diff --git a/.gitignore b/.gitignore
index 8fa0d36751913400596408757340dc5a56ca4d97..34ea03ce96564582673101299044af3e7792dac1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,5 @@
+CTestConfig.cmake
+CTestTestfile.cmake
 CMakeFiles
 cmake_install.cmake
 stage
@@ -26,3 +28,8 @@ OpenStructure.cbp
 DartConfiguration.tcl
 Testing
 *~
+README.html
+CPackConfig.cmake
+CPackSourceConfig.cmake
+deployment/macos/DNG.app
+deployment/macos/standalone
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 3ca970cacbd9a0bff2b3138ab2f0d6f6febba7e1..5ed6abafccc0d47d949b11811f9a45fdebdddf84 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -30,7 +30,7 @@ option(USE_DOUBLE_PRECISION "whether to compile in double precision"
 option(ENABLE_SPNAV "whether 3DConnexion devices should be supported"
       OFF)
 option(STATIC_PROPERTY_WORKAROUND "workaround for static property bug with some boost/boost_python combinations" OFF)
-option(DEPLOYMENT "switch on deployment settings" OFF)
+option(DEPLOYMENT "switch on deployment settings" OFF)
 option(COMPILE_TESTS "wheter unit tests should be compiled by default" OFF)
 
 if (PREFIX)
@@ -77,12 +77,21 @@ if (USE_SHADER)
 else()
   set(_SHADER OFF)
 endif()
-
+if (COMPILE_TMTOOLS)
+  set(_TM_TOOLS ON)
+else()
+  set(_TM_TOOLS OFF)
+endif()
 if (ENABLE_IMG)
   set(_IMG ON)
 else()
   set(_IMG OFF)
 endif()
+if (PROFILE)
+  set(_PROFILE ON)
+else()
+  set(_PROFILE OFF)
+endif()
 
 if (COMPOUND_LIB)
   set(_COMP_LIB "${COMPOUND_LIB}")
@@ -194,11 +203,11 @@ set(BOOST_REGEX_LIBRARIES ${Boost_LIBRARIES})
 #find_package(Boost ${_BOOST_MIN_VERSION} COMPONENTS math REQUIRED)
 #set(BOOST_MATH_LIBRARIES ${Boost_LIBRARIES})
 
-find_package(Qt4 4.4.3 REQUIRED)
+find_package(Qt4 4.5.0 REQUIRED)
 find_package(OpenGL REQUIRED)
 find_package(PNG REQUIRED)
 find_package(Eigen 2.0.0 REQUIRED)
-find_package(Python 2.2.1 REQUIRED)
+find_package(Python 2.4 REQUIRED)
 
 if (ENABLE_IMG)
   find_package(FFTW REQUIRED)
@@ -238,8 +247,8 @@ endif()
 
 add_subdirectory(modules)
 add_subdirectory(scripts)
-add_subdirectory(deployment)
-set(FILES_TO_BE_REMOVED CMakeFiles stage tests)
+add_subdirectory(deployment)
+set(FILES_TO_BE_REMOVED CMakeFiles stage tests)
 set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES
                          "${FILES_TO_BE_REMOVED}")
 
@@ -247,18 +256,21 @@ set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES
 
 message(STATUS 
         "OpenStructure will be built with the following options:\n"
+        "   Install Prefix                  (-PREFIX) : ${CMAKE_INSTALL_PREFIX}\n"
         "   RPath in install            (-DUSE_RPATH) : ${_USE_RPATH}\n"
-        "   Graphical interface         (-DENABLE_UI) : ${_UI}\n"
+        "   Graphical interface        (-DENABLE_GUI) : ${_UI}\n"
         "   OpenGL support             (-DENABLE_GFX) : ${_OPENGL}\n"
-        "   Image Processing support   (-DENABLE_IMG) : ${_IMG}\n"        
+        "   Image Processing support   (-DENABLE_IMG) : ${_IMG}\n"
         "   Shader support             (-DUSE_SHADER) : ${_SHADER}\n"
         "   Optimize                     (-DOPTIMIZE) : ${_OPT}\n"
+        "   Profiling support             (-DPROFILE) : ${_PROFILE}\n"
         "   Double Precision (-DUSE_DOUBLE_PRECISION) : ${_DOUBLE_PREC}\n"
-        "   Compound Lib             (-DCOMPOUND_LIB) : ${_COMP_LIB}")
+        "   Compound Lib             (-DCOMPOUND_LIB) : ${_COMP_LIB}\n"
+        "   TMAlign and TMScore   (-DCOMPILE_TMTOOLS) : ${_TM_TOOLS}")
         
 # doc target to create HTML documentation
 #set(SPHINX sphinx-build)
 #set(SPHINX_OPTIONS -c doc/conf -b html -d doc/html/doctrees)
 #add_custom_target(doc COMMAND 
 #                  ${SPHINX} ${SPHINX_OPTIONS} modules doc/html
-#                  VERBATIM)
+#                  VERBATIM)
diff --git a/build_configs/darwin_macports.txt b/build_configs/darwin_macports.txt
index aca42ad9d64b67d60ae60a3870cef30cf854c89d..821e0c792aa36718fa7e773f82be8b0b8156b4df 100644
--- a/build_configs/darwin_macports.txt
+++ b/build_configs/darwin_macports.txt
@@ -2,5 +2,6 @@
 # the dependencies installed over MacPorts
 set(BOOST_ROOT "/opt/local" CACHE PATH "prefix for the boost")
 set(PYTHON_ROOT "/opt/local" CACHE PATH "prefix for python")
-set(QT_QMAKE_EXECUTABLE "/opt/local/bin/qmake-mac" CACHE PATH 
+set(QT_QMAKE_EXECUTABLE "/opt/local/bin/qmake" CACHE PATH 
     "absolute path to qt executable")
+set(CMAKE_Fortran_FLAGS "-freal-loops" CACHE STRING "fortran compiler flags")
diff --git a/cmake_support/Deployment.cmake b/cmake_support/Deployment.cmake
index 8f59a7dd4f229a4484050af8728363ffedc83f15..c8acd43f014c998c567819e799cbad3f7863b84b 100644
--- a/cmake_support/Deployment.cmake
+++ b/cmake_support/Deployment.cmake
@@ -7,14 +7,17 @@ set(CPACK_PACKAGE_DESCRIPTION_FILE "${CMAKE_SOURCE_DIR}/ReadMe.txt")
 set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/LICENSE.txt")
 set(CPACK_PACKAGE_VERSION_MAJOR "1")
 set(CPACK_PACKAGE_VERSION_MINOR "0")
-set(CPACK_PACKAGE_VERSION_PATCH "0a1_${OST_REV}")
+if (OST_REV)
+  set(CPACK_PACKAGE_VERSION_PATCH "0a1_${OST_REV}")
+else()
+  set(CPACK_PACKAGE_VERSION_PATCH "0a1")
+endif()
 set(OST_VERSION "${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}")
-message("building OST version: ${OST_VERSION}")
 set(CPACK_PACKAGE_INSTALL_DIRECTORY "openstructure ${OST_VERSION}" )
 
 IF(WIN32 AND NOT UNIX)
 # There is a bug in NSI that does not handle full unix paths properly. Make
-# sure there is at least one set of four (4) backlasshes.
+# sure there is at least one set of four (4) backlashes.
   set(CPACK_PACKAGE_ICON "${CMAKE_SOURCE_DIR}/graphics/\\\\icon_32.png")
   #set(CPACK_NSIS_INSTALLED_ICON_NAME "bin/\\\\gosty.exe")
   set(CPACK_NSIS_DISPLAY_NAME "${CPACK_PACKAGE_INSTALL_DIRECTORY}")
diff --git a/cmake_support/OST.cmake b/cmake_support/OST.cmake
index e46d6f53ca1474b85366ba2def8ef28a518c55c5..9d928f6c946de5ce7a3c3f1d64991a98b2392d02 100644
--- a/cmake_support/OST.cmake
+++ b/cmake_support/OST.cmake
@@ -629,10 +629,12 @@ endmacro()
 macro(get_ost_rev)
   if (NOT OST_REV)
     if (NOT WIN32)
-      exec_program("svn" 
-                   ARGS "info |grep Revision|awk '{print $2}'"
-                   OUTPUT_VARIABLE OST_REV
-      )
+      if (EXISTS .svn)
+        exec_program("svn" 
+                     ARGS "info |grep Revision|awk '{print $2}'"
+                     OUTPUT_VARIABLE OST_REV
+        )
+      endif()
     else()
       exec_program("svnversion.exe"
                    ARGS ""
@@ -642,5 +644,7 @@ macro(get_ost_rev)
       string(REGEX REPLACE "[A-Za-z]" "" OST_REV ${OST_REV})
     endif()
   endif()
-  message("Revision: ${OST_REV}")
+  if (OST_REV)
+    message("Revision: ${OST_REV}")
+  endif()
 endmacro()
diff --git a/deployment/CMakeLists.txt b/deployment/CMakeLists.txt
index eb3285eb9703f657c984face278d3e7bc016c113..6824a305d71c9870480e5e71687ea153284fb768 100644
--- a/deployment/CMakeLists.txt
+++ b/deployment/CMakeLists.txt
@@ -1 +1,7 @@
-add_subdirectory(win)
\ No newline at end of file
+get_ost_rev()
+include(Deployment)
+set(SUBST_DIC OST_VERSION="${OST_VERSION}")
+add_custom_target(deploymnt ALL)
+substitute(IN_FILE README.html.in OUT_FILE README.html 
+               DICT ${SUBST_DIC})
+add_subdirectory(win)
diff --git a/deployment/README.html.in b/deployment/README.html.in
new file mode 100644
index 0000000000000000000000000000000000000000..864ff6e750d30cfd5f2adb4fc2196b0de992e5d0
--- /dev/null
+++ b/deployment/README.html.in
@@ -0,0 +1,51 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html 
+     PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+    "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+
+<head>
+<title>Protein Model Portal - PSI SGKB</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="robots" content="noarchive" />
+<meta http-equiv="Content-Style-Type" content="text/css" />
+<link rel="icon" href="share/favicon.ico" type="image/x-icon" />
+<link rel="author" title="The OpenStructure Team" href="?pid=contact" />
+</head>
+<body>
+<p style="color:gray">
+
+-----------------------------README----------------------------------------<br/>
+ This file is part of the OpenStructure project <www.openstructure.org><br/>
+<br/>
+ Copyright (C) 2008-2010 by the OpenStructure authors<br/>
+<br/>
+ This library is free software; you can redistribute it and/or modify it under<br/>
+ the terms of the GNU Lesser General Public License as published by the Free<br/>
+ Software Foundation; either version 3.0 of the License, or (at your option)<br/>
+ any later version.<br/>
+ This library is distributed in the hope that it will be useful, but WITHOUT<br/>
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS<br/>
+ FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more<br/>
+ details.<br/>
+<br/>
+ You should have received a copy of the GNU Lesser General Public License<br/>
+ along with this library; if not, write to the Free Software Foundation, Inc.,<br/>
+ 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA<br/>
+------------------------------------------------------------------------------<br/>
+</p>
+<br/>
+Thank you for using OpenStructure!<br/>
+<br/>
+This is the current Version of OpenStructure.<br/>
+Version: @OST_VERSION@<br/>
+<br/>
+This is a major release containig many bugfixes and improvements considering rendering, GUI and further <br/>
+functionality.<br/>
+<br/>
+For feedback or suggestions please contact us at <a href="http://www.openstructure.org">www.openstructure.org!</a><br/>
+<br/>
+<br/>
+The OpenStructure Authors<br/>
+
+</body>
diff --git a/deployment/linux/create_bundle.py b/deployment/linux/create_bundle.py
index 8869c25a36c341e121e5e25b134143369ef95ae7..b5a6f281f602def83c1318c93112e4ffdb186555 100644
--- a/deployment/linux/create_bundle.py
+++ b/deployment/linux/create_bundle.py
@@ -7,16 +7,20 @@ import sys
 
 # custom parameters
 
+if len(sys.argv) < 2:
+  print 'usage: create_bundle.py  additional_label'
+  sys.exit()
+
 boost_string='\".so.1.40.0\"'
-system_python_bin='/usr/bin/python2.6'
-name_python_bin='python2.6'
-system_python_libs='/usr/lib/python2.6'
+system_python_version='python2.6'
+system_python_bin='/usr/bin/'+system_python_version
+system_python_libs='/usr/lib/'+system_python_version
 second_system_python_libs_flag=True
-second_system_python_libs='/usr/lib/pymodules/python2.6'
+second_system_python_libs='/usr/lib/pymodules/'+system_python_version
+python_bin_in_bundle='python'
 qt4_plugins='/usr/lib/qt4/plugins'
-additional_label='ubuntu'
+additional_label=sys.argv[1]
 list_of_excluded_libraries=['ld-linux','libexpat','libgcc_s','libglib','cmov','libice','libSM','libX','libg','libGL.so','libfontconfig','libfreetype','libdrm','libxcb','libICE']
-
 currdir=os.getcwd()
 if currdir.find('deployment')==-1 or currdir.find('linux')==-1:
   print '\n'
@@ -41,10 +45,10 @@ svninfo_split=string.split(svninfo_lines[4])
 revstring=svninfo_split[1]
 directory_name='openstructure-linux-'+archstring+'-'+additional_label+'-rev'+revstring
 print 'Stripping subversion information to avoid accidental commit'
-#subprocess.call('rm -rf $(find . -name .svn)',shell=True,cwd='../../')
+subprocess.call('rm -rf $(find . -name .svn)',shell=True,cwd='../../')
 print 'Hardcoding package python binary path in openstructure executables'
 subprocess.call('mv scripts/ost.in scripts/ost.in.backup',shell=True,cwd='../../')
-subprocess.call('sed "s/@PYTHON_BINARY@/\$DNG_ROOT\/bin\/'+name_python_bin+'/g" scripts/ost.in.backup > scripts/ost.in.prepreprepre',shell=True,cwd='../../')
+subprocess.call('sed "s/@PYTHON_BINARY@/\$DNG_ROOT\/bin\/'+python_bin_in_bundle+'/g" scripts/ost.in.backup > scripts/ost.in.prepreprepre',shell=True,cwd='../../')
 subprocess.call('sed "s/\#export LD_LIBRARY_PATH/ export LD_LIBRARY_PATH/g" scripts/ost.in.prepreprepre > scripts/ost.in.preprepre',shell=True,cwd='../../')
 subprocess.call('sed "s/\#export PYTHONHOME/ export PYTHONHOME/g" scripts/ost.in.preprepre > scripts/ost.in.prepre',shell=True,cwd='../../')
 subprocess.call('sed "s/\#export PYTHONPATH/ export PYTHONPATH/g" scripts/ost.in.prepre > scripts/ost.in.pre',shell=True,cwd='../../')
@@ -52,18 +56,34 @@ subprocess.call('sed "s/\#export QT_PLUGIN_PATH/ export QT_PLUGIN_PATH/g" script
 subprocess.call('mv scripts/dng.in scripts/dng.in.backup',shell=True,cwd='../../')
 subprocess.call('sed "s/\#export LD_LIBRARY_PATH/ export LD_LIBRARY_PATH/g" scripts/dng.in.backup > scripts/dng.in.preprepre',shell=True,cwd='../../')
 subprocess.call('sed "s/\#export PYTHONHOME/ export PYTHONHOME/g" scripts/dng.in.preprepre > scripts/dng.in.prepre',shell=True,cwd='../../')
-subprocess.call('sed "s/\#export PYTHONPATH/ export PYTHONPATH/g" scripts/ost.in.prepre > scripts/ost.in.pre',shell=True,cwd='../../')
+subprocess.call('sed "s/\#export PYTHONPATH/ export PYTHONPATH/g" scripts/dng.in.prepre > scripts/dng.in.pre',shell=True,cwd='../../')
 subprocess.call('sed "s/\#export QT_PLUGIN_PATH/ export QT_PLUGIN_PATH/g" scripts/dng.in.pre > scripts/dng.in',shell=True,cwd='../../')
+#print 'Downloading Chemlib dictionary'
+#subprocess.call('wget ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif', shell=True, cwd='../../')
+#print 'Compiling Openstructure'
+#subprocess.call('cmake ./ -DCMAKE_BUILD_TYPE=Release -DPREFIX='+directory_name+' -DBoost_COMPILER='+boost_string+'-DENABLE_IMG=OFF -DENABLE_UI=OFF -DENABLE_GFX=OFF', shell=True,cwd='../../')
+#subprocess.call('make -j5',shell=True,cwd='../../')
+#print 'Converting Chemlib dictionary'
+#subprocess.call('stage/bin/chemdict_tool create components.cif compounds.chemlib', shell=True, cwd='../../')
+#print '\nStaging Chemlib dictionary'
 print 'Compiling Openstructure'
-subprocess.call('cmake ./ -DCMAKE_BUILD_TYPE=Release -DPREFIX='+directory_name+' -DBoost_COMPILER='+boost_string, shell=True,cwd='../../')
-subprocess.call('make',shell=True,cwd='../../')
+subprocess.call('cmake ./ -DCMAKE_BUILD_TYPE=Release -DPREFIX='+directory_name+' -DBoost_COMPILER='+boost_string+' -DCOMPOUND_LIB=ChemLib/compounds.chemlib -DENABLE_IMG=ON -DENABLE_UI=ON -DENABLE_GFX=ON -DOPTIMIZE=ON',shell=True,cwd='../../')
+subprocess.call('make -j2',shell=True,cwd='../../')
 print 'Removing obsolete packages and package directory'
 subprocess.call('rm -fr openstructure-linux*',shell=True,cwd='../../')
 print 'Creating new package directory'
 subprocess.call('mkdir '+directory_name,shell=True,cwd='../../')
 subprocess.call('mkdir '+directory_name+'/bin',shell=True,cwd='../../')
-so_list=[]
+print 'Copy python executable into stage for dependency detection'
+subprocess.call('cp '+system_python_bin+ ' stage/bin/python',shell=True,cwd='../../')
+print 'Copy python libraries into the stage for dependency detection'
+subprocess.call('cp -pRL '+system_python_libs+' stage/'+libdir,shell=True,cwd='../../')
+subprocess.call('rm -fr stage/'+libdir+'/'+system_python_version+'/dist-packages',shell=True,cwd='../../')
+if second_system_python_libs_flag==True:
+  subprocess.call('cp -pRL '+second_system_python_libs+'/sip* stage/'+libdir+'/'+system_python_version,shell=True,cwd='../../')
+  subprocess.call('cp -pRL '+second_system_python_libs+'/PyQt* stage/'+libdir+'/'+system_python_version,shell=True,cwd='../../')
 print 'Creating new dependency list'
+so_list=[]
 walk_list=os.walk('../../stage')
 for dir_entry in walk_list:
   for file_entry in dir_entry[2]:
@@ -91,19 +111,36 @@ subprocess.call('mkdir '+directory_name+'/'+libdir,shell=True,cwd='../../')
 for entry in filtered_dep_list:
   subprocess.call('cp '+entry+' '+directory_name+'/'+libdir,shell=True,cwd='../../')
 print 'Copy python executable into package directory structure'
-subprocess.call('cp '+system_python_bin+ ' '+directory_name+'/bin',shell=True,cwd='../../')
+subprocess.call('cp '+system_python_bin+ ' '+directory_name+'/bin/python',shell=True,cwd='../../')
 print 'Copy python libraries into package directory structure'
 subprocess.call('cp -pRL '+system_python_libs+' '+directory_name+'/'+libdir,shell=True,cwd='../../')
+subprocess.call('rm -fr '+directory_name+'/'+libdir+'/'+system_python_version+'/dist-packages',shell=True,cwd='../../')
 if second_system_python_libs_flag==True:
-  subprocess.call('cp -pRL '+second_system_python_libs+'/* '+directory_name+'/'+libdir+'/'+name_python_bin,shell=True,cwd='../../')
+  subprocess.call('cp -pRL '+second_system_python_libs+'/sip* '+directory_name+'/'+libdir+'/'+system_python_version,shell=True,cwd='../../')
+  subprocess.call('cp -pRL '+second_system_python_libs+'/PyQt* '+directory_name+'/'+libdir+'/'+system_python_version,shell=True,cwd='../../')
 print 'Copy Qt 4 plugins into package directory structure'
 subprocess.call('cp -pRL '+qt4_plugins+' '+directory_name+'/bin/',shell=True,cwd='../../')
 print 'Installing OpenStructure into package directory structure'
 subprocess.call('make install',shell=True,cwd='../../')
-print 'Copy examples into package directory structure'
+print 'Copying supplementary material into package directory structure'
+subprocess.call('cp -pRL  stage/share/openstructure  '+directory_name+'/share/',shell=True,cwd='../../')
+print 'Copying examples into package directory structure'
 subprocess.call('cp -pRL  examples  '+directory_name+'/share/openstructure/',shell=True,cwd='../../')
+print 'Copying ReadMe file into package directory structure'
+subprocess.call('cp deployment/README.html '+directory_name,shell=True,cwd='../../')
+print 'Creating executables at the top level of the package directory structure'
+subprocess.call('ln -sf bin/dng ./dng',shell=True,cwd='../../'+directory_name)
+subprocess.call('ln -sf bin/ost ./ost',shell=True,cwd='../../'+directory_name)
+print 'Copying additional libraries in the package directory structure'
+subprocess.call('cp /usr/lib/libssl.so.0.9.8   '+directory_name+'/'+libdir,shell=True,cwd='../../')
+subprocess.call('cp /usr/lib/libcrypto.so.0.9.8   '+directory_name+'/'+libdir,shell=True,cwd='../../')
 print 'Removing headers from package directory structure'
 subprocess.call('rm -fr   '+directory_name+'/include',shell=True,cwd='../../')
+print 'Stripping pyc files from bundle'
+subprocess.call('rm -rf $(find . -name *.pyc)',shell=True,cwd='../../')
+print 'removing dokk and harmony examples from bundle'
+subprocess.call('rm -rf '+directory_name+'/share/openstructure/examples/code_fragments/dokk',shell=True,cwd='../../')
+subprocess.call('rm -rf '+directory_name+'/share/openstructure/examples/code_fragments/harmony',shell=True,cwd='../../')
 print 'De-hardcoding package python binary path from openstructure executables'
 subprocess.call('rm scripts/ost.in',shell=True,cwd='../../')
 subprocess.call('rm scripts/ost.in.pre*',shell=True,cwd='../../')
diff --git a/deployment/linux/create_bundle_alt.py b/deployment/linux/create_bundle_alt.py
new file mode 100755
index 0000000000000000000000000000000000000000..6e5cf9bcf26311b4d7e1acd2ee61a18b9fc36a9f
--- /dev/null
+++ b/deployment/linux/create_bundle_alt.py
@@ -0,0 +1,183 @@
+import os,os.path
+import shutil
+import sys
+import tarfile
+import subprocess
+import re
+
+def get_libdir():
+  machine=os.uname()[4]
+  if machine.find('x86_64') !=-1:
+    return 'lib64'
+  else: 
+    return 'lib'
+    
+def get_arch():
+  machine=os.uname()[4]
+  if machine.find('x86_64') !=-1:
+    return '64bit'
+  else: 
+    return '32bit'
+
+def clean(standalonedir):
+  if os.path.exists(standalonedir):
+    shutil.rmtree(standalonedir)
+
+def copy_stage(stagedir,standalonedir):
+  libdir=get_libdir()
+  copytree_ex(os.path.join(stagedir,'bin'),os.path.join(standalonedir,'bin'))
+  copytree_ex(os.path.join(stagedir,libdir),os.path.join(standalonedir,libdir))
+  if os.path.exists(os.path.join(stagedir,'share')):
+    copytree_ex(os.path.join(stagedir,'share'),os.path.join(standalonedir,'share'))
+
+def collect_deps(binaries,exclude_list):
+  dependencies=set()
+  for binary in binaries:
+    collect_deps_recursive_(binary,dependencies,exclude_list)
+  return dependencies
+  
+def collect_deps_recursive_(binary,collected,exclude_list):
+  ldd_stdout=subprocess.Popen(['ldd',binary],stdout=subprocess.PIPE).stdout
+  output=ldd_stdout.readlines()
+  new_dependencies=set()
+  for entry in output:
+    if entry.find("statically linked")!=-1:
+      continue
+    sp=entry.split('(0x')
+    if len(sp)>0: # only continue if line is dependency
+     sp2=sp[0].split('=>',1)[-1].split()
+     if sp2: #ensure libname exists (fix for virtual linux-gate)
+       text=sp2[0]
+       if not text.split('.')[0].split('/')[-1] in exclude_list and not text in collected:
+         collect_deps_recursive_(text,collected,exclude_list)
+         collected.add(text) 
+  
+
+def copy_deps(binaries,standalonedir,exclude_list):
+  dependencies=set()
+  walk_list=os.walk(standalonedir)
+  binaries_list=[]
+  for dir_entry in walk_list:
+    for file_entry in dir_entry[2]:
+      if file_entry.endswith('.so') or file_entry in binaries:
+        filepath=os.path.join(dir_entry[0],file_entry)
+        binaries_list.append(filepath)  
+  dependencies=collect_deps(binaries_list,exclude_list)
+  for dep in dependencies:
+    shutil.copy2(dep,os.path.join(standalonedir,get_libdir()))
+
+def copy_examples(stagedir):
+  #todo
+  pass
+def copy_qt_plugins():
+  #todo
+  pass
+
+def process_scripts(scripts,standalonedir):
+  for script in scripts:
+    fp=open(os.path.join(standalonedir,'bin',script),'r')
+    text=fp.read()
+    fp.close()
+    text=re.sub('#export PYTHONPATH','export PYTHONPATH',text)
+    fp=open(os.path.join(standalonedir,'bin',script),'w')
+    fp.write(text)
+    fp.close()
+
+def create_package(name,standalonedir):
+  try:
+    import pysvn
+    try:
+      client=pysvn.Client()
+      svn_info=client.info('.')
+      revstring='-rev'+str(svn_info['revision'.number])
+    except pysvn.ClientError:
+      print 'No svn directory found. Addin no revision number.'
+      revstring=''
+  except ImportError:
+    print 'Pysvn not installed. Adding no revision number.'
+    revstring=''
+  tar_name=name+'-linux-'+get_arch()+revstring+'.tgz'
+  if os.path.exists(tar_name):
+    os.remove(tar_name)
+  tar = tarfile.open(tar_name, "w:gz")
+  tar.add(standalonedir,name+'-linux-'+get_arch()+revstring)
+  tar.close()
+
+def ignorer(dirpath,files):
+  ignores=[]
+  for f in files:
+    base=os.path.splitext(f)[0]
+    if f.endswith('.py'):
+      if base+'.pyc' in files or base+'.pyo' in files:
+        ignores.append(f)
+    elif f.endswith('.pyc'):
+      if base+'.pyo' in files:
+        ignores.append(f)
+  return ignores
+
+def copy_python_dirs(standalonedir):
+  dirs=sys.path[1:]
+  dirs.sort() #get toplevel dir to the beginning
+  toplevel=dirs[0]
+  shutil.copytree(toplevel,os.path.join(standalonedir,get_libdir(),'python'),ignore=ignorer)
+  for d in dirs[1:]:
+    if not d.startswith(toplevel) and os.path.isdir(d):
+      toplevel=d
+      copytree_ex(toplevel,os.path.join(standalonedir,get_libdir(),'python'),ignore=ignorer)
+
+
+def copytree_ex(source,destination, symlinks=False,ignore=None):
+  if not os.path.exists(destination):
+   shutil.copytree(source,destination,symlinks,ignore)
+  elif os.path.isdir(destination):
+    files=os.listdir(source)
+    if ignore:
+      ignores=ignore(source,files)
+    else:
+      ignores=[]
+    for f in files:
+      srcname=os.path.join(source,f)
+      dstname=os.path.join(destination,f)
+      if os.path.isdir(os.path.join(source,f)):
+        copytree_ex(srcname,dstname,symlinks,ignore=ignorer)
+      elif f not in ignores:
+        if symlinks and os.path.islink(srcname):
+          linkto = os.readlink(srcname)
+          os.symlink(linkto, dstname)
+        else:
+          shutil.copy2(srcname, dstname)
+  else:
+    raise IOError("destination is not a directory")
+    
+
+       
+############   main script ####################
+
+stagedir='../../stage'
+ost_stagedir='../../../openstructure/stage'
+standalonedir=os.path.join(os.getcwd(),'standalone')
+binaries=['gosty']
+exclude_list=['ld-linux','libexpat','libgcc_s','libglib','cmov','libice','libSM','libX','libg','libGL','libfontconfig','libfreetype','libdrm','libxcb','libICE']
+scripts=['dng','ost']
+
+#compile_stage()
+
+clean(standalonedir)
+print 'copying stage'
+copy_stage(stagedir,standalonedir)
+print 'copying ost stage'
+copy_stage(ost_stagedir,standalonedir)
+print 'copying python'
+shutil.copy(sys.executable,os.path.join(stagedir,'bin'))
+copy_python_dirs(standalonedir)
+print 'copying dependencies'
+binaries.append(sys.executable)
+copy_deps(binaries,standalonedir,exclude_list)
+print 'copying examples'
+copy_examples(stagedir)
+print 'copying plugins'
+copy_qt_plugins()
+print 'processing scripts'
+process_scripts(scripts,standalonedir)
+print 'creating package'
+create_package('openstructure','standalone')
diff --git a/deployment/linux/create_qmean_bundle.py b/deployment/linux/create_qmean_bundle.py
index d62c348bdd0e846f1f9075be778d79fd39fe67f5..e8743cb03106a2819475635a4353f5dcee39a1b0 100644
--- a/deployment/linux/create_qmean_bundle.py
+++ b/deployment/linux/create_qmean_bundle.py
@@ -60,9 +60,16 @@ subprocess.call('sed "s/\#export LD_LIBRARY_PATH/ export LD_LIBRARY_PATH/g" scri
 subprocess.call('sed "s/\#export PYTHONHOME/ export PYTHONHOME/g" scripts/dng.in.preprepre > scripts/dng.in.prepre',shell=True,cwd='../../')
 subprocess.call('sed "s/\#export PYTHONPATH/ export PYTHONPATH/g" scripts/ost.in.prepre > scripts/ost.in.pre',shell=True,cwd='../../')
 subprocess.call('sed "s/\#export QT_PLUGIN_PATH/ export QT_PLUGIN_PATH/g" scripts/dng.in.pre > scripts/dng.in',shell=True,cwd='../../')
+print 'Downloading Chemlib dictionary'
+subprocess.call('wget ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif', shell=True, cwd='../../')
 print 'Compiling Openstructure/Qmean'
 subprocess.call('cmake ./ -DCMAKE_BUILD_TYPE=Release -DPREFIX='+directory_name+' -DBoost_COMPILER='+boost_string+' -DONLY_QMEAN=ON -DENABLE_IMG=OFF -DENABLE_UI=OFF -DENABLE_GFX=OFF -DCOMPOUND_LIB=ChemLib/compounds.chemlib', shell=True,cwd='../../')
 subprocess.call('make',shell=True,cwd='../../')
+print 'Converting Chemlib dictionary'
+subprocess.call('stage/bin/chemdict_tool create components.cif compounds.chemlib', shell=True, cwd='../../')
+print '\nStaging Chemlib dictionary'
+subprocess.call('cmake ./ -DCOMPOUND_LIB=compounds.chemlib',shell=True,cwd='../../')
+subprocess.call('make',shell=True,cwd='../../')
 print 'Removing obsolete packages and package directory'
 subprocess.call('rm -fr qmean-*',shell=True,cwd='../../')
 print 'Creating new package directory'
@@ -110,6 +117,8 @@ print 'Copy examples into package directory structure'
 subprocess.call('cp -pRL  examples  '+directory_name+'/share/openstructure/',shell=True,cwd='../../')
 print 'Removing headers from package directory structure'
 subprocess.call('rm -fr   '+directory_name+'/include',shell=True,cwd='../../')
+print 'Copying supplementary material into package directory structure'
+subprocess.call('cp -pRL  stage/share/openstructure  '+directory_name+'/share/',shell=True,cwd='../../')
 print 'Copy qmean examples into package directory structure'
 subprocess.call('cp -pRL  modules/scratch/qmean/examples '+directory_name+'',shell=True,cwd='../../')
 print 'Copy readme and license files into package directory structure'
diff --git a/deployment/macos/Installer.pmdoc/01dng-contents.xml b/deployment/macos/Installer.pmdoc/01dng-contents.xml
deleted file mode 100644
index 61b6589190a24ad8a3f71f550a63eec92cf1af14..0000000000000000000000000000000000000000
--- a/deployment/macos/Installer.pmdoc/01dng-contents.xml
+++ /dev/null
@@ -1 +0,0 @@
-<pkg-contents spec="1.12"><f n="DNG.app" o="marco" g="staff" p="16893" pt="/Users/marco/Projects/ost/deployment/macos/DNG.app" m="true" t="file"><f n="Contents" o="marco" g="staff" p="16893"><f n="Info.plist" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="MacOS" o="marco" g="staff" p="16893"><f n="dng" o="marco" g="staff" p="33277"><mod>mode</mod></f><mod>mode</mod></f><f n="PkgInfo" o="marco" g="staff" p="33204"><mod>mode</mod></f><mod>mode</mod></f><mod>mode</mod></f></pkg-contents>
\ No newline at end of file
diff --git a/deployment/macos/Installer.pmdoc/01dng.xml b/deployment/macos/Installer.pmdoc/01dng.xml
deleted file mode 100644
index 728c5d6e076e6fc602f056ad2fd17de29a976a3d..0000000000000000000000000000000000000000
--- a/deployment/macos/Installer.pmdoc/01dng.xml
+++ /dev/null
@@ -1 +0,0 @@
-<pkgref spec="1.12" uuid="4C7C03C1-13A5-49A8-8A66-B35160BCA334"><config><identifier>org.openstructure.DNG.pkg</identifier><version>1</version><description></description><post-install type="none"/><requireAuthorization/><installFrom relative="true" mod="true" includeRoot="true">DNG.app</installFrom><installTo mod="true">/Applications/OpenStructure</installTo><flags><followSymbolicLinks/></flags><packageStore type="internal"></packageStore><mod>parent</mod><mod>requireAuthorization</mod><mod>relocatable</mod><mod>installTo.path</mod><mod>installFrom.path</mod><mod>installTo</mod><mod>identifier</mod></config><contents><file-list>01dng-contents.xml</file-list><component id="org.openstructure.OpenStructure" path="/Users/marco/Projects/ost/deployment/macos/DNG.app" version="" isRelocatable="true"><locator-info><token title="pkmk-token-10"><search-rule><combo identifier="org.openstructure.OpenStructure" default-path="/Applications/DNG.app"/></search-rule></token></locator-info></component><filter>/CVS$</filter><filter>/\.svn$</filter><filter>/\.cvsignore$</filter><filter>/\.cvspass$</filter><filter>/\.DS_Store$</filter></contents></pkgref>
\ No newline at end of file
diff --git a/deployment/macos/Installer.pmdoc/02openstructure-contents.xml b/deployment/macos/Installer.pmdoc/02openstructure-contents.xml
deleted file mode 100644
index 7fde158fb0a196b859f68b515017ac7d1c4d02e0..0000000000000000000000000000000000000000
--- a/deployment/macos/Installer.pmdoc/02openstructure-contents.xml
+++ /dev/null
@@ -1 +0,0 @@
-<pkg-contents spec="1.12"><f n="openstructure" o="root" g="wheel" p="16877" pt="/usr/openstructure" m="false" t="file"><f n="bin" o="root" g="wheel" p="16877"><f n="2to3" o="root" g="wheel" p="33261"/><f n="bmp2tiff" o="root" g="wheel" p="33261"/><f n="chemdict_tool" o="root" g="wheel" p="33261"/><f n="dng" o="root" g="wheel" p="33133"/><f n="fax2ps" o="root" g="wheel" p="33261"/><f n="fax2tiff" o="root" g="wheel" p="33261"/><f n="fftw-wisdom-to-conf" o="root" g="wheel" p="33261"/><f n="fftwf-wisdom" o="root" g="wheel" p="33261"/><f n="gif2tiff" o="root" g="wheel" p="33261"/><f n="gipltng" o="root" g="wheel" p="33133"/><f n="gosty" o="root" g="wheel" p="33261"/><f n="idle" o="root" g="wheel" p="33261"/><f n="init.py" o="root" g="wheel" p="33204"><mod>mode</mod></f><f n="init_cl.py" o="root" g="wheel" p="33204"><mod>mode</mod></f><f n="init_iplt.py" o="root" g="wheel" p="33204"><mod>mode</mod></f><f n="lconvert" o="root" g="wheel" p="33261"/><f n="libpng-config" o="root" g="wheel" p="33261"/><f n="libpng12-config" o="root" g="wheel" p="33261"/><f n="lrelease" o="root" g="wheel" p="33261"/><f n="lupdate" o="root" g="wheel" p="33261"/><f n="macdeployqt" o="root" g="wheel" p="33261"/><f n="moc" o="root" g="wheel" p="33261"/><f n="ost" o="root" g="wheel" p="33133"/><f n="pal2rgb" o="root" g="wheel" p="33261"/><f n="ppm2tiff" o="root" g="wheel" p="33261"/><f n="pydoc" o="root" g="wheel" p="33261"/><f n="pylupdate4" o="root" g="wheel" p="33261"/><f n="pyrcc4" o="root" g="wheel" p="33261"/><f n="python" o="root" g="wheel" p="33261"/><f n="python-config" o="root" g="wheel" p="33261"/><f n="python2.6" o="root" g="wheel" p="33261"/><f n="python2.6-config" o="root" g="wheel" p="33261"/><f n="pyuic4" o="root" g="wheel" p="33261"/><f n="qcollectiongenerator" o="root" g="wheel" p="33261"/><f n="qdbus" o="root" g="wheel" p="33261"/><f n="qdbuscpp2xml" o="root" g="wheel" p="33261"/><f n="qdbusxml2cpp" o="root" g="wheel" p="33261"/><f n="qhelpgenerator" o="root" g="wheel" p="33261"/><f n="qmake" o="root" g="wheel" p="33261"/><f n="qt3to4" o="root" g="wheel" p="33261"/><f n="ras2tiff" o="root" g="wheel" p="33261"/><f n="raw2tiff" o="root" g="wheel" p="33261"/><f n="rcc" o="root" g="wheel" p="33261"/><f n="rgb2ycbcr" o="root" g="wheel" p="33261"/><f n="sip" o="root" g="wheel" p="33261"/><f n="smtpd.py" o="root" g="wheel" p="33261"/><f n="thumbnail" o="root" g="wheel" p="33261"/><f n="tiff2bw" o="root" g="wheel" p="33261"/><f n="tiff2pdf" o="root" g="wheel" p="33261"/><f n="tiff2ps" o="root" g="wheel" p="33261"/><f n="tiff2rgba" o="root" g="wheel" p="33261"/><f n="tiffcmp" o="root" g="wheel" p="33261"/><f n="tiffcp" o="root" g="wheel" p="33261"/><f n="tiffdither" o="root" g="wheel" p="33261"/><f n="tiffdump" o="root" g="wheel" p="33261"/><f n="tiffinfo" o="root" g="wheel" p="33261"/><f n="tiffmedian" o="root" g="wheel" p="33261"/><f n="tiffset" o="root" g="wheel" p="33261"/><f n="tiffsplit" o="root" g="wheel" p="33261"/><f n="uic" o="root" g="wheel" p="33261"/><f n="xmlpatterns" o="root" g="wheel" p="33261"/></f><f n="include" o="root" g="wheel" p="16877"><f n="boost-1.41.0" o="root" g="wheel" p="16877"><f n="boost" o="root" g="wheel" p="16877"><f n="accumulators" o="root" g="wheel" p="16877"><f n="accumulators.hpp" o="root" g="wheel" p="33188"/><f n="accumulators_fwd.hpp" o="root" g="wheel" p="33188"/><f n="framework" o="root" g="wheel" p="16877"><f n="accumulator_base.hpp" o="root" g="wheel" p="33188"/><f n="accumulator_concept.hpp" o="root" g="wheel" p="33188"/><f n="accumulator_set.hpp" o="root" g="wheel" p="33188"/><f n="accumulators" o="root" g="wheel" p="16877"><f n="droppable_accumulator.hpp" o="root" g="wheel" p="33188"/><f n="external_accumulator.hpp" o="root" g="wheel" p="33188"/><f n="reference_accumulator.hpp" o="root" g="wheel" p="33188"/><f n="value_accumulator.hpp" o="root" g="wheel" p="33188"/></f><f n="depends_on.hpp" o="root" g="wheel" p="33188"/><f n="external.hpp" o="root" g="wheel" p="33188"/><f n="extractor.hpp" o="root" g="wheel" p="33188"/><f n="features.hpp" o="root" g="wheel" p="33188"/><f n="parameters" o="root" g="wheel" p="16877"><f n="accumulator.hpp" o="root" g="wheel" p="33188"/><f n="sample.hpp" o="root" g="wheel" p="33188"/><f n="weight.hpp" o="root" g="wheel" p="33188"/><f n="weights.hpp" o="root" g="wheel" p="33188"/></f></f><f n="numeric" o="root" g="wheel" p="16877"><f n="detail" o="root" g="wheel" p="16877"><f n="function1.hpp" o="root" g="wheel" p="33188"/><f n="function2.hpp" o="root" g="wheel" p="33188"/><f n="function3.hpp" o="root" g="wheel" p="33188"/><f n="function4.hpp" o="root" g="wheel" p="33188"/><f n="function_n.hpp" o="root" g="wheel" p="33188"/><f n="pod_singleton.hpp" o="root" g="wheel" p="33188"/></f><f n="functional" o="root" g="wheel" p="16877"><f n="complex.hpp" o="root" g="wheel" p="33188"/><f n="valarray.hpp" o="root" g="wheel" p="33188"/><f n="vector.hpp" o="root" g="wheel" p="33188"/></f><f n="functional.hpp" o="root" g="wheel" p="33188"/><f n="functional_fwd.hpp" o="root" g="wheel" p="33188"/></f><f n="statistics" o="root" g="wheel" p="16877"><f n="count.hpp" o="root" g="wheel" p="33188"/><f n="covariance.hpp" o="root" g="wheel" p="33188"/><f n="density.hpp" o="root" g="wheel" p="33188"/><f n="error_of.hpp" o="root" g="wheel" p="33188"/><f n="error_of_mean.hpp" o="root" g="wheel" p="33188"/><f n="extended_p_square.hpp" o="root" g="wheel" p="33188"/><f n="extended_p_square_quantile.hpp" o="root" g="wheel" p="33188"/><f n="kurtosis.hpp" o="root" g="wheel" p="33188"/><f n="max.hpp" o="root" g="wheel" p="33188"/><f n="mean.hpp" o="root" g="wheel" p="33188"/><f n="median.hpp" o="root" g="wheel" p="33188"/><f n="min.hpp" o="root" g="wheel" p="33188"/><f n="moment.hpp" o="root" g="wheel" p="33188"/><f n="p_square_cumulative_distribution.hpp" o="root" g="wheel" p="33188"/><f n="p_square_quantile.hpp" o="root" g="wheel" p="33188"/><f n="parameters" o="root" g="wheel" p="16877"><f n="quantile_probability.hpp" o="root" g="wheel" p="33188"/></f><f n="peaks_over_threshold.hpp" o="root" g="wheel" p="33188"/><f n="pot_quantile.hpp" o="root" g="wheel" p="33188"/><f n="pot_tail_mean.hpp" o="root" g="wheel" p="33188"/><f n="rolling_count.hpp" o="root" g="wheel" p="33188"/><f n="rolling_mean.hpp" o="root" g="wheel" p="33188"/><f n="rolling_sum.hpp" o="root" g="wheel" p="33188"/><f n="rolling_window.hpp" o="root" g="wheel" p="33188"/><f n="skewness.hpp" o="root" g="wheel" p="33188"/><f n="stats.hpp" o="root" g="wheel" p="33188"/><f n="sum.hpp" o="root" g="wheel" p="33188"/><f n="tail.hpp" o="root" g="wheel" p="33188"/><f n="tail_mean.hpp" o="root" g="wheel" p="33188"/><f n="tail_quantile.hpp" o="root" g="wheel" p="33188"/><f n="tail_variate.hpp" o="root" g="wheel" p="33188"/><f n="tail_variate_means.hpp" o="root" g="wheel" p="33188"/><f n="times2_iterator.hpp" o="root" g="wheel" p="33188"/><f n="variance.hpp" o="root" g="wheel" p="33188"/><f n="variates" o="root" g="wheel" p="16877"><f n="covariate.hpp" o="root" g="wheel" p="33188"/></f><f n="weighted_covariance.hpp" o="root" g="wheel" p="33188"/><f n="weighted_density.hpp" o="root" g="wheel" p="33188"/><f n="weighted_extended_p_square.hpp" o="root" g="wheel" p="33188"/><f n="weighted_kurtosis.hpp" o="root" g="wheel" p="33188"/><f n="weighted_mean.hpp" o="root" g="wheel" p="33188"/><f n="weighted_median.hpp" o="root" g="wheel" p="33188"/><f n="weighted_moment.hpp" o="root" g="wheel" p="33188"/><f n="weighted_p_square_cumulative_distribution.hpp" o="root" g="wheel" p="33188"/><f n="weighted_p_square_quantile.hpp" o="root" g="wheel" p="33188"/><f n="weighted_peaks_over_threshold.hpp" o="root" g="wheel" p="33188"/><f n="weighted_skewness.hpp" o="root" g="wheel" p="33188"/><f n="weighted_sum.hpp" o="root" g="wheel" p="33188"/><f n="weighted_tail_mean.hpp" o="root" g="wheel" p="33188"/><f n="weighted_tail_quantile.hpp" o="root" g="wheel" p="33188"/><f n="weighted_tail_variate_means.hpp" o="root" g="wheel" p="33188"/><f n="weighted_variance.hpp" o="root" g="wheel" p="33188"/><f n="with_error.hpp" o="root" g="wheel" p="33188"/></f><f n="statistics.hpp" o="root" g="wheel" p="33188"/><f n="statistics_fwd.hpp" o="root" g="wheel" p="33188"/></f><f n="algorithm" o="root" g="wheel" p="16877"><f n="minmax.hpp" o="root" g="wheel" p="33188"/><f n="minmax_element.hpp" o="root" g="wheel" p="33188"/><f n="string" o="root" g="wheel" p="16877"><f n="case_conv.hpp" o="root" g="wheel" p="33188"/><f n="classification.hpp" o="root" g="wheel" p="33188"/><f n="compare.hpp" o="root" g="wheel" p="33188"/><f n="concept.hpp" o="root" g="wheel" p="33188"/><f n="config.hpp" o="root" g="wheel" p="33188"/><f n="constants.hpp" o="root" g="wheel" p="33188"/><f n="detail" o="root" g="wheel" p="16877"><f n="case_conv.hpp" o="root" g="wheel" p="33188"/><f n="classification.hpp" o="root" g="wheel" p="33188"/><f n="find_format.hpp" o="root" g="wheel" p="33188"/><f n="find_format_all.hpp" o="root" g="wheel" p="33188"/><f 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diff --git a/deployment/macos/Installer.pmdoc/02openstructure.xml b/deployment/macos/Installer.pmdoc/02openstructure.xml
deleted file mode 100644
index 24daef59a833cdb44b5fd035d6a3cb7c954bfa52..0000000000000000000000000000000000000000
--- a/deployment/macos/Installer.pmdoc/02openstructure.xml
+++ /dev/null
@@ -1 +0,0 @@
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\ No newline at end of file
diff --git a/deployment/macos/Installer.pmdoc/03examples-contents.xml b/deployment/macos/Installer.pmdoc/03examples-contents.xml
deleted file mode 100644
index d0ea01668515fc9f9b0a4f8833856d330997dd0f..0000000000000000000000000000000000000000
--- a/deployment/macos/Installer.pmdoc/03examples-contents.xml
+++ /dev/null
@@ -1 +0,0 @@
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p="33204"><mod>mode</mod></f><f n="mdi_example.py.svn-base" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="menubar_example.py.svn-base" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="widget_example.py.svn-base" o="marco" g="staff" p="33204"><mod>mode</mod></f><mod>mode</mod></f><f n="tmp" o="marco" g="staff" p="16893"><f n="prop-base" o="marco" g="staff" p="16820"><mod>mode</mod></f><f n="props" o="marco" g="staff" p="16820"><mod>mode</mod></f><f n="tempfile.3.tmp" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="tempfile.4.tmp" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="tempfile.5.tmp" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="tempfile.6.tmp" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="tempfile.tmp" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="text-base" o="marco" g="staff" p="16820"><mod>mode</mod></f><mod>mode</mod></f><mod>mode</mod></f><f n="board.py" o="marco" g="staff" p="33277"><mod>mode</mod></f><f n="color_tool.py" o="marco" g="staff" p="33277"><mod>mode</mod></f><f n="mdi_example.py" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="menubar_example.py" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="widget_example.py" o="marco" g="staff" p="33204"><mod>mode</mod></f><mod>mode</mod></f></f></pkg-contents>
\ No newline at end of file
diff --git a/deployment/macos/Installer.pmdoc/03examples.xml b/deployment/macos/Installer.pmdoc/03examples.xml
deleted file mode 100644
index eb3e19890eb4607fce33cdb92fecf1ab39b30bc4..0000000000000000000000000000000000000000
--- a/deployment/macos/Installer.pmdoc/03examples.xml
+++ /dev/null
@@ -1 +0,0 @@
-<pkgref spec="1.12" uuid="3B183244-2EEB-4A57-B208-AC7286128C55"><config><identifier>org.openstructure.OST.examples.pkg</identifier><version>1</version><description></description><post-install type="none"/><requireAuthorization/><installFrom>/Users/marco/Projects/ost/examples</installFrom><installTo mod="true">/Applications/OpenStructure/Examples</installTo><flags><followSymbolicLinks/></flags><packageStore type="internal"></packageStore><mod>parent</mod><mod>installTo.path</mod><mod>installTo</mod><mod>identifier</mod></config><contents><file-list>03examples-contents.xml</file-list><filter>/CVS$</filter><filter>/\.svn$</filter><filter>/\.cvsignore$</filter><filter>/\.cvspass$</filter><filter>/\.DS_Store$</filter></contents></pkgref>
\ No newline at end of file
diff --git a/deployment/macos/Installer.pmdoc/index.xml b/deployment/macos/Installer.pmdoc/index.xml
deleted file mode 100644
index 905606181a707e6cd0e8bc8500414b4b2cfb0924..0000000000000000000000000000000000000000
--- a/deployment/macos/Installer.pmdoc/index.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<pkmkdoc spec="1.12"><properties><title>OpenStructure</title><build>/Users/marco/Projects/ost/deployment/macos/openstructure_1.0a_1655.pkg</build><organization>org.openstructure</organization><userSees ui="both"/><min-target os="3"/><domain anywhere="true"/></properties><distribution><versions min-spec="1.000000"/><scripts></scripts></distribution><contents><choice title="DNG" id="choice1" starts_selected="true" starts_enabled="true" starts_hidden="false"><pkgref id="org.openstructure.DNG.pkg"/></choice><choice title="OpenStructure" id="choice2" starts_selected="true" starts_enabled="true" starts_hidden="false"><pkgref id="org.openstructure.OST.pkg"/></choice><choice title="Examples" id="choice3" starts_selected="true" starts_enabled="true" starts_hidden="false"><pkgref id="org.openstructure.OST.examples.pkg"/></choice></contents><resources bg-scale="none" bg-align="topleft"><locale lang="en"><resource relative="true" mod="true" type="license">../../LICENSE.txt</resource><resource mime-type="text/rtf" kind="embedded" type="conclusion"><![CDATA[{\rtf1\ansi\ansicpg1252\cocoartf949\cocoasubrtf540
-{\fonttbl\f0\fnil\fcharset0 LucidaGrande;\f1\fmodern\fcharset0 Courier;}
-{\colortbl;\red255\green255\blue255;}
-\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\ql\qnatural\pardirnatural
-
-\f0\fs26 \cf0 If you would like to run OpenStructure from the commandline, please add the following line to 
-\f1 .bashrc
-\f0  or 
-\f1 .bash_profile:\
-\
-export PATH=/usr/openstructure/bin:$PATH}]]></resource></locale></resources><flags/><item type="file">01dng.xml</item><item type="file">02openstructure.xml</item><item type="file">03examples.xml</item><mod>properties.title</mod></pkmkdoc>
\ No newline at end of file
diff --git a/deployment/macos/OpenStructure.pmdoc/01dng-contents.xml b/deployment/macos/OpenStructure.pmdoc/01dng-contents.xml
new file mode 100644
index 0000000000000000000000000000000000000000..07ba5eb54bb1bc79de429156dc817df23e274fb8
--- /dev/null
+++ b/deployment/macos/OpenStructure.pmdoc/01dng-contents.xml
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/deployment/macos/OpenStructure.pmdoc/01dng.xml b/deployment/macos/OpenStructure.pmdoc/01dng.xml
new file mode 100644
index 0000000000000000000000000000000000000000..08783eb2be2b5b349a3690e009ed429d67353a0d
--- /dev/null
+++ b/deployment/macos/OpenStructure.pmdoc/01dng.xml
@@ -0,0 +1 @@
+<pkgref spec="1.12" uuid="2FD6FA09-D2A6-4765-A83C-B0F8E372E8FD"><config><identifier>org.openstructure.DNG.pkg</identifier><version>1.0</version><description></description><post-install type="none"/><requireAuthorization/><installFrom relative="true" includeRoot="true">DNG.app</installFrom><installTo>/Applications</installTo><flags><followSymbolicLinks/></flags><packageStore type="internal"></packageStore><mod>parent</mod><mod>requireAuthorization</mod><mod>relocatable</mod><mod>installFrom.isRelativeType</mod><mod>includeRoot</mod><mod>identifier</mod></config><contents><file-list>01dng-contents.xml</file-list><component id="org.openstructure.OpenStructure" path="/Users/marco/Projects/prod_ost/deployment/macos/DNG.app" version="" isRelocatable="true"><locator-info><token title="pkmk-token-18"><search-rule><combo identifier="org.openstructure.OpenStructure" default-path="/Applications/DNG.app"/></search-rule></token></locator-info></component><filter>/CVS$</filter><filter>/\.svn$</filter><filter>/\.cvsignore$</filter><filter>/\.cvspass$</filter><filter>/\.DS_Store$</filter></contents></pkgref>
\ No newline at end of file
diff --git a/deployment/macos/OpenStructure.pmdoc/02standalone-contents.xml b/deployment/macos/OpenStructure.pmdoc/02standalone-contents.xml
new file mode 100644
index 0000000000000000000000000000000000000000..017395170b0b9af69db19dd8ec696b7bd3ebe17a
--- /dev/null
+++ b/deployment/macos/OpenStructure.pmdoc/02standalone-contents.xml
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diff --git a/deployment/macos/OpenStructure.pmdoc/02standalone.xml b/deployment/macos/OpenStructure.pmdoc/02standalone.xml
new file mode 100644
index 0000000000000000000000000000000000000000..7a54f677ae14a43721dfa5a7e3a665ac77f7f68e
--- /dev/null
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diff --git a/deployment/macos/OpenStructure.pmdoc/03examples-contents.xml b/deployment/macos/OpenStructure.pmdoc/03examples-contents.xml
new file mode 100644
index 0000000000000000000000000000000000000000..f18a985612230d440ca95a85e4f7440be08ac5e1
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o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="sdh.face.svn-base" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="sdh.pdb.svn-base" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="sdh.vert.svn-base" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="test_surf.py.svn-base" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="test_surf_pov.py.svn-base" o="marco" g="staff" p="33204"><mod>mode</mod></f><mod>mode</mod></f><f n="tmp" o="marco" g="staff" p="16893"><f n="prop-base" o="marco" g="staff" p="16893"><mod>mode</mod></f><f n="props" o="marco" g="staff" p="16893"><mod>mode</mod></f><f n="text-base" o="marco" g="staff" p="16893"><mod>mode</mod></f><mod>mode</mod></f><mod>mode</mod></f><f n="fragment.pdb" o="marco" g="staff" p="33204"/><f n="sdh.face" o="marco" g="staff" p="33277"/><f n="sdh.pdb" o="marco" g="staff" p="33204"/><f n="sdh.vert" o="marco" g="staff" p="33277"/><f n="test_surf.py" o="marco" g="staff" p="33204"/><f n="test_surf_pov.py" o="marco" g="staff" p="33204"/></f><f n="trj" o="marco" g="staff" p="16893"><f n=".svn" o="marco" g="staff" p="16893"><f n="all-wcprops" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="dir-prop-base" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="entries" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="prop-base" o="marco" g="staff" p="16893"><f n="mpor_trj.crd.svn-base" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="mpor_trj_short.trj.svn-base" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="sample.dcd.svn-base" o="marco" g="staff" p="33204"><mod>mode</mod></f><mod>mode</mod></f><f n="props" o="marco" g="staff" p="16893"><mod>mode</mod></f><f n="text-base" o="marco" g="staff" p="16893"><f n="fragment.pdb.svn-base" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="mpor_trj.crd.svn-base" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="mpor_trj_short.trj.svn-base" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="sample.dcd.svn-base" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="sample.pdb.svn-base" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="test_trj.py.svn-base" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="test_trj_blur.py.svn-base" o="marco" g="staff" p="33204"><mod>mode</mod></f><mod>mode</mod></f><f n="tmp" o="marco" g="staff" p="16893"><f n="prop-base" o="marco" g="staff" p="16893"><mod>mode</mod></f><f n="props" o="marco" g="staff" p="16893"><mod>mode</mod></f><f n="text-base" o="marco" g="staff" p="16893"><mod>mode</mod></f><mod>mode</mod></f><mod>mode</mod></f><f n="fragment.pdb" o="marco" g="staff" p="33204"/><f n="mpor_trj.crd" o="marco" g="staff" p="33277"/><f n="mpor_trj_short.trj" o="marco" g="staff" p="33277"/><f n="sample.dcd" o="marco" g="staff" p="33204"/><f n="sample.pdb" o="marco" g="staff" p="33204"/><f n="test_trj.py" o="marco" g="staff" p="33204"/><f n="test_trj_blur.py" o="marco" g="staff" p="33204"/></f><f n="ui" o="marco" g="staff" p="16893"><f n=".svn" o="marco" g="staff" p="16893"><f n="all-wcprops" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="dir-prop-base" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="entries" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="prop-base" o="marco" g="staff" p="16893"><mod>mode</mod></f><f n="props" o="marco" g="staff" p="16893"><mod>mode</mod></f><f n="text-base" o="marco" g="staff" p="16893"><f n="board.py.svn-base" o="marco" g="staff" p="33277"><mod>mode</mod></f><f n="color_tool.py.svn-base" o="marco" g="staff" p="33277"><mod>mode</mod></f><f n="mdi_example.py.svn-base" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="menubar_example.py.svn-base" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="widget_example.py.svn-base" o="marco" g="staff" p="33204"><mod>mode</mod></f><mod>mode</mod></f><f n="tmp" o="marco" g="staff" p="16893"><f n="prop-base" o="marco" g="staff" p="16893"><mod>mode</mod></f><f n="props" o="marco" g="staff" p="16893"><mod>mode</mod></f><f n="text-base" o="marco" g="staff" p="16893"><mod>mode</mod></f><mod>mode</mod></f><mod>mode</mod></f><f n="board.py" o="marco" g="staff" p="33277"/><f n="board.pyc" o="marco" g="staff" p="33204"/><f n="color_tool.py" o="marco" g="staff" p="33277"/><f n="mdi_example.py" o="marco" g="staff" p="33204"/><f n="menubar_example.py" o="marco" g="staff" p="33204"/><f n="widget_example.py" o="marco" g="staff" p="33204"/></f></f></pkg-contents>
\ No newline at end of file
diff --git a/deployment/macos/OpenStructure.pmdoc/03examples.xml b/deployment/macos/OpenStructure.pmdoc/03examples.xml
new file mode 100644
index 0000000000000000000000000000000000000000..ff0317996f21014d462583eae994b0775529ce4b
--- /dev/null
+++ b/deployment/macos/OpenStructure.pmdoc/03examples.xml
@@ -0,0 +1 @@
+<pkgref spec="1.12" uuid="C2FAE439-87F5-415C-91EE-0436CC2E4D66"><config><identifier>org.openstructure.Examples.pkg</identifier><version>1.0</version><description></description><post-install type="none"/><requireAuthorization/><installFrom relative="true" mod="true">../../examples</installFrom><installTo mod="true">/Library/OpenStructure/examples</installTo><flags><followSymbolicLinks/></flags><packageStore type="internal"></packageStore><mod>parent</mod><mod>installFrom.isRelativeType</mod><mod>installTo.path</mod><mod>installFrom.path</mod><mod>installTo</mod><mod>identifier</mod></config><contents><file-list>03examples-contents.xml</file-list><filter>/CVS$</filter><filter>/\.svn$</filter><filter>/\.cvsignore$</filter><filter>/\.cvspass$</filter><filter>/\.DS_Store$</filter></contents></pkgref>
\ No newline at end of file
diff --git a/deployment/macos/OpenStructure.pmdoc/index.xml b/deployment/macos/OpenStructure.pmdoc/index.xml
new file mode 100644
index 0000000000000000000000000000000000000000..58623dbf2cb0cf54e05205cd5611105624528a24
--- /dev/null
+++ b/deployment/macos/OpenStructure.pmdoc/index.xml
@@ -0,0 +1 @@
+<pkmkdoc spec="1.12"><properties><title>OpenStructure</title><build>/Users/marco/Sites/ost-leopard.pkg</build><organization>org.openstructure</organization><userSees ui="easy"/><min-target os="3"/><domain system="true" user="true"/></properties><distribution><versions min-spec="1.000000"/><scripts></scripts></distribution><contents><choice title="DNG" id="choice6" description="DNG Graphical Frontend" starts_selected="true" starts_enabled="true" starts_hidden="false"><pkgref id="org.openstructure.DNG.pkg"/></choice><choice title="OpenStructure" id="choice7" description="The OpenStructure Framework" starts_selected="true" starts_enabled="true" starts_hidden="false"><pkgref id="org.openstructure.OpenStructure.pkg"/></choice><choice title="examples" id="choice8" description="OpenStructure Example Files" starts_selected="true" starts_enabled="true" starts_hidden="false"><pkgref id="org.openstructure.Examples.pkg"/></choice></contents><resources bg-scale="none" bg-align="topleft"><locale lang="en"/></resources><flags/><item type="file">01dng.xml</item><item type="file">02standalone.xml</item><item type="file">03examples.xml</item><mod>properties.customizeOption</mod><mod>properties.userDomain</mod><mod>properties.title</mod><mod>properties.anywhereDomain</mod><mod>properties.systemDomain</mod></pkmkdoc>
\ No newline at end of file
diff --git a/deployment/macos/bundle.py b/deployment/macos/bundle.py
new file mode 100644
index 0000000000000000000000000000000000000000..01d25441be9c6678576cd25f075f6496c28bbe89
--- /dev/null
+++ b/deployment/macos/bundle.py
@@ -0,0 +1,85 @@
+INFO_PLIST="""<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" 
+    "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+<dict>
+  <key>CFBundleDevelopmentRegion</key>
+  <string>English</string>
+  <key>CFBundleExecutable</key>
+  <string>dng</string>
+  <key>CFBundleHelpBookFolder</key>
+  <string>OpenStructure Manual</string>
+  <key>CFBundleHelpBookName</key>
+  <string>_BUNDLE_ Help</string>
+  <key>CFBundleIconFile</key>
+  <string>icon.icns</string>
+  <key>CFBundleIdentifier</key>
+  <string>org.openstructure.OpenStructure</string>
+  <key>CFBundleInfoDictionaryVersion</key>
+  <string>6.0</string>
+  <key>CFBundlePackageType</key>
+  <string>APPL</string>
+  <key>CFBundleSignature</key>
+  <string>????</string>
+  <key>CFBundleVersion</key>
+  <string></string>
+  <key>NSMainNibFile</key>
+  <string>MainMenu</string>
+  <key>NSPrincipalClass</key>
+  <string>NSApplication</string>
+</dict>
+</plist>"""
+
+import os
+from shutil import copy
+import stat
+def _WritePkgInfo(bundle):
+    pkg_info=open(os.path.join(bundle+'.app', 'Contents/PkgInfo'), 'w+')
+    pkg_info.write('APPL????')
+    pkg_info.close()
+
+def _WriteInfoPList(bundle):
+    info_plist=open(os.path.join(bundle+'.app', 'Contents/Info.plist'), 'w+')
+    info_plist.write(INFO_PLIST)
+    info_plist.close()
+
+def _WriteScript(bundle, standalone):
+  if standalone:
+    script="""#!/bin/sh
+if [ -h "$0" ] ; then
+  SCRIPT_NAME=`readlink "$0"`
+else
+  SCRIPT_NAME="$0"
+fi
+`dirname "$SCRIPT_NAME"`/../bin/dng
+    """
+  else:
+    script="""#!/bin/sh
+if [ -e $HOME/Library/OpenStructure/bin/dng ]; then
+  $HOME/Library/OpenStructure/bin/dng
+else
+  /Library/OpenStructure/bin/dng
+fi
+    """
+  bin_path=os.path.join('%s.app' % bundle, 'Contents/MacOS/dng')
+  bin=open(bin_path, 'w+')
+  bin.write(script)
+  bin.close()
+  os.system('chmod a+x %s' % bin_path)
+
+def _CreateBundleSkeleton(bundle, standalone):
+  bin_path=os.path.join('%s.app' % bundle, 'Contents/MacOS')
+  if not os.path.exists(bin_path):
+    os.makedirs(bin_path)
+  _WritePkgInfo(bundle)
+  _WriteInfoPList(bundle)
+  _WriteScript(bundle, standalone)
+  res_dir='%s.app/Contents/Resources' % bundle
+  if not os.path.exists(res_dir):
+    os.makedirs(res_dir)  
+  copy('../../graphics/icon.icns', res_dir)
+
+def create_bundle(bundle_name, standalone=False):
+  _CreateBundleSkeleton(bundle_name, standalone)
+  if standalone:
+    os.system('mv standalone/* DNG.app/Contents/')
\ No newline at end of file
diff --git a/deployment/macos/create_bundle.py b/deployment/macos/create_bundle.py
index 74f8b486621d53acfe73fd4e4242aeebcfc877a8..6a00d75db3bba9f127b6527b2fa91b6046837580 100644
--- a/deployment/macos/create_bundle.py
+++ b/deployment/macos/create_bundle.py
@@ -7,6 +7,10 @@ INFO_PLIST="""<?xml version="1.0" encoding="UTF-8"?>
   <string>English</string>
   <key>CFBundleExecutable</key>
   <string>dng</string>
+  <key>CFBundleName</key>
+  <string>DNG</string>  
+  <key>CFBundleDisplayName</key>
+  <string>DNG</string>  
   <key>CFBundleHelpBookFolder</key>
   <string>OpenStructure Manual</string>
   <key>CFBundleHelpBookName</key>
diff --git a/deployment/macos/deploy.py b/deployment/macos/deploy.py
new file mode 100644
index 0000000000000000000000000000000000000000..60d45e647da40c0b94d806b6a8107cdc6569049e
--- /dev/null
+++ b/deployment/macos/deploy.py
@@ -0,0 +1,23 @@
+import bundle
+import deps
+import sys
+from optparse import OptionParser
+import shutil
+import os
+p=OptionParser()
+p.add_option('--bundle', action='store_true', default=False)
+p.add_option('--no_rpath', action='store_true',
+             default=False)
+p.add_option('--macports_workaround', action='store_true', default=False)
+opts, args=p.parse_args()
+deps.make_standalone('../../stage', 'standalone', True, 
+                     opts.no_rpath, 
+                     macports_workaround=opts.macports_workaround)
+if os.path.exists('DNG.app'):
+  shutil.rmtree('DNG.app')
+bundle.create_bundle('DNG', opts.bundle)
+if opts.bundle:
+  shutil.copytree('../../examples', 'DNG.app/Contents/examples')
+  os.system('rm `find DNG.app/Contents/examples/ -name "*.pyc"`')
+  os.system('rm -rf DNG.app/Contents/examples/harmony')
+  os.system('rm -rf DNG.app/Contents/examples/dokk')  
\ No newline at end of file
diff --git a/deployment/macos/deps.py b/deployment/macos/deps.py
new file mode 100644
index 0000000000000000000000000000000000000000..460071d1b7effb0eb7477549f9495699891729da
--- /dev/null
+++ b/deployment/macos/deps.py
@@ -0,0 +1,319 @@
+import os
+import subprocess
+import shutil
+import sys
+import glob
+
+def _lib_name(component):
+  return 'libost_%s.dylib' % component
+
+def _deps_for_lib(lib, pool, recursive=True):
+  if lib in pool:
+    return
+  otool=subprocess.Popen(['otool', '-L', lib], stdout=subprocess.PIPE)
+  output=otool.communicate()[0]
+  lines=output.split('\n')[1:]
+  for line in lines:
+    d=line.split(' ')[0].strip()
+    if len(d)>0:
+      if d==lib:
+        continue
+      if d not in pool:
+        if d.startswith('/System') or d.startswith('/usr/lib'):
+          continue
+        if recursive:
+          _deps_for_lib(d, pool)
+        pool.add(d)        
+  return
+
+def collect_deps(stage_dir, components, binaries, site_packages, 
+                 site_packages_dir):
+  """
+  Collect the dependencies for the given components and returns a list of 
+  frameworks/libraries that the component depends on.
+  """
+  pool=set()
+  for component in components:
+    lib_name=os.path.abspath(os.path.join(stage_dir, 'lib', 
+                                          _lib_name(component)))  
+    if not os.path.exists(lib_name):
+      print 'WARNING:', lib_name, 'does not exist'
+    if lib_name not in pool:
+      _deps_for_lib(lib_name, pool)
+      pool.add(lib_name)    
+  for bin in binaries:  
+    bin_name=os.path.abspath(os.path.join(stage_dir, 'bin', 
+                                          bin))  
+    if not os.path.exists(bin_name):
+      print 'WARNING:', bin_name, 'does not exist'
+      continue
+    if bin_name not in pool:
+      _deps_for_lib(bin_name, pool)
+  for site_package in site_packages:
+    full_path=os.path.join(site_packages_dir, site_package)
+    if not os.path.exists(full_path):
+      print 'WARNING', site_package, 'does not exists'
+      continue
+    if os.path.isdir(full_path):
+      for so_file in glob.glob(os.path.join(full_path, '*.so')):
+        _deps_for_lib(so_file, pool)
+  return pool
+
+BINARIES=['gosty', 'chemdict_tool']
+COMPONENTS=['mol', 'geom', 'conop', 'gfx', 'gui', 'seq_alg', 'seq', 
+            'img', 'img_alg', 'qa', 'info', 'io', 'db', 'base']
+SCRIPTS=['dng', 'ost']
+CHANGE_ID_RPATH='install_name_tool -id @rpath/%s %s'   
+CHANGE_ID='install_name_tool -id @executable_path/%s %s'   
+CHANGE_LOAD_CMD_RPATH='install_name_tool -change %s @rpath/%s %s'
+CHANGE_LOAD_CMD='install_name_tool -change %s @executable_path/%s %s'
+ADD_RPATH='install_name_tool -add_rpath %s %s 2> /dev/null'
+SITE_PACKAGES=['sip.so', 'sipconfig.py', 'sipdistutils.py', 'PyQt4']
+REMOVE_HEADERS='rm -rf `find %s/lib -type d -name Headers`'
+REMOVE_CURRENT='rm -rf `find %s/lib -type d -name Current`'
+# collect libs of non-standard libraries/frameworks we depend on
+
+def copy_binaries(stage_dir, outdir, binary_names, scripts, use_rpath, 
+                  append_bin=True):
+
+  exe_path=os.path.abspath(os.path.join(outdir, 'bin'))
+  for binary_name in binary_names:
+    if append_bin:
+      bin_name=os.path.join(stage_dir, 'bin', binary_name)
+    else:
+      bin_name=os.path.join(stage_dir, binary_name)
+    if not os.path.exists(bin_name):
+      print 'WARNING:', binary_name, 'does not exist'
+      continue
+    dst_name=os.path.join(outdir, 'bin', os.path.basename(bin_name))
+    shutil.copy(bin_name, dst_name)
+    update_load_commands(dst_name, True, use_rpath, exe_path)
+    os.system(ADD_RPATH % ('../lib', dst_name))
+  for script in scripts:
+    shutil.copy(os.path.join(stage_dir, 'bin', script), 
+                os.path.join(outdir,'bin', script))
+
+def split_framework_components(abs_path):
+    """
+    Splits the path pointing to a dynamic library within a framework
+    
+    '/System/Frameworks/A.framework/Versions/4/A' =>
+    ['/System/Frameworks/A.framework', 'Versions/4/A']
+    """
+    parts=abs_path.split('/')
+    for i, s in enumerate(parts):
+      if s.endswith('.framework'):
+        lead=os.path.join('/', *parts[:i+1])
+        trail=os.path.join(*parts[i+1:])
+        return lead, trail
+
+def change_id(id, lib, use_rpath):
+  os.chmod(lib, 0666)
+  if use_rpath:
+    os.system(CHANGE_ID_RPATH % (id,lib))
+  else:
+    os.system(CHANGE_ID % (id,lib))
+  os.chmod(lib, 0444)
+
+def update_load_commands(lib, exe, use_rpath, exe_path):
+  direct_deps=set()
+  _deps_for_lib(lib, direct_deps, recursive=False)
+  os.chmod(lib, 0666)
+  for direct_dep in direct_deps:
+    if direct_dep.endswith('.dylib'):
+      if use_rpath:
+        new_name=os.path.basename(direct_dep)
+        os.system(CHANGE_LOAD_CMD_RPATH % (direct_dep, new_name, lib))
+      else:
+        new_name=os.path.join('../lib', os.path.basename(direct_dep))
+        os.system(CHANGE_LOAD_CMD % (direct_dep, new_name, lib))
+    else:
+      assert direct_dep.find('.framework/')>=0
+      if use_rpath:
+        framework_path, rel_path=split_framework_components(direct_dep)
+        framework_name=os.path.basename(framework_path)
+        new_name=os.path.join(framework_name, rel_path)
+        os.system(CHANGE_LOAD_CMD_RPATH % (direct_dep, new_name, lib))
+      else:
+        framework_path, rel_path=split_framework_components(direct_dep)
+        framework_name=os.path.basename(framework_path)      
+        new_name=os.path.join('../lib', framework_name, rel_path)
+        os.system(CHANGE_LOAD_CMD % (direct_dep, new_name, lib))
+  if use_rpath:
+    os.system(ADD_RPATH % ('.', lib))
+  if exe:
+    os.chmod(lib, 0555)
+  else:
+    os.chmod(lib, 0444)
+
+def copy_deps(dependencies, outdir, use_rpath):
+  exe_path=os.path.join(outdir, 'bin')
+  for dep in dependencies:
+    if dep.endswith('.dylib'):
+      dst_name=os.path.join(outdir, 'lib', os.path.basename(dep))
+      if not os.path.exists(dep):
+        continue
+      shutil.copy(dep, dst_name)
+      if use_rpath:
+        change_id(os.path.basename(dep), dst_name, use_rpath)
+      else:
+        change_id('../lib/%s' % os.path.basename(dep), dst_name, use_rpath)
+      update_load_commands(dst_name, False, use_rpath, exe_path)
+    else:
+      assert dep.find('.framework/')>=0
+      framework_path, rel_path=split_framework_components(dep)
+      framework_name=os.path.basename(framework_path)
+      dst_name=os.path.join(outdir, 'lib', framework_name)
+      shutil.copytree(framework_path, dst_name)
+      if use_rpath:
+        change_id(os.path.join(dst_name, rel_path), 
+                  os.path.join(dst_name, rel_path), use_rpath)
+      else:
+        change_id(os.path.join('../lib', framework_name, rel_path), 
+                  os.path.join(dst_name, rel_path), use_rpath)
+      os.unlink(os.path.join(dst_name, os.path.splitext(framework_name)[0]))
+      update_load_commands(os.path.join(dst_name, rel_path), False, 
+                           use_rpath, exe_path)
+
+def update_pymod_shared_objects(args, path, files):
+  lib_path, use_rpath=args
+  exe_path=os.path.abspath(os.path.join(lib_path, '../bin'))
+  for f in files:
+    if not os.path.exists(os.path.join(path, f)):
+      continue
+    base, ext=os.path.splitext(f)
+    if  ext=='.so':
+      path_to_lib_path=os.path.relpath(lib_path, path)
+      abs_name=os.path.join(path, f)
+      os.system(ADD_RPATH % (path_to_lib_path, abs_name))
+      update_load_commands(abs_name, False, use_rpath, exe_path)
+    elif ext in ('.pyc', '.pyo'):
+      os.unlink(os.path.join(path, f))
+
+def get_site_package_dir():
+  """
+  Get site-package directory of this python installation. This assumes 
+  that ost was linked against the same version of Python
+  """
+  for p in sys.path:
+    pattern='/site-packages'
+    index=p.find(pattern)
+    if index>=0:
+      return p[:index+len(pattern)]
+  raise RuntimeError("Couldn't determine site-packages location")
+
+def get_python_home():
+  """
+  Derive Python home by looking at the location of the os module
+  """
+  return os.path.dirname(sys.modules['os'].__file__)
+
+def check_install_name_tool_capabilities():
+  """
+  Find out whether install_name_tool supports the add_rpath option.
+  """
+  inst_name_tool=subprocess.Popen('install_name_tool', shell=True, 
+                                  stderr=subprocess.PIPE)
+  output=inst_name_tool.communicate()[1]
+  return output.find('-add_rpath')!=-1
+
+def make_standalone(stage_dir, outdir, no_includes, force_no_rpath=False,
+                    macports_workaround=False):
+  site_packages=get_site_package_dir()                    
+  # figure out if install_name_tool supports the -add_rpath option.
+  use_rpath=True
+  if not check_install_name_tool_capabilities():
+    print "install_name_tool doesn't support the -add_rpath option."
+    print "I will fallback to the more arcane @executable_path"
+    use_rpath=False
+  elif force_no_rpath:
+    print "I will use the arcane @executable_path"
+    use_rpath=False
+
+  if os.path.exists(outdir):
+    shutil.rmtree(outdir)
+  os.system('mkdir -p "%s"' % outdir)
+  os.system('mkdir -p "%s/lib"' % outdir)
+  os.system('mkdir -p "%s/bin"' % outdir)
+  print 'copying shared datafiles'
+  shutil.copytree(os.path.join(stage_dir, 'share'), 
+                  os.path.join(outdir, 'share'))
+  print 'collecting dependencies'
+  deps=collect_deps(stage_dir, COMPONENTS, BINARIES, SITE_PACKAGES, 
+                    site_packages)
+  print 'copying dependencies'
+  copy_deps(deps, outdir, use_rpath)
+  print 'copying binaries'
+  copy_binaries(stage_dir, outdir, BINARIES, SCRIPTS, use_rpath)
+  print 'copying pymod'
+  shutil.copytree(os.path.join(stage_dir, 'lib/openstructure'), 
+                  os.path.join(outdir, 'lib/openstructure'))
+  copied_py_framework=False
+  non_std_python=False
+  if os.path.exists(os.path.join(outdir, 'lib/Python.framework')):
+    framework_path=os.path.join(outdir, 'lib/Python.framework')
+    nonstd_python=True
+    copied_py_framework=True
+  if len(glob.glob(os.path.join(outdir, 'lib', 'libpython*')))>0:
+    non_std_python=True
+  if non_std_python:
+    print 'looks like we are using a non-standard python.'
+    python_home=get_python_home()    
+    if not copied_py_framework:
+      print 'also copying python modules from %s' % python_home
+      modules_dst=os.path.join(outdir, 'lib', os.path.basename(python_home))
+      shutil.copytree(python_home, modules_dst)
+      if os.path.exists(os.path.join(modules_dst, 'site-packages')):
+        shutil.rmtree(os.path.join(modules_dst, 'site-packages'))
+      copy_binaries(os.path.join(python_home, '../..'), outdir, 
+                    ['python'], [], use_rpath)
+      python_bin=os.path.abspath(os.path.join(python_home, '../../bin/python'))
+    else:
+      # For MacPorts it's even more involved. Python is not executed directly 
+      # but rather uses a wrapper executable that calls the actual python exe.
+      # We have to include that one into the bundle.
+      if macports_workaround:
+        path_to_app='../../Resources/Python.app/Contents/MacOS/'
+        exe_path=os.path.join(python_home, path_to_app)
+        copy_binaries(exe_path, outdir, ['python'], [], 
+                      use_rpath, append_bin=False)
+        python_bin=os.path.join('/opt/local/bin/python')
+      else:
+        copy_binaries(os.path.join(python_home, '../..'), outdir, 
+                      ['python'], [], use_rpath)
+        python_bin=os.path.abspath(os.path.join(python_home, '../../bin/python'))
+      # remove all versions but the one we are using
+      version_string=sys.version[0:3]
+      prefix, postfix=split_framework_components(python_home)
+      site_packages_dir=os.path.join(outdir, 'lib', 'Python.framework', 
+                                 postfix, 'site-packages')
+      if os.path.exists(site_packages_dir):
+        shutil.rmtree(site_packages_dir)
+      for directory in glob.glob(os.path.join(framework_path, 'Versions/*')):
+        if os.path.basename(directory)!=version_string:
+          shutil.rmtree(directory)
+    # replace the python executable
+    ost_script=os.path.join(outdir, 'bin', 'ost')
+    os.chmod(ost_script, 0666)
+    script=''.join(open(ost_script, 'r').readlines())
+    script=script.replace(python_bin, '$BIN_DIR/python')
+    open(ost_script, 'w').write(script)
+    os.chmod(ost_script, 0555)
+  elif use_rpath==False:
+    print 'BIG FAT WARNING: Creation bundle with @executable_path and default'
+    print 'Python might not work. Test carefully before deploying.'
+
+  if no_includes:
+    os.system(REMOVE_HEADERS % outdir)
+    os.system(REMOVE_CURRENT % outdir)  
+  print 'copying site-packages'
+  for sp in SITE_PACKAGES:
+    src=os.path.join(site_packages, sp)  
+    if os.path.isdir(src):
+      shutil.copytree(src, os.path.join(outdir, 'lib/openstructure', sp))
+    else:
+      shutil.copy(src, os.path.join(outdir, 'lib/openstructure', sp))
+  print 'updating link commands of python shared objects'
+  os.path.walk(os.path.join(outdir, 'lib'), 
+               update_pymod_shared_objects, 
+               (os.path.join(outdir, 'lib'), use_rpath))
diff --git a/deployment/win/CMakeLists.txt b/deployment/win/CMakeLists.txt
index 931ed78e0d78b3601ac87d8e62618cbd57a2af19..01c1a1d7a1ad9dab4b969f5516fdc071dc6bd440 100644
--- a/deployment/win/CMakeLists.txt
+++ b/deployment/win/CMakeLists.txt
@@ -1,5 +1,5 @@
 if(DEPLOYMENT)
-  get_ost_rev()
+#  get_ost_rev()
   include(Deployment)
   set(SUBST_DICT OST_VERSION="${OST_VERSION}")
   add_custom_target(deployment ALL)
diff --git a/deployment/win/create_archive.bat b/deployment/win/create_archive.bat
deleted file mode 100644
index 06902f502663f74180ca21132c842f14d606a6e4..0000000000000000000000000000000000000000
--- a/deployment/win/create_archive.bat
+++ /dev/null
@@ -1,24 +0,0 @@
-@ECHO OFF
-REM create a zip archive for deployment on windows
-REM no regisrty entries
-REM no PATHs will be changed except in the DNG session
-set inst_dir=openstructure1.0.0a1_1885
-set archive_name=OpenStructureWin32
-if exist "%inst_dir%" rmdir /S /Q "%inst_dir%" 
-if exist %archive_name%.zip del %archive_name%.zip*.*
-REM dir /S %inst_dir%
-mkdir "%inst_dir%\share\openstructure\examples"
-mkdir "%inst_dir%\lib\site-packages"
-mkdir "%inst_dir%\bin"
-xcopy  /E /I ..\..\examples "%inst_dir%\share\openstructure\examples"
-xcopy  /E /I ..\..\stage\share "%inst_dir%\share\"
-REM xcopy  /E /I ..\..\website\html "%inst_dir%\share\doc"
-copy  d:\programs\bin\python.exe "%inst_dir%\bin"
-
-xcopy  /E /I /EXCLUDE:excludes d:\programs\lib "%inst_dir%\lib"
-xcopy  /E /I ..\..\stage\lib "%inst_dir%\lib"
-xcopy /E /I /EXCLUDE:excludes ..\..\stage\bin "%inst_dir%\bin"
-set PATH="c:\Program Files (x86)"\7-Zip\;%PATH%
-REM 7z a -r -t7z %archive_name% "%inst_dir%" > log
-REM if exist %archive_name%.7z copy /b 7zS.sfx + config.txt + %archive_name%.7z %archive_name%.exe
-7z a -r -tzip %archive_name% "%inst_dir%" > log
diff --git a/deployment/win/create_archive.bat.in b/deployment/win/create_archive.bat.in
index de67e8fa0f02c9f63b504245de6a4d3f5123818d..47168bf3fe90c02e5ecec263efb8a1e9299f2688 100644
--- a/deployment/win/create_archive.bat.in
+++ b/deployment/win/create_archive.bat.in
@@ -1,7 +1,10 @@
 @ECHO OFF
 REM create a zip archive for deployment on windows
-REM no regisrty entries
+REM no registry entries
 REM no PATHs will be changed except in the DNG session
+REM 
+REM Author Juergen Haas
+REM
 set inst_dir=openstructure@OST_VERSION@
 set archive_name=OpenStructureWin32
 if exist "%inst_dir%" rmdir /S /Q "%inst_dir%" 
@@ -10,15 +13,19 @@ REM dir /S %inst_dir%
 mkdir "%inst_dir%\share\openstructure\examples"
 mkdir "%inst_dir%\lib\site-packages"
 mkdir "%inst_dir%\bin"
-xcopy  /E /I ..\..\examples "%inst_dir%\share\openstructure\examples"
-xcopy  /E /I ..\..\stage\share "%inst_dir%\share\"
+xcopy  /E /I /Y /EXCLUDE:exclude_file_types  ..\..\examples "%inst_dir%\share\openstructure\examples"
+xcopy  /E /I /Y /EXCLUDE:exclude_file_types ..\..\stage\share "%inst_dir%\share\"
 REM xcopy  /E /I ..\..\website\html "%inst_dir%\share\doc"
 copy  d:\programs\bin\python.exe "%inst_dir%\bin"
-
-xcopy  /E /I /EXCLUDE:excludes d:\programs\lib "%inst_dir%\lib"
-xcopy  /E /I ..\..\stage\lib "%inst_dir%\lib"
-xcopy /E /I /EXCLUDE:excludes ..\..\stage\bin "%inst_dir%\bin"
+copy ..\README.html "%inst_dir%" 
+copy ..\..\graphics\favicon.ico "%inst_dir%\share"
+copy dng.bat "%inst_dir%" 
+xcopy  /E /I /Y /EXCLUDE:excludes+exclude_file_types d:\programs\lib "%inst_dir%\lib"
+xcopy  /E /I /Y /EXCLUDE:excludes+exclude_file_types  ..\..\stage\lib "%inst_dir%\lib"
+xcopy /E /I /Y /EXCLUDE:excludes+exclude_file_types ..\..\stage\bin "%inst_dir%\bin"
 set PATH="c:\Program Files (x86)"\7-Zip\;%PATH%
 REM 7z a -r -t7z %archive_name% "%inst_dir%" > log
 REM if exist %archive_name%.7z copy /b 7zS.sfx + config.txt + %archive_name%.7z %archive_name%.exe
+if exist \TMTools\TMalign.exe copy /B \TMTools\TMalign.exe "%inst_dir%\bin\Release"
+if exist \TMTools\TMscore.exe copy /B \TMTools\TMscore.exe "%inst_dir%\bin\Release"
 7z a -r -tzip %archive_name% "%inst_dir%" > log
\ No newline at end of file
diff --git a/deployment/win/dng.bat b/deployment/win/dng.bat
new file mode 100644
index 0000000000000000000000000000000000000000..388e79e936dc18abd87c3902f3819b44a22f4869
--- /dev/null
+++ b/deployment/win/dng.bat
@@ -0,0 +1,23 @@
+@ECHO OFF
+REM ------------------------------------------------------------------------------
+REM This file is part of the OpenStructure project <www.openstructure.org>
+REM
+REM Copyright (C) 2008-2010 by the OpenStructure authors
+REM
+REM This library is free software; you can redistribute it and/or modify it under
+REM the terms of the GNU Lesser General Public License as published by the Free
+REM Software Foundation; either version 3.0 of the License, or (at your option)
+REM any later version.
+REM This library is distributed in the hope that it will be useful, but WITHOUT
+REM ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+REM FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+REM details.
+REM
+REM You should have received a copy of the GNU Lesser General Public License
+REM along with this library; if not, write to the Free Software Foundation, Inc.,
+REM 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+REM ------------------------------------------------------------------------------
+REM Windows startup script for a protein-centric user interface
+REM Author: Juergen Haas
+
+call "%~dp0\bin\dng.bat" %*
diff --git a/deployment/win/exclude_file_types b/deployment/win/exclude_file_types
new file mode 100644
index 0000000000000000000000000000000000000000..2ef73e4f551bffe1190f5eb9902bc69e7ec7a9a4
--- /dev/null
+++ b/deployment/win/exclude_file_types
@@ -0,0 +1,7 @@
+.lib
+.exp
+.pyc
+.idb
+dokk
+harmony
+README
diff --git a/deployment/win/excludes b/deployment/win/excludes
index cd3894ade9c8cd5571d39e7d2c84bb571ac97f35..9e8fc733f560afd6a1ac1eeb5f34b27e1921cc7d 100644
--- a/deployment/win/excludes
+++ b/deployment/win/excludes
@@ -3,4 +3,7 @@ graph
 prg_exec
 signals
 libboost
-create_archive
\ No newline at end of file
+create_archive
+.pdb
+markdown
+pygments
\ No newline at end of file
diff --git a/deployment/win/log b/deployment/win/log
deleted file mode 100644
index e599d7444e0d8461dd2f5f901a5dc3a40701cb30..0000000000000000000000000000000000000000
--- a/deployment/win/log
+++ /dev/null
@@ -1,2542 +0,0 @@
-
-7-Zip 4.65  Copyright (c) 1999-2009 Igor Pavlov  2009-02-03
-Scanning
-
-Creating archive OpenStructure_WIN32.zip
-
-Compressing  openstructure\bin\bjam.exe
-Compressing  openstructure\bin\dng.bat
-Compressing  openstructure\bin\Eula.txt
-Compressing  openstructure\bin\gipltng.bat
-Compressing  openstructure\bin\init.py
-Compressing  openstructure\bin\init_cl.py
-Compressing  openstructure\bin\init_iplt.py
-Compressing  openstructure\bin\jom.exe
-Compressing  openstructure\bin\ost.bat
-Compressing  openstructure\bin\pexports.exe
-Compressing  openstructure\bin\phonon4.dll
-Compressing  openstructure\bin\phonond4.dll
-Compressing  openstructure\bin\procmon.chm
-Compressing  openstructure\bin\Procmon.exe
-Compressing  openstructure\bin\python.exe
-Compressing  openstructure\bin\python.suo
-Compressing  openstructure\bin\Qt3Support4.dll
-Compressing  openstructure\bin\Qt3Supportd4.dll
-Compressing  openstructure\bin\QtCore4.dll
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-Compressing  openstructure\lib\xml\parsers\expat.py
-Compressing  openstructure\lib\xml\parsers\__init__.py
-Compressing  openstructure\lib\xml\sax\expatreader.py
-Compressing  openstructure\lib\xml\sax\handler.py
-Compressing  openstructure\lib\xml\sax\saxutils.py
-Compressing  openstructure\lib\xml\sax\xmlreader.py
-Compressing  openstructure\lib\xml\sax\_exceptions.py
-Compressing  openstructure\lib\xml\sax\__init__.py
-Compressing  openstructure\lib\xml\__init__.py
-Compressing  openstructure\lib\xml\__init__.pyc
-Compressing  openstructure\lib\zdll.exp
-Compressing  openstructure\lib\zdll.lib
-Compressing  openstructure\lib\zipfile.py
-Compressing  openstructure\lib\zlib.def
-Compressing  openstructure\lib\zlib1.dll
-Compressing  openstructure\lib\zlib1.exp
-Compressing  openstructure\lib\zlib1.lib
-Compressing  openstructure\lib\zlib1d.dll
-Compressing  openstructure\lib\zlib1d.lib
-Compressing  openstructure\lib\_abcoll.py
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-Compressing  openstructure\lib\_ctypes_test.lib
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-Compressing  openstructure\lib\_LWPCookieJar.py
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-
-Everything is Ok
diff --git a/doc/.gitignore b/doc/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..7c5f0a3725c4e27a34fd5a500aaae8dc224f880f
--- /dev/null
+++ b/doc/.gitignore
@@ -0,0 +1,2 @@
+build
+source
diff --git a/doc/conf/conf.py b/doc/conf/conf.py
index d7a1455a17fa44609c07625ed99d33de930ce6f1..e37ac88a4dba6c8b16869ba1964cb688104aa527 100644
--- a/doc/conf/conf.py
+++ b/doc/conf/conf.py
@@ -16,8 +16,10 @@ import sys, os
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-#sys.path.append(os.path.abspath('.'))
-
+sys.path.append(os.path.join(os.path.abspath('../..'), 
+                             'stage/lib/openstructure'))
+sys.path.append(os.path.join(os.path.abspath('../..'), 
+                             'stage/lib64/openstructure'))
 # -- General configuration -----------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
@@ -86,7 +88,7 @@ exclude_trees = []
 pygments_style = 'sphinx'
 
 # A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
+modindex_common_prefix = ['ost.']
 
 
 # -- Options for HTML output ---------------------------------------------------
@@ -162,7 +164,6 @@ html_static_path = ['_static']
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'openstructure-doc'
 
-
 # -- Options for LaTeX output --------------------------------------------------
 
 # The paper size ('letter' or 'a4').
diff --git a/doc/make.py b/doc/make.py
new file mode 100644
index 0000000000000000000000000000000000000000..1653dc73eb1ba177b05530200027f5e3bf90dd61
--- /dev/null
+++ b/doc/make.py
@@ -0,0 +1,97 @@
+import os, sys, re
+import shutil
+from ost import settings
+from optparse import OptionParser
+
+
+if len(sys.argv)==2:
+  root_dir=sys.argv[1]
+else:
+  root_dir='.'
+
+def _OutputPath(inpath, outdir):
+  parts=inpath.split(os.path.sep)
+  filtered_parts=[outdir]
+  index=parts.index('modules')
+  for part in parts[index+1:]:
+    if part!='doc':
+      filtered_parts.append(part)
+  return os.path.join(*filtered_parts)
+
+def _RequireCopy(in_name, out_name):
+  if not os.path.exists(out_name):
+    return True
+  if os.path.getmtime(in_name)>os.path.getmtime(out_name):
+    return True
+  return False
+
+
+pattern = re.compile('[a-zA-Z0-9_//]+\.png|[a-zA-Z0-9_//]+\.jpg')
+def _CheckImage(in_name):
+  file = open(in_name, "r")
+  text = file.read()
+  picture_list = pattern.findall(text)
+  file.close()
+  return picture_list
+
+def _CreateAndCopy(in_name, outdir):
+  out_name=_OutputPath(in_name, outdir)
+  out_dir=os.path.dirname(out_name)
+  if not os.path.exists(out_dir):
+    _MkDir(out_dir)
+  if _RequireCopy(in_name, out_name):
+    print 'cp %s %s' % (in_name, out_name)
+    os.system('cp %s %s' % (in_name, out_name))
+
+def _MkDir(dirname):
+  """
+  Recursively create directories if they don't exist
+  """
+  parts=dirname.split(os.path.sep)
+  for i, d in enumerate(parts):
+    n=os.path.join(*parts[:1+i])
+    if not os.path.exists(n):
+      os.mkdir(n)
+
+def _CollectRstDocs(outdir, dirname, fnames):
+  for fname in fnames:
+    if fname.endswith('.rst'):
+      in_name=os.path.join(dirname, fname)
+      _CreateAndCopy(in_name,outdir)
+      img_list = _CheckImage(in_name)
+      for img in img_list:
+        img_name = os.path.join(dirname,img)
+        _CreateAndCopy(img_name, outdir)
+
+
+def ParseArgs():
+  parser = OptionParser("usage: ost make.py [options] ")
+  parser.add_option("-l","--linkcheck", action="store_true", default=False, dest="linkcheck", help="validate all external links")
+  parser.add_option("-b", "--build-html", action="store_true", default=False, dest="html", help="build html documentation")
+  parser.add_option("-d", "--doctest", action="store_true", default=False, dest="doctest", help="run all test")
+  parser.add_option("-q", "--quiet", action="store_true", default=False, dest="quiet", help="run all test")
+  return parser.parse_args()
+
+opts, args=ParseArgs()
+if not opts.html and\
+   not opts.linkcheck and\
+   not opts.doctest:
+     opts.html=True
+
+opt_str='' 
+if opts.quiet:
+  opt_str=' -Q '
+
+for sub_dir in ('modules',):
+  os.path.walk(sub_dir, _CollectRstDocs, 'doc/source')
+sphinx_bin=settings.Locate(['sphinx-build', 'sphinx-build-2.6'])
+
+if opts.html:
+  os.system('%s %s -b html -c %s %s %s' % (sphinx_bin, opt_str, 'doc/conf', 'doc/source', 
+                                      'doc/build'))
+if opts.doctest:
+  os.system('%s %s -b doctest -c %s %s %s' % (sphinx_bin, opt_str, 'doc/conf', 'doc/source', 
+                                      'doc/build'))
+if opts.linkcheck:
+  os.system('%s %s -b linkcheck -c %s %s %s' % (sphinx_bin, opt_str, 'doc/conf', 'doc/source', 
+                                      'doc/build'))
diff --git a/doc/to_sphinx.py b/doc/to_sphinx.py
new file mode 100644
index 0000000000000000000000000000000000000000..09809d2351170a195c26aeada9f2c28b6d4a62fa
--- /dev/null
+++ b/doc/to_sphinx.py
@@ -0,0 +1,78 @@
+import re
+to_document=sys.argv[1]
+parts=to_document.split('.')
+module='.'.join(parts[:-1])
+class_name=parts[-1]
+__import__(module, globals(), locals())
+mod=sys.modules[module]
+the_class=getattr(mod, class_name)
+print '.. currentmodule:: %s' % module
+print ''
+print '.. class:: %s' % class_name
+
+def _arg_type(arg_type):
+  if arg_type not in ('str', 'int', 'bool', 'float', 'None'):
+    return ':class:`%s`' % arg_type
+  return arg_type
+class TypedArgument:
+  def __init__(self, name, arg_type):
+    self.name=name
+    self.type=_arg_type(arg_type)
+
+class Method:
+  def __init__(self, name, rtype, args, optional):
+    self.name=name
+    self.rtype=rtype
+    self.args=args
+    self.opt=optional
+  def to_sphinx(self):
+    if len(self.opt)>0:
+      signature='%s(%s%s)' % (self.name, ', '.join([a.name for a in self.args]), 
+                            '[, %s]' % ', '.join([a.name for a in self.opt]))
+    else:
+      signature='%s(%s)' % (self.name, ', '.join([a.name for a in self.args]))
+    val='  .. method:: %s\n\n' % signature
+    for arg in self.args+self.opt:
+      val+='    :param %s:\n' % arg.name
+      val+='    :type  %s: %s\n' % (arg.name, arg.type)
+    val+='    :rtype: %s\n' % self.rtype
+    return val
+
+def parse_signature(signature):
+  arg=re.compile(r'\s*(\((?P<type>\w+)\)(?P<name>\w+),?\s*)*')
+  opt_args=re.compile(r'(?P<args>.*)(:?\[,(?P<kwargs>.*)\])')
+  method=re.compile(r'(?P<name>\w+)\((?P<args>.*)\) -> (?P<rtype>\w+)')
+  method_match=method.match(signature)
+  if method_match:
+    optional=opt_args.match(method_match.groupdict()['args'])
+    opt_args=[]
+    if optional:
+      for opt_arg in optional.groupdict()['kwargs'].split(','):
+        a=arg.match(opt_arg)
+        assert a
+        opt_args.append(TypedArgument(a.groupdict()['name'], a.groupdict()['type']))
+      arg_string=optional.groupdict()['args']
+    else:
+      arg_string=method_match.groupdict()['args']
+    args=[]
+    for aarg in arg_string.split(','):
+      a=arg.match(aarg)
+      assert a
+      args.append(TypedArgument(a.groupdict()['name'], a.groupdict()['type']))  
+    
+    return Method(method_match.groupdict()['name'], 
+                  _arg_type(method_match.groupdict()['rtype']), 
+                  args[1:], opt_args)
+  print signature, 'not matched'
+
+if '--no-derived' in sys.argv:
+  members=the_class.__dict__.keys()
+else:
+  members=dir(the_class)
+for m in members:
+  if m.startswith('__'):
+    continue
+  member_doc=getattr(the_class, m).__doc__
+  if member_doc:
+    method=parse_signature(member_doc.split('\n')[1])
+    print method.to_sphinx()
\ No newline at end of file
diff --git a/examples/dokk/KEYS b/examples/code_fragments/dokk/KEYS
similarity index 100%
rename from examples/dokk/KEYS
rename to examples/code_fragments/dokk/KEYS
diff --git a/examples/dokk/config.py b/examples/code_fragments/dokk/config.py
similarity index 100%
rename from examples/dokk/config.py
rename to examples/code_fragments/dokk/config.py
diff --git a/examples/dokk/datafiles/dengue/level.ini b/examples/code_fragments/dokk/datafiles/dengue/level.ini
similarity index 100%
rename from examples/dokk/datafiles/dengue/level.ini
rename to examples/code_fragments/dokk/datafiles/dengue/level.ini
diff --git a/examples/dokk/datafiles/dengue/levelF.ini b/examples/code_fragments/dokk/datafiles/dengue/levelF.ini
similarity index 100%
rename from examples/dokk/datafiles/dengue/levelF.ini
rename to examples/code_fragments/dokk/datafiles/dengue/levelF.ini
diff --git a/examples/dokk/datafiles/dengue/ligand.sdf b/examples/code_fragments/dokk/datafiles/dengue/ligand.sdf
similarity index 100%
rename from examples/dokk/datafiles/dengue/ligand.sdf
rename to examples/code_fragments/dokk/datafiles/dengue/ligand.sdf
diff --git a/examples/dokk/datafiles/dengue/protein.pdb b/examples/code_fragments/dokk/datafiles/dengue/protein.pdb
similarity index 100%
rename from examples/dokk/datafiles/dengue/protein.pdb
rename to examples/code_fragments/dokk/datafiles/dengue/protein.pdb
diff --git a/examples/dokk/datafiles/dengue/surface.face b/examples/code_fragments/dokk/datafiles/dengue/surface.face
similarity index 100%
rename from examples/dokk/datafiles/dengue/surface.face
rename to examples/code_fragments/dokk/datafiles/dengue/surface.face
diff --git a/examples/dokk/datafiles/dengue/surface.vert b/examples/code_fragments/dokk/datafiles/dengue/surface.vert
similarity index 100%
rename from examples/dokk/datafiles/dengue/surface.vert
rename to examples/code_fragments/dokk/datafiles/dengue/surface.vert
diff --git a/examples/dokk/datafiles/dengue/top_ten.ini b/examples/code_fragments/dokk/datafiles/dengue/top_ten.ini
similarity index 100%
rename from examples/dokk/datafiles/dengue/top_ten.ini
rename to examples/code_fragments/dokk/datafiles/dengue/top_ten.ini
diff --git a/examples/dokk/datafiles/glyoxalase/level.ini b/examples/code_fragments/dokk/datafiles/glyoxalase/level.ini
similarity index 100%
rename from examples/dokk/datafiles/glyoxalase/level.ini
rename to examples/code_fragments/dokk/datafiles/glyoxalase/level.ini
diff --git a/examples/dokk/datafiles/glyoxalase/levelF.ini b/examples/code_fragments/dokk/datafiles/glyoxalase/levelF.ini
similarity index 100%
rename from examples/dokk/datafiles/glyoxalase/levelF.ini
rename to examples/code_fragments/dokk/datafiles/glyoxalase/levelF.ini
diff --git a/examples/dokk/datafiles/glyoxalase/ligand.sdf b/examples/code_fragments/dokk/datafiles/glyoxalase/ligand.sdf
similarity index 100%
rename from examples/dokk/datafiles/glyoxalase/ligand.sdf
rename to examples/code_fragments/dokk/datafiles/glyoxalase/ligand.sdf
diff --git a/examples/dokk/datafiles/glyoxalase/protein.pdb b/examples/code_fragments/dokk/datafiles/glyoxalase/protein.pdb
similarity index 100%
rename from examples/dokk/datafiles/glyoxalase/protein.pdb
rename to examples/code_fragments/dokk/datafiles/glyoxalase/protein.pdb
diff --git a/examples/dokk/datafiles/glyoxalase/surface.face b/examples/code_fragments/dokk/datafiles/glyoxalase/surface.face
similarity index 100%
rename from examples/dokk/datafiles/glyoxalase/surface.face
rename to examples/code_fragments/dokk/datafiles/glyoxalase/surface.face
diff --git a/examples/dokk/datafiles/glyoxalase/surface.vert b/examples/code_fragments/dokk/datafiles/glyoxalase/surface.vert
similarity index 100%
rename from examples/dokk/datafiles/glyoxalase/surface.vert
rename to examples/code_fragments/dokk/datafiles/glyoxalase/surface.vert
diff --git a/examples/dokk/datafiles/glyoxalase/top_ten.ini b/examples/code_fragments/dokk/datafiles/glyoxalase/top_ten.ini
similarity index 100%
rename from examples/dokk/datafiles/glyoxalase/top_ten.ini
rename to examples/code_fragments/dokk/datafiles/glyoxalase/top_ten.ini
diff --git a/examples/dokk/datafiles/hud.ini b/examples/code_fragments/dokk/datafiles/hud.ini
similarity index 100%
rename from examples/dokk/datafiles/hud.ini
rename to examples/code_fragments/dokk/datafiles/hud.ini
diff --git a/examples/dokk/datafiles/hudF.ini b/examples/code_fragments/dokk/datafiles/hudF.ini
similarity index 100%
rename from examples/dokk/datafiles/hudF.ini
rename to examples/code_fragments/dokk/datafiles/hudF.ini
diff --git a/examples/dokk/datafiles/retinol/level.ini b/examples/code_fragments/dokk/datafiles/retinol/level.ini
similarity index 100%
rename from examples/dokk/datafiles/retinol/level.ini
rename to examples/code_fragments/dokk/datafiles/retinol/level.ini
diff --git a/examples/dokk/datafiles/retinol/levelF.ini b/examples/code_fragments/dokk/datafiles/retinol/levelF.ini
similarity index 100%
rename from examples/dokk/datafiles/retinol/levelF.ini
rename to examples/code_fragments/dokk/datafiles/retinol/levelF.ini
diff --git a/examples/dokk/datafiles/retinol/ligand.sdf b/examples/code_fragments/dokk/datafiles/retinol/ligand.sdf
similarity index 100%
rename from examples/dokk/datafiles/retinol/ligand.sdf
rename to examples/code_fragments/dokk/datafiles/retinol/ligand.sdf
diff --git a/examples/dokk/datafiles/retinol/protein.pdb b/examples/code_fragments/dokk/datafiles/retinol/protein.pdb
similarity index 100%
rename from examples/dokk/datafiles/retinol/protein.pdb
rename to examples/code_fragments/dokk/datafiles/retinol/protein.pdb
diff --git a/examples/dokk/datafiles/retinol/surface.face b/examples/code_fragments/dokk/datafiles/retinol/surface.face
similarity index 100%
rename from examples/dokk/datafiles/retinol/surface.face
rename to examples/code_fragments/dokk/datafiles/retinol/surface.face
diff --git a/examples/dokk/datafiles/retinol/surface.vert b/examples/code_fragments/dokk/datafiles/retinol/surface.vert
similarity index 100%
rename from examples/dokk/datafiles/retinol/surface.vert
rename to examples/code_fragments/dokk/datafiles/retinol/surface.vert
diff --git a/examples/dokk/datafiles/retinol/top_ten.ini b/examples/code_fragments/dokk/datafiles/retinol/top_ten.ini
similarity index 100%
rename from examples/dokk/datafiles/retinol/top_ten.ini
rename to examples/code_fragments/dokk/datafiles/retinol/top_ten.ini
diff --git a/examples/dokk/datafiles/thrombin/level.ini b/examples/code_fragments/dokk/datafiles/thrombin/level.ini
similarity index 100%
rename from examples/dokk/datafiles/thrombin/level.ini
rename to examples/code_fragments/dokk/datafiles/thrombin/level.ini
diff --git a/examples/dokk/datafiles/thrombin/levelF.ini b/examples/code_fragments/dokk/datafiles/thrombin/levelF.ini
similarity index 100%
rename from examples/dokk/datafiles/thrombin/levelF.ini
rename to examples/code_fragments/dokk/datafiles/thrombin/levelF.ini
diff --git a/examples/dokk/datafiles/thrombin/ligand.sdf b/examples/code_fragments/dokk/datafiles/thrombin/ligand.sdf
similarity index 100%
rename from examples/dokk/datafiles/thrombin/ligand.sdf
rename to examples/code_fragments/dokk/datafiles/thrombin/ligand.sdf
diff --git a/examples/dokk/datafiles/thrombin/protein.pdb b/examples/code_fragments/dokk/datafiles/thrombin/protein.pdb
similarity index 100%
rename from examples/dokk/datafiles/thrombin/protein.pdb
rename to examples/code_fragments/dokk/datafiles/thrombin/protein.pdb
diff --git a/examples/dokk/datafiles/thrombin/surface.face b/examples/code_fragments/dokk/datafiles/thrombin/surface.face
similarity index 100%
rename from examples/dokk/datafiles/thrombin/surface.face
rename to examples/code_fragments/dokk/datafiles/thrombin/surface.face
diff --git a/examples/dokk/datafiles/thrombin/surface.vert b/examples/code_fragments/dokk/datafiles/thrombin/surface.vert
similarity index 100%
rename from examples/dokk/datafiles/thrombin/surface.vert
rename to examples/code_fragments/dokk/datafiles/thrombin/surface.vert
diff --git a/examples/dokk/datafiles/thrombin/top_ten.ini b/examples/code_fragments/dokk/datafiles/thrombin/top_ten.ini
similarity index 100%
rename from examples/dokk/datafiles/thrombin/top_ten.ini
rename to examples/code_fragments/dokk/datafiles/thrombin/top_ten.ini
diff --git a/examples/dokk/datafiles/tutorial_1/level.ini b/examples/code_fragments/dokk/datafiles/tutorial_1/level.ini
similarity index 100%
rename from examples/dokk/datafiles/tutorial_1/level.ini
rename to examples/code_fragments/dokk/datafiles/tutorial_1/level.ini
diff --git a/examples/dokk/datafiles/tutorial_1/levelF.ini b/examples/code_fragments/dokk/datafiles/tutorial_1/levelF.ini
similarity index 100%
rename from examples/dokk/datafiles/tutorial_1/levelF.ini
rename to examples/code_fragments/dokk/datafiles/tutorial_1/levelF.ini
diff --git a/examples/dokk/datafiles/tutorial_1/ligand.sdf b/examples/code_fragments/dokk/datafiles/tutorial_1/ligand.sdf
similarity index 100%
rename from examples/dokk/datafiles/tutorial_1/ligand.sdf
rename to examples/code_fragments/dokk/datafiles/tutorial_1/ligand.sdf
diff --git a/examples/dokk/datafiles/tutorial_1/protein.pdb b/examples/code_fragments/dokk/datafiles/tutorial_1/protein.pdb
similarity index 100%
rename from examples/dokk/datafiles/tutorial_1/protein.pdb
rename to examples/code_fragments/dokk/datafiles/tutorial_1/protein.pdb
diff --git a/examples/dokk/datafiles/tutorial_1/surface.face b/examples/code_fragments/dokk/datafiles/tutorial_1/surface.face
similarity index 100%
rename from examples/dokk/datafiles/tutorial_1/surface.face
rename to examples/code_fragments/dokk/datafiles/tutorial_1/surface.face
diff --git a/examples/dokk/datafiles/tutorial_1/surface.vert b/examples/code_fragments/dokk/datafiles/tutorial_1/surface.vert
similarity index 100%
rename from examples/dokk/datafiles/tutorial_1/surface.vert
rename to examples/code_fragments/dokk/datafiles/tutorial_1/surface.vert
diff --git a/examples/dokk/datafiles/tutorial_1/top_ten.ini b/examples/code_fragments/dokk/datafiles/tutorial_1/top_ten.ini
similarity index 100%
rename from examples/dokk/datafiles/tutorial_1/top_ten.ini
rename to examples/code_fragments/dokk/datafiles/tutorial_1/top_ten.ini
diff --git a/examples/dokk/datafiles/tutorial_2/level.ini b/examples/code_fragments/dokk/datafiles/tutorial_2/level.ini
similarity index 100%
rename from examples/dokk/datafiles/tutorial_2/level.ini
rename to examples/code_fragments/dokk/datafiles/tutorial_2/level.ini
diff --git a/examples/dokk/datafiles/tutorial_2/levelF.ini b/examples/code_fragments/dokk/datafiles/tutorial_2/levelF.ini
similarity index 100%
rename from examples/dokk/datafiles/tutorial_2/levelF.ini
rename to examples/code_fragments/dokk/datafiles/tutorial_2/levelF.ini
diff --git a/examples/dokk/datafiles/tutorial_2/ligand.sdf b/examples/code_fragments/dokk/datafiles/tutorial_2/ligand.sdf
similarity index 100%
rename from examples/dokk/datafiles/tutorial_2/ligand.sdf
rename to examples/code_fragments/dokk/datafiles/tutorial_2/ligand.sdf
diff --git a/examples/dokk/datafiles/tutorial_2/protein.pdb b/examples/code_fragments/dokk/datafiles/tutorial_2/protein.pdb
similarity index 100%
rename from examples/dokk/datafiles/tutorial_2/protein.pdb
rename to examples/code_fragments/dokk/datafiles/tutorial_2/protein.pdb
diff --git a/examples/dokk/datafiles/tutorial_2/surface.face b/examples/code_fragments/dokk/datafiles/tutorial_2/surface.face
similarity index 100%
rename from examples/dokk/datafiles/tutorial_2/surface.face
rename to examples/code_fragments/dokk/datafiles/tutorial_2/surface.face
diff --git a/examples/dokk/datafiles/tutorial_2/surface.vert b/examples/code_fragments/dokk/datafiles/tutorial_2/surface.vert
similarity index 100%
rename from examples/dokk/datafiles/tutorial_2/surface.vert
rename to examples/code_fragments/dokk/datafiles/tutorial_2/surface.vert
diff --git a/examples/dokk/datafiles/tutorial_2/top_ten.ini b/examples/code_fragments/dokk/datafiles/tutorial_2/top_ten.ini
similarity index 100%
rename from examples/dokk/datafiles/tutorial_2/top_ten.ini
rename to examples/code_fragments/dokk/datafiles/tutorial_2/top_ten.ini
diff --git a/examples/dokk/dokk b/examples/code_fragments/dokk/dokk
similarity index 100%
rename from examples/dokk/dokk
rename to examples/code_fragments/dokk/dokk
diff --git a/examples/dokk/dokk.py b/examples/code_fragments/dokk/dokk.py
similarity index 100%
rename from examples/dokk/dokk.py
rename to examples/code_fragments/dokk/dokk.py
diff --git a/examples/dokk/glwin.py b/examples/code_fragments/dokk/glwin.py
similarity index 100%
rename from examples/dokk/glwin.py
rename to examples/code_fragments/dokk/glwin.py
diff --git a/examples/dokk/hud.py b/examples/code_fragments/dokk/hud.py
similarity index 100%
rename from examples/dokk/hud.py
rename to examples/code_fragments/dokk/hud.py
diff --git a/examples/dokk/images/openstructure.png b/examples/code_fragments/dokk/images/openstructure.png
similarity index 100%
rename from examples/dokk/images/openstructure.png
rename to examples/code_fragments/dokk/images/openstructure.png
diff --git a/examples/dokk/images/rotation.png b/examples/code_fragments/dokk/images/rotation.png
similarity index 100%
rename from examples/dokk/images/rotation.png
rename to examples/code_fragments/dokk/images/rotation.png
diff --git a/examples/dokk/images/translation.png b/examples/code_fragments/dokk/images/translation.png
similarity index 100%
rename from examples/dokk/images/translation.png
rename to examples/code_fragments/dokk/images/translation.png
diff --git a/examples/dokk/level.py b/examples/code_fragments/dokk/level.py
similarity index 100%
rename from examples/dokk/level.py
rename to examples/code_fragments/dokk/level.py
diff --git a/examples/dokk/level_info.py b/examples/code_fragments/dokk/level_info.py
similarity index 100%
rename from examples/dokk/level_info.py
rename to examples/code_fragments/dokk/level_info.py
diff --git a/examples/dokk/level_intro.py b/examples/code_fragments/dokk/level_intro.py
similarity index 100%
rename from examples/dokk/level_intro.py
rename to examples/code_fragments/dokk/level_intro.py
diff --git a/examples/dokk/level_messages.py b/examples/code_fragments/dokk/level_messages.py
similarity index 100%
rename from examples/dokk/level_messages.py
rename to examples/code_fragments/dokk/level_messages.py
diff --git a/examples/dokk/ligand.py b/examples/code_fragments/dokk/ligand.py
similarity index 100%
rename from examples/dokk/ligand.py
rename to examples/code_fragments/dokk/ligand.py
diff --git a/examples/dokk/name_enter.py b/examples/code_fragments/dokk/name_enter.py
similarity index 100%
rename from examples/dokk/name_enter.py
rename to examples/code_fragments/dokk/name_enter.py
diff --git a/examples/dokk/protein.py b/examples/code_fragments/dokk/protein.py
similarity index 100%
rename from examples/dokk/protein.py
rename to examples/code_fragments/dokk/protein.py
diff --git a/examples/dokk/score_updater.py b/examples/code_fragments/dokk/score_updater.py
similarity index 100%
rename from examples/dokk/score_updater.py
rename to examples/code_fragments/dokk/score_updater.py
diff --git a/examples/dokk/spacenav_connect.py b/examples/code_fragments/dokk/spacenav_connect.py
similarity index 100%
rename from examples/dokk/spacenav_connect.py
rename to examples/code_fragments/dokk/spacenav_connect.py
diff --git a/examples/dokk/spnav_input.py b/examples/code_fragments/dokk/spnav_input.py
similarity index 100%
rename from examples/dokk/spnav_input.py
rename to examples/code_fragments/dokk/spnav_input.py
diff --git a/examples/dokk/start_dokk.py b/examples/code_fragments/dokk/start_dokk.py
similarity index 100%
rename from examples/dokk/start_dokk.py
rename to examples/code_fragments/dokk/start_dokk.py
diff --git a/examples/dokk/surface.py b/examples/code_fragments/dokk/surface.py
similarity index 100%
rename from examples/dokk/surface.py
rename to examples/code_fragments/dokk/surface.py
diff --git a/examples/entity/color_by_property.py b/examples/code_fragments/entity/color_by_property.py
similarity index 100%
rename from examples/entity/color_by_property.py
rename to examples/code_fragments/entity/color_by_property.py
diff --git a/examples/entity/fragment.pdb b/examples/code_fragments/entity/fragment.pdb
similarity index 100%
rename from examples/entity/fragment.pdb
rename to examples/code_fragments/entity/fragment.pdb
diff --git a/examples/entity/fragment2.pdb b/examples/code_fragments/entity/fragment2.pdb
similarity index 100%
rename from examples/entity/fragment2.pdb
rename to examples/code_fragments/entity/fragment2.pdb
diff --git a/examples/entity/gfx_selection.py b/examples/code_fragments/entity/gfx_selection.py
similarity index 100%
rename from examples/entity/gfx_selection.py
rename to examples/code_fragments/entity/gfx_selection.py
diff --git a/examples/entity/gfx_symmetry.py b/examples/code_fragments/entity/gfx_symmetry.py
similarity index 100%
rename from examples/entity/gfx_symmetry.py
rename to examples/code_fragments/entity/gfx_symmetry.py
diff --git a/examples/entity/gradient.py b/examples/code_fragments/entity/gradient.py
similarity index 100%
rename from examples/entity/gradient.py
rename to examples/code_fragments/entity/gradient.py
diff --git a/examples/entity/pdb1ake.ent b/examples/code_fragments/entity/pdb1ake.ent
similarity index 100%
rename from examples/entity/pdb1ake.ent
rename to examples/code_fragments/entity/pdb1ake.ent
diff --git a/examples/entity/pdb4ake.ent b/examples/code_fragments/entity/pdb4ake.ent
similarity index 100%
rename from examples/entity/pdb4ake.ent
rename to examples/code_fragments/entity/pdb4ake.ent
diff --git a/examples/entity/primitives.py b/examples/code_fragments/entity/primitives.py
similarity index 100%
rename from examples/entity/primitives.py
rename to examples/code_fragments/entity/primitives.py
diff --git a/examples/entity/random_lines.py b/examples/code_fragments/entity/random_lines.py
similarity index 100%
rename from examples/entity/random_lines.py
rename to examples/code_fragments/entity/random_lines.py
diff --git a/examples/entity/sdh.pdb b/examples/code_fragments/entity/sdh.pdb
similarity index 100%
rename from examples/entity/sdh.pdb
rename to examples/code_fragments/entity/sdh.pdb
diff --git a/examples/entity/superpose.py b/examples/code_fragments/entity/superpose.py
similarity index 100%
rename from examples/entity/superpose.py
rename to examples/code_fragments/entity/superpose.py
diff --git a/examples/harmony/glwin.py b/examples/code_fragments/harmony/glwin.py
similarity index 100%
rename from examples/harmony/glwin.py
rename to examples/code_fragments/harmony/glwin.py
diff --git a/examples/harmony/harmony b/examples/code_fragments/harmony/harmony
similarity index 100%
rename from examples/harmony/harmony
rename to examples/code_fragments/harmony/harmony
diff --git a/examples/harmony/harmony.py b/examples/code_fragments/harmony/harmony.py
similarity index 100%
rename from examples/harmony/harmony.py
rename to examples/code_fragments/harmony/harmony.py
diff --git a/examples/code_fragments/img/circle.png b/examples/code_fragments/img/circle.png
new file mode 100644
index 0000000000000000000000000000000000000000..61efe392847e7425ccb90aef460c2c0411de6abd
Binary files /dev/null and b/examples/code_fragments/img/circle.png differ
diff --git a/examples/img/create_split_image.py b/examples/code_fragments/img/create_split_image.py
similarity index 85%
rename from examples/img/create_split_image.py
rename to examples/code_fragments/img/create_split_image.py
index 084244455aa1de3a693cfb13297556c161c1c899..1da640423d02826a41233e42ec4904609898ffba 100644
--- a/examples/img/create_split_image.py
+++ b/examples/code_fragments/img/create_split_image.py
@@ -35,7 +35,12 @@ def CreateSplitImage(imagelist, start_at_y=True):
         count+=1
     return result
 
-imagelist=io.LoadImageList(sys.argv[1:-1])
+if len(sys.argv)<3:
+  imagelist=io.LoadImageList(['circle.png', 'square.png'])
+else:
+  imagelist=io.LoadImageList(sys.argv[1:-1])
+
 result=CreateSplitImage(imagelist)
 v_result=gui.CreateDataViewer(result)
-io.SaveImage(result,sys.argv[-1])
+main_area=gui.GostyApp.Instance().perspective.main_area
+main_area.AddWidget("Split Image", v_result)
diff --git a/examples/code_fragments/img/fft_li.py b/examples/code_fragments/img/fft_li.py
new file mode 100644
index 0000000000000000000000000000000000000000..73681183e786e7d46f0505721470a2a4ea8e6cdf
--- /dev/null
+++ b/examples/code_fragments/img/fft_li.py
@@ -0,0 +1,16 @@
+import sys
+import ost.img.alg
+if len(sys.argv)<2:
+  images=io.LoadImageList(['square.png','circle.png'])  
+else:
+  images=io.LoadImageList(sys.argv[1:])
+viewers=[]
+i=1
+main_area=gui.GostyApp.Instance().perspective.main_area
+for im in images:
+   im.CenterSpatialOrigin()
+   im.ApplyIP(img.alg.DFT()) 
+   v=gui.CreateDataViewer(im)
+   viewers.append(v)
+   main_area.AddWidget('Image' + str(i), v)
+   i+=1
\ No newline at end of file
diff --git a/examples/img/modulate_image.py b/examples/code_fragments/img/modulate_image.py
similarity index 78%
rename from examples/img/modulate_image.py
rename to examples/code_fragments/img/modulate_image.py
index d81fd59cb43884ac6b66113a77f226db309e64ab..bed29c56557019684e6291b9337b77a63a4d13dd 100644
--- a/examples/img/modulate_image.py
+++ b/examples/code_fragments/img/modulate_image.py
@@ -20,4 +20,6 @@ im3 = img.CreateImage(img.Size(400,400))
 im3.Paste(im)
 im3.Paste(im2)
 
-v=gui.CreateDataViewer(im3)
\ No newline at end of file
+v=gui.CreateDataViewer(im3)
+main_area=gui.GostyApp.Instance().perspective.main_area
+main_area.AddWidget("Modulated Image", v)
\ No newline at end of file
diff --git a/examples/img/spoke_pattern.py b/examples/code_fragments/img/spoke_pattern.py
similarity index 74%
rename from examples/img/spoke_pattern.py
rename to examples/code_fragments/img/spoke_pattern.py
index 7a11e42a1e60a0337e96ce01dac6e9c701c03618..c0a43b0013bb3d91d8391b25ca84d8e96e0bbe0a 100644
--- a/examples/img/spoke_pattern.py
+++ b/examples/code_fragments/img/spoke_pattern.py
@@ -2,15 +2,12 @@ import math
 import sys
 import ost.img.alg
 
-if len(sys.argv)!=2:
-  raise RuntimeError('Wrong number of command line arguments. The name of the output file should be the only argument.')
-
 # Tweakable parameters
-wedge_start = 80 # Width of wedge at the narrower point
-wedge_end = 2000 # Width of wedge at the broader point
+wedge_start = 20 # Width of wedge at the narrower point
+wedge_end = 500 # Width of wedge at the broader point
 number_of_bands = 11 # Number of alternating bands (must be odd)
-size_of_image_x = 2000 # Size of the image (X)
-size_of_image_y = 2000 # Size of the image (Y)
+size_of_image_x = 500 # Size of the image (X)
+size_of_image_y = 500 # Size of the image (Y)
 pixel_sampling = 1.0 * Units.A # Pixel width
 threshold = 2.0 * Units.A # Threshold for low pass filtering
 amplitude = 255 # amplitude of the obscillations
@@ -42,8 +39,7 @@ for y in range (start_y,end_y+1):
 filter=ost.img.alg.GaussianLowPassFilter(threshold)
 image.ApplyIP(filter)
 
-# Image is saved
-io.SaveImage(image,sys.argv[1])
-
 # Viewer is launched to show the result
-v=gui.CreateDataViewer(image)
\ No newline at end of file
+v=gui.CreateDataViewer(image)
+main_area=gui.GostyApp.Instance().perspective.main_area
+main_area.AddWidget("Modulated Image", v)
\ No newline at end of file
diff --git a/examples/img/square.png b/examples/code_fragments/img/square.png
similarity index 100%
rename from examples/img/square.png
rename to examples/code_fragments/img/square.png
diff --git a/examples/img/tone1.png b/examples/code_fragments/img/tone1.png
similarity index 100%
rename from examples/img/tone1.png
rename to examples/code_fragments/img/tone1.png
diff --git a/examples/img/tone2.png b/examples/code_fragments/img/tone2.png
similarity index 100%
rename from examples/img/tone2.png
rename to examples/code_fragments/img/tone2.png
diff --git a/examples/img/tone3.png b/examples/code_fragments/img/tone3.png
similarity index 100%
rename from examples/img/tone3.png
rename to examples/code_fragments/img/tone3.png
diff --git a/examples/img/tone4.png b/examples/code_fragments/img/tone4.png
similarity index 100%
rename from examples/img/tone4.png
rename to examples/code_fragments/img/tone4.png
diff --git a/examples/img/tone5.png b/examples/code_fragments/img/tone5.png
similarity index 100%
rename from examples/img/tone5.png
rename to examples/code_fragments/img/tone5.png
diff --git a/examples/img/view_phase_diff.py b/examples/code_fragments/img/view_phase_diff.py
similarity index 68%
rename from examples/img/view_phase_diff.py
rename to examples/code_fragments/img/view_phase_diff.py
index 0228a0e02fcc36190d8308940409b58daf0e0f00..4a395a50b094f008e15a8ec23bbf2f4d146a7c92 100644
--- a/examples/img/view_phase_diff.py
+++ b/examples/code_fragments/img/view_phase_diff.py
@@ -2,8 +2,12 @@ import sys
 import math
 import ost.img.alg
 
-image1=io.LoadImage(sys.argv[1])
-image2=io.LoadImage(sys.argv[2])
+if len(sys.argv)==2:
+  image1=io.LoadImage(sys.argv[1])
+  image2=io.LoadImage(sys.argv[2])
+else:
+  image1=io.LoadImage('square.png')
+  image2=io.LoadImage('circle.png')
 if image1.GetExtent() != image2.GetExtent():
   raise RuntimeError('The input images should have the same size.')
 image1.CenterSpatialOrigin()
@@ -18,4 +22,5 @@ for pixel in ex_it:
   phase_diff=phase1-phase2
   diff_image.SetReal(pixel,180.0*float(phase_diff)/math.pi)
 v=gui.CreateDataViewer(diff_image)
-v.SetName("Phase difference (in degrees)")
+main_area=gui.GostyApp.Instance().perspective.main_area
+main_area.AddWidget("Phase difference (in degrees)", v)
\ No newline at end of file
diff --git a/examples/map/1ppt.map b/examples/code_fragments/map/1ppt.map
similarity index 100%
rename from examples/map/1ppt.map
rename to examples/code_fragments/map/1ppt.map
diff --git a/examples/map/1ppt.pdb b/examples/code_fragments/map/1ppt.pdb
similarity index 100%
rename from examples/map/1ppt.pdb
rename to examples/code_fragments/map/1ppt.pdb
diff --git a/examples/map/gfx_mapiso.py b/examples/code_fragments/map/gfx_mapiso.py
similarity index 100%
rename from examples/map/gfx_mapiso.py
rename to examples/code_fragments/map/gfx_mapiso.py
diff --git a/examples/misc/bitmap_export.py b/examples/code_fragments/misc/bitmap_export.py
similarity index 100%
rename from examples/misc/bitmap_export.py
rename to examples/code_fragments/misc/bitmap_export.py
diff --git a/examples/misc/export_pov.py b/examples/code_fragments/misc/export_pov.py
similarity index 100%
rename from examples/misc/export_pov.py
rename to examples/code_fragments/misc/export_pov.py
diff --git a/examples/misc/fragment.face b/examples/code_fragments/misc/fragment.face
similarity index 100%
rename from examples/misc/fragment.face
rename to examples/code_fragments/misc/fragment.face
diff --git a/examples/misc/fragment.pdb b/examples/code_fragments/misc/fragment.pdb
similarity index 100%
rename from examples/misc/fragment.pdb
rename to examples/code_fragments/misc/fragment.pdb
diff --git a/examples/misc/fragment.vert b/examples/code_fragments/misc/fragment.vert
similarity index 100%
rename from examples/misc/fragment.vert
rename to examples/code_fragments/misc/fragment.vert
diff --git a/examples/modelling/roll_helix.py b/examples/code_fragments/misc/roll_helix.py
similarity index 100%
rename from examples/modelling/roll_helix.py
rename to examples/code_fragments/misc/roll_helix.py
diff --git a/examples/modelling/sdh.pdb b/examples/code_fragments/misc/sdh.pdb
similarity index 100%
rename from examples/modelling/sdh.pdb
rename to examples/code_fragments/misc/sdh.pdb
diff --git a/examples/modelling/strip_sidechains.py b/examples/code_fragments/misc/strip_sidechains.py
similarity index 100%
rename from examples/modelling/strip_sidechains.py
rename to examples/code_fragments/misc/strip_sidechains.py
diff --git a/examples/code_fragments/seq/seq_viewer.py b/examples/code_fragments/seq/seq_viewer.py
new file mode 100644
index 0000000000000000000000000000000000000000..1ca2535e805a2b00cf0dcaff5fd8cea1a178163c
--- /dev/null
+++ b/examples/code_fragments/seq/seq_viewer.py
@@ -0,0 +1,4 @@
+aln=io.LoadAlignment('sh2.aln')
+v=gui.SequenceViewer()
+v.AddAlignment(aln)
+v.Show()
diff --git a/examples/surf/fragment.pdb b/examples/code_fragments/surf/fragment.pdb
similarity index 100%
rename from examples/surf/fragment.pdb
rename to examples/code_fragments/surf/fragment.pdb
diff --git a/examples/surf/sdh.face b/examples/code_fragments/surf/sdh.face
similarity index 100%
rename from examples/surf/sdh.face
rename to examples/code_fragments/surf/sdh.face
diff --git a/examples/surf/sdh.pdb b/examples/code_fragments/surf/sdh.pdb
similarity index 100%
rename from examples/surf/sdh.pdb
rename to examples/code_fragments/surf/sdh.pdb
diff --git a/examples/surf/sdh.vert b/examples/code_fragments/surf/sdh.vert
similarity index 100%
rename from examples/surf/sdh.vert
rename to examples/code_fragments/surf/sdh.vert
diff --git a/examples/surf/test_surf.py b/examples/code_fragments/surf/test_surf.py
similarity index 100%
rename from examples/surf/test_surf.py
rename to examples/code_fragments/surf/test_surf.py
diff --git a/examples/surf/test_surf_pov.py b/examples/code_fragments/surf/test_surf_pov.py
similarity index 100%
rename from examples/surf/test_surf_pov.py
rename to examples/code_fragments/surf/test_surf_pov.py
diff --git a/examples/trj/fragment.pdb b/examples/code_fragments/trj/fragment.pdb
similarity index 100%
rename from examples/trj/fragment.pdb
rename to examples/code_fragments/trj/fragment.pdb
diff --git a/examples/trj/mpor_trj.crd b/examples/code_fragments/trj/mpor_trj.crd
similarity index 100%
rename from examples/trj/mpor_trj.crd
rename to examples/code_fragments/trj/mpor_trj.crd
diff --git a/examples/trj/mpor_trj_short.trj b/examples/code_fragments/trj/mpor_trj_short.trj
similarity index 100%
rename from examples/trj/mpor_trj_short.trj
rename to examples/code_fragments/trj/mpor_trj_short.trj
diff --git a/examples/trj/test_trj.py b/examples/code_fragments/trj/test_trj.py
similarity index 87%
rename from examples/trj/test_trj.py
rename to examples/code_fragments/trj/test_trj.py
index ae23e827465a0580c6e33f69a4c256a7f6b11366..0c3ed1f310eacb6e6e2a2dcc03af26a3aa077258 100644
--- a/examples/trj/test_trj.py
+++ b/examples/code_fragments/trj/test_trj.py
@@ -26,6 +26,4 @@ scene.SetCenter(go.GetCenter())
 scene.AutoAutoslab(True)
 
 anim=Anim(cg,go)
-
-print "enter anim.start(10) to start trajectory animation; use anim.stop() to turn it off again."
-
+anim.start(10)
diff --git a/examples/ui/board.py b/examples/code_fragments/ui/board.py
similarity index 100%
rename from examples/ui/board.py
rename to examples/code_fragments/ui/board.py
diff --git a/examples/ui/color_tool.py b/examples/code_fragments/ui/color_tool.py
similarity index 100%
rename from examples/ui/color_tool.py
rename to examples/code_fragments/ui/color_tool.py
diff --git a/examples/ui/mdi_example.py b/examples/code_fragments/ui/mdi_example.py
similarity index 100%
rename from examples/ui/mdi_example.py
rename to examples/code_fragments/ui/mdi_example.py
diff --git a/examples/ui/menubar_example.py b/examples/code_fragments/ui/menubar_example.py
similarity index 100%
rename from examples/ui/menubar_example.py
rename to examples/code_fragments/ui/menubar_example.py
diff --git a/examples/ui/widget_example.py b/examples/code_fragments/ui/widget_example.py
similarity index 97%
rename from examples/ui/widget_example.py
rename to examples/code_fragments/ui/widget_example.py
index a59847093e0f139199743b1f1eabe49aeea21904..733e9dcdb37de9be61eb7cbd4e4b6ed313fcaf5f 100644
--- a/examples/ui/widget_example.py
+++ b/examples/code_fragments/ui/widget_example.py
@@ -29,7 +29,7 @@ panels=gui.GostyApp.Instance().perspective.panels
 tetris=Board(panels.qobject)
 
 #Wrap widget to Qt Widget
-wid=gui.WrappedWidget(tetris)
+wid=gui.Widget(tetris)
 
 #Add Widget to widget pool
 panels.AddWidgetToPool("Break Widget",wid)
diff --git a/examples/demos/bbox.py b/examples/demos/bbox.py
new file mode 100644
index 0000000000000000000000000000000000000000..fa85b9a26676e876beb53f44494b44db108ff19a
--- /dev/null
+++ b/examples/demos/bbox.py
@@ -0,0 +1,26 @@
+# This code example shows how to calculate and display an oriented bounding box 
+# that contains all the atoms of an entity.
+
+# remove all objects from scene, just in case
+scene.RemoveAll()
+
+# Load sdh molecule
+sdh=io.LoadPDB('data/sdh.pdb')
+# Select backbone atoms of residues 99-128, which form a helix.
+helix=sdh.Select('rnum=99:128 and cname=A and aname=CA,C,N,O')
+# create a graphical representation of the helix and render it with simple 
+# lines.
+go=gfx.Entity('helix', gfx.SIMPLE, helix)
+# add it to the scene
+scene.Add(go)
+
+# calculate the bounding box for the helix
+bbox=mol.BoundingBoxFromEntity(helix)
+
+# create a graphical representation of the bounding box and add it to the scene
+bb=gfx.Cuboid('xxx', bbox)
+bb.SetFillColor(gfx.Color(0.5, 0.8, 0.5, 0.2))
+scene.Add(bb)
+
+# center the camera on the graphical object
+scene.center=go.center
diff --git a/examples/demos/charmm_trj_blur.py b/examples/demos/charmm_trj_blur.py
new file mode 100644
index 0000000000000000000000000000000000000000..8edfdc0c2768007b83698acf22cd8f2caa012da7
--- /dev/null
+++ b/examples/demos/charmm_trj_blur.py
@@ -0,0 +1,45 @@
+# trajectory generated by Raimund Dutzler
+from PyQt4 import QtCore
+scene.RemoveAll()
+
+
+class Anim(QtCore.QTimer):
+  """
+  Timer used to animate the trajectory on screen. Each time the OnTimer
+  method gets called we advance the trajectory by one step and render
+  the scene on the screen.
+  """
+  def __init__(self,cg,go):
+      QtCore.QTimer.__init__(self)
+      self.cg_=cg
+      self.go_=go
+      self.frame_=0
+      QtCore.QObject.connect(self, QtCore.SIGNAL("timeout()"), self.OnTimer)
+      
+  def OnTimer(self):
+    self.frame_=(self.frame_+1)%self.cg_.GetFrameCount()
+    self.go_.BlurSnapshot()
+    self.cg_.CopyFrame(self.frame_)
+    self.go_.UpdatePositions()
+        
+
+# load CHARMM trajectory from sample.pdb and sample.dcd
+cg = io.LoadCHARMMTraj("data/sample.pdb","data/sample.dcd")
+# create graphical representation of the entity
+eh=cg.GetEntity()
+# we don't want to display the hydrogen atoms, so select everything that is 
+# not a hydrogen and pass that view to the gfx.Entity() constructor.
+ev=eh.Select("not ele=H")
+go=gfx.Entity("mol",gfx.SIMPLE, ev)
+# enable the blur effect
+go.SetBlur(True)
+
+# add it to the scene for rendering
+scene.Add(go)
+scene.SetCenter(go.GetCenter())
+scene.AutoAutoslab(True)
+
+# create an animation timer and start it
+anim=Anim(cg,go)
+print 'Demo 6: Import of a CHARMM trajectory. Type anim.stop() to halt animation, anim.start(100) to start it again with stepsize 100!Starting animation now....'
+anim.start(50)
diff --git a/examples/demos/conservation.py b/examples/demos/conservation.py
new file mode 100644
index 0000000000000000000000000000000000000000..e4a254448462f41a68c15ff048fa6dc67dfe09ab
--- /dev/null
+++ b/examples/demos/conservation.py
@@ -0,0 +1,49 @@
+from ost.seq import alg
+scene.RemoveAll()
+#-------------------------------------------------------------------------------
+# Loading structure and alignment
+#-------------------------------------------------------------------------------
+m=io.LoadPDB('data/sh2.pdb')
+mp=m.Select('ishetatm=false')
+aln=io.LoadAlignment('data/sh2.aln')
+aln.AttachView(0, mp)
+aln.SetSequenceOffset(0, 1)
+#-------------------------------------------------------------------------------
+# Calculate conservation of alignment
+# First we set all properties to zero, then let alg.Conservation assign the
+# conservation scores to the residues
+#-------------------------------------------------------------------------------
+alg.Conservation(aln)
+
+#-------------------------------------------------------------------------------
+# Setup Graphical Objects for Rendering
+#-------------------------------------------------------------------------------
+g=gfx.Entity('SH2', m)
+s=io.LoadSurface('data/sh2.vert')
+gs=gfx.Surface('SH2-surf', s)
+scene.Add(gs)
+scene.Add(g)
+scene.CenterOn(g)
+
+s.Attach(mp.Select('ishetatm=false'), 8.0)
+
+gr=gfx.Gradient()
+gr.SetColorAt(0.0, gfx.Color(0.1, 0.1, 0.8))
+gr.SetColorAt(1.0, gfx.Color(0.8, 0.1, 0.1))
+
+gs.ColorBy('cons', gr, 0.8, 1.0, 
+           mol.Prop.Level.RESIDUE)
+g.SetRenderMode(gfx.HSC, 
+                m.Select('ishetatm=false'))
+g.SetRenderMode(gfx.CUSTOM, 
+                m.Select('ishetatm=true'))
+g.SetColor(gfx.YELLOW, 'ishetatm=true')
+
+#-------------------------------------------------------------------------------
+# Create alignment viewer and show it on the screen
+#-------------------------------------------------------------------------------
+seq_viewer=gui.SequenceViewer()
+seq_viewer.AddAlignment(aln)
+seq_viewer.Show()
+
+
diff --git a/examples/demos/correlate.py b/examples/demos/correlate.py
new file mode 100644
index 0000000000000000000000000000000000000000..55bb4d068002e6de2d4f38ece15a8236fa467b37
--- /dev/null
+++ b/examples/demos/correlate.py
@@ -0,0 +1,91 @@
+# this script shows how to score a set of candidate fragments according to their 
+# correlation with a density map. fragments with a higher correlation are ranked 
+# better than fragments with a low correlation.
+#
+
+# tabula rasa first
+scene.RemoveAll()
+
+
+import ost.img.alg as img_alg
+from ost.mol.alg import EntityToDensityRosetta, HIGH_RESOLUTION
+sdh=io.LoadPDB('data/sdh-complete.pdb')
+sdh_within=sdh.Select('rnum=94:101 and aname=CA,C,N,O')
+
+padding=4
+# we use a isotropic sampling of 1Anstroem
+bounds=sdh_within.bounds
+actual_size=bounds.max-bounds.min
+size=img.Size(int(actual_size.x+2*padding), 
+              int(actual_size.y+2*padding), 
+              int(actual_size.x+2*padding))
+
+def CreateDensityMap(size, origin):
+  # create 3D image to hold the density information. Pixel sampling is 1A
+  # by default. The image is empty
+  dmap=img.CreateImage(size)
+  dmap.SetAbsoluteOrigin(origin)  
+  return dmap
+origin=bounds.min-geom.Vec3(padding, padding, padding)
+dmap=CreateDensityMap(size, origin)
+cmap=CreateDensityMap(size, origin)
+
+# create density for residue 94 to residue 101
+EntityToDensityRosetta(sdh_within, dmap, HIGH_RESOLUTION, 5.0)
+map_go=gfx.MapIso('Density', dmap, 0.0)
+map_go.SetLevel(map_go.GetMean()*2.0)
+scene.Add(map_go)
+scene.CenterOn(map_go)
+
+# load all loop candidates stored in the PDB file. note the use of the 
+# load_multi parameter
+candidates=io.LoadPDB('data/loop-candidates.pdb', 
+                      load_multi=True)
+
+print len(candidates)
+#-------------------------------------------------------------------------------
+def Correlate(candidates):
+  # this function converts the candidate loop into a density and calculates the 
+  # real-spatial cross correlation with the actual density. The correlation 
+  # coefficient is stored as the "correl" property
+  
+  for index, candidate in enumerate(candidates):
+    EntityToDensityRosetta(candidate.CreateFullView(), cmap, 
+                           HIGH_RESOLUTION, 5.0, True)
+  
+    correl=img_alg.RealSpatialCrossCorrelation(dmap, cmap, dmap.GetExtent())
+    candidate.SetFloatProp('correl', correl)
+#-------------------------------------------------------------------------------  
+  
+  
+def Visualize(candidates):  
+  # finally, sort the candidates by correlation and display them. 
+  min_correl=min([c.GetFloatProp('correl') for c in candidates])
+  max_correl=max([c.GetFloatProp('correl') for c in candidates])
+
+  gradient=gfx.Gradient()
+  gradient.SetColorAt(0.0, gfx.RED)
+  gradient.SetColorAt(1.0, gfx.GREEN)
+
+  # sort candidates by correlation
+  def cmp_correl(lhs, rhs):
+    lhs_correl=lhs.GetFloatProp('correl')
+    rhs_correl=rhs.GetFloatProp('correl')
+    if lhs_correl>rhs_correl:
+      return -1
+    elif lhs_correl==rhs_correl:
+      return 0
+    else:
+      return 1
+  candidates=sorted(candidates, cmp_correl)
+
+  # create render objects and add to scene
+  for index, candidate in enumerate(candidates):
+    candidate_go=gfx.Entity('candidate %03d' % index, candidate)
+    norm=candidate.GetFloatProp('correl')/(max_correl-min_correl)
+    candidate_go.SetColor(gradient.GetColorAt(norm))
+    scene.Add(candidate_go)
+
+
+Correlate(candidates)
+Visualize(candidates)
diff --git a/examples/demos/data/1crn.pdb b/examples/demos/data/1crn.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..8ce00cb3b36a2cd63533355d085ae71a5cc1a651
--- /dev/null
+++ b/examples/demos/data/1crn.pdb
@@ -0,0 +1,611 @@
+HEADER    PLANT SEED PROTEIN                      30-APR-81   1CRN
+TITLE     WATER STRUCTURE OF A HYDROPHOBIC PROTEIN AT ATOMIC
+TITLE    2 RESOLUTION. PENTAGON RINGS OF WATER MOLECULES IN CRYSTALS
+TITLE    3 OF CRAMBIN
+COMPND    MOL_ID: 1;
+COMPND   2 MOLECULE: CRAMBIN;
+COMPND   3 CHAIN: A;
+COMPND   4 ENGINEERED: YES
+SOURCE    MOL_ID: 1;
+SOURCE   2 ORGANISM_SCIENTIFIC: CRAMBE HISPANICA SUBSP. ABYSSINICA;
+SOURCE   3 ORGANISM_TAXID: 3721;
+SOURCE   4 STRAIN: SUBSP. ABYSSINICA
+KEYWDS    PLANT SEED PROTEIN
+EXPDTA    X-RAY DIFFRACTION
+AUTHOR    W.A.HENDRICKSON,M.M.TEETER
+REVDAT   6   24-FEB-09 1CRN    1       VERSN
+REVDAT   5   16-APR-87 1CRN    1       HEADER
+REVDAT   4   04-MAR-85 1CRN    1       REMARK
+REVDAT   3   30-SEP-83 1CRN    1       REVDAT
+REVDAT   2   03-DEC-81 1CRN    1       SHEET
+REVDAT   1   28-JUL-81 1CRN    0
+JRNL        AUTH   M.M.TEETER
+JRNL        TITL   WATER STRUCTURE OF A HYDROPHOBIC PROTEIN AT ATOMIC
+JRNL        TITL 2 RESOLUTION: PENTAGON RINGS OF WATER MOLECULES IN
+JRNL        TITL 3 CRYSTALS OF CRAMBIN.
+JRNL        REF    PROC.NATL.ACAD.SCI.USA        V.  81  6014 1984
+JRNL        REFN                   ISSN 0027-8424
+JRNL        PMID   16593516
+JRNL        DOI    10.1073/PNAS.81.19.6014
+REMARK   1
+REMARK   1 REFERENCE 1
+REMARK   1  AUTH   W.A.HENDRICKSON,M.M.TEETER
+REMARK   1  TITL   STRUCTURE OF THE HYDROPHOBIC PROTEIN CRAMBIN
+REMARK   1  TITL 2 DETERMINED DIRECTLY FROM THE ANOMALOUS SCATTERING
+REMARK   1  TITL 3 OF SULPHUR
+REMARK   1  REF    NATURE                        V. 290   107 1981
+REMARK   1  REFN                   ISSN 0028-0836
+REMARK   1 REFERENCE 2
+REMARK   1  AUTH   M.M.TEETER,W.A.HENDRICKSON
+REMARK   1  TITL   HIGHLY ORDERED CRYSTALS OF THE PLANT SEED PROTEIN
+REMARK   1  TITL 2 CRAMBIN
+REMARK   1  REF    J.MOL.BIOL.                   V. 127   219 1979
+REMARK   1  REFN                   ISSN 0022-2836
+REMARK   2
+REMARK   2 RESOLUTION.    1.50 ANGSTROMS.
+REMARK   3
+REMARK   3 REFINEMENT.
+REMARK   3   PROGRAM     : PROLSQ
+REMARK   3   AUTHORS     : KONNERT,HENDRICKSON
+REMARK   3
+REMARK   3  DATA USED IN REFINEMENT.
+REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50
+REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : NULL
+REMARK   3   DATA CUTOFF            (SIGMA(F)) : NULL
+REMARK   3   COMPLETENESS FOR RANGE        (%) : NULL
+REMARK   3   NUMBER OF REFLECTIONS             : NULL
+REMARK   3
+REMARK   3  FIT TO DATA USED IN REFINEMENT.
+REMARK   3   CROSS-VALIDATION METHOD          : NULL
+REMARK   3   FREE R VALUE TEST SET SELECTION  : NULL
+REMARK   3   R VALUE     (WORKING + TEST SET) : NULL
+REMARK   3   R VALUE            (WORKING SET) : NULL
+REMARK   3   FREE R VALUE                     : NULL
+REMARK   3   FREE R VALUE TEST SET SIZE   (%) : NULL
+REMARK   3   FREE R VALUE TEST SET COUNT      : NULL
+REMARK   3
+REMARK   3  FIT/AGREEMENT OF MODEL WITH ALL DATA.
+REMARK   3   R VALUE   (WORKING + TEST SET, NO CUTOFF) : NULL
+REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : NULL
+REMARK   3   FREE R VALUE                  (NO CUTOFF) : NULL
+REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
+REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) : NULL
+REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : NULL
+REMARK   3
+REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
+REMARK   3   PROTEIN ATOMS            : 327
+REMARK   3   NUCLEIC ACID ATOMS       : 0
+REMARK   3   HETEROGEN ATOMS          : 0
+REMARK   3   SOLVENT ATOMS            : 0
+REMARK   3
+REMARK   3  B VALUES.
+REMARK   3   FROM WILSON PLOT           (A**2) : NULL
+REMARK   3   MEAN B VALUE      (OVERALL, A**2) : NULL
+REMARK   3   OVERALL ANISOTROPIC B VALUE.
+REMARK   3    B11 (A**2) : NULL
+REMARK   3    B22 (A**2) : NULL
+REMARK   3    B33 (A**2) : NULL
+REMARK   3    B12 (A**2) : NULL
+REMARK   3    B13 (A**2) : NULL
+REMARK   3    B23 (A**2) : NULL
+REMARK   3
+REMARK   3  ESTIMATED COORDINATE ERROR.
+REMARK   3   ESD FROM LUZZATI PLOT        (A) : NULL
+REMARK   3   ESD FROM SIGMAA              (A) : NULL
+REMARK   3   LOW RESOLUTION CUTOFF        (A) : NULL
+REMARK   3
+REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.
+REMARK   3   DISTANCE RESTRAINTS.                    RMS    SIGMA
+REMARK   3    BOND LENGTH                     (A) : NULL  ; NULL
+REMARK   3    ANGLE DISTANCE                  (A) : NULL  ; NULL
+REMARK   3    INTRAPLANAR 1-4 DISTANCE        (A) : NULL  ; NULL
+REMARK   3    H-BOND OR METAL COORDINATION    (A) : NULL  ; NULL
+REMARK   3
+REMARK   3   PLANE RESTRAINT                  (A) : NULL  ; NULL
+REMARK   3   CHIRAL-CENTER RESTRAINT       (A**3) : NULL  ; NULL
+REMARK   3
+REMARK   3   NON-BONDED CONTACT RESTRAINTS.
+REMARK   3    SINGLE TORSION                  (A) : NULL  ; NULL
+REMARK   3    MULTIPLE TORSION                (A) : NULL  ; NULL
+REMARK   3    H-BOND (X...Y)                  (A) : NULL  ; NULL
+REMARK   3    H-BOND (X-H...Y)                (A) : NULL  ; NULL
+REMARK   3
+REMARK   3   CONFORMATIONAL TORSION ANGLE RESTRAINTS.
+REMARK   3    SPECIFIED                 (DEGREES) : NULL  ; NULL
+REMARK   3    PLANAR                    (DEGREES) : NULL  ; NULL
+REMARK   3    STAGGERED                 (DEGREES) : NULL  ; NULL
+REMARK   3    TRANSVERSE                (DEGREES) : NULL  ; NULL
+REMARK   3
+REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA
+REMARK   3   MAIN-CHAIN BOND               (A**2) : NULL  ; NULL
+REMARK   3   MAIN-CHAIN ANGLE              (A**2) : NULL  ; NULL
+REMARK   3   SIDE-CHAIN BOND               (A**2) : NULL  ; NULL
+REMARK   3   SIDE-CHAIN ANGLE              (A**2) : NULL  ; NULL
+REMARK   3
+REMARK   3  OTHER REFINEMENT REMARKS: NULL
+REMARK   4
+REMARK   4 1CRN COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
+REMARK 100
+REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
+REMARK 200
+REMARK 200 EXPERIMENTAL DETAILS
+REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
+REMARK 200  DATE OF DATA COLLECTION        : NULL
+REMARK 200  TEMPERATURE           (KELVIN) : NULL
+REMARK 200  PH                             : NULL
+REMARK 200  NUMBER OF CRYSTALS USED        : NULL
+REMARK 200
+REMARK 200  SYNCHROTRON              (Y/N) : NULL
+REMARK 200  RADIATION SOURCE               : NULL
+REMARK 200  BEAMLINE                       : NULL
+REMARK 200  X-RAY GENERATOR MODEL          : NULL
+REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : NULL
+REMARK 200  WAVELENGTH OR RANGE        (A) : NULL
+REMARK 200  MONOCHROMATOR                  : NULL
+REMARK 200  OPTICS                         : NULL
+REMARK 200
+REMARK 200  DETECTOR TYPE                  : NULL
+REMARK 200  DETECTOR MANUFACTURER          : NULL
+REMARK 200  INTENSITY-INTEGRATION SOFTWARE : NULL
+REMARK 200  DATA SCALING SOFTWARE          : NULL
+REMARK 200
+REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : NULL
+REMARK 200  RESOLUTION RANGE HIGH      (A) : NULL
+REMARK 200  RESOLUTION RANGE LOW       (A) : NULL
+REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL
+REMARK 200
+REMARK 200 OVERALL.
+REMARK 200  COMPLETENESS FOR RANGE     (%) : NULL
+REMARK 200  DATA REDUNDANCY                : NULL
+REMARK 200  R MERGE                    (I) : NULL
+REMARK 200  R SYM                      (I) : NULL
+REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : NULL
+REMARK 200
+REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
+REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
+REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : NULL
+REMARK 200  COMPLETENESS FOR SHELL     (%) : NULL
+REMARK 200  DATA REDUNDANCY IN SHELL       : NULL
+REMARK 200  R MERGE FOR SHELL          (I) : NULL
+REMARK 200  R SYM FOR SHELL            (I) : NULL
+REMARK 200  <I/SIGMA(I)> FOR SHELL         : NULL
+REMARK 200
+REMARK 200 DIFFRACTION PROTOCOL: NULL
+REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
+REMARK 200 SOFTWARE USED: NULL
+REMARK 200 STARTING MODEL: NULL
+REMARK 200
+REMARK 200 REMARK: NULL
+REMARK 280
+REMARK 280 CRYSTAL
+REMARK 280 SOLVENT CONTENT, VS   (%): 32.16
+REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81
+REMARK 280
+REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
+REMARK 290
+REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
+REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
+REMARK 290
+REMARK 290      SYMOP   SYMMETRY
+REMARK 290     NNNMMM   OPERATOR
+REMARK 290       1555   X,Y,Z
+REMARK 290       2555   -X,Y+1/2,-Z
+REMARK 290
+REMARK 290     WHERE NNN -> OPERATOR NUMBER
+REMARK 290           MMM -> TRANSLATION VECTOR
+REMARK 290
+REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
+REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
+REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
+REMARK 290 RELATED MOLECULES.
+REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000
+REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000
+REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000
+REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000        0.00000
+REMARK 290   SMTRY2   2  0.000000  1.000000  0.000000        9.32505
+REMARK 290   SMTRY3   2  0.000000  0.000000 -1.000000        0.00000
+REMARK 290
+REMARK 290 REMARK: NULL
+REMARK 300
+REMARK 300 BIOMOLECULE: 1
+REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
+REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
+REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
+REMARK 300 BURIED SURFACE AREA.
+REMARK 350
+REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
+REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
+REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
+REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND
+REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
+REMARK 350
+REMARK 350 BIOMOLECULE: 1
+REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
+REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
+REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000
+REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000
+REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000
+REMARK 400
+REMARK 400 COMPOUND
+REMARK 400
+REMARK 400 THE SECONDARY STRUCTURE SPECIFICATIONS ARE THOSE DEFINED
+REMARK 400 IN REFERENCE 1 ABOVE AND DEPEND ON PARTICULAR DEFINITIONS
+REMARK 400 THAT MAY AFFECT THE DETERMINATION OF END POINTS.  PLEASE
+REMARK 400 CONSULT THE PRIMARY REFERENCE AND EXAMINE STRUCTURAL
+REMARK 400 DETAILS SUCH AS HYDROGEN BONDING AND CONFORMATION ANGLES
+REMARK 400 WHEN MAKING USE OF THE SPECIFICATIONS.
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
+REMARK 500
+REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
+REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
+REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
+REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
+REMARK 500
+REMARK 500 STANDARD TABLE:
+REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
+REMARK 500
+REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
+REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
+REMARK 500
+REMARK 500  M RES CSSEQI ATM1   ATM2   ATM3
+REMARK 500    ARG A  10   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.6 DEGREES
+REMARK 500    TYR A  29   CB  -  CG  -  CD1 ANGL. DEV. =  -4.7 DEGREES
+REMARK 500
+REMARK 500 REMARK: NULL
+DBREF  1CRN A    1    46  UNP    P01542   CRAM_CRAAB       1     46
+SEQRES   1 A   46  THR THR CYS CYS PRO SER ILE VAL ALA ARG SER ASN PHE
+SEQRES   2 A   46  ASN VAL CYS ARG LEU PRO GLY THR PRO GLU ALA ILE CYS
+SEQRES   3 A   46  ALA THR TYR THR GLY CYS ILE ILE ILE PRO GLY ALA THR
+SEQRES   4 A   46  CYS PRO GLY ASP TYR ALA ASN
+HELIX    1  H1 ILE A    7  PRO A   19  13/10 CONFORMATION RES 17,19       13
+HELIX    2  H2 GLU A   23  THR A   30  1DISTORTED 3/10 AT RES 30           8
+SHEET    1  S1 2 THR A   1  CYS A   4  0
+SHEET    2  S1 2 CYS A  32  ILE A  35 -1
+SSBOND   1 CYS A    3    CYS A   40                          1555   1555  2.00
+SSBOND   2 CYS A    4    CYS A   32                          1555   1555  2.04
+SSBOND   3 CYS A   16    CYS A   26                          1555   1555  2.05
+CRYST1   40.960   18.650   22.520  90.00  90.77  90.00 P 1 21 1      2
+ORIGX1      1.000000  0.000000  0.000000        0.00000
+ORIGX2      0.000000  1.000000  0.000000        0.00000
+ORIGX3      0.000000  0.000000  1.000000        0.00000
+SCALE1      0.024414  0.000000 -0.000328        0.00000
+SCALE2      0.000000  0.053619  0.000000        0.00000
+SCALE3      0.000000  0.000000  0.044409        0.00000
+ATOM      1  N   THR A   1      17.047  14.099   3.625  1.00 13.79           N
+ATOM      2  CA  THR A   1      16.967  12.784   4.338  1.00 10.80           C
+ATOM      3  C   THR A   1      15.685  12.755   5.133  1.00  9.19           C
+ATOM      4  O   THR A   1      15.268  13.825   5.594  1.00  9.85           O
+ATOM      5  CB  THR A   1      18.170  12.703   5.337  1.00 13.02           C
+ATOM      6  OG1 THR A   1      19.334  12.829   4.463  1.00 15.06           O
+ATOM      7  CG2 THR A   1      18.150  11.546   6.304  1.00 14.23           C
+ATOM      8  N   THR A   2      15.115  11.555   5.265  1.00  7.81           N
+ATOM      9  CA  THR A   2      13.856  11.469   6.066  1.00  8.31           C
+ATOM     10  C   THR A   2      14.164  10.785   7.379  1.00  5.80           C
+ATOM     11  O   THR A   2      14.993   9.862   7.443  1.00  6.94           O
+ATOM     12  CB  THR A   2      12.732  10.711   5.261  1.00 10.32           C
+ATOM     13  OG1 THR A   2      13.308   9.439   4.926  1.00 12.81           O
+ATOM     14  CG2 THR A   2      12.484  11.442   3.895  1.00 11.90           C
+ATOM     15  N   CYS A   3      13.488  11.241   8.417  1.00  5.24           N
+ATOM     16  CA  CYS A   3      13.660  10.707   9.787  1.00  5.39           C
+ATOM     17  C   CYS A   3      12.269  10.431  10.323  1.00  4.45           C
+ATOM     18  O   CYS A   3      11.393  11.308  10.185  1.00  6.54           O
+ATOM     19  CB  CYS A   3      14.368  11.748  10.691  1.00  5.99           C
+ATOM     20  SG  CYS A   3      15.885  12.426  10.016  1.00  7.01           S
+ATOM     21  N   CYS A   4      12.019   9.272  10.928  1.00  3.90           N
+ATOM     22  CA  CYS A   4      10.646   8.991  11.408  1.00  4.24           C
+ATOM     23  C   CYS A   4      10.654   8.793  12.919  1.00  3.72           C
+ATOM     24  O   CYS A   4      11.659   8.296  13.491  1.00  5.30           O
+ATOM     25  CB  CYS A   4      10.057   7.752  10.682  1.00  4.41           C
+ATOM     26  SG  CYS A   4       9.837   8.018   8.904  1.00  4.72           S
+ATOM     27  N   PRO A   5       9.561   9.108  13.563  1.00  3.96           N
+ATOM     28  CA  PRO A   5       9.448   9.034  15.012  1.00  4.25           C
+ATOM     29  C   PRO A   5       9.288   7.670  15.606  1.00  4.96           C
+ATOM     30  O   PRO A   5       9.490   7.519  16.819  1.00  7.44           O
+ATOM     31  CB  PRO A   5       8.230   9.957  15.345  1.00  5.11           C
+ATOM     32  CG  PRO A   5       7.338   9.786  14.114  1.00  5.24           C
+ATOM     33  CD  PRO A   5       8.366   9.804  12.958  1.00  5.20           C
+ATOM     34  N   SER A   6       8.875   6.686  14.796  1.00  4.83           N
+ATOM     35  CA  SER A   6       8.673   5.314  15.279  1.00  4.45           C
+ATOM     36  C   SER A   6       8.753   4.376  14.083  1.00  4.99           C
+ATOM     37  O   SER A   6       8.726   4.858  12.923  1.00  4.61           O
+ATOM     38  CB  SER A   6       7.340   5.121  15.996  1.00  5.05           C
+ATOM     39  OG  SER A   6       6.274   5.220  15.031  1.00  6.39           O
+ATOM     40  N   ILE A   7       8.881   3.075  14.358  1.00  4.94           N
+ATOM     41  CA  ILE A   7       8.912   2.083  13.258  1.00  6.33           C
+ATOM     42  C   ILE A   7       7.581   2.090  12.506  1.00  5.32           C
+ATOM     43  O   ILE A   7       7.670   2.031  11.245  1.00  6.85           O
+ATOM     44  CB  ILE A   7       9.207   0.677  13.924  1.00  8.43           C
+ATOM     45  CG1 ILE A   7      10.714   0.702  14.312  1.00  9.78           C
+ATOM     46  CG2 ILE A   7       8.811  -0.477  12.969  1.00 11.70           C
+ATOM     47  CD1 ILE A   7      11.185  -0.516  15.142  1.00  9.92           C
+ATOM     48  N   VAL A   8       6.458   2.162  13.159  1.00  5.02           N
+ATOM     49  CA  VAL A   8       5.145   2.209  12.453  1.00  6.93           C
+ATOM     50  C   VAL A   8       5.115   3.379  11.461  1.00  5.39           C
+ATOM     51  O   VAL A   8       4.664   3.268  10.343  1.00  6.30           O
+ATOM     52  CB  VAL A   8       3.995   2.354  13.478  1.00  9.64           C
+ATOM     53  CG1 VAL A   8       2.716   2.891  12.869  1.00 13.85           C
+ATOM     54  CG2 VAL A   8       3.758   1.032  14.208  1.00 11.97           C
+ATOM     55  N   ALA A   9       5.606   4.546  11.941  1.00  3.73           N
+ATOM     56  CA  ALA A   9       5.598   5.767  11.082  1.00  3.56           C
+ATOM     57  C   ALA A   9       6.441   5.527   9.850  1.00  4.13           C
+ATOM     58  O   ALA A   9       6.052   5.933   8.744  1.00  4.36           O
+ATOM     59  CB  ALA A   9       6.022   6.977  11.891  1.00  4.80           C
+ATOM     60  N   ARG A  10       7.647   4.909  10.005  1.00  3.73           N
+ATOM     61  CA  ARG A  10       8.496   4.609   8.837  1.00  3.38           C
+ATOM     62  C   ARG A  10       7.798   3.609   7.876  1.00  3.47           C
+ATOM     63  O   ARG A  10       7.878   3.778   6.651  1.00  4.67           O
+ATOM     64  CB  ARG A  10       9.847   4.020   9.305  1.00  3.95           C
+ATOM     65  CG  ARG A  10      10.752   3.607   8.149  1.00  4.55           C
+ATOM     66  CD  ARG A  10      11.226   4.699   7.244  1.00  5.89           C
+ATOM     67  NE  ARG A  10      12.143   5.571   8.035  1.00  6.20           N
+ATOM     68  CZ  ARG A  10      12.758   6.609   7.443  1.00  7.52           C
+ATOM     69  NH1 ARG A  10      12.539   6.932   6.158  1.00 10.68           N
+ATOM     70  NH2 ARG A  10      13.601   7.322   8.202  1.00  9.48           N
+ATOM     71  N   SER A  11       7.186   2.582   8.445  1.00  5.19           N
+ATOM     72  CA  SER A  11       6.500   1.584   7.565  1.00  4.60           C
+ATOM     73  C   SER A  11       5.382   2.313   6.773  1.00  4.84           C
+ATOM     74  O   SER A  11       5.213   2.016   5.557  1.00  5.84           O
+ATOM     75  CB  SER A  11       5.908   0.462   8.400  1.00  5.91           C
+ATOM     76  OG  SER A  11       6.990  -0.272   9.012  1.00  8.38           O
+ATOM     77  N   ASN A  12       4.648   3.182   7.446  1.00  3.54           N
+ATOM     78  CA  ASN A  12       3.545   3.935   6.751  1.00  4.57           C
+ATOM     79  C   ASN A  12       4.107   4.851   5.691  1.00  4.14           C
+ATOM     80  O   ASN A  12       3.536   5.001   4.617  1.00  5.52           O
+ATOM     81  CB  ASN A  12       2.663   4.677   7.748  1.00  6.42           C
+ATOM     82  CG  ASN A  12       1.802   3.735   8.610  1.00  8.25           C
+ATOM     83  OD1 ASN A  12       1.567   2.613   8.165  1.00 12.72           O
+ATOM     84  ND2 ASN A  12       1.394   4.252   9.767  1.00  9.92           N
+ATOM     85  N   PHE A  13       5.259   5.498   6.005  1.00  3.43           N
+ATOM     86  CA  PHE A  13       5.929   6.358   5.055  1.00  3.49           C
+ATOM     87  C   PHE A  13       6.304   5.578   3.799  1.00  3.40           C
+ATOM     88  O   PHE A  13       6.136   6.072   2.653  1.00  4.07           O
+ATOM     89  CB  PHE A  13       7.183   6.994   5.754  1.00  5.48           C
+ATOM     90  CG  PHE A  13       7.884   8.006   4.883  1.00  5.57           C
+ATOM     91  CD1 PHE A  13       8.906   7.586   4.027  1.00  6.99           C
+ATOM     92  CD2 PHE A  13       7.532   9.373   4.983  1.00  6.52           C
+ATOM     93  CE1 PHE A  13       9.560   8.539   3.194  1.00  8.20           C
+ATOM     94  CE2 PHE A  13       8.176  10.281   4.145  1.00  6.34           C
+ATOM     95  CZ  PHE A  13       9.141   9.845   3.292  1.00  6.84           C
+ATOM     96  N   ASN A  14       6.900   4.390   3.989  1.00  3.64           N
+ATOM     97  CA  ASN A  14       7.331   3.607   2.791  1.00  4.31           C
+ATOM     98  C   ASN A  14       6.116   3.210   1.915  1.00  3.98           C
+ATOM     99  O   ASN A  14       6.240   3.144   0.684  1.00  6.22           O
+ATOM    100  CB  ASN A  14       8.145   2.404   3.240  1.00  5.81           C
+ATOM    101  CG  ASN A  14       9.555   2.856   3.730  1.00  6.82           C
+ATOM    102  OD1 ASN A  14      10.013   3.895   3.323  1.00  9.43           O
+ATOM    103  ND2 ASN A  14      10.120   1.956   4.539  1.00  8.21           N
+ATOM    104  N   VAL A  15       4.993   2.927   2.571  1.00  3.76           N
+ATOM    105  CA  VAL A  15       3.782   2.599   1.742  1.00  3.98           C
+ATOM    106  C   VAL A  15       3.296   3.871   1.004  1.00  3.80           C
+ATOM    107  O   VAL A  15       2.947   3.817  -0.189  1.00  4.85           O
+ATOM    108  CB  VAL A  15       2.698   1.953   2.608  1.00  4.71           C
+ATOM    109  CG1 VAL A  15       1.384   1.826   1.806  1.00  6.67           C
+ATOM    110  CG2 VAL A  15       3.174   0.533   3.005  1.00  6.26           C
+ATOM    111  N   CYS A  16       3.321   4.987   1.720  1.00  3.79           N
+ATOM    112  CA  CYS A  16       2.890   6.285   1.126  1.00  3.54           C
+ATOM    113  C   CYS A  16       3.687   6.597  -0.111  1.00  3.48           C
+ATOM    114  O   CYS A  16       3.200   7.147  -1.103  1.00  4.63           O
+ATOM    115  CB  CYS A  16       3.039   7.369   2.240  1.00  4.58           C
+ATOM    116  SG  CYS A  16       2.559   9.014   1.649  1.00  5.66           S
+ATOM    117  N   ARG A  17       4.997   6.227  -0.100  1.00  3.99           N
+ATOM    118  CA  ARG A  17       5.895   6.489  -1.213  1.00  3.83           C
+ATOM    119  C   ARG A  17       5.738   5.560  -2.409  1.00  3.79           C
+ATOM    120  O   ARG A  17       6.228   5.901  -3.507  1.00  5.39           O
+ATOM    121  CB  ARG A  17       7.370   6.507  -0.731  1.00  4.11           C
+ATOM    122  CG  ARG A  17       7.717   7.687   0.206  1.00  4.69           C
+ATOM    123  CD  ARG A  17       7.949   8.947  -0.615  1.00  5.10           C
+ATOM    124  NE  ARG A  17       9.212   8.856  -1.337  1.00  4.71           N
+ATOM    125  CZ  ARG A  17       9.537   9.533  -2.431  1.00  5.28           C
+ATOM    126  NH1 ARG A  17       8.659  10.350  -3.032  1.00  6.67           N
+ATOM    127  NH2 ARG A  17      10.793   9.491  -2.899  1.00  6.41           N
+ATOM    128  N   LEU A  18       5.051   4.411  -2.204  1.00  4.70           N
+ATOM    129  CA  LEU A  18       4.933   3.431  -3.326  1.00  5.46           C
+ATOM    130  C   LEU A  18       4.397   4.014  -4.620  1.00  5.13           C
+ATOM    131  O   LEU A  18       4.988   3.755  -5.687  1.00  5.55           O
+ATOM    132  CB  LEU A  18       4.196   2.184  -2.863  1.00  6.47           C
+ATOM    133  CG  LEU A  18       4.960   1.178  -1.991  1.00  7.43           C
+ATOM    134  CD1 LEU A  18       3.907   0.097  -1.634  1.00  8.70           C
+ATOM    135  CD2 LEU A  18       6.129   0.606  -2.768  1.00  9.39           C
+ATOM    136  N   PRO A  19       3.329   4.795  -4.543  1.00  4.28           N
+ATOM    137  CA  PRO A  19       2.792   5.376  -5.797  1.00  5.38           C
+ATOM    138  C   PRO A  19       3.573   6.540  -6.322  1.00  6.30           C
+ATOM    139  O   PRO A  19       3.260   7.045  -7.422  1.00  9.62           O
+ATOM    140  CB  PRO A  19       1.358   5.766  -5.472  1.00  5.87           C
+ATOM    141  CG  PRO A  19       1.223   5.694  -3.993  1.00  6.47           C
+ATOM    142  CD  PRO A  19       2.421   4.941  -3.408  1.00  6.45           C
+ATOM    143  N   GLY A  20       4.565   7.047  -5.559  1.00  4.94           N
+ATOM    144  CA  GLY A  20       5.366   8.191  -6.018  1.00  5.39           C
+ATOM    145  C   GLY A  20       5.007   9.481  -5.280  1.00  5.03           C
+ATOM    146  O   GLY A  20       5.535  10.510  -5.730  1.00  7.34           O
+ATOM    147  N   THR A  21       4.181   9.438  -4.262  1.00  4.10           N
+ATOM    148  CA  THR A  21       3.767  10.609  -3.513  1.00  3.94           C
+ATOM    149  C   THR A  21       5.017  11.397  -3.042  1.00  3.96           C
+ATOM    150  O   THR A  21       5.947  10.757  -2.523  1.00  5.82           O
+ATOM    151  CB  THR A  21       2.992  10.188  -2.225  1.00  4.13           C
+ATOM    152  OG1 THR A  21       2.051   9.144  -2.623  1.00  5.45           O
+ATOM    153  CG2 THR A  21       2.260  11.349  -1.551  1.00  5.41           C
+ATOM    154  N   PRO A  22       4.971  12.703  -3.176  1.00  5.04           N
+ATOM    155  CA  PRO A  22       6.143  13.513  -2.696  1.00  4.69           C
+ATOM    156  C   PRO A  22       6.400  13.233  -1.225  1.00  4.19           C
+ATOM    157  O   PRO A  22       5.485  13.061  -0.382  1.00  4.47           O
+ATOM    158  CB  PRO A  22       5.703  14.969  -2.920  1.00  7.12           C
+ATOM    159  CG  PRO A  22       4.676  14.893  -3.996  1.00  7.03           C
+ATOM    160  CD  PRO A  22       3.964  13.567  -3.811  1.00  4.90           C
+ATOM    161  N   GLU A  23       7.728  13.297  -0.921  1.00  5.16           N
+ATOM    162  CA  GLU A  23       8.114  13.103   0.500  1.00  5.31           C
+ATOM    163  C   GLU A  23       7.427  14.073   1.410  1.00  4.11           C
+ATOM    164  O   GLU A  23       7.036  13.682   2.540  1.00  5.11           O
+ATOM    165  CB  GLU A  23       9.648  13.285   0.660  1.00  6.16           C
+ATOM    166  CG  GLU A  23      10.440  12.093   0.063  1.00  7.48           C
+ATOM    167  CD  GLU A  23      11.941  12.170   0.391  1.00  9.40           C
+ATOM    168  OE1 GLU A  23      12.416  13.225   0.681  1.00 10.40           O
+ATOM    169  OE2 GLU A  23      12.539  11.070   0.292  1.00 13.32           O
+ATOM    170  N   ALA A  24       7.212  15.334   0.966  1.00  4.56           N
+ATOM    171  CA  ALA A  24       6.614  16.317   1.913  1.00  4.49           C
+ATOM    172  C   ALA A  24       5.212  15.936   2.350  1.00  4.10           C
+ATOM    173  O   ALA A  24       4.782  16.166   3.495  1.00  5.64           O
+ATOM    174  CB  ALA A  24       6.605  17.695   1.246  1.00  5.80           C
+ATOM    175  N   ILE A  25       4.445  15.318   1.405  1.00  4.37           N
+ATOM    176  CA  ILE A  25       3.074  14.894   1.756  1.00  5.44           C
+ATOM    177  C   ILE A  25       3.085  13.643   2.645  1.00  4.32           C
+ATOM    178  O   ILE A  25       2.315  13.523   3.578  1.00  4.72           O
+ATOM    179  CB  ILE A  25       2.204  14.637   0.462  1.00  6.42           C
+ATOM    180  CG1 ILE A  25       1.815  16.048  -0.129  1.00  7.50           C
+ATOM    181  CG2 ILE A  25       0.903  13.864   0.811  1.00  7.65           C
+ATOM    182  CD1 ILE A  25       0.756  16.761   0.757  1.00  7.80           C
+ATOM    183  N   CYS A  26       4.032  12.764   2.313  1.00  3.92           N
+ATOM    184  CA  CYS A  26       4.180  11.549   3.187  1.00  4.37           C
+ATOM    185  C   CYS A  26       4.632  11.944   4.596  1.00  3.95           C
+ATOM    186  O   CYS A  26       4.227  11.252   5.547  1.00  4.74           O
+ATOM    187  CB  CYS A  26       5.038  10.518   2.539  1.00  4.63           C
+ATOM    188  SG  CYS A  26       4.349   9.794   1.022  1.00  5.61           S
+ATOM    189  N   ALA A  27       5.408  13.012   4.694  1.00  3.89           N
+ATOM    190  CA  ALA A  27       5.879  13.502   6.026  1.00  4.43           C
+ATOM    191  C   ALA A  27       4.696  13.908   6.882  1.00  4.26           C
+ATOM    192  O   ALA A  27       4.528  13.422   8.025  1.00  5.44           O
+ATOM    193  CB  ALA A  27       6.880  14.615   5.830  1.00  5.36           C
+ATOM    194  N   THR A  28       3.827  14.802   6.358  1.00  4.53           N
+ATOM    195  CA  THR A  28       2.691  15.221   7.194  1.00  5.08           C
+ATOM    196  C   THR A  28       1.672  14.132   7.434  1.00  4.62           C
+ATOM    197  O   THR A  28       0.947  14.112   8.468  1.00  7.80           O
+ATOM    198  CB  THR A  28       1.986  16.520   6.614  1.00  6.03           C
+ATOM    199  OG1 THR A  28       1.664  16.221   5.230  1.00  7.19           O
+ATOM    200  CG2 THR A  28       2.914  17.739   6.700  1.00  7.34           C
+ATOM    201  N   TYR A  29       1.621  13.190   6.511  1.00  5.01           N
+ATOM    202  CA  TYR A  29       0.715  12.045   6.657  1.00  6.60           C
+ATOM    203  C   TYR A  29       1.125  11.125   7.815  1.00  4.92           C
+ATOM    204  O   TYR A  29       0.286  10.632   8.545  1.00  7.13           O
+ATOM    205  CB  TYR A  29       0.755  11.229   5.322  1.00  9.66           C
+ATOM    206  CG  TYR A  29      -0.203  10.044   5.354  1.00 11.56           C
+ATOM    207  CD1 TYR A  29      -1.547  10.337   5.645  1.00 12.85           C
+ATOM    208  CD2 TYR A  29       0.193   8.750   5.100  1.00 14.44           C
+ATOM    209  CE1 TYR A  29      -2.496   9.329   5.673  1.00 16.61           C
+ATOM    210  CE2 TYR A  29      -0.801   7.705   5.156  1.00 17.11           C
+ATOM    211  CZ  TYR A  29      -2.079   8.031   5.430  1.00 19.99           C
+ATOM    212  OH  TYR A  29      -3.097   7.057   5.458  1.00 28.98           O
+ATOM    213  N   THR A  30       2.470  10.984   7.995  1.00  5.31           N
+ATOM    214  CA  THR A  30       2.986   9.994   8.950  1.00  5.70           C
+ATOM    215  C   THR A  30       3.609  10.505  10.230  1.00  6.28           C
+ATOM    216  O   THR A  30       3.766   9.715  11.186  1.00  8.77           O
+ATOM    217  CB  THR A  30       4.076   9.103   8.225  1.00  6.55           C
+ATOM    218  OG1 THR A  30       5.125  10.027   7.824  1.00  6.57           O
+ATOM    219  CG2 THR A  30       3.493   8.324   7.035  1.00  7.29           C
+ATOM    220  N   GLY A  31       3.984  11.764  10.241  1.00  4.99           N
+ATOM    221  CA  GLY A  31       4.769  12.336  11.360  1.00  5.50           C
+ATOM    222  C   GLY A  31       6.255  12.243  11.106  1.00  4.19           C
+ATOM    223  O   GLY A  31       7.037  12.750  11.954  1.00  6.12           O
+ATOM    224  N   CYS A  32       6.710  11.631   9.992  1.00  4.30           N
+ATOM    225  CA  CYS A  32       8.140  11.694   9.635  1.00  4.89           C
+ATOM    226  C   CYS A  32       8.500  13.141   9.206  1.00  5.50           C
+ATOM    227  O   CYS A  32       7.581  13.949   8.944  1.00  5.82           O
+ATOM    228  CB  CYS A  32       8.504  10.686   8.530  1.00  4.66           C
+ATOM    229  SG  CYS A  32       8.048   8.987   8.881  1.00  5.33           S
+ATOM    230  N   ILE A  33       9.793  13.410   9.173  1.00  6.02           N
+ATOM    231  CA  ILE A  33      10.280  14.760   8.823  1.00  5.24           C
+ATOM    232  C   ILE A  33      11.346  14.658   7.743  1.00  5.16           C
+ATOM    233  O   ILE A  33      11.971  13.583   7.552  1.00  7.19           O
+ATOM    234  CB  ILE A  33      10.790  15.535  10.085  1.00  5.49           C
+ATOM    235  CG1 ILE A  33      12.059  14.803  10.671  1.00  6.85           C
+ATOM    236  CG2 ILE A  33       9.684  15.686  11.138  1.00  6.45           C
+ATOM    237  CD1 ILE A  33      12.733  15.676  11.781  1.00  8.94           C
+ATOM    238  N   ILE A  34      11.490  15.773   7.038  1.00  5.52           N
+ATOM    239  CA  ILE A  34      12.552  15.877   6.036  1.00  6.82           C
+ATOM    240  C   ILE A  34      13.590  16.917   6.560  1.00  6.92           C
+ATOM    241  O   ILE A  34      13.168  18.006   6.945  1.00  9.22           O
+ATOM    242  CB  ILE A  34      11.987  16.360   4.681  1.00  8.11           C
+ATOM    243  CG1 ILE A  34      10.914  15.338   4.163  1.00  9.59           C
+ATOM    244  CG2 ILE A  34      13.131  16.517   3.629  1.00  9.73           C
+ATOM    245  CD1 ILE A  34      10.151  16.024   2.938  1.00 13.41           C
+ATOM    246  N   ILE A  35      14.856  16.493   6.536  1.00  7.06           N
+ATOM    247  CA  ILE A  35      15.930  17.454   6.941  1.00  7.52           C
+ATOM    248  C   ILE A  35      16.913  17.550   5.819  1.00  6.63           C
+ATOM    249  O   ILE A  35      17.097  16.660   4.970  1.00  7.90           O
+ATOM    250  CB  ILE A  35      16.622  16.995   8.285  1.00  8.07           C
+ATOM    251  CG1 ILE A  35      17.360  15.651   8.067  1.00  9.41           C
+ATOM    252  CG2 ILE A  35      15.592  16.974   9.434  1.00  9.46           C
+ATOM    253  CD1 ILE A  35      18.298  15.206   9.219  1.00  9.85           C
+ATOM    254  N   PRO A  36      17.664  18.669   5.806  1.00  8.07           N
+ATOM    255  CA  PRO A  36      18.635  18.861   4.738  1.00  8.78           C
+ATOM    256  C   PRO A  36      19.925  18.042   4.949  1.00  8.31           C
+ATOM    257  O   PRO A  36      20.593  17.742   3.945  1.00  9.09           O
+ATOM    258  CB  PRO A  36      18.945  20.364   4.783  1.00  9.67           C
+ATOM    259  CG  PRO A  36      18.238  20.937   5.908  1.00 10.15           C
+ATOM    260  CD  PRO A  36      17.371  19.900   6.596  1.00  9.53           C
+ATOM    261  N   GLY A  37      20.172  17.730   6.217  1.00  8.48           N
+ATOM    262  CA  GLY A  37      21.452  16.969   6.513  1.00  9.20           C
+ATOM    263  C   GLY A  37      21.143  15.478   6.427  1.00 10.41           C
+ATOM    264  O   GLY A  37      20.138  15.023   5.878  1.00 12.06           O
+ATOM    265  N   ALA A  38      22.055  14.701   7.032  1.00  9.24           N
+ATOM    266  CA  ALA A  38      22.019  13.242   7.020  1.00  9.24           C
+ATOM    267  C   ALA A  38      21.944  12.628   8.396  1.00  9.60           C
+ATOM    268  O   ALA A  38      21.869  11.387   8.435  1.00 13.65           O
+ATOM    269  CB  ALA A  38      23.246  12.697   6.275  1.00 10.43           C
+ATOM    270  N   THR A  39      21.894  13.435   9.436  1.00  8.70           N
+ATOM    271  CA  THR A  39      21.936  12.911  10.809  1.00  9.46           C
+ATOM    272  C   THR A  39      20.615  13.191  11.521  1.00  8.32           C
+ATOM    273  O   THR A  39      20.357  14.317  11.948  1.00  9.89           O
+ATOM    274  CB  THR A  39      23.131  13.601  11.593  1.00 10.72           C
+ATOM    275  OG1 THR A  39      24.284  13.401  10.709  1.00 11.66           O
+ATOM    276  CG2 THR A  39      23.340  12.935  12.962  1.00 11.81           C
+ATOM    277  N   CYS A  40      19.827  12.110  11.642  1.00  7.64           N
+ATOM    278  CA  CYS A  40      18.504  12.312  12.298  1.00  8.05           C
+ATOM    279  C   CYS A  40      18.684  12.451  13.784  1.00  7.63           C
+ATOM    280  O   CYS A  40      19.533  11.718  14.362  1.00  9.64           O
+ATOM    281  CB  CYS A  40      17.582  11.117  11.996  1.00  7.80           C
+ATOM    282  SG  CYS A  40      17.199  10.929  10.237  1.00  7.30           S
+ATOM    283  N   PRO A  41      17.880  13.266  14.426  1.00  8.00           N
+ATOM    284  CA  PRO A  41      17.924  13.421  15.877  1.00  8.96           C
+ATOM    285  C   PRO A  41      17.392  12.206  16.594  1.00  9.06           C
+ATOM    286  O   PRO A  41      16.652  11.368  16.033  1.00  8.82           O
+ATOM    287  CB  PRO A  41      17.076  14.658  16.145  1.00 10.39           C
+ATOM    288  CG  PRO A  41      16.098  14.689  14.997  1.00 10.99           C
+ATOM    289  CD  PRO A  41      16.859  14.150  13.779  1.00 10.49           C
+ATOM    290  N   GLY A  42      17.728  12.124  17.884  1.00  7.55           N
+ATOM    291  CA  GLY A  42      17.334  10.956  18.691  1.00  8.00           C
+ATOM    292  C   GLY A  42      15.875  10.688  18.871  1.00  7.22           C
+ATOM    293  O   GLY A  42      15.434   9.550  19.166  1.00  8.41           O
+ATOM    294  N   ASP A  43      15.036  11.747  18.715  1.00  5.54           N
+ATOM    295  CA  ASP A  43      13.564  11.573  18.836  1.00  5.85           C
+ATOM    296  C   ASP A  43      12.936  11.227  17.470  1.00  5.87           C
+ATOM    297  O   ASP A  43      11.720  11.040  17.428  1.00  7.29           O
+ATOM    298  CB  ASP A  43      12.933  12.737  19.580  1.00  6.72           C
+ATOM    299  CG  ASP A  43      13.140  14.094  18.958  1.00  8.59           C
+ATOM    300  OD1 ASP A  43      14.109  14.303  18.212  1.00  9.59           O
+ATOM    301  OD2 ASP A  43      12.267  14.963  19.265  1.00 11.45           O
+ATOM    302  N   TYR A  44      13.725  11.174  16.425  1.00  5.22           N
+ATOM    303  CA  TYR A  44      13.257  10.745  15.081  1.00  5.56           C
+ATOM    304  C   TYR A  44      14.275   9.687  14.612  1.00  4.61           C
+ATOM    305  O   TYR A  44      14.930   9.862  13.568  1.00  6.04           O
+ATOM    306  CB  TYR A  44      13.200  11.914  14.071  1.00  5.41           C
+ATOM    307  CG  TYR A  44      12.000  12.819  14.399  1.00  5.34           C
+ATOM    308  CD1 TYR A  44      12.119  13.853  15.332  1.00  6.59           C
+ATOM    309  CD2 TYR A  44      10.775  12.617  13.762  1.00  5.94           C
+ATOM    310  CE1 TYR A  44      11.045  14.675  15.610  1.00  5.97           C
+ATOM    311  CE2 TYR A  44       9.676  13.433  14.048  1.00  5.17           C
+ATOM    312  CZ  TYR A  44       9.802  14.456  14.996  1.00  5.96           C
+ATOM    313  OH  TYR A  44       8.740  15.265  15.269  1.00  8.60           O
+ATOM    314  N   ALA A  45      14.342   8.640  15.422  1.00  4.76           N
+ATOM    315  CA  ALA A  45      15.445   7.667  15.246  1.00  5.89           C
+ATOM    316  C   ALA A  45      15.171   6.533  14.280  1.00  6.67           C
+ATOM    317  O   ALA A  45      16.093   5.705  14.039  1.00  7.56           O
+ATOM    318  CB  ALA A  45      15.680   7.099  16.682  1.00  6.82           C
+ATOM    319  N   ASN A  46      13.966   6.502  13.739  1.00  5.80           N
+ATOM    320  CA  ASN A  46      13.512   5.395  12.878  1.00  6.15           C
+ATOM    321  C   ASN A  46      13.311   5.853  11.455  1.00  6.61           C
+ATOM    322  O   ASN A  46      13.733   6.929  11.026  1.00  7.18           O
+ATOM    323  CB  ASN A  46      12.266   4.769  13.501  1.00  7.27           C
+ATOM    324  CG  ASN A  46      12.538   4.304  14.922  1.00  7.98           C
+ATOM    325  OD1 ASN A  46      11.982   4.849  15.886  1.00 11.00           O
+ATOM    326  ND2 ASN A  46      13.407   3.298  15.015  1.00 10.32           N
+ATOM    327  OXT ASN A  46      12.703   4.973  10.746  1.00  7.86           O
+TER     328      ASN A  46
+CONECT   20  282
+CONECT   26  229
+CONECT  116  188
+CONECT  188  116
+CONECT  229   26
+CONECT  282   20
+MASTER      227    0    0    2    2    1    0    6  327    1    6    4
+END
\ No newline at end of file
diff --git a/examples/demos/data/loop-candidates.pdb b/examples/demos/data/loop-candidates.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..ffe1f2131b09b24b08aa08194ef6b4d216c92090
--- /dev/null
+++ b/examples/demos/data/loop-candidates.pdb
@@ -0,0 +1,2653 @@
+MODEL     1
+ATOM      1  N   GLY A   1      38.710   1.038  82.108  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      37.883   0.416  83.169  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.130   1.383  84.091  1.00  0.00           C  
+ATOM      4  O   GLY A   1      36.425   0.948  85.043  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.284   2.688  83.864  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      36.545   3.637  84.693  1.00  0.00           C  
+ATOM      7  C   GLY A   2      36.251   4.894  83.921  1.00  0.00           C  
+ATOM      8  O   GLY A   2      36.800   5.105  82.842  1.00  0.00           O  
+ATOM      9  N   GLY A   3      35.362   5.719  84.474  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      35.067   7.002  83.865  1.00  0.00           C  
+ATOM     11  C   GLY A   3      34.851   8.017  84.963  1.00  0.00           C  
+ATOM     12  O   GLY A   3      34.138   7.742  85.934  1.00  0.00           O  
+ATOM     13  N   GLY A   4      35.432   9.200  84.792  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      35.208  10.231  85.789  1.00  0.00           C  
+ATOM     15  C   GLY A   4      33.904  10.992  85.530  1.00  0.00           C  
+ATOM     16  O   GLY A   4      33.665  11.438  84.396  1.00  0.00           O  
+ATOM     17  N   GLY A   5      33.088  11.162  86.578  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      31.857  11.927  86.457  1.00  0.00           C  
+ATOM     19  C   GLY A   5      32.011  13.248  87.199  1.00  0.00           C  
+ATOM     20  O   GLY A   5      33.024  13.530  87.835  1.00  0.00           O  
+ATOM     21  N   GLY A   6      30.995  14.080  87.139  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      31.028  15.352  87.848  1.00  0.00           C  
+ATOM     23  C   GLY A   6      31.072  15.151  89.369  1.00  0.00           C  
+ATOM     24  O   GLY A   6      31.772  15.913  90.062  1.00  0.00           O  
+ATOM     25  N   GLY A   7      30.377  14.144  89.904  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      30.434  13.930  91.366  1.00  0.00           C  
+ATOM     27  C   GLY A   7      30.872  12.547  91.763  1.00  0.00           C  
+ATOM     28  O   GLY A   7      31.198  12.335  92.930  1.00  0.00           O  
+ATOM     29  N   GLY A   8      30.900  11.606  90.829  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.273  10.230  91.170  1.00  0.00           C  
+ATOM     31  C   GLY A   8      32.201   9.611  90.119  1.00  0.00           C  
+ATOM     32  O   GLY A   8      32.232  10.048  88.945  1.00  0.00           O  
+ENDMDL
+MODEL     2
+ATOM      1  N   GLY A   1      38.694   1.543  80.899  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      37.811   0.422  81.162  1.00  0.00           C  
+ATOM      3  C   GLY A   1      36.813   0.739  82.269  1.00  0.00           C  
+ATOM      4  O   GLY A   1      36.463  -0.139  83.053  1.00  0.00           O  
+ATOM      5  N   GLY A   2      36.346   1.992  82.355  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      35.665   2.472  83.574  1.00  0.00           C  
+ATOM      7  C   GLY A   2      34.159   2.214  83.809  1.00  0.00           C  
+ATOM      8  O   GLY A   2      33.771   1.351  84.600  1.00  0.00           O  
+ATOM      9  N   GLY A   3      33.352   2.956  83.052  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      31.921   3.300  83.269  1.00  0.00           C  
+ATOM     11  C   GLY A   3      32.019   4.574  83.999  1.00  0.00           C  
+ATOM     12  O   GLY A   3      31.244   5.489  83.769  1.00  0.00           O  
+ATOM     13  N   GLY A   4      32.990   4.583  84.911  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      33.441   5.749  85.631  1.00  0.00           C  
+ATOM     15  C   GLY A   4      32.618   6.160  86.832  1.00  0.00           C  
+ATOM     16  O   GLY A   4      32.927   7.160  87.474  1.00  0.00           O  
+ATOM     17  N   GLY A   5      31.565   5.399  87.135  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      30.952   5.520  88.450  1.00  0.00           C  
+ATOM     19  C   GLY A   5      31.908   4.985  89.503  1.00  0.00           C  
+ATOM     20  O   GLY A   5      32.967   4.457  89.168  1.00  0.00           O  
+ATOM     21  N   GLY A   6      31.540   5.138  90.772  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      32.398   4.804  91.910  1.00  0.00           C  
+ATOM     23  C   GLY A   6      33.617   5.704  91.979  1.00  0.00           C  
+ATOM     24  O   GLY A   6      34.000   6.132  93.058  1.00  0.00           O  
+ATOM     25  N   GLY A   7      34.213   6.004  90.833  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      35.205   7.050  90.732  1.00  0.00           C  
+ATOM     27  C   GLY A   7      34.526   8.366  91.057  1.00  0.00           C  
+ATOM     28  O   GLY A   7      35.012   9.145  91.867  1.00  0.00           O  
+ATOM     29  N   GLY A   8      33.376   8.575  90.425  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      32.545   9.749  90.628  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.847   9.644  91.961  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.720  10.629  92.682  1.00  0.00           O  
+ENDMDL
+MODEL     3
+ATOM      1  N   GLY A   1      37.941   0.894  83.211  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.351   0.100  82.048  1.00  0.00           C  
+ATOM      3  C   GLY A   1      38.070  -1.376  82.274  1.00  0.00           C  
+ATOM      4  O   GLY A   1      38.284  -2.201  81.376  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.577  -1.720  83.456  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      37.305  -3.108  83.793  1.00  0.00           C  
+ATOM      7  C   GLY A   2      35.817  -3.450  83.857  1.00  0.00           C  
+ATOM      8  O   GLY A   2      35.261  -3.793  84.918  1.00  0.00           O  
+ATOM      9  N   GLY A   3      35.172  -3.308  82.705  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      33.763  -3.637  82.556  1.00  0.00           C  
+ATOM     11  C   GLY A   3      32.846  -2.989  83.603  1.00  0.00           C  
+ATOM     12  O   GLY A   3      31.974  -3.651  84.174  1.00  0.00           O  
+ATOM     13  N   GLY A   4      33.052  -1.709  83.860  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      32.217  -0.991  84.809  1.00  0.00           C  
+ATOM     15  C   GLY A   4      32.148   0.461  84.395  1.00  0.00           C  
+ATOM     16  O   GLY A   4      33.131   1.048  83.942  1.00  0.00           O  
+ATOM     17  N   GLY A   5      30.962   1.045  84.532  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      30.769   2.453  84.213  1.00  0.00           C  
+ATOM     19  C   GLY A   5      30.966   3.174  85.535  1.00  0.00           C  
+ATOM     20  O   GLY A   5      30.385   2.783  86.551  1.00  0.00           O  
+ATOM     21  N   GLY A   6      31.820   4.186  85.540  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      32.099   4.919  86.770  1.00  0.00           C  
+ATOM     23  C   GLY A   6      31.756   6.388  86.635  1.00  0.00           C  
+ATOM     24  O   GLY A   6      32.114   7.016  85.634  1.00  0.00           O  
+ATOM     25  N   GLY A   7      31.066   6.921  87.634  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      30.704   8.337  87.675  1.00  0.00           C  
+ATOM     27  C   GLY A   7      31.026   8.785  89.086  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.343   8.389  90.032  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.072   9.583  89.225  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      32.490  10.046  90.544  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.536  11.097  91.116  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.042  11.965  90.410  1.00  0.00           O  
+ENDMDL
+MODEL     4
+ATOM      1  N   GLY A   1      39.299   0.095  81.830  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      39.119   0.759  83.108  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.764   1.452  83.184  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.537   2.450  82.498  1.00  0.00           O  
+ATOM      5  N   GLY A   2      36.868   0.917  84.007  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      35.494   1.405  83.993  1.00  0.00           C  
+ATOM      7  C   GLY A   2      35.271   2.570  84.917  1.00  0.00           C  
+ATOM      8  O   GLY A   2      34.915   2.402  86.104  1.00  0.00           O  
+ATOM      9  N   GLY A   3      35.453   3.778  84.371  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      35.322   5.017  85.129  1.00  0.00           C  
+ATOM     11  C   GLY A   3      33.950   5.151  85.795  1.00  0.00           C  
+ATOM     12  O   GLY A   3      33.791   5.918  86.743  1.00  0.00           O  
+ATOM     13  N   GLY A   4      32.968   4.412  85.289  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      31.638   4.395  85.942  1.00  0.00           C  
+ATOM     15  C   GLY A   4      31.632   3.697  87.308  1.00  0.00           C  
+ATOM     16  O   GLY A   4      30.722   3.904  88.135  1.00  0.00           O  
+ATOM     17  N   GLY A   5      32.652   2.890  87.543  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      32.844   2.171  88.786  1.00  0.00           C  
+ATOM     19  C   GLY A   5      33.566   3.031  89.829  1.00  0.00           C  
+ATOM     20  O   GLY A   5      33.797   2.588  90.956  1.00  0.00           O  
+ATOM     21  N   GLY A   6      33.925   4.254  89.433  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      34.406   5.252  90.385  1.00  0.00           C  
+ATOM     23  C   GLY A   6      33.271   5.638  91.330  1.00  0.00           C  
+ATOM     24  O   GLY A   6      33.528   6.067  92.445  1.00  0.00           O  
+ATOM     25  N   GLY A   7      32.033   5.455  90.876  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      30.831   5.799  91.649  1.00  0.00           C  
+ATOM     27  C   GLY A   7      30.954   7.251  92.113  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.787   7.549  93.287  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.268   8.153  91.192  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.516   9.552  91.546  1.00  0.00           C  
+ATOM     31  C   GLY A   8      30.747  10.448  90.577  1.00  0.00           C  
+ATOM     32  O   GLY A   8      30.985  10.420  89.357  1.00  0.00           O  
+ENDMDL
+MODEL     5
+ATOM      1  N   GLY A   1      39.744  -0.325  82.421  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      39.895   0.901  83.202  1.00  0.00           C  
+ATOM      3  C   GLY A   1      38.762   1.066  84.196  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.599   0.811  83.892  1.00  0.00           O  
+ATOM      5  N   GLY A   2      39.113   1.524  85.386  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      38.138   1.717  86.453  1.00  0.00           C  
+ATOM      7  C   GLY A   2      37.298   2.967  86.290  1.00  0.00           C  
+ATOM      8  O   GLY A   2      37.799   4.031  85.918  1.00  0.00           O  
+ATOM      9  N   GLY A   3      36.005   2.819  86.581  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      35.075   3.936  86.547  1.00  0.00           C  
+ATOM     11  C   GLY A   3      35.445   4.681  87.829  1.00  0.00           C  
+ATOM     12  O   GLY A   3      35.957   4.072  88.768  1.00  0.00           O  
+ATOM     13  N   GLY A   4      35.207   5.994  87.886  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      35.551   6.745  89.102  1.00  0.00           C  
+ATOM     15  C   GLY A   4      34.529   6.479  90.214  1.00  0.00           C  
+ATOM     16  O   GLY A   4      33.829   7.384  90.661  1.00  0.00           O  
+ATOM     17  N   GLY A   5      34.473   5.223  90.650  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      33.540   4.769  91.678  1.00  0.00           C  
+ATOM     19  C   GLY A   5      33.338   5.695  92.884  1.00  0.00           C  
+ATOM     20  O   GLY A   5      32.206   6.074  93.207  1.00  0.00           O  
+ATOM     21  N   GLY A   6      34.439   6.038  93.527  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      34.445   6.908  94.697  1.00  0.00           C  
+ATOM     23  C   GLY A   6      33.809   8.300  94.412  1.00  0.00           C  
+ATOM     24  O   GLY A   6      33.108   8.857  95.260  1.00  0.00           O  
+ATOM     25  N   GLY A   7      34.046   8.822  93.207  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      33.586  10.164  92.797  1.00  0.00           C  
+ATOM     27  C   GLY A   7      32.333  10.292  91.927  1.00  0.00           C  
+ATOM     28  O   GLY A   7      31.781  11.389  91.815  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.896   9.211  91.298  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      30.770   9.242  90.365  1.00  0.00           C  
+ATOM     31  C   GLY A   8      30.018  10.561  90.198  1.00  0.00           C  
+ATOM     32  O   GLY A   8      30.241  11.281  89.220  1.00  0.00           O  
+ENDMDL
+MODEL     6
+ATOM      1  N   GLY A   1      38.845   0.036  81.682  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.666   1.380  82.229  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.534   1.444  83.244  1.00  0.00           C  
+ATOM      4  O   GLY A   1      36.451   1.975  82.953  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.779   0.917  84.460  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      36.852   0.846  85.602  1.00  0.00           C  
+ATOM      7  C   GLY A   2      36.486   2.204  86.189  1.00  0.00           C  
+ATOM      8  O   GLY A   2      36.941   3.246  85.708  1.00  0.00           O  
+ATOM      9  N   GLY A   3      35.683   2.185  87.251  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      35.240   3.424  87.881  1.00  0.00           C  
+ATOM     11  C   GLY A   3      36.365   4.153  88.606  1.00  0.00           C  
+ATOM     12  O   GLY A   3      37.218   3.523  89.237  1.00  0.00           O  
+ATOM     13  N   GLY A   4      36.363   5.489  88.522  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      37.393   6.314  89.170  1.00  0.00           C  
+ATOM     15  C   GLY A   4      37.494   6.138  90.673  1.00  0.00           C  
+ATOM     16  O   GLY A   4      36.500   6.133  91.396  1.00  0.00           O  
+ATOM     17  N   GLY A   5      38.732   5.986  91.135  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      39.040   5.810  92.544  1.00  0.00           C  
+ATOM     19  C   GLY A   5      38.724   7.052  93.392  1.00  0.00           C  
+ATOM     20  O   GLY A   5      38.194   6.935  94.494  1.00  0.00           O  
+ATOM     21  N   GLY A   6      39.034   8.229  92.873  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      38.811   9.444  93.642  1.00  0.00           C  
+ATOM     23  C   GLY A   6      37.654  10.346  93.213  1.00  0.00           C  
+ATOM     24  O   GLY A   6      37.661  11.548  93.504  1.00  0.00           O  
+ATOM     25  N   GLY A   7      36.664   9.768  92.554  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      35.506  10.537  92.103  1.00  0.00           C  
+ATOM     27  C   GLY A   7      34.300   9.629  91.948  1.00  0.00           C  
+ATOM     28  O   GLY A   7      34.441   8.425  91.728  1.00  0.00           O  
+ATOM     29  N   GLY A   8      33.103  10.186  92.089  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.883   9.408  91.889  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.594   9.739  90.427  1.00  0.00           C  
+ATOM     32  O   GLY A   8      30.907  10.720  90.130  1.00  0.00           O  
+ENDMDL
+MODEL     7
+ATOM      1  N   GLY A   1      37.351   1.566  82.295  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.039   0.665  81.359  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.830  -0.812  81.756  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.763  -1.698  80.888  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.702  -1.064  83.062  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      37.456  -2.413  83.589  1.00  0.00           C  
+ATOM      7  C   GLY A   2      35.968  -2.766  83.742  1.00  0.00           C  
+ATOM      8  O   GLY A   2      35.620  -3.876  84.189  1.00  0.00           O  
+ATOM      9  N   GLY A   3      35.090  -1.845  83.354  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      33.658  -2.115  83.335  1.00  0.00           C  
+ATOM     11  C   GLY A   3      32.979  -2.182  84.690  1.00  0.00           C  
+ATOM     12  O   GLY A   3      31.916  -2.801  84.800  1.00  0.00           O  
+ATOM     13  N   GLY A   4      33.578  -1.567  85.705  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      32.956  -1.513  87.034  1.00  0.00           C  
+ATOM     15  C   GLY A   4      31.843  -0.476  87.066  1.00  0.00           C  
+ATOM     16  O   GLY A   4      31.939   0.550  86.399  1.00  0.00           O  
+ATOM     17  N   GLY A   5      30.799  -0.755  87.834  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      29.668   0.170  87.970  1.00  0.00           C  
+ATOM     19  C   GLY A   5      30.020   1.264  88.976  1.00  0.00           C  
+ATOM     20  O   GLY A   5      29.487   1.282  90.091  1.00  0.00           O  
+ATOM     21  N   GLY A   6      30.919   2.171  88.585  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      31.533   3.125  89.513  1.00  0.00           C  
+ATOM     23  C   GLY A   6      31.207   4.575  89.179  1.00  0.00           C  
+ATOM     24  O   GLY A   6      31.261   4.957  88.015  1.00  0.00           O  
+ATOM     25  N   GLY A   7      30.837   5.361  90.194  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      30.699   6.804  90.041  1.00  0.00           C  
+ATOM     27  C   GLY A   7      31.675   7.523  90.960  1.00  0.00           C  
+ATOM     28  O   GLY A   7      31.924   7.093  92.102  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.239   8.616  90.471  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      32.972   9.541  91.321  1.00  0.00           C  
+ATOM     31  C   GLY A   8      32.023  10.616  91.820  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.214  11.149  91.052  1.00  0.00           O  
+ENDMDL
+MODEL     8
+ATOM      1  N   GLY A   1      40.155  -0.234  82.459  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.773  -0.322  82.937  1.00  0.00           C  
+ATOM      3  C   GLY A   1      38.504   0.803  83.932  1.00  0.00           C  
+ATOM      4  O   GLY A   1      39.316   1.039  84.830  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.372   1.475  83.781  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      37.052   2.577  84.667  1.00  0.00           C  
+ATOM      7  C   GLY A   2      36.704   2.204  86.100  1.00  0.00           C  
+ATOM      8  O   GLY A   2      36.356   1.060  86.386  1.00  0.00           O  
+ATOM      9  N   GLY A   3      36.814   3.182  87.000  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      36.485   2.969  88.407  1.00  0.00           C  
+ATOM     11  C   GLY A   3      36.007   4.296  89.005  1.00  0.00           C  
+ATOM     12  O   GLY A   3      36.180   5.355  88.408  1.00  0.00           O  
+ATOM     13  N   GLY A   4      35.405   4.217  90.188  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      34.882   5.394  90.870  1.00  0.00           C  
+ATOM     15  C   GLY A   4      35.755   5.806  92.044  1.00  0.00           C  
+ATOM     16  O   GLY A   4      35.297   6.519  92.940  1.00  0.00           O  
+ATOM     17  N   GLY A   5      37.018   5.390  92.031  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      37.934   5.685  93.128  1.00  0.00           C  
+ATOM     19  C   GLY A   5      38.069   7.173  93.478  1.00  0.00           C  
+ATOM     20  O   GLY A   5      38.299   7.510  94.634  1.00  0.00           O  
+ATOM     21  N   GLY A   6      37.925   8.062  92.493  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      38.021   9.494  92.796  1.00  0.00           C  
+ATOM     23  C   GLY A   6      36.727  10.236  92.491  1.00  0.00           C  
+ATOM     24  O   GLY A   6      36.744  11.433  92.185  1.00  0.00           O  
+ATOM     25  N   GLY A   7      35.596   9.546  92.577  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      34.339  10.229  92.336  1.00  0.00           C  
+ATOM     27  C   GLY A   7      33.536   9.740  91.148  1.00  0.00           C  
+ATOM     28  O   GLY A   7      34.041   9.004  90.291  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.290  10.176  91.084  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.387   9.769  90.018  1.00  0.00           C  
+ATOM     31  C   GLY A   8      30.394  10.903  89.722  1.00  0.00           C  
+ATOM     32  O   GLY A   8      30.216  11.806  90.533  1.00  0.00           O  
+ENDMDL
+MODEL     9
+ATOM      1  N   GLY A   1      37.374  -0.731  81.136  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      37.800   0.432  81.902  1.00  0.00           C  
+ATOM      3  C   GLY A   1      36.895   0.678  83.101  1.00  0.00           C  
+ATOM      4  O   GLY A   1      35.690   0.418  83.052  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.479   1.184  84.189  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      36.706   1.475  85.386  1.00  0.00           C  
+ATOM      7  C   GLY A   2      35.756   2.667  85.232  1.00  0.00           C  
+ATOM      8  O   GLY A   2      34.893   2.892  86.090  1.00  0.00           O  
+ATOM      9  N   GLY A   3      35.889   3.418  84.145  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      34.861   4.387  83.776  1.00  0.00           C  
+ATOM     11  C   GLY A   3      33.488   3.725  83.637  1.00  0.00           C  
+ATOM     12  O   GLY A   3      32.471   4.310  84.020  1.00  0.00           O  
+ATOM     13  N   GLY A   4      33.472   2.504  83.100  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      32.247   1.734  82.880  1.00  0.00           C  
+ATOM     15  C   GLY A   4      31.757   1.027  84.145  1.00  0.00           C  
+ATOM     16  O   GLY A   4      30.795   0.271  84.099  1.00  0.00           O  
+ATOM     17  N   GLY A   5      32.442   1.267  85.255  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      32.296   0.432  86.446  1.00  0.00           C  
+ATOM     19  C   GLY A   5      31.821   1.338  87.569  1.00  0.00           C  
+ATOM     20  O   GLY A   5      31.144   0.897  88.500  1.00  0.00           O  
+ATOM     21  N   GLY A   6      32.209   2.603  87.456  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      32.437   3.460  88.611  1.00  0.00           C  
+ATOM     23  C   GLY A   6      32.079   4.925  88.377  1.00  0.00           C  
+ATOM     24  O   GLY A   6      32.329   5.490  87.311  1.00  0.00           O  
+ATOM     25  N   GLY A   7      31.478   5.523  89.404  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      31.118   6.929  89.379  1.00  0.00           C  
+ATOM     27  C   GLY A   7      31.647   7.587  90.641  1.00  0.00           C  
+ATOM     28  O   GLY A   7      31.635   6.970  91.709  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.114   8.821  90.500  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      32.738   9.602  91.564  1.00  0.00           C  
+ATOM     31  C   GLY A   8      32.223  11.044  91.461  1.00  0.00           C  
+ATOM     32  O   GLY A   8      32.400  11.701  90.438  1.00  0.00           O  
+ENDMDL
+MODEL     10
+ATOM      1  N   GLY A   1      39.541   0.503  82.277  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.394   0.734  83.188  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.854  -0.517  83.923  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.196  -0.427  84.945  1.00  0.00           O  
+ATOM      5  N   GLY A   2      38.125  -1.671  83.352  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      37.855  -2.942  83.977  1.00  0.00           C  
+ATOM      7  C   GLY A   2      38.757  -3.176  85.219  1.00  0.00           C  
+ATOM      8  O   GLY A   2      38.420  -3.960  86.070  1.00  0.00           O  
+ATOM      9  N   GLY A   3      39.841  -2.415  85.338  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      40.856  -2.641  86.363  1.00  0.00           C  
+ATOM     11  C   GLY A   3      40.992  -1.561  87.421  1.00  0.00           C  
+ATOM     12  O   GLY A   3      42.004  -1.491  88.124  1.00  0.00           O  
+ATOM     13  N   GLY A   4      39.964  -0.738  87.514  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      39.921   0.411  88.397  1.00  0.00           C  
+ATOM     15  C   GLY A   4      38.457   0.665  88.745  1.00  0.00           C  
+ATOM     16  O   GLY A   4      37.572   0.189  88.029  1.00  0.00           O  
+ATOM     17  N   GLY A   5      38.194   1.382  89.826  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      36.834   1.703  90.210  1.00  0.00           C  
+ATOM     19  C   GLY A   5      36.634   3.239  90.178  1.00  0.00           C  
+ATOM     20  O   GLY A   5      36.532   3.868  91.227  1.00  0.00           O  
+ATOM     21  N   GLY A   6      36.579   3.855  88.993  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      36.211   5.276  88.904  1.00  0.00           C  
+ATOM     23  C   GLY A   6      34.764   5.553  89.322  1.00  0.00           C  
+ATOM     24  O   GLY A   6      33.860   4.815  88.924  1.00  0.00           O  
+ATOM     25  N   GLY A   7      34.530   6.615  90.085  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      33.176   6.939  90.563  1.00  0.00           C  
+ATOM     27  C   GLY A   7      32.891   8.448  90.633  1.00  0.00           C  
+ATOM     28  O   GLY A   7      33.780   9.283  90.563  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.615   8.757  90.751  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.153  10.058  91.188  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.066  11.103  90.093  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.422  10.845  88.934  1.00  0.00           O  
+ENDMDL
+MODEL     11
+ATOM      1  N   GLY A   1      38.620   1.006  81.483  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.588  -0.066  82.452  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.849   0.257  83.755  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.412  -0.646  84.458  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.666   1.542  84.052  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      37.002   1.912  85.301  1.00  0.00           C  
+ATOM      7  C   GLY A   2      35.912   2.978  85.151  1.00  0.00           C  
+ATOM      8  O   GLY A   2      35.639   3.726  86.094  1.00  0.00           O  
+ATOM      9  N   GLY A   3      35.284   3.033  83.975  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      34.240   4.031  83.687  1.00  0.00           C  
+ATOM     11  C   GLY A   3      33.102   4.085  84.701  1.00  0.00           C  
+ATOM     12  O   GLY A   3      32.537   5.151  84.941  1.00  0.00           O  
+ATOM     13  N   GLY A   4      32.772   2.945  85.284  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      31.696   2.889  86.280  1.00  0.00           C  
+ATOM     15  C   GLY A   4      32.066   3.712  87.511  1.00  0.00           C  
+ATOM     16  O   GLY A   4      31.267   4.526  87.996  1.00  0.00           O  
+ATOM     17  N   GLY A   5      33.274   3.513  88.012  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      33.745   4.237  89.188  1.00  0.00           C  
+ATOM     19  C   GLY A   5      33.992   5.717  88.891  1.00  0.00           C  
+ATOM     20  O   GLY A   5      33.590   6.587  89.657  1.00  0.00           O  
+ATOM     21  N   GLY A   6      34.642   5.978  87.774  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      34.966   7.349  87.378  1.00  0.00           C  
+ATOM     23  C   GLY A   6      33.759   8.251  87.147  1.00  0.00           C  
+ATOM     24  O   GLY A   6      33.838   9.465  87.361  1.00  0.00           O  
+ATOM     25  N   GLY A   7      32.625   7.690  86.732  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      31.438   8.499  86.503  1.00  0.00           C  
+ATOM     27  C   GLY A   7      30.977   9.227  87.755  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.245  10.224  87.670  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.407   8.762  88.925  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.053   9.378  90.195  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.840  10.665  90.433  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.479  11.486  91.283  1.00  0.00           O  
+ENDMDL
+MODEL     12
+ATOM      1  N   GLY A   1      39.953  -0.206  81.840  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      39.805   1.058  82.531  1.00  0.00           C  
+ATOM      3  C   GLY A   1      38.486   1.156  83.278  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.448   0.639  82.819  1.00  0.00           O  
+ATOM      5  N   GLY A   2      38.505   1.872  84.391  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      37.258   2.310  85.016  1.00  0.00           C  
+ATOM      7  C   GLY A   2      37.077   3.772  84.687  1.00  0.00           C  
+ATOM      8  O   GLY A   2      38.039   4.579  84.800  1.00  0.00           O  
+ATOM      9  N   GLY A   3      35.867   4.137  84.263  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      35.573   5.530  84.015  1.00  0.00           C  
+ATOM     11  C   GLY A   3      35.176   6.150  85.343  1.00  0.00           C  
+ATOM     12  O   GLY A   3      34.005   6.038  85.782  1.00  0.00           O  
+ATOM     13  N   GLY A   4      36.155   6.824  85.953  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      36.035   7.451  87.280  1.00  0.00           C  
+ATOM     15  C   GLY A   4      34.937   8.505  87.320  1.00  0.00           C  
+ATOM     16  O   GLY A   4      34.229   8.662  88.308  1.00  0.00           O  
+ATOM     17  N   GLY A   5      34.813   9.216  86.222  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      33.855  10.288  86.072  1.00  0.00           C  
+ATOM     19  C   GLY A   5      32.421   9.770  86.087  1.00  0.00           C  
+ATOM     20  O   GLY A   5      31.618  10.230  86.914  1.00  0.00           O  
+ATOM     21  N   GLY A   6      32.122   8.772  85.255  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      30.801   8.141  85.245  1.00  0.00           C  
+ATOM     23  C   GLY A   6      30.468   7.572  86.635  1.00  0.00           C  
+ATOM     24  O   GLY A   6      29.393   7.792  87.160  1.00  0.00           O  
+ATOM     25  N   GLY A   7      31.421   6.851  87.241  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      31.171   6.158  88.511  1.00  0.00           C  
+ATOM     27  C   GLY A   7      30.974   7.151  89.653  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.375   6.817  90.677  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.458   8.371  89.444  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.353   9.436  90.436  1.00  0.00           C  
+ATOM     31  C   GLY A   8      30.061  10.226  90.334  1.00  0.00           C  
+ATOM     32  O   GLY A   8      29.773  11.056  91.183  1.00  0.00           O  
+ENDMDL
+MODEL     13
+ATOM      1  N   GLY A   1      38.683   1.333  82.516  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.307   0.664  81.278  1.00  0.00           C  
+ATOM      3  C   GLY A   1      36.802   0.574  81.321  1.00  0.00           C  
+ATOM      4  O   GLY A   1      36.192   0.835  82.372  1.00  0.00           O  
+ATOM      5  N   GLY A   2      36.115   0.175  80.239  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      34.667   0.042  80.383  1.00  0.00           C  
+ATOM      7  C   GLY A   2      34.428  -1.204  81.224  1.00  0.00           C  
+ATOM      8  O   GLY A   2      35.211  -2.183  81.211  1.00  0.00           O  
+ATOM      9  N   GLY A   3      33.386  -1.153  82.028  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      33.079  -2.228  82.926  1.00  0.00           C  
+ATOM     11  C   GLY A   3      33.935  -2.106  84.169  1.00  0.00           C  
+ATOM     12  O   GLY A   3      33.808  -2.959  85.032  1.00  0.00           O  
+ATOM     13  N   GLY A   4      34.842  -1.149  84.344  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      35.665  -1.122  85.547  1.00  0.00           C  
+ATOM     15  C   GLY A   4      34.843  -0.423  86.596  1.00  0.00           C  
+ATOM     16  O   GLY A   4      34.271   0.625  86.346  1.00  0.00           O  
+ATOM     17  N   GLY A   5      34.710  -1.002  87.775  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      33.910  -0.447  88.835  1.00  0.00           C  
+ATOM     19  C   GLY A   5      34.709   0.668  89.482  1.00  0.00           C  
+ATOM     20  O   GLY A   5      35.882   0.506  89.820  1.00  0.00           O  
+ATOM     21  N   GLY A   6      34.090   1.829  89.696  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      34.783   3.000  90.243  1.00  0.00           C  
+ATOM     23  C   GLY A   6      33.741   4.016  90.726  1.00  0.00           C  
+ATOM     24  O   GLY A   6      32.564   3.912  90.327  1.00  0.00           O  
+ATOM     25  N   GLY A   7      34.166   4.969  91.553  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      33.341   6.047  92.072  1.00  0.00           C  
+ATOM     27  C   GLY A   7      33.759   7.481  91.689  1.00  0.00           C  
+ATOM     28  O   GLY A   7      34.946   7.876  91.749  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.766   8.265  91.234  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      32.951   9.668  90.928  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.907  10.479  91.685  1.00  0.00           C  
+ATOM     32  O   GLY A   8      30.779  10.007  91.874  1.00  0.00           O  
+ENDMDL
+MODEL     14
+ATOM      1  N   GLY A   1      37.182   1.742  82.428  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      37.643   0.667  81.549  1.00  0.00           C  
+ATOM      3  C   GLY A   1      39.072   0.216  81.809  1.00  0.00           C  
+ATOM      4  O   GLY A   1      39.439  -0.904  81.465  1.00  0.00           O  
+ATOM      5  N   GLY A   2      39.886   1.086  82.407  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      41.281   0.757  82.663  1.00  0.00           C  
+ATOM      7  C   GLY A   2      41.649   0.350  84.088  1.00  0.00           C  
+ATOM      8  O   GLY A   2      42.512  -0.503  84.274  1.00  0.00           O  
+ATOM      9  N   GLY A   3      41.013   0.958  85.086  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      41.340   0.624  86.474  1.00  0.00           C  
+ATOM     11  C   GLY A   3      40.145   0.074  87.259  1.00  0.00           C  
+ATOM     12  O   GLY A   3      40.287  -0.304  88.424  1.00  0.00           O  
+ATOM     13  N   GLY A   4      38.979   0.065  86.625  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      37.739  -0.439  87.221  1.00  0.00           C  
+ATOM     15  C   GLY A   4      37.185   0.382  88.383  1.00  0.00           C  
+ATOM     16  O   GLY A   4      36.354  -0.115  89.161  1.00  0.00           O  
+ATOM     17  N   GLY A   5      37.640   1.625  88.513  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      37.140   2.513  89.569  1.00  0.00           C  
+ATOM     19  C   GLY A   5      35.659   2.777  89.303  1.00  0.00           C  
+ATOM     20  O   GLY A   5      35.243   2.927  88.154  1.00  0.00           O  
+ATOM     21  N   GLY A   6      34.858   2.815  90.368  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      33.427   3.069  90.241  1.00  0.00           C  
+ATOM     23  C   GLY A   6      33.207   4.559  90.022  1.00  0.00           C  
+ATOM     24  O   GLY A   6      33.856   5.378  90.674  1.00  0.00           O  
+ATOM     25  N   GLY A   7      32.326   4.924  89.095  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      32.070   6.343  88.841  1.00  0.00           C  
+ATOM     27  C   GLY A   7      31.645   6.953  90.167  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.921   6.330  90.948  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.113   8.167  90.440  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.839   8.828  91.709  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.749  10.354  91.593  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.945  10.919  90.513  1.00  0.00           O  
+ENDMDL
+MODEL     15
+ATOM      1  N   GLY A   1      39.641  -0.389  81.968  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.975  -0.190  83.251  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.895   0.867  83.050  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.961   1.655  82.107  1.00  0.00           O  
+ATOM      5  N   GLY A   2      36.915   0.880  83.945  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      35.838   1.849  83.854  1.00  0.00           C  
+ATOM      7  C   GLY A   2      36.340   3.259  84.158  1.00  0.00           C  
+ATOM      8  O   GLY A   2      37.301   3.443  84.908  1.00  0.00           O  
+ATOM      9  N   GLY A   3      35.687   4.248  83.555  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      36.026   5.653  83.763  1.00  0.00           C  
+ATOM     11  C   GLY A   3      35.367   6.063  85.078  1.00  0.00           C  
+ATOM     12  O   GLY A   3      34.277   6.614  85.081  1.00  0.00           O  
+ATOM     13  N   GLY A   4      36.042   5.794  86.189  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      35.487   6.105  87.491  1.00  0.00           C  
+ATOM     15  C   GLY A   4      35.279   7.581  87.813  1.00  0.00           C  
+ATOM     16  O   GLY A   4      34.380   7.929  88.572  1.00  0.00           O  
+ATOM     17  N   GLY A   5      36.089   8.456  87.234  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      35.932   9.873  87.510  1.00  0.00           C  
+ATOM     19  C   GLY A   5      34.578  10.342  86.961  1.00  0.00           C  
+ATOM     20  O   GLY A   5      33.831  11.034  87.654  1.00  0.00           O  
+ATOM     21  N   GLY A   6      34.262   9.937  85.734  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      32.983  10.318  85.121  1.00  0.00           C  
+ATOM     23  C   GLY A   6      31.840   9.747  85.938  1.00  0.00           C  
+ATOM     24  O   GLY A   6      30.828  10.409  86.188  1.00  0.00           O  
+ATOM     25  N   GLY A   7      32.000   8.496  86.359  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      30.998   7.809  87.160  1.00  0.00           C  
+ATOM     27  C   GLY A   7      30.757   8.566  88.457  1.00  0.00           C  
+ATOM     28  O   GLY A   7      29.623   8.722  88.905  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.840   9.034  89.080  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.720   9.787  90.321  1.00  0.00           C  
+ATOM     31  C   GLY A   8      30.980  11.103  90.082  1.00  0.00           C  
+ATOM     32  O   GLY A   8      30.219  11.548  90.931  1.00  0.00           O  
+ENDMDL
+MODEL     16
+ATOM      1  N   GLY A   1      38.167   0.379  81.889  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      37.050  -0.373  82.486  1.00  0.00           C  
+ATOM      3  C   GLY A   1      36.575   0.380  83.751  1.00  0.00           C  
+ATOM      4  O   GLY A   1      35.357   0.571  83.942  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.510   0.835  84.589  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      37.169   1.497  85.861  1.00  0.00           C  
+ATOM      7  C   GLY A   2      36.490   2.858  85.616  1.00  0.00           C  
+ATOM      8  O   GLY A   2      35.541   3.231  86.317  1.00  0.00           O  
+ATOM      9  N   GLY A   3      36.983   3.578  84.608  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      36.472   4.918  84.289  1.00  0.00           C  
+ATOM     11  C   GLY A   3      35.003   4.848  83.856  1.00  0.00           C  
+ATOM     12  O   GLY A   3      34.246   5.754  84.089  1.00  0.00           O  
+ATOM     13  N   GLY A   4      34.583   3.753  83.265  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      33.202   3.598  82.814  1.00  0.00           C  
+ATOM     15  C   GLY A   4      32.195   3.522  83.952  1.00  0.00           C  
+ATOM     16  O   GLY A   4      31.042   3.830  83.743  1.00  0.00           O  
+ATOM     17  N   GLY A   5      32.626   3.152  85.149  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      31.691   3.034  86.287  1.00  0.00           C  
+ATOM     19  C   GLY A   5      32.046   3.719  87.599  1.00  0.00           C  
+ATOM     20  O   GLY A   5      31.208   3.754  88.525  1.00  0.00           O  
+ATOM     21  N   GLY A   6      33.251   4.287  87.716  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      33.657   4.992  88.937  1.00  0.00           C  
+ATOM     23  C   GLY A   6      32.570   5.984  89.344  1.00  0.00           C  
+ATOM     24  O   GLY A   6      32.355   6.946  88.608  1.00  0.00           O  
+ATOM     25  N   GLY A   7      31.831   5.753  90.439  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      30.685   6.624  90.766  1.00  0.00           C  
+ATOM     27  C   GLY A   7      31.021   8.145  90.799  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.230   8.924  90.280  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.170   8.519  91.307  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      32.538   9.943  91.436  1.00  0.00           C  
+ATOM     31  C   GLY A   8      32.697  10.602  90.083  1.00  0.00           C  
+ATOM     32  O   GLY A   8      32.403  11.795  89.956  1.00  0.00           O  
+ENDMDL
+MODEL     17
+ATOM      1  N   GLY A   1      38.218   0.458  80.761  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      37.387   1.339  81.552  1.00  0.00           C  
+ATOM      3  C   GLY A   1      36.739   0.563  82.702  1.00  0.00           C  
+ATOM      4  O   GLY A   1      35.939  -0.359  82.478  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.113   0.911  83.924  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      36.557   0.280  85.117  1.00  0.00           C  
+ATOM      7  C   GLY A   2      35.228   0.898  85.518  1.00  0.00           C  
+ATOM      8  O   GLY A   2      34.968   2.075  85.248  1.00  0.00           O  
+ATOM      9  N   GLY A   3      34.375   0.091  86.143  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      33.101   0.563  86.700  1.00  0.00           C  
+ATOM     11  C   GLY A   3      33.229   0.760  88.205  1.00  0.00           C  
+ATOM     12  O   GLY A   3      33.659  -0.160  88.917  1.00  0.00           O  
+ATOM     13  N   GLY A   4      32.876   1.950  88.698  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      32.931   2.246  90.139  1.00  0.00           C  
+ATOM     15  C   GLY A   4      31.917   1.430  90.937  1.00  0.00           C  
+ATOM     16  O   GLY A   4      30.769   1.261  90.522  1.00  0.00           O  
+ATOM     17  N   GLY A   5      32.369   0.902  92.079  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      31.493   0.182  92.985  1.00  0.00           C  
+ATOM     19  C   GLY A   5      30.694   1.175  93.835  1.00  0.00           C  
+ATOM     20  O   GLY A   5      29.521   0.944  94.131  1.00  0.00           O  
+ATOM     21  N   GLY A   6      31.347   2.277  94.218  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      30.679   3.418  94.847  1.00  0.00           C  
+ATOM     23  C   GLY A   6      30.788   4.659  93.964  1.00  0.00           C  
+ATOM     24  O   GLY A   6      31.772   4.821  93.235  1.00  0.00           O  
+ATOM     25  N   GLY A   7      29.797   5.545  94.049  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      29.766   6.765  93.227  1.00  0.00           C  
+ATOM     27  C   GLY A   7      30.935   7.728  93.484  1.00  0.00           C  
+ATOM     28  O   GLY A   7      31.381   7.886  94.613  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.418   8.361  92.415  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      32.544   9.289  92.496  1.00  0.00           C  
+ATOM     31  C   GLY A   8      32.300  10.571  91.667  1.00  0.00           C  
+ATOM     32  O   GLY A   8      32.242  10.506  90.424  1.00  0.00           O  
+ENDMDL
+MODEL     18
+ATOM      1  N   GLY A   1      38.480   2.260  82.127  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.883   0.857  82.108  1.00  0.00           C  
+ATOM      3  C   GLY A   1      38.363  -0.018  83.231  1.00  0.00           C  
+ATOM      4  O   GLY A   1      38.512  -1.246  83.186  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.758   0.581  84.244  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      37.245  -0.198  85.377  1.00  0.00           C  
+ATOM      7  C   GLY A   2      36.081  -1.066  84.921  1.00  0.00           C  
+ATOM      8  O   GLY A   2      35.106  -0.562  84.369  1.00  0.00           O  
+ATOM      9  N   GLY A   3      36.172  -2.385  85.133  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      35.104  -3.303  84.719  1.00  0.00           C  
+ATOM     11  C   GLY A   3      33.954  -3.172  85.712  1.00  0.00           C  
+ATOM     12  O   GLY A   3      32.797  -3.013  85.307  1.00  0.00           O  
+ATOM     13  N   GLY A   4      34.268  -3.279  86.992  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      33.283  -3.106  88.044  1.00  0.00           C  
+ATOM     15  C   GLY A   4      33.149  -1.588  88.042  1.00  0.00           C  
+ATOM     16  O   GLY A   4      34.144  -0.872  88.117  1.00  0.00           O  
+ATOM     17  N   GLY A   5      31.926  -1.075  87.959  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      31.743   0.372  87.850  1.00  0.00           C  
+ATOM     19  C   GLY A   5      31.054   1.128  88.978  1.00  0.00           C  
+ATOM     20  O   GLY A   5      30.053   0.689  89.541  1.00  0.00           O  
+ATOM     21  N   GLY A   6      31.643   2.274  89.298  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      31.097   3.200  90.290  1.00  0.00           C  
+ATOM     23  C   GLY A   6      31.355   4.567  89.686  1.00  0.00           C  
+ATOM     24  O   GLY A   6      32.481   5.070  89.686  1.00  0.00           O  
+ATOM     25  N   GLY A   7      30.300   5.155  89.119  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      30.384   6.468  88.506  1.00  0.00           C  
+ATOM     27  C   GLY A   7      30.286   7.484  89.637  1.00  0.00           C  
+ATOM     28  O   GLY A   7      29.198   7.927  90.002  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.432   7.845  90.186  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.498   8.772  91.296  1.00  0.00           C  
+ATOM     31  C   GLY A   8      30.978  10.162  90.962  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.228  10.693  89.878  1.00  0.00           O  
+ENDMDL
+MODEL     19
+ATOM      1  N   GLY A   1      36.903   0.607  83.038  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      37.620  -0.348  82.184  1.00  0.00           C  
+ATOM      3  C   GLY A   1      36.819  -1.673  82.072  1.00  0.00           C  
+ATOM      4  O   GLY A   1      36.542  -2.174  80.969  1.00  0.00           O  
+ATOM      5  N   GLY A   2      36.358  -2.164  83.201  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      35.716  -3.450  83.259  1.00  0.00           C  
+ATOM      7  C   GLY A   2      34.316  -3.408  82.795  1.00  0.00           C  
+ATOM      8  O   GLY A   2      33.707  -4.457  82.654  1.00  0.00           O  
+ATOM      9  N   GLY A   3      33.799  -2.215  82.529  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      32.465  -2.058  81.965  1.00  0.00           C  
+ATOM     11  C   GLY A   3      31.366  -1.635  82.914  1.00  0.00           C  
+ATOM     12  O   GLY A   3      30.171  -1.564  82.503  1.00  0.00           O  
+ATOM     13  N   GLY A   4      31.710  -1.373  84.170  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      30.698  -0.955  85.153  1.00  0.00           C  
+ATOM     15  C   GLY A   4      30.549   0.573  85.096  1.00  0.00           C  
+ATOM     16  O   GLY A   4      31.521   1.292  85.352  1.00  0.00           O  
+ATOM     17  N   GLY A   5      29.364   1.089  84.716  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      29.179   2.543  84.634  1.00  0.00           C  
+ATOM     19  C   GLY A   5      29.519   3.169  85.989  1.00  0.00           C  
+ATOM     20  O   GLY A   5      28.931   2.767  86.990  1.00  0.00           O  
+ATOM     21  N   GLY A   6      30.432   4.140  85.989  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      31.010   4.725  87.210  1.00  0.00           C  
+ATOM     23  C   GLY A   6      31.263   6.227  87.050  1.00  0.00           C  
+ATOM     24  O   GLY A   6      31.497   6.713  85.950  1.00  0.00           O  
+ATOM     25  N   GLY A   7      31.077   6.991  88.145  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      31.292   8.435  88.122  1.00  0.00           C  
+ATOM     27  C   GLY A   7      31.868   8.867  89.490  1.00  0.00           C  
+ATOM     28  O   GLY A   7      31.490   8.328  90.515  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.833   9.783  89.453  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      33.435  10.345  90.659  1.00  0.00           C  
+ATOM     31  C   GLY A   8      32.570  11.473  91.200  1.00  0.00           C  
+ATOM     32  O   GLY A   8      32.084  12.323  90.449  1.00  0.00           O  
+ENDMDL
+MODEL     20
+ATOM      1  N   GLY A   1      38.166   1.246  81.226  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      37.189   0.831  82.229  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.039   1.957  83.240  1.00  0.00           C  
+ATOM      4  O   GLY A   1      38.009   2.659  83.543  1.00  0.00           O  
+ATOM      5  N   GLY A   2      35.830   2.145  83.771  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      35.607   3.174  84.765  1.00  0.00           C  
+ATOM      7  C   GLY A   2      34.796   2.638  85.930  1.00  0.00           C  
+ATOM      8  O   GLY A   2      34.136   1.606  85.817  1.00  0.00           O  
+ATOM      9  N   GLY A   3      34.866   3.335  87.056  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      34.112   2.956  88.255  1.00  0.00           C  
+ATOM     11  C   GLY A   3      33.585   4.247  88.866  1.00  0.00           C  
+ATOM     12  O   GLY A   3      34.169   5.313  88.679  1.00  0.00           O  
+ATOM     13  N   GLY A   4      32.470   4.154  89.579  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      31.875   5.314  90.203  1.00  0.00           C  
+ATOM     15  C   GLY A   4      31.776   5.061  91.703  1.00  0.00           C  
+ATOM     16  O   GLY A   4      31.495   3.947  92.136  1.00  0.00           O  
+ATOM     17  N   GLY A   5      32.016   6.105  92.485  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      31.936   6.022  93.928  1.00  0.00           C  
+ATOM     19  C   GLY A   5      31.661   7.428  94.470  1.00  0.00           C  
+ATOM     20  O   GLY A   5      32.153   8.423  93.940  1.00  0.00           O  
+ATOM     21  N   GLY A   6      30.850   7.483  95.525  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      30.517   8.750  96.174  1.00  0.00           C  
+ATOM     23  C   GLY A   6      30.046   9.835  95.200  1.00  0.00           C  
+ATOM     24  O   GLY A   6      30.419  11.001  95.345  1.00  0.00           O  
+ATOM     25  N   GLY A   7      29.242   9.430  94.230  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      28.700  10.371  93.262  1.00  0.00           C  
+ATOM     27  C   GLY A   7      29.661  10.880  92.207  1.00  0.00           C  
+ATOM     28  O   GLY A   7      29.342  11.798  91.449  1.00  0.00           O  
+ATOM     29  N   GLY A   8      30.846  10.291  92.147  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.815  10.711  91.155  1.00  0.00           C  
+ATOM     31  C   GLY A   8      32.597   9.534  90.589  1.00  0.00           C  
+ATOM     32  O   GLY A   8      32.625   8.448  91.164  1.00  0.00           O  
+ENDMDL
+MODEL     21
+ATOM      1  N   GLY A   1      38.724   0.189  81.459  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.338  -0.291  82.779  1.00  0.00           C  
+ATOM      3  C   GLY A   1      38.044   0.928  83.654  1.00  0.00           C  
+ATOM      4  O   GLY A   1      38.699   1.956  83.528  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.054   0.794  84.526  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      36.717   1.873  85.448  1.00  0.00           C  
+ATOM      7  C   GLY A   2      36.076   1.272  86.679  1.00  0.00           C  
+ATOM      8  O   GLY A   2      35.559   0.141  86.633  1.00  0.00           O  
+ATOM      9  N   GLY A   3      36.125   2.002  87.778  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      35.535   1.532  89.019  1.00  0.00           C  
+ATOM     11  C   GLY A   3      34.521   2.519  89.552  1.00  0.00           C  
+ATOM     12  O   GLY A   3      34.178   3.488  88.873  1.00  0.00           O  
+ATOM     13  N   GLY A   4      34.047   2.277  90.766  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      33.059   3.143  91.402  1.00  0.00           C  
+ATOM     15  C   GLY A   4      33.484   4.619  91.496  1.00  0.00           C  
+ATOM     16  O   GLY A   4      32.662   5.513  91.270  1.00  0.00           O  
+ATOM     17  N   GLY A   5      34.743   4.857  91.820  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      35.248   6.216  91.942  1.00  0.00           C  
+ATOM     19  C   GLY A   5      35.169   6.974  90.633  1.00  0.00           C  
+ATOM     20  O   GLY A   5      34.803   8.157  90.591  1.00  0.00           O  
+ATOM     21  N   GLY A   6      35.519   6.306  89.546  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      35.456   6.933  88.233  1.00  0.00           C  
+ATOM     23  C   GLY A   6      34.024   7.414  87.949  1.00  0.00           C  
+ATOM     24  O   GLY A   6      33.826   8.586  87.617  1.00  0.00           O  
+ATOM     25  N   GLY A   7      33.037   6.541  88.107  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      31.629   6.893  87.855  1.00  0.00           C  
+ATOM     27  C   GLY A   7      31.079   8.013  88.738  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.057   8.616  88.397  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.727   8.304  89.866  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.275   9.371  90.746  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.808  10.749  90.305  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.240  11.780  90.659  1.00  0.00           O  
+ENDMDL
+MODEL     22
+ATOM      1  N   GLY A   1      39.069  -0.340  82.442  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.719   1.050  82.701  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.365   1.261  83.446  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.076   2.380  83.867  1.00  0.00           O  
+ATOM      5  N   GLY A   2      36.550   0.222  83.619  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      35.307   0.390  84.391  1.00  0.00           C  
+ATOM      7  C   GLY A   2      35.410  -0.076  85.836  1.00  0.00           C  
+ATOM      8  O   GLY A   2      34.546   0.274  86.629  1.00  0.00           O  
+ATOM      9  N   GLY A   3      36.469  -0.838  86.162  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      36.567  -1.577  87.427  1.00  0.00           C  
+ATOM     11  C   GLY A   3      37.202  -0.784  88.557  1.00  0.00           C  
+ATOM     12  O   GLY A   3      36.851  -0.972  89.725  1.00  0.00           O  
+ATOM     13  N   GLY A   4      38.154   0.089  88.216  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      38.785   0.904  89.219  1.00  0.00           C  
+ATOM     15  C   GLY A   4      38.508   2.390  89.005  1.00  0.00           C  
+ATOM     16  O   GLY A   4      39.178   3.229  89.600  1.00  0.00           O  
+ATOM     17  N   GLY A   5      37.529   2.752  88.186  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      37.308   4.177  87.980  1.00  0.00           C  
+ATOM     19  C   GLY A   5      36.650   4.779  89.226  1.00  0.00           C  
+ATOM     20  O   GLY A   5      35.979   4.038  89.981  1.00  0.00           O  
+ATOM     21  N   GLY A   6      36.864   6.107  89.472  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      36.392   6.705  90.708  1.00  0.00           C  
+ATOM     23  C   GLY A   6      34.892   6.648  90.739  1.00  0.00           C  
+ATOM     24  O   GLY A   6      34.243   6.819  89.707  1.00  0.00           O  
+ATOM     25  N   GLY A   7      34.346   6.392  91.912  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      32.917   6.248  92.057  1.00  0.00           C  
+ATOM     27  C   GLY A   7      32.092   7.474  91.624  1.00  0.00           C  
+ATOM     28  O   GLY A   7      31.030   7.320  91.047  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.579   8.697  91.876  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.810   9.916  91.501  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.666  10.048  89.996  1.00  0.00           C  
+ATOM     32  O   GLY A   8      30.801  10.791  89.517  1.00  0.00           O  
+ENDMDL
+MODEL     23
+ATOM      1  N   GLY A   1      38.583   0.593  81.223  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      37.539  -0.319  81.698  1.00  0.00           C  
+ATOM      3  C   GLY A   1      36.664   0.136  82.867  1.00  0.00           C  
+ATOM      4  O   GLY A   1      35.712  -0.558  83.242  1.00  0.00           O  
+ATOM      5  N   GLY A   2      36.961   1.288  83.435  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      36.242   1.763  84.611  1.00  0.00           C  
+ATOM      7  C   GLY A   2      35.514   3.074  84.376  1.00  0.00           C  
+ATOM      8  O   GLY A   2      35.601   3.659  83.320  1.00  0.00           O  
+ATOM      9  N   GLY A   3      34.760   3.546  85.384  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      34.101   4.829  85.146  1.00  0.00           C  
+ATOM     11  C   GLY A   3      35.171   5.937  85.157  1.00  0.00           C  
+ATOM     12  O   GLY A   3      36.258   5.761  85.726  1.00  0.00           O  
+ATOM     13  N   GLY A   4      34.879   7.053  84.523  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      35.791   8.192  84.483  1.00  0.00           C  
+ATOM     15  C   GLY A   4      35.867   8.795  85.912  1.00  0.00           C  
+ATOM     16  O   GLY A   4      34.862   8.795  86.635  1.00  0.00           O  
+ATOM     17  N   GLY A   5      37.023   9.317  86.310  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      37.134   9.902  87.658  1.00  0.00           C  
+ATOM     19  C   GLY A   5      36.199  11.093  87.748  1.00  0.00           C  
+ATOM     20  O   GLY A   5      35.674  11.389  88.803  1.00  0.00           O  
+ATOM     21  N   GLY A   6      35.954  11.766  86.619  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      35.070  12.938  86.587  1.00  0.00           C  
+ATOM     23  C   GLY A   6      33.592  12.644  86.816  1.00  0.00           C  
+ATOM     24  O   GLY A   6      32.773  13.551  86.744  1.00  0.00           O  
+ATOM     25  N   GLY A   7      33.250  11.374  87.036  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      31.863  11.010  87.288  1.00  0.00           C  
+ATOM     27  C   GLY A   7      31.699  10.356  88.663  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.619   9.910  89.009  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.784  10.263  89.433  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      32.690   9.679  90.766  1.00  0.00           C  
+ATOM     31  C   GLY A   8      32.066  10.731  91.714  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.887  11.905  91.334  1.00  0.00           O  
+ENDMDL
+MODEL     24
+ATOM      1  N   GLY A   1      38.196  -0.187  81.440  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      39.051   0.635  82.304  1.00  0.00           C  
+ATOM      3  C   GLY A   1      38.192   1.666  83.033  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.416   2.395  82.405  1.00  0.00           O  
+ATOM      5  N   GLY A   2      38.303   1.695  84.358  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      37.594   2.647  85.196  1.00  0.00           C  
+ATOM      7  C   GLY A   2      38.662   3.579  85.784  1.00  0.00           C  
+ATOM      8  O   GLY A   2      39.564   3.090  86.455  1.00  0.00           O  
+ATOM      9  N   GLY A   3      38.601   4.880  85.496  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      39.570   5.880  85.991  1.00  0.00           C  
+ATOM     11  C   GLY A   3      39.189   6.331  87.419  1.00  0.00           C  
+ATOM     12  O   GLY A   3      38.016   6.609  87.678  1.00  0.00           O  
+ATOM     13  N   GLY A   4      40.161   6.430  88.335  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      39.800   6.776  89.700  1.00  0.00           C  
+ATOM     15  C   GLY A   4      39.037   8.098  89.748  1.00  0.00           C  
+ATOM     16  O   GLY A   4      39.524   9.118  89.252  1.00  0.00           O  
+ATOM     17  N   GLY A   5      37.860   8.060  90.352  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      37.011   9.236  90.425  1.00  0.00           C  
+ATOM     19  C   GLY A   5      35.893   9.191  89.367  1.00  0.00           C  
+ATOM     20  O   GLY A   5      34.844   9.784  89.564  1.00  0.00           O  
+ATOM     21  N   GLY A   6      36.134   8.491  88.252  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      35.121   8.352  87.183  1.00  0.00           C  
+ATOM     23  C   GLY A   6      33.841   7.758  87.762  1.00  0.00           C  
+ATOM     24  O   GLY A   6      32.736   8.220  87.466  1.00  0.00           O  
+ATOM     25  N   GLY A   7      34.014   6.756  88.632  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      32.906   6.059  89.265  1.00  0.00           C  
+ATOM     27  C   GLY A   7      32.005   6.952  90.102  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.839   6.613  90.337  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.514   8.107  90.569  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.625   9.009  91.314  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.371  10.285  90.489  1.00  0.00           C  
+ATOM     32  O   GLY A   8      30.995  11.319  91.023  1.00  0.00           O  
+ENDMDL
+MODEL     25
+ATOM      1  N   GLY A   1      37.751   2.143  82.171  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      37.583   1.238  81.043  1.00  0.00           C  
+ATOM      3  C   GLY A   1      36.549   0.164  81.327  1.00  0.00           C  
+ATOM      4  O   GLY A   1      36.173  -0.575  80.425  1.00  0.00           O  
+ATOM      5  N   GLY A   2      35.979   0.070  82.532  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      34.861  -0.819  82.743  1.00  0.00           C  
+ATOM      7  C   GLY A   2      33.572  -0.051  82.957  1.00  0.00           C  
+ATOM      8  O   GLY A   2      33.396   0.596  83.983  1.00  0.00           O  
+ATOM      9  N   GLY A   3      32.592  -0.180  82.073  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      31.468   0.714  82.116  1.00  0.00           C  
+ATOM     11  C   GLY A   3      30.484   0.279  83.162  1.00  0.00           C  
+ATOM     12  O   GLY A   3      29.517   1.012  83.305  1.00  0.00           O  
+ATOM     13  N   GLY A   4      30.651  -0.822  83.915  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      29.822  -1.108  85.071  1.00  0.00           C  
+ATOM     15  C   GLY A   4      30.384  -0.569  86.370  1.00  0.00           C  
+ATOM     16  O   GLY A   4      29.786  -0.818  87.407  1.00  0.00           O  
+ATOM     17  N   GLY A   5      31.553   0.062  86.428  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      32.114   0.432  87.724  1.00  0.00           C  
+ATOM     19  C   GLY A   5      31.321   1.646  88.271  1.00  0.00           C  
+ATOM     20  O   GLY A   5      30.940   2.528  87.499  1.00  0.00           O  
+ATOM     21  N   GLY A   6      31.018   1.823  89.546  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      30.430   3.041  90.096  1.00  0.00           C  
+ATOM     23  C   GLY A   6      31.377   4.224  89.874  1.00  0.00           C  
+ATOM     24  O   GLY A   6      32.598   4.085  90.057  1.00  0.00           O  
+ATOM     25  N   GLY A   7      30.858   5.406  89.532  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      31.664   6.615  89.495  1.00  0.00           C  
+ATOM     27  C   GLY A   7      31.772   7.287  90.852  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.849   7.296  91.663  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.920   7.870  91.174  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      33.048   8.763  92.312  1.00  0.00           C  
+ATOM     31  C   GLY A   8      32.343  10.050  91.962  1.00  0.00           C  
+ATOM     32  O   GLY A   8      32.155  10.368  90.787  1.00  0.00           O  
+ENDMDL
+MODEL     26
+ATOM      1  N   GLY A   1      37.411   1.343  82.224  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.024   0.076  81.827  1.00  0.00           C  
+ATOM      3  C   GLY A   1      38.768  -0.546  83.011  1.00  0.00           C  
+ATOM      4  O   GLY A   1      38.706  -1.754  83.239  1.00  0.00           O  
+ATOM      5  N   GLY A   2      39.436   0.293  83.808  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      40.235  -0.195  84.923  1.00  0.00           C  
+ATOM      7  C   GLY A   2      39.409  -0.555  86.137  1.00  0.00           C  
+ATOM      8  O   GLY A   2      39.736  -1.503  86.840  1.00  0.00           O  
+ATOM      9  N   GLY A   3      38.336   0.183  86.396  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      37.663   0.101  87.690  1.00  0.00           C  
+ATOM     11  C   GLY A   3      36.183  -0.299  87.669  1.00  0.00           C  
+ATOM     12  O   GLY A   3      35.584  -0.479  88.740  1.00  0.00           O  
+ATOM     13  N   GLY A   4      35.577  -0.414  86.500  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      34.131  -0.508  86.425  1.00  0.00           C  
+ATOM     15  C   GLY A   4      33.463   0.851  86.656  1.00  0.00           C  
+ATOM     16  O   GLY A   4      34.142   1.865  86.810  1.00  0.00           O  
+ATOM     17  N   GLY A   5      32.135   0.846  86.699  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      31.345   2.064  86.829  1.00  0.00           C  
+ATOM     19  C   GLY A   5      31.153   2.389  88.288  1.00  0.00           C  
+ATOM     20  O   GLY A   5      30.464   1.637  89.014  1.00  0.00           O  
+ATOM     21  N   GLY A   6      31.776   3.475  88.721  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      31.831   3.846  90.105  1.00  0.00           C  
+ATOM     23  C   GLY A   6      30.933   5.045  90.366  1.00  0.00           C  
+ATOM     24  O   GLY A   6      30.453   5.685  89.428  1.00  0.00           O  
+ATOM     25  N   GLY A   7      30.698   5.338  91.631  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      29.959   6.525  92.045  1.00  0.00           C  
+ATOM     27  C   GLY A   7      30.832   7.737  91.743  1.00  0.00           C  
+ATOM     28  O   GLY A   7      31.872   7.937  92.386  1.00  0.00           O  
+ATOM     29  N   GLY A   8      30.447   8.528  90.755  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.329   9.574  90.232  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.433  10.789  91.136  1.00  0.00           C  
+ATOM     32  O   GLY A   8      32.464  11.490  91.172  1.00  0.00           O  
+ENDMDL
+MODEL     27
+ATOM      1  N   GLY A   1      39.153   0.625  82.874  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.021   0.979  82.086  1.00  0.00           C  
+ATOM      3  C   GLY A   1      36.898   1.713  82.802  1.00  0.00           C  
+ATOM      4  O   GLY A   1      36.537   2.769  82.329  1.00  0.00           O  
+ATOM      5  N   GLY A   2      36.353   1.126  83.882  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      35.087   1.567  84.467  1.00  0.00           C  
+ATOM      7  C   GLY A   2      35.209   1.802  85.977  1.00  0.00           C  
+ATOM      8  O   GLY A   2      34.392   1.397  86.802  1.00  0.00           O  
+ATOM      9  N   GLY A   3      36.308   2.557  86.284  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      36.485   2.878  87.716  1.00  0.00           C  
+ATOM     11  C   GLY A   3      36.254   4.330  88.038  1.00  0.00           C  
+ATOM     12  O   GLY A   3      36.241   4.727  89.223  1.00  0.00           O  
+ATOM     13  N   GLY A   4      35.999   5.187  87.048  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      35.708   6.596  87.408  1.00  0.00           C  
+ATOM     15  C   GLY A   4      34.469   6.667  88.311  1.00  0.00           C  
+ATOM     16  O   GLY A   4      34.414   7.511  89.202  1.00  0.00           O  
+ATOM     17  N   GLY A   5      33.505   5.758  88.098  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      32.324   5.744  88.958  1.00  0.00           C  
+ATOM     19  C   GLY A   5      32.644   5.452  90.429  1.00  0.00           C  
+ATOM     20  O   GLY A   5      31.785   5.716  91.288  1.00  0.00           O  
+ATOM     21  N   GLY A   6      33.814   4.940  90.761  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      34.243   4.704  92.134  1.00  0.00           C  
+ATOM     23  C   GLY A   6      34.957   5.924  92.708  1.00  0.00           C  
+ATOM     24  O   GLY A   6      35.312   5.873  93.897  1.00  0.00           O  
+ATOM     25  N   GLY A   7      35.109   6.968  91.934  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      35.547   8.251  92.400  1.00  0.00           C  
+ATOM     27  C   GLY A   7      34.409   9.305  92.518  1.00  0.00           C  
+ATOM     28  O   GLY A   7      34.328  10.051  93.505  1.00  0.00           O  
+ATOM     29  N   GLY A   8      33.537   9.399  91.520  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      32.499  10.390  91.475  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.323   9.939  90.618  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.536   9.081  89.747  1.00  0.00           O  
+ENDMDL
+MODEL     28
+ATOM      1  N   GLY A   1      38.932   0.106  80.893  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.326  -0.059  82.213  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.375   1.105  82.454  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.713   2.262  82.196  1.00  0.00           O  
+ATOM      5  N   GLY A   2      36.178   0.807  82.950  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      35.196   1.851  83.204  1.00  0.00           C  
+ATOM      7  C   GLY A   2      34.992   2.115  84.692  1.00  0.00           C  
+ATOM      8  O   GLY A   2      34.114   2.886  85.077  1.00  0.00           O  
+ATOM      9  N   GLY A   3      35.827   1.485  85.531  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      35.682   1.623  86.978  1.00  0.00           C  
+ATOM     11  C   GLY A   3      35.661   3.060  87.515  1.00  0.00           C  
+ATOM     12  O   GLY A   3      34.894   3.374  88.422  1.00  0.00           O  
+ATOM     13  N   GLY A   4      36.482   3.929  86.937  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      36.538   5.316  87.406  1.00  0.00           C  
+ATOM     15  C   GLY A   4      35.178   6.004  87.358  1.00  0.00           C  
+ATOM     16  O   GLY A   4      34.832   6.764  88.255  1.00  0.00           O  
+ATOM     17  N   GLY A   5      34.398   5.731  86.312  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      33.087   6.351  86.168  1.00  0.00           C  
+ATOM     19  C   GLY A   5      32.140   6.003  87.316  1.00  0.00           C  
+ATOM     20  O   GLY A   5      31.267   6.791  87.658  1.00  0.00           O  
+ATOM     21  N   GLY A   6      32.328   4.825  87.917  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      31.483   4.402  89.024  1.00  0.00           C  
+ATOM     23  C   GLY A   6      31.960   4.916  90.373  1.00  0.00           C  
+ATOM     24  O   GLY A   6      31.434   4.520  91.422  1.00  0.00           O  
+ATOM     25  N   GLY A   7      32.953   5.811  90.354  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      33.489   6.373  91.595  1.00  0.00           C  
+ATOM     27  C   GLY A   7      33.184   7.875  91.693  1.00  0.00           C  
+ATOM     28  O   GLY A   7      33.427   8.488  92.730  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.644   8.441  90.620  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      32.366   9.866  90.560  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.156  10.367  91.364  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.275  11.340  92.118  1.00  0.00           O  
+ENDMDL
+MODEL     29
+ATOM      1  N   GLY A   1      38.462   2.172  81.070  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      37.778   1.172  81.882  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.322   1.903  83.149  1.00  0.00           C  
+ATOM      4  O   GLY A   1      38.150   2.426  83.893  1.00  0.00           O  
+ATOM      5  N   GLY A   2      36.014   1.930  83.380  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      35.451   2.564  84.561  1.00  0.00           C  
+ATOM      7  C   GLY A   2      34.681   1.461  85.288  1.00  0.00           C  
+ATOM      8  O   GLY A   2      33.774   0.870  84.715  1.00  0.00           O  
+ATOM      9  N   GLY A   3      35.031   1.198  86.555  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      34.380   0.118  87.296  1.00  0.00           C  
+ATOM     11  C   GLY A   3      33.416   0.511  88.389  1.00  0.00           C  
+ATOM     12  O   GLY A   3      33.243   1.697  88.724  1.00  0.00           O  
+ATOM     13  N   GLY A   4      32.801  -0.518  88.960  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      31.840  -0.367  90.041  1.00  0.00           C  
+ATOM     15  C   GLY A   4      32.595   0.121  91.271  1.00  0.00           C  
+ATOM     16  O   GLY A   4      32.001   0.567  92.249  1.00  0.00           O  
+ATOM     17  N   GLY A   5      33.922   0.056  91.222  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      34.754   0.509  92.335  1.00  0.00           C  
+ATOM     19  C   GLY A   5      35.210   1.962  92.193  1.00  0.00           C  
+ATOM     20  O   GLY A   5      35.909   2.480  93.069  1.00  0.00           O  
+ATOM     21  N   GLY A   6      34.839   2.605  91.092  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      35.202   4.005  90.864  1.00  0.00           C  
+ATOM     23  C   GLY A   6      33.894   4.766  90.833  1.00  0.00           C  
+ATOM     24  O   GLY A   6      33.714   5.692  90.041  1.00  0.00           O  
+ATOM     25  N   GLY A   7      32.987   4.369  91.724  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      31.641   4.904  91.791  1.00  0.00           C  
+ATOM     27  C   GLY A   7      31.368   6.260  92.458  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.781   6.323  93.535  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.791   7.335  91.792  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.523   8.681  92.263  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.809   9.588  91.081  1.00  0.00           C  
+ATOM     32  O   GLY A   8      32.537   9.209  90.157  1.00  0.00           O  
+ENDMDL
+MODEL     30
+ATOM      1  N   GLY A   1      37.996   0.156  81.281  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.922   0.251  82.391  1.00  0.00           C  
+ATOM      3  C   GLY A   1      38.192   0.988  83.507  1.00  0.00           C  
+ATOM      4  O   GLY A   1      38.189   2.215  83.559  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.566   0.230  84.399  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      36.831   0.820  85.516  1.00  0.00           C  
+ATOM      7  C   GLY A   2      37.715   1.475  86.574  1.00  0.00           C  
+ATOM      8  O   GLY A   2      37.220   1.998  87.565  1.00  0.00           O  
+ATOM      9  N   GLY A   3      39.029   1.389  86.413  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      39.936   2.021  87.348  1.00  0.00           C  
+ATOM     11  C   GLY A   3      40.227   3.431  86.834  1.00  0.00           C  
+ATOM     12  O   GLY A   3      39.780   4.420  87.413  1.00  0.00           O  
+ATOM     13  N   GLY A   4      40.882   3.510  85.686  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      41.246   4.777  85.086  1.00  0.00           C  
+ATOM     15  C   GLY A   4      40.069   5.636  84.638  1.00  0.00           C  
+ATOM     16  O   GLY A   4      40.073   6.852  84.842  1.00  0.00           O  
+ATOM     17  N   GLY A   5      39.048   5.012  84.058  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      37.907   5.763  83.551  1.00  0.00           C  
+ATOM     19  C   GLY A   5      36.633   5.821  84.377  1.00  0.00           C  
+ATOM     20  O   GLY A   5      35.579   6.212  83.867  1.00  0.00           O  
+ATOM     21  N   GLY A   6      36.719   5.423  85.642  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      35.558   5.469  86.499  1.00  0.00           C  
+ATOM     23  C   GLY A   6      35.244   6.927  86.822  1.00  0.00           C  
+ATOM     24  O   GLY A   6      36.156   7.750  86.904  1.00  0.00           O  
+ATOM     25  N   GLY A   7      33.952   7.242  86.929  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      33.478   8.586  87.269  1.00  0.00           C  
+ATOM     27  C   GLY A   7      32.480   8.369  88.414  1.00  0.00           C  
+ATOM     28  O   GLY A   7      31.917   7.294  88.540  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.271   9.377  89.260  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.352   9.241  90.394  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.070  10.592  91.053  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.899  11.498  90.977  1.00  0.00           O  
+ENDMDL
+MODEL     31
+ATOM      1  N   GLY A   1      38.313  -1.305  82.154  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.583  -0.444  83.300  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.675   0.776  83.192  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.558   1.351  82.102  1.00  0.00           O  
+ATOM      5  N   GLY A   2      36.988   1.086  84.287  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      36.195   2.349  84.414  1.00  0.00           C  
+ATOM      7  C   GLY A   2      36.949   3.414  85.205  1.00  0.00           C  
+ATOM      8  O   GLY A   2      37.501   3.107  86.250  1.00  0.00           O  
+ATOM      9  N   GLY A   3      36.994   4.646  84.729  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      37.732   5.710  85.345  1.00  0.00           C  
+ATOM     11  C   GLY A   3      36.884   6.374  86.378  1.00  0.00           C  
+ATOM     12  O   GLY A   3      35.751   6.774  86.103  1.00  0.00           O  
+ATOM     13  N   GLY A   4      37.441   6.528  87.597  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      36.687   7.180  88.659  1.00  0.00           C  
+ATOM     15  C   GLY A   4      36.165   8.563  88.254  1.00  0.00           C  
+ATOM     16  O   GLY A   4      35.015   8.925  88.641  1.00  0.00           O  
+ATOM     17  N   GLY A   5      36.930   9.334  87.519  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      36.468  10.687  87.203  1.00  0.00           C  
+ATOM     19  C   GLY A   5      35.179  10.582  86.379  1.00  0.00           C  
+ATOM     20  O   GLY A   5      34.197  11.350  86.604  1.00  0.00           O  
+ATOM     21  N   GLY A   6      35.097   9.662  85.434  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      33.887   9.539  84.638  1.00  0.00           C  
+ATOM     23  C   GLY A   6      32.724   9.159  85.526  1.00  0.00           C  
+ATOM     24  O   GLY A   6      31.600   9.677  85.386  1.00  0.00           O  
+ATOM     25  N   GLY A   7      32.946   8.214  86.442  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      31.852   7.563  87.191  1.00  0.00           C  
+ATOM     27  C   GLY A   7      31.310   8.541  88.245  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.069   8.731  88.310  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.199   9.181  89.000  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.781   9.986  90.130  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.853  11.488  89.989  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.226  12.224  90.837  1.00  0.00           O  
+ENDMDL
+MODEL     32
+ATOM      1  N   GLY A   1      39.092   1.113  81.936  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      39.129   1.651  83.290  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.829   2.421  83.637  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.176   2.887  82.674  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.430   2.570  84.901  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      36.265   3.411  85.247  1.00  0.00           C  
+ATOM      7  C   GLY A   2      36.375   4.911  84.856  1.00  0.00           C  
+ATOM      8  O   GLY A   2      37.507   5.388  84.665  1.00  0.00           O  
+ATOM      9  N   GLY A   3      35.211   5.617  84.805  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      35.169   7.079  84.730  1.00  0.00           C  
+ATOM     11  C   GLY A   3      34.777   7.690  86.091  1.00  0.00           C  
+ATOM     12  O   GLY A   3      34.030   7.025  86.870  1.00  0.00           O  
+ATOM     13  N   GLY A   4      35.214   8.912  86.435  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      34.774   9.619  87.646  1.00  0.00           C  
+ATOM     15  C   GLY A   4      34.406  11.048  87.237  1.00  0.00           C  
+ATOM     16  O   GLY A   4      35.222  11.774  86.613  1.00  0.00           O  
+ATOM     17  N   GLY A   5      33.161  11.485  87.552  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      32.755  12.889  87.289  1.00  0.00           C  
+ATOM     19  C   GLY A   5      31.732  13.337  88.342  1.00  0.00           C  
+ATOM     20  O   GLY A   5      30.797  12.619  88.722  1.00  0.00           O  
+ATOM     21  N   GLY A   6      31.887  14.539  88.886  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      30.902  15.077  89.829  1.00  0.00           C  
+ATOM     23  C   GLY A   6      30.559  14.171  91.020  1.00  0.00           C  
+ATOM     24  O   GLY A   6      29.387  14.001  91.357  1.00  0.00           O  
+ATOM     25  N   GLY A   7      31.546  13.574  91.643  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      31.333  12.784  92.850  1.00  0.00           C  
+ATOM     27  C   GLY A   7      30.795  11.380  92.647  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.437  10.761  93.695  1.00  0.00           O  
+ATOM     29  N   GLY A   8      30.753  10.892  91.375  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      30.234   9.536  91.068  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.228   8.703  90.249  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.918   9.302  89.423  1.00  0.00           O  
+ENDMDL
+MODEL     33
+ATOM      1  N   GLY A   1      38.954   0.169  81.633  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.349   0.999  82.677  1.00  0.00           C  
+ATOM      3  C   GLY A   1      38.739   2.481  82.521  1.00  0.00           C  
+ATOM      4  O   GLY A   1      39.946   2.825  82.657  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.791   3.413  82.284  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      38.040   4.869  82.188  1.00  0.00           C  
+ATOM      7  C   GLY A   2      37.725   5.647  83.470  1.00  0.00           C  
+ATOM      8  O   GLY A   2      38.519   6.544  83.869  1.00  0.00           O  
+ATOM      9  N   GLY A   3      36.601   5.381  84.107  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      36.033   6.096  85.262  1.00  0.00           C  
+ATOM     11  C   GLY A   3      35.642   5.151  86.417  1.00  0.00           C  
+ATOM     12  O   GLY A   3      35.204   4.016  86.122  1.00  0.00           O  
+ATOM     13  N   GLY A   4      35.759   5.526  87.699  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      35.514   4.679  88.892  1.00  0.00           C  
+ATOM     15  C   GLY A   4      34.271   5.107  89.680  1.00  0.00           C  
+ATOM     16  O   GLY A   4      34.222   6.173  90.302  1.00  0.00           O  
+ATOM     17  N   GLY A   5      33.199   4.289  89.706  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      31.966   4.656  90.445  1.00  0.00           C  
+ATOM     19  C   GLY A   5      32.199   4.809  91.963  1.00  0.00           C  
+ATOM     20  O   GLY A   5      31.419   5.510  92.651  1.00  0.00           O  
+ATOM     21  N   GLY A   6      33.245   4.239  92.557  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      33.461   4.357  93.988  1.00  0.00           C  
+ATOM     23  C   GLY A   6      33.845   5.772  94.491  1.00  0.00           C  
+ATOM     24  O   GLY A   6      33.758   6.072  95.712  1.00  0.00           O  
+ATOM     25  N   GLY A   7      34.284   6.668  93.584  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      34.507   8.080  93.866  1.00  0.00           C  
+ATOM     27  C   GLY A   7      33.443   8.958  93.172  1.00  0.00           C  
+ATOM     28  O   GLY A   7      33.657  10.189  93.078  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.309   8.403  92.712  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.244   9.202  92.091  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.413   9.480  90.606  1.00  0.00           C  
+ATOM     32  O   GLY A   8      30.732  10.396  90.073  1.00  0.00           O  
+ENDMDL
+MODEL     34
+ATOM      1  N   GLY A   1      38.627   2.438  81.755  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.954   1.036  81.541  1.00  0.00           C  
+ATOM      3  C   GLY A   1      38.007   0.093  82.240  1.00  0.00           C  
+ATOM      4  O   GLY A   1      38.132  -1.105  82.068  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.085   0.605  83.047  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      36.004  -0.177  83.594  1.00  0.00           C  
+ATOM      7  C   GLY A   2      34.901  -0.135  82.565  1.00  0.00           C  
+ATOM      8  O   GLY A   2      34.402   0.920  82.210  1.00  0.00           O  
+ATOM      9  N   GLY A   3      34.532  -1.287  82.066  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      33.591  -1.375  81.033  1.00  0.00           C  
+ATOM     11  C   GLY A   3      32.141  -1.267  81.537  1.00  0.00           C  
+ATOM     12  O   GLY A   3      31.273  -0.767  80.818  1.00  0.00           O  
+ATOM     13  N   GLY A   4      31.886  -1.674  82.760  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      30.570  -1.493  83.406  1.00  0.00           C  
+ATOM     15  C   GLY A   4      30.304  -0.012  83.683  1.00  0.00           C  
+ATOM     16  O   GLY A   4      31.234   0.735  83.836  1.00  0.00           O  
+ATOM     17  N   GLY A   5      29.017   0.401  83.763  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      28.708   1.823  84.060  1.00  0.00           C  
+ATOM     19  C   GLY A   5      29.156   2.167  85.458  1.00  0.00           C  
+ATOM     20  O   GLY A   5      28.885   1.403  86.365  1.00  0.00           O  
+ATOM     21  N   GLY A   6      29.847   3.288  85.618  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      30.395   3.710  86.906  1.00  0.00           C  
+ATOM     23  C   GLY A   6      29.927   5.123  87.165  1.00  0.00           C  
+ATOM     24  O   GLY A   6      29.857   5.953  86.238  1.00  0.00           O  
+ATOM     25  N   GLY A   7      29.658   5.402  88.441  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      29.435   6.733  88.884  1.00  0.00           C  
+ATOM     27  C   GLY A   7      30.392   6.979  90.064  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.575   6.102  90.901  1.00  0.00           O  
+ATOM     29  N   GLY A   8      30.962   8.175  90.140  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.793   8.561  91.228  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.171   9.823  91.796  1.00  0.00           C  
+ATOM     32  O   GLY A   8      30.878  10.775  91.042  1.00  0.00           O  
+ENDMDL
+MODEL     35
+ATOM      1  N   GLY A   1      36.607  -0.710  81.680  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      37.298   0.454  82.225  1.00  0.00           C  
+ATOM      3  C   GLY A   1      36.369   1.285  83.104  1.00  0.00           C  
+ATOM      4  O   GLY A   1      36.754   1.743  84.183  1.00  0.00           O  
+ATOM      5  N   GLY A   2      35.148   1.479  82.654  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      34.168   2.243  83.404  1.00  0.00           C  
+ATOM      7  C   GLY A   2      33.825   1.524  84.726  1.00  0.00           C  
+ATOM      8  O   GLY A   2      33.645   2.159  85.758  1.00  0.00           O  
+ATOM      9  N   GLY A   3      33.766   0.200  84.682  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      33.433  -0.577  85.882  1.00  0.00           C  
+ATOM     11  C   GLY A   3      34.421  -0.425  87.033  1.00  0.00           C  
+ATOM     12  O   GLY A   3      34.027  -0.488  88.195  1.00  0.00           O  
+ATOM     13  N   GLY A   4      35.690  -0.229  86.710  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      36.729  -0.102  87.727  1.00  0.00           C  
+ATOM     15  C   GLY A   4      36.841   1.286  88.347  1.00  0.00           C  
+ATOM     16  O   GLY A   4      37.532   1.459  89.343  1.00  0.00           O  
+ATOM     17  N   GLY A   5      36.174   2.255  87.745  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      36.231   3.647  88.209  1.00  0.00           C  
+ATOM     19  C   GLY A   5      35.616   3.879  89.592  1.00  0.00           C  
+ATOM     20  O   GLY A   5      34.615   3.256  89.932  1.00  0.00           O  
+ATOM     21  N   GLY A   6      36.214   4.784  90.381  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      35.671   5.081  91.719  1.00  0.00           C  
+ATOM     23  C   GLY A   6      34.334   5.797  91.567  1.00  0.00           C  
+ATOM     24  O   GLY A   6      34.067   6.409  90.536  1.00  0.00           O  
+ATOM     25  N   GLY A   7      33.492   5.721  92.591  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      32.172   6.346  92.545  1.00  0.00           C  
+ATOM     27  C   GLY A   7      32.112   7.784  92.018  1.00  0.00           C  
+ATOM     28  O   GLY A   7      31.253   8.088  91.200  1.00  0.00           O  
+ATOM     29  N   GLY A   8      33.021   8.647  92.455  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      32.974  10.045  92.034  1.00  0.00           C  
+ATOM     31  C   GLY A   8      33.281  10.306  90.552  1.00  0.00           C  
+ATOM     32  O   GLY A   8      32.902  11.345  90.006  1.00  0.00           O  
+ENDMDL
+MODEL     36
+ATOM      1  N   GLY A   1      40.266   0.182  82.567  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      39.138  -0.340  83.307  1.00  0.00           C  
+ATOM      3  C   GLY A   1      38.324   0.793  83.934  1.00  0.00           C  
+ATOM      4  O   GLY A   1      38.870   1.768  84.394  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.010   0.625  84.006  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      36.153   1.639  84.581  1.00  0.00           C  
+ATOM      7  C   GLY A   2      36.352   1.730  86.092  1.00  0.00           C  
+ATOM      8  O   GLY A   2      36.711   0.744  86.749  1.00  0.00           O  
+ATOM      9  N   GLY A   3      36.111   2.922  86.632  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      36.209   3.190  88.047  1.00  0.00           C  
+ATOM     11  C   GLY A   3      35.026   4.083  88.337  1.00  0.00           C  
+ATOM     12  O   GLY A   3      35.165   5.258  88.633  1.00  0.00           O  
+ATOM     13  N   GLY A   4      33.855   3.480  88.218  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      32.588   4.207  88.110  1.00  0.00           C  
+ATOM     15  C   GLY A   4      32.274   5.085  89.307  1.00  0.00           C  
+ATOM     16  O   GLY A   4      31.847   6.221  89.146  1.00  0.00           O  
+ATOM     17  N   GLY A   5      32.483   4.556  90.508  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      32.168   5.294  91.716  1.00  0.00           C  
+ATOM     19  C   GLY A   5      33.029   6.547  91.860  1.00  0.00           C  
+ATOM     20  O   GLY A   5      32.523   7.602  92.242  1.00  0.00           O  
+ATOM     21  N   GLY A   6      34.323   6.437  91.558  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      35.195   7.631  91.547  1.00  0.00           C  
+ATOM     23  C   GLY A   6      34.825   8.598  90.408  1.00  0.00           C  
+ATOM     24  O   GLY A   6      34.721   9.805  90.626  1.00  0.00           O  
+ATOM     25  N   GLY A   7      34.639   8.085  89.192  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      34.314   8.955  88.062  1.00  0.00           C  
+ATOM     27  C   GLY A   7      33.017   9.717  88.321  1.00  0.00           C  
+ATOM     28  O   GLY A   7      32.989  10.924  88.176  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.980   9.024  88.777  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      30.719   9.675  89.179  1.00  0.00           C  
+ATOM     31  C   GLY A   8      30.846  10.705  90.313  1.00  0.00           C  
+ATOM     32  O   GLY A   8      30.137  11.711  90.302  1.00  0.00           O  
+ENDMDL
+MODEL     37
+ATOM      1  N   GLY A   1      39.038   2.060  81.426  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      39.548   0.816  82.014  1.00  0.00           C  
+ATOM      3  C   GLY A   1      39.349   0.759  83.540  1.00  0.00           C  
+ATOM      4  O   GLY A   1      39.486  -0.353  84.105  1.00  0.00           O  
+ATOM      5  N   GLY A   2      39.051   1.870  84.196  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      38.928   1.921  85.639  1.00  0.00           C  
+ATOM      7  C   GLY A   2      37.452   2.151  86.010  1.00  0.00           C  
+ATOM      8  O   GLY A   2      36.922   3.238  85.850  1.00  0.00           O  
+ATOM      9  N   GLY A   3      36.756   1.109  86.464  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      35.345   1.277  86.777  1.00  0.00           C  
+ATOM     11  C   GLY A   3      35.053   2.356  87.826  1.00  0.00           C  
+ATOM     12  O   GLY A   3      33.954   2.932  87.855  1.00  0.00           O  
+ATOM     13  N   GLY A   4      36.034   2.659  88.677  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      35.828   3.688  89.696  1.00  0.00           C  
+ATOM     15  C   GLY A   4      35.541   5.089  89.160  1.00  0.00           C  
+ATOM     16  O   GLY A   4      34.884   5.884  89.855  1.00  0.00           O  
+ATOM     17  N   GLY A   5      36.019   5.416  87.947  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      35.787   6.757  87.395  1.00  0.00           C  
+ATOM     19  C   GLY A   5      34.412   6.830  86.721  1.00  0.00           C  
+ATOM     20  O   GLY A   5      33.938   7.965  86.437  1.00  0.00           O  
+ATOM     21  N   GLY A   6      33.789   5.695  86.374  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      32.563   5.651  85.633  1.00  0.00           C  
+ATOM     23  C   GLY A   6      31.364   5.867  86.577  1.00  0.00           C  
+ATOM     24  O   GLY A   6      31.071   4.976  87.355  1.00  0.00           O  
+ATOM     25  N   GLY A   7      30.712   7.007  86.503  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      29.506   7.266  87.289  1.00  0.00           C  
+ATOM     27  C   GLY A   7      29.728   7.770  88.697  1.00  0.00           C  
+ATOM     28  O   GLY A   7      28.761   7.832  89.452  1.00  0.00           O  
+ATOM     29  N   GLY A   8      30.941   8.181  89.061  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.142   8.691  90.394  1.00  0.00           C  
+ATOM     31  C   GLY A   8      30.418  10.054  90.567  1.00  0.00           C  
+ATOM     32  O   GLY A   8      29.935  10.345  91.662  1.00  0.00           O  
+ENDMDL
+MODEL     38
+ATOM      1  N   GLY A   1      39.593   0.822  82.094  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.674  -0.251  82.478  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.426   0.213  83.240  1.00  0.00           C  
+ATOM      4  O   GLY A   1      36.544  -0.598  83.540  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.354   1.509  83.544  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      36.202   2.083  84.233  1.00  0.00           C  
+ATOM      7  C   GLY A   2      35.820   3.411  83.586  1.00  0.00           C  
+ATOM      8  O   GLY A   2      36.679   4.238  83.299  1.00  0.00           O  
+ATOM      9  N   GLY A   3      34.517   3.622  83.355  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      34.021   4.952  83.026  1.00  0.00           C  
+ATOM     11  C   GLY A   3      33.823   5.735  84.327  1.00  0.00           C  
+ATOM     12  O   GLY A   3      32.778   5.628  84.977  1.00  0.00           O  
+ATOM     13  N   GLY A   4      34.839   6.507  84.695  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      34.833   7.254  85.938  1.00  0.00           C  
+ATOM     15  C   GLY A   4      33.924   8.481  85.911  1.00  0.00           C  
+ATOM     16  O   GLY A   4      33.514   8.955  86.973  1.00  0.00           O  
+ATOM     17  N   GLY A   5      33.597   8.984  84.724  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      32.628  10.078  84.607  1.00  0.00           C  
+ATOM     19  C   GLY A   5      31.264   9.612  85.111  1.00  0.00           C  
+ATOM     20  O   GLY A   5      30.546  10.370  85.784  1.00  0.00           O  
+ATOM     21  N   GLY A   6      30.921   8.367  84.796  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      29.717   7.710  85.282  1.00  0.00           C  
+ATOM     23  C   GLY A   6      29.793   7.433  86.784  1.00  0.00           C  
+ATOM     24  O   GLY A   6      28.899   7.826  87.536  1.00  0.00           O  
+ATOM     25  N   GLY A   7      30.867   6.780  87.225  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      31.023   6.403  88.630  1.00  0.00           C  
+ATOM     27  C   GLY A   7      31.060   7.604  89.586  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.468   7.555  90.674  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.743   8.667  89.175  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      32.046   9.797  90.061  1.00  0.00           C  
+ATOM     31  C   GLY A   8      30.827  10.691  90.383  1.00  0.00           C  
+ATOM     32  O   GLY A   8      30.864  11.455  91.347  1.00  0.00           O  
+ENDMDL
+MODEL     39
+ATOM      1  N   GLY A   1      38.470   1.627  82.416  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      37.696   0.419  82.171  1.00  0.00           C  
+ATOM      3  C   GLY A   1      36.434   0.547  83.010  1.00  0.00           C  
+ATOM      4  O   GLY A   1      36.330   1.435  83.844  1.00  0.00           O  
+ATOM      5  N   GLY A   2      35.469  -0.347  82.780  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      34.234  -0.306  83.543  1.00  0.00           C  
+ATOM      7  C   GLY A   2      34.470  -0.614  85.027  1.00  0.00           C  
+ATOM      8  O   GLY A   2      33.838  -0.025  85.904  1.00  0.00           O  
+ATOM      9  N   GLY A   3      35.398  -1.531  85.308  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      35.731  -1.945  86.681  1.00  0.00           C  
+ATOM     11  C   GLY A   3      36.388  -0.899  87.570  1.00  0.00           C  
+ATOM     12  O   GLY A   3      36.156  -0.874  88.775  1.00  0.00           O  
+ATOM     13  N   GLY A   4      37.216  -0.031  86.979  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      37.904   0.997  87.746  1.00  0.00           C  
+ATOM     15  C   GLY A   4      37.022   2.221  88.035  1.00  0.00           C  
+ATOM     16  O   GLY A   4      37.385   3.071  88.844  1.00  0.00           O  
+ATOM     17  N   GLY A   5      35.886   2.307  87.348  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      34.975   3.424  87.528  1.00  0.00           C  
+ATOM     19  C   GLY A   5      34.634   3.694  88.997  1.00  0.00           C  
+ATOM     20  O   GLY A   5      33.820   2.995  89.600  1.00  0.00           O  
+ATOM     21  N   GLY A   6      35.254   4.729  89.548  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      35.050   5.163  90.917  1.00  0.00           C  
+ATOM     23  C   GLY A   6      33.580   5.527  91.106  1.00  0.00           C  
+ATOM     24  O   GLY A   6      32.856   5.689  90.118  1.00  0.00           O  
+ATOM     25  N   GLY A   7      33.099   5.620  92.359  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      31.690   5.980  92.528  1.00  0.00           C  
+ATOM     27  C   GLY A   7      31.480   7.428  92.087  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.413   7.790  91.599  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.525   8.231  92.246  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      32.484   9.646  91.865  1.00  0.00           C  
+ATOM     31  C   GLY A   8      32.481   9.784  90.341  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.865  10.704  89.799  1.00  0.00           O  
+ENDMDL
+MODEL     40
+ATOM      1  N   GLY A   1      38.618  -0.755  82.798  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      39.414   0.455  83.005  1.00  0.00           C  
+ATOM      3  C   GLY A   1      38.648   1.567  83.710  1.00  0.00           C  
+ATOM      4  O   GLY A   1      39.248   2.544  84.154  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.344   1.443  83.783  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      36.560   2.493  84.409  1.00  0.00           C  
+ATOM      7  C   GLY A   2      36.741   2.454  85.945  1.00  0.00           C  
+ATOM      8  O   GLY A   2      36.482   1.425  86.577  1.00  0.00           O  
+ATOM      9  N   GLY A   3      37.178   3.583  86.524  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      37.454   3.736  87.960  1.00  0.00           C  
+ATOM     11  C   GLY A   3      36.282   4.251  88.791  1.00  0.00           C  
+ATOM     12  O   GLY A   3      35.329   4.821  88.260  1.00  0.00           O  
+ATOM     13  N   GLY A   4      36.380   4.098  90.116  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      35.332   4.589  91.015  1.00  0.00           C  
+ATOM     15  C   GLY A   4      35.197   6.163  90.831  1.00  0.00           C  
+ATOM     16  O   GLY A   4      34.100   6.737  90.832  1.00  0.00           O  
+ATOM     17  N   GLY A   5      36.334   6.853  90.647  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      36.268   8.269  90.372  1.00  0.00           C  
+ATOM     19  C   GLY A   5      35.484   8.534  89.021  1.00  0.00           C  
+ATOM     20  O   GLY A   5      34.659   9.454  88.947  1.00  0.00           O  
+ATOM     21  N   GLY A   6      35.745   7.737  87.972  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      35.043   7.899  86.680  1.00  0.00           C  
+ATOM     23  C   GLY A   6      33.518   7.781  86.909  1.00  0.00           C  
+ATOM     24  O   GLY A   6      32.748   8.593  86.371  1.00  0.00           O  
+ATOM     25  N   GLY A   7      33.099   6.795  87.710  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      31.676   6.564  87.990  1.00  0.00           C  
+ATOM     27  C   GLY A   7      31.050   7.633  88.836  1.00  0.00           C  
+ATOM     28  O   GLY A   7      29.853   7.946  88.640  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.812   8.216  89.745  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.262   9.340  90.533  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.187  10.639  89.680  1.00  0.00           C  
+ATOM     32  O   GLY A   8      30.301  11.480  89.876  1.00  0.00           O  
+ENDMDL
+MODEL     41
+ATOM      1  N   GLY A   1      37.440   0.602  80.564  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      37.653   0.169  81.954  1.00  0.00           C  
+ATOM      3  C   GLY A   1      36.818   0.949  82.964  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.350   1.778  83.706  1.00  0.00           O  
+ATOM      5  N   GLY A   2      35.501   0.699  83.015  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      34.623   1.397  83.960  1.00  0.00           C  
+ATOM      7  C   GLY A   2      35.085   1.183  85.402  1.00  0.00           C  
+ATOM      8  O   GLY A   2      35.917   0.311  85.663  1.00  0.00           O  
+ATOM      9  N   GLY A   3      34.535   1.961  86.321  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      34.867   1.868  87.734  1.00  0.00           C  
+ATOM     11  C   GLY A   3      34.024   2.884  88.510  1.00  0.00           C  
+ATOM     12  O   GLY A   3      33.849   4.017  88.053  1.00  0.00           O  
+ATOM     13  N   GLY A   4      33.508   2.483  89.667  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      32.682   3.394  90.448  1.00  0.00           C  
+ATOM     15  C   GLY A   4      33.433   4.665  90.844  1.00  0.00           C  
+ATOM     16  O   GLY A   4      32.874   5.764  90.766  1.00  0.00           O  
+ATOM     17  N   GLY A   5      34.689   4.521  91.253  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      35.513   5.649  91.683  1.00  0.00           C  
+ATOM     19  C   GLY A   5      35.897   6.607  90.558  1.00  0.00           C  
+ATOM     20  O   GLY A   5      36.412   7.698  90.812  1.00  0.00           O  
+ATOM     21  N   GLY A   6      35.661   6.191  89.315  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      35.956   7.023  88.154  1.00  0.00           C  
+ATOM     23  C   GLY A   6      34.749   7.894  87.822  1.00  0.00           C  
+ATOM     24  O   GLY A   6      34.888   8.984  87.260  1.00  0.00           O  
+ATOM     25  N   GLY A   7      33.566   7.399  88.167  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      32.320   8.104  87.875  1.00  0.00           C  
+ATOM     27  C   GLY A   7      31.813   8.909  89.068  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.992   9.814  88.915  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.326   8.574  90.241  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.893   9.222  91.470  1.00  0.00           C  
+ATOM     31  C   GLY A   8      32.350  10.655  91.652  1.00  0.00           C  
+ATOM     32  O   GLY A   8      33.276  11.129  90.997  1.00  0.00           O  
+ENDMDL
+MODEL     42
+ATOM      1  N   GLY A   1      39.776   2.585  82.143  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      39.130   1.611  83.025  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.963   2.169  83.838  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.169   1.401  84.367  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.877   3.487  83.951  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      36.995   4.095  84.938  1.00  0.00           C  
+ATOM      7  C   GLY A   2      36.767   5.572  84.655  1.00  0.00           C  
+ATOM      8  O   GLY A   2      37.653   6.264  84.142  1.00  0.00           O  
+ATOM      9  N   GLY A   3      35.566   6.045  84.995  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      35.225   7.457  84.972  1.00  0.00           C  
+ATOM     11  C   GLY A   3      34.681   7.868  86.327  1.00  0.00           C  
+ATOM     12  O   GLY A   3      33.989   7.083  86.974  1.00  0.00           O  
+ATOM     13  N   GLY A   4      35.021   9.077  86.766  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      34.487   9.643  88.004  1.00  0.00           C  
+ATOM     15  C   GLY A   4      33.871  11.009  87.696  1.00  0.00           C  
+ATOM     16  O   GLY A   4      34.591  11.942  87.290  1.00  0.00           O  
+ATOM     17  N   GLY A   5      32.563  11.112  87.871  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      31.789  12.310  87.547  1.00  0.00           C  
+ATOM     19  C   GLY A   5      31.379  12.920  88.882  1.00  0.00           C  
+ATOM     20  O   GLY A   5      30.431  12.445  89.520  1.00  0.00           O  
+ATOM     21  N   GLY A   6      32.110  13.938  89.324  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      31.869  14.568  90.632  1.00  0.00           C  
+ATOM     23  C   GLY A   6      31.683  13.533  91.742  1.00  0.00           C  
+ATOM     24  O   GLY A   6      30.653  13.495  92.425  1.00  0.00           O  
+ATOM     25  N   GLY A   7      32.692  12.678  91.905  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      32.743  11.620  92.925  1.00  0.00           C  
+ATOM     27  C   GLY A   7      31.902  10.371  92.659  1.00  0.00           C  
+ATOM     28  O   GLY A   7      32.001   9.419  93.419  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.094  10.364  91.601  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      30.272   9.197  91.261  1.00  0.00           C  
+ATOM     31  C   GLY A   8      30.997   8.343  90.219  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.292   8.821  89.115  1.00  0.00           O  
+ENDMDL
+MODEL     43
+ATOM      1  N   GLY A   1      39.259   2.934  81.550  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.246   1.923  81.859  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.198   2.357  82.850  1.00  0.00           C  
+ATOM      4  O   GLY A   1      36.218   1.632  83.078  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.386   3.529  83.444  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      36.442   4.071  84.414  1.00  0.00           C  
+ATOM      7  C   GLY A   2      35.752   5.319  83.914  1.00  0.00           C  
+ATOM      8  O   GLY A   2      36.245   6.015  83.017  1.00  0.00           O  
+ATOM      9  N   GLY A   3      34.607   5.602  84.515  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      33.834   6.790  84.214  1.00  0.00           C  
+ATOM     11  C   GLY A   3      33.756   7.532  85.538  1.00  0.00           C  
+ATOM     12  O   GLY A   3      33.150   7.071  86.516  1.00  0.00           O  
+ATOM     13  N   GLY A   4      34.403   8.695  85.577  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      34.453   9.521  86.759  1.00  0.00           C  
+ATOM     15  C   GLY A   4      33.368  10.565  86.783  1.00  0.00           C  
+ATOM     16  O   GLY A   4      33.389  11.527  86.043  1.00  0.00           O  
+ATOM     17  N   GLY A   5      32.390  10.337  87.648  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      31.277  11.236  87.824  1.00  0.00           C  
+ATOM     19  C   GLY A   5      31.606  12.076  89.041  1.00  0.00           C  
+ATOM     20  O   GLY A   5      32.519  11.744  89.789  1.00  0.00           O  
+ATOM     21  N   GLY A   6      30.874  13.165  89.260  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      31.073  14.075  90.388  1.00  0.00           C  
+ATOM     23  C   GLY A   6      31.056  13.461  91.789  1.00  0.00           C  
+ATOM     24  O   GLY A   6      31.872  13.830  92.641  1.00  0.00           O  
+ATOM     25  N   GLY A   7      30.142  12.544  92.042  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      30.033  11.950  93.368  1.00  0.00           C  
+ATOM     27  C   GLY A   7      30.474  10.487  93.471  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.533   9.923  94.565  1.00  0.00           O  
+ATOM     29  N   GLY A   8      30.778   9.867  92.328  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.211   8.487  92.325  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.769   8.113  90.979  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.747   8.912  90.040  1.00  0.00           O  
+ENDMDL
+MODEL     44
+ATOM      1  N   GLY A   1      38.563  -0.489  81.994  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.146   0.687  82.742  1.00  0.00           C  
+ATOM      3  C   GLY A   1      38.503   0.672  84.197  1.00  0.00           C  
+ATOM      4  O   GLY A   1      38.352  -0.352  84.820  1.00  0.00           O  
+ATOM      5  N   GLY A   2      39.002   1.791  84.733  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      39.240   1.873  86.167  1.00  0.00           C  
+ATOM      7  C   GLY A   2      37.921   2.517  86.590  1.00  0.00           C  
+ATOM      8  O   GLY A   2      37.591   3.634  86.206  1.00  0.00           O  
+ATOM      9  N   GLY A   3      37.114   1.773  87.344  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      35.826   2.316  87.778  1.00  0.00           C  
+ATOM     11  C   GLY A   3      36.052   3.339  88.856  1.00  0.00           C  
+ATOM     12  O   GLY A   3      37.172   3.475  89.323  1.00  0.00           O  
+ATOM     13  N   GLY A   4      35.048   4.152  89.167  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      35.224   5.076  90.279  1.00  0.00           C  
+ATOM     15  C   GLY A   4      34.225   4.637  91.324  1.00  0.00           C  
+ATOM     16  O   GLY A   4      33.235   3.950  91.020  1.00  0.00           O  
+ATOM     17  N   GLY A   5      34.403   5.110  92.532  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      33.524   4.716  93.614  1.00  0.00           C  
+ATOM     19  C   GLY A   5      32.210   5.462  93.599  1.00  0.00           C  
+ATOM     20  O   GLY A   5      32.188   6.689  93.375  1.00  0.00           O  
+ATOM     21  N   GLY A   6      31.118   4.713  93.767  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      29.788   5.307  93.809  1.00  0.00           C  
+ATOM     23  C   GLY A   6      29.458   6.047  92.511  1.00  0.00           C  
+ATOM     24  O   GLY A   6      28.598   6.918  92.497  1.00  0.00           O  
+ATOM     25  N   GLY A   7      30.137   5.691  91.421  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      29.901   6.321  90.123  1.00  0.00           C  
+ATOM     27  C   GLY A   7      30.006   7.832  90.107  1.00  0.00           C  
+ATOM     28  O   GLY A   7      29.414   8.508  89.248  1.00  0.00           O  
+ATOM     29  N   GLY A   8      30.777   8.365  91.036  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      30.945   9.799  91.117  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.698  10.430  89.918  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.574  11.627  89.634  1.00  0.00           O  
+ENDMDL
+MODEL     45
+ATOM      1  N   GLY A   1      38.403  -1.404  82.273  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      37.654  -0.171  82.087  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.445   0.534  83.417  1.00  0.00           C  
+ATOM      4  O   GLY A   1      36.380   0.429  84.027  1.00  0.00           O  
+ATOM      5  N   GLY A   2      38.474   1.238  83.871  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      38.424   1.953  85.147  1.00  0.00           C  
+ATOM      7  C   GLY A   2      37.414   3.089  85.128  1.00  0.00           C  
+ATOM      8  O   GLY A   2      37.056   3.614  84.063  1.00  0.00           O  
+ATOM      9  N   GLY A   3      36.935   3.488  86.323  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      35.954   4.570  86.450  1.00  0.00           C  
+ATOM     11  C   GLY A   3      36.612   5.838  85.960  1.00  0.00           C  
+ATOM     12  O   GLY A   3      37.811   6.031  86.163  1.00  0.00           O  
+ATOM     13  N   GLY A   4      35.861   6.702  85.291  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      36.486   7.933  84.842  1.00  0.00           C  
+ATOM     15  C   GLY A   4      36.170   8.965  85.916  1.00  0.00           C  
+ATOM     16  O   GLY A   4      35.013   9.106  86.329  1.00  0.00           O  
+ATOM     17  N   GLY A   5      37.194   9.697  86.375  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      37.035  10.720  87.416  1.00  0.00           C  
+ATOM     19  C   GLY A   5      35.807  11.621  87.253  1.00  0.00           C  
+ATOM     20  O   GLY A   5      35.215  12.042  88.244  1.00  0.00           O  
+ATOM     21  N   GLY A   6      35.424  11.915  86.008  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      34.269  12.784  85.774  1.00  0.00           C  
+ATOM     23  C   GLY A   6      32.973  12.091  86.161  1.00  0.00           C  
+ATOM     24  O   GLY A   6      31.918  12.728  86.321  1.00  0.00           O  
+ATOM     25  N   GLY A   7      33.050  10.770  86.339  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      31.863  10.016  86.728  1.00  0.00           C  
+ATOM     27  C   GLY A   7      31.663   9.923  88.234  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.582   9.565  88.712  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.710  10.241  88.977  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      32.658  10.192  90.432  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.783  11.284  91.025  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.487  12.292  90.369  1.00  0.00           O  
+ENDMDL
+MODEL     46
+ATOM      1  N   GLY A   1      39.770   0.835  82.050  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.584   0.016  82.083  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.587   0.830  82.895  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.580   0.766  84.106  1.00  0.00           O  
+ATOM      5  N   GLY A   2      36.787   1.628  82.189  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      35.876   2.609  82.771  1.00  0.00           C  
+ATOM      7  C   GLY A   2      35.063   2.203  83.987  1.00  0.00           C  
+ATOM      8  O   GLY A   2      34.925   2.983  84.914  1.00  0.00           O  
+ATOM      9  N   GLY A   3      34.548   0.983  83.969  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      33.732   0.462  85.050  1.00  0.00           C  
+ATOM     11  C   GLY A   3      34.467   0.315  86.389  1.00  0.00           C  
+ATOM     12  O   GLY A   3      33.824   0.348  87.438  1.00  0.00           O  
+ATOM     13  N   GLY A   4      35.789   0.178  86.370  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      36.556   0.034  87.606  1.00  0.00           C  
+ATOM     15  C   GLY A   4      37.627   1.096  87.800  1.00  0.00           C  
+ATOM     16  O   GLY A   4      38.484   0.946  88.684  1.00  0.00           O  
+ATOM     17  N   GLY A   5      37.565   2.191  87.039  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      38.578   3.238  87.171  1.00  0.00           C  
+ATOM     19  C   GLY A   5      38.226   4.262  88.229  1.00  0.00           C  
+ATOM     20  O   GLY A   5      38.931   4.350  89.233  1.00  0.00           O  
+ATOM     21  N   GLY A   6      37.173   5.045  88.023  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      36.771   6.045  89.008  1.00  0.00           C  
+ATOM     23  C   GLY A   6      35.265   6.276  88.932  1.00  0.00           C  
+ATOM     24  O   GLY A   6      34.747   6.594  87.862  1.00  0.00           O  
+ATOM     25  N   GLY A   7      34.581   6.091  90.064  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      33.141   6.289  90.147  1.00  0.00           C  
+ATOM     27  C   GLY A   7      32.828   7.678  90.634  1.00  0.00           C  
+ATOM     28  O   GLY A   7      32.900   7.970  91.834  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.424   8.544  89.723  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      32.118   9.904  90.137  1.00  0.00           C  
+ATOM     31  C   GLY A   8      30.748  10.114  90.808  1.00  0.00           C  
+ATOM     32  O   GLY A   8      30.624  11.028  91.629  1.00  0.00           O  
+ENDMDL
+MODEL     47
+ATOM      1  N   GLY A   1      38.510  -0.099  81.982  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.333   1.361  82.050  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.471   1.766  83.262  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.834   2.654  84.030  1.00  0.00           O  
+ATOM      5  N   GLY A   2      36.349   1.055  83.446  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      35.415   1.334  84.560  1.00  0.00           C  
+ATOM      7  C   GLY A   2      36.114   1.125  85.900  1.00  0.00           C  
+ATOM      8  O   GLY A   2      35.877   1.850  86.852  1.00  0.00           O  
+ATOM      9  N   GLY A   3      36.995   0.136  85.964  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      37.732  -0.084  87.189  1.00  0.00           C  
+ATOM     11  C   GLY A   3      38.781   1.014  87.450  1.00  0.00           C  
+ATOM     12  O   GLY A   3      39.260   1.141  88.582  1.00  0.00           O  
+ATOM     13  N   GLY A   4      39.164   1.797  86.439  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      40.157   2.856  86.672  1.00  0.00           C  
+ATOM     15  C   GLY A   4      39.530   4.127  87.186  1.00  0.00           C  
+ATOM     16  O   GLY A   4      40.211   4.974  87.723  1.00  0.00           O  
+ATOM     17  N   GLY A   5      38.225   4.259  87.013  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      37.502   5.447  87.431  1.00  0.00           C  
+ATOM     19  C   GLY A   5      37.257   5.487  88.910  1.00  0.00           C  
+ATOM     20  O   GLY A   5      37.016   4.466  89.577  1.00  0.00           O  
+ATOM     21  N   GLY A   6      37.328   6.715  89.424  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      37.050   6.973  90.833  1.00  0.00           C  
+ATOM     23  C   GLY A   6      35.549   6.674  91.058  1.00  0.00           C  
+ATOM     24  O   GLY A   6      34.749   6.704  90.097  1.00  0.00           O  
+ATOM     25  N   GLY A   7      35.138   6.368  92.302  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      33.715   6.077  92.503  1.00  0.00           C  
+ATOM     27  C   GLY A   7      32.740   7.156  91.978  1.00  0.00           C  
+ATOM     28  O   GLY A   7      31.809   6.856  91.252  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.984   8.406  92.343  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      32.093   9.488  91.936  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.985   9.761  90.410  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.039  10.449  89.963  1.00  0.00           O  
+ENDMDL
+MODEL     48
+ATOM      1  N   GLY A   1      38.701   2.524  82.446  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.474   1.142  82.082  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.392   0.556  82.986  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.482   0.665  84.233  1.00  0.00           O  
+ATOM      5  N   GLY A   2      36.361  -0.063  82.382  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      35.259  -0.682  83.135  1.00  0.00           C  
+ATOM      7  C   GLY A   2      35.784  -1.676  84.134  1.00  0.00           C  
+ATOM      8  O   GLY A   2      36.610  -2.493  83.798  1.00  0.00           O  
+ATOM      9  N   GLY A   3      35.312  -1.585  85.381  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      35.838  -2.416  86.439  1.00  0.00           C  
+ATOM     11  C   GLY A   3      36.908  -1.748  87.285  1.00  0.00           C  
+ATOM     12  O   GLY A   3      37.189  -2.202  88.364  1.00  0.00           O  
+ATOM     13  N   GLY A   4      37.502  -0.669  86.777  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      38.470   0.135  87.520  1.00  0.00           C  
+ATOM     15  C   GLY A   4      37.955   1.540  87.853  1.00  0.00           C  
+ATOM     16  O   GLY A   4      38.561   2.241  88.676  1.00  0.00           O  
+ATOM     17  N   GLY A   5      36.816   1.931  87.270  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      36.266   3.268  87.486  1.00  0.00           C  
+ATOM     19  C   GLY A   5      35.472   3.371  88.800  1.00  0.00           C  
+ATOM     20  O   GLY A   5      34.627   2.522  89.090  1.00  0.00           O  
+ATOM     21  N   GLY A   6      35.758   4.419  89.568  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      35.182   4.585  90.906  1.00  0.00           C  
+ATOM     23  C   GLY A   6      33.726   5.026  90.825  1.00  0.00           C  
+ATOM     24  O   GLY A   6      33.319   5.584  89.818  1.00  0.00           O  
+ATOM     25  N   GLY A   7      32.923   4.743  91.869  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      31.510   5.142  91.923  1.00  0.00           C  
+ATOM     27  C   GLY A   7      31.201   6.601  91.564  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.278   6.852  90.779  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.942   7.542  92.128  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.716   8.966  91.851  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.904   9.324  90.382  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.243  10.214  89.854  1.00  0.00           O  
+ENDMDL
+MODEL     49
+ATOM      1  N   GLY A   1      38.423   0.523  82.473  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      37.931  -0.608  83.263  1.00  0.00           C  
+ATOM      3  C   GLY A   1      36.940  -0.095  84.280  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.039   1.040  84.751  1.00  0.00           O  
+ATOM      5  N   GLY A   2      36.040  -0.994  84.690  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      35.109  -0.692  85.755  1.00  0.00           C  
+ATOM      7  C   GLY A   2      33.730  -0.326  85.281  1.00  0.00           C  
+ATOM      8  O   GLY A   2      33.432  -0.217  84.059  1.00  0.00           O  
+ATOM      9  N   GLY A   3      32.846  -0.101  86.255  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      31.446   0.184  85.957  1.00  0.00           C  
+ATOM     11  C   GLY A   3      31.166   1.659  85.708  1.00  0.00           C  
+ATOM     12  O   GLY A   3      31.761   2.544  86.341  1.00  0.00           O  
+ATOM     13  N   GLY A   4      30.247   1.951  84.769  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      29.786   3.298  84.521  1.00  0.00           C  
+ATOM     15  C   GLY A   4      29.247   3.901  85.808  1.00  0.00           C  
+ATOM     16  O   GLY A   4      29.439   5.071  86.102  1.00  0.00           O  
+ATOM     17  N   GLY A   5      28.462   3.099  86.527  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      27.715   3.604  87.693  1.00  0.00           C  
+ATOM     19  C   GLY A   5      28.578   4.160  88.827  1.00  0.00           C  
+ATOM     20  O   GLY A   5      28.083   4.926  89.671  1.00  0.00           O  
+ATOM     21  N   GLY A   6      29.800   3.694  88.897  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      30.689   4.103  90.000  1.00  0.00           C  
+ATOM     23  C   GLY A   6      31.553   5.297  89.704  1.00  0.00           C  
+ATOM     24  O   GLY A   6      32.428   5.634  90.542  1.00  0.00           O  
+ATOM     25  N   GLY A   7      31.304   5.998  88.580  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      32.031   7.232  88.249  1.00  0.00           C  
+ATOM     27  C   GLY A   7      31.603   8.287  89.286  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.450   8.367  89.677  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.560   9.076  89.750  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      32.241  10.083  90.723  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.910  11.370  90.051  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.985  11.453  88.811  1.00  0.00           O  
+ENDMDL
+MODEL     50
+ATOM      1  N   GLY A   1      38.184   1.163  83.396  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.703   0.241  82.394  1.00  0.00           C  
+ATOM      3  C   GLY A   1      38.151  -1.173  82.602  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.900  -1.897  81.635  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.976  -1.565  83.856  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      37.448  -2.891  84.202  1.00  0.00           C  
+ATOM      7  C   GLY A   2      35.930  -2.879  84.115  1.00  0.00           C  
+ATOM      8  O   GLY A   2      35.278  -3.936  84.168  1.00  0.00           O  
+ATOM      9  N   GLY A   3      35.363  -1.685  83.994  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      33.922  -1.483  83.914  1.00  0.00           C  
+ATOM     11  C   GLY A   3      33.189  -1.926  85.183  1.00  0.00           C  
+ATOM     12  O   GLY A   3      32.098  -2.486  85.121  1.00  0.00           O  
+ATOM     13  N   GLY A   4      33.813  -1.657  86.324  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      33.210  -1.970  87.620  1.00  0.00           C  
+ATOM     15  C   GLY A   4      32.345  -0.758  87.986  1.00  0.00           C  
+ATOM     16  O   GLY A   4      32.734   0.382  87.734  1.00  0.00           O  
+ATOM     17  N   GLY A   5      31.192  -0.991  88.604  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      30.320   0.106  88.986  1.00  0.00           C  
+ATOM     19  C   GLY A   5      30.985   1.109  89.897  1.00  0.00           C  
+ATOM     20  O   GLY A   5      31.705   0.743  90.826  1.00  0.00           O  
+ATOM     21  N   GLY A   6      30.738   2.383  89.629  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      31.282   3.468  90.429  1.00  0.00           C  
+ATOM     23  C   GLY A   6      30.473   4.729  90.204  1.00  0.00           C  
+ATOM     24  O   GLY A   6      29.827   4.905  89.164  1.00  0.00           O  
+ATOM     25  N   GLY A   7      30.485   5.611  91.202  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      29.792   6.877  91.112  1.00  0.00           C  
+ATOM     27  C   GLY A   7      30.806   7.947  91.496  1.00  0.00           C  
+ATOM     28  O   GLY A   7      31.227   8.026  92.654  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.223   8.749  90.511  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      32.187   9.833  90.737  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.329  11.098  90.758  1.00  0.00           C  
+ATOM     32  O   GLY A   8      30.876  11.565  89.715  1.00  0.00           O  
+ENDMDL
+MODEL     51
+ATOM      1  N   GLY A   1      38.014   1.823  82.115  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      39.063   0.799  82.064  1.00  0.00           C  
+ATOM      3  C   GLY A   1      39.544   0.512  83.481  1.00  0.00           C  
+ATOM      4  O   GLY A   1      39.195   1.240  84.413  1.00  0.00           O  
+ATOM      5  N   GLY A   2      40.344  -0.530  83.652  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      40.802  -0.920  84.983  1.00  0.00           C  
+ATOM      7  C   GLY A   2      41.777   0.034  85.671  1.00  0.00           C  
+ATOM      8  O   GLY A   2      42.161  -0.198  86.830  1.00  0.00           O  
+ATOM      9  N   GLY A   3      42.172   1.102  84.997  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      43.095   2.061  85.596  1.00  0.00           C  
+ATOM     11  C   GLY A   3      42.366   3.155  86.382  1.00  0.00           C  
+ATOM     12  O   GLY A   3      43.001   3.942  87.095  1.00  0.00           O  
+ATOM     13  N   GLY A   4      41.046   3.215  86.279  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      40.309   4.244  86.996  1.00  0.00           C  
+ATOM     15  C   GLY A   4      39.254   3.674  87.934  1.00  0.00           C  
+ATOM     16  O   GLY A   4      38.783   2.550  87.769  1.00  0.00           O  
+ATOM     17  N   GLY A   5      38.890   4.460  88.937  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      37.867   4.038  89.882  1.00  0.00           C  
+ATOM     19  C   GLY A   5      36.541   4.169  89.157  1.00  0.00           C  
+ATOM     20  O   GLY A   5      36.420   4.926  88.201  1.00  0.00           O  
+ATOM     21  N   GLY A   6      35.515   3.419  89.600  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      34.216   3.524  88.940  1.00  0.00           C  
+ATOM     23  C   GLY A   6      33.691   4.959  88.938  1.00  0.00           C  
+ATOM     24  O   GLY A   6      34.013   5.744  89.840  1.00  0.00           O  
+ATOM     25  N   GLY A   7      32.888   5.327  87.934  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      32.341   6.686  87.856  1.00  0.00           C  
+ATOM     27  C   GLY A   7      31.538   7.033  89.100  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.686   6.262  89.539  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.800   8.205  89.675  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.088   8.609  90.876  1.00  0.00           C  
+ATOM     31  C   GLY A   8      30.589  10.055  90.863  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.131  10.929  90.203  1.00  0.00           O  
+ENDMDL
+MODEL     52
+ATOM      1  N   GLY A   1      38.035  -0.676  81.845  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      37.256  -0.967  83.032  1.00  0.00           C  
+ATOM      3  C   GLY A   1      36.862   0.321  83.700  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.693   1.058  84.180  1.00  0.00           O  
+ATOM      5  N   GLY A   2      35.565   0.606  83.670  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      35.061   1.797  84.295  1.00  0.00           C  
+ATOM      7  C   GLY A   2      34.430   1.468  85.668  1.00  0.00           C  
+ATOM      8  O   GLY A   2      33.444   0.717  85.754  1.00  0.00           O  
+ATOM      9  N   GLY A   3      35.005   2.048  86.726  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      34.501   1.897  88.113  1.00  0.00           C  
+ATOM     11  C   GLY A   3      33.492   2.995  88.453  1.00  0.00           C  
+ATOM     12  O   GLY A   3      33.407   3.993  87.764  1.00  0.00           O  
+ATOM     13  N   GLY A   4      32.745   2.797  89.517  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      31.845   3.831  90.045  1.00  0.00           C  
+ATOM     15  C   GLY A   4      32.576   5.138  90.333  1.00  0.00           C  
+ATOM     16  O   GLY A   4      32.101   6.218  89.989  1.00  0.00           O  
+ATOM     17  N   GLY A   5      33.757   5.037  90.958  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      34.569   6.223  91.224  1.00  0.00           C  
+ATOM     19  C   GLY A   5      34.944   6.983  89.950  1.00  0.00           C  
+ATOM     20  O   GLY A   5      34.983   8.210  89.960  1.00  0.00           O  
+ATOM     21  N   GLY A   6      35.119   6.274  88.819  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      35.502   6.934  87.568  1.00  0.00           C  
+ATOM     23  C   GLY A   6      34.349   7.818  87.110  1.00  0.00           C  
+ATOM     24  O   GLY A   6      34.550   8.908  86.586  1.00  0.00           O  
+ATOM     25  N   GLY A   7      33.144   7.281  87.291  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      31.883   7.940  86.941  1.00  0.00           C  
+ATOM     27  C   GLY A   7      31.599   9.195  87.762  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.916  10.184  87.271  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.118   9.244  88.995  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.781  10.303  89.963  1.00  0.00           C  
+ATOM     31  C   GLY A   8      32.851  11.402  90.144  1.00  0.00           C  
+ATOM     32  O   GLY A   8      32.644  12.344  90.918  1.00  0.00           O  
+ENDMDL
+MODEL     53
+ATOM      1  N   GLY A   1      39.380   0.420  83.735  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.555   0.224  82.551  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.208   0.962  82.519  1.00  0.00           C  
+ATOM      4  O   GLY A   1      36.653   1.164  81.432  1.00  0.00           O  
+ATOM      5  N   GLY A   2      36.689   1.363  83.673  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      35.400   2.057  83.738  1.00  0.00           C  
+ATOM      7  C   GLY A   2      35.374   3.202  82.730  1.00  0.00           C  
+ATOM      8  O   GLY A   2      36.328   3.977  82.642  1.00  0.00           O  
+ATOM      9  N   GLY A   3      34.297   3.309  81.928  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      34.123   4.342  80.901  1.00  0.00           C  
+ATOM     11  C   GLY A   3      34.286   5.771  81.404  1.00  0.00           C  
+ATOM     12  O   GLY A   3      34.730   6.648  80.664  1.00  0.00           O  
+ATOM     13  N   GLY A   4      33.886   6.007  82.657  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      33.973   7.323  83.265  1.00  0.00           C  
+ATOM     15  C   GLY A   4      34.872   7.253  84.487  1.00  0.00           C  
+ATOM     16  O   GLY A   4      35.563   6.256  84.713  1.00  0.00           O  
+ATOM     17  N   GLY A   5      34.901   8.329  85.269  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      35.697   8.340  86.490  1.00  0.00           C  
+ATOM     19  C   GLY A   5      34.843   7.612  87.514  1.00  0.00           C  
+ATOM     20  O   GLY A   5      33.760   8.088  87.869  1.00  0.00           O  
+ATOM     21  N   GLY A   6      35.313   6.463  87.993  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      34.546   5.694  88.983  1.00  0.00           C  
+ATOM     23  C   GLY A   6      34.300   6.448  90.300  1.00  0.00           C  
+ATOM     24  O   GLY A   6      33.400   6.092  91.064  1.00  0.00           O  
+ATOM     25  N   GLY A   7      35.064   7.517  90.528  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      34.930   8.321  91.742  1.00  0.00           C  
+ATOM     27  C   GLY A   7      34.125   9.604  91.483  1.00  0.00           C  
+ATOM     28  O   GLY A   7      34.169  10.531  92.285  1.00  0.00           O  
+ATOM     29  N   GLY A   8      33.418   9.650  90.355  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      32.603  10.801  89.979  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.216  10.605  90.604  1.00  0.00           C  
+ATOM     32  O   GLY A   8      30.468   9.715  90.215  1.00  0.00           O  
+ENDMDL
+MODEL     54
+ATOM      1  N   GLY A   1      37.664   1.038  81.407  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.496   0.429  82.457  1.00  0.00           C  
+ATOM      3  C   GLY A   1      38.084   0.844  83.862  1.00  0.00           C  
+ATOM      4  O   GLY A   1      38.098   0.033  84.783  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.734   2.111  84.033  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      37.510   2.626  85.390  1.00  0.00           C  
+ATOM      7  C   GLY A   2      36.135   3.213  85.616  1.00  0.00           C  
+ATOM      8  O   GLY A   2      35.504   2.908  86.634  1.00  0.00           O  
+ATOM      9  N   GLY A   3      35.695   4.099  84.721  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      34.516   4.918  84.998  1.00  0.00           C  
+ATOM     11  C   GLY A   3      33.176   4.196  84.909  1.00  0.00           C  
+ATOM     12  O   GLY A   3      32.222   4.643  85.515  1.00  0.00           O  
+ATOM     13  N   GLY A   4      33.121   3.082  84.177  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      31.914   2.261  84.160  1.00  0.00           C  
+ATOM     15  C   GLY A   4      31.596   1.708  85.559  1.00  0.00           C  
+ATOM     16  O   GLY A   4      30.425   1.640  85.953  1.00  0.00           O  
+ATOM     17  N   GLY A   5      32.635   1.353  86.308  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      32.508   0.983  87.717  1.00  0.00           C  
+ATOM     19  C   GLY A   5      32.431   2.223  88.628  1.00  0.00           C  
+ATOM     20  O   GLY A   5      31.683   2.227  89.609  1.00  0.00           O  
+ATOM     21  N   GLY A   6      33.211   3.260  88.322  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      33.310   4.421  89.209  1.00  0.00           C  
+ATOM     23  C   GLY A   6      32.506   5.613  88.657  1.00  0.00           C  
+ATOM     24  O   GLY A   6      33.073   6.621  88.217  1.00  0.00           O  
+ATOM     25  N   GLY A   7      31.177   5.488  88.701  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      30.244   6.471  88.118  1.00  0.00           C  
+ATOM     27  C   GLY A   7      30.322   7.857  88.752  1.00  0.00           C  
+ATOM     28  O   GLY A   7      29.944   8.864  88.142  1.00  0.00           O  
+ATOM     29  N   GLY A   8      30.821   7.905  89.984  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      30.921   9.148  90.765  1.00  0.00           C  
+ATOM     31  C   GLY A   8      32.075  10.059  90.327  1.00  0.00           C  
+ATOM     32  O   GLY A   8      32.189  11.208  90.783  1.00  0.00           O  
+ENDMDL
+MODEL     55
+ATOM      1  N   GLY A   1      38.228   0.952  81.047  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      37.631   1.889  82.004  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.280   1.204  83.313  1.00  0.00           C  
+ATOM      4  O   GLY A   1      36.967   0.015  83.342  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.320   1.979  84.393  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      36.989   1.467  85.719  1.00  0.00           C  
+ATOM      7  C   GLY A   2      35.513   1.057  85.725  1.00  0.00           C  
+ATOM      8  O   GLY A   2      34.726   1.527  84.906  1.00  0.00           O  
+ATOM      9  N   GLY A   3      35.162   0.182  86.653  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      33.792  -0.298  86.771  1.00  0.00           C  
+ATOM     11  C   GLY A   3      33.155   0.177  88.064  1.00  0.00           C  
+ATOM     12  O   GLY A   3      31.954   0.008  88.281  1.00  0.00           O  
+ATOM     13  N   GLY A   4      33.978   0.773  88.915  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      33.516   1.283  90.205  1.00  0.00           C  
+ATOM     15  C   GLY A   4      32.495   2.401  90.005  1.00  0.00           C  
+ATOM     16  O   GLY A   4      32.492   3.074  88.964  1.00  0.00           O  
+ATOM     17  N   GLY A   5      31.638   2.610  91.004  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      30.594   3.620  90.892  1.00  0.00           C  
+ATOM     19  C   GLY A   5      30.368   4.477  92.128  1.00  0.00           C  
+ATOM     20  O   GLY A   5      29.785   5.563  92.044  1.00  0.00           O  
+ATOM     21  N   GLY A   6      30.799   3.993  93.291  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      30.603   4.749  94.523  1.00  0.00           C  
+ATOM     23  C   GLY A   6      31.407   6.038  94.597  1.00  0.00           C  
+ATOM     24  O   GLY A   6      32.456   6.177  93.966  1.00  0.00           O  
+ATOM     25  N   GLY A   7      30.887   6.969  95.373  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      31.512   8.271  95.610  1.00  0.00           C  
+ATOM     27  C   GLY A   7      32.050   9.007  94.393  1.00  0.00           C  
+ATOM     28  O   GLY A   7      33.191   9.445  94.369  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.196   9.155  93.382  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.571   9.880  92.181  1.00  0.00           C  
+ATOM     31  C   GLY A   8      32.260   9.118  91.069  1.00  0.00           C  
+ATOM     32  O   GLY A   8      32.461   9.684  89.988  1.00  0.00           O  
+ENDMDL
+MODEL     56
+ATOM      1  N   GLY A   1      38.796   2.120  82.098  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.931   0.723  82.487  1.00  0.00           C  
+ATOM      3  C   GLY A   1      38.010   0.438  83.675  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.672  -0.712  83.926  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.612   1.481  84.391  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      36.662   1.394  85.485  1.00  0.00           C  
+ATOM      7  C   GLY A   2      35.216   1.444  85.019  1.00  0.00           C  
+ATOM      8  O   GLY A   2      34.869   2.334  84.225  1.00  0.00           O  
+ATOM      9  N   GLY A   3      34.320   0.582  85.467  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      32.892   0.712  85.145  1.00  0.00           C  
+ATOM     11  C   GLY A   3      32.315   2.057  85.583  1.00  0.00           C  
+ATOM     12  O   GLY A   3      32.574   2.552  86.683  1.00  0.00           O  
+ATOM     13  N   GLY A   4      31.529   2.652  84.694  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      30.885   3.959  84.859  1.00  0.00           C  
+ATOM     15  C   GLY A   4      30.237   4.109  86.225  1.00  0.00           C  
+ATOM     16  O   GLY A   4      30.196   5.155  86.874  1.00  0.00           O  
+ATOM     17  N   GLY A   5      29.707   2.993  86.694  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      29.031   2.899  87.971  1.00  0.00           C  
+ATOM     19  C   GLY A   5      29.965   2.561  89.126  1.00  0.00           C  
+ATOM     20  O   GLY A   5      29.437   2.395  90.218  1.00  0.00           O  
+ATOM     21  N   GLY A   6      31.268   2.408  88.925  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      32.154   1.888  89.959  1.00  0.00           C  
+ATOM     23  C   GLY A   6      32.680   2.991  90.847  1.00  0.00           C  
+ATOM     24  O   GLY A   6      33.148   2.716  91.959  1.00  0.00           O  
+ATOM     25  N   GLY A   7      32.548   4.235  90.402  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      32.921   5.450  91.117  1.00  0.00           C  
+ATOM     27  C   GLY A   7      31.852   6.515  90.920  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.904   6.180  90.201  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.927   7.708  91.454  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.001   8.799  91.207  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.559   9.754  90.136  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.132  10.892  89.998  1.00  0.00           O  
+ENDMDL
+MODEL     57
+ATOM      1  N   GLY A   1      38.632   1.099  81.688  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.819  -0.082  82.545  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.847  -0.160  83.718  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.387  -1.252  84.085  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.554   0.988  84.318  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      36.874   1.004  85.614  1.00  0.00           C  
+ATOM      7  C   GLY A   2      35.796   2.070  85.762  1.00  0.00           C  
+ATOM      8  O   GLY A   2      35.773   3.042  85.014  1.00  0.00           O  
+ATOM      9  N   GLY A   3      34.917   1.852  86.725  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      33.956   2.853  87.195  1.00  0.00           C  
+ATOM     11  C   GLY A   3      34.035   2.940  88.718  1.00  0.00           C  
+ATOM     12  O   GLY A   3      34.584   2.036  89.375  1.00  0.00           O  
+ATOM     13  N   GLY A   4      33.492   4.004  89.288  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      33.424   4.135  90.745  1.00  0.00           C  
+ATOM     15  C   GLY A   4      32.192   3.449  91.316  1.00  0.00           C  
+ATOM     16  O   GLY A   4      31.084   3.594  90.789  1.00  0.00           O  
+ATOM     17  N   GLY A   5      32.376   2.692  92.397  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      31.256   2.097  93.111  1.00  0.00           C  
+ATOM     19  C   GLY A   5      30.407   3.224  93.684  1.00  0.00           C  
+ATOM     20  O   GLY A   5      30.903   4.059  94.448  1.00  0.00           O  
+ATOM     21  N   GLY A   6      29.135   3.270  93.290  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      28.229   4.304  93.763  1.00  0.00           C  
+ATOM     23  C   GLY A   6      28.136   5.550  92.902  1.00  0.00           C  
+ATOM     24  O   GLY A   6      27.324   6.425  93.191  1.00  0.00           O  
+ATOM     25  N   GLY A   7      28.968   5.641  91.867  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      28.896   6.747  90.886  1.00  0.00           C  
+ATOM     27  C   GLY A   7      29.969   7.806  91.057  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.441   8.041  92.175  1.00  0.00           O  
+ATOM     29  N   GLY A   8      30.330   8.459  89.948  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.394   9.488  89.969  1.00  0.00           C  
+ATOM     31  C   GLY A   8      30.946  10.791  90.622  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.791  11.589  91.061  1.00  0.00           O  
+ENDMDL
+MODEL     58
+ATOM      1  N   GLY A   1      38.254  -0.499  83.354  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      36.868  -0.171  83.098  1.00  0.00           C  
+ATOM      3  C   GLY A   1      36.342   0.763  84.177  1.00  0.00           C  
+ATOM      4  O   GLY A   1      36.439   0.439  85.363  1.00  0.00           O  
+ATOM      5  N   GLY A   2      35.805   1.914  83.795  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      35.223   2.884  84.725  1.00  0.00           C  
+ATOM      7  C   GLY A   2      33.706   2.726  84.744  1.00  0.00           C  
+ATOM      8  O   GLY A   2      33.044   2.616  83.684  1.00  0.00           O  
+ATOM      9  N   GLY A   3      33.096   2.691  85.916  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      31.605   2.607  85.984  1.00  0.00           C  
+ATOM     11  C   GLY A   3      31.147   4.028  85.647  1.00  0.00           C  
+ATOM     12  O   GLY A   3      31.258   4.911  86.539  1.00  0.00           O  
+ATOM     13  N   GLY A   4      30.718   4.270  84.393  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      30.382   5.632  83.963  1.00  0.00           C  
+ATOM     15  C   GLY A   4      29.188   6.254  84.664  1.00  0.00           C  
+ATOM     16  O   GLY A   4      28.978   7.470  84.653  1.00  0.00           O  
+ATOM     17  N   GLY A   5      28.325   5.440  85.272  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      27.155   5.888  85.980  1.00  0.00           C  
+ATOM     19  C   GLY A   5      27.365   6.147  87.445  1.00  0.00           C  
+ATOM     20  O   GLY A   5      26.442   6.620  88.130  1.00  0.00           O  
+ATOM     21  N   GLY A   6      28.539   5.893  88.014  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      28.746   6.076  89.452  1.00  0.00           C  
+ATOM     23  C   GLY A   6      29.604   7.275  89.761  1.00  0.00           C  
+ATOM     24  O   GLY A   6      30.745   7.448  89.368  1.00  0.00           O  
+ATOM     25  N   GLY A   7      29.022   8.175  90.577  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      29.712   9.405  91.011  1.00  0.00           C  
+ATOM     27  C   GLY A   7      30.908   9.017  91.859  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.826   8.126  92.665  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.004   9.704  91.698  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      32.200  10.817  90.819  1.00  0.00           C  
+ATOM     31  C   GLY A   8      32.678  10.450  89.431  1.00  0.00           C  
+ATOM     32  O   GLY A   8      33.089  11.366  88.722  1.00  0.00           O  
+ENDMDL
+MODEL     59
+ATOM      1  N   GLY A   1      39.206  -0.938  83.320  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.373   0.258  83.318  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.866   0.381  84.752  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.238  -0.548  85.258  1.00  0.00           O  
+ATOM      5  N   GLY A   2      38.148   1.490  85.403  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      37.719   1.651  86.785  1.00  0.00           C  
+ATOM      7  C   GLY A   2      37.143   3.010  87.142  1.00  0.00           C  
+ATOM      8  O   GLY A   2      37.617   4.045  86.688  1.00  0.00           O  
+ATOM      9  N   GLY A   3      36.123   2.977  87.987  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      35.421   4.158  88.456  1.00  0.00           C  
+ATOM     11  C   GLY A   3      35.673   4.306  89.955  1.00  0.00           C  
+ATOM     12  O   GLY A   3      36.138   3.371  90.595  1.00  0.00           O  
+ATOM     13  N   GLY A   4      35.363   5.475  90.519  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      35.536   5.642  91.952  1.00  0.00           C  
+ATOM     15  C   GLY A   4      34.352   4.933  92.625  1.00  0.00           C  
+ATOM     16  O   GLY A   4      33.438   4.448  91.934  1.00  0.00           O  
+ATOM     17  N   GLY A   5      34.351   4.852  93.954  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      33.268   4.156  94.662  1.00  0.00           C  
+ATOM     19  C   GLY A   5      31.856   4.551  94.267  1.00  0.00           C  
+ATOM     20  O   GLY A   5      30.958   3.714  94.272  1.00  0.00           O  
+ATOM     21  N   GLY A   6      31.658   5.813  93.923  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      30.331   6.278  93.564  1.00  0.00           C  
+ATOM     23  C   GLY A   6      30.144   6.525  92.071  1.00  0.00           C  
+ATOM     24  O   GLY A   6      29.068   6.968  91.654  1.00  0.00           O  
+ATOM     25  N   GLY A   7      31.167   6.238  91.280  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      31.068   6.488  89.851  1.00  0.00           C  
+ATOM     27  C   GLY A   7      30.788   7.967  89.643  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.048   8.346  88.720  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.378   8.800  90.489  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.149  10.242  90.404  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.648  10.856  89.105  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.188  11.926  88.703  1.00  0.00           O  
+ENDMDL
+MODEL     60
+ATOM      1  N   GLY A   1      38.605  -0.705  81.438  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      39.046   0.334  82.369  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.822   0.727  83.183  1.00  0.00           C  
+ATOM      4  O   GLY A   1      36.938   1.420  82.692  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.797   0.284  84.427  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      36.673   0.565  85.298  1.00  0.00           C  
+ATOM      7  C   GLY A   2      36.709   1.908  86.012  1.00  0.00           C  
+ATOM      8  O   GLY A   2      37.758   2.445  86.359  1.00  0.00           O  
+ATOM      9  N   GLY A   3      35.515   2.452  86.200  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      35.318   3.710  86.895  1.00  0.00           C  
+ATOM     11  C   GLY A   3      34.336   3.331  88.007  1.00  0.00           C  
+ATOM     12  O   GLY A   3      33.403   2.556  87.764  1.00  0.00           O  
+ATOM     13  N   GLY A   4      34.537   3.831  89.217  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      33.645   3.453  90.305  1.00  0.00           C  
+ATOM     15  C   GLY A   4      32.789   4.589  90.858  1.00  0.00           C  
+ATOM     16  O   GLY A   4      32.982   5.758  90.528  1.00  0.00           O  
+ATOM     17  N   GLY A   5      31.847   4.203  91.718  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      30.908   5.114  92.350  1.00  0.00           C  
+ATOM     19  C   GLY A   5      31.593   6.262  93.091  1.00  0.00           C  
+ATOM     20  O   GLY A   5      31.072   7.373  93.126  1.00  0.00           O  
+ATOM     21  N   GLY A   6      32.759   5.995  93.674  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      33.503   7.019  94.413  1.00  0.00           C  
+ATOM     23  C   GLY A   6      34.131   8.069  93.498  1.00  0.00           C  
+ATOM     24  O   GLY A   6      34.204   9.238  93.859  1.00  0.00           O  
+ATOM     25  N   GLY A   7      34.604   7.646  92.320  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      35.183   8.581  91.364  1.00  0.00           C  
+ATOM     27  C   GLY A   7      34.081   9.534  90.912  1.00  0.00           C  
+ATOM     28  O   GLY A   7      34.310  10.731  90.742  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.891   8.985  90.708  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.730   9.750  90.268  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.320  10.750  91.328  1.00  0.00           C  
+ATOM     32  O   GLY A   8      30.908  11.870  91.016  1.00  0.00           O  
+ENDMDL
+MODEL     61
+ATOM      1  N   GLY A   1      39.222   2.594  82.608  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.824   1.304  82.039  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.582   0.778  82.752  1.00  0.00           C  
+ATOM      4  O   GLY A   1      36.582   0.469  82.114  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.648   0.674  84.081  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      36.522   0.220  84.880  1.00  0.00           C  
+ATOM      7  C   GLY A   2      36.218   1.293  85.919  1.00  0.00           C  
+ATOM      8  O   GLY A   2      37.115   2.013  86.370  1.00  0.00           O  
+ATOM      9  N   GLY A   3      34.943   1.407  86.301  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      34.527   2.448  87.225  1.00  0.00           C  
+ATOM     11  C   GLY A   3      34.742   2.239  88.708  1.00  0.00           C  
+ATOM     12  O   GLY A   3      34.354   3.072  89.521  1.00  0.00           O  
+ATOM     13  N   GLY A   4      35.371   1.120  89.077  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      35.666   0.889  90.487  1.00  0.00           C  
+ATOM     15  C   GLY A   4      36.845   1.811  90.735  1.00  0.00           C  
+ATOM     16  O   GLY A   4      37.168   2.147  91.872  1.00  0.00           O  
+ATOM     17  N   GLY A   5      37.468   2.241  89.637  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      38.609   3.148  89.657  1.00  0.00           C  
+ATOM     19  C   GLY A   5      38.190   4.602  89.888  1.00  0.00           C  
+ATOM     20  O   GLY A   5      39.037   5.447  90.180  1.00  0.00           O  
+ATOM     21  N   GLY A   6      36.905   4.886  89.740  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      36.365   6.235  89.937  1.00  0.00           C  
+ATOM     23  C   GLY A   6      34.884   6.076  90.209  1.00  0.00           C  
+ATOM     24  O   GLY A   6      34.034   6.447  89.381  1.00  0.00           O  
+ATOM     25  N   GLY A   7      34.537   5.545  91.386  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      33.163   5.296  91.824  1.00  0.00           C  
+ATOM     27  C   GLY A   7      32.169   6.446  91.740  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.970   6.206  91.570  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.635   7.683  91.866  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.732   8.843  91.808  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.455   9.176  90.357  1.00  0.00           C  
+ATOM     32  O   GLY A   8      30.615  10.031  90.038  1.00  0.00           O  
+ENDMDL
+MODEL     62
+ATOM      1  N   GLY A   1      39.731   0.494  81.927  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      39.269  -0.046  83.188  1.00  0.00           C  
+ATOM      3  C   GLY A   1      38.227   0.762  83.936  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.555   1.628  83.366  1.00  0.00           O  
+ATOM      5  N   GLY A   2      38.118   0.485  85.234  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      37.097   1.077  86.105  1.00  0.00           C  
+ATOM      7  C   GLY A   2      37.452   2.522  86.504  1.00  0.00           C  
+ATOM      8  O   GLY A   2      36.596   3.315  86.870  1.00  0.00           O  
+ATOM      9  N   GLY A   3      38.767   2.810  86.469  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      39.225   4.192  86.657  1.00  0.00           C  
+ATOM     11  C   GLY A   3      38.554   4.878  87.856  1.00  0.00           C  
+ATOM     12  O   GLY A   3      37.803   5.829  87.710  1.00  0.00           O  
+ATOM     13  N   GLY A   4      38.861   4.279  89.014  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      38.271   4.708  90.291  1.00  0.00           C  
+ATOM     15  C   GLY A   4      38.363   6.192  90.660  1.00  0.00           C  
+ATOM     16  O   GLY A   4      37.469   6.705  91.317  1.00  0.00           O  
+ATOM     17  N   GLY A   5      39.413   6.882  90.216  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      39.545   8.290  90.554  1.00  0.00           C  
+ATOM     19  C   GLY A   5      38.550   9.183  89.814  1.00  0.00           C  
+ATOM     20  O   GLY A   5      38.417  10.362  90.149  1.00  0.00           O  
+ATOM     21  N   GLY A   6      37.846   8.621  88.840  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      36.862   9.397  88.082  1.00  0.00           C  
+ATOM     23  C   GLY A   6      35.441   8.928  88.341  1.00  0.00           C  
+ATOM     24  O   GLY A   6      34.482   9.595  87.970  1.00  0.00           O  
+ATOM     25  N   GLY A   7      35.305   7.771  88.986  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      33.972   7.228  89.262  1.00  0.00           C  
+ATOM     27  C   GLY A   7      33.080   8.199  90.016  1.00  0.00           C  
+ATOM     28  O   GLY A   7      33.496   8.790  91.025  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.862   8.369  89.517  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      30.900   9.248  90.160  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.080  10.744  89.977  1.00  0.00           C  
+ATOM     32  O   GLY A   8      30.222  11.524  90.414  1.00  0.00           O  
+ENDMDL
+MODEL     63
+ATOM      1  N   GLY A   1      38.279   0.586  81.977  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.778   1.851  82.504  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.748   2.418  83.473  1.00  0.00           C  
+ATOM      4  O   GLY A   1      36.547   2.421  83.177  1.00  0.00           O  
+ATOM      5  N   GLY A   2      38.208   2.879  84.640  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      37.354   3.605  85.592  1.00  0.00           C  
+ATOM      7  C   GLY A   2      37.050   5.015  85.101  1.00  0.00           C  
+ATOM      8  O   GLY A   2      37.924   5.686  84.538  1.00  0.00           O  
+ATOM      9  N   GLY A   3      35.809   5.469  85.314  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      35.359   6.802  84.892  1.00  0.00           C  
+ATOM     11  C   GLY A   3      35.078   7.700  86.081  1.00  0.00           C  
+ATOM     12  O   GLY A   3      34.779   7.209  87.169  1.00  0.00           O  
+ATOM     13  N   GLY A   4      35.214   9.014  85.882  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      35.009   9.999  86.960  1.00  0.00           C  
+ATOM     15  C   GLY A   4      33.936  11.053  86.662  1.00  0.00           C  
+ATOM     16  O   GLY A   4      33.788  11.494  85.516  1.00  0.00           O  
+ATOM     17  N   GLY A   5      33.206  11.427  87.698  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      32.267  12.555  87.636  1.00  0.00           C  
+ATOM     19  C   GLY A   5      32.147  13.146  89.034  1.00  0.00           C  
+ATOM     20  O   GLY A   5      32.522  12.493  90.019  1.00  0.00           O  
+ATOM     21  N   GLY A   6      31.644  14.402  89.152  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      31.269  14.941  90.466  1.00  0.00           C  
+ATOM     23  C   GLY A   6      30.434  13.934  91.290  1.00  0.00           C  
+ATOM     24  O   GLY A   6      30.741  13.689  92.469  1.00  0.00           O  
+ATOM     25  N   GLY A   7      29.432  13.325  90.649  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      28.513  12.395  91.301  1.00  0.00           C  
+ATOM     27  C   GLY A   7      29.084  10.989  91.574  1.00  0.00           C  
+ATOM     28  O   GLY A   7      28.334  10.080  91.914  1.00  0.00           O  
+ATOM     29  N   GLY A   8      30.398  10.825  91.422  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.058   9.532  91.708  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.728   8.867  90.510  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.838   9.473  89.430  1.00  0.00           O  
+ENDMDL
+MODEL     64
+ATOM      1  N   GLY A   1      39.045   0.158  82.105  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      37.783  -0.494  82.330  1.00  0.00           C  
+ATOM      3  C   GLY A   1      36.946   0.182  83.389  1.00  0.00           C  
+ATOM      4  O   GLY A   1      35.741  -0.001  83.433  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.585   0.818  84.349  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      36.805   1.352  85.463  1.00  0.00           C  
+ATOM      7  C   GLY A   2      36.195   2.766  85.225  1.00  0.00           C  
+ATOM      8  O   GLY A   2      35.365   3.135  86.032  1.00  0.00           O  
+ATOM      9  N   GLY A   3      36.769   3.595  84.312  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      36.206   4.913  83.990  1.00  0.00           C  
+ATOM     11  C   GLY A   3      35.999   5.706  85.263  1.00  0.00           C  
+ATOM     12  O   GLY A   3      34.922   6.248  85.523  1.00  0.00           O  
+ATOM     13  N   GLY A   4      36.995   5.605  86.156  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      36.873   6.137  87.453  1.00  0.00           C  
+ATOM     15  C   GLY A   4      36.328   7.564  87.529  1.00  0.00           C  
+ATOM     16  O   GLY A   4      35.478   7.825  88.373  1.00  0.00           O  
+ATOM     17  N   GLY A   5      36.949   8.513  86.777  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      36.537   9.919  86.848  1.00  0.00           C  
+ATOM     19  C   GLY A   5      35.112  10.092  86.365  1.00  0.00           C  
+ATOM     20  O   GLY A   5      34.326  10.868  86.954  1.00  0.00           O  
+ATOM     21  N   GLY A   6      34.748   9.392  85.318  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      33.362   9.441  84.913  1.00  0.00           C  
+ATOM     23  C   GLY A   6      32.462   9.011  86.078  1.00  0.00           C  
+ATOM     24  O   GLY A   6      31.689   9.815  86.551  1.00  0.00           O  
+ATOM     25  N   GLY A   7      32.551   7.771  86.574  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      31.820   7.401  87.799  1.00  0.00           C  
+ATOM     27  C   GLY A   7      32.398   8.364  88.811  1.00  0.00           C  
+ATOM     28  O   GLY A   7      33.471   8.880  88.657  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.803   8.749  89.788  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      32.520   9.875  90.499  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.879  11.200  90.198  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.257  11.806  91.081  1.00  0.00           O  
+ENDMDL
+MODEL     65
+ATOM      1  N   GLY A   1      39.303   0.275  82.106  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.025  -0.383  82.303  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.094   0.240  83.351  1.00  0.00           C  
+ATOM      4  O   GLY A   1      35.879   0.187  83.203  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.648   0.841  84.392  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      36.824   1.411  85.456  1.00  0.00           C  
+ATOM      7  C   GLY A   2      36.228   2.808  85.244  1.00  0.00           C  
+ATOM      8  O   GLY A   2      35.351   3.213  86.005  1.00  0.00           O  
+ATOM      9  N   GLY A   3      36.687   3.551  84.235  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      36.145   4.905  83.962  1.00  0.00           C  
+ATOM     11  C   GLY A   3      35.864   5.666  85.267  1.00  0.00           C  
+ATOM     12  O   GLY A   3      34.807   6.282  85.411  1.00  0.00           O  
+ATOM     13  N   GLY A   4      36.810   5.613  86.199  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      36.672   6.223  87.517  1.00  0.00           C  
+ATOM     15  C   GLY A   4      36.176   7.680  87.593  1.00  0.00           C  
+ATOM     16  O   GLY A   4      35.231   7.965  88.312  1.00  0.00           O  
+ATOM     17  N   GLY A   5      36.839   8.592  86.890  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      36.441  10.001  86.935  1.00  0.00           C  
+ATOM     19  C   GLY A   5      34.963  10.178  86.559  1.00  0.00           C  
+ATOM     20  O   GLY A   5      34.218  10.871  87.237  1.00  0.00           O  
+ATOM     21  N   GLY A   6      34.549   9.519  85.485  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      33.162   9.590  85.050  1.00  0.00           C  
+ATOM     23  C   GLY A   6      32.224   9.080  86.142  1.00  0.00           C  
+ATOM     24  O   GLY A   6      31.212   9.729  86.454  1.00  0.00           O  
+ATOM     25  N   GLY A   7      32.545   7.928  86.724  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      31.693   7.371  87.765  1.00  0.00           C  
+ATOM     27  C   GLY A   7      31.481   8.306  88.953  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.351   8.479  89.412  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.543   8.917  89.464  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      32.384   9.800  90.606  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.625  11.066  90.196  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.000  11.728  91.041  1.00  0.00           O  
+ENDMDL
+MODEL     66
+ATOM      1  N   GLY A   1      37.807   0.777  80.802  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.033   0.069  82.059  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.583   0.823  83.300  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.266   0.211  84.321  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.547   2.152  83.204  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      37.147   2.976  84.347  1.00  0.00           C  
+ATOM      7  C   GLY A   2      35.714   3.487  84.258  1.00  0.00           C  
+ATOM      8  O   GLY A   2      35.345   4.451  84.938  1.00  0.00           O  
+ATOM      9  N   GLY A   3      34.914   2.829  83.420  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      33.531   3.248  83.254  1.00  0.00           C  
+ATOM     11  C   GLY A   3      32.756   3.283  84.556  1.00  0.00           C  
+ATOM     12  O   GLY A   3      31.815   4.057  84.689  1.00  0.00           O  
+ATOM     13  N   GLY A   4      33.142   2.452  85.512  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      32.439   2.441  86.775  1.00  0.00           C  
+ATOM     15  C   GLY A   4      33.003   3.469  87.742  1.00  0.00           C  
+ATOM     16  O   GLY A   4      32.351   3.874  88.704  1.00  0.00           O  
+ATOM     17  N   GLY A   5      34.232   3.891  87.484  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      34.909   4.856  88.339  1.00  0.00           C  
+ATOM     19  C   GLY A   5      34.610   6.300  87.910  1.00  0.00           C  
+ATOM     20  O   GLY A   5      34.519   7.211  88.741  1.00  0.00           O  
+ATOM     21  N   GLY A   6      34.432   6.500  86.600  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      34.135   7.818  86.051  1.00  0.00           C  
+ATOM     23  C   GLY A   6      32.898   8.527  86.627  1.00  0.00           C  
+ATOM     24  O   GLY A   6      32.951   9.704  86.932  1.00  0.00           O  
+ATOM     25  N   GLY A   7      31.784   7.804  86.794  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      30.573   8.444  87.334  1.00  0.00           C  
+ATOM     27  C   GLY A   7      30.700   9.210  88.649  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.246  10.340  88.753  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.302   8.572  89.648  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.478   9.211  90.943  1.00  0.00           C  
+ATOM     31  C   GLY A   8      32.367  10.440  90.878  1.00  0.00           C  
+ATOM     32  O   GLY A   8      32.162  11.406  91.620  1.00  0.00           O  
+ENDMDL
+MODEL     67
+ATOM      1  N   GLY A   1      39.077  -0.146  81.424  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      39.108   0.468  82.738  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.709   0.797  83.207  1.00  0.00           C  
+ATOM      4  O   GLY A   1      36.916   1.402  82.455  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.399   0.399  84.439  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      36.101   0.670  85.033  1.00  0.00           C  
+ATOM      7  C   GLY A   2      36.381   1.259  86.414  1.00  0.00           C  
+ATOM      8  O   GLY A   2      36.686   0.549  87.374  1.00  0.00           O  
+ATOM      9  N   GLY A   3      36.309   2.579  86.472  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      36.865   3.354  87.561  1.00  0.00           C  
+ATOM     11  C   GLY A   3      35.734   3.922  88.372  1.00  0.00           C  
+ATOM     12  O   GLY A   3      34.828   4.529  87.810  1.00  0.00           O  
+ATOM     13  N   GLY A   4      35.773   3.732  89.691  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      34.790   4.339  90.611  1.00  0.00           C  
+ATOM     15  C   GLY A   4      34.906   5.862  90.707  1.00  0.00           C  
+ATOM     16  O   GLY A   4      33.902   6.550  90.815  1.00  0.00           O  
+ATOM     17  N   GLY A   5      36.116   6.410  90.663  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      36.242   7.876  90.617  1.00  0.00           C  
+ATOM     19  C   GLY A   5      35.680   8.485  89.355  1.00  0.00           C  
+ATOM     20  O   GLY A   5      35.211   9.600  89.374  1.00  0.00           O  
+ATOM     21  N   GLY A   6      35.704   7.767  88.243  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      35.017   8.251  87.036  1.00  0.00           C  
+ATOM     23  C   GLY A   6      33.479   8.184  87.216  1.00  0.00           C  
+ATOM     24  O   GLY A   6      32.779   9.158  86.935  1.00  0.00           O  
+ATOM     25  N   GLY A   7      32.976   7.063  87.742  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      31.526   6.967  88.082  1.00  0.00           C  
+ATOM     27  C   GLY A   7      31.074   8.058  89.042  1.00  0.00           C  
+ATOM     28  O   GLY A   7      29.967   8.590  88.936  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.922   8.384  89.995  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.553   9.353  91.011  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.391  10.725  90.379  1.00  0.00           C  
+ATOM     32  O   GLY A   8      30.592  11.529  90.843  1.00  0.00           O  
+ENDMDL
+MODEL     68
+ATOM      1  N   GLY A   1      39.190  -0.950  81.799  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.476   0.314  82.011  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.921   0.286  83.428  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.000  -0.477  83.731  1.00  0.00           O  
+ATOM      5  N   GLY A   2      38.485   1.119  84.293  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      38.158   1.113  85.705  1.00  0.00           C  
+ATOM      7  C   GLY A   2      37.209   2.250  86.072  1.00  0.00           C  
+ATOM      8  O   GLY A   2      37.583   3.426  86.018  1.00  0.00           O  
+ATOM      9  N   GLY A   3      35.976   1.880  86.422  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      34.967   2.830  86.888  1.00  0.00           C  
+ATOM     11  C   GLY A   3      35.011   2.956  88.407  1.00  0.00           C  
+ATOM     12  O   GLY A   3      35.118   1.956  89.121  1.00  0.00           O  
+ATOM     13  N   GLY A   4      34.934   4.189  88.899  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      35.149   4.484  90.319  1.00  0.00           C  
+ATOM     15  C   GLY A   4      34.125   5.457  90.893  1.00  0.00           C  
+ATOM     16  O   GLY A   4      33.714   6.407  90.225  1.00  0.00           O  
+ATOM     17  N   GLY A   5      33.733   5.218  92.141  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      32.793   6.076  92.870  1.00  0.00           C  
+ATOM     19  C   GLY A   5      33.407   7.433  93.192  1.00  0.00           C  
+ATOM     20  O   GLY A   5      32.720   8.464  93.127  1.00  0.00           O  
+ATOM     21  N   GLY A   6      34.693   7.430  93.536  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      35.426   8.650  93.879  1.00  0.00           C  
+ATOM     23  C   GLY A   6      35.418   9.660  92.725  1.00  0.00           C  
+ATOM     24  O   GLY A   6      35.188  10.853  92.940  1.00  0.00           O  
+ATOM     25  N   GLY A   7      35.667   9.162  91.515  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      35.628   9.976  90.297  1.00  0.00           C  
+ATOM     27  C   GLY A   7      34.205  10.502  90.050  1.00  0.00           C  
+ATOM     28  O   GLY A   7      34.025  11.651  89.639  1.00  0.00           O  
+ATOM     29  N   GLY A   8      33.211   9.656  90.327  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.806  10.023  90.191  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.402  11.064  91.234  1.00  0.00           C  
+ATOM     32  O   GLY A   8      30.635  11.989  90.938  1.00  0.00           O  
+ENDMDL
+MODEL     69
+ATOM      1  N   GLY A   1      38.071  -1.691  83.155  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      37.483  -0.512  83.711  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.698   0.729  82.884  1.00  0.00           C  
+ATOM      4  O   GLY A   1      38.779   0.987  82.371  1.00  0.00           O  
+ATOM      5  N   GLY A   2      36.692   1.560  82.836  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      36.803   2.917  82.301  1.00  0.00           C  
+ATOM      7  C   GLY A   2      36.748   4.036  83.326  1.00  0.00           C  
+ATOM      8  O   GLY A   2      36.413   3.820  84.496  1.00  0.00           O  
+ATOM      9  N   GLY A   3      36.963   5.284  82.909  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      36.854   6.358  83.912  1.00  0.00           C  
+ATOM     11  C   GLY A   3      35.423   6.580  84.397  1.00  0.00           C  
+ATOM     12  O   GLY A   3      35.201   7.264  85.423  1.00  0.00           O  
+ATOM     13  N   GLY A   4      34.425   6.032  83.678  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      33.055   6.236  84.107  1.00  0.00           C  
+ATOM     15  C   GLY A   4      32.616   5.069  84.931  1.00  0.00           C  
+ATOM     16  O   GLY A   4      31.462   5.039  85.375  1.00  0.00           O  
+ATOM     17  N   GLY A   5      33.509   4.102  85.147  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      33.220   3.113  86.165  1.00  0.00           C  
+ATOM     19  C   GLY A   5      33.816   3.594  87.506  1.00  0.00           C  
+ATOM     20  O   GLY A   5      34.579   2.870  88.201  1.00  0.00           O  
+ATOM     21  N   GLY A   6      33.488   4.842  87.854  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      33.932   5.469  89.104  1.00  0.00           C  
+ATOM     23  C   GLY A   6      32.844   6.319  89.692  1.00  0.00           C  
+ATOM     24  O   GLY A   6      31.937   6.727  88.998  1.00  0.00           O  
+ATOM     25  N   GLY A   7      33.002   6.625  90.976  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      31.977   7.311  91.751  1.00  0.00           C  
+ATOM     27  C   GLY A   7      31.803   8.760  91.281  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.666   9.241  91.094  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.913   9.474  91.150  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      32.789  10.921  90.882  1.00  0.00           C  
+ATOM     31  C   GLY A   8      32.057  11.159  89.559  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.331  12.120  89.412  1.00  0.00           O  
+ENDMDL
+MODEL     70
+ATOM      1  N   GLY A   1      37.362   0.673  83.667  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      37.884  -0.582  83.128  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.111  -1.807  83.634  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.072  -2.846  82.960  1.00  0.00           O  
+ATOM      5  N   GLY A   2      36.515  -1.682  84.806  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      35.779  -2.797  85.374  1.00  0.00           C  
+ATOM      7  C   GLY A   2      34.814  -2.396  86.487  1.00  0.00           C  
+ATOM      8  O   GLY A   2      33.612  -2.629  86.382  1.00  0.00           O  
+ATOM      9  N   GLY A   3      35.345  -1.787  87.544  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      34.534  -1.418  88.703  1.00  0.00           C  
+ATOM     11  C   GLY A   3      33.745  -0.110  88.676  1.00  0.00           C  
+ATOM     12  O   GLY A   3      32.961   0.159  89.588  1.00  0.00           O  
+ATOM     13  N   GLY A   4      33.969   0.696  87.637  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      33.282   1.978  87.523  1.00  0.00           C  
+ATOM     15  C   GLY A   4      34.293   3.079  87.273  1.00  0.00           C  
+ATOM     16  O   GLY A   4      35.484   2.793  87.135  1.00  0.00           O  
+ATOM     17  N   GLY A   5      33.828   4.321  87.179  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      34.718   5.461  86.965  1.00  0.00           C  
+ATOM     19  C   GLY A   5      35.110   5.897  88.390  1.00  0.00           C  
+ATOM     20  O   GLY A   5      34.252   6.236  89.199  1.00  0.00           O  
+ATOM     21  N   GLY A   6      36.404   5.910  88.709  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      36.905   6.282  90.034  1.00  0.00           C  
+ATOM     23  C   GLY A   6      36.901   7.754  90.430  1.00  0.00           C  
+ATOM     24  O   GLY A   6      37.281   8.078  91.557  1.00  0.00           O  
+ATOM     25  N   GLY A   7      36.463   8.635  89.550  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      36.500  10.061  89.852  1.00  0.00           C  
+ATOM     27  C   GLY A   7      35.175  10.764  89.993  1.00  0.00           C  
+ATOM     28  O   GLY A   7      35.085  11.972  89.796  1.00  0.00           O  
+ATOM     29  N   GLY A   8      34.141  10.013  90.349  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      32.799  10.568  90.498  1.00  0.00           C  
+ATOM     31  C   GLY A   8      32.440  11.402  89.281  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.834  12.472  89.394  1.00  0.00           O  
+ENDMDL
+MODEL     71
+ATOM      1  N   GLY A   1      38.705  -0.723  81.652  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      37.858  -0.776  82.835  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.151   0.590  82.928  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.780   1.589  83.341  1.00  0.00           O  
+ATOM      5  N   GLY A   2      35.904   0.556  82.527  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      35.211   1.852  82.459  1.00  0.00           C  
+ATOM      7  C   GLY A   2      34.198   2.248  83.506  1.00  0.00           C  
+ATOM      8  O   GLY A   2      33.769   1.511  84.401  1.00  0.00           O  
+ATOM      9  N   GLY A   3      33.734   3.499  83.330  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      32.700   4.123  84.121  1.00  0.00           C  
+ATOM     11  C   GLY A   3      33.140   4.728  85.428  1.00  0.00           C  
+ATOM     12  O   GLY A   3      32.312   5.179  86.233  1.00  0.00           O  
+ATOM     13  N   GLY A   4      34.462   4.816  85.574  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      35.079   5.380  86.767  1.00  0.00           C  
+ATOM     15  C   GLY A   4      34.943   6.922  86.693  1.00  0.00           C  
+ATOM     16  O   GLY A   4      34.945   7.606  87.698  1.00  0.00           O  
+ATOM     17  N   GLY A   5      34.800   7.479  85.480  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      34.696   8.953  85.464  1.00  0.00           C  
+ATOM     19  C   GLY A   5      33.283   9.366  85.850  1.00  0.00           C  
+ATOM     20  O   GLY A   5      33.118  10.234  86.704  1.00  0.00           O  
+ATOM     21  N   GLY A   6      32.312   8.712  85.232  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      30.921   8.998  85.492  1.00  0.00           C  
+ATOM     23  C   GLY A   6      30.531   8.695  86.939  1.00  0.00           C  
+ATOM     24  O   GLY A   6      29.696   9.392  87.536  1.00  0.00           O  
+ATOM     25  N   GLY A   7      31.184   7.677  87.515  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      30.875   7.290  88.872  1.00  0.00           C  
+ATOM     27  C   GLY A   7      31.308   8.334  89.859  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.835   8.391  91.006  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.271   9.157  89.427  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      32.652  10.231  90.390  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.576  11.301  90.432  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.489  12.102  91.365  1.00  0.00           O  
+ENDMDL
+MODEL     72
+ATOM      1  N   GLY A   1      39.129   1.753  81.267  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      39.295   2.047  82.683  1.00  0.00           C  
+ATOM      3  C   GLY A   1      38.013   2.684  83.171  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.538   2.395  84.252  1.00  0.00           O  
+ATOM      5  N   GLY A   2      37.434   3.574  82.368  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      36.329   4.370  82.856  1.00  0.00           C  
+ATOM      7  C   GLY A   2      35.125   3.477  83.044  1.00  0.00           C  
+ATOM      8  O   GLY A   2      34.402   3.664  84.014  1.00  0.00           O  
+ATOM      9  N   GLY A   3      34.905   2.559  82.094  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      33.750   1.668  82.135  1.00  0.00           C  
+ATOM     11  C   GLY A   3      33.737   0.723  83.314  1.00  0.00           C  
+ATOM     12  O   GLY A   3      32.627   0.331  83.782  1.00  0.00           O  
+ATOM     13  N   GLY A   4      34.923   0.366  83.866  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      34.961  -0.458  85.126  1.00  0.00           C  
+ATOM     15  C   GLY A   4      34.418   0.262  86.359  1.00  0.00           C  
+ATOM     16  O   GLY A   4      33.885  -0.356  87.308  1.00  0.00           O  
+ATOM     17  N   GLY A   5      34.541   1.581  86.350  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      34.264   2.358  87.557  1.00  0.00           C  
+ATOM     19  C   GLY A   5      32.786   2.366  87.959  1.00  0.00           C  
+ATOM     20  O   GLY A   5      31.914   2.397  87.104  1.00  0.00           O  
+ATOM     21  N   GLY A   6      32.570   2.337  89.260  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      31.235   2.338  89.853  1.00  0.00           C  
+ATOM     23  C   GLY A   6      31.078   3.507  90.809  1.00  0.00           C  
+ATOM     24  O   GLY A   6      31.994   4.276  90.986  1.00  0.00           O  
+ATOM     25  N   GLY A   7      29.886   3.651  91.398  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      29.632   4.726  92.355  1.00  0.00           C  
+ATOM     27  C   GLY A   7      29.659   6.127  91.734  1.00  0.00           C  
+ATOM     28  O   GLY A   7      29.163   6.329  90.626  1.00  0.00           O  
+ATOM     29  N   GLY A   8      30.246   7.076  92.453  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      30.441   8.449  91.930  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.378   8.508  90.746  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.173   9.284  89.805  1.00  0.00           O  
+ENDMDL
+MODEL     73
+ATOM      1  N   GLY A   1      38.360   0.778  83.823  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      39.291  -0.040  83.064  1.00  0.00           C  
+ATOM      3  C   GLY A   1      38.835  -1.482  83.014  1.00  0.00           C  
+ATOM      4  O   GLY A   1      39.191  -2.218  82.087  1.00  0.00           O  
+ATOM      5  N   GLY A   2      38.038  -1.893  83.996  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      37.512  -3.245  84.059  1.00  0.00           C  
+ATOM      7  C   GLY A   2      36.294  -3.362  83.140  1.00  0.00           C  
+ATOM      8  O   GLY A   2      35.592  -4.373  83.159  1.00  0.00           O  
+ATOM      9  N   GLY A   3      36.041  -2.312  82.363  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      34.922  -2.312  81.431  1.00  0.00           C  
+ATOM     11  C   GLY A   3      33.589  -1.830  81.958  1.00  0.00           C  
+ATOM     12  O   GLY A   3      32.592  -1.885  81.243  1.00  0.00           O  
+ATOM     13  N   GLY A   4      33.560  -1.363  83.194  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      32.318  -0.893  83.791  1.00  0.00           C  
+ATOM     15  C   GLY A   4      31.984   0.549  83.435  1.00  0.00           C  
+ATOM     16  O   GLY A   4      32.874   1.369  83.198  1.00  0.00           O  
+ATOM     17  N   GLY A   5      30.700   0.851  83.381  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      30.234   2.204  83.119  1.00  0.00           C  
+ATOM     19  C   GLY A   5      30.188   2.833  84.504  1.00  0.00           C  
+ATOM     20  O   GLY A   5      29.537   2.307  85.414  1.00  0.00           O  
+ATOM     21  N   GLY A   6      30.901   3.935  84.667  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      30.989   4.590  85.964  1.00  0.00           C  
+ATOM     23  C   GLY A   6      30.716   6.088  85.945  1.00  0.00           C  
+ATOM     24  O   GLY A   6      31.028   6.781  84.967  1.00  0.00           O  
+ATOM     25  N   GLY A   7      30.122   6.575  87.022  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      29.837   7.995  87.179  1.00  0.00           C  
+ATOM     27  C   GLY A   7      30.312   8.427  88.565  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.035   7.756  89.570  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.061   9.517  88.618  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.573  10.029  89.875  1.00  0.00           C  
+ATOM     31  C   GLY A   8      30.789  11.263  90.302  1.00  0.00           C  
+ATOM     32  O   GLY A   8      30.582  12.180  89.523  1.00  0.00           O  
+ENDMDL
+MODEL     74
+ATOM      1  N   GLY A   1      39.102   2.551  81.072  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.697   1.150  81.129  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.922   0.814  82.399  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.180  -0.165  82.439  1.00  0.00           O  
+ATOM      5  N   GLY A   2      38.116   1.627  83.435  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      37.431   1.440  84.720  1.00  0.00           C  
+ATOM      7  C   GLY A   2      36.941   2.816  85.154  1.00  0.00           C  
+ATOM      8  O   GLY A   2      37.455   3.407  86.108  1.00  0.00           O  
+ATOM      9  N   GLY A   3      35.920   3.304  84.453  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      35.345   4.626  84.691  1.00  0.00           C  
+ATOM     11  C   GLY A   3      34.442   4.739  85.915  1.00  0.00           C  
+ATOM     12  O   GLY A   3      34.167   5.849  86.383  1.00  0.00           O  
+ATOM     13  N   GLY A   4      33.982   3.609  86.435  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      33.076   3.590  87.582  1.00  0.00           C  
+ATOM     15  C   GLY A   4      33.500   4.511  88.731  1.00  0.00           C  
+ATOM     16  O   GLY A   4      32.694   5.299  89.228  1.00  0.00           O  
+ATOM     17  N   GLY A   5      34.753   4.409  89.145  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      35.244   5.214  90.265  1.00  0.00           C  
+ATOM     19  C   GLY A   5      35.162   6.692  89.935  1.00  0.00           C  
+ATOM     20  O   GLY A   5      34.574   7.481  90.672  1.00  0.00           O  
+ATOM     21  N   GLY A   6      35.776   7.029  88.814  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      35.810   8.391  88.328  1.00  0.00           C  
+ATOM     23  C   GLY A   6      34.386   8.960  88.231  1.00  0.00           C  
+ATOM     24  O   GLY A   6      34.085  10.000  88.800  1.00  0.00           O  
+ATOM     25  N   GLY A   7      33.509   8.262  87.517  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      32.123   8.703  87.357  1.00  0.00           C  
+ATOM     27  C   GLY A   7      31.462   9.015  88.686  1.00  0.00           C  
+ATOM     28  O   GLY A   7      30.726   9.995  88.818  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.739   8.168  89.666  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.196   8.311  91.004  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.651   9.608  91.676  1.00  0.00           C  
+ATOM     32  O   GLY A   8      30.862  10.292  92.323  1.00  0.00           O  
+ENDMDL
+MODEL     75
+ATOM      1  N   GLY A   1      39.477   1.172  82.998  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.582   0.149  82.482  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.132   0.396  82.864  1.00  0.00           C  
+ATOM      4  O   GLY A   1      36.242  -0.398  82.543  1.00  0.00           O  
+ATOM      5  N   GLY A   2      36.887   1.508  83.554  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      35.538   1.873  83.952  1.00  0.00           C  
+ATOM      7  C   GLY A   2      34.924   1.061  85.073  1.00  0.00           C  
+ATOM      8  O   GLY A   2      33.706   1.032  85.222  1.00  0.00           O  
+ATOM      9  N   GLY A   3      35.772   0.413  85.874  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      35.285  -0.401  86.974  1.00  0.00           C  
+ATOM     11  C   GLY A   3      34.809   0.425  88.169  1.00  0.00           C  
+ATOM     12  O   GLY A   3      34.141  -0.103  89.060  1.00  0.00           O  
+ATOM     13  N   GLY A   4      35.148   1.711  88.199  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      34.748   2.559  89.313  1.00  0.00           C  
+ATOM     15  C   GLY A   4      33.960   3.802  88.904  1.00  0.00           C  
+ATOM     16  O   GLY A   4      33.955   4.797  89.638  1.00  0.00           O  
+ATOM     17  N   GLY A   5      33.297   3.762  87.757  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      32.533   4.912  87.276  1.00  0.00           C  
+ATOM     19  C   GLY A   5      31.520   5.454  88.290  1.00  0.00           C  
+ATOM     20  O   GLY A   5      31.305   6.665  88.365  1.00  0.00           O  
+ATOM     21  N   GLY A   6      30.905   4.564  89.054  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      29.891   4.962  90.038  1.00  0.00           C  
+ATOM     23  C   GLY A   6      30.461   5.619  91.284  1.00  0.00           C  
+ATOM     24  O   GLY A   6      29.717   5.973  92.213  1.00  0.00           O  
+ATOM     25  N   GLY A   7      31.779   5.798  91.327  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      32.417   6.399  92.484  1.00  0.00           C  
+ATOM     27  C   GLY A   7      32.870   7.836  92.217  1.00  0.00           C  
+ATOM     28  O   GLY A   7      33.776   8.354  92.873  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.208   8.479  91.254  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      32.507   9.865  90.880  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.158  10.569  90.730  1.00  0.00           C  
+ATOM     32  O   GLY A   8      30.574  10.574  89.648  1.00  0.00           O  
+ENDMDL
+MODEL     76
+ATOM      1  N   GLY A   1      38.970  -0.729  81.676  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.693   0.612  82.190  1.00  0.00           C  
+ATOM      3  C   GLY A   1      38.108   0.525  83.598  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.650   1.523  84.136  1.00  0.00           O  
+ATOM      5  N   GLY A   2      38.153  -0.651  84.205  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      37.481  -0.902  85.485  1.00  0.00           C  
+ATOM      7  C   GLY A   2      37.836   0.074  86.607  1.00  0.00           C  
+ATOM      8  O   GLY A   2      37.006   0.353  87.473  1.00  0.00           O  
+ATOM      9  N   GLY A   3      39.073   0.578  86.616  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      39.498   1.485  87.685  1.00  0.00           C  
+ATOM     11  C   GLY A   3      39.182   2.967  87.390  1.00  0.00           C  
+ATOM     12  O   GLY A   3      39.408   3.835  88.227  1.00  0.00           O  
+ATOM     13  N   GLY A   4      38.638   3.249  86.203  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      38.247   4.631  85.829  1.00  0.00           C  
+ATOM     15  C   GLY A   4      37.174   5.120  86.832  1.00  0.00           C  
+ATOM     16  O   GLY A   4      36.308   4.351  87.244  1.00  0.00           O  
+ATOM     17  N   GLY A   5      37.271   6.378  87.280  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      36.411   6.889  88.369  1.00  0.00           C  
+ATOM     19  C   GLY A   5      35.160   7.658  87.952  1.00  0.00           C  
+ATOM     20  O   GLY A   5      34.550   8.362  88.768  1.00  0.00           O  
+ATOM     21  N   GLY A   6      34.765   7.494  86.690  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      33.698   8.288  86.049  1.00  0.00           C  
+ATOM     23  C   GLY A   6      32.276   8.162  86.668  1.00  0.00           C  
+ATOM     24  O   GLY A   6      31.432   9.063  86.495  1.00  0.00           O  
+ATOM     25  N   GLY A   7      32.019   7.051  87.356  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      30.755   6.847  88.042  1.00  0.00           C  
+ATOM     27  C   GLY A   7      30.556   7.826  89.213  1.00  0.00           C  
+ATOM     28  O   GLY A   7      29.471   7.868  89.801  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.584   8.599  89.539  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.499   9.540  90.651  1.00  0.00           C  
+ATOM     31  C   GLY A   8      31.246  10.995  90.300  1.00  0.00           C  
+ATOM     32  O   GLY A   8      30.913  11.783  91.187  1.00  0.00           O  
+ENDMDL
+MODEL     77
+ATOM      1  N   GLY A   1      39.403   1.379  81.921  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      38.845   0.068  82.272  1.00  0.00           C  
+ATOM      3  C   GLY A   1      37.793   0.199  83.362  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.990   0.908  84.348  1.00  0.00           O  
+ATOM      5  N   GLY A   2      36.675  -0.521  83.213  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      35.657  -0.431  84.298  1.00  0.00           C  
+ATOM      7  C   GLY A   2      36.254  -1.144  85.545  1.00  0.00           C  
+ATOM      8  O   GLY A   2      35.675  -1.085  86.620  1.00  0.00           O  
+ATOM      9  N   GLY A   3      37.398  -1.766  85.290  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      38.194  -2.482  86.266  1.00  0.00           C  
+ATOM     11  C   GLY A   3      38.514  -1.595  87.464  1.00  0.00           C  
+ATOM     12  O   GLY A   3      37.984  -1.753  88.554  1.00  0.00           O  
+ATOM     13  N   GLY A   4      39.394  -0.607  87.232  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      39.714   0.317  88.295  1.00  0.00           C  
+ATOM     15  C   GLY A   4      38.828   1.486  88.380  1.00  0.00           C  
+ATOM     16  O   GLY A   4      38.778   2.395  87.535  1.00  0.00           O  
+ATOM     17  N   GLY A   5      37.953   1.521  89.403  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      37.004   2.620  89.484  1.00  0.00           C  
+ATOM     19  C   GLY A   5      37.501   3.845  90.216  1.00  0.00           C  
+ATOM     20  O   GLY A   5      38.489   3.824  90.944  1.00  0.00           O  
+ATOM     21  N   GLY A   6      36.762   4.928  90.029  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      36.947   6.185  90.714  1.00  0.00           C  
+ATOM     23  C   GLY A   6      35.558   6.586  91.295  1.00  0.00           C  
+ATOM     24  O   GLY A   6      34.554   6.051  90.838  1.00  0.00           O  
+ATOM     25  N   GLY A   7      35.558   7.472  92.270  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      34.273   7.907  92.880  1.00  0.00           C  
+ATOM     27  C   GLY A   7      33.587   8.848  91.914  1.00  0.00           C  
+ATOM     28  O   GLY A   7      34.113   9.892  91.525  1.00  0.00           O  
+ATOM     29  N   GLY A   8      32.413   8.437  91.420  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.778   9.304  90.412  1.00  0.00           C  
+ATOM     31  C   GLY A   8      30.880  10.320  91.057  1.00  0.00           C  
+ATOM     32  O   GLY A   8      30.731  11.456  90.578  1.00  0.00           O  
+ENDMDL
+MODEL     78
+ATOM      1  N   GLY A   1      38.919   1.043  82.749  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      37.743   0.182  82.786  1.00  0.00           C  
+ATOM      3  C   GLY A   1      36.746   0.581  83.905  1.00  0.00           C  
+ATOM      4  O   GLY A   1      37.146   0.901  85.022  1.00  0.00           O  
+ATOM      5  N   GLY A   2      35.468   0.697  83.518  1.00  0.00           N  
+ATOM      6  CA  GLY A   2      34.252   0.697  84.387  1.00  0.00           C  
+ATOM      7  C   GLY A   2      34.246  -0.125  85.695  1.00  0.00           C  
+ATOM      8  O   GLY A   2      33.588   0.224  86.651  1.00  0.00           O  
+ATOM      9  N   GLY A   3      34.904  -1.279  85.677  1.00  0.00           N  
+ATOM     10  CA  GLY A   3      35.010  -2.130  86.847  1.00  0.00           C  
+ATOM     11  C   GLY A   3      35.552  -1.344  88.055  1.00  0.00           C  
+ATOM     12  O   GLY A   3      35.078  -1.548  89.185  1.00  0.00           O  
+ATOM     13  N   GLY A   4      36.478  -0.423  87.797  1.00  0.00           N  
+ATOM     14  CA  GLY A   4      37.238   0.277  88.841  1.00  0.00           C  
+ATOM     15  C   GLY A   4      36.745   1.695  89.141  1.00  0.00           C  
+ATOM     16  O   GLY A   4      37.243   2.350  90.053  1.00  0.00           O  
+ATOM     17  N   GLY A   5      35.786   2.169  88.353  1.00  0.00           N  
+ATOM     18  CA  GLY A   5      35.164   3.475  88.585  1.00  0.00           C  
+ATOM     19  C   GLY A   5      34.384   3.515  89.907  1.00  0.00           C  
+ATOM     20  O   GLY A   5      33.890   2.493  90.391  1.00  0.00           O  
+ATOM     21  N   GLY A   6      34.289   4.704  90.474  1.00  0.00           N  
+ATOM     22  CA  GLY A   6      33.533   4.981  91.675  1.00  0.00           C  
+ATOM     23  C   GLY A   6      32.200   5.627  91.329  1.00  0.00           C  
+ATOM     24  O   GLY A   6      31.832   5.748  90.158  1.00  0.00           O  
+ATOM     25  N   GLY A   7      31.460   6.021  92.356  1.00  0.00           N  
+ATOM     26  CA  GLY A   7      30.194   6.718  92.162  1.00  0.00           C  
+ATOM     27  C   GLY A   7      30.417   8.162  91.753  1.00  0.00           C  
+ATOM     28  O   GLY A   7      29.441   8.854  91.450  1.00  0.00           O  
+ATOM     29  N   GLY A   8      31.647   8.654  91.799  1.00  0.00           N  
+ATOM     30  CA  GLY A   8      31.946   9.995  91.299  1.00  0.00           C  
+ATOM     31  C   GLY A   8      32.140   9.963  89.771  1.00  0.00           C  
+ATOM     32  O   GLY A   8      31.936  10.963  89.093  1.00  0.00           O  
+ENDMDL
+END   
\ No newline at end of file
diff --git a/examples/trj/sample.dcd b/examples/demos/data/sample.dcd
similarity index 100%
rename from examples/trj/sample.dcd
rename to examples/demos/data/sample.dcd
diff --git a/examples/trj/sample.pdb b/examples/demos/data/sample.pdb
similarity index 100%
rename from examples/trj/sample.pdb
rename to examples/demos/data/sample.pdb
diff --git a/examples/demos/data/sdh-complete.pdb b/examples/demos/data/sdh-complete.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..af4812d0333a88029cf48c05a0a06a7a2d762395
--- /dev/null
+++ b/examples/demos/data/sdh-complete.pdb
@@ -0,0 +1,1942 @@
+HELIX    1   1 ARG A   15  GLU A   28  1                                  14    
+HELIX    2   2 ASN A   38  GLY A   50  1                                  13    
+HELIX    3   3 ASP A   62  GLY A   78  1                                  17    
+HELIX    4   4 PRO A   94  ILE A   98  5                                   5    
+HELIX    5   5 THR A   99  VAL A  111  1                                  13    
+HELIX    6   6 VAL A  111  GLY A  129  1                                  19    
+HELIX    7   7 SER A  139  ARG A  143  5                                   5    
+HELIX    8   8 VAL A  149  ILE A  171  1                                  23    
+HELIX    9   9 HIS A  189  ASN A  202  1                                  14    
+HELIX   10  10 GLY A  206  VAL A  216  1                                  11    
+HELIX   11  11 ARG A  223  LEU A  234  1                                  12    
+HELIX   12  12 ALA A  235  ASP A  240  5                                   6    
+HELIX   13  13 ARG B   15  GLU B   28  1                                  14    
+HELIX   14  14 ASN B   38  GLY B   50  1                                  13    
+HELIX   15  15 ASP B   62  GLY B   78  1                                  17    
+HELIX   16  16 PRO B   94  ILE B   98  5                                   5    
+HELIX   17  17 THR B   99  VAL B  111  1                                  13    
+HELIX   18  18 VAL B  111  GLY B  129  1                                  19    
+HELIX   19  19 SER B  139  ARG B  143  5                                   5    
+HELIX   20  20 VAL B  149  ILE B  171  1                                  23    
+HELIX   21  21 HIS B  189  GLU B  201  1                                  13    
+HELIX   22  22 GLY B  206  VAL B  216  1                                  11    
+HELIX   23  23 ARG B  223  LEU B  234  1                                  12    
+HELIX   24  24 ALA B  235  ASP B  240  5                                   6    
+SHEET    1   A 7 ALA A  53  ALA A  57  0                                        
+SHEET    2   A 7 ALA A  30  ASP A  36  1  N  ILE A  34   O  CYS A  54           
+SHEET    3   A 7 LYS A   6  THR A  11  1  N  LYS A   6   O  ARG A  31           
+SHEET    4   A 7 ILE A  82  ASN A  85  1  O  ILE A  82   N  LEU A   9           
+SHEET    5   A 7 GLY A 132  MET A 137  1  O  ILE A 135   N  LEU A  83           
+SHEET    6   A 7 ILE A 175  PRO A 182  1  O  ASN A 176   N  ILE A 134           
+SHEET    7   A 7 THR A 246  VAL A 249  1  O  TYR A 247   N  ALA A 181           
+SHEET    1   B 7 ALA B  53  ALA B  57  0                                        
+SHEET    2   B 7 ARG B  31  ASP B  36  1  N  ILE B  34   O  CYS B  54           
+SHEET    3   B 7 THR B   7  THR B  11  1  N  ALA B   8   O  ARG B  31           
+SHEET    4   B 7 ILE B  82  ASN B  85  1  O  VAL B  84   N  LEU B   9           
+SHEET    5   B 7 GLY B 132  MET B 137  1  O  ILE B 135   N  LEU B  83           
+SHEET    6   B 7 ILE B 175  PRO B 182  1  O  ASN B 176   N  ILE B 134           
+SHEET    7   B 7 THR B 246  VAL B 249  1  O  TYR B 247   N  ALA B 181           
+CRYST1   67.465   67.465  191.044  90.00  90.00 120.00 P 31 2 1     12          
+ORIGX1      1.000000  0.000000  0.000000        0.00000                         
+ORIGX2      0.000000  1.000000  0.000000        0.00000                         
+ORIGX3      0.000000  0.000000  1.000000        0.00000                         
+SCALE1      0.014823  0.008558  0.000000        0.00000                         
+SCALE2      0.000000  0.017116  0.000000        0.00000                         
+SCALE3      0.000000  0.000000  0.005234        0.00000                         
+ATOM      1  N   MET A   1      21.609  35.384  56.705  1.00 41.48           N  
+ATOM      2  CA  MET A   1      20.601  35.494  57.793  1.00 41.58           C  
+ATOM      3  C   MET A   1      19.654  34.300  57.789  1.00 39.51           C  
+ATOM      4  O   MET A   1      18.447  34.456  57.595  1.00 38.98           O  
+ATOM      5  CB  MET A   1      19.789  36.783  57.639  1.00 45.90           C  
+ATOM      6  CG  MET A   1      20.629  38.055  57.606  1.00 51.18           C  
+ATOM      7  SD  MET A   1      21.638  38.325  59.084  1.00 55.83           S  
+ATOM      8  CE  MET A   1      23.233  37.697  58.529  1.00 54.59           C  
+ATOM      9  N   ARG A   2      20.202  33.112  58.011  1.00 36.39           N  
+ATOM     10  CA  ARG A   2      19.396  31.903  58.033  1.00 34.35           C  
+ATOM     11  C   ARG A   2      18.608  31.739  59.328  1.00 34.20           C  
+ATOM     12  O   ARG A   2      17.651  30.965  59.381  1.00 32.64           O  
+ATOM     13  CB  ARG A   2      20.284  30.681  57.801  1.00 33.48           C  
+ATOM     14  CG  ARG A   2      20.665  30.488  56.342  1.00 31.69           C  
+ATOM     15  CD  ARG A   2      21.557  29.281  56.154  1.00 29.91           C  
+ATOM     16  NE  ARG A   2      22.931  29.557  56.551  1.00 28.95           N  
+ATOM     17  CZ  ARG A   2      23.901  28.653  56.528  1.00 30.21           C  
+ATOM     18  NH1 ARG A   2      23.640  27.417  56.130  1.00 32.54           N  
+ATOM     19  NH2 ARG A   2      25.132  28.980  56.893  1.00 29.14           N  
+ATOM     20  N   LEU A   3      19.003  32.473  60.366  1.00 35.07           N  
+ATOM     21  CA  LEU A   3      18.330  32.402  61.664  1.00 34.70           C  
+ATOM     22  C   LEU A   3      17.884  33.787  62.117  1.00 35.41           C  
+ATOM     23  O   LEU A   3      17.853  34.091  63.308  1.00 35.91           O  
+ATOM     24  CB  LEU A   3      19.269  31.793  62.710  1.00 31.47           C  
+ATOM     25  CG  LEU A   3      19.695  30.340  62.501  1.00 29.10           C  
+ATOM     26  CD1 LEU A   3      20.585  29.897  63.648  1.00 26.97           C  
+ATOM     27  CD2 LEU A   3      18.461  29.459  62.420  1.00 27.95           C  
+ATOM     28  N   ASP A   4      17.517  34.614  61.149  1.00 36.70           N  
+ATOM     29  CA  ASP A   4      17.099  35.980  61.411  1.00 37.42           C  
+ATOM     30  C   ASP A   4      15.897  36.114  62.343  1.00 37.20           C  
+ATOM     31  O   ASP A   4      14.839  35.529  62.107  1.00 35.42           O  
+ATOM     32  CB  ASP A   4      16.814  36.671  60.079  1.00 40.33           C  
+ATOM     33  CG  ASP A   4      17.023  38.166  60.142  1.00 43.16           C  
+ATOM     34  OD1 ASP A   4      16.121  38.876  60.638  1.00 44.42           O  
+ATOM     35  OD2 ASP A   4      18.100  38.629  59.699  1.00 45.27           O  
+ATOM     36  N   GLY A   5      16.085  36.893  63.408  1.00 38.60           N  
+ATOM     37  CA  GLY A   5      15.027  37.141  64.378  1.00 40.00           C  
+ATOM     38  C   GLY A   5      14.640  35.963  65.253  1.00 40.53           C  
+ATOM     39  O   GLY A   5      13.475  35.828  65.645  1.00 40.48           O  
+ATOM     40  N   LYS A   6      15.612  35.110  65.565  1.00 39.87           N  
+ATOM     41  CA  LYS A   6      15.354  33.938  66.391  1.00 38.75           C  
+ATOM     42  C   LYS A   6      16.248  33.899  67.615  1.00 37.16           C  
+ATOM     43  O   LYS A   6      17.363  34.427  67.602  1.00 36.93           O  
+ATOM     44  CB  LYS A   6      15.548  32.665  65.571  1.00 39.36           C  
+ATOM     45  CG  LYS A   6      14.498  32.476  64.504  1.00 40.15           C  
+ATOM     46  CD  LYS A   6      14.601  31.107  63.866  1.00 41.73           C  
+ATOM     47  CE  LYS A   6      13.463  30.880  62.879  1.00 44.93           C  
+ATOM     48  NZ  LYS A   6      12.132  31.017  63.537  1.00 44.56           N  
+ATOM     49  N   THR A   7      15.750  33.261  68.670  1.00 34.56           N  
+ATOM     50  CA  THR A   7      16.484  33.152  69.925  1.00 31.14           C  
+ATOM     51  C   THR A   7      16.945  31.728  70.188  1.00 30.82           C  
+ATOM     52  O   THR A   7      16.175  30.775  70.059  1.00 31.78           O  
+ATOM     53  CB  THR A   7      15.618  33.605  71.114  1.00 30.89           C  
+ATOM     54  OG1 THR A   7      14.409  32.837  71.147  1.00 31.28           O  
+ATOM     55  CG2 THR A   7      15.263  35.077  70.991  1.00 32.31           C  
+ATOM     56  N   ALA A   8      18.205  31.586  70.573  1.00 29.62           N  
+ATOM     57  CA  ALA A   8      18.759  30.274  70.854  1.00 29.72           C  
+ATOM     58  C   ALA A   8      19.461  30.202  72.215  1.00 30.28           C  
+ATOM     59  O   ALA A   8      20.244  31.084  72.579  1.00 30.25           O  
+ATOM     60  CB  ALA A   8      19.732  29.874  69.745  1.00 29.05           C  
+ATOM     61  N   LEU A   9      19.163  29.146  72.964  1.00 28.68           N  
+ATOM     62  CA  LEU A   9      19.784  28.923  74.261  1.00 26.72           C  
+ATOM     63  C   LEU A   9      20.780  27.790  74.007  1.00 26.04           C  
+ATOM     64  O   LEU A   9      20.390  26.713  73.554  1.00 26.45           O  
+ATOM     65  CB  LEU A   9      18.733  28.471  75.291  1.00 26.06           C  
+ATOM     66  CG  LEU A   9      19.044  28.458  76.801  1.00 25.33           C  
+ATOM     67  CD1 LEU A   9      17.929  27.731  77.537  1.00 23.24           C  
+ATOM     68  CD2 LEU A   9      20.359  27.772  77.089  1.00 25.34           C  
+ATOM     69  N   ILE A  10      22.056  28.036  74.278  1.00 23.49           N  
+ATOM     70  CA  ILE A  10      23.077  27.016  74.090  1.00 24.46           C  
+ATOM     71  C   ILE A  10      23.777  26.777  75.422  1.00 27.09           C  
+ATOM     72  O   ILE A  10      24.431  27.677  75.953  1.00 27.64           O  
+ATOM     73  CB  ILE A  10      24.124  27.460  73.057  1.00 24.13           C  
+ATOM     74  CG1 ILE A  10      23.427  27.822  71.747  1.00 22.48           C  
+ATOM     75  CG2 ILE A  10      25.153  26.351  72.842  1.00 17.46           C  
+ATOM     76  CD1 ILE A  10      24.360  28.402  70.719  1.00 24.59           C  
+ATOM     77  N   THR A  11      23.650  25.565  75.955  1.00 27.49           N  
+ATOM     78  CA  THR A  11      24.256  25.247  77.240  1.00 28.56           C  
+ATOM     79  C   THR A  11      25.740  24.948  77.123  1.00 29.62           C  
+ATOM     80  O   THR A  11      26.186  24.359  76.138  1.00 32.36           O  
+ATOM     81  CB  THR A  11      23.551  24.043  77.899  1.00 27.97           C  
+ATOM     82  OG1 THR A  11      23.883  22.839  77.199  1.00 27.93           O  
+ATOM     83  CG2 THR A  11      22.050  24.235  77.863  1.00 27.09           C  
+ATOM     84  N   GLY A  12      26.499  25.356  78.137  1.00 29.33           N  
+ATOM     85  CA  GLY A  12      27.934  25.121  78.150  1.00 29.86           C  
+ATOM     86  C   GLY A  12      28.634  25.744  76.963  1.00 31.12           C  
+ATOM     87  O   GLY A  12      29.570  25.170  76.407  1.00 32.13           O  
+ATOM     88  N   SER A  13      28.186  26.939  76.592  1.00 32.78           N  
+ATOM     89  CA  SER A  13      28.721  27.662  75.443  1.00 33.66           C  
+ATOM     90  C   SER A  13      29.757  28.737  75.764  1.00 35.28           C  
+ATOM     91  O   SER A  13      30.039  29.600  74.933  1.00 36.10           O  
+ATOM     92  CB  SER A  13      27.561  28.292  74.674  1.00 32.16           C  
+ATOM     93  OG  SER A  13      26.712  29.012  75.550  1.00 31.20           O  
+ATOM     94  N   ALA A  14      30.323  28.696  76.963  1.00 36.42           N  
+ATOM     95  CA  ALA A  14      31.320  29.688  77.335  1.00 36.95           C  
+ATOM     96  C   ALA A  14      32.594  29.418  76.550  1.00 37.21           C  
+ATOM     97  O   ALA A  14      33.338  30.338  76.218  1.00 36.96           O  
+ATOM     98  CB  ALA A  14      31.600  29.621  78.834  1.00 36.61           C  
+ATOM     99  N   ARG A  15      32.833  28.146  76.249  1.00 37.46           N  
+ATOM    100  CA  ARG A  15      34.025  27.749  75.511  1.00 38.19           C  
+ATOM    101  C   ARG A  15      33.755  26.585  74.573  1.00 36.88           C  
+ATOM    102  O   ARG A  15      32.648  26.040  74.533  1.00 36.88           O  
+ATOM    103  CB  ARG A  15      35.136  27.342  76.484  1.00 40.06           C  
+ATOM    104  CG  ARG A  15      35.555  28.438  77.445  1.00 43.70           C  
+ATOM    105  CD  ARG A  15      36.475  27.902  78.531  1.00 44.19           C  
+ATOM    106  NE  ARG A  15      36.657  28.880  79.598  0.00 44.00           N  
+ATOM    107  CZ  ARG A  15      37.270  28.625  80.748  0.00 44.01           C  
+ATOM    108  NH1 ARG A  15      37.389  29.576  81.664  0.00 43.97           N  
+ATOM    109  NH2 ARG A  15      37.761  27.416  80.985  0.00 43.97           N  
+ATOM    110  N   GLY A  16      34.791  26.214  73.825  1.00 35.61           N  
+ATOM    111  CA  GLY A  16      34.707  25.101  72.898  1.00 34.73           C  
+ATOM    112  C   GLY A  16      33.653  25.160  71.808  1.00 33.39           C  
+ATOM    113  O   GLY A  16      33.297  26.227  71.306  1.00 33.46           O  
+ATOM    114  N   ILE A  17      33.164  23.980  71.445  1.00 32.78           N  
+ATOM    115  CA  ILE A  17      32.152  23.820  70.409  1.00 31.95           C  
+ATOM    116  C   ILE A  17      30.913  24.653  70.699  1.00 31.77           C  
+ATOM    117  O   ILE A  17      30.311  25.231  69.789  1.00 32.50           O  
+ATOM    118  CB  ILE A  17      31.747  22.340  70.285  1.00 30.90           C  
+ATOM    119  CG1 ILE A  17      32.954  21.519  69.822  1.00 31.07           C  
+ATOM    120  CG2 ILE A  17      30.574  22.194  69.336  1.00 32.31           C  
+ATOM    121  CD1 ILE A  17      32.682  20.030  69.689  1.00 31.10           C  
+ATOM    122  N   GLY A  18      30.533  24.711  71.968  1.00 30.54           N  
+ATOM    123  CA  GLY A  18      29.362  25.475  72.340  1.00 30.57           C  
+ATOM    124  C   GLY A  18      29.499  26.918  71.916  1.00 31.00           C  
+ATOM    125  O   GLY A  18      28.548  27.511  71.403  1.00 30.12           O  
+ATOM    126  N   ARG A  19      30.685  27.484  72.133  1.00 32.12           N  
+ATOM    127  CA  ARG A  19      30.947  28.870  71.768  1.00 34.24           C  
+ATOM    128  C   ARG A  19      30.840  29.036  70.263  1.00 34.09           C  
+ATOM    129  O   ARG A  19      30.246  30.000  69.775  1.00 34.42           O  
+ATOM    130  CB  ARG A  19      32.341  29.306  72.227  1.00 35.54           C  
+ATOM    131  CG  ARG A  19      32.719  30.675  71.700  1.00 37.76           C  
+ATOM    132  CD  ARG A  19      33.872  31.311  72.446  1.00 41.26           C  
+ATOM    133  NE  ARG A  19      34.100  32.671  71.961  1.00 45.22           N  
+ATOM    134  CZ  ARG A  19      34.886  33.567  72.552  1.00 47.24           C  
+ATOM    135  NH1 ARG A  19      35.538  33.261  73.668  1.00 47.45           N  
+ATOM    136  NH2 ARG A  19      35.014  34.779  72.026  1.00 48.67           N  
+ATOM    137  N   ALA A  20      31.420  28.084  69.537  1.00 33.55           N  
+ATOM    138  CA  ALA A  20      31.395  28.100  68.081  1.00 32.10           C  
+ATOM    139  C   ALA A  20      29.960  28.244  67.579  1.00 31.27           C  
+ATOM    140  O   ALA A  20      29.657  29.151  66.801  1.00 30.43           O  
+ATOM    141  CB  ALA A  20      32.014  26.822  67.542  1.00 33.12           C  
+ATOM    142  N   PHE A  21      29.078  27.355  68.031  1.00 29.80           N  
+ATOM    143  CA  PHE A  21      27.681  27.410  67.616  1.00 30.38           C  
+ATOM    144  C   PHE A  21      27.098  28.791  67.875  1.00 31.24           C  
+ATOM    145  O   PHE A  21      26.382  29.341  67.041  1.00 31.23           O  
+ATOM    146  CB  PHE A  21      26.849  26.371  68.372  1.00 31.41           C  
+ATOM    147  CG  PHE A  21      27.159  24.947  68.004  1.00 31.93           C  
+ATOM    148  CD1 PHE A  21      26.580  23.898  68.713  1.00 32.29           C  
+ATOM    149  CD2 PHE A  21      28.021  24.649  66.951  1.00 31.51           C  
+ATOM    150  CE1 PHE A  21      26.858  22.570  68.385  1.00 32.16           C  
+ATOM    151  CE2 PHE A  21      28.304  23.327  66.615  1.00 31.35           C  
+ATOM    152  CZ  PHE A  21      27.718  22.286  67.334  1.00 32.56           C  
+ATOM    153  N   ALA A  22      27.407  29.349  69.040  1.00 32.80           N  
+ATOM    154  CA  ALA A  22      26.898  30.661  69.410  1.00 32.66           C  
+ATOM    155  C   ALA A  22      27.351  31.695  68.394  1.00 33.14           C  
+ATOM    156  O   ALA A  22      26.539  32.453  67.870  1.00 33.21           O  
+ATOM    157  CB  ALA A  22      27.384  31.037  70.797  1.00 32.85           C  
+ATOM    158  N   GLU A  23      28.649  31.723  68.120  1.00 33.91           N  
+ATOM    159  CA  GLU A  23      29.184  32.667  67.152  1.00 36.31           C  
+ATOM    160  C   GLU A  23      28.513  32.448  65.792  1.00 36.26           C  
+ATOM    161  O   GLU A  23      28.056  33.402  65.158  1.00 37.82           O  
+ATOM    162  CB  GLU A  23      30.713  32.521  67.046  1.00 36.10           C  
+ATOM    163  CG  GLU A  23      31.437  32.932  68.324  1.00 40.69           C  
+ATOM    164  CD  GLU A  23      32.958  32.853  68.229  1.00 43.33           C  
+ATOM    165  OE1 GLU A  23      33.481  31.834  67.729  1.00 45.41           O  
+ATOM    166  OE2 GLU A  23      33.635  33.805  68.678  1.00 45.19           O  
+ATOM    167  N   ALA A  24      28.428  31.196  65.355  1.00 35.52           N  
+ATOM    168  CA  ALA A  24      27.799  30.893  64.076  1.00 35.70           C  
+ATOM    169  C   ALA A  24      26.343  31.359  64.068  1.00 36.18           C  
+ATOM    170  O   ALA A  24      25.894  32.018  63.131  1.00 38.13           O  
+ATOM    171  CB  ALA A  24      27.874  29.403  63.802  1.00 35.57           C  
+ATOM    172  N   TYR A  25      25.609  31.018  65.120  1.00 35.70           N  
+ATOM    173  CA  TYR A  25      24.209  31.409  65.240  1.00 34.64           C  
+ATOM    174  C   TYR A  25      24.019  32.924  65.172  1.00 35.28           C  
+ATOM    175  O   TYR A  25      23.109  33.417  64.498  1.00 34.85           O  
+ATOM    176  CB  TYR A  25      23.638  30.869  66.553  1.00 32.65           C  
+ATOM    177  CG  TYR A  25      23.047  29.482  66.442  1.00 31.55           C  
+ATOM    178  CD1 TYR A  25      23.584  28.537  65.564  1.00 29.81           C  
+ATOM    179  CD2 TYR A  25      21.943  29.113  67.212  1.00 32.84           C  
+ATOM    180  CE1 TYR A  25      23.033  27.262  65.452  1.00 28.86           C  
+ATOM    181  CE2 TYR A  25      21.384  27.835  67.109  1.00 31.38           C  
+ATOM    182  CZ  TYR A  25      21.935  26.917  66.226  1.00 29.78           C  
+ATOM    183  OH  TYR A  25      21.383  25.660  66.120  1.00 28.89           O  
+ATOM    184  N   VAL A  26      24.872  33.660  65.878  1.00 36.23           N  
+ATOM    185  CA  VAL A  26      24.792  35.115  65.884  1.00 37.22           C  
+ATOM    186  C   VAL A  26      25.032  35.634  64.475  1.00 38.84           C  
+ATOM    187  O   VAL A  26      24.326  36.525  64.003  1.00 38.94           O  
+ATOM    188  CB  VAL A  26      25.840  35.733  66.833  1.00 36.95           C  
+ATOM    189  CG1 VAL A  26      25.880  37.247  66.655  1.00 36.32           C  
+ATOM    190  CG2 VAL A  26      25.497  35.381  68.278  1.00 35.50           C  
+ATOM    191  N   ARG A  27      26.021  35.055  63.803  1.00 39.22           N  
+ATOM    192  CA  ARG A  27      26.359  35.452  62.444  1.00 40.94           C  
+ATOM    193  C   ARG A  27      25.161  35.300  61.511  1.00 40.42           C  
+ATOM    194  O   ARG A  27      25.075  35.985  60.492  1.00 42.12           O  
+ATOM    195  CB  ARG A  27      27.507  34.597  61.915  1.00 43.30           C  
+ATOM    196  CG  ARG A  27      28.427  35.315  60.945  1.00 47.74           C  
+ATOM    197  CD  ARG A  27      28.992  34.355  59.908  1.00 51.22           C  
+ATOM    198  NE  ARG A  27      29.188  32.999  60.427  1.00 55.99           N  
+ATOM    199  CZ  ARG A  27      28.554  31.917  59.964  1.00 58.56           C  
+ATOM    200  NH1 ARG A  27      28.791  30.722  60.490  1.00 58.38           N  
+ATOM    201  NH2 ARG A  27      27.680  32.024  58.969  1.00 60.19           N  
+ATOM    202  N   GLU A  28      24.241  34.402  61.856  1.00 38.14           N  
+ATOM    203  CA  GLU A  28      23.060  34.163  61.031  1.00 36.10           C  
+ATOM    204  C   GLU A  28      21.870  35.017  61.452  1.00 36.39           C  
+ATOM    205  O   GLU A  28      20.727  34.740  61.076  1.00 34.91           O  
+ATOM    206  CB  GLU A  28      22.667  32.682  61.071  1.00 35.69           C  
+ATOM    207  CG  GLU A  28      23.663  31.726  60.403  1.00 33.17           C  
+ATOM    208  CD  GLU A  28      23.837  31.979  58.905  1.00 32.01           C  
+ATOM    209  OE1 GLU A  28      22.832  32.201  58.195  1.00 28.70           O  
+ATOM    210  OE2 GLU A  28      24.989  31.942  58.433  1.00 31.55           O  
+ATOM    211  N   GLY A  29      22.149  36.047  62.247  1.00 37.61           N  
+ATOM    212  CA  GLY A  29      21.108  36.956  62.694  1.00 39.19           C  
+ATOM    213  C   GLY A  29      20.233  36.496  63.845  1.00 40.36           C  
+ATOM    214  O   GLY A  29      19.062  36.883  63.935  1.00 40.61           O  
+ATOM    215  N   ALA A  30      20.788  35.682  64.736  1.00 40.68           N  
+ATOM    216  CA  ALA A  30      20.023  35.190  65.876  1.00 40.66           C  
+ATOM    217  C   ALA A  30      20.555  35.725  67.199  1.00 40.40           C  
+ATOM    218  O   ALA A  30      21.729  36.081  67.308  1.00 40.37           O  
+ATOM    219  CB  ALA A  30      20.042  33.676  65.895  1.00 40.55           C  
+ATOM    220  N   ARG A  31      19.674  35.795  68.193  1.00 40.42           N  
+ATOM    221  CA  ARG A  31      20.044  36.250  69.532  1.00 40.52           C  
+ATOM    222  C   ARG A  31      20.339  34.996  70.352  1.00 39.11           C  
+ATOM    223  O   ARG A  31      19.508  34.094  70.439  1.00 38.13           O  
+ATOM    224  CB  ARG A  31      18.899  37.053  70.158  1.00 42.90           C  
+ATOM    225  CG  ARG A  31      18.781  38.467  69.597  1.00 46.44           C  
+ATOM    226  CD  ARG A  31      17.354  38.820  69.230  1.00 48.95           C  
+ATOM    227  NE  ARG A  31      16.476  38.861  70.394  1.00 53.95           N  
+ATOM    228  CZ  ARG A  31      15.162  39.061  70.330  1.00 56.89           C  
+ATOM    229  NH1 ARG A  31      14.573  39.237  69.151  1.00 58.47           N  
+ATOM    230  NH2 ARG A  31      14.433  39.087  71.441  1.00 57.00           N  
+ATOM    231  N   VAL A  32      21.529  34.935  70.938  1.00 37.80           N  
+ATOM    232  CA  VAL A  32      21.924  33.765  71.711  1.00 36.59           C  
+ATOM    233  C   VAL A  32      22.185  34.035  73.183  1.00 36.34           C  
+ATOM    234  O   VAL A  32      22.528  35.146  73.578  1.00 35.13           O  
+ATOM    235  CB  VAL A  32      23.194  33.133  71.128  1.00 36.30           C  
+ATOM    236  CG1 VAL A  32      23.024  32.916  69.627  1.00 37.03           C  
+ATOM    237  CG2 VAL A  32      24.390  34.025  71.416  1.00 35.06           C  
+ATOM    238  N   ALA A  33      22.040  32.986  73.984  1.00 37.38           N  
+ATOM    239  CA  ALA A  33      22.261  33.058  75.421  1.00 36.31           C  
+ATOM    240  C   ALA A  33      23.443  32.179  75.785  1.00 36.88           C  
+ATOM    241  O   ALA A  33      23.386  30.961  75.625  1.00 37.35           O  
+ATOM    242  CB  ALA A  33      21.025  32.588  76.159  1.00 35.42           C  
+ATOM    243  N   ILE A  34      24.518  32.795  76.264  1.00 38.13           N  
+ATOM    244  CA  ILE A  34      25.699  32.038  76.657  1.00 38.94           C  
+ATOM    245  C   ILE A  34      25.498  31.538  78.080  1.00 40.59           C  
+ATOM    246  O   ILE A  34      25.831  32.227  79.043  1.00 40.22           O  
+ATOM    247  CB  ILE A  34      26.975  32.904  76.619  1.00 38.37           C  
+ATOM    248  CG1 ILE A  34      27.170  33.497  75.222  1.00 38.46           C  
+ATOM    249  CG2 ILE A  34      28.185  32.057  76.997  1.00 37.39           C  
+ATOM    250  CD1 ILE A  34      27.420  32.462  74.150  1.00 38.95           C  
+ATOM    251  N   ALA A  35      24.941  30.339  78.205  1.00 41.92           N  
+ATOM    252  CA  ALA A  35      24.695  29.745  79.508  1.00 43.18           C  
+ATOM    253  C   ALA A  35      25.878  28.894  79.938  1.00 44.41           C  
+ATOM    254  O   ALA A  35      26.433  28.139  79.146  1.00 45.46           O  
+ATOM    255  CB  ALA A  35      23.438  28.901  79.465  1.00 42.44           C  
+ATOM    256  N   ASP A  36      26.262  29.028  81.200  1.00 46.15           N  
+ATOM    257  CA  ASP A  36      27.373  28.265  81.745  1.00 47.31           C  
+ATOM    258  C   ASP A  36      27.265  28.297  83.267  1.00 48.60           C  
+ATOM    259  O   ASP A  36      26.596  29.168  83.829  1.00 49.31           O  
+ATOM    260  CB  ASP A  36      28.699  28.877  81.297  1.00 46.39           C  
+ATOM    261  CG  ASP A  36      29.828  27.871  81.287  1.00 45.88           C  
+ATOM    262  OD1 ASP A  36      29.800  26.960  80.432  1.00 45.19           O  
+ATOM    263  OD2 ASP A  36      30.738  27.988  82.136  1.00 45.12           O  
+ATOM    264  N   ILE A  37      27.915  27.351  83.936  1.00 50.09           N  
+ATOM    265  CA  ILE A  37      27.863  27.297  85.392  1.00 51.95           C  
+ATOM    266  C   ILE A  37      28.675  28.423  86.033  1.00 53.37           C  
+ATOM    267  O   ILE A  37      28.359  28.876  87.135  1.00 53.50           O  
+ATOM    268  CB  ILE A  37      28.371  25.949  85.917  1.00 51.56           C  
+ATOM    269  CG1 ILE A  37      28.119  25.865  87.423  1.00 51.91           C  
+ATOM    270  CG2 ILE A  37      29.850  25.790  85.595  1.00 51.01           C  
+ATOM    271  CD1 ILE A  37      28.295  24.481  88.004  1.00 52.00           C  
+ATOM    272  N   ASN A  38      29.720  28.865  85.335  1.00 54.64           N  
+ATOM    273  CA  ASN A  38      30.572  29.955  85.808  1.00 55.52           C  
+ATOM    274  C   ASN A  38      30.205  31.247  85.084  1.00 54.73           C  
+ATOM    275  O   ASN A  38      30.615  31.463  83.940  1.00 55.80           O  
+ATOM    276  CB  ASN A  38      32.046  29.639  85.552  1.00 56.47           C  
+ATOM    277  CG  ASN A  38      32.936  30.854  85.732  1.00 57.78           C  
+ATOM    278  OD1 ASN A  38      32.920  31.504  86.782  1.00 57.89           O  
+ATOM    279  ND2 ASN A  38      33.717  31.170  84.706  1.00 58.70           N  
+ATOM    280  N   LEU A  39      29.447  32.105  85.757  1.00 53.84           N  
+ATOM    281  CA  LEU A  39      29.002  33.363  85.173  1.00 54.57           C  
+ATOM    282  C   LEU A  39      30.136  34.284  84.727  1.00 55.54           C  
+ATOM    283  O   LEU A  39      29.931  35.148  83.876  1.00 56.03           O  
+ATOM    284  CB  LEU A  39      28.090  34.097  86.154  1.00 53.87           C  
+ATOM    285  CG  LEU A  39      27.369  35.328  85.603  1.00 54.60           C  
+ATOM    286  CD1 LEU A  39      26.591  34.951  84.350  1.00 54.32           C  
+ATOM    287  CD2 LEU A  39      26.433  35.892  86.665  1.00 54.58           C  
+ATOM    288  N   GLU A  40      31.327  34.104  85.295  1.00 56.31           N  
+ATOM    289  CA  GLU A  40      32.472  34.933  84.916  1.00 57.01           C  
+ATOM    290  C   GLU A  40      32.787  34.722  83.441  1.00 56.41           C  
+ATOM    291  O   GLU A  40      32.757  35.662  82.649  1.00 57.32           O  
+ATOM    292  CB  GLU A  40      33.716  34.579  85.745  1.00 57.92           C  
+ATOM    293  CG  GLU A  40      33.674  35.022  87.199  1.00 57.86           C  
+ATOM    294  CD  GLU A  40      34.962  34.708  87.935  0.00 57.81           C  
+ATOM    295  OE1 GLU A  40      36.020  35.241  87.537  0.00 57.80           O  
+ATOM    296  OE2 GLU A  40      34.918  33.927  88.909  0.00 57.80           O  
+ATOM    297  N   ALA A  41      33.087  33.477  83.085  1.00 55.70           N  
+ATOM    298  CA  ALA A  41      33.413  33.119  81.710  1.00 55.07           C  
+ATOM    299  C   ALA A  41      32.261  33.441  80.760  1.00 54.36           C  
+ATOM    300  O   ALA A  41      32.485  33.884  79.631  1.00 55.50           O  
+ATOM    301  CB  ALA A  41      33.759  31.637  81.628  1.00 54.86           C  
+ATOM    302  N   ALA A  42      31.033  33.217  81.220  1.00 51.88           N  
+ATOM    303  CA  ALA A  42      29.860  33.487  80.406  1.00 50.49           C  
+ATOM    304  C   ALA A  42      29.833  34.951  79.984  1.00 50.10           C  
+ATOM    305  O   ALA A  42      29.768  35.254  78.795  1.00 50.28           O  
+ATOM    306  CB  ALA A  42      28.595  33.138  81.176  1.00 49.63           C  
+ATOM    307  N   ARG A  43      29.889  35.855  80.960  1.00 49.94           N  
+ATOM    308  CA  ARG A  43      29.873  37.291  80.683  1.00 49.15           C  
+ATOM    309  C   ARG A  43      31.008  37.677  79.745  1.00 48.09           C  
+ATOM    310  O   ARG A  43      30.836  38.518  78.864  1.00 47.84           O  
+ATOM    311  CB  ARG A  43      30.007  38.101  81.977  1.00 49.16           C  
+ATOM    312  CG  ARG A  43      28.905  37.872  82.993  1.00 49.68           C  
+ATOM    313  CD  ARG A  43      28.432  39.193  83.580  1.00 49.79           C  
+ATOM    314  NE  ARG A  43      29.543  40.037  84.010  0.00 49.84           N  
+ATOM    315  CZ  ARG A  43      30.359  39.749  85.018  0.00 49.87           C  
+ATOM    316  NH1 ARG A  43      30.194  38.631  85.712  0.00 49.88           N  
+ATOM    317  NH2 ARG A  43      31.344  40.580  85.331  0.00 49.88           N  
+ATOM    318  N   ALA A  44      32.168  37.058  79.948  1.00 46.99           N  
+ATOM    319  CA  ALA A  44      33.347  37.326  79.134  1.00 47.53           C  
+ATOM    320  C   ALA A  44      33.092  37.017  77.663  1.00 48.09           C  
+ATOM    321  O   ALA A  44      33.331  37.854  76.789  1.00 48.80           O  
+ATOM    322  CB  ALA A  44      34.517  36.499  79.640  1.00 46.98           C  
+ATOM    323  N   THR A  45      32.613  35.805  77.401  1.00 48.24           N  
+ATOM    324  CA  THR A  45      32.315  35.359  76.046  1.00 47.85           C  
+ATOM    325  C   THR A  45      31.174  36.166  75.430  1.00 48.44           C  
+ATOM    326  O   THR A  45      31.248  36.574  74.271  1.00 48.68           O  
+ATOM    327  CB  THR A  45      31.932  33.864  76.037  1.00 47.38           C  
+ATOM    328  OG1 THR A  45      33.031  33.089  76.529  1.00 45.66           O  
+ATOM    329  CG2 THR A  45      31.589  33.403  74.631  1.00 47.55           C  
+ATOM    330  N   ALA A  46      30.121  36.396  76.207  1.00 49.20           N  
+ATOM    331  CA  ALA A  46      28.970  37.147  75.722  1.00 50.60           C  
+ATOM    332  C   ALA A  46      29.372  38.548  75.281  1.00 51.74           C  
+ATOM    333  O   ALA A  46      28.896  39.053  74.260  1.00 52.51           O  
+ATOM    334  CB  ALA A  46      27.906  37.228  76.806  1.00 50.87           C  
+ATOM    335  N   ALA A  47      30.248  39.174  76.059  1.00 52.05           N  
+ATOM    336  CA  ALA A  47      30.707  40.523  75.755  1.00 52.69           C  
+ATOM    337  C   ALA A  47      31.644  40.502  74.553  1.00 51.52           C  
+ATOM    338  O   ALA A  47      31.737  41.470  73.799  1.00 51.19           O  
+ATOM    339  CB  ALA A  47      31.419  41.112  76.969  1.00 52.78           C  
+ATOM    340  N   GLU A  48      32.330  39.380  74.388  1.00 51.09           N  
+ATOM    341  CA  GLU A  48      33.274  39.192  73.301  1.00 51.37           C  
+ATOM    342  C   GLU A  48      32.542  39.009  71.972  1.00 51.47           C  
+ATOM    343  O   GLU A  48      33.058  39.387  70.918  1.00 52.14           O  
+ATOM    344  CB  GLU A  48      34.139  37.968  73.606  1.00 52.10           C  
+ATOM    345  CG  GLU A  48      35.520  37.991  72.994  1.00 54.21           C  
+ATOM    346  CD  GLU A  48      36.492  37.099  73.748  1.00 54.75           C  
+ATOM    347  OE1 GLU A  48      36.631  37.285  74.974  1.00 56.29           O  
+ATOM    348  OE2 GLU A  48      37.119  36.218  73.125  1.00 55.57           O  
+ATOM    349  N   ILE A  49      31.336  38.442  72.035  1.00 50.68           N  
+ATOM    350  CA  ILE A  49      30.522  38.190  70.846  1.00 49.69           C  
+ATOM    351  C   ILE A  49      29.723  39.410  70.390  1.00 49.67           C  
+ATOM    352  O   ILE A  49      29.548  39.630  69.192  1.00 49.69           O  
+ATOM    353  CB  ILE A  49      29.549  36.999  71.076  1.00 49.01           C  
+ATOM    354  CG1 ILE A  49      30.350  35.705  71.233  1.00 48.28           C  
+ATOM    355  CG2 ILE A  49      28.568  36.880  69.916  1.00 47.17           C  
+ATOM    356  CD1 ILE A  49      29.499  34.463  71.377  1.00 47.96           C  
+ATOM    357  N   GLY A  50      29.228  40.200  71.335  1.00 49.39           N  
+ATOM    358  CA  GLY A  50      28.476  41.377  70.949  1.00 49.47           C  
+ATOM    359  C   GLY A  50      27.117  41.538  71.598  1.00 50.11           C  
+ATOM    360  O   GLY A  50      26.726  40.737  72.449  1.00 50.29           O  
+ATOM    361  N   PRO A  51      26.372  42.587  71.207  1.00 50.40           N  
+ATOM    362  CA  PRO A  51      25.034  42.921  71.712  1.00 49.58           C  
+ATOM    363  C   PRO A  51      23.998  41.830  71.457  1.00 49.02           C  
+ATOM    364  O   PRO A  51      22.927  41.829  72.067  1.00 49.15           O  
+ATOM    365  CB  PRO A  51      24.695  44.209  70.962  1.00 50.07           C  
+ATOM    366  CG  PRO A  51      26.039  44.821  70.704  1.00 49.86           C  
+ATOM    367  CD  PRO A  51      26.847  43.628  70.278  1.00 49.89           C  
+ATOM    368  N   ALA A  52      24.318  40.909  70.553  1.00 48.54           N  
+ATOM    369  CA  ALA A  52      23.401  39.823  70.213  1.00 48.72           C  
+ATOM    370  C   ALA A  52      23.466  38.671  71.213  1.00 48.10           C  
+ATOM    371  O   ALA A  52      22.586  37.809  71.240  1.00 48.18           O  
+ATOM    372  CB  ALA A  52      23.698  39.313  68.809  1.00 47.21           C  
+ATOM    373  N   ALA A  53      24.508  38.661  72.035  1.00 47.86           N  
+ATOM    374  CA  ALA A  53      24.677  37.611  73.028  1.00 48.97           C  
+ATOM    375  C   ALA A  53      24.611  38.150  74.458  1.00 49.45           C  
+ATOM    376  O   ALA A  53      25.078  39.251  74.743  1.00 50.94           O  
+ATOM    377  CB  ALA A  53      26.007  36.901  72.803  1.00 48.79           C  
+ATOM    378  N   CYS A  54      24.015  37.370  75.351  1.00 48.98           N  
+ATOM    379  CA  CYS A  54      23.913  37.747  76.749  1.00 48.17           C  
+ATOM    380  C   CYS A  54      24.262  36.524  77.589  1.00 47.49           C  
+ATOM    381  O   CYS A  54      24.032  35.389  77.168  1.00 47.24           O  
+ATOM    382  CB  CYS A  54      22.505  38.250  77.070  1.00 49.09           C  
+ATOM    383  SG  CYS A  54      21.176  37.139  76.603  1.00 53.63           S  
+ATOM    384  N   ALA A  55      24.835  36.757  78.766  1.00 46.35           N  
+ATOM    385  CA  ALA A  55      25.234  35.670  79.651  1.00 44.77           C  
+ATOM    386  C   ALA A  55      24.166  35.313  80.682  1.00 44.27           C  
+ATOM    387  O   ALA A  55      23.260  36.099  80.968  1.00 44.34           O  
+ATOM    388  CB  ALA A  55      26.541  36.029  80.353  1.00 44.16           C  
+ATOM    389  N   ILE A  56      24.274  34.107  81.224  1.00 43.29           N  
+ATOM    390  CA  ILE A  56      23.343  33.630  82.237  1.00 42.02           C  
+ATOM    391  C   ILE A  56      23.912  32.391  82.914  1.00 41.19           C  
+ATOM    392  O   ILE A  56      24.461  31.500  82.259  1.00 40.62           O  
+ATOM    393  CB  ILE A  56      21.952  33.301  81.641  1.00 41.75           C  
+ATOM    394  CG1 ILE A  56      20.980  32.970  82.770  1.00 41.95           C  
+ATOM    395  CG2 ILE A  56      22.037  32.118  80.696  1.00 41.03           C  
+ATOM    396  CD1 ILE A  56      19.538  32.936  82.327  1.00 42.82           C  
+ATOM    397  N   ALA A  57      23.793  32.349  84.235  1.00 39.65           N  
+ATOM    398  CA  ALA A  57      24.308  31.232  85.012  1.00 38.36           C  
+ATOM    399  C   ALA A  57      23.370  30.037  84.907  1.00 37.61           C  
+ATOM    400  O   ALA A  57      22.146  30.182  84.994  1.00 36.56           O  
+ATOM    401  CB  ALA A  57      24.475  31.649  86.468  1.00 37.83           C  
+ATOM    402  N   LEU A  58      23.947  28.855  84.717  1.00 36.28           N  
+ATOM    403  CA  LEU A  58      23.140  27.651  84.599  1.00 35.96           C  
+ATOM    404  C   LEU A  58      23.840  26.388  85.066  1.00 35.93           C  
+ATOM    405  O   LEU A  58      24.970  26.097  84.670  1.00 36.09           O  
+ATOM    406  CB  LEU A  58      22.692  27.458  83.152  1.00 35.23           C  
+ATOM    407  CG  LEU A  58      21.843  26.214  82.879  1.00 33.94           C  
+ATOM    408  CD1 LEU A  58      20.495  26.339  83.567  1.00 30.46           C  
+ATOM    409  CD2 LEU A  58      21.654  26.060  81.378  1.00 33.43           C  
+ATOM    410  N   ASP A  59      23.156  25.643  85.921  1.00 35.71           N  
+ATOM    411  CA  ASP A  59      23.674  24.380  86.417  1.00 35.86           C  
+ATOM    412  C   ASP A  59      22.624  23.368  85.984  1.00 35.81           C  
+ATOM    413  O   ASP A  59      21.618  23.187  86.673  1.00 35.94           O  
+ATOM    414  CB  ASP A  59      23.780  24.396  87.938  1.00 36.21           C  
+ATOM    415  CG  ASP A  59      24.445  23.156  88.474  1.00 37.33           C  
+ATOM    416  OD1 ASP A  59      24.050  22.047  88.059  1.00 36.23           O  
+ATOM    417  OD2 ASP A  59      25.362  23.291  89.307  1.00 40.49           O  
+ATOM    418  N   VAL A  60      22.845  22.723  84.838  1.00 34.59           N  
+ATOM    419  CA  VAL A  60      21.877  21.764  84.314  1.00 33.19           C  
+ATOM    420  C   VAL A  60      21.534  20.613  85.254  1.00 33.10           C  
+ATOM    421  O   VAL A  60      20.557  19.899  85.025  1.00 31.94           O  
+ATOM    422  CB  VAL A  60      22.331  21.174  82.945  1.00 32.86           C  
+ATOM    423  CG1 VAL A  60      22.377  22.279  81.896  1.00 30.34           C  
+ATOM    424  CG2 VAL A  60      23.684  20.491  83.078  1.00 31.52           C  
+ATOM    425  N   THR A  61      22.321  20.434  86.312  1.00 33.07           N  
+ATOM    426  CA  THR A  61      22.057  19.356  87.259  1.00 34.49           C  
+ATOM    427  C   THR A  61      21.128  19.803  88.388  1.00 35.19           C  
+ATOM    428  O   THR A  61      20.699  18.986  89.201  1.00 36.31           O  
+ATOM    429  CB  THR A  61      23.344  18.836  87.901  1.00 34.05           C  
+ATOM    430  OG1 THR A  61      23.795  19.777  88.879  1.00 36.43           O  
+ATOM    431  CG2 THR A  61      24.422  18.655  86.856  1.00 33.40           C  
+ATOM    432  N   ASP A  62      20.818  21.098  88.433  1.00 36.00           N  
+ATOM    433  CA  ASP A  62      19.945  21.644  89.473  1.00 35.14           C  
+ATOM    434  C   ASP A  62      18.631  22.188  88.916  1.00 34.81           C  
+ATOM    435  O   ASP A  62      18.615  23.185  88.194  1.00 34.83           O  
+ATOM    436  CB  ASP A  62      20.663  22.760  90.228  1.00 37.13           C  
+ATOM    437  CG  ASP A  62      19.817  23.336  91.339  1.00 38.64           C  
+ATOM    438  OD1 ASP A  62      19.553  22.601  92.314  1.00 40.81           O  
+ATOM    439  OD2 ASP A  62      19.407  24.512  91.235  1.00 38.60           O  
+ATOM    440  N   GLN A  63      17.527  21.546  89.275  1.00 33.87           N  
+ATOM    441  CA  GLN A  63      16.217  21.962  88.794  1.00 33.52           C  
+ATOM    442  C   GLN A  63      15.944  23.448  89.021  1.00 34.72           C  
+ATOM    443  O   GLN A  63      15.393  24.129  88.158  1.00 35.13           O  
+ATOM    444  CB  GLN A  63      15.128  21.138  89.477  1.00 32.53           C  
+ATOM    445  CG  GLN A  63      13.749  21.322  88.871  1.00 32.39           C  
+ATOM    446  CD  GLN A  63      13.678  20.827  87.437  1.00 32.46           C  
+ATOM    447  OE1 GLN A  63      13.977  19.666  87.154  1.00 31.56           O  
+ATOM    448  NE2 GLN A  63      13.279  21.707  86.526  1.00 30.21           N  
+ATOM    449  N   ALA A  64      16.329  23.955  90.187  1.00 35.86           N  
+ATOM    450  CA  ALA A  64      16.097  25.362  90.506  1.00 34.48           C  
+ATOM    451  C   ALA A  64      16.796  26.271  89.506  1.00 32.80           C  
+ATOM    452  O   ALA A  64      16.200  27.223  89.001  1.00 32.43           O  
+ATOM    453  CB  ALA A  64      16.579  25.670  91.924  1.00 35.25           C  
+ATOM    454  N   SER A  65      18.062  25.976  89.227  1.00 31.21           N  
+ATOM    455  CA  SER A  65      18.843  26.772  88.284  1.00 30.13           C  
+ATOM    456  C   SER A  65      18.215  26.692  86.894  1.00 29.47           C  
+ATOM    457  O   SER A  65      18.210  27.665  86.144  1.00 27.80           O  
+ATOM    458  CB  SER A  65      20.284  26.266  88.238  1.00 29.21           C  
+ATOM    459  OG  SER A  65      21.095  27.121  87.457  1.00 30.51           O  
+ATOM    460  N   ILE A  66      17.674  25.523  86.567  1.00 29.84           N  
+ATOM    461  CA  ILE A  66      17.037  25.306  85.277  1.00 30.26           C  
+ATOM    462  C   ILE A  66      15.785  26.169  85.134  1.00 32.24           C  
+ATOM    463  O   ILE A  66      15.634  26.890  84.147  1.00 32.91           O  
+ATOM    464  CB  ILE A  66      16.686  23.801  85.077  1.00 27.13           C  
+ATOM    465  CG1 ILE A  66      17.952  23.026  84.702  1.00 24.91           C  
+ATOM    466  CG2 ILE A  66      15.609  23.636  84.022  1.00 24.45           C  
+ATOM    467  CD1 ILE A  66      17.751  21.532  84.563  1.00 26.91           C  
+ATOM    468  N   ASP A  67      14.893  26.108  86.117  1.00 34.00           N  
+ATOM    469  CA  ASP A  67      13.664  26.895  86.059  1.00 35.40           C  
+ATOM    470  C   ASP A  67      13.937  28.400  86.059  1.00 36.75           C  
+ATOM    471  O   ASP A  67      13.202  29.176  85.442  1.00 36.01           O  
+ATOM    472  CB  ASP A  67      12.742  26.532  87.225  1.00 36.58           C  
+ATOM    473  CG  ASP A  67      12.308  25.081  87.193  1.00 38.36           C  
+ATOM    474  OD1 ASP A  67      11.931  24.610  86.103  1.00 39.81           O  
+ATOM    475  OD2 ASP A  67      12.336  24.413  88.252  1.00 38.47           O  
+ATOM    476  N   ARG A  68      14.985  28.819  86.758  1.00 38.36           N  
+ATOM    477  CA  ARG A  68      15.316  30.231  86.796  1.00 40.77           C  
+ATOM    478  C   ARG A  68      15.752  30.657  85.408  1.00 41.08           C  
+ATOM    479  O   ARG A  68      15.227  31.623  84.852  1.00 40.58           O  
+ATOM    480  CB  ARG A  68      16.445  30.508  87.788  1.00 44.09           C  
+ATOM    481  CG  ARG A  68      15.981  30.904  89.178  1.00 48.76           C  
+ATOM    482  CD  ARG A  68      17.099  31.640  89.915  1.00 53.27           C  
+ATOM    483  NE  ARG A  68      18.266  30.792  90.159  1.00 54.86           N  
+ATOM    484  CZ  ARG A  68      18.303  29.815  91.061  1.00 54.87           C  
+ATOM    485  NH1 ARG A  68      17.235  29.562  91.810  1.00 55.06           N  
+ATOM    486  NH2 ARG A  68      19.406  29.090  91.213  1.00 54.48           N  
+ATOM    487  N   CYS A  69      16.712  29.918  84.856  1.00 40.06           N  
+ATOM    488  CA  CYS A  69      17.252  30.191  83.531  1.00 39.62           C  
+ATOM    489  C   CYS A  69      16.169  30.403  82.475  1.00 38.72           C  
+ATOM    490  O   CYS A  69      16.150  31.422  81.783  1.00 37.80           O  
+ATOM    491  CB  CYS A  69      18.165  29.044  83.100  1.00 39.99           C  
+ATOM    492  SG  CYS A  69      18.689  29.125  81.368  1.00 42.49           S  
+ATOM    493  N   VAL A  70      15.265  29.438  82.361  1.00 38.16           N  
+ATOM    494  CA  VAL A  70      14.189  29.507  81.384  1.00 37.40           C  
+ATOM    495  C   VAL A  70      13.238  30.673  81.619  1.00 38.38           C  
+ATOM    496  O   VAL A  70      12.861  31.369  80.679  1.00 40.49           O  
+ATOM    497  CB  VAL A  70      13.381  28.194  81.370  1.00 36.15           C  
+ATOM    498  CG1 VAL A  70      12.103  28.367  80.558  1.00 34.94           C  
+ATOM    499  CG2 VAL A  70      14.233  27.081  80.784  1.00 34.51           C  
+ATOM    500  N   ALA A  71      12.843  30.881  82.868  1.00 38.72           N  
+ATOM    501  CA  ALA A  71      11.934  31.969  83.201  1.00 38.96           C  
+ATOM    502  C   ALA A  71      12.553  33.335  82.885  1.00 39.02           C  
+ATOM    503  O   ALA A  71      11.873  34.233  82.394  1.00 37.96           O  
+ATOM    504  CB  ALA A  71      11.554  31.891  84.680  1.00 39.38           C  
+ATOM    505  N   GLU A  72      13.844  33.483  83.160  1.00 38.71           N  
+ATOM    506  CA  GLU A  72      14.534  34.741  82.913  1.00 40.87           C  
+ATOM    507  C   GLU A  72      14.619  35.073  81.427  1.00 42.58           C  
+ATOM    508  O   GLU A  72      14.327  36.200  81.017  1.00 43.89           O  
+ATOM    509  CB  GLU A  72      15.936  34.691  83.515  1.00 41.27           C  
+ATOM    510  CG  GLU A  72      16.717  35.978  83.370  1.00 44.16           C  
+ATOM    511  CD  GLU A  72      17.913  36.020  84.299  1.00 46.54           C  
+ATOM    512  OE1 GLU A  72      18.684  37.003  84.250  1.00 46.48           O  
+ATOM    513  OE2 GLU A  72      18.076  35.063  85.086  1.00 48.50           O  
+ATOM    514  N   LEU A  73      15.021  34.094  80.622  1.00 42.36           N  
+ATOM    515  CA  LEU A  73      15.134  34.288  79.183  1.00 40.61           C  
+ATOM    516  C   LEU A  73      13.766  34.552  78.574  1.00 41.27           C  
+ATOM    517  O   LEU A  73      13.641  35.313  77.613  1.00 40.27           O  
+ATOM    518  CB  LEU A  73      15.770  33.060  78.536  1.00 40.13           C  
+ATOM    519  CG  LEU A  73      17.241  32.840  78.898  1.00 38.89           C  
+ATOM    520  CD1 LEU A  73      17.704  31.513  78.328  1.00 38.35           C  
+ATOM    521  CD2 LEU A  73      18.090  33.994  78.365  1.00 37.11           C  
+ATOM    522  N   LEU A  74      12.738  33.925  79.135  1.00 42.57           N  
+ATOM    523  CA  LEU A  74      11.384  34.124  78.639  1.00 45.20           C  
+ATOM    524  C   LEU A  74      10.957  35.578  78.780  1.00 47.81           C  
+ATOM    525  O   LEU A  74      10.206  36.089  77.953  1.00 48.42           O  
+ATOM    526  CB  LEU A  74      10.395  33.229  79.386  1.00 43.87           C  
+ATOM    527  CG  LEU A  74      10.201  31.823  78.817  1.00 44.62           C  
+ATOM    528  CD1 LEU A  74       9.162  31.074  79.643  1.00 45.12           C  
+ATOM    529  CD2 LEU A  74       9.745  31.919  77.367  1.00 44.40           C  
+ATOM    530  N   ASP A  75      11.432  36.243  79.830  1.00 50.76           N  
+ATOM    531  CA  ASP A  75      11.076  37.637  80.051  1.00 52.76           C  
+ATOM    532  C   ASP A  75      11.948  38.559  79.219  1.00 52.17           C  
+ATOM    533  O   ASP A  75      11.502  39.623  78.803  1.00 52.65           O  
+ATOM    534  CB  ASP A  75      11.193  38.005  81.535  1.00 56.34           C  
+ATOM    535  CG  ASP A  75      10.282  37.165  82.419  1.00 59.85           C  
+ATOM    536  OD1 ASP A  75       9.204  36.740  81.942  1.00 60.41           O  
+ATOM    537  OD2 ASP A  75      10.641  36.942  83.596  1.00 62.77           O  
+ATOM    538  N   ARG A  76      13.189  38.152  78.972  1.00 51.65           N  
+ATOM    539  CA  ARG A  76      14.096  38.966  78.170  1.00 50.77           C  
+ATOM    540  C   ARG A  76      13.787  38.837  76.680  1.00 48.49           C  
+ATOM    541  O   ARG A  76      13.930  39.802  75.932  1.00 48.31           O  
+ATOM    542  CB  ARG A  76      15.558  38.560  78.388  1.00 52.74           C  
+ATOM    543  CG  ARG A  76      16.071  38.633  79.814  1.00 56.53           C  
+ATOM    544  CD  ARG A  76      17.593  38.707  79.785  1.00 60.30           C  
+ATOM    545  NE  ARG A  76      18.226  38.126  80.965  1.00 64.33           N  
+ATOM    546  CZ  ARG A  76      19.544  38.051  81.138  1.00 66.39           C  
+ATOM    547  NH1 ARG A  76      20.364  38.528  80.207  1.00 66.95           N  
+ATOM    548  NH2 ARG A  76      20.046  37.489  82.233  1.00 67.54           N  
+ATOM    549  N   TRP A  77      13.367  37.649  76.250  1.00 45.41           N  
+ATOM    550  CA  TRP A  77      13.073  37.420  74.835  1.00 42.13           C  
+ATOM    551  C   TRP A  77      11.604  37.231  74.487  1.00 41.62           C  
+ATOM    552  O   TRP A  77      11.191  37.532  73.372  1.00 42.05           O  
+ATOM    553  CB  TRP A  77      13.828  36.196  74.313  1.00 40.03           C  
+ATOM    554  CG  TRP A  77      15.319  36.285  74.371  1.00 37.51           C  
+ATOM    555  CD1 TRP A  77      16.080  37.418  74.381  1.00 36.49           C  
+ATOM    556  CD2 TRP A  77      16.236  35.186  74.343  1.00 36.56           C  
+ATOM    557  NE1 TRP A  77      17.415  37.092  74.356  1.00 36.46           N  
+ATOM    558  CE2 TRP A  77      17.538  35.726  74.331  1.00 35.91           C  
+ATOM    559  CE3 TRP A  77      16.083  33.793  74.319  1.00 36.20           C  
+ATOM    560  CZ2 TRP A  77      18.682  34.926  74.301  1.00 36.10           C  
+ATOM    561  CZ3 TRP A  77      17.218  32.997  74.289  1.00 35.54           C  
+ATOM    562  CH2 TRP A  77      18.501  33.567  74.278  1.00 35.62           C  
+ATOM    563  N   GLY A  78      10.817  36.722  75.427  1.00 41.28           N  
+ATOM    564  CA  GLY A  78       9.413  36.492  75.148  1.00 39.86           C  
+ATOM    565  C   GLY A  78       9.199  35.091  74.606  1.00 39.97           C  
+ATOM    566  O   GLY A  78       8.073  34.603  74.550  1.00 40.78           O  
+ATOM    567  N   SER A  79      10.281  34.441  74.189  1.00 39.94           N  
+ATOM    568  CA  SER A  79      10.198  33.078  73.665  1.00 40.25           C  
+ATOM    569  C   SER A  79      11.570  32.517  73.303  1.00 39.63           C  
+ATOM    570  O   SER A  79      12.458  33.249  72.854  1.00 39.90           O  
+ATOM    571  CB  SER A  79       9.300  33.022  72.426  1.00 40.29           C  
+ATOM    572  OG  SER A  79       9.923  33.655  71.324  1.00 41.43           O  
+ATOM    573  N   ILE A  80      11.733  31.214  73.509  1.00 37.58           N  
+ATOM    574  CA  ILE A  80      12.976  30.529  73.189  1.00 35.51           C  
+ATOM    575  C   ILE A  80      12.668  29.699  71.951  1.00 34.68           C  
+ATOM    576  O   ILE A  80      11.840  28.787  72.008  1.00 35.20           O  
+ATOM    577  CB  ILE A  80      13.401  29.597  74.332  1.00 35.48           C  
+ATOM    578  CG1 ILE A  80      13.495  30.395  75.631  1.00 36.66           C  
+ATOM    579  CG2 ILE A  80      14.737  28.950  74.013  1.00 34.17           C  
+ATOM    580  CD1 ILE A  80      13.798  29.547  76.843  1.00 38.10           C  
+ATOM    581  N   ASP A  81      13.314  30.021  70.832  1.00 31.81           N  
+ATOM    582  CA  ASP A  81      13.066  29.295  69.590  1.00 29.02           C  
+ATOM    583  C   ASP A  81      13.932  28.060  69.419  1.00 26.87           C  
+ATOM    584  O   ASP A  81      13.478  27.046  68.891  1.00 25.72           O  
+ATOM    585  CB  ASP A  81      13.288  30.199  68.377  1.00 30.39           C  
+ATOM    586  CG  ASP A  81      12.416  31.436  68.400  1.00 32.09           C  
+ATOM    587  OD1 ASP A  81      11.213  31.313  68.725  1.00 32.38           O  
+ATOM    588  OD2 ASP A  81      12.938  32.527  68.081  1.00 32.67           O  
+ATOM    589  N   ILE A  82      15.177  28.146  69.872  1.00 24.06           N  
+ATOM    590  CA  ILE A  82      16.111  27.042  69.710  1.00 23.63           C  
+ATOM    591  C   ILE A  82      16.885  26.710  70.981  1.00 23.22           C  
+ATOM    592  O   ILE A  82      17.361  27.601  71.683  1.00 23.85           O  
+ATOM    593  CB  ILE A  82      17.145  27.369  68.607  1.00 23.10           C  
+ATOM    594  CG1 ILE A  82      16.439  27.943  67.373  1.00 24.17           C  
+ATOM    595  CG2 ILE A  82      17.930  26.127  68.255  1.00 20.12           C  
+ATOM    596  CD1 ILE A  82      17.391  28.510  66.314  1.00 21.60           C  
+ATOM    597  N   LEU A  83      17.036  25.419  71.249  1.00 22.50           N  
+ATOM    598  CA  LEU A  83      17.762  24.955  72.423  1.00 21.46           C  
+ATOM    599  C   LEU A  83      18.813  23.938  72.002  1.00 21.96           C  
+ATOM    600  O   LEU A  83      18.507  22.958  71.319  1.00 23.88           O  
+ATOM    601  CB  LEU A  83      16.781  24.334  73.430  1.00 21.20           C  
+ATOM    602  CG  LEU A  83      17.255  23.705  74.752  1.00 22.02           C  
+ATOM    603  CD1 LEU A  83      17.386  22.220  74.577  1.00 24.56           C  
+ATOM    604  CD2 LEU A  83      18.561  24.314  75.223  1.00 21.61           C  
+ATOM    605  N   VAL A  84      20.057  24.181  72.403  1.00 21.01           N  
+ATOM    606  CA  VAL A  84      21.145  23.284  72.067  1.00 20.11           C  
+ATOM    607  C   VAL A  84      21.814  22.744  73.319  1.00 20.79           C  
+ATOM    608  O   VAL A  84      22.588  23.445  73.971  1.00 22.04           O  
+ATOM    609  CB  VAL A  84      22.218  23.995  71.203  1.00 21.55           C  
+ATOM    610  CG1 VAL A  84      23.360  23.030  70.890  1.00 18.11           C  
+ATOM    611  CG2 VAL A  84      21.589  24.518  69.912  1.00 20.98           C  
+ATOM    612  N   ASN A  85      21.509  21.496  73.656  1.00 20.08           N  
+ATOM    613  CA  ASN A  85      22.106  20.862  74.819  1.00 18.51           C  
+ATOM    614  C   ASN A  85      23.548  20.468  74.495  1.00 18.52           C  
+ATOM    615  O   ASN A  85      23.817  19.350  74.057  1.00 19.21           O  
+ATOM    616  CB  ASN A  85      21.304  19.622  75.233  1.00 18.41           C  
+ATOM    617  CG  ASN A  85      19.937  19.970  75.824  1.00 18.99           C  
+ATOM    618  OD1 ASN A  85      19.813  20.879  76.644  1.00 16.61           O  
+ATOM    619  ND2 ASN A  85      18.908  19.230  75.419  1.00 18.55           N  
+ATOM    620  N   ASN A  86      24.468  21.402  74.713  1.00 18.04           N  
+ATOM    621  CA  ASN A  86      25.885  21.179  74.452  1.00 18.54           C  
+ATOM    622  C   ASN A  86      26.713  20.843  75.712  1.00 18.47           C  
+ATOM    623  O   ASN A  86      27.798  20.269  75.608  1.00 14.60           O  
+ATOM    624  CB  ASN A  86      26.474  22.420  73.771  1.00 18.83           C  
+ATOM    625  CG  ASN A  86      27.958  22.285  73.500  1.00 23.16           C  
+ATOM    626  OD1 ASN A  86      28.385  21.440  72.711  1.00 24.69           O  
+ATOM    627  ND2 ASN A  86      28.758  23.114  74.164  1.00 27.29           N  
+ATOM    628  N   ALA A  87      26.208  21.199  76.895  1.00 18.54           N  
+ATOM    629  CA  ALA A  87      26.934  20.936  78.146  1.00 18.23           C  
+ATOM    630  C   ALA A  87      27.198  19.454  78.361  1.00 17.40           C  
+ATOM    631  O   ALA A  87      26.286  18.635  78.299  1.00 18.97           O  
+ATOM    632  CB  ALA A  87      26.164  21.504  79.332  1.00 18.39           C  
+ATOM    633  N   ALA A  88      28.449  19.106  78.629  1.00 17.55           N  
+ATOM    634  CA  ALA A  88      28.793  17.712  78.827  1.00 18.66           C  
+ATOM    635  C   ALA A  88      30.147  17.528  79.504  1.00 20.46           C  
+ATOM    636  O   ALA A  88      30.954  18.452  79.575  1.00 21.40           O  
+ATOM    637  CB  ALA A  88      28.783  16.992  77.480  1.00 18.28           C  
+ATOM    638  N   LEU A  89      30.384  16.322  80.004  1.00 22.35           N  
+ATOM    639  CA  LEU A  89      31.637  15.993  80.661  1.00 22.91           C  
+ATOM    640  C   LEU A  89      32.177  14.702  80.088  1.00 21.30           C  
+ATOM    641  O   LEU A  89      31.428  13.839  79.646  1.00 19.69           O  
+ATOM    642  CB  LEU A  89      31.445  15.823  82.173  1.00 27.01           C  
+ATOM    643  CG  LEU A  89      31.564  17.045  83.089  1.00 29.37           C  
+ATOM    644  CD1 LEU A  89      31.381  16.585  84.531  1.00 30.12           C  
+ATOM    645  CD2 LEU A  89      32.931  17.704  82.926  1.00 29.29           C  
+ATOM    646  N   PHE A  90      33.491  14.578  80.114  1.00 22.22           N  
+ATOM    647  CA  PHE A  90      34.151  13.400  79.595  1.00 22.86           C  
+ATOM    648  C   PHE A  90      35.035  12.768  80.668  1.00 24.47           C  
+ATOM    649  O   PHE A  90      35.492  13.445  81.588  1.00 25.08           O  
+ATOM    650  CB  PHE A  90      34.986  13.782  78.373  1.00 19.71           C  
+ATOM    651  CG  PHE A  90      35.767  12.648  77.812  1.00 20.71           C  
+ATOM    652  CD1 PHE A  90      37.100  12.473  78.154  1.00 20.21           C  
+ATOM    653  CD2 PHE A  90      35.162  11.731  76.961  1.00 20.67           C  
+ATOM    654  CE1 PHE A  90      37.821  11.396  77.662  1.00 20.92           C  
+ATOM    655  CE2 PHE A  90      35.873  10.650  76.463  1.00 19.79           C  
+ATOM    656  CZ  PHE A  90      37.208  10.485  76.812  1.00 21.68           C  
+ATOM    657  N   ASP A  91      35.272  11.468  80.543  1.00 25.32           N  
+ATOM    658  CA  ASP A  91      36.094  10.747  81.500  1.00 25.52           C  
+ATOM    659  C   ASP A  91      36.311   9.346  80.941  1.00 26.06           C  
+ATOM    660  O   ASP A  91      35.546   8.882  80.094  1.00 25.43           O  
+ATOM    661  CB  ASP A  91      35.366  10.668  82.844  1.00 28.34           C  
+ATOM    662  CG  ASP A  91      36.315  10.550  84.033  1.00 28.51           C  
+ATOM    663  OD1 ASP A  91      35.804  10.377  85.159  1.00 32.55           O  
+ATOM    664  OD2 ASP A  91      37.551  10.635  83.857  1.00 25.53           O  
+ATOM    665  N   LEU A  92      37.354   8.671  81.406  1.00 25.99           N  
+ATOM    666  CA  LEU A  92      37.626   7.326  80.930  1.00 25.97           C  
+ATOM    667  C   LEU A  92      38.276   6.478  82.000  1.00 24.25           C  
+ATOM    668  O   LEU A  92      38.981   6.986  82.864  1.00 25.34           O  
+ATOM    669  CB  LEU A  92      38.512   7.376  79.679  1.00 28.10           C  
+ATOM    670  CG  LEU A  92      39.851   8.112  79.755  1.00 29.37           C  
+ATOM    671  CD1 LEU A  92      40.986   7.107  79.781  1.00 31.08           C  
+ATOM    672  CD2 LEU A  92      39.999   9.018  78.551  1.00 30.89           C  
+ATOM    673  N   ALA A  93      38.021   5.179  81.939  1.00 22.01           N  
+ATOM    674  CA  ALA A  93      38.583   4.244  82.895  1.00 21.68           C  
+ATOM    675  C   ALA A  93      38.022   2.870  82.587  1.00 19.84           C  
+ATOM    676  O   ALA A  93      36.883   2.756  82.135  1.00 20.46           O  
+ATOM    677  CB  ALA A  93      38.203   4.658  84.326  1.00 22.18           C  
+ATOM    678  N   PRO A  94      38.820   1.809  82.805  1.00 18.44           N  
+ATOM    679  CA  PRO A  94      38.352   0.445  82.542  1.00 18.56           C  
+ATOM    680  C   PRO A  94      37.196   0.101  83.484  1.00 19.10           C  
+ATOM    681  O   PRO A  94      36.959   0.790  84.482  1.00 17.96           O  
+ATOM    682  CB  PRO A  94      39.587  -0.414  82.829  1.00 17.65           C  
+ATOM    683  CG  PRO A  94      40.720   0.506  82.557  1.00 16.82           C  
+ATOM    684  CD  PRO A  94      40.258   1.815  83.132  1.00 17.44           C  
+ATOM    685  N   ILE A  95      36.486  -0.972  83.167  1.00 19.35           N  
+ATOM    686  CA  ILE A  95      35.367  -1.411  83.984  1.00 19.77           C  
+ATOM    687  C   ILE A  95      35.747  -1.563  85.463  1.00 19.74           C  
+ATOM    688  O   ILE A  95      35.127  -0.953  86.328  1.00 18.49           O  
+ATOM    689  CB  ILE A  95      34.809  -2.762  83.478  1.00 19.29           C  
+ATOM    690  CG1 ILE A  95      34.212  -2.590  82.077  1.00 19.44           C  
+ATOM    691  CG2 ILE A  95      33.753  -3.292  84.451  1.00 19.79           C  
+ATOM    692  CD1 ILE A  95      33.033  -1.623  82.015  1.00 17.09           C  
+ATOM    693  N   VAL A  96      36.770  -2.361  85.750  1.00 19.67           N  
+ATOM    694  CA  VAL A  96      37.171  -2.584  87.137  1.00 21.64           C  
+ATOM    695  C   VAL A  96      37.706  -1.357  87.881  1.00 22.62           C  
+ATOM    696  O   VAL A  96      38.021  -1.454  89.060  1.00 24.28           O  
+ATOM    697  CB  VAL A  96      38.231  -3.719  87.257  1.00 20.39           C  
+ATOM    698  CG1 VAL A  96      37.755  -4.962  86.525  1.00 19.41           C  
+ATOM    699  CG2 VAL A  96      39.563  -3.254  86.712  1.00 19.92           C  
+ATOM    700  N   GLU A  97      37.802  -0.210  87.212  1.00 22.01           N  
+ATOM    701  CA  GLU A  97      38.312   0.998  87.861  1.00 20.95           C  
+ATOM    702  C   GLU A  97      37.306   2.130  87.898  1.00 21.11           C  
+ATOM    703  O   GLU A  97      37.590   3.202  88.427  1.00 22.26           O  
+ATOM    704  CB  GLU A  97      39.578   1.496  87.161  1.00 21.10           C  
+ATOM    705  CG  GLU A  97      40.823   0.688  87.471  1.00 23.62           C  
+ATOM    706  CD  GLU A  97      42.031   1.163  86.693  1.00 23.81           C  
+ATOM    707  OE1 GLU A  97      42.268   2.387  86.640  1.00 26.41           O  
+ATOM    708  OE2 GLU A  97      42.750   0.312  86.139  1.00 27.00           O  
+ATOM    709  N   ILE A  98      36.132   1.903  87.330  1.00 20.73           N  
+ATOM    710  CA  ILE A  98      35.115   2.938  87.310  1.00 19.76           C  
+ATOM    711  C   ILE A  98      34.722   3.267  88.748  1.00 20.11           C  
+ATOM    712  O   ILE A  98      34.584   2.374  89.579  1.00 20.28           O  
+ATOM    713  CB  ILE A  98      33.885   2.469  86.500  1.00 18.40           C  
+ATOM    714  CG1 ILE A  98      34.294   2.236  85.045  1.00 18.46           C  
+ATOM    715  CG2 ILE A  98      32.776   3.503  86.575  1.00 17.99           C  
+ATOM    716  CD1 ILE A  98      33.172   1.715  84.173  1.00 18.69           C  
+ATOM    717  N   THR A  99      34.547   4.549  89.033  1.00 19.91           N  
+ATOM    718  CA  THR A  99      34.184   4.991  90.370  1.00 20.47           C  
+ATOM    719  C   THR A  99      32.757   5.507  90.386  1.00 21.49           C  
+ATOM    720  O   THR A  99      32.218   5.877  89.345  1.00 22.14           O  
+ATOM    721  CB  THR A  99      35.098   6.114  90.830  1.00 20.02           C  
+ATOM    722  OG1 THR A  99      34.848   7.281  90.037  1.00 21.23           O  
+ATOM    723  CG2 THR A  99      36.557   5.699  90.675  1.00 18.99           C  
+ATOM    724  N   ARG A 100      32.147   5.533  91.567  1.00 20.86           N  
+ATOM    725  CA  ARG A 100      30.775   6.008  91.693  1.00 21.25           C  
+ATOM    726  C   ARG A 100      30.714   7.495  91.425  1.00 22.04           C  
+ATOM    727  O   ARG A 100      29.669   8.028  91.049  1.00 21.32           O  
+ATOM    728  CB  ARG A 100      30.229   5.733  93.096  1.00 21.99           C  
+ATOM    729  CG  ARG A 100      30.030   4.270  93.416  1.00 21.45           C  
+ATOM    730  CD  ARG A 100      28.595   4.022  93.803  1.00 21.05           C  
+ATOM    731  NE  ARG A 100      28.301   2.599  93.840  1.00 21.89           N  
+ATOM    732  CZ  ARG A 100      27.092   2.096  93.632  1.00 21.17           C  
+ATOM    733  NH1 ARG A 100      26.901   0.786  93.683  1.00 22.28           N  
+ATOM    734  NH2 ARG A 100      26.080   2.908  93.361  1.00 19.13           N  
+ATOM    735  N   GLU A 101      31.837   8.172  91.634  1.00 22.16           N  
+ATOM    736  CA  GLU A 101      31.873   9.605  91.408  1.00 25.43           C  
+ATOM    737  C   GLU A 101      31.900   9.901  89.908  1.00 23.60           C  
+ATOM    738  O   GLU A 101      31.289  10.865  89.455  1.00 23.03           O  
+ATOM    739  CB  GLU A 101      33.089  10.227  92.102  1.00 28.13           C  
+ATOM    740  CG  GLU A 101      34.409   9.639  91.670  1.00 37.06           C  
+ATOM    741  CD  GLU A 101      35.225  10.609  90.858  1.00 41.38           C  
+ATOM    742  OE1 GLU A 101      35.562  10.294  89.700  1.00 43.62           O  
+ATOM    743  OE2 GLU A 101      35.532  11.691  91.387  1.00 47.06           O  
+ATOM    744  N   SER A 102      32.595   9.075  89.135  1.00 22.31           N  
+ATOM    745  CA  SER A 102      32.640   9.299  87.697  1.00 23.09           C  
+ATOM    746  C   SER A 102      31.236   9.078  87.138  1.00 22.44           C  
+ATOM    747  O   SER A 102      30.685   9.925  86.425  1.00 22.31           O  
+ATOM    748  CB  SER A 102      33.622   8.342  87.034  1.00 25.08           C  
+ATOM    749  OG  SER A 102      33.800   8.704  85.675  1.00 28.87           O  
+ATOM    750  N   TYR A 103      30.656   7.937  87.481  1.00 18.65           N  
+ATOM    751  CA  TYR A 103      29.314   7.609  87.044  1.00 21.34           C  
+ATOM    752  C   TYR A 103      28.317   8.715  87.418  1.00 21.94           C  
+ATOM    753  O   TYR A 103      27.665   9.296  86.552  1.00 23.56           O  
+ATOM    754  CB  TYR A 103      28.872   6.288  87.679  1.00 21.53           C  
+ATOM    755  CG  TYR A 103      27.416   5.967  87.449  1.00 23.00           C  
+ATOM    756  CD1 TYR A 103      26.987   5.416  86.243  1.00 22.62           C  
+ATOM    757  CD2 TYR A 103      26.455   6.268  88.417  1.00 22.76           C  
+ATOM    758  CE1 TYR A 103      25.640   5.177  86.002  1.00 22.98           C  
+ATOM    759  CE2 TYR A 103      25.098   6.032  88.183  1.00 23.79           C  
+ATOM    760  CZ  TYR A 103      24.702   5.488  86.970  1.00 23.99           C  
+ATOM    761  OH  TYR A 103      23.371   5.262  86.708  1.00 25.68           O  
+ATOM    762  N   ASP A 104      28.207   8.991  88.714  1.00 22.49           N  
+ATOM    763  CA  ASP A 104      27.284  10.000  89.238  1.00 23.01           C  
+ATOM    764  C   ASP A 104      27.349  11.332  88.516  1.00 22.19           C  
+ATOM    765  O   ASP A 104      26.316  11.929  88.203  1.00 21.72           O  
+ATOM    766  CB  ASP A 104      27.558  10.261  90.724  1.00 24.41           C  
+ATOM    767  CG  ASP A 104      27.167   9.095  91.619  1.00 26.69           C  
+ATOM    768  OD1 ASP A 104      27.576   9.116  92.797  1.00 29.39           O  
+ATOM    769  OD2 ASP A 104      26.455   8.171  91.169  1.00 25.80           O  
+ATOM    770  N   ARG A 105      28.566  11.802  88.275  1.00 20.95           N  
+ATOM    771  CA  ARG A 105      28.783  13.085  87.625  1.00 22.47           C  
+ATOM    772  C   ARG A 105      28.437  13.138  86.119  1.00 22.12           C  
+ATOM    773  O   ARG A 105      27.695  14.023  85.679  1.00 19.28           O  
+ATOM    774  CB  ARG A 105      30.233  13.518  87.860  1.00 25.69           C  
+ATOM    775  CG  ARG A 105      30.365  14.897  88.479  1.00 29.95           C  
+ATOM    776  CD  ARG A 105      31.812  15.233  88.813  1.00 33.99           C  
+ATOM    777  NE  ARG A 105      32.745  14.942  87.725  1.00 37.09           N  
+ATOM    778  CZ  ARG A 105      33.587  13.912  87.719  1.00 39.00           C  
+ATOM    779  NH1 ARG A 105      33.616  13.065  88.745  1.00 41.45           N  
+ATOM    780  NH2 ARG A 105      34.412  13.734  86.696  1.00 39.59           N  
+ATOM    781  N   LEU A 106      28.957  12.193  85.337  1.00 21.14           N  
+ATOM    782  CA  LEU A 106      28.688  12.186  83.905  1.00 19.92           C  
+ATOM    783  C   LEU A 106      27.204  12.029  83.595  1.00 19.76           C  
+ATOM    784  O   LEU A 106      26.673  12.740  82.735  1.00 18.73           O  
+ATOM    785  CB  LEU A 106      29.484  11.078  83.204  1.00 20.49           C  
+ATOM    786  CG  LEU A 106      31.016  11.112  83.295  1.00 19.85           C  
+ATOM    787  CD1 LEU A 106      31.598  10.429  82.066  1.00 17.67           C  
+ATOM    788  CD2 LEU A 106      31.518  12.538  83.366  1.00 19.59           C  
+ATOM    789  N   PHE A 107      26.527  11.114  84.286  1.00 17.48           N  
+ATOM    790  CA  PHE A 107      25.104  10.928  84.029  1.00 18.47           C  
+ATOM    791  C   PHE A 107      24.287  12.135  84.462  1.00 19.90           C  
+ATOM    792  O   PHE A 107      23.299  12.495  83.811  1.00 20.21           O  
+ATOM    793  CB  PHE A 107      24.575   9.664  84.712  1.00 18.99           C  
+ATOM    794  CG  PHE A 107      24.696   8.424  83.865  1.00 17.93           C  
+ATOM    795  CD1 PHE A 107      25.901   7.745  83.767  1.00 16.68           C  
+ATOM    796  CD2 PHE A 107      23.605   7.961  83.135  1.00 17.68           C  
+ATOM    797  CE1 PHE A 107      26.020   6.622  82.950  1.00 19.17           C  
+ATOM    798  CE2 PHE A 107      23.713   6.844  82.318  1.00 18.06           C  
+ATOM    799  CZ  PHE A 107      24.922   6.172  82.223  1.00 17.93           C  
+ATOM    800  N   ALA A 108      24.699  12.770  85.556  1.00 20.29           N  
+ATOM    801  CA  ALA A 108      23.997  13.949  86.050  1.00 20.07           C  
+ATOM    802  C   ALA A 108      24.004  15.079  85.011  1.00 20.51           C  
+ATOM    803  O   ALA A 108      22.982  15.712  84.752  1.00 21.81           O  
+ATOM    804  CB  ALA A 108      24.640  14.424  87.339  1.00 20.59           C  
+ATOM    805  N   ILE A 109      25.153  15.319  84.399  1.00 20.73           N  
+ATOM    806  CA  ILE A 109      25.262  16.382  83.411  1.00 22.03           C  
+ATOM    807  C   ILE A 109      24.875  16.005  81.984  1.00 20.38           C  
+ATOM    808  O   ILE A 109      24.061  16.683  81.367  1.00 21.07           O  
+ATOM    809  CB  ILE A 109      26.686  16.937  83.384  1.00 25.48           C  
+ATOM    810  CG1 ILE A 109      27.046  17.449  84.780  1.00 26.67           C  
+ATOM    811  CG2 ILE A 109      26.798  18.044  82.322  1.00 24.01           C  
+ATOM    812  CD1 ILE A 109      28.508  17.733  84.966  1.00 30.52           C  
+ATOM    813  N   ASN A 110      25.460  14.928  81.466  1.00 19.70           N  
+ATOM    814  CA  ASN A 110      25.198  14.479  80.099  1.00 18.57           C  
+ATOM    815  C   ASN A 110      23.767  14.025  79.835  1.00 18.89           C  
+ATOM    816  O   ASN A 110      23.135  14.459  78.870  1.00 20.23           O  
+ATOM    817  CB  ASN A 110      26.157  13.345  79.734  1.00 16.62           C  
+ATOM    818  CG  ASN A 110      27.614  13.775  79.784  1.00 18.15           C  
+ATOM    819  OD1 ASN A 110      27.928  14.921  80.134  1.00 16.03           O  
+ATOM    820  ND2 ASN A 110      28.515  12.855  79.435  1.00 15.67           N  
+ATOM    821  N   VAL A 111      23.266  13.142  80.692  1.00 18.51           N  
+ATOM    822  CA  VAL A 111      21.915  12.597  80.567  1.00 16.00           C  
+ATOM    823  C   VAL A 111      20.874  13.482  81.245  1.00 19.45           C  
+ATOM    824  O   VAL A 111      20.111  14.186  80.572  1.00 20.05           O  
+ATOM    825  CB  VAL A 111      21.851  11.194  81.187  1.00 12.54           C  
+ATOM    826  CG1 VAL A 111      20.482  10.578  80.969  1.00 11.01           C  
+ATOM    827  CG2 VAL A 111      22.933  10.329  80.587  1.00 14.15           C  
+ATOM    828  N   SER A 112      20.853  13.444  82.578  1.00 20.67           N  
+ATOM    829  CA  SER A 112      19.916  14.231  83.381  1.00 20.34           C  
+ATOM    830  C   SER A 112      19.820  15.688  82.933  1.00 19.69           C  
+ATOM    831  O   SER A 112      18.725  16.234  82.783  1.00 19.30           O  
+ATOM    832  CB  SER A 112      20.334  14.183  84.853  1.00 21.15           C  
+ATOM    833  OG  SER A 112      19.541  15.059  85.628  1.00 23.67           O  
+ATOM    834  N   GLY A 113      20.971  16.319  82.736  1.00 20.05           N  
+ATOM    835  CA  GLY A 113      20.981  17.705  82.301  1.00 20.56           C  
+ATOM    836  C   GLY A 113      20.255  17.912  80.983  1.00 20.79           C  
+ATOM    837  O   GLY A 113      19.447  18.832  80.845  1.00 21.68           O  
+ATOM    838  N   THR A 114      20.533  17.052  80.008  1.00 20.29           N  
+ATOM    839  CA  THR A 114      19.891  17.154  78.700  1.00 19.33           C  
+ATOM    840  C   THR A 114      18.387  16.920  78.787  1.00 19.05           C  
+ATOM    841  O   THR A 114      17.593  17.664  78.200  1.00 18.95           O  
+ATOM    842  CB  THR A 114      20.497  16.139  77.713  1.00 19.60           C  
+ATOM    843  OG1 THR A 114      21.835  16.535  77.391  1.00 19.37           O  
+ATOM    844  CG2 THR A 114      19.663  16.057  76.445  1.00 19.59           C  
+ATOM    845  N   LEU A 115      17.994  15.890  79.530  1.00 18.82           N  
+ATOM    846  CA  LEU A 115      16.582  15.569  79.677  1.00 19.61           C  
+ATOM    847  C   LEU A 115      15.744  16.683  80.292  1.00 20.46           C  
+ATOM    848  O   LEU A 115      14.806  17.181  79.665  1.00 21.53           O  
+ATOM    849  CB  LEU A 115      16.405  14.295  80.508  1.00 20.85           C  
+ATOM    850  CG  LEU A 115      14.952  13.919  80.845  1.00 22.57           C  
+ATOM    851  CD1 LEU A 115      14.116  13.802  79.573  1.00 22.28           C  
+ATOM    852  CD2 LEU A 115      14.937  12.609  81.608  1.00 23.14           C  
+ATOM    853  N   PHE A 116      16.069  17.079  81.517  1.00 20.51           N  
+ATOM    854  CA  PHE A 116      15.280  18.113  82.187  1.00 20.87           C  
+ATOM    855  C   PHE A 116      15.379  19.487  81.546  1.00 20.41           C  
+ATOM    856  O   PHE A 116      14.469  20.308  81.678  1.00 20.80           O  
+ATOM    857  CB  PHE A 116      15.629  18.143  83.682  1.00 18.66           C  
+ATOM    858  CG  PHE A 116      15.251  16.871  84.389  1.00 15.88           C  
+ATOM    859  CD1 PHE A 116      13.913  16.548  84.587  1.00 14.86           C  
+ATOM    860  CD2 PHE A 116      16.220  15.938  84.735  1.00 16.05           C  
+ATOM    861  CE1 PHE A 116      13.546  15.305  85.106  1.00 16.33           C  
+ATOM    862  CE2 PHE A 116      15.861  14.696  85.253  1.00 15.00           C  
+ATOM    863  CZ  PHE A 116      14.524  14.379  85.438  1.00 13.88           C  
+ATOM    864  N   MET A 117      16.471  19.734  80.832  1.00 21.77           N  
+ATOM    865  CA  MET A 117      16.632  21.007  80.139  1.00 22.20           C  
+ATOM    866  C   MET A 117      15.644  20.960  78.957  1.00 21.64           C  
+ATOM    867  O   MET A 117      15.004  21.955  78.626  1.00 21.47           O  
+ATOM    868  CB  MET A 117      18.073  21.152  79.655  1.00 23.05           C  
+ATOM    869  CG  MET A 117      18.524  22.578  79.398  1.00 28.50           C  
+ATOM    870  SD  MET A 117      18.551  23.661  80.862  1.00 29.23           S  
+ATOM    871  CE  MET A 117      17.487  24.948  80.296  1.00 28.57           C  
+ATOM    872  N   MET A 118      15.508  19.786  78.341  1.00 22.05           N  
+ATOM    873  CA  MET A 118      14.574  19.596  77.230  1.00 22.31           C  
+ATOM    874  C   MET A 118      13.153  19.802  77.736  1.00 23.71           C  
+ATOM    875  O   MET A 118      12.328  20.469  77.104  1.00 23.35           O  
+ATOM    876  CB  MET A 118      14.654  18.170  76.674  1.00 20.90           C  
+ATOM    877  CG  MET A 118      15.500  17.977  75.430  1.00 23.11           C  
+ATOM    878  SD  MET A 118      14.977  16.476  74.535  1.00 22.63           S  
+ATOM    879  CE  MET A 118      15.543  15.185  75.629  1.00 23.25           C  
+ATOM    880  N   GLN A 119      12.869  19.195  78.882  1.00 25.13           N  
+ATOM    881  CA  GLN A 119      11.548  19.276  79.477  1.00 25.60           C  
+ATOM    882  C   GLN A 119      11.169  20.713  79.807  1.00 25.48           C  
+ATOM    883  O   GLN A 119      10.057  21.152  79.521  1.00 25.67           O  
+ATOM    884  CB  GLN A 119      11.511  18.424  80.734  1.00 26.26           C  
+ATOM    885  CG  GLN A 119      10.141  18.293  81.353  1.00 27.78           C  
+ATOM    886  CD  GLN A 119      10.219  17.718  82.746  1.00 26.91           C  
+ATOM    887  OE1 GLN A 119      10.850  18.303  83.629  1.00 26.42           O  
+ATOM    888  NE2 GLN A 119       9.592  16.564  82.951  1.00 24.18           N  
+ATOM    889  N   ALA A 120      12.097  21.449  80.403  1.00 25.78           N  
+ATOM    890  CA  ALA A 120      11.831  22.835  80.753  1.00 27.01           C  
+ATOM    891  C   ALA A 120      11.499  23.684  79.516  1.00 28.88           C  
+ATOM    892  O   ALA A 120      10.482  24.383  79.487  1.00 29.66           O  
+ATOM    893  CB  ALA A 120      13.025  23.412  81.481  1.00 27.01           C  
+ATOM    894  N   VAL A 121      12.355  23.621  78.495  1.00 29.43           N  
+ATOM    895  CA  VAL A 121      12.145  24.390  77.263  1.00 28.82           C  
+ATOM    896  C   VAL A 121      10.920  23.912  76.471  1.00 28.60           C  
+ATOM    897  O   VAL A 121      10.148  24.719  75.956  1.00 28.22           O  
+ATOM    898  CB  VAL A 121      13.390  24.325  76.350  1.00 28.69           C  
+ATOM    899  CG1 VAL A 121      13.077  24.935  75.002  1.00 28.19           C  
+ATOM    900  CG2 VAL A 121      14.552  25.063  77.004  1.00 26.94           C  
+ATOM    901  N   ALA A 122      10.742  22.601  76.379  1.00 28.03           N  
+ATOM    902  CA  ALA A 122       9.602  22.051  75.660  1.00 28.61           C  
+ATOM    903  C   ALA A 122       8.283  22.558  76.251  1.00 29.97           C  
+ATOM    904  O   ALA A 122       7.343  22.873  75.510  1.00 28.96           O  
+ATOM    905  CB  ALA A 122       9.643  20.531  75.705  1.00 27.15           C  
+ATOM    906  N   ARG A 123       8.209  22.628  77.581  1.00 29.83           N  
+ATOM    907  CA  ARG A 123       6.992  23.097  78.240  1.00 30.06           C  
+ATOM    908  C   ARG A 123       6.700  24.532  77.846  1.00 29.11           C  
+ATOM    909  O   ARG A 123       5.543  24.904  77.656  1.00 28.37           O  
+ATOM    910  CB  ARG A 123       7.093  22.966  79.772  1.00 31.03           C  
+ATOM    911  CG  ARG A 123       6.661  21.586  80.275  1.00 33.90           C  
+ATOM    912  CD  ARG A 123       6.420  21.507  81.786  1.00 35.16           C  
+ATOM    913  NE  ARG A 123       7.652  21.407  82.567  1.00 37.11           N  
+ATOM    914  CZ  ARG A 123       7.826  20.563  83.583  1.00 37.79           C  
+ATOM    915  NH1 ARG A 123       6.849  19.738  83.941  1.00 36.14           N  
+ATOM    916  NH2 ARG A 123       8.976  20.547  84.249  1.00 38.09           N  
+ATOM    917  N   ALA A 124       7.755  25.332  77.710  1.00 28.70           N  
+ATOM    918  CA  ALA A 124       7.602  26.726  77.310  1.00 28.61           C  
+ATOM    919  C   ALA A 124       7.128  26.802  75.856  1.00 29.37           C  
+ATOM    920  O   ALA A 124       6.189  27.532  75.542  1.00 29.55           O  
+ATOM    921  CB  ALA A 124       8.922  27.466  77.466  1.00 25.88           C  
+ATOM    922  N   MET A 125       7.776  26.037  74.979  1.00 28.86           N  
+ATOM    923  CA  MET A 125       7.419  26.033  73.565  1.00 29.90           C  
+ATOM    924  C   MET A 125       5.969  25.639  73.359  1.00 30.75           C  
+ATOM    925  O   MET A 125       5.251  26.270  72.588  1.00 32.33           O  
+ATOM    926  CB  MET A 125       8.342  25.090  72.782  1.00 27.85           C  
+ATOM    927  CG  MET A 125       9.752  25.623  72.668  1.00 26.04           C  
+ATOM    928  SD  MET A 125      10.951  24.448  72.031  1.00 29.91           S  
+ATOM    929  CE  MET A 125      12.401  25.529  71.840  1.00 24.28           C  
+ATOM    930  N   ILE A 126       5.529  24.598  74.050  1.00 32.14           N  
+ATOM    931  CA  ILE A 126       4.150  24.164  73.920  1.00 33.78           C  
+ATOM    932  C   ILE A 126       3.215  25.327  74.265  1.00 35.78           C  
+ATOM    933  O   ILE A 126       2.251  25.600  73.545  1.00 36.73           O  
+ATOM    934  CB  ILE A 126       3.875  22.948  74.832  1.00 33.34           C  
+ATOM    935  CG1 ILE A 126       4.761  21.780  74.385  1.00 33.90           C  
+ATOM    936  CG2 ILE A 126       2.398  22.566  74.776  1.00 32.20           C  
+ATOM    937  CD1 ILE A 126       4.585  20.505  75.165  1.00 32.43           C  
+ATOM    938  N   ALA A 127       3.518  26.022  75.358  1.00 38.03           N  
+ATOM    939  CA  ALA A 127       2.718  27.164  75.791  1.00 38.24           C  
+ATOM    940  C   ALA A 127       2.785  28.257  74.733  1.00 38.06           C  
+ATOM    941  O   ALA A 127       1.771  28.851  74.382  1.00 38.38           O  
+ATOM    942  CB  ALA A 127       3.233  27.692  77.128  1.00 38.48           C  
+ATOM    943  N   GLY A 128       3.987  28.514  74.227  1.00 39.05           N  
+ATOM    944  CA  GLY A 128       4.162  29.525  73.198  1.00 39.65           C  
+ATOM    945  C   GLY A 128       3.233  29.306  72.013  1.00 41.06           C  
+ATOM    946  O   GLY A 128       2.808  30.260  71.366  1.00 42.05           O  
+ATOM    947  N   GLY A 129       2.922  28.047  71.720  1.00 40.32           N  
+ATOM    948  CA  GLY A 129       2.022  27.750  70.623  1.00 40.33           C  
+ATOM    949  C   GLY A 129       2.581  27.847  69.213  1.00 40.71           C  
+ATOM    950  O   GLY A 129       1.820  27.773  68.249  1.00 40.37           O  
+ATOM    951  N   ARG A 130       3.892  28.012  69.070  1.00 40.56           N  
+ATOM    952  CA  ARG A 130       4.476  28.099  67.735  1.00 39.75           C  
+ATOM    953  C   ARG A 130       5.716  27.214  67.544  1.00 37.42           C  
+ATOM    954  O   ARG A 130       6.677  27.595  66.872  1.00 35.99           O  
+ATOM    955  CB  ARG A 130       4.783  29.563  67.392  1.00 41.96           C  
+ATOM    956  CG  ARG A 130       5.719  30.268  68.350  1.00 45.95           C  
+ATOM    957  CD  ARG A 130       5.420  31.758  68.392  1.00 48.73           C  
+ATOM    958  NE  ARG A 130       6.545  32.526  68.917  1.00 53.36           N  
+ATOM    959  CZ  ARG A 130       7.662  32.772  68.236  1.00 55.86           C  
+ATOM    960  NH1 ARG A 130       7.806  32.312  66.996  1.00 56.76           N  
+ATOM    961  NH2 ARG A 130       8.637  33.481  68.791  1.00 56.58           N  
+ATOM    962  N   GLY A 131       5.665  26.025  68.142  1.00 34.51           N  
+ATOM    963  CA  GLY A 131       6.745  25.057  68.035  1.00 31.01           C  
+ATOM    964  C   GLY A 131       8.140  25.535  68.390  1.00 28.67           C  
+ATOM    965  O   GLY A 131       8.309  26.505  69.127  1.00 28.29           O  
+ATOM    966  N   GLY A 132       9.141  24.836  67.859  1.00 26.33           N  
+ATOM    967  CA  GLY A 132      10.524  25.192  68.113  1.00 23.68           C  
+ATOM    968  C   GLY A 132      11.477  24.103  67.660  1.00 22.44           C  
+ATOM    969  O   GLY A 132      11.050  23.060  67.166  1.00 21.64           O  
+ATOM    970  N   LYS A 133      12.772  24.348  67.828  1.00 21.27           N  
+ATOM    971  CA  LYS A 133      13.795  23.386  67.445  1.00 21.71           C  
+ATOM    972  C   LYS A 133      14.684  23.020  68.636  1.00 21.26           C  
+ATOM    973  O   LYS A 133      15.133  23.895  69.379  1.00 20.38           O  
+ATOM    974  CB  LYS A 133      14.693  23.964  66.343  1.00 23.68           C  
+ATOM    975  CG  LYS A 133      13.987  24.412  65.069  1.00 24.24           C  
+ATOM    976  CD  LYS A 133      13.427  23.235  64.299  1.00 24.24           C  
+ATOM    977  CE  LYS A 133      12.870  23.676  62.960  1.00 21.90           C  
+ATOM    978  NZ  LYS A 133      12.283  22.503  62.259  1.00 24.56           N  
+ATOM    979  N   ILE A 134      14.939  21.728  68.813  1.00 20.43           N  
+ATOM    980  CA  ILE A 134      15.814  21.273  69.889  1.00 20.62           C  
+ATOM    981  C   ILE A 134      16.877  20.375  69.291  1.00 20.28           C  
+ATOM    982  O   ILE A 134      16.568  19.405  68.593  1.00 20.31           O  
+ATOM    983  CB  ILE A 134      15.059  20.471  70.991  1.00 21.36           C  
+ATOM    984  CG1 ILE A 134      14.103  21.388  71.750  1.00 18.16           C  
+ATOM    985  CG2 ILE A 134      16.066  19.879  71.984  1.00 19.10           C  
+ATOM    986  CD1 ILE A 134      13.185  20.658  72.688  1.00 22.19           C  
+ATOM    987  N   ILE A 135      18.132  20.703  69.569  1.00 20.25           N  
+ATOM    988  CA  ILE A 135      19.249  19.928  69.060  1.00 19.84           C  
+ATOM    989  C   ILE A 135      20.095  19.402  70.208  1.00 19.85           C  
+ATOM    990  O   ILE A 135      20.602  20.181  71.017  1.00 20.82           O  
+ATOM    991  CB  ILE A 135      20.147  20.790  68.156  1.00 20.63           C  
+ATOM    992  CG1 ILE A 135      19.316  21.393  67.027  1.00 21.25           C  
+ATOM    993  CG2 ILE A 135      21.286  19.956  67.603  1.00 16.92           C  
+ATOM    994  CD1 ILE A 135      20.084  22.389  66.188  1.00 22.38           C  
+ATOM    995  N   ASN A 136      20.242  18.083  70.285  1.00 19.12           N  
+ATOM    996  CA  ASN A 136      21.061  17.483  71.327  1.00 19.66           C  
+ATOM    997  C   ASN A 136      22.407  17.123  70.748  1.00 19.41           C  
+ATOM    998  O   ASN A 136      22.533  16.892  69.551  1.00 22.83           O  
+ATOM    999  CB  ASN A 136      20.409  16.223  71.898  1.00 18.43           C  
+ATOM   1000  CG  ASN A 136      19.079  16.509  72.539  1.00 20.02           C  
+ATOM   1001  OD1 ASN A 136      18.873  17.594  73.095  1.00 18.24           O  
+ATOM   1002  ND2 ASN A 136      18.163  15.541  72.475  1.00 15.50           N  
+ATOM   1003  N   MET A 137      23.416  17.085  71.602  1.00 18.84           N  
+ATOM   1004  CA  MET A 137      24.750  16.741  71.167  1.00 19.71           C  
+ATOM   1005  C   MET A 137      25.118  15.339  71.639  1.00 20.72           C  
+ATOM   1006  O   MET A 137      25.384  15.108  72.824  1.00 23.43           O  
+ATOM   1007  CB  MET A 137      25.757  17.755  71.711  1.00 20.02           C  
+ATOM   1008  CG  MET A 137      25.652  19.142  71.089  1.00 23.09           C  
+ATOM   1009  SD  MET A 137      26.076  19.168  69.318  1.00 22.73           S  
+ATOM   1010  CE  MET A 137      27.855  19.057  69.408  1.00 23.85           C  
+ATOM   1011  N   ALA A 138      25.105  14.393  70.714  1.00 18.57           N  
+ATOM   1012  CA  ALA A 138      25.474  13.032  71.047  1.00 18.03           C  
+ATOM   1013  C   ALA A 138      26.960  12.943  70.742  1.00 17.33           C  
+ATOM   1014  O   ALA A 138      27.712  13.876  71.033  1.00 17.16           O  
+ATOM   1015  CB  ALA A 138      24.682  12.037  70.197  1.00 16.15           C  
+ATOM   1016  N   SER A 139      27.378  11.840  70.136  1.00 16.62           N  
+ATOM   1017  CA  SER A 139      28.785  11.635  69.806  1.00 16.28           C  
+ATOM   1018  C   SER A 139      28.960  10.227  69.278  1.00 15.83           C  
+ATOM   1019  O   SER A 139      28.139   9.352  69.548  1.00 15.25           O  
+ATOM   1020  CB  SER A 139      29.655  11.809  71.054  1.00 16.49           C  
+ATOM   1021  OG  SER A 139      30.775  10.932  71.030  1.00 17.38           O  
+ATOM   1022  N   GLN A 140      30.028  10.005  68.525  1.00 16.70           N  
+ATOM   1023  CA  GLN A 140      30.286   8.676  67.997  1.00 19.84           C  
+ATOM   1024  C   GLN A 140      30.321   7.671  69.151  1.00 19.01           C  
+ATOM   1025  O   GLN A 140      29.987   6.496  68.979  1.00 17.76           O  
+ATOM   1026  CB  GLN A 140      31.624   8.648  67.257  1.00 22.44           C  
+ATOM   1027  CG  GLN A 140      32.817   9.036  68.107  1.00 26.33           C  
+ATOM   1028  CD  GLN A 140      34.137   8.760  67.407  1.00 30.24           C  
+ATOM   1029  OE1 GLN A 140      34.353   9.203  66.277  1.00 30.88           O  
+ATOM   1030  NE2 GLN A 140      35.031   8.024  68.077  1.00 30.11           N  
+ATOM   1031  N   ALA A 141      30.729   8.145  70.327  1.00 19.37           N  
+ATOM   1032  CA  ALA A 141      30.823   7.288  71.508  1.00 18.60           C  
+ATOM   1033  C   ALA A 141      29.474   6.669  71.842  1.00 17.25           C  
+ATOM   1034  O   ALA A 141      29.411   5.561  72.367  1.00 14.43           O  
+ATOM   1035  CB  ALA A 141      31.342   8.081  72.691  1.00 17.72           C  
+ATOM   1036  N   GLY A 142      28.402   7.386  71.515  1.00 17.68           N  
+ATOM   1037  CA  GLY A 142      27.066   6.890  71.785  1.00 18.97           C  
+ATOM   1038  C   GLY A 142      26.553   5.866  70.787  1.00 20.14           C  
+ATOM   1039  O   GLY A 142      25.454   5.339  70.965  1.00 19.86           O  
+ATOM   1040  N   ARG A 143      27.340   5.583  69.748  1.00 21.05           N  
+ATOM   1041  CA  ARG A 143      26.961   4.624  68.703  1.00 20.57           C  
+ATOM   1042  C   ARG A 143      27.436   3.215  69.022  1.00 21.89           C  
+ATOM   1043  O   ARG A 143      26.758   2.242  68.706  1.00 24.11           O  
+ATOM   1044  CB  ARG A 143      27.552   5.036  67.352  1.00 19.46           C  
+ATOM   1045  CG  ARG A 143      27.044   6.359  66.796  1.00 18.05           C  
+ATOM   1046  CD  ARG A 143      25.587   6.273  66.365  1.00 16.48           C  
+ATOM   1047  NE  ARG A 143      25.222   7.405  65.519  1.00 17.15           N  
+ATOM   1048  CZ  ARG A 143      24.004   7.627  65.035  1.00 15.24           C  
+ATOM   1049  NH1 ARG A 143      23.785   8.686  64.275  1.00 15.49           N  
+ATOM   1050  NH2 ARG A 143      23.007   6.800  65.313  1.00 13.65           N  
+ATOM   1051  N   ARG A 144      28.615   3.112  69.628  1.00 22.09           N  
+ATOM   1052  CA  ARG A 144      29.182   1.819  69.997  1.00 21.38           C  
+ATOM   1053  C   ARG A 144      30.032   1.970  71.254  1.00 21.68           C  
+ATOM   1054  O   ARG A 144      30.651   3.010  71.474  1.00 20.35           O  
+ATOM   1055  CB  ARG A 144      30.045   1.252  68.855  1.00 22.18           C  
+ATOM   1056  CG  ARG A 144      31.409   1.918  68.663  1.00 21.83           C  
+ATOM   1057  CD  ARG A 144      31.289   3.345  68.152  1.00 25.39           C  
+ATOM   1058  NE  ARG A 144      32.552   4.069  68.273  1.00 30.20           N  
+ATOM   1059  CZ  ARG A 144      33.186   4.286  69.424  1.00 33.72           C  
+ATOM   1060  NH1 ARG A 144      32.680   3.838  70.571  1.00 33.69           N  
+ATOM   1061  NH2 ARG A 144      34.334   4.951  69.430  1.00 34.47           N  
+ATOM   1062  N   GLY A 145      30.060   0.929  72.078  1.00 22.26           N  
+ATOM   1063  CA  GLY A 145      30.841   0.994  73.299  1.00 22.50           C  
+ATOM   1064  C   GLY A 145      32.327   0.922  73.023  1.00 24.41           C  
+ATOM   1065  O   GLY A 145      32.736   0.555  71.919  1.00 24.30           O  
+ATOM   1066  N   GLU A 146      33.126   1.291  74.025  1.00 24.94           N  
+ATOM   1067  CA  GLU A 146      34.591   1.260  73.963  1.00 24.35           C  
+ATOM   1068  C   GLU A 146      35.117   0.706  75.282  1.00 23.71           C  
+ATOM   1069  O   GLU A 146      34.540   0.950  76.344  1.00 23.59           O  
+ATOM   1070  CB  GLU A 146      35.173   2.656  73.757  1.00 27.30           C  
+ATOM   1071  CG  GLU A 146      34.969   3.237  72.379  1.00 30.94           C  
+ATOM   1072  CD  GLU A 146      35.747   4.525  72.192  1.00 34.30           C  
+ATOM   1073  OE1 GLU A 146      36.998   4.465  72.222  1.00 34.64           O  
+ATOM   1074  OE2 GLU A 146      35.108   5.593  72.027  1.00 36.59           O  
+ATOM   1075  N   ALA A 147      36.227  -0.016  75.211  1.00 21.29           N  
+ATOM   1076  CA  ALA A 147      36.822  -0.638  76.385  1.00 20.14           C  
+ATOM   1077  C   ALA A 147      37.123   0.289  77.563  1.00 19.98           C  
+ATOM   1078  O   ALA A 147      36.817  -0.052  78.708  1.00 21.78           O  
+ATOM   1079  CB  ALA A 147      38.088  -1.385  75.981  1.00 17.96           C  
+ATOM   1080  N   LEU A 148      37.711   1.451  77.300  1.00 18.18           N  
+ATOM   1081  CA  LEU A 148      38.056   2.372  78.380  1.00 16.96           C  
+ATOM   1082  C   LEU A 148      37.144   3.586  78.514  1.00 16.48           C  
+ATOM   1083  O   LEU A 148      37.491   4.539  79.210  1.00 16.83           O  
+ATOM   1084  CB  LEU A 148      39.491   2.872  78.199  1.00 16.32           C  
+ATOM   1085  CG  LEU A 148      40.585   1.838  77.941  1.00 16.15           C  
+ATOM   1086  CD1 LEU A 148      41.905   2.557  77.783  1.00 16.30           C  
+ATOM   1087  CD2 LEU A 148      40.652   0.843  79.082  1.00 16.62           C  
+ATOM   1088  N   VAL A 149      35.987   3.572  77.862  1.00 16.80           N  
+ATOM   1089  CA  VAL A 149      35.092   4.732  77.938  1.00 16.61           C  
+ATOM   1090  C   VAL A 149      33.651   4.344  78.246  1.00 16.36           C  
+ATOM   1091  O   VAL A 149      32.705   5.004  77.799  1.00 16.06           O  
+ATOM   1092  CB  VAL A 149      35.111   5.539  76.605  1.00 17.74           C  
+ATOM   1093  CG1 VAL A 149      34.578   6.944  76.842  1.00 15.17           C  
+ATOM   1094  CG2 VAL A 149      36.530   5.585  76.034  1.00 13.64           C  
+ATOM   1095  N   GLY A 150      33.501   3.272  79.018  1.00 15.60           N  
+ATOM   1096  CA  GLY A 150      32.186   2.779  79.385  1.00 14.75           C  
+ATOM   1097  C   GLY A 150      31.181   3.808  79.859  1.00 15.37           C  
+ATOM   1098  O   GLY A 150      30.080   3.888  79.299  1.00 15.20           O  
+ATOM   1099  N   VAL A 151      31.541   4.594  80.878  1.00 14.19           N  
+ATOM   1100  CA  VAL A 151      30.620   5.595  81.422  1.00 14.53           C  
+ATOM   1101  C   VAL A 151      30.240   6.677  80.428  1.00 14.06           C  
+ATOM   1102  O   VAL A 151      29.063   6.968  80.258  1.00 17.92           O  
+ATOM   1103  CB  VAL A 151      31.190   6.277  82.698  1.00 16.19           C  
+ATOM   1104  CG1 VAL A 151      30.226   7.348  83.200  1.00 14.78           C  
+ATOM   1105  CG2 VAL A 151      31.413   5.243  83.789  1.00 15.99           C  
+ATOM   1106  N   TYR A 152      31.222   7.284  79.772  1.00 15.98           N  
+ATOM   1107  CA  TYR A 152      30.922   8.330  78.791  1.00 17.81           C  
+ATOM   1108  C   TYR A 152      30.028   7.791  77.657  1.00 16.55           C  
+ATOM   1109  O   TYR A 152      29.004   8.392  77.327  1.00 13.34           O  
+ATOM   1110  CB  TYR A 152      32.214   8.902  78.199  1.00 18.53           C  
+ATOM   1111  CG  TYR A 152      31.976   9.985  77.166  1.00 21.15           C  
+ATOM   1112  CD1 TYR A 152      31.471  11.230  77.541  1.00 20.27           C  
+ATOM   1113  CD2 TYR A 152      32.245   9.761  75.808  1.00 19.65           C  
+ATOM   1114  CE1 TYR A 152      31.242  12.228  76.596  1.00 21.19           C  
+ATOM   1115  CE2 TYR A 152      32.014  10.754  74.853  1.00 17.35           C  
+ATOM   1116  CZ  TYR A 152      31.516  11.981  75.255  1.00 21.77           C  
+ATOM   1117  OH  TYR A 152      31.297  12.976  74.329  1.00 22.64           O  
+ATOM   1118  N   CYS A 153      30.424   6.652  77.085  1.00 15.84           N  
+ATOM   1119  CA  CYS A 153      29.675   6.020  76.002  1.00 16.54           C  
+ATOM   1120  C   CYS A 153      28.224   5.802  76.370  1.00 16.71           C  
+ATOM   1121  O   CYS A 153      27.327   6.112  75.584  1.00 18.01           O  
+ATOM   1122  CB  CYS A 153      30.294   4.672  75.633  1.00 15.99           C  
+ATOM   1123  SG  CYS A 153      31.808   4.781  74.650  1.00 17.20           S  
+ATOM   1124  N   ALA A 154      27.996   5.276  77.571  1.00 17.44           N  
+ATOM   1125  CA  ALA A 154      26.642   5.000  78.047  1.00 15.73           C  
+ATOM   1126  C   ALA A 154      25.799   6.255  78.160  1.00 14.77           C  
+ATOM   1127  O   ALA A 154      24.591   6.199  77.962  1.00 15.79           O  
+ATOM   1128  CB  ALA A 154      26.687   4.276  79.388  1.00 16.69           C  
+ATOM   1129  N   THR A 155      26.415   7.390  78.480  1.00 14.37           N  
+ATOM   1130  CA  THR A 155      25.637   8.621  78.587  1.00 14.85           C  
+ATOM   1131  C   THR A 155      25.218   9.078  77.198  1.00 15.17           C  
+ATOM   1132  O   THR A 155      24.095   9.551  76.988  1.00 15.78           O  
+ATOM   1133  CB  THR A 155      26.434   9.765  79.241  1.00 15.92           C  
+ATOM   1134  OG1 THR A 155      27.517  10.144  78.379  1.00 12.15           O  
+ATOM   1135  CG2 THR A 155      26.975   9.332  80.611  1.00 13.53           C  
+ATOM   1136  N   LYS A 156      26.121   8.940  76.238  1.00 16.19           N  
+ATOM   1137  CA  LYS A 156      25.801   9.357  74.887  1.00 17.27           C  
+ATOM   1138  C   LYS A 156      24.752   8.453  74.256  1.00 16.60           C  
+ATOM   1139  O   LYS A 156      23.866   8.930  73.543  1.00 15.42           O  
+ATOM   1140  CB  LYS A 156      27.072   9.436  74.053  1.00 18.41           C  
+ATOM   1141  CG  LYS A 156      27.961  10.605  74.490  1.00 19.98           C  
+ATOM   1142  CD  LYS A 156      27.158  11.905  74.555  1.00 19.81           C  
+ATOM   1143  CE  LYS A 156      28.058  13.092  74.852  1.00 25.05           C  
+ATOM   1144  NZ  LYS A 156      27.297  14.376  74.954  1.00 26.40           N  
+ATOM   1145  N   ALA A 157      24.820   7.157  74.544  1.00 15.12           N  
+ATOM   1146  CA  ALA A 157      23.817   6.246  74.008  1.00 16.09           C  
+ATOM   1147  C   ALA A 157      22.451   6.686  74.542  1.00 16.14           C  
+ATOM   1148  O   ALA A 157      21.448   6.656  73.826  1.00 17.97           O  
+ATOM   1149  CB  ALA A 157      24.116   4.814  74.431  1.00 14.14           C  
+ATOM   1150  N   ALA A 158      22.420   7.106  75.803  1.00 15.79           N  
+ATOM   1151  CA  ALA A 158      21.180   7.561  76.425  1.00 14.27           C  
+ATOM   1152  C   ALA A 158      20.654   8.829  75.751  1.00 12.98           C  
+ATOM   1153  O   ALA A 158      19.443   9.011  75.598  1.00 11.65           O  
+ATOM   1154  CB  ALA A 158      21.404   7.816  77.906  1.00 13.63           C  
+ATOM   1155  N   VAL A 159      21.562   9.713  75.357  1.00 14.09           N  
+ATOM   1156  CA  VAL A 159      21.161  10.950  74.701  1.00 15.94           C  
+ATOM   1157  C   VAL A 159      20.473  10.648  73.377  1.00 16.91           C  
+ATOM   1158  O   VAL A 159      19.471  11.284  73.021  1.00 18.62           O  
+ATOM   1159  CB  VAL A 159      22.373  11.848  74.418  1.00 19.36           C  
+ATOM   1160  CG1 VAL A 159      21.985  12.959  73.430  1.00 17.95           C  
+ATOM   1161  CG2 VAL A 159      22.886  12.434  75.720  1.00 16.29           C  
+ATOM   1162  N   ILE A 160      21.019   9.678  72.650  1.00 15.23           N  
+ATOM   1163  CA  ILE A 160      20.455   9.282  71.372  1.00 15.18           C  
+ATOM   1164  C   ILE A 160      19.058   8.728  71.612  1.00 16.04           C  
+ATOM   1165  O   ILE A 160      18.108   9.050  70.883  1.00 16.42           O  
+ATOM   1166  CB  ILE A 160      21.359   8.227  70.675  1.00 14.97           C  
+ATOM   1167  CG1 ILE A 160      22.633   8.914  70.163  1.00 11.63           C  
+ATOM   1168  CG2 ILE A 160      20.609   7.539  69.539  1.00 13.25           C  
+ATOM   1169  CD1 ILE A 160      23.622   7.982  69.527  1.00  9.69           C  
+ATOM   1170  N   SER A 161      18.929   7.912  72.654  1.00 16.35           N  
+ATOM   1171  CA  SER A 161      17.634   7.322  72.994  1.00 16.15           C  
+ATOM   1172  C   SER A 161      16.607   8.401  73.340  1.00 15.16           C  
+ATOM   1173  O   SER A 161      15.473   8.377  72.850  1.00 16.17           O  
+ATOM   1174  CB  SER A 161      17.786   6.352  74.168  1.00 15.04           C  
+ATOM   1175  OG  SER A 161      16.537   5.776  74.501  1.00 16.19           O  
+ATOM   1176  N   LEU A 162      17.006   9.351  74.179  1.00 14.13           N  
+ATOM   1177  CA  LEU A 162      16.112  10.432  74.578  1.00 15.33           C  
+ATOM   1178  C   LEU A 162      15.708  11.329  73.402  1.00 16.38           C  
+ATOM   1179  O   LEU A 162      14.595  11.868  73.374  1.00 16.59           O  
+ATOM   1180  CB  LEU A 162      16.773  11.274  75.669  1.00 16.85           C  
+ATOM   1181  CG  LEU A 162      16.979  10.572  77.017  1.00 17.26           C  
+ATOM   1182  CD1 LEU A 162      17.834  11.443  77.909  1.00 16.81           C  
+ATOM   1183  CD2 LEU A 162      15.637  10.292  77.660  1.00 13.61           C  
+ATOM   1184  N   THR A 163      16.614  11.501  72.441  1.00 16.75           N  
+ATOM   1185  CA  THR A 163      16.327  12.323  71.264  1.00 17.10           C  
+ATOM   1186  C   THR A 163      15.199  11.668  70.456  1.00 16.30           C  
+ATOM   1187  O   THR A 163      14.300  12.345  69.943  1.00 17.26           O  
+ATOM   1188  CB  THR A 163      17.581  12.479  70.367  1.00 19.11           C  
+ATOM   1189  OG1 THR A 163      18.609  13.174  71.085  1.00 19.02           O  
+ATOM   1190  CG2 THR A 163      17.247  13.262  69.116  1.00 20.19           C  
+ATOM   1191  N   GLN A 164      15.232  10.345  70.360  1.00 15.12           N  
+ATOM   1192  CA  GLN A 164      14.196   9.631  69.626  1.00 15.44           C  
+ATOM   1193  C   GLN A 164      12.866   9.703  70.365  1.00 15.95           C  
+ATOM   1194  O   GLN A 164      11.827  10.002  69.768  1.00 16.78           O  
+ATOM   1195  CB  GLN A 164      14.594   8.171  69.436  1.00 14.78           C  
+ATOM   1196  CG  GLN A 164      15.960   8.006  68.828  1.00 15.84           C  
+ATOM   1197  CD  GLN A 164      16.342   6.556  68.675  1.00 19.19           C  
+ATOM   1198  OE1 GLN A 164      15.880   5.699  69.433  1.00 20.32           O  
+ATOM   1199  NE2 GLN A 164      17.206   6.270  67.709  1.00 16.87           N  
+ATOM   1200  N   SER A 165      12.894   9.435  71.669  1.00 16.16           N  
+ATOM   1201  CA  SER A 165      11.671   9.476  72.461  1.00 14.84           C  
+ATOM   1202  C   SER A 165      11.068  10.873  72.475  1.00 12.80           C  
+ATOM   1203  O   SER A 165       9.867  11.041  72.257  1.00 13.05           O  
+ATOM   1204  CB  SER A 165      11.942   9.012  73.894  1.00 15.53           C  
+ATOM   1205  OG  SER A 165      12.432   7.684  73.900  1.00 15.44           O  
+ATOM   1206  N   ALA A 166      11.894  11.879  72.726  1.00 11.66           N  
+ATOM   1207  CA  ALA A 166      11.383  13.244  72.752  1.00 13.41           C  
+ATOM   1208  C   ALA A 166      10.881  13.601  71.361  1.00 16.14           C  
+ATOM   1209  O   ALA A 166       9.799  14.167  71.215  1.00 18.02           O  
+ATOM   1210  CB  ALA A 166      12.480  14.221  73.188  1.00 11.62           C  
+ATOM   1211  N   GLY A 167      11.668  13.245  70.345  1.00 17.23           N  
+ATOM   1212  CA  GLY A 167      11.309  13.538  68.971  1.00 18.65           C  
+ATOM   1213  C   GLY A 167       9.927  13.067  68.568  1.00 19.67           C  
+ATOM   1214  O   GLY A 167       9.132  13.843  68.040  1.00 20.49           O  
+ATOM   1215  N   LEU A 168       9.634  11.795  68.810  1.00 19.99           N  
+ATOM   1216  CA  LEU A 168       8.331  11.240  68.463  1.00 21.31           C  
+ATOM   1217  C   LEU A 168       7.215  11.866  69.294  1.00 23.15           C  
+ATOM   1218  O   LEU A 168       6.094  12.054  68.812  1.00 24.54           O  
+ATOM   1219  CB  LEU A 168       8.319   9.726  68.692  1.00 19.65           C  
+ATOM   1220  CG  LEU A 168       9.337   8.869  67.934  1.00 23.11           C  
+ATOM   1221  CD1 LEU A 168       9.266   7.438  68.448  1.00 21.84           C  
+ATOM   1222  CD2 LEU A 168       9.063   8.915  66.433  1.00 22.24           C  
+ATOM   1223  N   ASN A 169       7.531  12.194  70.545  1.00 24.02           N  
+ATOM   1224  CA  ASN A 169       6.549  12.754  71.466  1.00 23.10           C  
+ATOM   1225  C   ASN A 169       6.266  14.231  71.281  1.00 22.53           C  
+ATOM   1226  O   ASN A 169       5.136  14.669  71.454  1.00 22.07           O  
+ATOM   1227  CB  ASN A 169       6.990  12.496  72.916  1.00 23.60           C  
+ATOM   1228  CG  ASN A 169       5.961  12.959  73.936  1.00 22.75           C  
+ATOM   1229  OD1 ASN A 169       4.781  12.639  73.833  1.00 22.50           O  
+ATOM   1230  ND2 ASN A 169       6.411  13.706  74.929  1.00 22.50           N  
+ATOM   1231  N   LEU A 170       7.280  14.998  70.907  1.00 22.86           N  
+ATOM   1232  CA  LEU A 170       7.094  16.434  70.758  1.00 23.51           C  
+ATOM   1233  C   LEU A 170       6.769  16.972  69.368  1.00 24.90           C  
+ATOM   1234  O   LEU A 170       6.344  18.122  69.241  1.00 23.81           O  
+ATOM   1235  CB  LEU A 170       8.324  17.165  71.301  1.00 23.37           C  
+ATOM   1236  CG  LEU A 170       8.609  16.983  72.796  1.00 22.33           C  
+ATOM   1237  CD1 LEU A 170       9.751  17.884  73.208  1.00 19.90           C  
+ATOM   1238  CD2 LEU A 170       7.364  17.320  73.603  1.00 22.34           C  
+ATOM   1239  N   ILE A 171       6.960  16.158  68.330  1.00 25.65           N  
+ATOM   1240  CA  ILE A 171       6.692  16.617  66.973  1.00 25.81           C  
+ATOM   1241  C   ILE A 171       5.238  17.038  66.758  1.00 27.43           C  
+ATOM   1242  O   ILE A 171       4.957  17.870  65.900  1.00 27.46           O  
+ATOM   1243  CB  ILE A 171       7.073  15.547  65.919  1.00 24.70           C  
+ATOM   1244  CG1 ILE A 171       6.946  16.142  64.514  1.00 22.26           C  
+ATOM   1245  CG2 ILE A 171       6.178  14.328  66.049  1.00 23.61           C  
+ATOM   1246  CD1 ILE A 171       7.824  17.352  64.287  1.00 18.76           C  
+ATOM   1247  N   ARG A 172       4.323  16.475  67.545  1.00 29.18           N  
+ATOM   1248  CA  ARG A 172       2.900  16.801  67.435  1.00 30.92           C  
+ATOM   1249  C   ARG A 172       2.662  18.266  67.803  1.00 29.99           C  
+ATOM   1250  O   ARG A 172       1.680  18.861  67.384  1.00 29.53           O  
+ATOM   1251  CB  ARG A 172       2.061  15.911  68.367  1.00 35.19           C  
+ATOM   1252  CG  ARG A 172       2.675  14.538  68.698  1.00 43.55           C  
+ATOM   1253  CD  ARG A 172       2.946  13.704  67.444  1.00 50.59           C  
+ATOM   1254  NE  ARG A 172       3.530  12.391  67.732  1.00 55.89           N  
+ATOM   1255  CZ  ARG A 172       2.868  11.368  68.269  1.00 59.21           C  
+ATOM   1256  NH1 ARG A 172       1.583  11.496  68.587  1.00 60.66           N  
+ATOM   1257  NH2 ARG A 172       3.488  10.209  68.477  1.00 59.15           N  
+ATOM   1258  N   HIS A 173       3.559  18.843  68.597  1.00 30.06           N  
+ATOM   1259  CA  HIS A 173       3.425  20.237  69.011  1.00 29.38           C  
+ATOM   1260  C   HIS A 173       4.262  21.152  68.143  1.00 28.54           C  
+ATOM   1261  O   HIS A 173       4.419  22.333  68.450  1.00 29.83           O  
+ATOM   1262  CB  HIS A 173       3.852  20.425  70.473  1.00 30.23           C  
+ATOM   1263  CG  HIS A 173       2.985  19.703  71.452  1.00 31.94           C  
+ATOM   1264  ND1 HIS A 173       3.316  18.468  71.971  1.00 33.73           N  
+ATOM   1265  CD2 HIS A 173       1.775  20.017  71.973  1.00 31.84           C  
+ATOM   1266  CE1 HIS A 173       2.348  18.053  72.766  1.00 34.56           C  
+ATOM   1267  NE2 HIS A 173       1.400  18.975  72.785  1.00 34.51           N  
+ATOM   1268  N   GLY A 174       4.811  20.600  67.067  1.00 27.07           N  
+ATOM   1269  CA  GLY A 174       5.625  21.396  66.167  1.00 24.63           C  
+ATOM   1270  C   GLY A 174       7.044  21.592  66.647  1.00 23.40           C  
+ATOM   1271  O   GLY A 174       7.710  22.553  66.264  1.00 24.50           O  
+ATOM   1272  N   ILE A 175       7.515  20.681  67.491  1.00 22.24           N  
+ATOM   1273  CA  ILE A 175       8.871  20.766  68.012  1.00 20.63           C  
+ATOM   1274  C   ILE A 175       9.708  19.642  67.419  1.00 21.17           C  
+ATOM   1275  O   ILE A 175       9.385  18.465  67.598  1.00 20.43           O  
+ATOM   1276  CB  ILE A 175       8.905  20.619  69.547  1.00 20.05           C  
+ATOM   1277  CG1 ILE A 175       8.014  21.676  70.199  1.00 21.88           C  
+ATOM   1278  CG2 ILE A 175      10.333  20.755  70.046  1.00 16.31           C  
+ATOM   1279  CD1 ILE A 175       7.888  21.532  71.712  1.00 20.44           C  
+ATOM   1280  N   ASN A 176      10.771  20.010  66.706  1.00 20.73           N  
+ATOM   1281  CA  ASN A 176      11.665  19.029  66.100  1.00 20.36           C  
+ATOM   1282  C   ASN A 176      12.803  18.757  67.060  1.00 18.91           C  
+ATOM   1283  O   ASN A 176      13.425  19.695  67.568  1.00 17.94           O  
+ATOM   1284  CB  ASN A 176      12.287  19.545  64.791  1.00 20.67           C  
+ATOM   1285  CG  ASN A 176      11.263  19.820  63.714  1.00 23.34           C  
+ATOM   1286  OD1 ASN A 176      10.635  20.881  63.692  1.00 25.32           O  
+ATOM   1287  ND2 ASN A 176      11.084  18.859  62.812  1.00 20.98           N  
+ATOM   1288  N   VAL A 177      13.076  17.481  67.301  1.00 15.54           N  
+ATOM   1289  CA  VAL A 177      14.179  17.110  68.168  1.00 16.40           C  
+ATOM   1290  C   VAL A 177      15.119  16.164  67.409  1.00 15.61           C  
+ATOM   1291  O   VAL A 177      14.715  15.089  66.975  1.00 15.59           O  
+ATOM   1292  CB  VAL A 177      13.684  16.407  69.470  1.00 18.18           C  
+ATOM   1293  CG1 VAL A 177      14.871  16.167  70.412  1.00 15.32           C  
+ATOM   1294  CG2 VAL A 177      12.617  17.256  70.161  1.00 15.53           C  
+ATOM   1295  N   ASN A 178      16.367  16.577  67.241  1.00 14.59           N  
+ATOM   1296  CA  ASN A 178      17.356  15.764  66.547  1.00 16.00           C  
+ATOM   1297  C   ASN A 178      18.671  15.956  67.290  1.00 17.44           C  
+ATOM   1298  O   ASN A 178      18.761  16.804  68.175  1.00 18.35           O  
+ATOM   1299  CB  ASN A 178      17.524  16.229  65.092  1.00 14.42           C  
+ATOM   1300  CG  ASN A 178      16.262  16.057  64.268  1.00 13.37           C  
+ATOM   1301  OD1 ASN A 178      15.859  14.939  63.950  1.00 11.38           O  
+ATOM   1302  ND2 ASN A 178      15.628  17.169  63.924  1.00 11.38           N  
+ATOM   1303  N   ALA A 179      19.688  15.186  66.925  1.00 16.81           N  
+ATOM   1304  CA  ALA A 179      20.989  15.304  67.572  1.00 17.70           C  
+ATOM   1305  C   ALA A 179      22.123  15.270  66.553  1.00 18.08           C  
+ATOM   1306  O   ALA A 179      21.953  14.787  65.435  1.00 18.21           O  
+ATOM   1307  CB  ALA A 179      21.173  14.179  68.583  1.00 16.58           C  
+ATOM   1308  N   ILE A 180      23.276  15.795  66.948  1.00 18.15           N  
+ATOM   1309  CA  ILE A 180      24.461  15.798  66.094  1.00 18.35           C  
+ATOM   1310  C   ILE A 180      25.481  14.913  66.804  1.00 18.11           C  
+ATOM   1311  O   ILE A 180      25.656  15.030  68.012  1.00 20.45           O  
+ATOM   1312  CB  ILE A 180      25.058  17.219  65.955  1.00 18.29           C  
+ATOM   1313  CG1 ILE A 180      24.052  18.151  65.279  1.00 16.41           C  
+ATOM   1314  CG2 ILE A 180      26.357  17.168  65.177  1.00 15.58           C  
+ATOM   1315  CD1 ILE A 180      24.489  19.593  65.282  1.00 16.74           C  
+ATOM   1316  N   ALA A 181      26.143  14.025  66.072  1.00 17.12           N  
+ATOM   1317  CA  ALA A 181      27.132  13.147  66.683  1.00 17.03           C  
+ATOM   1318  C   ALA A 181      28.529  13.392  66.124  1.00 18.92           C  
+ATOM   1319  O   ALA A 181      28.909  12.838  65.093  1.00 18.45           O  
+ATOM   1320  CB  ALA A 181      26.740  11.693  66.487  1.00 15.64           C  
+ATOM   1321  N   PRO A 182      29.311  14.249  66.799  1.00 19.68           N  
+ATOM   1322  CA  PRO A 182      30.670  14.542  66.338  1.00 19.64           C  
+ATOM   1323  C   PRO A 182      31.542  13.292  66.450  1.00 22.18           C  
+ATOM   1324  O   PRO A 182      31.157  12.306  67.080  1.00 22.23           O  
+ATOM   1325  CB  PRO A 182      31.132  15.638  67.299  1.00 17.46           C  
+ATOM   1326  CG  PRO A 182      29.844  16.304  67.729  1.00 17.22           C  
+ATOM   1327  CD  PRO A 182      28.925  15.130  67.919  1.00 17.83           C  
+ATOM   1328  N   GLY A 183      32.712  13.332  65.831  1.00 24.56           N  
+ATOM   1329  CA  GLY A 183      33.623  12.212  65.920  1.00 29.35           C  
+ATOM   1330  C   GLY A 183      34.672  12.638  66.923  1.00 33.20           C  
+ATOM   1331  O   GLY A 183      34.347  12.963  68.069  1.00 34.83           O  
+ATOM   1332  N   VAL A 184      35.929  12.651  66.503  1.00 35.67           N  
+ATOM   1333  CA  VAL A 184      37.002  13.089  67.382  1.00 40.16           C  
+ATOM   1334  C   VAL A 184      37.278  14.560  67.066  1.00 42.25           C  
+ATOM   1335  O   VAL A 184      37.712  14.896  65.969  1.00 42.64           O  
+ATOM   1336  CB  VAL A 184      38.275  12.242  67.168  1.00 40.51           C  
+ATOM   1337  CG1 VAL A 184      38.078  10.861  67.770  1.00 39.63           C  
+ATOM   1338  CG2 VAL A 184      38.572  12.108  65.677  1.00 42.18           C  
+ATOM   1339  N   VAL A 185      36.990  15.440  68.017  1.00 45.34           N  
+ATOM   1340  CA  VAL A 185      37.209  16.866  67.814  1.00 49.56           C  
+ATOM   1341  C   VAL A 185      38.413  17.329  68.610  1.00 53.11           C  
+ATOM   1342  O   VAL A 185      38.526  17.042  69.803  1.00 53.93           O  
+ATOM   1343  CB  VAL A 185      35.991  17.699  68.258  1.00 49.58           C  
+ATOM   1344  CG1 VAL A 185      36.274  19.185  68.049  1.00 48.44           C  
+ATOM   1345  CG2 VAL A 185      34.763  17.274  67.475  1.00 49.21           C  
+ATOM   1346  N   ASP A 186      39.313  18.050  67.950  1.00 56.68           N  
+ATOM   1347  CA  ASP A 186      40.503  18.541  68.622  1.00 60.24           C  
+ATOM   1348  C   ASP A 186      40.135  19.607  69.646  1.00 62.23           C  
+ATOM   1349  O   ASP A 186      39.107  20.279  69.539  1.00 62.03           O  
+ATOM   1350  CB  ASP A 186      41.504  19.109  67.612  1.00 61.15           C  
+ATOM   1351  CG  ASP A 186      42.919  19.189  68.171  1.00 63.02           C  
+ATOM   1352  OD1 ASP A 186      43.123  18.821  69.348  1.00 64.60           O  
+ATOM   1353  OD2 ASP A 186      43.833  19.618  67.432  1.00 63.98           O  
+ATOM   1354  N   GLY A 187      41.003  19.740  70.638  1.00 65.34           N  
+ATOM   1355  CA  GLY A 187      40.821  20.690  71.715  1.00 68.73           C  
+ATOM   1356  C   GLY A 187      41.956  20.428  72.685  1.00 70.64           C  
+ATOM   1357  O   GLY A 187      42.683  19.439  72.548  1.00 71.06           O  
+ATOM   1358  N   GLU A 188      42.121  21.299  73.668  1.00 72.17           N  
+ATOM   1359  CA  GLU A 188      43.197  21.121  74.630  1.00 73.53           C  
+ATOM   1360  C   GLU A 188      43.054  19.842  75.458  1.00 73.25           C  
+ATOM   1361  O   GLU A 188      44.049  19.200  75.784  1.00 74.21           O  
+ATOM   1362  CB  GLU A 188      43.271  22.342  75.543  1.00 74.81           C  
+ATOM   1363  CG  GLU A 188      41.928  22.763  76.092  1.00 76.65           C  
+ATOM   1364  CD  GLU A 188      41.994  24.089  76.813  1.00 78.01           C  
+ATOM   1365  OE1 GLU A 188      43.107  24.642  76.944  1.00 79.12           O  
+ATOM   1366  OE2 GLU A 188      40.932  24.580  77.251  1.00 79.03           O  
+ATOM   1367  N   HIS A 189      41.821  19.466  75.785  1.00 71.89           N  
+ATOM   1368  CA  HIS A 189      41.573  18.263  76.580  1.00 70.38           C  
+ATOM   1369  C   HIS A 189      42.370  17.050  76.095  1.00 69.41           C  
+ATOM   1370  O   HIS A 189      42.613  16.111  76.857  1.00 69.33           O  
+ATOM   1371  CB  HIS A 189      40.085  17.922  76.557  1.00 70.47           C  
+ATOM   1372  CG  HIS A 189      39.545  17.702  75.178  1.00 71.14           C  
+ATOM   1373  ND1 HIS A 189      39.521  18.695  74.224  1.00 70.60           N  
+ATOM   1374  CD2 HIS A 189      39.030  16.598  74.587  1.00 71.47           C  
+ATOM   1375  CE1 HIS A 189      39.016  18.214  73.103  1.00 70.66           C  
+ATOM   1376  NE2 HIS A 189      38.710  16.942  73.296  1.00 71.08           N  
+ATOM   1377  N   TRP A 190      42.779  17.073  74.830  1.00 67.92           N  
+ATOM   1378  CA  TRP A 190      43.533  15.962  74.262  1.00 66.94           C  
+ATOM   1379  C   TRP A 190      44.908  15.743  74.875  1.00 67.66           C  
+ATOM   1380  O   TRP A 190      45.518  14.692  74.680  1.00 68.15           O  
+ATOM   1381  CB  TRP A 190      43.659  16.118  72.742  1.00 64.11           C  
+ATOM   1382  CG  TRP A 190      42.594  15.354  72.011  1.00 60.92           C  
+ATOM   1383  CD1 TRP A 190      41.423  15.844  71.506  1.00 59.84           C  
+ATOM   1384  CD2 TRP A 190      42.559  13.939  71.804  1.00 58.82           C  
+ATOM   1385  NE1 TRP A 190      40.659  14.819  71.002  1.00 58.65           N  
+ATOM   1386  CE2 TRP A 190      41.332  13.638  71.174  1.00 58.69           C  
+ATOM   1387  CE3 TRP A 190      43.444  12.893  72.096  1.00 58.51           C  
+ATOM   1388  CZ2 TRP A 190      40.968  12.334  70.828  1.00 58.32           C  
+ATOM   1389  CZ3 TRP A 190      43.081  11.596  71.753  1.00 58.65           C  
+ATOM   1390  CH2 TRP A 190      41.853  11.329  71.126  1.00 58.40           C  
+ATOM   1391  N   ASP A 191      45.395  16.728  75.620  1.00 68.65           N  
+ATOM   1392  CA  ASP A 191      46.702  16.612  76.258  1.00 69.33           C  
+ATOM   1393  C   ASP A 191      46.625  15.519  77.322  1.00 68.31           C  
+ATOM   1394  O   ASP A 191      47.409  14.566  77.316  1.00 68.22           O  
+ATOM   1395  CB  ASP A 191      47.091  17.933  76.934  1.00 71.80           C  
+ATOM   1396  CG  ASP A 191      46.715  19.154  76.108  1.00 73.75           C  
+ATOM   1397  OD1 ASP A 191      46.139  20.104  76.687  1.00 74.00           O  
+ATOM   1398  OD2 ASP A 191      46.997  19.172  74.890  1.00 74.44           O  
+ATOM   1399  N   GLY A 192      45.665  15.674  78.231  1.00 66.70           N  
+ATOM   1400  CA  GLY A 192      45.484  14.717  79.309  1.00 64.71           C  
+ATOM   1401  C   GLY A 192      44.892  13.401  78.852  1.00 63.30           C  
+ATOM   1402  O   GLY A 192      45.316  12.335  79.301  1.00 62.40           O  
+ATOM   1403  N   VAL A 193      43.905  13.477  77.963  1.00 62.43           N  
+ATOM   1404  CA  VAL A 193      43.255  12.283  77.439  1.00 60.31           C  
+ATOM   1405  C   VAL A 193      44.321  11.369  76.855  1.00 59.50           C  
+ATOM   1406  O   VAL A 193      44.338  10.164  77.114  1.00 58.71           O  
+ATOM   1407  CB  VAL A 193      42.238  12.639  76.335  1.00 59.25           C  
+ATOM   1408  CG1 VAL A 193      41.577  11.375  75.802  1.00 58.69           C  
+ATOM   1409  CG2 VAL A 193      41.197  13.594  76.886  1.00 58.50           C  
+ATOM   1410  N   ASP A 194      45.215  11.962  76.072  1.00 59.03           N  
+ATOM   1411  CA  ASP A 194      46.304  11.229  75.441  1.00 58.59           C  
+ATOM   1412  C   ASP A 194      47.185  10.585  76.515  1.00 57.85           C  
+ATOM   1413  O   ASP A 194      47.600   9.427  76.391  1.00 57.67           O  
+ATOM   1414  CB  ASP A 194      47.133  12.182  74.578  1.00 58.32           C  
+ATOM   1415  CG  ASP A 194      48.300  11.494  73.915  1.00 58.85           C  
+ATOM   1416  OD1 ASP A 194      48.063  10.640  73.033  1.00 58.08           O  
+ATOM   1417  OD2 ASP A 194      49.452  11.804  74.287  1.00 58.45           O  
+ATOM   1418  N   ALA A 195      47.464  11.347  77.569  1.00 56.42           N  
+ATOM   1419  CA  ALA A 195      48.283  10.861  78.674  1.00 55.64           C  
+ATOM   1420  C   ALA A 195      47.628   9.632  79.285  1.00 54.70           C  
+ATOM   1421  O   ALA A 195      48.298   8.649  79.614  1.00 53.94           O  
+ATOM   1422  CB  ALA A 195      48.429  11.947  79.728  1.00 55.46           C  
+ATOM   1423  N   LYS A 196      46.311   9.707  79.437  1.00 54.16           N  
+ATOM   1424  CA  LYS A 196      45.529   8.617  79.998  1.00 53.98           C  
+ATOM   1425  C   LYS A 196      45.733   7.338  79.193  1.00 53.52           C  
+ATOM   1426  O   LYS A 196      46.170   6.320  79.736  1.00 53.23           O  
+ATOM   1427  CB  LYS A 196      44.047   8.993  80.005  1.00 54.35           C  
+ATOM   1428  CG  LYS A 196      43.696  10.096  80.979  1.00 56.27           C  
+ATOM   1429  CD  LYS A 196      43.783   9.592  82.407  1.00 58.25           C  
+ATOM   1430  CE  LYS A 196      43.293  10.636  83.400  1.00 59.44           C  
+ATOM   1431  NZ  LYS A 196      43.173  10.073  84.778  1.00 60.85           N  
+ATOM   1432  N   PHE A 197      45.417   7.394  77.900  1.00 52.11           N  
+ATOM   1433  CA  PHE A 197      45.566   6.233  77.029  1.00 51.19           C  
+ATOM   1434  C   PHE A 197      47.010   5.746  76.998  1.00 51.30           C  
+ATOM   1435  O   PHE A 197      47.270   4.541  77.045  1.00 50.40           O  
+ATOM   1436  CB  PHE A 197      45.109   6.556  75.600  1.00 49.19           C  
+ATOM   1437  CG  PHE A 197      43.616   6.671  75.443  1.00 46.86           C  
+ATOM   1438  CD1 PHE A 197      42.996   7.915  75.417  1.00 45.15           C  
+ATOM   1439  CD2 PHE A 197      42.831   5.530  75.310  1.00 46.08           C  
+ATOM   1440  CE1 PHE A 197      41.618   8.020  75.256  1.00 44.34           C  
+ATOM   1441  CE2 PHE A 197      41.455   5.626  75.149  1.00 44.65           C  
+ATOM   1442  CZ  PHE A 197      40.847   6.873  75.121  1.00 43.84           C  
+ATOM   1443  N   ALA A 198      47.948   6.683  76.914  1.00 52.00           N  
+ATOM   1444  CA  ALA A 198      49.363   6.330  76.881  1.00 53.89           C  
+ATOM   1445  C   ALA A 198      49.704   5.450  78.084  1.00 54.91           C  
+ATOM   1446  O   ALA A 198      50.444   4.468  77.970  1.00 53.95           O  
+ATOM   1447  CB  ALA A 198      50.216   7.595  76.895  1.00 51.77           C  
+ATOM   1448  N   ASP A 199      49.138   5.806  79.231  1.00 56.75           N  
+ATOM   1449  CA  ASP A 199      49.374   5.082  80.469  1.00 58.72           C  
+ATOM   1450  C   ASP A 199      48.558   3.789  80.559  1.00 58.47           C  
+ATOM   1451  O   ASP A 199      49.040   2.780  81.076  1.00 58.04           O  
+ATOM   1452  CB  ASP A 199      49.055   5.992  81.659  1.00 61.40           C  
+ATOM   1453  CG  ASP A 199      49.597   5.452  82.966  1.00 64.83           C  
+ATOM   1454  OD1 ASP A 199      50.822   5.204  83.045  1.00 66.81           O  
+ATOM   1455  OD2 ASP A 199      48.803   5.278  83.916  1.00 66.48           O  
+ATOM   1456  N   TYR A 200      47.327   3.826  80.054  1.00 57.94           N  
+ATOM   1457  CA  TYR A 200      46.440   2.663  80.075  1.00 57.30           C  
+ATOM   1458  C   TYR A 200      46.791   1.606  79.027  1.00 58.08           C  
+ATOM   1459  O   TYR A 200      46.448   0.433  79.192  1.00 58.00           O  
+ATOM   1460  CB  TYR A 200      44.986   3.088  79.837  1.00 54.81           C  
+ATOM   1461  CG  TYR A 200      44.243   3.630  81.041  1.00 54.29           C  
+ATOM   1462  CD1 TYR A 200      43.683   4.909  81.018  1.00 53.72           C  
+ATOM   1463  CD2 TYR A 200      44.057   2.851  82.184  1.00 54.57           C  
+ATOM   1464  CE1 TYR A 200      42.952   5.400  82.100  1.00 53.10           C  
+ATOM   1465  CE2 TYR A 200      43.325   3.334  83.278  1.00 53.99           C  
+ATOM   1466  CZ  TYR A 200      42.777   4.609  83.225  1.00 53.47           C  
+ATOM   1467  OH  TYR A 200      42.052   5.094  84.288  1.00 52.20           O  
+ATOM   1468  N   GLU A 201      47.471   2.010  77.956  1.00 58.77           N  
+ATOM   1469  CA  GLU A 201      47.796   1.072  76.885  1.00 60.18           C  
+ATOM   1470  C   GLU A 201      49.277   0.900  76.553  1.00 60.32           C  
+ATOM   1471  O   GLU A 201      49.615   0.309  75.526  1.00 59.03           O  
+ATOM   1472  CB  GLU A 201      47.040   1.470  75.613  1.00 61.22           C  
+ATOM   1473  CG  GLU A 201      45.736   2.205  75.889  1.00 63.44           C  
+ATOM   1474  CD  GLU A 201      44.867   2.370  74.656  1.00 64.50           C  
+ATOM   1475  OE1 GLU A 201      44.289   1.362  74.196  1.00 64.36           O  
+ATOM   1476  OE2 GLU A 201      44.763   3.507  74.148  1.00 64.74           O  
+ATOM   1477  N   ASN A 202      50.158   1.404  77.410  1.00 60.96           N  
+ATOM   1478  CA  ASN A 202      51.591   1.270  77.168  1.00 61.64           C  
+ATOM   1479  C   ASN A 202      51.925   1.851  75.792  1.00 61.22           C  
+ATOM   1480  O   ASN A 202      52.417   1.154  74.904  1.00 60.33           O  
+ATOM   1481  CB  ASN A 202      51.986  -0.214  77.244  1.00 62.95           C  
+ATOM   1482  CG  ASN A 202      53.487  -0.435  77.135  1.00 64.07           C  
+ATOM   1483  OD1 ASN A 202      54.276   0.209  77.830  1.00 64.55           O  
+ATOM   1484  ND2 ASN A 202      53.887  -1.363  76.268  1.00 64.74           N  
+ATOM   1485  N   LEU A 203      51.639   3.138  75.626  1.00 60.87           N  
+ATOM   1486  CA  LEU A 203      51.895   3.835  74.373  1.00 60.56           C  
+ATOM   1487  C   LEU A 203      52.716   5.089  74.643  1.00 60.41           C  
+ATOM   1488  O   LEU A 203      52.573   5.717  75.691  1.00 60.44           O  
+ATOM   1489  CB  LEU A 203      50.574   4.238  73.709  1.00 60.79           C  
+ATOM   1490  CG  LEU A 203      49.587   3.146  73.281  1.00 61.14           C  
+ATOM   1491  CD1 LEU A 203      48.275   3.787  72.850  1.00 60.55           C  
+ATOM   1492  CD2 LEU A 203      50.182   2.319  72.147  1.00 60.88           C  
+ATOM   1493  N   PRO A 204      53.594   5.467  73.701  1.00 60.19           N  
+ATOM   1494  CA  PRO A 204      54.427   6.664  73.866  1.00 60.30           C  
+ATOM   1495  C   PRO A 204      53.537   7.894  74.018  1.00 60.41           C  
+ATOM   1496  O   PRO A 204      52.481   7.977  73.395  1.00 60.34           O  
+ATOM   1497  CB  PRO A 204      55.237   6.703  72.570  1.00 60.07           C  
+ATOM   1498  CG  PRO A 204      55.349   5.254  72.197  1.00 60.33           C  
+ATOM   1499  CD  PRO A 204      53.954   4.742  72.470  1.00 60.03           C  
+ATOM   1500  N   ARG A 205      53.956   8.843  74.843  1.00 60.69           N  
+ATOM   1501  CA  ARG A 205      53.171  10.052  75.047  1.00 62.34           C  
+ATOM   1502  C   ARG A 205      52.963  10.758  73.706  1.00 61.75           C  
+ATOM   1503  O   ARG A 205      53.929  11.175  73.066  1.00 62.25           O  
+ATOM   1504  CB  ARG A 205      53.895  10.993  76.007  1.00 65.20           C  
+ATOM   1505  CG  ARG A 205      54.473  10.317  77.238  1.00 71.21           C  
+ATOM   1506  CD  ARG A 205      55.347  11.294  78.010  1.00 75.99           C  
+ATOM   1507  NE  ARG A 205      56.194  10.634  79.002  1.00 80.68           N  
+ATOM   1508  CZ  ARG A 205      57.146  11.250  79.701  1.00 82.80           C  
+ATOM   1509  NH1 ARG A 205      57.375  12.547  79.520  1.00 83.42           N  
+ATOM   1510  NH2 ARG A 205      57.876  10.569  80.578  1.00 83.44           N  
+ATOM   1511  N   GLY A 206      51.709  10.885  73.280  1.00 60.65           N  
+ATOM   1512  CA  GLY A 206      51.414  11.553  72.021  1.00 58.74           C  
+ATOM   1513  C   GLY A 206      51.039  10.648  70.858  1.00 57.72           C  
+ATOM   1514  O   GLY A 206      50.530  11.116  69.840  1.00 57.45           O  
+ATOM   1515  N   GLU A 207      51.288   9.353  71.005  1.00 56.61           N  
+ATOM   1516  CA  GLU A 207      50.983   8.390  69.957  1.00 56.75           C  
+ATOM   1517  C   GLU A 207      49.481   8.210  69.758  1.00 56.35           C  
+ATOM   1518  O   GLU A 207      49.008   8.095  68.630  1.00 56.37           O  
+ATOM   1519  CB  GLU A 207      51.619   7.035  70.289  1.00 58.24           C  
+ATOM   1520  CG  GLU A 207      51.245   5.907  69.328  1.00 61.56           C  
+ATOM   1521  CD  GLU A 207      51.943   6.005  67.978  1.00 63.92           C  
+ATOM   1522  OE1 GLU A 207      52.271   7.134  67.547  1.00 64.56           O  
+ATOM   1523  OE2 GLU A 207      52.148   4.946  67.340  1.00 64.66           O  
+ATOM   1524  N   LYS A 208      48.736   8.184  70.858  1.00 55.81           N  
+ATOM   1525  CA  LYS A 208      47.291   7.994  70.803  1.00 54.47           C  
+ATOM   1526  C   LYS A 208      46.591   9.054  69.968  1.00 54.10           C  
+ATOM   1527  O   LYS A 208      45.808   8.731  69.076  1.00 54.24           O  
+ATOM   1528  CB  LYS A 208      46.695   7.998  72.215  1.00 53.61           C  
+ATOM   1529  CG  LYS A 208      45.220   7.622  72.257  1.00 51.11           C  
+ATOM   1530  CD  LYS A 208      45.027   6.180  71.831  1.00 49.58           C  
+ATOM   1531  CE  LYS A 208      43.572   5.785  71.839  1.00 46.85           C  
+ATOM   1532  NZ  LYS A 208      43.441   4.340  71.534  1.00 46.61           N  
+ATOM   1533  N   LYS A 209      46.868  10.319  70.265  1.00 53.65           N  
+ATOM   1534  CA  LYS A 209      46.248  11.420  69.535  1.00 53.32           C  
+ATOM   1535  C   LYS A 209      46.620  11.367  68.062  1.00 54.50           C  
+ATOM   1536  O   LYS A 209      45.845  11.783  67.202  1.00 54.77           O  
+ATOM   1537  CB  LYS A 209      46.683  12.763  70.116  1.00 51.21           C  
+ATOM   1538  CG  LYS A 209      46.033  13.946  69.436  1.00 48.73           C  
+ATOM   1539  CD  LYS A 209      46.562  15.259  69.976  1.00 48.11           C  
+ATOM   1540  CE  LYS A 209      45.841  16.435  69.349  1.00 46.46           C  
+ATOM   1541  NZ  LYS A 209      46.410  17.738  69.771  1.00 47.55           N  
+ATOM   1542  N   ARG A 210      47.813  10.858  67.777  1.00 55.70           N  
+ATOM   1543  CA  ARG A 210      48.287  10.749  66.406  1.00 56.99           C  
+ATOM   1544  C   ARG A 210      47.528   9.641  65.680  1.00 56.95           C  
+ATOM   1545  O   ARG A 210      47.042   9.840  64.564  1.00 56.48           O  
+ATOM   1546  CB  ARG A 210      49.784  10.440  66.385  1.00 58.95           C  
+ATOM   1547  CG  ARG A 210      50.405  10.512  65.001  1.00 61.02           C  
+ATOM   1548  CD  ARG A 210      51.718   9.749  64.944  1.00 63.75           C  
+ATOM   1549  NE  ARG A 210      51.524   8.322  65.202  1.00 65.84           N  
+ATOM   1550  CZ  ARG A 210      50.788   7.512  64.442  1.00 66.16           C  
+ATOM   1551  NH1 ARG A 210      50.170   7.983  63.366  1.00 66.15           N  
+ATOM   1552  NH2 ARG A 210      50.667   6.228  64.759  1.00 65.33           N  
+ATOM   1553  N   GLN A 211      47.438   8.476  66.319  1.00 56.05           N  
+ATOM   1554  CA  GLN A 211      46.735   7.331  65.748  1.00 55.34           C  
+ATOM   1555  C   GLN A 211      45.298   7.708  65.427  1.00 53.74           C  
+ATOM   1556  O   GLN A 211      44.826   7.499  64.309  1.00 53.99           O  
+ATOM   1557  CB  GLN A 211      46.732   6.146  66.727  1.00 57.24           C  
+ATOM   1558  CG  GLN A 211      48.058   5.403  66.842  1.00 60.85           C  
+ATOM   1559  CD  GLN A 211      47.982   4.210  67.784  1.00 62.89           C  
+ATOM   1560  OE1 GLN A 211      47.139   3.324  67.620  1.00 63.24           O  
+ATOM   1561  NE2 GLN A 211      48.868   4.182  68.773  1.00 63.72           N  
+ATOM   1562  N   VAL A 212      44.615   8.273  66.419  1.00 51.56           N  
+ATOM   1563  CA  VAL A 212      43.216   8.679  66.295  1.00 48.04           C  
+ATOM   1564  C   VAL A 212      42.937   9.604  65.116  1.00 45.48           C  
+ATOM   1565  O   VAL A 212      42.021   9.362  64.334  1.00 43.48           O  
+ATOM   1566  CB  VAL A 212      42.735   9.375  67.585  1.00 46.87           C  
+ATOM   1567  CG1 VAL A 212      41.301   9.839  67.425  1.00 47.50           C  
+ATOM   1568  CG2 VAL A 212      42.853   8.419  68.756  1.00 45.84           C  
+ATOM   1569  N   GLY A 213      43.728  10.664  65.000  1.00 44.03           N  
+ATOM   1570  CA  GLY A 213      43.542  11.616  63.919  1.00 43.19           C  
+ATOM   1571  C   GLY A 213      43.835  11.061  62.538  1.00 42.50           C  
+ATOM   1572  O   GLY A 213      43.246  11.501  61.552  1.00 42.61           O  
+ATOM   1573  N   ALA A 214      44.744  10.093  62.468  1.00 41.63           N  
+ATOM   1574  CA  ALA A 214      45.119   9.474  61.203  1.00 39.58           C  
+ATOM   1575  C   ALA A 214      44.128   8.385  60.793  1.00 38.85           C  
+ATOM   1576  O   ALA A 214      44.039   8.032  59.619  1.00 39.86           O  
+ATOM   1577  CB  ALA A 214      46.525   8.886  61.313  1.00 39.82           C  
+ATOM   1578  N   ALA A 215      43.381   7.856  61.757  1.00 36.60           N  
+ATOM   1579  CA  ALA A 215      42.414   6.801  61.472  1.00 33.99           C  
+ATOM   1580  C   ALA A 215      41.119   7.352  60.886  1.00 32.84           C  
+ATOM   1581  O   ALA A 215      40.317   6.603  60.317  1.00 32.52           O  
+ATOM   1582  CB  ALA A 215      42.118   6.010  62.738  1.00 33.98           C  
+ATOM   1583  N   VAL A 216      40.911   8.658  61.033  1.00 31.30           N  
+ATOM   1584  CA  VAL A 216      39.713   9.302  60.498  1.00 30.33           C  
+ATOM   1585  C   VAL A 216      39.781   9.256  58.980  1.00 29.51           C  
+ATOM   1586  O   VAL A 216      40.721   9.778  58.388  1.00 29.59           O  
+ATOM   1587  CB  VAL A 216      39.629  10.780  60.920  1.00 30.17           C  
+ATOM   1588  CG1 VAL A 216      38.431  11.439  60.253  1.00 28.16           C  
+ATOM   1589  CG2 VAL A 216      39.532  10.885  62.433  1.00 29.30           C  
+ATOM   1590  N   PRO A 217      38.790   8.624  58.331  1.00 28.53           N  
+ATOM   1591  CA  PRO A 217      38.765   8.523  56.867  1.00 27.89           C  
+ATOM   1592  C   PRO A 217      39.094   9.848  56.183  1.00 26.79           C  
+ATOM   1593  O   PRO A 217      39.957   9.895  55.316  1.00 25.32           O  
+ATOM   1594  CB  PRO A 217      37.342   8.054  56.582  1.00 28.59           C  
+ATOM   1595  CG  PRO A 217      37.060   7.170  57.762  1.00 28.21           C  
+ATOM   1596  CD  PRO A 217      37.598   7.987  58.920  1.00 28.45           C  
+ATOM   1597  N   PHE A 218      38.410  10.916  56.589  1.00 26.23           N  
+ATOM   1598  CA  PHE A 218      38.634  12.243  56.020  1.00 26.96           C  
+ATOM   1599  C   PHE A 218      40.113  12.639  56.061  1.00 28.62           C  
+ATOM   1600  O   PHE A 218      40.557  13.473  55.273  1.00 29.39           O  
+ATOM   1601  CB  PHE A 218      37.813  13.294  56.771  1.00 25.34           C  
+ATOM   1602  CG  PHE A 218      37.843  14.663  56.135  1.00 26.10           C  
+ATOM   1603  CD1 PHE A 218      36.899  15.020  55.175  1.00 26.93           C  
+ATOM   1604  CD2 PHE A 218      38.807  15.600  56.501  1.00 26.10           C  
+ATOM   1605  CE1 PHE A 218      36.912  16.287  54.594  1.00 24.35           C  
+ATOM   1606  CE2 PHE A 218      38.828  16.870  55.925  1.00 25.01           C  
+ATOM   1607  CZ  PHE A 218      37.879  17.213  54.972  1.00 24.55           C  
+ATOM   1608  N   GLY A 219      40.870  12.068  56.992  1.00 29.98           N  
+ATOM   1609  CA  GLY A 219      42.286  12.383  57.062  1.00 31.28           C  
+ATOM   1610  C   GLY A 219      42.759  13.360  58.125  1.00 32.62           C  
+ATOM   1611  O   GLY A 219      43.926  13.766  58.115  1.00 32.48           O  
+ATOM   1612  N   ARG A 220      41.872  13.752  59.034  1.00 32.75           N  
+ATOM   1613  CA  ARG A 220      42.264  14.667  60.099  1.00 32.67           C  
+ATOM   1614  C   ARG A 220      41.242  14.715  61.222  1.00 33.39           C  
+ATOM   1615  O   ARG A 220      40.089  14.311  61.058  1.00 33.04           O  
+ATOM   1616  CB  ARG A 220      42.488  16.080  59.549  1.00 32.06           C  
+ATOM   1617  CG  ARG A 220      41.264  16.982  59.553  1.00 31.62           C  
+ATOM   1618  CD  ARG A 220      41.560  18.295  58.836  1.00 31.43           C  
+ATOM   1619  NE  ARG A 220      40.436  19.233  58.714  1.00 32.68           N  
+ATOM   1620  CZ  ARG A 220      39.176  18.996  59.067  1.00 34.77           C  
+ATOM   1621  NH1 ARG A 220      38.819  17.833  59.589  1.00 40.13           N  
+ATOM   1622  NH2 ARG A 220      38.260  19.936  58.887  1.00 33.56           N  
+ATOM   1623  N   MET A 221      41.685  15.210  62.369  1.00 34.46           N  
+ATOM   1624  CA  MET A 221      40.823  15.330  63.526  1.00 36.12           C  
+ATOM   1625  C   MET A 221      39.796  16.421  63.233  1.00 35.62           C  
+ATOM   1626  O   MET A 221      40.037  17.306  62.409  1.00 35.49           O  
+ATOM   1627  CB  MET A 221      41.665  15.687  64.752  1.00 39.51           C  
+ATOM   1628  CG  MET A 221      40.999  15.396  66.074  1.00 41.17           C  
+ATOM   1629  SD  MET A 221      42.254  15.072  67.311  1.00 48.07           S  
+ATOM   1630  CE  MET A 221      42.587  13.344  67.007  1.00 44.94           C  
+ATOM   1631  N   GLY A 222      38.651  16.349  63.903  1.00 35.13           N  
+ATOM   1632  CA  GLY A 222      37.597  17.323  63.689  1.00 34.04           C  
+ATOM   1633  C   GLY A 222      37.910  18.728  64.160  1.00 34.46           C  
+ATOM   1634  O   GLY A 222      38.894  18.968  64.856  1.00 32.50           O  
+ATOM   1635  N   ARG A 223      37.043  19.660  63.779  1.00 35.55           N  
+ATOM   1636  CA  ARG A 223      37.194  21.064  64.128  1.00 37.27           C  
+ATOM   1637  C   ARG A 223      35.792  21.624  64.353  1.00 37.14           C  
+ATOM   1638  O   ARG A 223      34.829  21.146  63.758  1.00 37.79           O  
+ATOM   1639  CB  ARG A 223      37.882  21.789  62.973  1.00 40.76           C  
+ATOM   1640  CG  ARG A 223      38.869  22.866  63.374  1.00 46.38           C  
+ATOM   1641  CD  ARG A 223      40.052  22.861  62.420  1.00 48.38           C  
+ATOM   1642  NE  ARG A 223      39.629  22.531  61.062  1.00 51.61           N  
+ATOM   1643  CZ  ARG A 223      40.445  22.473  60.012  1.00 52.89           C  
+ATOM   1644  NH1 ARG A 223      41.738  22.727  60.162  1.00 54.40           N  
+ATOM   1645  NH2 ARG A 223      39.969  22.155  58.813  1.00 52.64           N  
+ATOM   1646  N   ALA A 224      35.666  22.629  65.208  1.00 36.60           N  
+ATOM   1647  CA  ALA A 224      34.352  23.200  65.480  1.00 36.54           C  
+ATOM   1648  C   ALA A 224      33.659  23.649  64.195  1.00 36.01           C  
+ATOM   1649  O   ALA A 224      32.459  23.456  64.030  1.00 35.98           O  
+ATOM   1650  CB  ALA A 224      34.479  24.371  66.450  1.00 36.19           C  
+ATOM   1651  N   GLU A 225      34.427  24.239  63.285  1.00 36.54           N  
+ATOM   1652  CA  GLU A 225      33.897  24.725  62.015  1.00 36.13           C  
+ATOM   1653  C   GLU A 225      33.254  23.635  61.161  1.00 33.95           C  
+ATOM   1654  O   GLU A 225      32.456  23.929  60.276  1.00 33.83           O  
+ATOM   1655  CB  GLU A 225      35.006  25.414  61.213  1.00 38.60           C  
+ATOM   1656  CG  GLU A 225      35.567  26.663  61.881  1.00 43.71           C  
+ATOM   1657  CD  GLU A 225      36.398  26.357  63.118  1.00 46.36           C  
+ATOM   1658  OE1 GLU A 225      36.616  27.290  63.919  1.00 49.37           O  
+ATOM   1659  OE2 GLU A 225      36.842  25.199  63.285  1.00 46.89           O  
+ATOM   1660  N   ASP A 226      33.600  22.380  61.418  1.00 30.48           N  
+ATOM   1661  CA  ASP A 226      33.019  21.290  60.651  1.00 28.59           C  
+ATOM   1662  C   ASP A 226      31.594  21.013  61.090  1.00 27.55           C  
+ATOM   1663  O   ASP A 226      30.814  20.431  60.341  1.00 26.90           O  
+ATOM   1664  CB  ASP A 226      33.837  20.012  60.819  1.00 27.46           C  
+ATOM   1665  CG  ASP A 226      35.259  20.175  60.355  1.00 29.29           C  
+ATOM   1666  OD1 ASP A 226      35.484  20.992  59.431  1.00 33.27           O  
+ATOM   1667  OD2 ASP A 226      36.149  19.482  60.894  1.00 26.89           O  
+ATOM   1668  N   LEU A 227      31.260  21.451  62.301  1.00 26.95           N  
+ATOM   1669  CA  LEU A 227      29.941  21.213  62.888  1.00 25.55           C  
+ATOM   1670  C   LEU A 227      28.897  22.318  62.761  1.00 24.79           C  
+ATOM   1671  O   LEU A 227      27.705  22.033  62.713  1.00 25.55           O  
+ATOM   1672  CB  LEU A 227      30.111  20.860  64.373  1.00 24.60           C  
+ATOM   1673  CG  LEU A 227      30.508  19.435  64.795  1.00 25.02           C  
+ATOM   1674  CD1 LEU A 227      31.388  18.770  63.767  1.00 22.80           C  
+ATOM   1675  CD2 LEU A 227      31.224  19.509  66.133  1.00 25.24           C  
+ATOM   1676  N   THR A 228      29.334  23.571  62.708  1.00 25.33           N  
+ATOM   1677  CA  THR A 228      28.405  24.699  62.631  1.00 26.26           C  
+ATOM   1678  C   THR A 228      27.376  24.663  61.496  1.00 25.76           C  
+ATOM   1679  O   THR A 228      26.234  25.099  61.683  1.00 27.50           O  
+ATOM   1680  CB  THR A 228      29.172  26.033  62.583  1.00 27.39           C  
+ATOM   1681  OG1 THR A 228      30.023  26.063  61.432  1.00 29.26           O  
+ATOM   1682  CG2 THR A 228      30.029  26.186  63.838  1.00 27.87           C  
+ATOM   1683  N   GLY A 229      27.762  24.143  60.332  1.00 23.67           N  
+ATOM   1684  CA  GLY A 229      26.829  24.065  59.218  1.00 20.40           C  
+ATOM   1685  C   GLY A 229      25.595  23.251  59.573  1.00 19.34           C  
+ATOM   1686  O   GLY A 229      24.463  23.688  59.356  1.00 18.85           O  
+ATOM   1687  N   MET A 230      25.812  22.059  60.120  1.00 19.43           N  
+ATOM   1688  CA  MET A 230      24.717  21.176  60.517  1.00 20.56           C  
+ATOM   1689  C   MET A 230      23.919  21.779  61.690  1.00 20.54           C  
+ATOM   1690  O   MET A 230      22.688  21.683  61.736  1.00 19.43           O  
+ATOM   1691  CB  MET A 230      25.279  19.802  60.898  1.00 21.95           C  
+ATOM   1692  CG  MET A 230      24.234  18.778  61.285  1.00 22.84           C  
+ATOM   1693  SD  MET A 230      23.037  18.482  59.979  1.00 25.30           S  
+ATOM   1694  CE  MET A 230      23.893  17.232  59.046  1.00 23.83           C  
+ATOM   1695  N   ALA A 231      24.622  22.409  62.628  1.00 19.80           N  
+ATOM   1696  CA  ALA A 231      23.976  23.043  63.774  1.00 19.79           C  
+ATOM   1697  C   ALA A 231      22.955  24.077  63.285  1.00 20.62           C  
+ATOM   1698  O   ALA A 231      21.874  24.224  63.863  1.00 20.55           O  
+ATOM   1699  CB  ALA A 231      25.024  23.716  64.657  1.00 18.85           C  
+ATOM   1700  N   ILE A 232      23.308  24.790  62.218  1.00 21.65           N  
+ATOM   1701  CA  ILE A 232      22.429  25.804  61.622  1.00 22.41           C  
+ATOM   1702  C   ILE A 232      21.302  25.157  60.798  1.00 22.34           C  
+ATOM   1703  O   ILE A 232      20.125  25.508  60.938  1.00 22.23           O  
+ATOM   1704  CB  ILE A 232      23.233  26.760  60.690  1.00 22.14           C  
+ATOM   1705  CG1 ILE A 232      24.255  27.553  61.510  1.00 21.71           C  
+ATOM   1706  CG2 ILE A 232      22.293  27.711  59.970  1.00 20.73           C  
+ATOM   1707  CD1 ILE A 232      25.247  28.342  60.672  1.00 21.14           C  
+ATOM   1708  N   PHE A 233      21.669  24.206  59.942  1.00 21.98           N  
+ATOM   1709  CA  PHE A 233      20.696  23.536  59.094  1.00 20.26           C  
+ATOM   1710  C   PHE A 233      19.520  22.942  59.863  1.00 20.62           C  
+ATOM   1711  O   PHE A 233      18.363  23.154  59.495  1.00 21.09           O  
+ATOM   1712  CB  PHE A 233      21.366  22.430  58.284  1.00 19.22           C  
+ATOM   1713  CG  PHE A 233      20.426  21.720  57.347  1.00 19.57           C  
+ATOM   1714  CD1 PHE A 233      19.952  22.355  56.203  1.00 20.24           C  
+ATOM   1715  CD2 PHE A 233      19.993  20.430  57.622  1.00 19.07           C  
+ATOM   1716  CE1 PHE A 233      19.057  21.715  55.347  1.00 20.20           C  
+ATOM   1717  CE2 PHE A 233      19.097  19.779  56.773  1.00 20.60           C  
+ATOM   1718  CZ  PHE A 233      18.628  20.424  55.632  1.00 20.62           C  
+ATOM   1719  N   LEU A 234      19.813  22.191  60.921  1.00 19.98           N  
+ATOM   1720  CA  LEU A 234      18.761  21.559  61.715  1.00 20.60           C  
+ATOM   1721  C   LEU A 234      17.793  22.544  62.361  1.00 21.64           C  
+ATOM   1722  O   LEU A 234      16.700  22.160  62.771  1.00 21.11           O  
+ATOM   1723  CB  LEU A 234      19.375  20.668  62.798  1.00 18.60           C  
+ATOM   1724  CG  LEU A 234      19.938  19.333  62.308  1.00 17.74           C  
+ATOM   1725  CD1 LEU A 234      20.567  18.564  63.458  1.00 15.97           C  
+ATOM   1726  CD2 LEU A 234      18.812  18.524  61.682  1.00 17.93           C  
+ATOM   1727  N   ALA A 235      18.192  23.812  62.439  1.00 22.87           N  
+ATOM   1728  CA  ALA A 235      17.355  24.841  63.045  1.00 25.13           C  
+ATOM   1729  C   ALA A 235      16.507  25.610  62.037  1.00 26.81           C  
+ATOM   1730  O   ALA A 235      15.700  26.459  62.423  1.00 28.97           O  
+ATOM   1731  CB  ALA A 235      18.229  25.820  63.833  1.00 24.33           C  
+ATOM   1732  N   THR A 236      16.679  25.320  60.752  1.00 26.60           N  
+ATOM   1733  CA  THR A 236      15.925  26.025  59.716  1.00 26.35           C  
+ATOM   1734  C   THR A 236      14.688  25.260  59.259  1.00 25.67           C  
+ATOM   1735  O   THR A 236      14.532  24.071  59.542  1.00 26.18           O  
+ATOM   1736  CB  THR A 236      16.804  26.292  58.486  1.00 26.23           C  
+ATOM   1737  OG1 THR A 236      17.209  25.042  57.917  1.00 25.70           O  
+ATOM   1738  CG2 THR A 236      18.039  27.087  58.877  1.00 24.61           C  
+ATOM   1739  N   PRO A 237      13.778  25.941  58.551  1.00 24.86           N  
+ATOM   1740  CA  PRO A 237      12.575  25.249  58.086  1.00 24.52           C  
+ATOM   1741  C   PRO A 237      12.850  24.220  56.990  1.00 25.24           C  
+ATOM   1742  O   PRO A 237      11.963  23.448  56.627  1.00 25.86           O  
+ATOM   1743  CB  PRO A 237      11.670  26.392  57.627  1.00 22.45           C  
+ATOM   1744  CG  PRO A 237      12.629  27.458  57.243  1.00 23.42           C  
+ATOM   1745  CD  PRO A 237      13.675  27.391  58.319  1.00 24.22           C  
+ATOM   1746  N   GLU A 238      14.072  24.200  56.463  1.00 25.76           N  
+ATOM   1747  CA  GLU A 238      14.415  23.223  55.440  1.00 26.78           C  
+ATOM   1748  C   GLU A 238      14.594  21.862  56.098  1.00 27.45           C  
+ATOM   1749  O   GLU A 238      14.824  20.858  55.417  1.00 28.63           O  
+ATOM   1750  CB  GLU A 238      15.705  23.607  54.707  1.00 28.34           C  
+ATOM   1751  CG  GLU A 238      15.549  24.748  53.720  1.00 29.47           C  
+ATOM   1752  CD  GLU A 238      16.743  24.880  52.781  1.00 31.84           C  
+ATOM   1753  OE1 GLU A 238      17.884  25.016  53.266  1.00 32.42           O  
+ATOM   1754  OE2 GLU A 238      16.541  24.850  51.549  1.00 33.50           O  
+ATOM   1755  N   ALA A 239      14.476  21.836  57.425  1.00 26.09           N  
+ATOM   1756  CA  ALA A 239      14.619  20.605  58.196  1.00 24.01           C  
+ATOM   1757  C   ALA A 239      13.340  20.241  58.953  1.00 24.62           C  
+ATOM   1758  O   ALA A 239      13.337  19.321  59.780  1.00 25.04           O  
+ATOM   1759  CB  ALA A 239      15.778  20.741  59.175  1.00 23.04           C  
+ATOM   1760  N   ASP A 240      12.251  20.949  58.668  1.00 22.92           N  
+ATOM   1761  CA  ASP A 240      10.983  20.679  59.340  1.00 21.54           C  
+ATOM   1762  C   ASP A 240      10.523  19.235  59.247  1.00 21.09           C  
+ATOM   1763  O   ASP A 240       9.713  18.798  60.058  1.00 21.96           O  
+ATOM   1764  CB  ASP A 240       9.864  21.549  58.776  1.00 21.66           C  
+ATOM   1765  CG  ASP A 240       9.937  22.983  59.245  1.00 22.84           C  
+ATOM   1766  OD1 ASP A 240      10.857  23.337  60.015  1.00 23.30           O  
+ATOM   1767  OD2 ASP A 240       9.054  23.762  58.833  1.00 25.36           O  
+ATOM   1768  N   TYR A 241      11.009  18.494  58.260  1.00 19.28           N  
+ATOM   1769  CA  TYR A 241      10.574  17.113  58.113  1.00 18.03           C  
+ATOM   1770  C   TYR A 241      11.587  16.132  58.710  1.00 18.36           C  
+ATOM   1771  O   TYR A 241      11.430  14.915  58.583  1.00 18.99           O  
+ATOM   1772  CB  TYR A 241      10.320  16.795  56.629  1.00 16.72           C  
+ATOM   1773  CG  TYR A 241       9.357  15.646  56.381  1.00 14.84           C  
+ATOM   1774  CD1 TYR A 241       8.013  15.730  56.776  1.00 15.54           C  
+ATOM   1775  CD2 TYR A 241       9.787  14.472  55.761  1.00 12.80           C  
+ATOM   1776  CE1 TYR A 241       7.128  14.668  56.561  1.00 14.31           C  
+ATOM   1777  CE2 TYR A 241       8.912  13.410  55.539  1.00 12.47           C  
+ATOM   1778  CZ  TYR A 241       7.590  13.514  55.941  1.00 14.81           C  
+ATOM   1779  OH  TYR A 241       6.733  12.456  55.731  1.00 17.97           O  
+ATOM   1780  N   ILE A 242      12.624  16.659  59.360  1.00 18.06           N  
+ATOM   1781  CA  ILE A 242      13.632  15.802  59.990  1.00 18.59           C  
+ATOM   1782  C   ILE A 242      13.275  15.639  61.479  1.00 20.10           C  
+ATOM   1783  O   ILE A 242      13.363  16.584  62.262  1.00 18.52           O  
+ATOM   1784  CB  ILE A 242      15.044  16.401  59.828  1.00 16.72           C  
+ATOM   1785  CG1 ILE A 242      15.407  16.442  58.333  1.00 16.44           C  
+ATOM   1786  CG2 ILE A 242      16.056  15.562  60.591  1.00 15.55           C  
+ATOM   1787  CD1 ILE A 242      16.715  17.134  58.009  1.00 13.53           C  
+ATOM   1788  N   VAL A 243      12.864  14.430  61.854  1.00 20.04           N  
+ATOM   1789  CA  VAL A 243      12.441  14.145  63.225  1.00 18.99           C  
+ATOM   1790  C   VAL A 243      13.112  12.946  63.895  1.00 18.34           C  
+ATOM   1791  O   VAL A 243      13.210  11.873  63.303  1.00 18.35           O  
+ATOM   1792  CB  VAL A 243      10.923  13.896  63.262  1.00 18.93           C  
+ATOM   1793  CG1 VAL A 243      10.460  13.640  64.685  1.00 18.33           C  
+ATOM   1794  CG2 VAL A 243      10.198  15.083  62.658  1.00 17.52           C  
+ATOM   1795  N   ALA A 244      13.554  13.145  65.138  1.00 17.17           N  
+ATOM   1796  CA  ALA A 244      14.180  12.100  65.952  1.00 16.24           C  
+ATOM   1797  C   ALA A 244      15.363  11.404  65.300  1.00 15.92           C  
+ATOM   1798  O   ALA A 244      15.486  10.185  65.372  1.00 18.93           O  
+ATOM   1799  CB  ALA A 244      13.128  11.057  66.361  1.00 12.40           C  
+ATOM   1800  N   GLN A 245      16.247  12.179  64.689  1.00 15.76           N  
+ATOM   1801  CA  GLN A 245      17.418  11.619  64.031  1.00 14.89           C  
+ATOM   1802  C   GLN A 245      18.677  12.078  64.733  1.00 14.04           C  
+ATOM   1803  O   GLN A 245      18.679  13.107  65.421  1.00 13.19           O  
+ATOM   1804  CB  GLN A 245      17.496  12.098  62.566  1.00 16.43           C  
+ATOM   1805  CG  GLN A 245      16.248  11.831  61.733  1.00 14.23           C  
+ATOM   1806  CD  GLN A 245      15.967  10.355  61.600  1.00 13.84           C  
+ATOM   1807  OE1 GLN A 245      16.882   9.559  61.366  1.00 15.40           O  
+ATOM   1808  NE2 GLN A 245      14.700   9.975  61.740  1.00 12.98           N  
+ATOM   1809  N   THR A 246      19.746  11.311  64.532  1.00 13.90           N  
+ATOM   1810  CA  THR A 246      21.073  11.618  65.060  1.00 13.69           C  
+ATOM   1811  C   THR A 246      21.963  11.546  63.810  1.00 14.66           C  
+ATOM   1812  O   THR A 246      22.130  10.479  63.219  1.00 15.17           O  
+ATOM   1813  CB  THR A 246      21.543  10.573  66.112  1.00 13.15           C  
+ATOM   1814  OG1 THR A 246      20.665  10.607  67.247  1.00 14.80           O  
+ATOM   1815  CG2 THR A 246      22.958  10.882  66.581  1.00 10.43           C  
+ATOM   1816  N   TYR A 247      22.493  12.695  63.398  1.00 14.72           N  
+ATOM   1817  CA  TYR A 247      23.338  12.801  62.209  1.00 13.19           C  
+ATOM   1818  C   TYR A 247      24.814  12.835  62.562  1.00 14.07           C  
+ATOM   1819  O   TYR A 247      25.249  13.694  63.324  1.00 15.30           O  
+ATOM   1820  CB  TYR A 247      22.986  14.074  61.436  1.00 10.03           C  
+ATOM   1821  CG  TYR A 247      21.655  14.036  60.698  1.00 10.79           C  
+ATOM   1822  CD1 TYR A 247      21.058  15.210  60.240  1.00 10.59           C  
+ATOM   1823  CD2 TYR A 247      21.023  12.831  60.410  1.00  9.17           C  
+ATOM   1824  CE1 TYR A 247      19.871  15.181  59.514  1.00 11.19           C  
+ATOM   1825  CE2 TYR A 247      19.840  12.796  59.681  1.00  9.39           C  
+ATOM   1826  CZ  TYR A 247      19.274  13.973  59.238  1.00 10.28           C  
+ATOM   1827  OH  TYR A 247      18.108  13.938  58.506  1.00 16.71           O  
+ATOM   1828  N   ASN A 248      25.582  11.910  61.998  1.00 13.65           N  
+ATOM   1829  CA  ASN A 248      27.012  11.844  62.258  1.00 16.85           C  
+ATOM   1830  C   ASN A 248      27.802  12.808  61.380  1.00 18.74           C  
+ATOM   1831  O   ASN A 248      27.707  12.752  60.148  1.00 22.45           O  
+ATOM   1832  CB  ASN A 248      27.529  10.424  62.015  1.00 17.50           C  
+ATOM   1833  CG  ASN A 248      27.012   9.429  63.034  1.00 19.69           C  
+ATOM   1834  OD1 ASN A 248      26.091   9.720  63.800  1.00 18.80           O  
+ATOM   1835  ND2 ASN A 248      27.602   8.238  63.042  1.00 21.89           N  
+ATOM   1836  N   VAL A 249      28.572  13.690  62.014  1.00 18.57           N  
+ATOM   1837  CA  VAL A 249      29.420  14.646  61.301  1.00 18.70           C  
+ATOM   1838  C   VAL A 249      30.800  14.378  61.884  1.00 20.64           C  
+ATOM   1839  O   VAL A 249      31.308  15.149  62.698  1.00 22.16           O  
+ATOM   1840  CB  VAL A 249      28.997  16.110  61.576  1.00 18.65           C  
+ATOM   1841  CG1 VAL A 249      29.853  17.072  60.737  1.00 18.55           C  
+ATOM   1842  CG2 VAL A 249      27.526  16.300  61.236  1.00 15.89           C  
+ATOM   1843  N   ASP A 250      31.399  13.275  61.440  1.00 21.03           N  
+ATOM   1844  CA  ASP A 250      32.677  12.801  61.955  1.00 21.01           C  
+ATOM   1845  C   ASP A 250      33.738  12.428  60.914  1.00 21.15           C  
+ATOM   1846  O   ASP A 250      34.615  11.612  61.204  1.00 20.51           O  
+ATOM   1847  CB  ASP A 250      32.391  11.562  62.789  1.00 23.83           C  
+ATOM   1848  CG  ASP A 250      31.742  10.454  61.955  1.00 27.33           C  
+ATOM   1849  OD1 ASP A 250      31.203   9.479  62.526  1.00 28.60           O  
+ATOM   1850  OD2 ASP A 250      31.777  10.562  60.708  1.00 28.72           O  
+ATOM   1851  N   GLY A 251      33.659  12.986  59.709  1.00 20.11           N  
+ATOM   1852  CA  GLY A 251      34.647  12.657  58.691  1.00 17.10           C  
+ATOM   1853  C   GLY A 251      34.732  11.174  58.349  1.00 18.53           C  
+ATOM   1854  O   GLY A 251      35.765  10.691  57.867  1.00 17.43           O  
+ATOM   1855  N   GLY A 252      33.653  10.441  58.610  1.00 18.10           N  
+ATOM   1856  CA  GLY A 252      33.631   9.026  58.300  1.00 19.73           C  
+ATOM   1857  C   GLY A 252      33.998   8.089  59.440  1.00 23.83           C  
+ATOM   1858  O   GLY A 252      34.022   6.867  59.248  1.00 22.71           O  
+ATOM   1859  N   ASN A 253      34.276   8.640  60.623  1.00 25.53           N  
+ATOM   1860  CA  ASN A 253      34.653   7.820  61.778  1.00 25.63           C  
+ATOM   1861  C   ASN A 253      33.661   6.701  62.091  1.00 24.79           C  
+ATOM   1862  O   ASN A 253      34.053   5.594  62.456  1.00 25.09           O  
+ATOM   1863  CB  ASN A 253      34.850   8.707  63.001  1.00 27.95           C  
+ATOM   1864  CG  ASN A 253      36.241   8.580  63.574  1.00 32.16           C  
+ATOM   1865  OD1 ASN A 253      37.211   8.425  62.829  1.00 33.89           O  
+ATOM   1866  ND2 ASN A 253      36.355   8.652  64.898  1.00 33.82           N  
+ATOM   1867  N   TRP A 254      32.375   6.989  61.957  1.00 23.58           N  
+ATOM   1868  CA  TRP A 254      31.353   5.983  62.190  1.00 23.49           C  
+ATOM   1869  C   TRP A 254      30.267   6.167  61.134  1.00 24.70           C  
+ATOM   1870  O   TRP A 254      29.931   7.291  60.768  1.00 25.29           O  
+ATOM   1871  CB  TRP A 254      30.769   6.117  63.600  1.00 23.33           C  
+ATOM   1872  CG  TRP A 254      29.962   4.923  63.981  1.00 18.89           C  
+ATOM   1873  CD1 TRP A 254      28.604   4.811  63.964  1.00 19.59           C  
+ATOM   1874  CD2 TRP A 254      30.468   3.639  64.353  1.00 18.21           C  
+ATOM   1875  NE1 TRP A 254      28.229   3.532  64.301  1.00 18.41           N  
+ATOM   1876  CE2 TRP A 254      29.355   2.791  64.544  1.00 19.37           C  
+ATOM   1877  CE3 TRP A 254      31.756   3.121  64.540  1.00 17.89           C  
+ATOM   1878  CZ2 TRP A 254      29.489   1.449  64.921  1.00 19.13           C  
+ATOM   1879  CZ3 TRP A 254      31.890   1.790  64.912  1.00 19.67           C  
+ATOM   1880  CH2 TRP A 254      30.762   0.967  65.097  1.00 20.58           C  
+ATOM   1881  N   MET A 255      29.709   5.069  60.642  1.00 26.34           N  
+ATOM   1882  CA  MET A 255      28.701   5.164  59.592  1.00 27.93           C  
+ATOM   1883  C   MET A 255      27.302   4.748  60.005  1.00 27.64           C  
+ATOM   1884  O   MET A 255      27.057   3.586  60.326  1.00 29.54           O  
+ATOM   1885  CB  MET A 255      29.146   4.331  58.399  1.00 28.54           C  
+ATOM   1886  CG  MET A 255      30.558   4.642  57.948  1.00 30.99           C  
+ATOM   1887  SD  MET A 255      31.116   3.394  56.790  1.00 34.74           S  
+ATOM   1888  CE  MET A 255      31.526   2.062  57.912  1.00 35.45           C  
+ATOM   1889  N   SER A 256      26.376   5.699  59.965  1.00 26.90           N  
+ATOM   1890  CA  SER A 256      24.998   5.430  60.347  1.00 28.27           C  
+ATOM   1891  C   SER A 256      24.040   5.839  59.231  1.00 28.44           C  
+ATOM   1892  O   SER A 256      24.543   6.294  58.186  1.00 28.92           O  
+ATOM   1893  CB  SER A 256      24.664   6.188  61.642  1.00 28.64           C  
+ATOM   1894  OG  SER A 256      25.569   5.836  62.681  1.00 28.28           O  
+ATOM   1895  OXT SER A 256      22.811   5.701  59.408  1.00 27.92           O  
+TER    1896      SER A 256                                                      
+END
\ No newline at end of file
diff --git a/examples/demos/data/sdh.pdb b/examples/demos/data/sdh.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..796f7fa85f97be7d3cd7a3287225d36b06e4e39c
--- /dev/null
+++ b/examples/demos/data/sdh.pdb
@@ -0,0 +1,3838 @@
+HELIX    1   1 ARG A   15  GLU A   28  1                                  14    
+HELIX    2   2 ASN A   38  GLY A   50  1                                  13    
+HELIX    3   3 ASP A   62  GLY A   78  1                                  17    
+HELIX    4   4 PRO A   94  ILE A   98  5                                   5    
+HELIX    5   5 THR A   99  VAL A  111  1                                  13    
+HELIX    6   6 VAL A  111  GLY A  129  1                                  19    
+HELIX    7   7 SER A  139  ARG A  143  5                                   5    
+HELIX    8   8 VAL A  149  ILE A  171  1                                  23    
+HELIX    9   9 HIS A  189  ASN A  202  1                                  14    
+HELIX   10  10 GLY A  206  VAL A  216  1                                  11    
+HELIX   11  11 ARG A  223  LEU A  234  1                                  12    
+HELIX   12  12 ALA A  235  ASP A  240  5                                   6    
+HELIX   13  13 ARG B   15  GLU B   28  1                                  14    
+HELIX   14  14 ASN B   38  GLY B   50  1                                  13    
+HELIX   15  15 ASP B   62  GLY B   78  1                                  17    
+HELIX   16  16 PRO B   94  ILE B   98  5                                   5    
+HELIX   17  17 THR B   99  VAL B  111  1                                  13    
+HELIX   18  18 VAL B  111  GLY B  129  1                                  19    
+HELIX   19  19 SER B  139  ARG B  143  5                                   5    
+HELIX   20  20 VAL B  149  ILE B  171  1                                  23    
+HELIX   21  21 HIS B  189  GLU B  201  1                                  13    
+HELIX   22  22 GLY B  206  VAL B  216  1                                  11    
+HELIX   23  23 ARG B  223  LEU B  234  1                                  12    
+HELIX   24  24 ALA B  235  ASP B  240  5                                   6    
+SHEET    1   A 7 ALA A  53  ALA A  57  0                                        
+SHEET    2   A 7 ALA A  30  ASP A  36  1  N  ILE A  34   O  CYS A  54           
+SHEET    3   A 7 LYS A   6  THR A  11  1  N  LYS A   6   O  ARG A  31           
+SHEET    4   A 7 ILE A  82  ASN A  85  1  O  ILE A  82   N  LEU A   9           
+SHEET    5   A 7 GLY A 132  MET A 137  1  O  ILE A 135   N  LEU A  83           
+SHEET    6   A 7 ILE A 175  PRO A 182  1  O  ASN A 176   N  ILE A 134           
+SHEET    7   A 7 THR A 246  VAL A 249  1  O  TYR A 247   N  ALA A 181           
+SHEET    1   B 7 ALA B  53  ALA B  57  0                                        
+SHEET    2   B 7 ARG B  31  ASP B  36  1  N  ILE B  34   O  CYS B  54           
+SHEET    3   B 7 THR B   7  THR B  11  1  N  ALA B   8   O  ARG B  31           
+SHEET    4   B 7 ILE B  82  ASN B  85  1  O  VAL B  84   N  LEU B   9           
+SHEET    5   B 7 GLY B 132  MET B 137  1  O  ILE B 135   N  LEU B  83           
+SHEET    6   B 7 ILE B 175  PRO B 182  1  O  ASN B 176   N  ILE B 134           
+SHEET    7   B 7 THR B 246  VAL B 249  1  O  TYR B 247   N  ALA B 181           
+CRYST1   67.465   67.465  191.044  90.00  90.00 120.00 P 31 2 1     12          
+ORIGX1      1.000000  0.000000  0.000000        0.00000                         
+ORIGX2      0.000000  1.000000  0.000000        0.00000                         
+ORIGX3      0.000000  0.000000  1.000000        0.00000                         
+SCALE1      0.014823  0.008558  0.000000        0.00000                         
+SCALE2      0.000000  0.017116  0.000000        0.00000                         
+SCALE3      0.000000  0.000000  0.005234        0.00000                         
+ATOM      1  N   MET A   1      21.609  35.384  56.705  1.00 41.48           N  
+ATOM      2  CA  MET A   1      20.601  35.494  57.793  1.00 41.58           C  
+ATOM      3  C   MET A   1      19.654  34.300  57.789  1.00 39.51           C  
+ATOM      4  O   MET A   1      18.447  34.456  57.595  1.00 38.98           O  
+ATOM      5  CB  MET A   1      19.789  36.783  57.639  1.00 45.90           C  
+ATOM      6  CG  MET A   1      20.629  38.055  57.606  1.00 51.18           C  
+ATOM      7  SD  MET A   1      21.638  38.325  59.084  1.00 55.83           S  
+ATOM      8  CE  MET A   1      23.233  37.697  58.529  1.00 54.59           C  
+ATOM      9  N   ARG A   2      20.202  33.112  58.011  1.00 36.39           N  
+ATOM     10  CA  ARG A   2      19.396  31.903  58.033  1.00 34.35           C  
+ATOM     11  C   ARG A   2      18.608  31.739  59.328  1.00 34.20           C  
+ATOM     12  O   ARG A   2      17.651  30.965  59.381  1.00 32.64           O  
+ATOM     13  CB  ARG A   2      20.284  30.681  57.801  1.00 33.48           C  
+ATOM     14  CG  ARG A   2      20.665  30.488  56.342  1.00 31.69           C  
+ATOM     15  CD  ARG A   2      21.557  29.281  56.154  1.00 29.91           C  
+ATOM     16  NE  ARG A   2      22.931  29.557  56.551  1.00 28.95           N  
+ATOM     17  CZ  ARG A   2      23.901  28.653  56.528  1.00 30.21           C  
+ATOM     18  NH1 ARG A   2      23.640  27.417  56.130  1.00 32.54           N  
+ATOM     19  NH2 ARG A   2      25.132  28.980  56.893  1.00 29.14           N  
+ATOM     20  N   LEU A   3      19.003  32.473  60.366  1.00 35.07           N  
+ATOM     21  CA  LEU A   3      18.330  32.402  61.664  1.00 34.70           C  
+ATOM     22  C   LEU A   3      17.884  33.787  62.117  1.00 35.41           C  
+ATOM     23  O   LEU A   3      17.853  34.091  63.308  1.00 35.91           O  
+ATOM     24  CB  LEU A   3      19.269  31.793  62.710  1.00 31.47           C  
+ATOM     25  CG  LEU A   3      19.695  30.340  62.501  1.00 29.10           C  
+ATOM     26  CD1 LEU A   3      20.585  29.897  63.648  1.00 26.97           C  
+ATOM     27  CD2 LEU A   3      18.461  29.459  62.420  1.00 27.95           C  
+ATOM     28  N   ASP A   4      17.517  34.614  61.149  1.00 36.70           N  
+ATOM     29  CA  ASP A   4      17.099  35.980  61.411  1.00 37.42           C  
+ATOM     30  C   ASP A   4      15.897  36.114  62.343  1.00 37.20           C  
+ATOM     31  O   ASP A   4      14.839  35.529  62.107  1.00 35.42           O  
+ATOM     32  CB  ASP A   4      16.814  36.671  60.079  1.00 40.33           C  
+ATOM     33  CG  ASP A   4      17.023  38.166  60.142  1.00 43.16           C  
+ATOM     34  OD1 ASP A   4      16.121  38.876  60.638  1.00 44.42           O  
+ATOM     35  OD2 ASP A   4      18.100  38.629  59.699  1.00 45.27           O  
+ATOM     36  N   GLY A   5      16.085  36.893  63.408  1.00 38.60           N  
+ATOM     37  CA  GLY A   5      15.027  37.141  64.378  1.00 40.00           C  
+ATOM     38  C   GLY A   5      14.640  35.963  65.253  1.00 40.53           C  
+ATOM     39  O   GLY A   5      13.475  35.828  65.645  1.00 40.48           O  
+ATOM     40  N   LYS A   6      15.612  35.110  65.565  1.00 39.87           N  
+ATOM     41  CA  LYS A   6      15.354  33.938  66.391  1.00 38.75           C  
+ATOM     42  C   LYS A   6      16.248  33.899  67.615  1.00 37.16           C  
+ATOM     43  O   LYS A   6      17.363  34.427  67.602  1.00 36.93           O  
+ATOM     44  CB  LYS A   6      15.548  32.665  65.571  1.00 39.36           C  
+ATOM     45  CG  LYS A   6      14.498  32.476  64.504  1.00 40.15           C  
+ATOM     46  CD  LYS A   6      14.601  31.107  63.866  1.00 41.73           C  
+ATOM     47  CE  LYS A   6      13.463  30.880  62.879  1.00 44.93           C  
+ATOM     48  NZ  LYS A   6      12.132  31.017  63.537  1.00 44.56           N  
+ATOM     49  N   THR A   7      15.750  33.261  68.670  1.00 34.56           N  
+ATOM     50  CA  THR A   7      16.484  33.152  69.925  1.00 31.14           C  
+ATOM     51  C   THR A   7      16.945  31.728  70.188  1.00 30.82           C  
+ATOM     52  O   THR A   7      16.175  30.775  70.059  1.00 31.78           O  
+ATOM     53  CB  THR A   7      15.618  33.605  71.114  1.00 30.89           C  
+ATOM     54  OG1 THR A   7      14.409  32.837  71.147  1.00 31.28           O  
+ATOM     55  CG2 THR A   7      15.263  35.077  70.991  1.00 32.31           C  
+ATOM     56  N   ALA A   8      18.205  31.586  70.573  1.00 29.62           N  
+ATOM     57  CA  ALA A   8      18.759  30.274  70.854  1.00 29.72           C  
+ATOM     58  C   ALA A   8      19.461  30.202  72.215  1.00 30.28           C  
+ATOM     59  O   ALA A   8      20.244  31.084  72.579  1.00 30.25           O  
+ATOM     60  CB  ALA A   8      19.732  29.874  69.745  1.00 29.05           C  
+ATOM     61  N   LEU A   9      19.163  29.146  72.964  1.00 28.68           N  
+ATOM     62  CA  LEU A   9      19.784  28.923  74.261  1.00 26.72           C  
+ATOM     63  C   LEU A   9      20.780  27.790  74.007  1.00 26.04           C  
+ATOM     64  O   LEU A   9      20.390  26.713  73.554  1.00 26.45           O  
+ATOM     65  CB  LEU A   9      18.733  28.471  75.291  1.00 26.06           C  
+ATOM     66  CG  LEU A   9      19.044  28.458  76.801  1.00 25.33           C  
+ATOM     67  CD1 LEU A   9      17.929  27.731  77.537  1.00 23.24           C  
+ATOM     68  CD2 LEU A   9      20.359  27.772  77.089  1.00 25.34           C  
+ATOM     69  N   ILE A  10      22.056  28.036  74.278  1.00 23.49           N  
+ATOM     70  CA  ILE A  10      23.077  27.016  74.090  1.00 24.46           C  
+ATOM     71  C   ILE A  10      23.777  26.777  75.422  1.00 27.09           C  
+ATOM     72  O   ILE A  10      24.431  27.677  75.953  1.00 27.64           O  
+ATOM     73  CB  ILE A  10      24.124  27.460  73.057  1.00 24.13           C  
+ATOM     74  CG1 ILE A  10      23.427  27.822  71.747  1.00 22.48           C  
+ATOM     75  CG2 ILE A  10      25.153  26.351  72.842  1.00 17.46           C  
+ATOM     76  CD1 ILE A  10      24.360  28.402  70.719  1.00 24.59           C  
+ATOM     77  N   THR A  11      23.650  25.565  75.955  1.00 27.49           N  
+ATOM     78  CA  THR A  11      24.256  25.247  77.240  1.00 28.56           C  
+ATOM     79  C   THR A  11      25.740  24.948  77.123  1.00 29.62           C  
+ATOM     80  O   THR A  11      26.186  24.359  76.138  1.00 32.36           O  
+ATOM     81  CB  THR A  11      23.551  24.043  77.899  1.00 27.97           C  
+ATOM     82  OG1 THR A  11      23.883  22.839  77.199  1.00 27.93           O  
+ATOM     83  CG2 THR A  11      22.050  24.235  77.863  1.00 27.09           C  
+ATOM     84  N   GLY A  12      26.499  25.356  78.137  1.00 29.33           N  
+ATOM     85  CA  GLY A  12      27.934  25.121  78.150  1.00 29.86           C  
+ATOM     86  C   GLY A  12      28.634  25.744  76.963  1.00 31.12           C  
+ATOM     87  O   GLY A  12      29.570  25.170  76.407  1.00 32.13           O  
+ATOM     88  N   SER A  13      28.186  26.939  76.592  1.00 32.78           N  
+ATOM     89  CA  SER A  13      28.721  27.662  75.443  1.00 33.66           C  
+ATOM     90  C   SER A  13      29.757  28.737  75.764  1.00 35.28           C  
+ATOM     91  O   SER A  13      30.039  29.600  74.933  1.00 36.10           O  
+ATOM     92  CB  SER A  13      27.561  28.292  74.674  1.00 32.16           C  
+ATOM     93  OG  SER A  13      26.712  29.012  75.550  1.00 31.20           O  
+ATOM     94  N   ALA A  14      30.323  28.696  76.963  1.00 36.42           N  
+ATOM     95  CA  ALA A  14      31.320  29.688  77.335  1.00 36.95           C  
+ATOM     96  C   ALA A  14      32.594  29.418  76.550  1.00 37.21           C  
+ATOM     97  O   ALA A  14      33.338  30.338  76.218  1.00 36.96           O  
+ATOM     98  CB  ALA A  14      31.600  29.621  78.834  1.00 36.61           C  
+ATOM     99  N   ARG A  15      32.833  28.146  76.249  1.00 37.46           N  
+ATOM    100  CA  ARG A  15      34.025  27.749  75.511  1.00 38.19           C  
+ATOM    101  C   ARG A  15      33.755  26.585  74.573  1.00 36.88           C  
+ATOM    102  O   ARG A  15      32.648  26.040  74.533  1.00 36.88           O  
+ATOM    103  CB  ARG A  15      35.136  27.342  76.484  1.00 40.06           C  
+ATOM    104  CG  ARG A  15      35.555  28.438  77.445  1.00 43.70           C  
+ATOM    105  CD  ARG A  15      36.475  27.902  78.531  1.00 44.19           C  
+ATOM    106  NE  ARG A  15      36.657  28.880  79.598  0.00 44.00           N  
+ATOM    107  CZ  ARG A  15      37.270  28.625  80.748  0.00 44.01           C  
+ATOM    108  NH1 ARG A  15      37.389  29.576  81.664  0.00 43.97           N  
+ATOM    109  NH2 ARG A  15      37.761  27.416  80.985  0.00 43.97           N  
+ATOM    110  N   GLY A  16      34.791  26.214  73.825  1.00 35.61           N  
+ATOM    111  CA  GLY A  16      34.707  25.101  72.898  1.00 34.73           C  
+ATOM    112  C   GLY A  16      33.653  25.160  71.808  1.00 33.39           C  
+ATOM    113  O   GLY A  16      33.297  26.227  71.306  1.00 33.46           O  
+ATOM    114  N   ILE A  17      33.164  23.980  71.445  1.00 32.78           N  
+ATOM    115  CA  ILE A  17      32.152  23.820  70.409  1.00 31.95           C  
+ATOM    116  C   ILE A  17      30.913  24.653  70.699  1.00 31.77           C  
+ATOM    117  O   ILE A  17      30.311  25.231  69.789  1.00 32.50           O  
+ATOM    118  CB  ILE A  17      31.747  22.340  70.285  1.00 30.90           C  
+ATOM    119  CG1 ILE A  17      32.954  21.519  69.822  1.00 31.07           C  
+ATOM    120  CG2 ILE A  17      30.574  22.194  69.336  1.00 32.31           C  
+ATOM    121  CD1 ILE A  17      32.682  20.030  69.689  1.00 31.10           C  
+ATOM    122  N   GLY A  18      30.533  24.711  71.968  1.00 30.54           N  
+ATOM    123  CA  GLY A  18      29.362  25.475  72.340  1.00 30.57           C  
+ATOM    124  C   GLY A  18      29.499  26.918  71.916  1.00 31.00           C  
+ATOM    125  O   GLY A  18      28.548  27.511  71.403  1.00 30.12           O  
+ATOM    126  N   ARG A  19      30.685  27.484  72.133  1.00 32.12           N  
+ATOM    127  CA  ARG A  19      30.947  28.870  71.768  1.00 34.24           C  
+ATOM    128  C   ARG A  19      30.840  29.036  70.263  1.00 34.09           C  
+ATOM    129  O   ARG A  19      30.246  30.000  69.775  1.00 34.42           O  
+ATOM    130  CB  ARG A  19      32.341  29.306  72.227  1.00 35.54           C  
+ATOM    131  CG  ARG A  19      32.719  30.675  71.700  1.00 37.76           C  
+ATOM    132  CD  ARG A  19      33.872  31.311  72.446  1.00 41.26           C  
+ATOM    133  NE  ARG A  19      34.100  32.671  71.961  1.00 45.22           N  
+ATOM    134  CZ  ARG A  19      34.886  33.567  72.552  1.00 47.24           C  
+ATOM    135  NH1 ARG A  19      35.538  33.261  73.668  1.00 47.45           N  
+ATOM    136  NH2 ARG A  19      35.014  34.779  72.026  1.00 48.67           N  
+ATOM    137  N   ALA A  20      31.420  28.084  69.537  1.00 33.55           N  
+ATOM    138  CA  ALA A  20      31.395  28.100  68.081  1.00 32.10           C  
+ATOM    139  C   ALA A  20      29.960  28.244  67.579  1.00 31.27           C  
+ATOM    140  O   ALA A  20      29.657  29.151  66.801  1.00 30.43           O  
+ATOM    141  CB  ALA A  20      32.014  26.822  67.542  1.00 33.12           C  
+ATOM    142  N   PHE A  21      29.078  27.355  68.031  1.00 29.80           N  
+ATOM    143  CA  PHE A  21      27.681  27.410  67.616  1.00 30.38           C  
+ATOM    144  C   PHE A  21      27.098  28.791  67.875  1.00 31.24           C  
+ATOM    145  O   PHE A  21      26.382  29.341  67.041  1.00 31.23           O  
+ATOM    146  CB  PHE A  21      26.849  26.371  68.372  1.00 31.41           C  
+ATOM    147  CG  PHE A  21      27.159  24.947  68.004  1.00 31.93           C  
+ATOM    148  CD1 PHE A  21      26.580  23.898  68.713  1.00 32.29           C  
+ATOM    149  CD2 PHE A  21      28.021  24.649  66.951  1.00 31.51           C  
+ATOM    150  CE1 PHE A  21      26.858  22.570  68.385  1.00 32.16           C  
+ATOM    151  CE2 PHE A  21      28.304  23.327  66.615  1.00 31.35           C  
+ATOM    152  CZ  PHE A  21      27.718  22.286  67.334  1.00 32.56           C  
+ATOM    153  N   ALA A  22      27.407  29.349  69.040  1.00 32.80           N  
+ATOM    154  CA  ALA A  22      26.898  30.661  69.410  1.00 32.66           C  
+ATOM    155  C   ALA A  22      27.351  31.695  68.394  1.00 33.14           C  
+ATOM    156  O   ALA A  22      26.539  32.453  67.870  1.00 33.21           O  
+ATOM    157  CB  ALA A  22      27.384  31.037  70.797  1.00 32.85           C  
+ATOM    158  N   GLU A  23      28.649  31.723  68.120  1.00 33.91           N  
+ATOM    159  CA  GLU A  23      29.184  32.667  67.152  1.00 36.31           C  
+ATOM    160  C   GLU A  23      28.513  32.448  65.792  1.00 36.26           C  
+ATOM    161  O   GLU A  23      28.056  33.402  65.158  1.00 37.82           O  
+ATOM    162  CB  GLU A  23      30.713  32.521  67.046  1.00 36.10           C  
+ATOM    163  CG  GLU A  23      31.437  32.932  68.324  1.00 40.69           C  
+ATOM    164  CD  GLU A  23      32.958  32.853  68.229  1.00 43.33           C  
+ATOM    165  OE1 GLU A  23      33.481  31.834  67.729  1.00 45.41           O  
+ATOM    166  OE2 GLU A  23      33.635  33.805  68.678  1.00 45.19           O  
+ATOM    167  N   ALA A  24      28.428  31.196  65.355  1.00 35.52           N  
+ATOM    168  CA  ALA A  24      27.799  30.893  64.076  1.00 35.70           C  
+ATOM    169  C   ALA A  24      26.343  31.359  64.068  1.00 36.18           C  
+ATOM    170  O   ALA A  24      25.894  32.018  63.131  1.00 38.13           O  
+ATOM    171  CB  ALA A  24      27.874  29.403  63.802  1.00 35.57           C  
+ATOM    172  N   TYR A  25      25.609  31.018  65.120  1.00 35.70           N  
+ATOM    173  CA  TYR A  25      24.209  31.409  65.240  1.00 34.64           C  
+ATOM    174  C   TYR A  25      24.019  32.924  65.172  1.00 35.28           C  
+ATOM    175  O   TYR A  25      23.109  33.417  64.498  1.00 34.85           O  
+ATOM    176  CB  TYR A  25      23.638  30.869  66.553  1.00 32.65           C  
+ATOM    177  CG  TYR A  25      23.047  29.482  66.442  1.00 31.55           C  
+ATOM    178  CD1 TYR A  25      23.584  28.537  65.564  1.00 29.81           C  
+ATOM    179  CD2 TYR A  25      21.943  29.113  67.212  1.00 32.84           C  
+ATOM    180  CE1 TYR A  25      23.033  27.262  65.452  1.00 28.86           C  
+ATOM    181  CE2 TYR A  25      21.384  27.835  67.109  1.00 31.38           C  
+ATOM    182  CZ  TYR A  25      21.935  26.917  66.226  1.00 29.78           C  
+ATOM    183  OH  TYR A  25      21.383  25.660  66.120  1.00 28.89           O  
+ATOM    184  N   VAL A  26      24.872  33.660  65.878  1.00 36.23           N  
+ATOM    185  CA  VAL A  26      24.792  35.115  65.884  1.00 37.22           C  
+ATOM    186  C   VAL A  26      25.032  35.634  64.475  1.00 38.84           C  
+ATOM    187  O   VAL A  26      24.326  36.525  64.003  1.00 38.94           O  
+ATOM    188  CB  VAL A  26      25.840  35.733  66.833  1.00 36.95           C  
+ATOM    189  CG1 VAL A  26      25.880  37.247  66.655  1.00 36.32           C  
+ATOM    190  CG2 VAL A  26      25.497  35.381  68.278  1.00 35.50           C  
+ATOM    191  N   ARG A  27      26.021  35.055  63.803  1.00 39.22           N  
+ATOM    192  CA  ARG A  27      26.359  35.452  62.444  1.00 40.94           C  
+ATOM    193  C   ARG A  27      25.161  35.300  61.511  1.00 40.42           C  
+ATOM    194  O   ARG A  27      25.075  35.985  60.492  1.00 42.12           O  
+ATOM    195  CB  ARG A  27      27.507  34.597  61.915  1.00 43.30           C  
+ATOM    196  CG  ARG A  27      28.427  35.315  60.945  1.00 47.74           C  
+ATOM    197  CD  ARG A  27      28.992  34.355  59.908  1.00 51.22           C  
+ATOM    198  NE  ARG A  27      29.188  32.999  60.427  1.00 55.99           N  
+ATOM    199  CZ  ARG A  27      28.554  31.917  59.964  1.00 58.56           C  
+ATOM    200  NH1 ARG A  27      28.791  30.722  60.490  1.00 58.38           N  
+ATOM    201  NH2 ARG A  27      27.680  32.024  58.969  1.00 60.19           N  
+ATOM    202  N   GLU A  28      24.241  34.402  61.856  1.00 38.14           N  
+ATOM    203  CA  GLU A  28      23.060  34.163  61.031  1.00 36.10           C  
+ATOM    204  C   GLU A  28      21.870  35.017  61.452  1.00 36.39           C  
+ATOM    205  O   GLU A  28      20.727  34.740  61.076  1.00 34.91           O  
+ATOM    206  CB  GLU A  28      22.667  32.682  61.071  1.00 35.69           C  
+ATOM    207  CG  GLU A  28      23.663  31.726  60.403  1.00 33.17           C  
+ATOM    208  CD  GLU A  28      23.837  31.979  58.905  1.00 32.01           C  
+ATOM    209  OE1 GLU A  28      22.832  32.201  58.195  1.00 28.70           O  
+ATOM    210  OE2 GLU A  28      24.989  31.942  58.433  1.00 31.55           O  
+ATOM    211  N   GLY A  29      22.149  36.047  62.247  1.00 37.61           N  
+ATOM    212  CA  GLY A  29      21.108  36.956  62.694  1.00 39.19           C  
+ATOM    213  C   GLY A  29      20.233  36.496  63.845  1.00 40.36           C  
+ATOM    214  O   GLY A  29      19.062  36.883  63.935  1.00 40.61           O  
+ATOM    215  N   ALA A  30      20.788  35.682  64.736  1.00 40.68           N  
+ATOM    216  CA  ALA A  30      20.023  35.190  65.876  1.00 40.66           C  
+ATOM    217  C   ALA A  30      20.555  35.725  67.199  1.00 40.40           C  
+ATOM    218  O   ALA A  30      21.729  36.081  67.308  1.00 40.37           O  
+ATOM    219  CB  ALA A  30      20.042  33.676  65.895  1.00 40.55           C  
+ATOM    220  N   ARG A  31      19.674  35.795  68.193  1.00 40.42           N  
+ATOM    221  CA  ARG A  31      20.044  36.250  69.532  1.00 40.52           C  
+ATOM    222  C   ARG A  31      20.339  34.996  70.352  1.00 39.11           C  
+ATOM    223  O   ARG A  31      19.508  34.094  70.439  1.00 38.13           O  
+ATOM    224  CB  ARG A  31      18.899  37.053  70.158  1.00 42.90           C  
+ATOM    225  CG  ARG A  31      18.781  38.467  69.597  1.00 46.44           C  
+ATOM    226  CD  ARG A  31      17.354  38.820  69.230  1.00 48.95           C  
+ATOM    227  NE  ARG A  31      16.476  38.861  70.394  1.00 53.95           N  
+ATOM    228  CZ  ARG A  31      15.162  39.061  70.330  1.00 56.89           C  
+ATOM    229  NH1 ARG A  31      14.573  39.237  69.151  1.00 58.47           N  
+ATOM    230  NH2 ARG A  31      14.433  39.087  71.441  1.00 57.00           N  
+ATOM    231  N   VAL A  32      21.529  34.935  70.938  1.00 37.80           N  
+ATOM    232  CA  VAL A  32      21.924  33.765  71.711  1.00 36.59           C  
+ATOM    233  C   VAL A  32      22.185  34.035  73.183  1.00 36.34           C  
+ATOM    234  O   VAL A  32      22.528  35.146  73.578  1.00 35.13           O  
+ATOM    235  CB  VAL A  32      23.194  33.133  71.128  1.00 36.30           C  
+ATOM    236  CG1 VAL A  32      23.024  32.916  69.627  1.00 37.03           C  
+ATOM    237  CG2 VAL A  32      24.390  34.025  71.416  1.00 35.06           C  
+ATOM    238  N   ALA A  33      22.040  32.986  73.984  1.00 37.38           N  
+ATOM    239  CA  ALA A  33      22.261  33.058  75.421  1.00 36.31           C  
+ATOM    240  C   ALA A  33      23.443  32.179  75.785  1.00 36.88           C  
+ATOM    241  O   ALA A  33      23.386  30.961  75.625  1.00 37.35           O  
+ATOM    242  CB  ALA A  33      21.025  32.588  76.159  1.00 35.42           C  
+ATOM    243  N   ILE A  34      24.518  32.795  76.264  1.00 38.13           N  
+ATOM    244  CA  ILE A  34      25.699  32.038  76.657  1.00 38.94           C  
+ATOM    245  C   ILE A  34      25.498  31.538  78.080  1.00 40.59           C  
+ATOM    246  O   ILE A  34      25.831  32.227  79.043  1.00 40.22           O  
+ATOM    247  CB  ILE A  34      26.975  32.904  76.619  1.00 38.37           C  
+ATOM    248  CG1 ILE A  34      27.170  33.497  75.222  1.00 38.46           C  
+ATOM    249  CG2 ILE A  34      28.185  32.057  76.997  1.00 37.39           C  
+ATOM    250  CD1 ILE A  34      27.420  32.462  74.150  1.00 38.95           C  
+ATOM    251  N   ALA A  35      24.941  30.339  78.205  1.00 41.92           N  
+ATOM    252  CA  ALA A  35      24.695  29.745  79.508  1.00 43.18           C  
+ATOM    253  C   ALA A  35      25.878  28.894  79.938  1.00 44.41           C  
+ATOM    254  O   ALA A  35      26.433  28.139  79.146  1.00 45.46           O  
+ATOM    255  CB  ALA A  35      23.438  28.901  79.465  1.00 42.44           C  
+ATOM    256  N   ASP A  36      26.262  29.028  81.200  1.00 46.15           N  
+ATOM    257  CA  ASP A  36      27.373  28.265  81.745  1.00 47.31           C  
+ATOM    258  C   ASP A  36      27.265  28.297  83.267  1.00 48.60           C  
+ATOM    259  O   ASP A  36      26.596  29.168  83.829  1.00 49.31           O  
+ATOM    260  CB  ASP A  36      28.699  28.877  81.297  1.00 46.39           C  
+ATOM    261  CG  ASP A  36      29.828  27.871  81.287  1.00 45.88           C  
+ATOM    262  OD1 ASP A  36      29.800  26.960  80.432  1.00 45.19           O  
+ATOM    263  OD2 ASP A  36      30.738  27.988  82.136  1.00 45.12           O  
+ATOM    264  N   ILE A  37      27.915  27.351  83.936  1.00 50.09           N  
+ATOM    265  CA  ILE A  37      27.863  27.297  85.392  1.00 51.95           C  
+ATOM    266  C   ILE A  37      28.675  28.423  86.033  1.00 53.37           C  
+ATOM    267  O   ILE A  37      28.359  28.876  87.135  1.00 53.50           O  
+ATOM    268  CB  ILE A  37      28.371  25.949  85.917  1.00 51.56           C  
+ATOM    269  CG1 ILE A  37      28.119  25.865  87.423  1.00 51.91           C  
+ATOM    270  CG2 ILE A  37      29.850  25.790  85.595  1.00 51.01           C  
+ATOM    271  CD1 ILE A  37      28.295  24.481  88.004  1.00 52.00           C  
+ATOM    272  N   ASN A  38      29.720  28.865  85.335  1.00 54.64           N  
+ATOM    273  CA  ASN A  38      30.572  29.955  85.808  1.00 55.52           C  
+ATOM    274  C   ASN A  38      30.205  31.247  85.084  1.00 54.73           C  
+ATOM    275  O   ASN A  38      30.615  31.463  83.940  1.00 55.80           O  
+ATOM    276  CB  ASN A  38      32.046  29.639  85.552  1.00 56.47           C  
+ATOM    277  CG  ASN A  38      32.936  30.854  85.732  1.00 57.78           C  
+ATOM    278  OD1 ASN A  38      32.920  31.504  86.782  1.00 57.89           O  
+ATOM    279  ND2 ASN A  38      33.717  31.170  84.706  1.00 58.70           N  
+ATOM    280  N   LEU A  39      29.447  32.105  85.757  1.00 53.84           N  
+ATOM    281  CA  LEU A  39      29.002  33.363  85.173  1.00 54.57           C  
+ATOM    282  C   LEU A  39      30.136  34.284  84.727  1.00 55.54           C  
+ATOM    283  O   LEU A  39      29.931  35.148  83.876  1.00 56.03           O  
+ATOM    284  CB  LEU A  39      28.090  34.097  86.154  1.00 53.87           C  
+ATOM    285  CG  LEU A  39      27.369  35.328  85.603  1.00 54.60           C  
+ATOM    286  CD1 LEU A  39      26.591  34.951  84.350  1.00 54.32           C  
+ATOM    287  CD2 LEU A  39      26.433  35.892  86.665  1.00 54.58           C  
+ATOM    288  N   GLU A  40      31.327  34.104  85.295  1.00 56.31           N  
+ATOM    289  CA  GLU A  40      32.472  34.933  84.916  1.00 57.01           C  
+ATOM    290  C   GLU A  40      32.787  34.722  83.441  1.00 56.41           C  
+ATOM    291  O   GLU A  40      32.757  35.662  82.649  1.00 57.32           O  
+ATOM    292  CB  GLU A  40      33.716  34.579  85.745  1.00 57.92           C  
+ATOM    293  CG  GLU A  40      33.674  35.022  87.199  1.00 57.86           C  
+ATOM    294  CD  GLU A  40      34.962  34.708  87.935  0.00 57.81           C  
+ATOM    295  OE1 GLU A  40      36.020  35.241  87.537  0.00 57.80           O  
+ATOM    296  OE2 GLU A  40      34.918  33.927  88.909  0.00 57.80           O  
+ATOM    297  N   ALA A  41      33.087  33.477  83.085  1.00 55.70           N  
+ATOM    298  CA  ALA A  41      33.413  33.119  81.710  1.00 55.07           C  
+ATOM    299  C   ALA A  41      32.261  33.441  80.760  1.00 54.36           C  
+ATOM    300  O   ALA A  41      32.485  33.884  79.631  1.00 55.50           O  
+ATOM    301  CB  ALA A  41      33.759  31.637  81.628  1.00 54.86           C  
+ATOM    302  N   ALA A  42      31.033  33.217  81.220  1.00 51.88           N  
+ATOM    303  CA  ALA A  42      29.860  33.487  80.406  1.00 50.49           C  
+ATOM    304  C   ALA A  42      29.833  34.951  79.984  1.00 50.10           C  
+ATOM    305  O   ALA A  42      29.768  35.254  78.795  1.00 50.28           O  
+ATOM    306  CB  ALA A  42      28.595  33.138  81.176  1.00 49.63           C  
+ATOM    307  N   ARG A  43      29.889  35.855  80.960  1.00 49.94           N  
+ATOM    308  CA  ARG A  43      29.873  37.291  80.683  1.00 49.15           C  
+ATOM    309  C   ARG A  43      31.008  37.677  79.745  1.00 48.09           C  
+ATOM    310  O   ARG A  43      30.836  38.518  78.864  1.00 47.84           O  
+ATOM    311  CB  ARG A  43      30.007  38.101  81.977  1.00 49.16           C  
+ATOM    312  CG  ARG A  43      28.905  37.872  82.993  1.00 49.68           C  
+ATOM    313  CD  ARG A  43      28.432  39.193  83.580  1.00 49.79           C  
+ATOM    314  NE  ARG A  43      29.543  40.037  84.010  0.00 49.84           N  
+ATOM    315  CZ  ARG A  43      30.359  39.749  85.018  0.00 49.87           C  
+ATOM    316  NH1 ARG A  43      30.194  38.631  85.712  0.00 49.88           N  
+ATOM    317  NH2 ARG A  43      31.344  40.580  85.331  0.00 49.88           N  
+ATOM    318  N   ALA A  44      32.168  37.058  79.948  1.00 46.99           N  
+ATOM    319  CA  ALA A  44      33.347  37.326  79.134  1.00 47.53           C  
+ATOM    320  C   ALA A  44      33.092  37.017  77.663  1.00 48.09           C  
+ATOM    321  O   ALA A  44      33.331  37.854  76.789  1.00 48.80           O  
+ATOM    322  CB  ALA A  44      34.517  36.499  79.640  1.00 46.98           C  
+ATOM    323  N   THR A  45      32.613  35.805  77.401  1.00 48.24           N  
+ATOM    324  CA  THR A  45      32.315  35.359  76.046  1.00 47.85           C  
+ATOM    325  C   THR A  45      31.174  36.166  75.430  1.00 48.44           C  
+ATOM    326  O   THR A  45      31.248  36.574  74.271  1.00 48.68           O  
+ATOM    327  CB  THR A  45      31.932  33.864  76.037  1.00 47.38           C  
+ATOM    328  OG1 THR A  45      33.031  33.089  76.529  1.00 45.66           O  
+ATOM    329  CG2 THR A  45      31.589  33.403  74.631  1.00 47.55           C  
+ATOM    330  N   ALA A  46      30.121  36.396  76.207  1.00 49.20           N  
+ATOM    331  CA  ALA A  46      28.970  37.147  75.722  1.00 50.60           C  
+ATOM    332  C   ALA A  46      29.372  38.548  75.281  1.00 51.74           C  
+ATOM    333  O   ALA A  46      28.896  39.053  74.260  1.00 52.51           O  
+ATOM    334  CB  ALA A  46      27.906  37.228  76.806  1.00 50.87           C  
+ATOM    335  N   ALA A  47      30.248  39.174  76.059  1.00 52.05           N  
+ATOM    336  CA  ALA A  47      30.707  40.523  75.755  1.00 52.69           C  
+ATOM    337  C   ALA A  47      31.644  40.502  74.553  1.00 51.52           C  
+ATOM    338  O   ALA A  47      31.737  41.470  73.799  1.00 51.19           O  
+ATOM    339  CB  ALA A  47      31.419  41.112  76.969  1.00 52.78           C  
+ATOM    340  N   GLU A  48      32.330  39.380  74.388  1.00 51.09           N  
+ATOM    341  CA  GLU A  48      33.274  39.192  73.301  1.00 51.37           C  
+ATOM    342  C   GLU A  48      32.542  39.009  71.972  1.00 51.47           C  
+ATOM    343  O   GLU A  48      33.058  39.387  70.918  1.00 52.14           O  
+ATOM    344  CB  GLU A  48      34.139  37.968  73.606  1.00 52.10           C  
+ATOM    345  CG  GLU A  48      35.520  37.991  72.994  1.00 54.21           C  
+ATOM    346  CD  GLU A  48      36.492  37.099  73.748  1.00 54.75           C  
+ATOM    347  OE1 GLU A  48      36.631  37.285  74.974  1.00 56.29           O  
+ATOM    348  OE2 GLU A  48      37.119  36.218  73.125  1.00 55.57           O  
+ATOM    349  N   ILE A  49      31.336  38.442  72.035  1.00 50.68           N  
+ATOM    350  CA  ILE A  49      30.522  38.190  70.846  1.00 49.69           C  
+ATOM    351  C   ILE A  49      29.723  39.410  70.390  1.00 49.67           C  
+ATOM    352  O   ILE A  49      29.548  39.630  69.192  1.00 49.69           O  
+ATOM    353  CB  ILE A  49      29.549  36.999  71.076  1.00 49.01           C  
+ATOM    354  CG1 ILE A  49      30.350  35.705  71.233  1.00 48.28           C  
+ATOM    355  CG2 ILE A  49      28.568  36.880  69.916  1.00 47.17           C  
+ATOM    356  CD1 ILE A  49      29.499  34.463  71.377  1.00 47.96           C  
+ATOM    357  N   GLY A  50      29.228  40.200  71.335  1.00 49.39           N  
+ATOM    358  CA  GLY A  50      28.476  41.377  70.949  1.00 49.47           C  
+ATOM    359  C   GLY A  50      27.117  41.538  71.598  1.00 50.11           C  
+ATOM    360  O   GLY A  50      26.726  40.737  72.449  1.00 50.29           O  
+ATOM    361  N   PRO A  51      26.372  42.587  71.207  1.00 50.40           N  
+ATOM    362  CA  PRO A  51      25.034  42.921  71.712  1.00 49.58           C  
+ATOM    363  C   PRO A  51      23.998  41.830  71.457  1.00 49.02           C  
+ATOM    364  O   PRO A  51      22.927  41.829  72.067  1.00 49.15           O  
+ATOM    365  CB  PRO A  51      24.695  44.209  70.962  1.00 50.07           C  
+ATOM    366  CG  PRO A  51      26.039  44.821  70.704  1.00 49.86           C  
+ATOM    367  CD  PRO A  51      26.847  43.628  70.278  1.00 49.89           C  
+ATOM    368  N   ALA A  52      24.318  40.909  70.553  1.00 48.54           N  
+ATOM    369  CA  ALA A  52      23.401  39.823  70.213  1.00 48.72           C  
+ATOM    370  C   ALA A  52      23.466  38.671  71.213  1.00 48.10           C  
+ATOM    371  O   ALA A  52      22.586  37.809  71.240  1.00 48.18           O  
+ATOM    372  CB  ALA A  52      23.698  39.313  68.809  1.00 47.21           C  
+ATOM    373  N   ALA A  53      24.508  38.661  72.035  1.00 47.86           N  
+ATOM    374  CA  ALA A  53      24.677  37.611  73.028  1.00 48.97           C  
+ATOM    375  C   ALA A  53      24.611  38.150  74.458  1.00 49.45           C  
+ATOM    376  O   ALA A  53      25.078  39.251  74.743  1.00 50.94           O  
+ATOM    377  CB  ALA A  53      26.007  36.901  72.803  1.00 48.79           C  
+ATOM    378  N   CYS A  54      24.015  37.370  75.351  1.00 48.98           N  
+ATOM    379  CA  CYS A  54      23.913  37.747  76.749  1.00 48.17           C  
+ATOM    380  C   CYS A  54      24.262  36.524  77.589  1.00 47.49           C  
+ATOM    381  O   CYS A  54      24.032  35.389  77.168  1.00 47.24           O  
+ATOM    382  CB  CYS A  54      22.505  38.250  77.070  1.00 49.09           C  
+ATOM    383  SG  CYS A  54      21.176  37.139  76.603  1.00 53.63           S  
+ATOM    384  N   ALA A  55      24.835  36.757  78.766  1.00 46.35           N  
+ATOM    385  CA  ALA A  55      25.234  35.670  79.651  1.00 44.77           C  
+ATOM    386  C   ALA A  55      24.166  35.313  80.682  1.00 44.27           C  
+ATOM    387  O   ALA A  55      23.260  36.099  80.968  1.00 44.34           O  
+ATOM    388  CB  ALA A  55      26.541  36.029  80.353  1.00 44.16           C  
+ATOM    389  N   ILE A  56      24.274  34.107  81.224  1.00 43.29           N  
+ATOM    390  CA  ILE A  56      23.343  33.630  82.237  1.00 42.02           C  
+ATOM    391  C   ILE A  56      23.912  32.391  82.914  1.00 41.19           C  
+ATOM    392  O   ILE A  56      24.461  31.500  82.259  1.00 40.62           O  
+ATOM    393  CB  ILE A  56      21.952  33.301  81.641  1.00 41.75           C  
+ATOM    394  CG1 ILE A  56      20.980  32.970  82.770  1.00 41.95           C  
+ATOM    395  CG2 ILE A  56      22.037  32.118  80.696  1.00 41.03           C  
+ATOM    396  CD1 ILE A  56      19.538  32.936  82.327  1.00 42.82           C  
+ATOM    397  N   ALA A  57      23.793  32.349  84.235  1.00 39.65           N  
+ATOM    398  CA  ALA A  57      24.308  31.232  85.012  1.00 38.36           C  
+ATOM    399  C   ALA A  57      23.370  30.037  84.907  1.00 37.61           C  
+ATOM    400  O   ALA A  57      22.146  30.182  84.994  1.00 36.56           O  
+ATOM    401  CB  ALA A  57      24.475  31.649  86.468  1.00 37.83           C  
+ATOM    402  N   LEU A  58      23.947  28.855  84.717  1.00 36.28           N  
+ATOM    403  CA  LEU A  58      23.140  27.651  84.599  1.00 35.96           C  
+ATOM    404  C   LEU A  58      23.840  26.388  85.066  1.00 35.93           C  
+ATOM    405  O   LEU A  58      24.970  26.097  84.670  1.00 36.09           O  
+ATOM    406  CB  LEU A  58      22.692  27.458  83.152  1.00 35.23           C  
+ATOM    407  CG  LEU A  58      21.843  26.214  82.879  1.00 33.94           C  
+ATOM    408  CD1 LEU A  58      20.495  26.339  83.567  1.00 30.46           C  
+ATOM    409  CD2 LEU A  58      21.654  26.060  81.378  1.00 33.43           C  
+ATOM    410  N   ASP A  59      23.156  25.643  85.921  1.00 35.71           N  
+ATOM    411  CA  ASP A  59      23.674  24.380  86.417  1.00 35.86           C  
+ATOM    412  C   ASP A  59      22.624  23.368  85.984  1.00 35.81           C  
+ATOM    413  O   ASP A  59      21.618  23.187  86.673  1.00 35.94           O  
+ATOM    414  CB  ASP A  59      23.780  24.396  87.938  1.00 36.21           C  
+ATOM    415  CG  ASP A  59      24.445  23.156  88.474  1.00 37.33           C  
+ATOM    416  OD1 ASP A  59      24.050  22.047  88.059  1.00 36.23           O  
+ATOM    417  OD2 ASP A  59      25.362  23.291  89.307  1.00 40.49           O  
+ATOM    418  N   VAL A  60      22.845  22.723  84.838  1.00 34.59           N  
+ATOM    419  CA  VAL A  60      21.877  21.764  84.314  1.00 33.19           C  
+ATOM    420  C   VAL A  60      21.534  20.613  85.254  1.00 33.10           C  
+ATOM    421  O   VAL A  60      20.557  19.899  85.025  1.00 31.94           O  
+ATOM    422  CB  VAL A  60      22.331  21.174  82.945  1.00 32.86           C  
+ATOM    423  CG1 VAL A  60      22.377  22.279  81.896  1.00 30.34           C  
+ATOM    424  CG2 VAL A  60      23.684  20.491  83.078  1.00 31.52           C  
+ATOM    425  N   THR A  61      22.321  20.434  86.312  1.00 33.07           N  
+ATOM    426  CA  THR A  61      22.057  19.356  87.259  1.00 34.49           C  
+ATOM    427  C   THR A  61      21.128  19.803  88.388  1.00 35.19           C  
+ATOM    428  O   THR A  61      20.699  18.986  89.201  1.00 36.31           O  
+ATOM    429  CB  THR A  61      23.344  18.836  87.901  1.00 34.05           C  
+ATOM    430  OG1 THR A  61      23.795  19.777  88.879  1.00 36.43           O  
+ATOM    431  CG2 THR A  61      24.422  18.655  86.856  1.00 33.40           C  
+ATOM    432  N   ASP A  62      20.818  21.098  88.433  1.00 36.00           N  
+ATOM    433  CA  ASP A  62      19.945  21.644  89.473  1.00 35.14           C  
+ATOM    434  C   ASP A  62      18.631  22.188  88.916  1.00 34.81           C  
+ATOM    435  O   ASP A  62      18.615  23.185  88.194  1.00 34.83           O  
+ATOM    436  CB  ASP A  62      20.663  22.760  90.228  1.00 37.13           C  
+ATOM    437  CG  ASP A  62      19.817  23.336  91.339  1.00 38.64           C  
+ATOM    438  OD1 ASP A  62      19.553  22.601  92.314  1.00 40.81           O  
+ATOM    439  OD2 ASP A  62      19.407  24.512  91.235  1.00 38.60           O  
+ATOM    440  N   GLN A  63      17.527  21.546  89.275  1.00 33.87           N  
+ATOM    441  CA  GLN A  63      16.217  21.962  88.794  1.00 33.52           C  
+ATOM    442  C   GLN A  63      15.944  23.448  89.021  1.00 34.72           C  
+ATOM    443  O   GLN A  63      15.393  24.129  88.158  1.00 35.13           O  
+ATOM    444  CB  GLN A  63      15.128  21.138  89.477  1.00 32.53           C  
+ATOM    445  CG  GLN A  63      13.749  21.322  88.871  1.00 32.39           C  
+ATOM    446  CD  GLN A  63      13.678  20.827  87.437  1.00 32.46           C  
+ATOM    447  OE1 GLN A  63      13.977  19.666  87.154  1.00 31.56           O  
+ATOM    448  NE2 GLN A  63      13.279  21.707  86.526  1.00 30.21           N  
+ATOM    449  N   ALA A  64      16.329  23.955  90.187  1.00 35.86           N  
+ATOM    450  CA  ALA A  64      16.097  25.362  90.506  1.00 34.48           C  
+ATOM    451  C   ALA A  64      16.796  26.271  89.506  1.00 32.80           C  
+ATOM    452  O   ALA A  64      16.200  27.223  89.001  1.00 32.43           O  
+ATOM    453  CB  ALA A  64      16.579  25.670  91.924  1.00 35.25           C  
+ATOM    454  N   SER A  65      18.062  25.976  89.227  1.00 31.21           N  
+ATOM    455  CA  SER A  65      18.843  26.772  88.284  1.00 30.13           C  
+ATOM    456  C   SER A  65      18.215  26.692  86.894  1.00 29.47           C  
+ATOM    457  O   SER A  65      18.210  27.665  86.144  1.00 27.80           O  
+ATOM    458  CB  SER A  65      20.284  26.266  88.238  1.00 29.21           C  
+ATOM    459  OG  SER A  65      21.095  27.121  87.457  1.00 30.51           O  
+ATOM    460  N   ILE A  66      17.674  25.523  86.567  1.00 29.84           N  
+ATOM    461  CA  ILE A  66      17.037  25.306  85.277  1.00 30.26           C  
+ATOM    462  C   ILE A  66      15.785  26.169  85.134  1.00 32.24           C  
+ATOM    463  O   ILE A  66      15.634  26.890  84.147  1.00 32.91           O  
+ATOM    464  CB  ILE A  66      16.686  23.801  85.077  1.00 27.13           C  
+ATOM    465  CG1 ILE A  66      17.952  23.026  84.702  1.00 24.91           C  
+ATOM    466  CG2 ILE A  66      15.609  23.636  84.022  1.00 24.45           C  
+ATOM    467  CD1 ILE A  66      17.751  21.532  84.563  1.00 26.91           C  
+ATOM    468  N   ASP A  67      14.893  26.108  86.117  1.00 34.00           N  
+ATOM    469  CA  ASP A  67      13.664  26.895  86.059  1.00 35.40           C  
+ATOM    470  C   ASP A  67      13.937  28.400  86.059  1.00 36.75           C  
+ATOM    471  O   ASP A  67      13.202  29.176  85.442  1.00 36.01           O  
+ATOM    472  CB  ASP A  67      12.742  26.532  87.225  1.00 36.58           C  
+ATOM    473  CG  ASP A  67      12.308  25.081  87.193  1.00 38.36           C  
+ATOM    474  OD1 ASP A  67      11.931  24.610  86.103  1.00 39.81           O  
+ATOM    475  OD2 ASP A  67      12.336  24.413  88.252  1.00 38.47           O  
+ATOM    476  N   ARG A  68      14.985  28.819  86.758  1.00 38.36           N  
+ATOM    477  CA  ARG A  68      15.316  30.231  86.796  1.00 40.77           C  
+ATOM    478  C   ARG A  68      15.752  30.657  85.408  1.00 41.08           C  
+ATOM    479  O   ARG A  68      15.227  31.623  84.852  1.00 40.58           O  
+ATOM    480  CB  ARG A  68      16.445  30.508  87.788  1.00 44.09           C  
+ATOM    481  CG  ARG A  68      15.981  30.904  89.178  1.00 48.76           C  
+ATOM    482  CD  ARG A  68      17.099  31.640  89.915  1.00 53.27           C  
+ATOM    483  NE  ARG A  68      18.266  30.792  90.159  1.00 54.86           N  
+ATOM    484  CZ  ARG A  68      18.303  29.815  91.061  1.00 54.87           C  
+ATOM    485  NH1 ARG A  68      17.235  29.562  91.810  1.00 55.06           N  
+ATOM    486  NH2 ARG A  68      19.406  29.090  91.213  1.00 54.48           N  
+ATOM    487  N   CYS A  69      16.712  29.918  84.856  1.00 40.06           N  
+ATOM    488  CA  CYS A  69      17.252  30.191  83.531  1.00 39.62           C  
+ATOM    489  C   CYS A  69      16.169  30.403  82.475  1.00 38.72           C  
+ATOM    490  O   CYS A  69      16.150  31.422  81.783  1.00 37.80           O  
+ATOM    491  CB  CYS A  69      18.165  29.044  83.100  1.00 39.99           C  
+ATOM    492  SG  CYS A  69      18.689  29.125  81.368  1.00 42.49           S  
+ATOM    493  N   VAL A  70      15.265  29.438  82.361  1.00 38.16           N  
+ATOM    494  CA  VAL A  70      14.189  29.507  81.384  1.00 37.40           C  
+ATOM    495  C   VAL A  70      13.238  30.673  81.619  1.00 38.38           C  
+ATOM    496  O   VAL A  70      12.861  31.369  80.679  1.00 40.49           O  
+ATOM    497  CB  VAL A  70      13.381  28.194  81.370  1.00 36.15           C  
+ATOM    498  CG1 VAL A  70      12.103  28.367  80.558  1.00 34.94           C  
+ATOM    499  CG2 VAL A  70      14.233  27.081  80.784  1.00 34.51           C  
+ATOM    500  N   ALA A  71      12.843  30.881  82.868  1.00 38.72           N  
+ATOM    501  CA  ALA A  71      11.934  31.969  83.201  1.00 38.96           C  
+ATOM    502  C   ALA A  71      12.553  33.335  82.885  1.00 39.02           C  
+ATOM    503  O   ALA A  71      11.873  34.233  82.394  1.00 37.96           O  
+ATOM    504  CB  ALA A  71      11.554  31.891  84.680  1.00 39.38           C  
+ATOM    505  N   GLU A  72      13.844  33.483  83.160  1.00 38.71           N  
+ATOM    506  CA  GLU A  72      14.534  34.741  82.913  1.00 40.87           C  
+ATOM    507  C   GLU A  72      14.619  35.073  81.427  1.00 42.58           C  
+ATOM    508  O   GLU A  72      14.327  36.200  81.017  1.00 43.89           O  
+ATOM    509  CB  GLU A  72      15.936  34.691  83.515  1.00 41.27           C  
+ATOM    510  CG  GLU A  72      16.717  35.978  83.370  1.00 44.16           C  
+ATOM    511  CD  GLU A  72      17.913  36.020  84.299  1.00 46.54           C  
+ATOM    512  OE1 GLU A  72      18.684  37.003  84.250  1.00 46.48           O  
+ATOM    513  OE2 GLU A  72      18.076  35.063  85.086  1.00 48.50           O  
+ATOM    514  N   LEU A  73      15.021  34.094  80.622  1.00 42.36           N  
+ATOM    515  CA  LEU A  73      15.134  34.288  79.183  1.00 40.61           C  
+ATOM    516  C   LEU A  73      13.766  34.552  78.574  1.00 41.27           C  
+ATOM    517  O   LEU A  73      13.641  35.313  77.613  1.00 40.27           O  
+ATOM    518  CB  LEU A  73      15.770  33.060  78.536  1.00 40.13           C  
+ATOM    519  CG  LEU A  73      17.241  32.840  78.898  1.00 38.89           C  
+ATOM    520  CD1 LEU A  73      17.704  31.513  78.328  1.00 38.35           C  
+ATOM    521  CD2 LEU A  73      18.090  33.994  78.365  1.00 37.11           C  
+ATOM    522  N   LEU A  74      12.738  33.925  79.135  1.00 42.57           N  
+ATOM    523  CA  LEU A  74      11.384  34.124  78.639  1.00 45.20           C  
+ATOM    524  C   LEU A  74      10.957  35.578  78.780  1.00 47.81           C  
+ATOM    525  O   LEU A  74      10.206  36.089  77.953  1.00 48.42           O  
+ATOM    526  CB  LEU A  74      10.395  33.229  79.386  1.00 43.87           C  
+ATOM    527  CG  LEU A  74      10.201  31.823  78.817  1.00 44.62           C  
+ATOM    528  CD1 LEU A  74       9.162  31.074  79.643  1.00 45.12           C  
+ATOM    529  CD2 LEU A  74       9.745  31.919  77.367  1.00 44.40           C  
+ATOM    530  N   ASP A  75      11.432  36.243  79.830  1.00 50.76           N  
+ATOM    531  CA  ASP A  75      11.076  37.637  80.051  1.00 52.76           C  
+ATOM    532  C   ASP A  75      11.948  38.559  79.219  1.00 52.17           C  
+ATOM    533  O   ASP A  75      11.502  39.623  78.803  1.00 52.65           O  
+ATOM    534  CB  ASP A  75      11.193  38.005  81.535  1.00 56.34           C  
+ATOM    535  CG  ASP A  75      10.282  37.165  82.419  1.00 59.85           C  
+ATOM    536  OD1 ASP A  75       9.204  36.740  81.942  1.00 60.41           O  
+ATOM    537  OD2 ASP A  75      10.641  36.942  83.596  1.00 62.77           O  
+ATOM    538  N   ARG A  76      13.189  38.152  78.972  1.00 51.65           N  
+ATOM    539  CA  ARG A  76      14.096  38.966  78.170  1.00 50.77           C  
+ATOM    540  C   ARG A  76      13.787  38.837  76.680  1.00 48.49           C  
+ATOM    541  O   ARG A  76      13.930  39.802  75.932  1.00 48.31           O  
+ATOM    542  CB  ARG A  76      15.558  38.560  78.388  1.00 52.74           C  
+ATOM    543  CG  ARG A  76      16.071  38.633  79.814  1.00 56.53           C  
+ATOM    544  CD  ARG A  76      17.593  38.707  79.785  1.00 60.30           C  
+ATOM    545  NE  ARG A  76      18.226  38.126  80.965  1.00 64.33           N  
+ATOM    546  CZ  ARG A  76      19.544  38.051  81.138  1.00 66.39           C  
+ATOM    547  NH1 ARG A  76      20.364  38.528  80.207  1.00 66.95           N  
+ATOM    548  NH2 ARG A  76      20.046  37.489  82.233  1.00 67.54           N  
+ATOM    549  N   TRP A  77      13.367  37.649  76.250  1.00 45.41           N  
+ATOM    550  CA  TRP A  77      13.073  37.420  74.835  1.00 42.13           C  
+ATOM    551  C   TRP A  77      11.604  37.231  74.487  1.00 41.62           C  
+ATOM    552  O   TRP A  77      11.191  37.532  73.372  1.00 42.05           O  
+ATOM    553  CB  TRP A  77      13.828  36.196  74.313  1.00 40.03           C  
+ATOM    554  CG  TRP A  77      15.319  36.285  74.371  1.00 37.51           C  
+ATOM    555  CD1 TRP A  77      16.080  37.418  74.381  1.00 36.49           C  
+ATOM    556  CD2 TRP A  77      16.236  35.186  74.343  1.00 36.56           C  
+ATOM    557  NE1 TRP A  77      17.415  37.092  74.356  1.00 36.46           N  
+ATOM    558  CE2 TRP A  77      17.538  35.726  74.331  1.00 35.91           C  
+ATOM    559  CE3 TRP A  77      16.083  33.793  74.319  1.00 36.20           C  
+ATOM    560  CZ2 TRP A  77      18.682  34.926  74.301  1.00 36.10           C  
+ATOM    561  CZ3 TRP A  77      17.218  32.997  74.289  1.00 35.54           C  
+ATOM    562  CH2 TRP A  77      18.501  33.567  74.278  1.00 35.62           C  
+ATOM    563  N   GLY A  78      10.817  36.722  75.427  1.00 41.28           N  
+ATOM    564  CA  GLY A  78       9.413  36.492  75.148  1.00 39.86           C  
+ATOM    565  C   GLY A  78       9.199  35.091  74.606  1.00 39.97           C  
+ATOM    566  O   GLY A  78       8.073  34.603  74.550  1.00 40.78           O  
+ATOM    567  N   SER A  79      10.281  34.441  74.189  1.00 39.94           N  
+ATOM    568  CA  SER A  79      10.198  33.078  73.665  1.00 40.25           C  
+ATOM    569  C   SER A  79      11.570  32.517  73.303  1.00 39.63           C  
+ATOM    570  O   SER A  79      12.458  33.249  72.854  1.00 39.90           O  
+ATOM    571  CB  SER A  79       9.300  33.022  72.426  1.00 40.29           C  
+ATOM    572  OG  SER A  79       9.923  33.655  71.324  1.00 41.43           O  
+ATOM    573  N   ILE A  80      11.733  31.214  73.509  1.00 37.58           N  
+ATOM    574  CA  ILE A  80      12.976  30.529  73.189  1.00 35.51           C  
+ATOM    575  C   ILE A  80      12.668  29.699  71.951  1.00 34.68           C  
+ATOM    576  O   ILE A  80      11.840  28.787  72.008  1.00 35.20           O  
+ATOM    577  CB  ILE A  80      13.401  29.597  74.332  1.00 35.48           C  
+ATOM    578  CG1 ILE A  80      13.495  30.395  75.631  1.00 36.66           C  
+ATOM    579  CG2 ILE A  80      14.737  28.950  74.013  1.00 34.17           C  
+ATOM    580  CD1 ILE A  80      13.798  29.547  76.843  1.00 38.10           C  
+ATOM    581  N   ASP A  81      13.314  30.021  70.832  1.00 31.81           N  
+ATOM    582  CA  ASP A  81      13.066  29.295  69.590  1.00 29.02           C  
+ATOM    583  C   ASP A  81      13.932  28.060  69.419  1.00 26.87           C  
+ATOM    584  O   ASP A  81      13.478  27.046  68.891  1.00 25.72           O  
+ATOM    585  CB  ASP A  81      13.288  30.199  68.377  1.00 30.39           C  
+ATOM    586  CG  ASP A  81      12.416  31.436  68.400  1.00 32.09           C  
+ATOM    587  OD1 ASP A  81      11.213  31.313  68.725  1.00 32.38           O  
+ATOM    588  OD2 ASP A  81      12.938  32.527  68.081  1.00 32.67           O  
+ATOM    589  N   ILE A  82      15.177  28.146  69.872  1.00 24.06           N  
+ATOM    590  CA  ILE A  82      16.111  27.042  69.710  1.00 23.63           C  
+ATOM    591  C   ILE A  82      16.885  26.710  70.981  1.00 23.22           C  
+ATOM    592  O   ILE A  82      17.361  27.601  71.683  1.00 23.85           O  
+ATOM    593  CB  ILE A  82      17.145  27.369  68.607  1.00 23.10           C  
+ATOM    594  CG1 ILE A  82      16.439  27.943  67.373  1.00 24.17           C  
+ATOM    595  CG2 ILE A  82      17.930  26.127  68.255  1.00 20.12           C  
+ATOM    596  CD1 ILE A  82      17.391  28.510  66.314  1.00 21.60           C  
+ATOM    597  N   LEU A  83      17.036  25.419  71.249  1.00 22.50           N  
+ATOM    598  CA  LEU A  83      17.762  24.955  72.423  1.00 21.46           C  
+ATOM    599  C   LEU A  83      18.813  23.938  72.002  1.00 21.96           C  
+ATOM    600  O   LEU A  83      18.507  22.958  71.319  1.00 23.88           O  
+ATOM    601  CB  LEU A  83      16.781  24.334  73.430  1.00 21.20           C  
+ATOM    602  CG  LEU A  83      17.255  23.705  74.752  1.00 22.02           C  
+ATOM    603  CD1 LEU A  83      17.386  22.220  74.577  1.00 24.56           C  
+ATOM    604  CD2 LEU A  83      18.561  24.314  75.223  1.00 21.61           C  
+ATOM    605  N   VAL A  84      20.057  24.181  72.403  1.00 21.01           N  
+ATOM    606  CA  VAL A  84      21.145  23.284  72.067  1.00 20.11           C  
+ATOM    607  C   VAL A  84      21.814  22.744  73.319  1.00 20.79           C  
+ATOM    608  O   VAL A  84      22.588  23.445  73.971  1.00 22.04           O  
+ATOM    609  CB  VAL A  84      22.218  23.995  71.203  1.00 21.55           C  
+ATOM    610  CG1 VAL A  84      23.360  23.030  70.890  1.00 18.11           C  
+ATOM    611  CG2 VAL A  84      21.589  24.518  69.912  1.00 20.98           C  
+ATOM    612  N   ASN A  85      21.509  21.496  73.656  1.00 20.08           N  
+ATOM    613  CA  ASN A  85      22.106  20.862  74.819  1.00 18.51           C  
+ATOM    614  C   ASN A  85      23.548  20.468  74.495  1.00 18.52           C  
+ATOM    615  O   ASN A  85      23.817  19.350  74.057  1.00 19.21           O  
+ATOM    616  CB  ASN A  85      21.304  19.622  75.233  1.00 18.41           C  
+ATOM    617  CG  ASN A  85      19.937  19.970  75.824  1.00 18.99           C  
+ATOM    618  OD1 ASN A  85      19.813  20.879  76.644  1.00 16.61           O  
+ATOM    619  ND2 ASN A  85      18.908  19.230  75.419  1.00 18.55           N  
+ATOM    620  N   ASN A  86      24.468  21.402  74.713  1.00 18.04           N  
+ATOM    621  CA  ASN A  86      25.885  21.179  74.452  1.00 18.54           C  
+ATOM    622  C   ASN A  86      26.713  20.843  75.712  1.00 18.47           C  
+ATOM    623  O   ASN A  86      27.798  20.269  75.608  1.00 14.60           O  
+ATOM    624  CB  ASN A  86      26.474  22.420  73.771  1.00 18.83           C  
+ATOM    625  CG  ASN A  86      27.958  22.285  73.500  1.00 23.16           C  
+ATOM    626  OD1 ASN A  86      28.385  21.440  72.711  1.00 24.69           O  
+ATOM    627  ND2 ASN A  86      28.758  23.114  74.164  1.00 27.29           N  
+ATOM    628  N   ALA A  87      26.208  21.199  76.895  1.00 18.54           N  
+ATOM    629  CA  ALA A  87      26.934  20.936  78.146  1.00 18.23           C  
+ATOM    630  C   ALA A  87      27.198  19.454  78.361  1.00 17.40           C  
+ATOM    631  O   ALA A  87      26.286  18.635  78.299  1.00 18.97           O  
+ATOM    632  CB  ALA A  87      26.164  21.504  79.332  1.00 18.39           C  
+ATOM    633  N   ALA A  88      28.449  19.106  78.629  1.00 17.55           N  
+ATOM    634  CA  ALA A  88      28.793  17.712  78.827  1.00 18.66           C  
+ATOM    635  C   ALA A  88      30.147  17.528  79.504  1.00 20.46           C  
+ATOM    636  O   ALA A  88      30.954  18.452  79.575  1.00 21.40           O  
+ATOM    637  CB  ALA A  88      28.783  16.992  77.480  1.00 18.28           C  
+ATOM    638  N   LEU A  89      30.384  16.322  80.004  1.00 22.35           N  
+ATOM    639  CA  LEU A  89      31.637  15.993  80.661  1.00 22.91           C  
+ATOM    640  C   LEU A  89      32.177  14.702  80.088  1.00 21.30           C  
+ATOM    641  O   LEU A  89      31.428  13.839  79.646  1.00 19.69           O  
+ATOM    642  CB  LEU A  89      31.445  15.823  82.173  1.00 27.01           C  
+ATOM    643  CG  LEU A  89      31.564  17.045  83.089  1.00 29.37           C  
+ATOM    644  CD1 LEU A  89      31.381  16.585  84.531  1.00 30.12           C  
+ATOM    645  CD2 LEU A  89      32.931  17.704  82.926  1.00 29.29           C  
+ATOM    646  N   PHE A  90      33.491  14.578  80.114  1.00 22.22           N  
+ATOM    647  CA  PHE A  90      34.151  13.400  79.595  1.00 22.86           C  
+ATOM    648  C   PHE A  90      35.035  12.768  80.668  1.00 24.47           C  
+ATOM    649  O   PHE A  90      35.492  13.445  81.588  1.00 25.08           O  
+ATOM    650  CB  PHE A  90      34.986  13.782  78.373  1.00 19.71           C  
+ATOM    651  CG  PHE A  90      35.767  12.648  77.812  1.00 20.71           C  
+ATOM    652  CD1 PHE A  90      37.100  12.473  78.154  1.00 20.21           C  
+ATOM    653  CD2 PHE A  90      35.162  11.731  76.961  1.00 20.67           C  
+ATOM    654  CE1 PHE A  90      37.821  11.396  77.662  1.00 20.92           C  
+ATOM    655  CE2 PHE A  90      35.873  10.650  76.463  1.00 19.79           C  
+ATOM    656  CZ  PHE A  90      37.208  10.485  76.812  1.00 21.68           C  
+ATOM    657  N   ASP A  91      35.272  11.468  80.543  1.00 25.32           N  
+ATOM    658  CA  ASP A  91      36.094  10.747  81.500  1.00 25.52           C  
+ATOM    659  C   ASP A  91      36.311   9.346  80.941  1.00 26.06           C  
+ATOM    660  O   ASP A  91      35.546   8.882  80.094  1.00 25.43           O  
+ATOM    661  CB  ASP A  91      35.366  10.668  82.844  1.00 28.34           C  
+ATOM    662  CG  ASP A  91      36.315  10.550  84.033  1.00 28.51           C  
+ATOM    663  OD1 ASP A  91      35.804  10.377  85.159  1.00 32.55           O  
+ATOM    664  OD2 ASP A  91      37.551  10.635  83.857  1.00 25.53           O  
+ATOM    665  N   LEU A  92      37.354   8.671  81.406  1.00 25.99           N  
+ATOM    666  CA  LEU A  92      37.626   7.326  80.930  1.00 25.97           C  
+ATOM    667  C   LEU A  92      38.276   6.478  82.000  1.00 24.25           C  
+ATOM    668  O   LEU A  92      38.981   6.986  82.864  1.00 25.34           O  
+ATOM    669  CB  LEU A  92      38.512   7.376  79.679  1.00 28.10           C  
+ATOM    670  CG  LEU A  92      39.851   8.112  79.755  1.00 29.37           C  
+ATOM    671  CD1 LEU A  92      40.986   7.107  79.781  1.00 31.08           C  
+ATOM    672  CD2 LEU A  92      39.999   9.018  78.551  1.00 30.89           C  
+ATOM    673  N   ALA A  93      38.021   5.179  81.939  1.00 22.01           N  
+ATOM    674  CA  ALA A  93      38.583   4.244  82.895  1.00 21.68           C  
+ATOM    675  C   ALA A  93      38.022   2.870  82.587  1.00 19.84           C  
+ATOM    676  O   ALA A  93      36.883   2.756  82.135  1.00 20.46           O  
+ATOM    677  CB  ALA A  93      38.203   4.658  84.326  1.00 22.18           C  
+ATOM    678  N   PRO A  94      38.820   1.809  82.805  1.00 18.44           N  
+ATOM    679  CA  PRO A  94      38.352   0.445  82.542  1.00 18.56           C  
+ATOM    680  C   PRO A  94      37.196   0.101  83.484  1.00 19.10           C  
+ATOM    681  O   PRO A  94      36.959   0.790  84.482  1.00 17.96           O  
+ATOM    682  CB  PRO A  94      39.587  -0.414  82.829  1.00 17.65           C  
+ATOM    683  CG  PRO A  94      40.720   0.506  82.557  1.00 16.82           C  
+ATOM    684  CD  PRO A  94      40.258   1.815  83.132  1.00 17.44           C  
+ATOM    685  N   ILE A  95      36.486  -0.972  83.167  1.00 19.35           N  
+ATOM    686  CA  ILE A  95      35.367  -1.411  83.984  1.00 19.77           C  
+ATOM    687  C   ILE A  95      35.747  -1.563  85.463  1.00 19.74           C  
+ATOM    688  O   ILE A  95      35.127  -0.953  86.328  1.00 18.49           O  
+ATOM    689  CB  ILE A  95      34.809  -2.762  83.478  1.00 19.29           C  
+ATOM    690  CG1 ILE A  95      34.212  -2.590  82.077  1.00 19.44           C  
+ATOM    691  CG2 ILE A  95      33.753  -3.292  84.451  1.00 19.79           C  
+ATOM    692  CD1 ILE A  95      33.033  -1.623  82.015  1.00 17.09           C  
+ATOM    693  N   VAL A  96      36.770  -2.361  85.750  1.00 19.67           N  
+ATOM    694  CA  VAL A  96      37.171  -2.584  87.137  1.00 21.64           C  
+ATOM    695  C   VAL A  96      37.706  -1.357  87.881  1.00 22.62           C  
+ATOM    696  O   VAL A  96      38.021  -1.454  89.060  1.00 24.28           O  
+ATOM    697  CB  VAL A  96      38.231  -3.719  87.257  1.00 20.39           C  
+ATOM    698  CG1 VAL A  96      37.755  -4.962  86.525  1.00 19.41           C  
+ATOM    699  CG2 VAL A  96      39.563  -3.254  86.712  1.00 19.92           C  
+ATOM    700  N   GLU A  97      37.802  -0.210  87.212  1.00 22.01           N  
+ATOM    701  CA  GLU A  97      38.312   0.998  87.861  1.00 20.95           C  
+ATOM    702  C   GLU A  97      37.306   2.130  87.898  1.00 21.11           C  
+ATOM    703  O   GLU A  97      37.590   3.202  88.427  1.00 22.26           O  
+ATOM    704  CB  GLU A  97      39.578   1.496  87.161  1.00 21.10           C  
+ATOM    705  CG  GLU A  97      40.823   0.688  87.471  1.00 23.62           C  
+ATOM    706  CD  GLU A  97      42.031   1.163  86.693  1.00 23.81           C  
+ATOM    707  OE1 GLU A  97      42.268   2.387  86.640  1.00 26.41           O  
+ATOM    708  OE2 GLU A  97      42.750   0.312  86.139  1.00 27.00           O  
+ATOM    709  N   ILE A  98      36.132   1.903  87.330  1.00 20.73           N  
+ATOM    710  CA  ILE A  98      35.115   2.938  87.310  1.00 19.76           C  
+ATOM    711  C   ILE A  98      34.722   3.267  88.748  1.00 20.11           C  
+ATOM    712  O   ILE A  98      34.584   2.374  89.579  1.00 20.28           O  
+ATOM    713  CB  ILE A  98      33.885   2.469  86.500  1.00 18.40           C  
+ATOM    714  CG1 ILE A  98      34.294   2.236  85.045  1.00 18.46           C  
+ATOM    715  CG2 ILE A  98      32.776   3.503  86.575  1.00 17.99           C  
+ATOM    716  CD1 ILE A  98      33.172   1.715  84.173  1.00 18.69           C  
+ATOM    717  N   THR A  99      34.547   4.549  89.033  1.00 19.91           N  
+ATOM    718  CA  THR A  99      34.184   4.991  90.370  1.00 20.47           C  
+ATOM    719  C   THR A  99      32.757   5.507  90.386  1.00 21.49           C  
+ATOM    720  O   THR A  99      32.218   5.877  89.345  1.00 22.14           O  
+ATOM    721  CB  THR A  99      35.098   6.114  90.830  1.00 20.02           C  
+ATOM    722  OG1 THR A  99      34.848   7.281  90.037  1.00 21.23           O  
+ATOM    723  CG2 THR A  99      36.557   5.699  90.675  1.00 18.99           C  
+ATOM    724  N   ARG A 100      32.147   5.533  91.567  1.00 20.86           N  
+ATOM    725  CA  ARG A 100      30.775   6.008  91.693  1.00 21.25           C  
+ATOM    726  C   ARG A 100      30.714   7.495  91.425  1.00 22.04           C  
+ATOM    727  O   ARG A 100      29.669   8.028  91.049  1.00 21.32           O  
+ATOM    728  CB  ARG A 100      30.229   5.733  93.096  1.00 21.99           C  
+ATOM    729  CG  ARG A 100      30.030   4.270  93.416  1.00 21.45           C  
+ATOM    730  CD  ARG A 100      28.595   4.022  93.803  1.00 21.05           C  
+ATOM    731  NE  ARG A 100      28.301   2.599  93.840  1.00 21.89           N  
+ATOM    732  CZ  ARG A 100      27.092   2.096  93.632  1.00 21.17           C  
+ATOM    733  NH1 ARG A 100      26.901   0.786  93.683  1.00 22.28           N  
+ATOM    734  NH2 ARG A 100      26.080   2.908  93.361  1.00 19.13           N  
+ATOM    735  N   GLU A 101      31.837   8.172  91.634  1.00 22.16           N  
+ATOM    736  CA  GLU A 101      31.873   9.605  91.408  1.00 25.43           C  
+ATOM    737  C   GLU A 101      31.900   9.901  89.908  1.00 23.60           C  
+ATOM    738  O   GLU A 101      31.289  10.865  89.455  1.00 23.03           O  
+ATOM    739  CB  GLU A 101      33.089  10.227  92.102  1.00 28.13           C  
+ATOM    740  CG  GLU A 101      34.409   9.639  91.670  1.00 37.06           C  
+ATOM    741  CD  GLU A 101      35.225  10.609  90.858  1.00 41.38           C  
+ATOM    742  OE1 GLU A 101      35.562  10.294  89.700  1.00 43.62           O  
+ATOM    743  OE2 GLU A 101      35.532  11.691  91.387  1.00 47.06           O  
+ATOM    744  N   SER A 102      32.595   9.075  89.135  1.00 22.31           N  
+ATOM    745  CA  SER A 102      32.640   9.299  87.697  1.00 23.09           C  
+ATOM    746  C   SER A 102      31.236   9.078  87.138  1.00 22.44           C  
+ATOM    747  O   SER A 102      30.685   9.925  86.425  1.00 22.31           O  
+ATOM    748  CB  SER A 102      33.622   8.342  87.034  1.00 25.08           C  
+ATOM    749  OG  SER A 102      33.800   8.704  85.675  1.00 28.87           O  
+ATOM    750  N   TYR A 103      30.656   7.937  87.481  1.00 18.65           N  
+ATOM    751  CA  TYR A 103      29.314   7.609  87.044  1.00 21.34           C  
+ATOM    752  C   TYR A 103      28.317   8.715  87.418  1.00 21.94           C  
+ATOM    753  O   TYR A 103      27.665   9.296  86.552  1.00 23.56           O  
+ATOM    754  CB  TYR A 103      28.872   6.288  87.679  1.00 21.53           C  
+ATOM    755  CG  TYR A 103      27.416   5.967  87.449  1.00 23.00           C  
+ATOM    756  CD1 TYR A 103      26.987   5.416  86.243  1.00 22.62           C  
+ATOM    757  CD2 TYR A 103      26.455   6.268  88.417  1.00 22.76           C  
+ATOM    758  CE1 TYR A 103      25.640   5.177  86.002  1.00 22.98           C  
+ATOM    759  CE2 TYR A 103      25.098   6.032  88.183  1.00 23.79           C  
+ATOM    760  CZ  TYR A 103      24.702   5.488  86.970  1.00 23.99           C  
+ATOM    761  OH  TYR A 103      23.371   5.262  86.708  1.00 25.68           O  
+ATOM    762  N   ASP A 104      28.207   8.991  88.714  1.00 22.49           N  
+ATOM    763  CA  ASP A 104      27.284  10.000  89.238  1.00 23.01           C  
+ATOM    764  C   ASP A 104      27.349  11.332  88.516  1.00 22.19           C  
+ATOM    765  O   ASP A 104      26.316  11.929  88.203  1.00 21.72           O  
+ATOM    766  CB  ASP A 104      27.558  10.261  90.724  1.00 24.41           C  
+ATOM    767  CG  ASP A 104      27.167   9.095  91.619  1.00 26.69           C  
+ATOM    768  OD1 ASP A 104      27.576   9.116  92.797  1.00 29.39           O  
+ATOM    769  OD2 ASP A 104      26.455   8.171  91.169  1.00 25.80           O  
+ATOM    770  N   ARG A 105      28.566  11.802  88.275  1.00 20.95           N  
+ATOM    771  CA  ARG A 105      28.783  13.085  87.625  1.00 22.47           C  
+ATOM    772  C   ARG A 105      28.437  13.138  86.119  1.00 22.12           C  
+ATOM    773  O   ARG A 105      27.695  14.023  85.679  1.00 19.28           O  
+ATOM    774  CB  ARG A 105      30.233  13.518  87.860  1.00 25.69           C  
+ATOM    775  CG  ARG A 105      30.365  14.897  88.479  1.00 29.95           C  
+ATOM    776  CD  ARG A 105      31.812  15.233  88.813  1.00 33.99           C  
+ATOM    777  NE  ARG A 105      32.745  14.942  87.725  1.00 37.09           N  
+ATOM    778  CZ  ARG A 105      33.587  13.912  87.719  1.00 39.00           C  
+ATOM    779  NH1 ARG A 105      33.616  13.065  88.745  1.00 41.45           N  
+ATOM    780  NH2 ARG A 105      34.412  13.734  86.696  1.00 39.59           N  
+ATOM    781  N   LEU A 106      28.957  12.193  85.337  1.00 21.14           N  
+ATOM    782  CA  LEU A 106      28.688  12.186  83.905  1.00 19.92           C  
+ATOM    783  C   LEU A 106      27.204  12.029  83.595  1.00 19.76           C  
+ATOM    784  O   LEU A 106      26.673  12.740  82.735  1.00 18.73           O  
+ATOM    785  CB  LEU A 106      29.484  11.078  83.204  1.00 20.49           C  
+ATOM    786  CG  LEU A 106      31.016  11.112  83.295  1.00 19.85           C  
+ATOM    787  CD1 LEU A 106      31.598  10.429  82.066  1.00 17.67           C  
+ATOM    788  CD2 LEU A 106      31.518  12.538  83.366  1.00 19.59           C  
+ATOM    789  N   PHE A 107      26.527  11.114  84.286  1.00 17.48           N  
+ATOM    790  CA  PHE A 107      25.104  10.928  84.029  1.00 18.47           C  
+ATOM    791  C   PHE A 107      24.287  12.135  84.462  1.00 19.90           C  
+ATOM    792  O   PHE A 107      23.299  12.495  83.811  1.00 20.21           O  
+ATOM    793  CB  PHE A 107      24.575   9.664  84.712  1.00 18.99           C  
+ATOM    794  CG  PHE A 107      24.696   8.424  83.865  1.00 17.93           C  
+ATOM    795  CD1 PHE A 107      25.901   7.745  83.767  1.00 16.68           C  
+ATOM    796  CD2 PHE A 107      23.605   7.961  83.135  1.00 17.68           C  
+ATOM    797  CE1 PHE A 107      26.020   6.622  82.950  1.00 19.17           C  
+ATOM    798  CE2 PHE A 107      23.713   6.844  82.318  1.00 18.06           C  
+ATOM    799  CZ  PHE A 107      24.922   6.172  82.223  1.00 17.93           C  
+ATOM    800  N   ALA A 108      24.699  12.770  85.556  1.00 20.29           N  
+ATOM    801  CA  ALA A 108      23.997  13.949  86.050  1.00 20.07           C  
+ATOM    802  C   ALA A 108      24.004  15.079  85.011  1.00 20.51           C  
+ATOM    803  O   ALA A 108      22.982  15.712  84.752  1.00 21.81           O  
+ATOM    804  CB  ALA A 108      24.640  14.424  87.339  1.00 20.59           C  
+ATOM    805  N   ILE A 109      25.153  15.319  84.399  1.00 20.73           N  
+ATOM    806  CA  ILE A 109      25.262  16.382  83.411  1.00 22.03           C  
+ATOM    807  C   ILE A 109      24.875  16.005  81.984  1.00 20.38           C  
+ATOM    808  O   ILE A 109      24.061  16.683  81.367  1.00 21.07           O  
+ATOM    809  CB  ILE A 109      26.686  16.937  83.384  1.00 25.48           C  
+ATOM    810  CG1 ILE A 109      27.046  17.449  84.780  1.00 26.67           C  
+ATOM    811  CG2 ILE A 109      26.798  18.044  82.322  1.00 24.01           C  
+ATOM    812  CD1 ILE A 109      28.508  17.733  84.966  1.00 30.52           C  
+ATOM    813  N   ASN A 110      25.460  14.928  81.466  1.00 19.70           N  
+ATOM    814  CA  ASN A 110      25.198  14.479  80.099  1.00 18.57           C  
+ATOM    815  C   ASN A 110      23.767  14.025  79.835  1.00 18.89           C  
+ATOM    816  O   ASN A 110      23.135  14.459  78.870  1.00 20.23           O  
+ATOM    817  CB  ASN A 110      26.157  13.345  79.734  1.00 16.62           C  
+ATOM    818  CG  ASN A 110      27.614  13.775  79.784  1.00 18.15           C  
+ATOM    819  OD1 ASN A 110      27.928  14.921  80.134  1.00 16.03           O  
+ATOM    820  ND2 ASN A 110      28.515  12.855  79.435  1.00 15.67           N  
+ATOM    821  N   VAL A 111      23.266  13.142  80.692  1.00 18.51           N  
+ATOM    822  CA  VAL A 111      21.915  12.597  80.567  1.00 16.00           C  
+ATOM    823  C   VAL A 111      20.874  13.482  81.245  1.00 19.45           C  
+ATOM    824  O   VAL A 111      20.111  14.186  80.572  1.00 20.05           O  
+ATOM    825  CB  VAL A 111      21.851  11.194  81.187  1.00 12.54           C  
+ATOM    826  CG1 VAL A 111      20.482  10.578  80.969  1.00 11.01           C  
+ATOM    827  CG2 VAL A 111      22.933  10.329  80.587  1.00 14.15           C  
+ATOM    828  N   SER A 112      20.853  13.444  82.578  1.00 20.67           N  
+ATOM    829  CA  SER A 112      19.916  14.231  83.381  1.00 20.34           C  
+ATOM    830  C   SER A 112      19.820  15.688  82.933  1.00 19.69           C  
+ATOM    831  O   SER A 112      18.725  16.234  82.783  1.00 19.30           O  
+ATOM    832  CB  SER A 112      20.334  14.183  84.853  1.00 21.15           C  
+ATOM    833  OG  SER A 112      19.541  15.059  85.628  1.00 23.67           O  
+ATOM    834  N   GLY A 113      20.971  16.319  82.736  1.00 20.05           N  
+ATOM    835  CA  GLY A 113      20.981  17.705  82.301  1.00 20.56           C  
+ATOM    836  C   GLY A 113      20.255  17.912  80.983  1.00 20.79           C  
+ATOM    837  O   GLY A 113      19.447  18.832  80.845  1.00 21.68           O  
+ATOM    838  N   THR A 114      20.533  17.052  80.008  1.00 20.29           N  
+ATOM    839  CA  THR A 114      19.891  17.154  78.700  1.00 19.33           C  
+ATOM    840  C   THR A 114      18.387  16.920  78.787  1.00 19.05           C  
+ATOM    841  O   THR A 114      17.593  17.664  78.200  1.00 18.95           O  
+ATOM    842  CB  THR A 114      20.497  16.139  77.713  1.00 19.60           C  
+ATOM    843  OG1 THR A 114      21.835  16.535  77.391  1.00 19.37           O  
+ATOM    844  CG2 THR A 114      19.663  16.057  76.445  1.00 19.59           C  
+ATOM    845  N   LEU A 115      17.994  15.890  79.530  1.00 18.82           N  
+ATOM    846  CA  LEU A 115      16.582  15.569  79.677  1.00 19.61           C  
+ATOM    847  C   LEU A 115      15.744  16.683  80.292  1.00 20.46           C  
+ATOM    848  O   LEU A 115      14.806  17.181  79.665  1.00 21.53           O  
+ATOM    849  CB  LEU A 115      16.405  14.295  80.508  1.00 20.85           C  
+ATOM    850  CG  LEU A 115      14.952  13.919  80.845  1.00 22.57           C  
+ATOM    851  CD1 LEU A 115      14.116  13.802  79.573  1.00 22.28           C  
+ATOM    852  CD2 LEU A 115      14.937  12.609  81.608  1.00 23.14           C  
+ATOM    853  N   PHE A 116      16.069  17.079  81.517  1.00 20.51           N  
+ATOM    854  CA  PHE A 116      15.280  18.113  82.187  1.00 20.87           C  
+ATOM    855  C   PHE A 116      15.379  19.487  81.546  1.00 20.41           C  
+ATOM    856  O   PHE A 116      14.469  20.308  81.678  1.00 20.80           O  
+ATOM    857  CB  PHE A 116      15.629  18.143  83.682  1.00 18.66           C  
+ATOM    858  CG  PHE A 116      15.251  16.871  84.389  1.00 15.88           C  
+ATOM    859  CD1 PHE A 116      13.913  16.548  84.587  1.00 14.86           C  
+ATOM    860  CD2 PHE A 116      16.220  15.938  84.735  1.00 16.05           C  
+ATOM    861  CE1 PHE A 116      13.546  15.305  85.106  1.00 16.33           C  
+ATOM    862  CE2 PHE A 116      15.861  14.696  85.253  1.00 15.00           C  
+ATOM    863  CZ  PHE A 116      14.524  14.379  85.438  1.00 13.88           C  
+ATOM    864  N   MET A 117      16.471  19.734  80.832  1.00 21.77           N  
+ATOM    865  CA  MET A 117      16.632  21.007  80.139  1.00 22.20           C  
+ATOM    866  C   MET A 117      15.644  20.960  78.957  1.00 21.64           C  
+ATOM    867  O   MET A 117      15.004  21.955  78.626  1.00 21.47           O  
+ATOM    868  CB  MET A 117      18.073  21.152  79.655  1.00 23.05           C  
+ATOM    869  CG  MET A 117      18.524  22.578  79.398  1.00 28.50           C  
+ATOM    870  SD  MET A 117      18.551  23.661  80.862  1.00 29.23           S  
+ATOM    871  CE  MET A 117      17.487  24.948  80.296  1.00 28.57           C  
+ATOM    872  N   MET A 118      15.508  19.786  78.341  1.00 22.05           N  
+ATOM    873  CA  MET A 118      14.574  19.596  77.230  1.00 22.31           C  
+ATOM    874  C   MET A 118      13.153  19.802  77.736  1.00 23.71           C  
+ATOM    875  O   MET A 118      12.328  20.469  77.104  1.00 23.35           O  
+ATOM    876  CB  MET A 118      14.654  18.170  76.674  1.00 20.90           C  
+ATOM    877  CG  MET A 118      15.500  17.977  75.430  1.00 23.11           C  
+ATOM    878  SD  MET A 118      14.977  16.476  74.535  1.00 22.63           S  
+ATOM    879  CE  MET A 118      15.543  15.185  75.629  1.00 23.25           C  
+ATOM    880  N   GLN A 119      12.869  19.195  78.882  1.00 25.13           N  
+ATOM    881  CA  GLN A 119      11.548  19.276  79.477  1.00 25.60           C  
+ATOM    882  C   GLN A 119      11.169  20.713  79.807  1.00 25.48           C  
+ATOM    883  O   GLN A 119      10.057  21.152  79.521  1.00 25.67           O  
+ATOM    884  CB  GLN A 119      11.511  18.424  80.734  1.00 26.26           C  
+ATOM    885  CG  GLN A 119      10.141  18.293  81.353  1.00 27.78           C  
+ATOM    886  CD  GLN A 119      10.219  17.718  82.746  1.00 26.91           C  
+ATOM    887  OE1 GLN A 119      10.850  18.303  83.629  1.00 26.42           O  
+ATOM    888  NE2 GLN A 119       9.592  16.564  82.951  1.00 24.18           N  
+ATOM    889  N   ALA A 120      12.097  21.449  80.403  1.00 25.78           N  
+ATOM    890  CA  ALA A 120      11.831  22.835  80.753  1.00 27.01           C  
+ATOM    891  C   ALA A 120      11.499  23.684  79.516  1.00 28.88           C  
+ATOM    892  O   ALA A 120      10.482  24.383  79.487  1.00 29.66           O  
+ATOM    893  CB  ALA A 120      13.025  23.412  81.481  1.00 27.01           C  
+ATOM    894  N   VAL A 121      12.355  23.621  78.495  1.00 29.43           N  
+ATOM    895  CA  VAL A 121      12.145  24.390  77.263  1.00 28.82           C  
+ATOM    896  C   VAL A 121      10.920  23.912  76.471  1.00 28.60           C  
+ATOM    897  O   VAL A 121      10.148  24.719  75.956  1.00 28.22           O  
+ATOM    898  CB  VAL A 121      13.390  24.325  76.350  1.00 28.69           C  
+ATOM    899  CG1 VAL A 121      13.077  24.935  75.002  1.00 28.19           C  
+ATOM    900  CG2 VAL A 121      14.552  25.063  77.004  1.00 26.94           C  
+ATOM    901  N   ALA A 122      10.742  22.601  76.379  1.00 28.03           N  
+ATOM    902  CA  ALA A 122       9.602  22.051  75.660  1.00 28.61           C  
+ATOM    903  C   ALA A 122       8.283  22.558  76.251  1.00 29.97           C  
+ATOM    904  O   ALA A 122       7.343  22.873  75.510  1.00 28.96           O  
+ATOM    905  CB  ALA A 122       9.643  20.531  75.705  1.00 27.15           C  
+ATOM    906  N   ARG A 123       8.209  22.628  77.581  1.00 29.83           N  
+ATOM    907  CA  ARG A 123       6.992  23.097  78.240  1.00 30.06           C  
+ATOM    908  C   ARG A 123       6.700  24.532  77.846  1.00 29.11           C  
+ATOM    909  O   ARG A 123       5.543  24.904  77.656  1.00 28.37           O  
+ATOM    910  CB  ARG A 123       7.093  22.966  79.772  1.00 31.03           C  
+ATOM    911  CG  ARG A 123       6.661  21.586  80.275  1.00 33.90           C  
+ATOM    912  CD  ARG A 123       6.420  21.507  81.786  1.00 35.16           C  
+ATOM    913  NE  ARG A 123       7.652  21.407  82.567  1.00 37.11           N  
+ATOM    914  CZ  ARG A 123       7.826  20.563  83.583  1.00 37.79           C  
+ATOM    915  NH1 ARG A 123       6.849  19.738  83.941  1.00 36.14           N  
+ATOM    916  NH2 ARG A 123       8.976  20.547  84.249  1.00 38.09           N  
+ATOM    917  N   ALA A 124       7.755  25.332  77.710  1.00 28.70           N  
+ATOM    918  CA  ALA A 124       7.602  26.726  77.310  1.00 28.61           C  
+ATOM    919  C   ALA A 124       7.128  26.802  75.856  1.00 29.37           C  
+ATOM    920  O   ALA A 124       6.189  27.532  75.542  1.00 29.55           O  
+ATOM    921  CB  ALA A 124       8.922  27.466  77.466  1.00 25.88           C  
+ATOM    922  N   MET A 125       7.776  26.037  74.979  1.00 28.86           N  
+ATOM    923  CA  MET A 125       7.419  26.033  73.565  1.00 29.90           C  
+ATOM    924  C   MET A 125       5.969  25.639  73.359  1.00 30.75           C  
+ATOM    925  O   MET A 125       5.251  26.270  72.588  1.00 32.33           O  
+ATOM    926  CB  MET A 125       8.342  25.090  72.782  1.00 27.85           C  
+ATOM    927  CG  MET A 125       9.752  25.623  72.668  1.00 26.04           C  
+ATOM    928  SD  MET A 125      10.951  24.448  72.031  1.00 29.91           S  
+ATOM    929  CE  MET A 125      12.401  25.529  71.840  1.00 24.28           C  
+ATOM    930  N   ILE A 126       5.529  24.598  74.050  1.00 32.14           N  
+ATOM    931  CA  ILE A 126       4.150  24.164  73.920  1.00 33.78           C  
+ATOM    932  C   ILE A 126       3.215  25.327  74.265  1.00 35.78           C  
+ATOM    933  O   ILE A 126       2.251  25.600  73.545  1.00 36.73           O  
+ATOM    934  CB  ILE A 126       3.875  22.948  74.832  1.00 33.34           C  
+ATOM    935  CG1 ILE A 126       4.761  21.780  74.385  1.00 33.90           C  
+ATOM    936  CG2 ILE A 126       2.398  22.566  74.776  1.00 32.20           C  
+ATOM    937  CD1 ILE A 126       4.585  20.505  75.165  1.00 32.43           C  
+ATOM    938  N   ALA A 127       3.518  26.022  75.358  1.00 38.03           N  
+ATOM    939  CA  ALA A 127       2.718  27.164  75.791  1.00 38.24           C  
+ATOM    940  C   ALA A 127       2.785  28.257  74.733  1.00 38.06           C  
+ATOM    941  O   ALA A 127       1.771  28.851  74.382  1.00 38.38           O  
+ATOM    942  CB  ALA A 127       3.233  27.692  77.128  1.00 38.48           C  
+ATOM    943  N   GLY A 128       3.987  28.514  74.227  1.00 39.05           N  
+ATOM    944  CA  GLY A 128       4.162  29.525  73.198  1.00 39.65           C  
+ATOM    945  C   GLY A 128       3.233  29.306  72.013  1.00 41.06           C  
+ATOM    946  O   GLY A 128       2.808  30.260  71.366  1.00 42.05           O  
+ATOM    947  N   GLY A 129       2.922  28.047  71.720  1.00 40.32           N  
+ATOM    948  CA  GLY A 129       2.022  27.750  70.623  1.00 40.33           C  
+ATOM    949  C   GLY A 129       2.581  27.847  69.213  1.00 40.71           C  
+ATOM    950  O   GLY A 129       1.820  27.773  68.249  1.00 40.37           O  
+ATOM    951  N   ARG A 130       3.892  28.012  69.070  1.00 40.56           N  
+ATOM    952  CA  ARG A 130       4.476  28.099  67.735  1.00 39.75           C  
+ATOM    953  C   ARG A 130       5.716  27.214  67.544  1.00 37.42           C  
+ATOM    954  O   ARG A 130       6.677  27.595  66.872  1.00 35.99           O  
+ATOM    955  CB  ARG A 130       4.783  29.563  67.392  1.00 41.96           C  
+ATOM    956  CG  ARG A 130       5.719  30.268  68.350  1.00 45.95           C  
+ATOM    957  CD  ARG A 130       5.420  31.758  68.392  1.00 48.73           C  
+ATOM    958  NE  ARG A 130       6.545  32.526  68.917  1.00 53.36           N  
+ATOM    959  CZ  ARG A 130       7.662  32.772  68.236  1.00 55.86           C  
+ATOM    960  NH1 ARG A 130       7.806  32.312  66.996  1.00 56.76           N  
+ATOM    961  NH2 ARG A 130       8.637  33.481  68.791  1.00 56.58           N  
+ATOM    962  N   GLY A 131       5.665  26.025  68.142  1.00 34.51           N  
+ATOM    963  CA  GLY A 131       6.745  25.057  68.035  1.00 31.01           C  
+ATOM    964  C   GLY A 131       8.140  25.535  68.390  1.00 28.67           C  
+ATOM    965  O   GLY A 131       8.309  26.505  69.127  1.00 28.29           O  
+ATOM    966  N   GLY A 132       9.141  24.836  67.859  1.00 26.33           N  
+ATOM    967  CA  GLY A 132      10.524  25.192  68.113  1.00 23.68           C  
+ATOM    968  C   GLY A 132      11.477  24.103  67.660  1.00 22.44           C  
+ATOM    969  O   GLY A 132      11.050  23.060  67.166  1.00 21.64           O  
+ATOM    970  N   LYS A 133      12.772  24.348  67.828  1.00 21.27           N  
+ATOM    971  CA  LYS A 133      13.795  23.386  67.445  1.00 21.71           C  
+ATOM    972  C   LYS A 133      14.684  23.020  68.636  1.00 21.26           C  
+ATOM    973  O   LYS A 133      15.133  23.895  69.379  1.00 20.38           O  
+ATOM    974  CB  LYS A 133      14.693  23.964  66.343  1.00 23.68           C  
+ATOM    975  CG  LYS A 133      13.987  24.412  65.069  1.00 24.24           C  
+ATOM    976  CD  LYS A 133      13.427  23.235  64.299  1.00 24.24           C  
+ATOM    977  CE  LYS A 133      12.870  23.676  62.960  1.00 21.90           C  
+ATOM    978  NZ  LYS A 133      12.283  22.503  62.259  1.00 24.56           N  
+ATOM    979  N   ILE A 134      14.939  21.728  68.813  1.00 20.43           N  
+ATOM    980  CA  ILE A 134      15.814  21.273  69.889  1.00 20.62           C  
+ATOM    981  C   ILE A 134      16.877  20.375  69.291  1.00 20.28           C  
+ATOM    982  O   ILE A 134      16.568  19.405  68.593  1.00 20.31           O  
+ATOM    983  CB  ILE A 134      15.059  20.471  70.991  1.00 21.36           C  
+ATOM    984  CG1 ILE A 134      14.103  21.388  71.750  1.00 18.16           C  
+ATOM    985  CG2 ILE A 134      16.066  19.879  71.984  1.00 19.10           C  
+ATOM    986  CD1 ILE A 134      13.185  20.658  72.688  1.00 22.19           C  
+ATOM    987  N   ILE A 135      18.132  20.703  69.569  1.00 20.25           N  
+ATOM    988  CA  ILE A 135      19.249  19.928  69.060  1.00 19.84           C  
+ATOM    989  C   ILE A 135      20.095  19.402  70.208  1.00 19.85           C  
+ATOM    990  O   ILE A 135      20.602  20.181  71.017  1.00 20.82           O  
+ATOM    991  CB  ILE A 135      20.147  20.790  68.156  1.00 20.63           C  
+ATOM    992  CG1 ILE A 135      19.316  21.393  67.027  1.00 21.25           C  
+ATOM    993  CG2 ILE A 135      21.286  19.956  67.603  1.00 16.92           C  
+ATOM    994  CD1 ILE A 135      20.084  22.389  66.188  1.00 22.38           C  
+ATOM    995  N   ASN A 136      20.242  18.083  70.285  1.00 19.12           N  
+ATOM    996  CA  ASN A 136      21.061  17.483  71.327  1.00 19.66           C  
+ATOM    997  C   ASN A 136      22.407  17.123  70.748  1.00 19.41           C  
+ATOM    998  O   ASN A 136      22.533  16.892  69.551  1.00 22.83           O  
+ATOM    999  CB  ASN A 136      20.409  16.223  71.898  1.00 18.43           C  
+ATOM   1000  CG  ASN A 136      19.079  16.509  72.539  1.00 20.02           C  
+ATOM   1001  OD1 ASN A 136      18.873  17.594  73.095  1.00 18.24           O  
+ATOM   1002  ND2 ASN A 136      18.163  15.541  72.475  1.00 15.50           N  
+ATOM   1003  N   MET A 137      23.416  17.085  71.602  1.00 18.84           N  
+ATOM   1004  CA  MET A 137      24.750  16.741  71.167  1.00 19.71           C  
+ATOM   1005  C   MET A 137      25.118  15.339  71.639  1.00 20.72           C  
+ATOM   1006  O   MET A 137      25.384  15.108  72.824  1.00 23.43           O  
+ATOM   1007  CB  MET A 137      25.757  17.755  71.711  1.00 20.02           C  
+ATOM   1008  CG  MET A 137      25.652  19.142  71.089  1.00 23.09           C  
+ATOM   1009  SD  MET A 137      26.076  19.168  69.318  1.00 22.73           S  
+ATOM   1010  CE  MET A 137      27.855  19.057  69.408  1.00 23.85           C  
+ATOM   1011  N   ALA A 138      25.105  14.393  70.714  1.00 18.57           N  
+ATOM   1012  CA  ALA A 138      25.474  13.032  71.047  1.00 18.03           C  
+ATOM   1013  C   ALA A 138      26.960  12.943  70.742  1.00 17.33           C  
+ATOM   1014  O   ALA A 138      27.712  13.876  71.033  1.00 17.16           O  
+ATOM   1015  CB  ALA A 138      24.682  12.037  70.197  1.00 16.15           C  
+ATOM   1016  N   SER A 139      27.378  11.840  70.136  1.00 16.62           N  
+ATOM   1017  CA  SER A 139      28.785  11.635  69.806  1.00 16.28           C  
+ATOM   1018  C   SER A 139      28.960  10.227  69.278  1.00 15.83           C  
+ATOM   1019  O   SER A 139      28.139   9.352  69.548  1.00 15.25           O  
+ATOM   1020  CB  SER A 139      29.655  11.809  71.054  1.00 16.49           C  
+ATOM   1021  OG  SER A 139      30.775  10.932  71.030  1.00 17.38           O  
+ATOM   1022  N   GLN A 140      30.028  10.005  68.525  1.00 16.70           N  
+ATOM   1023  CA  GLN A 140      30.286   8.676  67.997  1.00 19.84           C  
+ATOM   1024  C   GLN A 140      30.321   7.671  69.151  1.00 19.01           C  
+ATOM   1025  O   GLN A 140      29.987   6.496  68.979  1.00 17.76           O  
+ATOM   1026  CB  GLN A 140      31.624   8.648  67.257  1.00 22.44           C  
+ATOM   1027  CG  GLN A 140      32.817   9.036  68.107  1.00 26.33           C  
+ATOM   1028  CD  GLN A 140      34.137   8.760  67.407  1.00 30.24           C  
+ATOM   1029  OE1 GLN A 140      34.353   9.203  66.277  1.00 30.88           O  
+ATOM   1030  NE2 GLN A 140      35.031   8.024  68.077  1.00 30.11           N  
+ATOM   1031  N   ALA A 141      30.729   8.145  70.327  1.00 19.37           N  
+ATOM   1032  CA  ALA A 141      30.823   7.288  71.508  1.00 18.60           C  
+ATOM   1033  C   ALA A 141      29.474   6.669  71.842  1.00 17.25           C  
+ATOM   1034  O   ALA A 141      29.411   5.561  72.367  1.00 14.43           O  
+ATOM   1035  CB  ALA A 141      31.342   8.081  72.691  1.00 17.72           C  
+ATOM   1036  N   GLY A 142      28.402   7.386  71.515  1.00 17.68           N  
+ATOM   1037  CA  GLY A 142      27.066   6.890  71.785  1.00 18.97           C  
+ATOM   1038  C   GLY A 142      26.553   5.866  70.787  1.00 20.14           C  
+ATOM   1039  O   GLY A 142      25.454   5.339  70.965  1.00 19.86           O  
+ATOM   1040  N   ARG A 143      27.340   5.583  69.748  1.00 21.05           N  
+ATOM   1041  CA  ARG A 143      26.961   4.624  68.703  1.00 20.57           C  
+ATOM   1042  C   ARG A 143      27.436   3.215  69.022  1.00 21.89           C  
+ATOM   1043  O   ARG A 143      26.758   2.242  68.706  1.00 24.11           O  
+ATOM   1044  CB  ARG A 143      27.552   5.036  67.352  1.00 19.46           C  
+ATOM   1045  CG  ARG A 143      27.044   6.359  66.796  1.00 18.05           C  
+ATOM   1046  CD  ARG A 143      25.587   6.273  66.365  1.00 16.48           C  
+ATOM   1047  NE  ARG A 143      25.222   7.405  65.519  1.00 17.15           N  
+ATOM   1048  CZ  ARG A 143      24.004   7.627  65.035  1.00 15.24           C  
+ATOM   1049  NH1 ARG A 143      23.785   8.686  64.275  1.00 15.49           N  
+ATOM   1050  NH2 ARG A 143      23.007   6.800  65.313  1.00 13.65           N  
+ATOM   1051  N   ARG A 144      28.615   3.112  69.628  1.00 22.09           N  
+ATOM   1052  CA  ARG A 144      29.182   1.819  69.997  1.00 21.38           C  
+ATOM   1053  C   ARG A 144      30.032   1.970  71.254  1.00 21.68           C  
+ATOM   1054  O   ARG A 144      30.651   3.010  71.474  1.00 20.35           O  
+ATOM   1055  CB  ARG A 144      30.045   1.252  68.855  1.00 22.18           C  
+ATOM   1056  CG  ARG A 144      31.409   1.918  68.663  1.00 21.83           C  
+ATOM   1057  CD  ARG A 144      31.289   3.345  68.152  1.00 25.39           C  
+ATOM   1058  NE  ARG A 144      32.552   4.069  68.273  1.00 30.20           N  
+ATOM   1059  CZ  ARG A 144      33.186   4.286  69.424  1.00 33.72           C  
+ATOM   1060  NH1 ARG A 144      32.680   3.838  70.571  1.00 33.69           N  
+ATOM   1061  NH2 ARG A 144      34.334   4.951  69.430  1.00 34.47           N  
+ATOM   1062  N   GLY A 145      30.060   0.929  72.078  1.00 22.26           N  
+ATOM   1063  CA  GLY A 145      30.841   0.994  73.299  1.00 22.50           C  
+ATOM   1064  C   GLY A 145      32.327   0.922  73.023  1.00 24.41           C  
+ATOM   1065  O   GLY A 145      32.736   0.555  71.919  1.00 24.30           O  
+ATOM   1066  N   GLU A 146      33.126   1.291  74.025  1.00 24.94           N  
+ATOM   1067  CA  GLU A 146      34.591   1.260  73.963  1.00 24.35           C  
+ATOM   1068  C   GLU A 146      35.117   0.706  75.282  1.00 23.71           C  
+ATOM   1069  O   GLU A 146      34.540   0.950  76.344  1.00 23.59           O  
+ATOM   1070  CB  GLU A 146      35.173   2.656  73.757  1.00 27.30           C  
+ATOM   1071  CG  GLU A 146      34.969   3.237  72.379  1.00 30.94           C  
+ATOM   1072  CD  GLU A 146      35.747   4.525  72.192  1.00 34.30           C  
+ATOM   1073  OE1 GLU A 146      36.998   4.465  72.222  1.00 34.64           O  
+ATOM   1074  OE2 GLU A 146      35.108   5.593  72.027  1.00 36.59           O  
+ATOM   1075  N   ALA A 147      36.227  -0.016  75.211  1.00 21.29           N  
+ATOM   1076  CA  ALA A 147      36.822  -0.638  76.385  1.00 20.14           C  
+ATOM   1077  C   ALA A 147      37.123   0.289  77.563  1.00 19.98           C  
+ATOM   1078  O   ALA A 147      36.817  -0.052  78.708  1.00 21.78           O  
+ATOM   1079  CB  ALA A 147      38.088  -1.385  75.981  1.00 17.96           C  
+ATOM   1080  N   LEU A 148      37.711   1.451  77.300  1.00 18.18           N  
+ATOM   1081  CA  LEU A 148      38.056   2.372  78.380  1.00 16.96           C  
+ATOM   1082  C   LEU A 148      37.144   3.586  78.514  1.00 16.48           C  
+ATOM   1083  O   LEU A 148      37.491   4.539  79.210  1.00 16.83           O  
+ATOM   1084  CB  LEU A 148      39.491   2.872  78.199  1.00 16.32           C  
+ATOM   1085  CG  LEU A 148      40.585   1.838  77.941  1.00 16.15           C  
+ATOM   1086  CD1 LEU A 148      41.905   2.557  77.783  1.00 16.30           C  
+ATOM   1087  CD2 LEU A 148      40.652   0.843  79.082  1.00 16.62           C  
+ATOM   1088  N   VAL A 149      35.987   3.572  77.862  1.00 16.80           N  
+ATOM   1089  CA  VAL A 149      35.092   4.732  77.938  1.00 16.61           C  
+ATOM   1090  C   VAL A 149      33.651   4.344  78.246  1.00 16.36           C  
+ATOM   1091  O   VAL A 149      32.705   5.004  77.799  1.00 16.06           O  
+ATOM   1092  CB  VAL A 149      35.111   5.539  76.605  1.00 17.74           C  
+ATOM   1093  CG1 VAL A 149      34.578   6.944  76.842  1.00 15.17           C  
+ATOM   1094  CG2 VAL A 149      36.530   5.585  76.034  1.00 13.64           C  
+ATOM   1095  N   GLY A 150      33.501   3.272  79.018  1.00 15.60           N  
+ATOM   1096  CA  GLY A 150      32.186   2.779  79.385  1.00 14.75           C  
+ATOM   1097  C   GLY A 150      31.181   3.808  79.859  1.00 15.37           C  
+ATOM   1098  O   GLY A 150      30.080   3.888  79.299  1.00 15.20           O  
+ATOM   1099  N   VAL A 151      31.541   4.594  80.878  1.00 14.19           N  
+ATOM   1100  CA  VAL A 151      30.620   5.595  81.422  1.00 14.53           C  
+ATOM   1101  C   VAL A 151      30.240   6.677  80.428  1.00 14.06           C  
+ATOM   1102  O   VAL A 151      29.063   6.968  80.258  1.00 17.92           O  
+ATOM   1103  CB  VAL A 151      31.190   6.277  82.698  1.00 16.19           C  
+ATOM   1104  CG1 VAL A 151      30.226   7.348  83.200  1.00 14.78           C  
+ATOM   1105  CG2 VAL A 151      31.413   5.243  83.789  1.00 15.99           C  
+ATOM   1106  N   TYR A 152      31.222   7.284  79.772  1.00 15.98           N  
+ATOM   1107  CA  TYR A 152      30.922   8.330  78.791  1.00 17.81           C  
+ATOM   1108  C   TYR A 152      30.028   7.791  77.657  1.00 16.55           C  
+ATOM   1109  O   TYR A 152      29.004   8.392  77.327  1.00 13.34           O  
+ATOM   1110  CB  TYR A 152      32.214   8.902  78.199  1.00 18.53           C  
+ATOM   1111  CG  TYR A 152      31.976   9.985  77.166  1.00 21.15           C  
+ATOM   1112  CD1 TYR A 152      31.471  11.230  77.541  1.00 20.27           C  
+ATOM   1113  CD2 TYR A 152      32.245   9.761  75.808  1.00 19.65           C  
+ATOM   1114  CE1 TYR A 152      31.242  12.228  76.596  1.00 21.19           C  
+ATOM   1115  CE2 TYR A 152      32.014  10.754  74.853  1.00 17.35           C  
+ATOM   1116  CZ  TYR A 152      31.516  11.981  75.255  1.00 21.77           C  
+ATOM   1117  OH  TYR A 152      31.297  12.976  74.329  1.00 22.64           O  
+ATOM   1118  N   CYS A 153      30.424   6.652  77.085  1.00 15.84           N  
+ATOM   1119  CA  CYS A 153      29.675   6.020  76.002  1.00 16.54           C  
+ATOM   1120  C   CYS A 153      28.224   5.802  76.370  1.00 16.71           C  
+ATOM   1121  O   CYS A 153      27.327   6.112  75.584  1.00 18.01           O  
+ATOM   1122  CB  CYS A 153      30.294   4.672  75.633  1.00 15.99           C  
+ATOM   1123  SG  CYS A 153      31.808   4.781  74.650  1.00 17.20           S  
+ATOM   1124  N   ALA A 154      27.996   5.276  77.571  1.00 17.44           N  
+ATOM   1125  CA  ALA A 154      26.642   5.000  78.047  1.00 15.73           C  
+ATOM   1126  C   ALA A 154      25.799   6.255  78.160  1.00 14.77           C  
+ATOM   1127  O   ALA A 154      24.591   6.199  77.962  1.00 15.79           O  
+ATOM   1128  CB  ALA A 154      26.687   4.276  79.388  1.00 16.69           C  
+ATOM   1129  N   THR A 155      26.415   7.390  78.480  1.00 14.37           N  
+ATOM   1130  CA  THR A 155      25.637   8.621  78.587  1.00 14.85           C  
+ATOM   1131  C   THR A 155      25.218   9.078  77.198  1.00 15.17           C  
+ATOM   1132  O   THR A 155      24.095   9.551  76.988  1.00 15.78           O  
+ATOM   1133  CB  THR A 155      26.434   9.765  79.241  1.00 15.92           C  
+ATOM   1134  OG1 THR A 155      27.517  10.144  78.379  1.00 12.15           O  
+ATOM   1135  CG2 THR A 155      26.975   9.332  80.611  1.00 13.53           C  
+ATOM   1136  N   LYS A 156      26.121   8.940  76.238  1.00 16.19           N  
+ATOM   1137  CA  LYS A 156      25.801   9.357  74.887  1.00 17.27           C  
+ATOM   1138  C   LYS A 156      24.752   8.453  74.256  1.00 16.60           C  
+ATOM   1139  O   LYS A 156      23.866   8.930  73.543  1.00 15.42           O  
+ATOM   1140  CB  LYS A 156      27.072   9.436  74.053  1.00 18.41           C  
+ATOM   1141  CG  LYS A 156      27.961  10.605  74.490  1.00 19.98           C  
+ATOM   1142  CD  LYS A 156      27.158  11.905  74.555  1.00 19.81           C  
+ATOM   1143  CE  LYS A 156      28.058  13.092  74.852  1.00 25.05           C  
+ATOM   1144  NZ  LYS A 156      27.297  14.376  74.954  1.00 26.40           N  
+ATOM   1145  N   ALA A 157      24.820   7.157  74.544  1.00 15.12           N  
+ATOM   1146  CA  ALA A 157      23.817   6.246  74.008  1.00 16.09           C  
+ATOM   1147  C   ALA A 157      22.451   6.686  74.542  1.00 16.14           C  
+ATOM   1148  O   ALA A 157      21.448   6.656  73.826  1.00 17.97           O  
+ATOM   1149  CB  ALA A 157      24.116   4.814  74.431  1.00 14.14           C  
+ATOM   1150  N   ALA A 158      22.420   7.106  75.803  1.00 15.79           N  
+ATOM   1151  CA  ALA A 158      21.180   7.561  76.425  1.00 14.27           C  
+ATOM   1152  C   ALA A 158      20.654   8.829  75.751  1.00 12.98           C  
+ATOM   1153  O   ALA A 158      19.443   9.011  75.598  1.00 11.65           O  
+ATOM   1154  CB  ALA A 158      21.404   7.816  77.906  1.00 13.63           C  
+ATOM   1155  N   VAL A 159      21.562   9.713  75.357  1.00 14.09           N  
+ATOM   1156  CA  VAL A 159      21.161  10.950  74.701  1.00 15.94           C  
+ATOM   1157  C   VAL A 159      20.473  10.648  73.377  1.00 16.91           C  
+ATOM   1158  O   VAL A 159      19.471  11.284  73.021  1.00 18.62           O  
+ATOM   1159  CB  VAL A 159      22.373  11.848  74.418  1.00 19.36           C  
+ATOM   1160  CG1 VAL A 159      21.985  12.959  73.430  1.00 17.95           C  
+ATOM   1161  CG2 VAL A 159      22.886  12.434  75.720  1.00 16.29           C  
+ATOM   1162  N   ILE A 160      21.019   9.678  72.650  1.00 15.23           N  
+ATOM   1163  CA  ILE A 160      20.455   9.282  71.372  1.00 15.18           C  
+ATOM   1164  C   ILE A 160      19.058   8.728  71.612  1.00 16.04           C  
+ATOM   1165  O   ILE A 160      18.108   9.050  70.883  1.00 16.42           O  
+ATOM   1166  CB  ILE A 160      21.359   8.227  70.675  1.00 14.97           C  
+ATOM   1167  CG1 ILE A 160      22.633   8.914  70.163  1.00 11.63           C  
+ATOM   1168  CG2 ILE A 160      20.609   7.539  69.539  1.00 13.25           C  
+ATOM   1169  CD1 ILE A 160      23.622   7.982  69.527  1.00  9.69           C  
+ATOM   1170  N   SER A 161      18.929   7.912  72.654  1.00 16.35           N  
+ATOM   1171  CA  SER A 161      17.634   7.322  72.994  1.00 16.15           C  
+ATOM   1172  C   SER A 161      16.607   8.401  73.340  1.00 15.16           C  
+ATOM   1173  O   SER A 161      15.473   8.377  72.850  1.00 16.17           O  
+ATOM   1174  CB  SER A 161      17.786   6.352  74.168  1.00 15.04           C  
+ATOM   1175  OG  SER A 161      16.537   5.776  74.501  1.00 16.19           O  
+ATOM   1176  N   LEU A 162      17.006   9.351  74.179  1.00 14.13           N  
+ATOM   1177  CA  LEU A 162      16.112  10.432  74.578  1.00 15.33           C  
+ATOM   1178  C   LEU A 162      15.708  11.329  73.402  1.00 16.38           C  
+ATOM   1179  O   LEU A 162      14.595  11.868  73.374  1.00 16.59           O  
+ATOM   1180  CB  LEU A 162      16.773  11.274  75.669  1.00 16.85           C  
+ATOM   1181  CG  LEU A 162      16.979  10.572  77.017  1.00 17.26           C  
+ATOM   1182  CD1 LEU A 162      17.834  11.443  77.909  1.00 16.81           C  
+ATOM   1183  CD2 LEU A 162      15.637  10.292  77.660  1.00 13.61           C  
+ATOM   1184  N   THR A 163      16.614  11.501  72.441  1.00 16.75           N  
+ATOM   1185  CA  THR A 163      16.327  12.323  71.264  1.00 17.10           C  
+ATOM   1186  C   THR A 163      15.199  11.668  70.456  1.00 16.30           C  
+ATOM   1187  O   THR A 163      14.300  12.345  69.943  1.00 17.26           O  
+ATOM   1188  CB  THR A 163      17.581  12.479  70.367  1.00 19.11           C  
+ATOM   1189  OG1 THR A 163      18.609  13.174  71.085  1.00 19.02           O  
+ATOM   1190  CG2 THR A 163      17.247  13.262  69.116  1.00 20.19           C  
+ATOM   1191  N   GLN A 164      15.232  10.345  70.360  1.00 15.12           N  
+ATOM   1192  CA  GLN A 164      14.196   9.631  69.626  1.00 15.44           C  
+ATOM   1193  C   GLN A 164      12.866   9.703  70.365  1.00 15.95           C  
+ATOM   1194  O   GLN A 164      11.827  10.002  69.768  1.00 16.78           O  
+ATOM   1195  CB  GLN A 164      14.594   8.171  69.436  1.00 14.78           C  
+ATOM   1196  CG  GLN A 164      15.960   8.006  68.828  1.00 15.84           C  
+ATOM   1197  CD  GLN A 164      16.342   6.556  68.675  1.00 19.19           C  
+ATOM   1198  OE1 GLN A 164      15.880   5.699  69.433  1.00 20.32           O  
+ATOM   1199  NE2 GLN A 164      17.206   6.270  67.709  1.00 16.87           N  
+ATOM   1200  N   SER A 165      12.894   9.435  71.669  1.00 16.16           N  
+ATOM   1201  CA  SER A 165      11.671   9.476  72.461  1.00 14.84           C  
+ATOM   1202  C   SER A 165      11.068  10.873  72.475  1.00 12.80           C  
+ATOM   1203  O   SER A 165       9.867  11.041  72.257  1.00 13.05           O  
+ATOM   1204  CB  SER A 165      11.942   9.012  73.894  1.00 15.53           C  
+ATOM   1205  OG  SER A 165      12.432   7.684  73.900  1.00 15.44           O  
+ATOM   1206  N   ALA A 166      11.894  11.879  72.726  1.00 11.66           N  
+ATOM   1207  CA  ALA A 166      11.383  13.244  72.752  1.00 13.41           C  
+ATOM   1208  C   ALA A 166      10.881  13.601  71.361  1.00 16.14           C  
+ATOM   1209  O   ALA A 166       9.799  14.167  71.215  1.00 18.02           O  
+ATOM   1210  CB  ALA A 166      12.480  14.221  73.188  1.00 11.62           C  
+ATOM   1211  N   GLY A 167      11.668  13.245  70.345  1.00 17.23           N  
+ATOM   1212  CA  GLY A 167      11.309  13.538  68.971  1.00 18.65           C  
+ATOM   1213  C   GLY A 167       9.927  13.067  68.568  1.00 19.67           C  
+ATOM   1214  O   GLY A 167       9.132  13.843  68.040  1.00 20.49           O  
+ATOM   1215  N   LEU A 168       9.634  11.795  68.810  1.00 19.99           N  
+ATOM   1216  CA  LEU A 168       8.331  11.240  68.463  1.00 21.31           C  
+ATOM   1217  C   LEU A 168       7.215  11.866  69.294  1.00 23.15           C  
+ATOM   1218  O   LEU A 168       6.094  12.054  68.812  1.00 24.54           O  
+ATOM   1219  CB  LEU A 168       8.319   9.726  68.692  1.00 19.65           C  
+ATOM   1220  CG  LEU A 168       9.337   8.869  67.934  1.00 23.11           C  
+ATOM   1221  CD1 LEU A 168       9.266   7.438  68.448  1.00 21.84           C  
+ATOM   1222  CD2 LEU A 168       9.063   8.915  66.433  1.00 22.24           C  
+ATOM   1223  N   ASN A 169       7.531  12.194  70.545  1.00 24.02           N  
+ATOM   1224  CA  ASN A 169       6.549  12.754  71.466  1.00 23.10           C  
+ATOM   1225  C   ASN A 169       6.266  14.231  71.281  1.00 22.53           C  
+ATOM   1226  O   ASN A 169       5.136  14.669  71.454  1.00 22.07           O  
+ATOM   1227  CB  ASN A 169       6.990  12.496  72.916  1.00 23.60           C  
+ATOM   1228  CG  ASN A 169       5.961  12.959  73.936  1.00 22.75           C  
+ATOM   1229  OD1 ASN A 169       4.781  12.639  73.833  1.00 22.50           O  
+ATOM   1230  ND2 ASN A 169       6.411  13.706  74.929  1.00 22.50           N  
+ATOM   1231  N   LEU A 170       7.280  14.998  70.907  1.00 22.86           N  
+ATOM   1232  CA  LEU A 170       7.094  16.434  70.758  1.00 23.51           C  
+ATOM   1233  C   LEU A 170       6.769  16.972  69.368  1.00 24.90           C  
+ATOM   1234  O   LEU A 170       6.344  18.122  69.241  1.00 23.81           O  
+ATOM   1235  CB  LEU A 170       8.324  17.165  71.301  1.00 23.37           C  
+ATOM   1236  CG  LEU A 170       8.609  16.983  72.796  1.00 22.33           C  
+ATOM   1237  CD1 LEU A 170       9.751  17.884  73.208  1.00 19.90           C  
+ATOM   1238  CD2 LEU A 170       7.364  17.320  73.603  1.00 22.34           C  
+ATOM   1239  N   ILE A 171       6.960  16.158  68.330  1.00 25.65           N  
+ATOM   1240  CA  ILE A 171       6.692  16.617  66.973  1.00 25.81           C  
+ATOM   1241  C   ILE A 171       5.238  17.038  66.758  1.00 27.43           C  
+ATOM   1242  O   ILE A 171       4.957  17.870  65.900  1.00 27.46           O  
+ATOM   1243  CB  ILE A 171       7.073  15.547  65.919  1.00 24.70           C  
+ATOM   1244  CG1 ILE A 171       6.946  16.142  64.514  1.00 22.26           C  
+ATOM   1245  CG2 ILE A 171       6.178  14.328  66.049  1.00 23.61           C  
+ATOM   1246  CD1 ILE A 171       7.824  17.352  64.287  1.00 18.76           C  
+ATOM   1247  N   ARG A 172       4.323  16.475  67.545  1.00 29.18           N  
+ATOM   1248  CA  ARG A 172       2.900  16.801  67.435  1.00 30.92           C  
+ATOM   1249  C   ARG A 172       2.662  18.266  67.803  1.00 29.99           C  
+ATOM   1250  O   ARG A 172       1.680  18.861  67.384  1.00 29.53           O  
+ATOM   1251  CB  ARG A 172       2.061  15.911  68.367  1.00 35.19           C  
+ATOM   1252  CG  ARG A 172       2.675  14.538  68.698  1.00 43.55           C  
+ATOM   1253  CD  ARG A 172       2.946  13.704  67.444  1.00 50.59           C  
+ATOM   1254  NE  ARG A 172       3.530  12.391  67.732  1.00 55.89           N  
+ATOM   1255  CZ  ARG A 172       2.868  11.368  68.269  1.00 59.21           C  
+ATOM   1256  NH1 ARG A 172       1.583  11.496  68.587  1.00 60.66           N  
+ATOM   1257  NH2 ARG A 172       3.488  10.209  68.477  1.00 59.15           N  
+ATOM   1258  N   HIS A 173       3.559  18.843  68.597  1.00 30.06           N  
+ATOM   1259  CA  HIS A 173       3.425  20.237  69.011  1.00 29.38           C  
+ATOM   1260  C   HIS A 173       4.262  21.152  68.143  1.00 28.54           C  
+ATOM   1261  O   HIS A 173       4.419  22.333  68.450  1.00 29.83           O  
+ATOM   1262  CB  HIS A 173       3.852  20.425  70.473  1.00 30.23           C  
+ATOM   1263  CG  HIS A 173       2.985  19.703  71.452  1.00 31.94           C  
+ATOM   1264  ND1 HIS A 173       3.316  18.468  71.971  1.00 33.73           N  
+ATOM   1265  CD2 HIS A 173       1.775  20.017  71.973  1.00 31.84           C  
+ATOM   1266  CE1 HIS A 173       2.348  18.053  72.766  1.00 34.56           C  
+ATOM   1267  NE2 HIS A 173       1.400  18.975  72.785  1.00 34.51           N  
+ATOM   1268  N   GLY A 174       4.811  20.600  67.067  1.00 27.07           N  
+ATOM   1269  CA  GLY A 174       5.625  21.396  66.167  1.00 24.63           C  
+ATOM   1270  C   GLY A 174       7.044  21.592  66.647  1.00 23.40           C  
+ATOM   1271  O   GLY A 174       7.710  22.553  66.264  1.00 24.50           O  
+ATOM   1272  N   ILE A 175       7.515  20.681  67.491  1.00 22.24           N  
+ATOM   1273  CA  ILE A 175       8.871  20.766  68.012  1.00 20.63           C  
+ATOM   1274  C   ILE A 175       9.708  19.642  67.419  1.00 21.17           C  
+ATOM   1275  O   ILE A 175       9.385  18.465  67.598  1.00 20.43           O  
+ATOM   1276  CB  ILE A 175       8.905  20.619  69.547  1.00 20.05           C  
+ATOM   1277  CG1 ILE A 175       8.014  21.676  70.199  1.00 21.88           C  
+ATOM   1278  CG2 ILE A 175      10.333  20.755  70.046  1.00 16.31           C  
+ATOM   1279  CD1 ILE A 175       7.888  21.532  71.712  1.00 20.44           C  
+ATOM   1280  N   ASN A 176      10.771  20.010  66.706  1.00 20.73           N  
+ATOM   1281  CA  ASN A 176      11.665  19.029  66.100  1.00 20.36           C  
+ATOM   1282  C   ASN A 176      12.803  18.757  67.060  1.00 18.91           C  
+ATOM   1283  O   ASN A 176      13.425  19.695  67.568  1.00 17.94           O  
+ATOM   1284  CB  ASN A 176      12.287  19.545  64.791  1.00 20.67           C  
+ATOM   1285  CG  ASN A 176      11.263  19.820  63.714  1.00 23.34           C  
+ATOM   1286  OD1 ASN A 176      10.635  20.881  63.692  1.00 25.32           O  
+ATOM   1287  ND2 ASN A 176      11.084  18.859  62.812  1.00 20.98           N  
+ATOM   1288  N   VAL A 177      13.076  17.481  67.301  1.00 15.54           N  
+ATOM   1289  CA  VAL A 177      14.179  17.110  68.168  1.00 16.40           C  
+ATOM   1290  C   VAL A 177      15.119  16.164  67.409  1.00 15.61           C  
+ATOM   1291  O   VAL A 177      14.715  15.089  66.975  1.00 15.59           O  
+ATOM   1292  CB  VAL A 177      13.684  16.407  69.470  1.00 18.18           C  
+ATOM   1293  CG1 VAL A 177      14.871  16.167  70.412  1.00 15.32           C  
+ATOM   1294  CG2 VAL A 177      12.617  17.256  70.161  1.00 15.53           C  
+ATOM   1295  N   ASN A 178      16.367  16.577  67.241  1.00 14.59           N  
+ATOM   1296  CA  ASN A 178      17.356  15.764  66.547  1.00 16.00           C  
+ATOM   1297  C   ASN A 178      18.671  15.956  67.290  1.00 17.44           C  
+ATOM   1298  O   ASN A 178      18.761  16.804  68.175  1.00 18.35           O  
+ATOM   1299  CB  ASN A 178      17.524  16.229  65.092  1.00 14.42           C  
+ATOM   1300  CG  ASN A 178      16.262  16.057  64.268  1.00 13.37           C  
+ATOM   1301  OD1 ASN A 178      15.859  14.939  63.950  1.00 11.38           O  
+ATOM   1302  ND2 ASN A 178      15.628  17.169  63.924  1.00 11.38           N  
+ATOM   1303  N   ALA A 179      19.688  15.186  66.925  1.00 16.81           N  
+ATOM   1304  CA  ALA A 179      20.989  15.304  67.572  1.00 17.70           C  
+ATOM   1305  C   ALA A 179      22.123  15.270  66.553  1.00 18.08           C  
+ATOM   1306  O   ALA A 179      21.953  14.787  65.435  1.00 18.21           O  
+ATOM   1307  CB  ALA A 179      21.173  14.179  68.583  1.00 16.58           C  
+ATOM   1308  N   ILE A 180      23.276  15.795  66.948  1.00 18.15           N  
+ATOM   1309  CA  ILE A 180      24.461  15.798  66.094  1.00 18.35           C  
+ATOM   1310  C   ILE A 180      25.481  14.913  66.804  1.00 18.11           C  
+ATOM   1311  O   ILE A 180      25.656  15.030  68.012  1.00 20.45           O  
+ATOM   1312  CB  ILE A 180      25.058  17.219  65.955  1.00 18.29           C  
+ATOM   1313  CG1 ILE A 180      24.052  18.151  65.279  1.00 16.41           C  
+ATOM   1314  CG2 ILE A 180      26.357  17.168  65.177  1.00 15.58           C  
+ATOM   1315  CD1 ILE A 180      24.489  19.593  65.282  1.00 16.74           C  
+ATOM   1316  N   ALA A 181      26.143  14.025  66.072  1.00 17.12           N  
+ATOM   1317  CA  ALA A 181      27.132  13.147  66.683  1.00 17.03           C  
+ATOM   1318  C   ALA A 181      28.529  13.392  66.124  1.00 18.92           C  
+ATOM   1319  O   ALA A 181      28.909  12.838  65.093  1.00 18.45           O  
+ATOM   1320  CB  ALA A 181      26.740  11.693  66.487  1.00 15.64           C  
+ATOM   1321  N   PRO A 182      29.311  14.249  66.799  1.00 19.68           N  
+ATOM   1322  CA  PRO A 182      30.670  14.542  66.338  1.00 19.64           C  
+ATOM   1323  C   PRO A 182      31.542  13.292  66.450  1.00 22.18           C  
+ATOM   1324  O   PRO A 182      31.157  12.306  67.080  1.00 22.23           O  
+ATOM   1325  CB  PRO A 182      31.132  15.638  67.299  1.00 17.46           C  
+ATOM   1326  CG  PRO A 182      29.844  16.304  67.729  1.00 17.22           C  
+ATOM   1327  CD  PRO A 182      28.925  15.130  67.919  1.00 17.83           C  
+ATOM   1328  N   GLY A 183      32.712  13.332  65.831  1.00 24.56           N  
+ATOM   1329  CA  GLY A 183      33.623  12.212  65.920  1.00 29.35           C  
+ATOM   1330  C   GLY A 183      34.672  12.638  66.923  1.00 33.20           C  
+ATOM   1331  O   GLY A 183      34.347  12.963  68.069  1.00 34.83           O  
+ATOM   1332  N   VAL A 184      35.929  12.651  66.503  1.00 35.67           N  
+ATOM   1333  CA  VAL A 184      37.002  13.089  67.382  1.00 40.16           C  
+ATOM   1334  C   VAL A 184      37.278  14.560  67.066  1.00 42.25           C  
+ATOM   1335  O   VAL A 184      37.712  14.896  65.969  1.00 42.64           O  
+ATOM   1336  CB  VAL A 184      38.275  12.242  67.168  1.00 40.51           C  
+ATOM   1337  CG1 VAL A 184      38.078  10.861  67.770  1.00 39.63           C  
+ATOM   1338  CG2 VAL A 184      38.572  12.108  65.677  1.00 42.18           C  
+ATOM   1339  N   VAL A 185      36.990  15.440  68.017  1.00 45.34           N  
+ATOM   1340  CA  VAL A 185      37.209  16.866  67.814  1.00 49.56           C  
+ATOM   1341  C   VAL A 185      38.413  17.329  68.610  1.00 53.11           C  
+ATOM   1342  O   VAL A 185      38.526  17.042  69.803  1.00 53.93           O  
+ATOM   1343  CB  VAL A 185      35.991  17.699  68.258  1.00 49.58           C  
+ATOM   1344  CG1 VAL A 185      36.274  19.185  68.049  1.00 48.44           C  
+ATOM   1345  CG2 VAL A 185      34.763  17.274  67.475  1.00 49.21           C  
+ATOM   1346  N   ASP A 186      39.313  18.050  67.950  1.00 56.68           N  
+ATOM   1347  CA  ASP A 186      40.503  18.541  68.622  1.00 60.24           C  
+ATOM   1348  C   ASP A 186      40.135  19.607  69.646  1.00 62.23           C  
+ATOM   1349  O   ASP A 186      39.107  20.279  69.539  1.00 62.03           O  
+ATOM   1350  CB  ASP A 186      41.504  19.109  67.612  1.00 61.15           C  
+ATOM   1351  CG  ASP A 186      42.919  19.189  68.171  1.00 63.02           C  
+ATOM   1352  OD1 ASP A 186      43.123  18.821  69.348  1.00 64.60           O  
+ATOM   1353  OD2 ASP A 186      43.833  19.618  67.432  1.00 63.98           O  
+ATOM   1354  N   GLY A 187      41.003  19.740  70.638  1.00 65.34           N  
+ATOM   1355  CA  GLY A 187      40.821  20.690  71.715  1.00 68.73           C  
+ATOM   1356  C   GLY A 187      41.956  20.428  72.685  1.00 70.64           C  
+ATOM   1357  O   GLY A 187      42.683  19.439  72.548  1.00 71.06           O  
+ATOM   1358  N   GLU A 188      42.121  21.299  73.668  1.00 72.17           N  
+ATOM   1359  CA  GLU A 188      43.197  21.121  74.630  1.00 73.53           C  
+ATOM   1360  C   GLU A 188      43.054  19.842  75.458  1.00 73.25           C  
+ATOM   1361  O   GLU A 188      44.049  19.200  75.784  1.00 74.21           O  
+ATOM   1362  CB  GLU A 188      43.271  22.342  75.543  1.00 74.81           C  
+ATOM   1363  CG  GLU A 188      41.928  22.763  76.092  1.00 76.65           C  
+ATOM   1364  CD  GLU A 188      41.994  24.089  76.813  1.00 78.01           C  
+ATOM   1365  OE1 GLU A 188      43.107  24.642  76.944  1.00 79.12           O  
+ATOM   1366  OE2 GLU A 188      40.932  24.580  77.251  1.00 79.03           O  
+ATOM   1367  N   HIS A 189      41.821  19.466  75.785  1.00 71.89           N  
+ATOM   1368  CA  HIS A 189      41.573  18.263  76.580  1.00 70.38           C  
+ATOM   1369  C   HIS A 189      42.370  17.050  76.095  1.00 69.41           C  
+ATOM   1370  O   HIS A 189      42.613  16.111  76.857  1.00 69.33           O  
+ATOM   1371  CB  HIS A 189      40.085  17.922  76.557  1.00 70.47           C  
+ATOM   1372  CG  HIS A 189      39.545  17.702  75.178  1.00 71.14           C  
+ATOM   1373  ND1 HIS A 189      39.521  18.695  74.224  1.00 70.60           N  
+ATOM   1374  CD2 HIS A 189      39.030  16.598  74.587  1.00 71.47           C  
+ATOM   1375  CE1 HIS A 189      39.016  18.214  73.103  1.00 70.66           C  
+ATOM   1376  NE2 HIS A 189      38.710  16.942  73.296  1.00 71.08           N  
+ATOM   1377  N   TRP A 190      42.779  17.073  74.830  1.00 67.92           N  
+ATOM   1378  CA  TRP A 190      43.533  15.962  74.262  1.00 66.94           C  
+ATOM   1379  C   TRP A 190      44.908  15.743  74.875  1.00 67.66           C  
+ATOM   1380  O   TRP A 190      45.518  14.692  74.680  1.00 68.15           O  
+ATOM   1381  CB  TRP A 190      43.659  16.118  72.742  1.00 64.11           C  
+ATOM   1382  CG  TRP A 190      42.594  15.354  72.011  1.00 60.92           C  
+ATOM   1383  CD1 TRP A 190      41.423  15.844  71.506  1.00 59.84           C  
+ATOM   1384  CD2 TRP A 190      42.559  13.939  71.804  1.00 58.82           C  
+ATOM   1385  NE1 TRP A 190      40.659  14.819  71.002  1.00 58.65           N  
+ATOM   1386  CE2 TRP A 190      41.332  13.638  71.174  1.00 58.69           C  
+ATOM   1387  CE3 TRP A 190      43.444  12.893  72.096  1.00 58.51           C  
+ATOM   1388  CZ2 TRP A 190      40.968  12.334  70.828  1.00 58.32           C  
+ATOM   1389  CZ3 TRP A 190      43.081  11.596  71.753  1.00 58.65           C  
+ATOM   1390  CH2 TRP A 190      41.853  11.329  71.126  1.00 58.40           C  
+ATOM   1391  N   ASP A 191      45.395  16.728  75.620  1.00 68.65           N  
+ATOM   1392  CA  ASP A 191      46.702  16.612  76.258  1.00 69.33           C  
+ATOM   1393  C   ASP A 191      46.625  15.519  77.322  1.00 68.31           C  
+ATOM   1394  O   ASP A 191      47.409  14.566  77.316  1.00 68.22           O  
+ATOM   1395  CB  ASP A 191      47.091  17.933  76.934  1.00 71.80           C  
+ATOM   1396  CG  ASP A 191      46.715  19.154  76.108  1.00 73.75           C  
+ATOM   1397  OD1 ASP A 191      46.139  20.104  76.687  1.00 74.00           O  
+ATOM   1398  OD2 ASP A 191      46.997  19.172  74.890  1.00 74.44           O  
+ATOM   1399  N   GLY A 192      45.665  15.674  78.231  1.00 66.70           N  
+ATOM   1400  CA  GLY A 192      45.484  14.717  79.309  1.00 64.71           C  
+ATOM   1401  C   GLY A 192      44.892  13.401  78.852  1.00 63.30           C  
+ATOM   1402  O   GLY A 192      45.316  12.335  79.301  1.00 62.40           O  
+ATOM   1403  N   VAL A 193      43.905  13.477  77.963  1.00 62.43           N  
+ATOM   1404  CA  VAL A 193      43.255  12.283  77.439  1.00 60.31           C  
+ATOM   1405  C   VAL A 193      44.321  11.369  76.855  1.00 59.50           C  
+ATOM   1406  O   VAL A 193      44.338  10.164  77.114  1.00 58.71           O  
+ATOM   1407  CB  VAL A 193      42.238  12.639  76.335  1.00 59.25           C  
+ATOM   1408  CG1 VAL A 193      41.577  11.375  75.802  1.00 58.69           C  
+ATOM   1409  CG2 VAL A 193      41.197  13.594  76.886  1.00 58.50           C  
+ATOM   1410  N   ASP A 194      45.215  11.962  76.072  1.00 59.03           N  
+ATOM   1411  CA  ASP A 194      46.304  11.229  75.441  1.00 58.59           C  
+ATOM   1412  C   ASP A 194      47.185  10.585  76.515  1.00 57.85           C  
+ATOM   1413  O   ASP A 194      47.600   9.427  76.391  1.00 57.67           O  
+ATOM   1414  CB  ASP A 194      47.133  12.182  74.578  1.00 58.32           C  
+ATOM   1415  CG  ASP A 194      48.300  11.494  73.915  1.00 58.85           C  
+ATOM   1416  OD1 ASP A 194      48.063  10.640  73.033  1.00 58.08           O  
+ATOM   1417  OD2 ASP A 194      49.452  11.804  74.287  1.00 58.45           O  
+ATOM   1418  N   ALA A 195      47.464  11.347  77.569  1.00 56.42           N  
+ATOM   1419  CA  ALA A 195      48.283  10.861  78.674  1.00 55.64           C  
+ATOM   1420  C   ALA A 195      47.628   9.632  79.285  1.00 54.70           C  
+ATOM   1421  O   ALA A 195      48.298   8.649  79.614  1.00 53.94           O  
+ATOM   1422  CB  ALA A 195      48.429  11.947  79.728  1.00 55.46           C  
+ATOM   1423  N   LYS A 196      46.311   9.707  79.437  1.00 54.16           N  
+ATOM   1424  CA  LYS A 196      45.529   8.617  79.998  1.00 53.98           C  
+ATOM   1425  C   LYS A 196      45.733   7.338  79.193  1.00 53.52           C  
+ATOM   1426  O   LYS A 196      46.170   6.320  79.736  1.00 53.23           O  
+ATOM   1427  CB  LYS A 196      44.047   8.993  80.005  1.00 54.35           C  
+ATOM   1428  CG  LYS A 196      43.696  10.096  80.979  1.00 56.27           C  
+ATOM   1429  CD  LYS A 196      43.783   9.592  82.407  1.00 58.25           C  
+ATOM   1430  CE  LYS A 196      43.293  10.636  83.400  1.00 59.44           C  
+ATOM   1431  NZ  LYS A 196      43.173  10.073  84.778  1.00 60.85           N  
+ATOM   1432  N   PHE A 197      45.417   7.394  77.900  1.00 52.11           N  
+ATOM   1433  CA  PHE A 197      45.566   6.233  77.029  1.00 51.19           C  
+ATOM   1434  C   PHE A 197      47.010   5.746  76.998  1.00 51.30           C  
+ATOM   1435  O   PHE A 197      47.270   4.541  77.045  1.00 50.40           O  
+ATOM   1436  CB  PHE A 197      45.109   6.556  75.600  1.00 49.19           C  
+ATOM   1437  CG  PHE A 197      43.616   6.671  75.443  1.00 46.86           C  
+ATOM   1438  CD1 PHE A 197      42.996   7.915  75.417  1.00 45.15           C  
+ATOM   1439  CD2 PHE A 197      42.831   5.530  75.310  1.00 46.08           C  
+ATOM   1440  CE1 PHE A 197      41.618   8.020  75.256  1.00 44.34           C  
+ATOM   1441  CE2 PHE A 197      41.455   5.626  75.149  1.00 44.65           C  
+ATOM   1442  CZ  PHE A 197      40.847   6.873  75.121  1.00 43.84           C  
+ATOM   1443  N   ALA A 198      47.948   6.683  76.914  1.00 52.00           N  
+ATOM   1444  CA  ALA A 198      49.363   6.330  76.881  1.00 53.89           C  
+ATOM   1445  C   ALA A 198      49.704   5.450  78.084  1.00 54.91           C  
+ATOM   1446  O   ALA A 198      50.444   4.468  77.970  1.00 53.95           O  
+ATOM   1447  CB  ALA A 198      50.216   7.595  76.895  1.00 51.77           C  
+ATOM   1448  N   ASP A 199      49.138   5.806  79.231  1.00 56.75           N  
+ATOM   1449  CA  ASP A 199      49.374   5.082  80.469  1.00 58.72           C  
+ATOM   1450  C   ASP A 199      48.558   3.789  80.559  1.00 58.47           C  
+ATOM   1451  O   ASP A 199      49.040   2.780  81.076  1.00 58.04           O  
+ATOM   1452  CB  ASP A 199      49.055   5.992  81.659  1.00 61.40           C  
+ATOM   1453  CG  ASP A 199      49.597   5.452  82.966  1.00 64.83           C  
+ATOM   1454  OD1 ASP A 199      50.822   5.204  83.045  1.00 66.81           O  
+ATOM   1455  OD2 ASP A 199      48.803   5.278  83.916  1.00 66.48           O  
+ATOM   1456  N   TYR A 200      47.327   3.826  80.054  1.00 57.94           N  
+ATOM   1457  CA  TYR A 200      46.440   2.663  80.075  1.00 57.30           C  
+ATOM   1458  C   TYR A 200      46.791   1.606  79.027  1.00 58.08           C  
+ATOM   1459  O   TYR A 200      46.448   0.433  79.192  1.00 58.00           O  
+ATOM   1460  CB  TYR A 200      44.986   3.088  79.837  1.00 54.81           C  
+ATOM   1461  CG  TYR A 200      44.243   3.630  81.041  1.00 54.29           C  
+ATOM   1462  CD1 TYR A 200      43.683   4.909  81.018  1.00 53.72           C  
+ATOM   1463  CD2 TYR A 200      44.057   2.851  82.184  1.00 54.57           C  
+ATOM   1464  CE1 TYR A 200      42.952   5.400  82.100  1.00 53.10           C  
+ATOM   1465  CE2 TYR A 200      43.325   3.334  83.278  1.00 53.99           C  
+ATOM   1466  CZ  TYR A 200      42.777   4.609  83.225  1.00 53.47           C  
+ATOM   1467  OH  TYR A 200      42.052   5.094  84.288  1.00 52.20           O  
+ATOM   1468  N   GLU A 201      47.471   2.010  77.956  1.00 58.77           N  
+ATOM   1469  CA  GLU A 201      47.796   1.072  76.885  1.00 60.18           C  
+ATOM   1470  C   GLU A 201      49.277   0.900  76.553  1.00 60.32           C  
+ATOM   1471  O   GLU A 201      49.615   0.309  75.526  1.00 59.03           O  
+ATOM   1472  CB  GLU A 201      47.040   1.470  75.613  1.00 61.22           C  
+ATOM   1473  CG  GLU A 201      45.736   2.205  75.889  1.00 63.44           C  
+ATOM   1474  CD  GLU A 201      44.867   2.370  74.656  1.00 64.50           C  
+ATOM   1475  OE1 GLU A 201      44.289   1.362  74.196  1.00 64.36           O  
+ATOM   1476  OE2 GLU A 201      44.763   3.507  74.148  1.00 64.74           O  
+ATOM   1477  N   ASN A 202      50.158   1.404  77.410  1.00 60.96           N  
+ATOM   1478  CA  ASN A 202      51.591   1.270  77.168  1.00 61.64           C  
+ATOM   1479  C   ASN A 202      51.925   1.851  75.792  1.00 61.22           C  
+ATOM   1480  O   ASN A 202      52.417   1.154  74.904  1.00 60.33           O  
+ATOM   1481  CB  ASN A 202      51.986  -0.214  77.244  1.00 62.95           C  
+ATOM   1482  CG  ASN A 202      53.487  -0.435  77.135  1.00 64.07           C  
+ATOM   1483  OD1 ASN A 202      54.276   0.209  77.830  1.00 64.55           O  
+ATOM   1484  ND2 ASN A 202      53.887  -1.363  76.268  1.00 64.74           N  
+ATOM   1485  N   LEU A 203      51.639   3.138  75.626  1.00 60.87           N  
+ATOM   1486  CA  LEU A 203      51.895   3.835  74.373  1.00 60.56           C  
+ATOM   1487  C   LEU A 203      52.716   5.089  74.643  1.00 60.41           C  
+ATOM   1488  O   LEU A 203      52.573   5.717  75.691  1.00 60.44           O  
+ATOM   1489  CB  LEU A 203      50.574   4.238  73.709  1.00 60.79           C  
+ATOM   1490  CG  LEU A 203      49.587   3.146  73.281  1.00 61.14           C  
+ATOM   1491  CD1 LEU A 203      48.275   3.787  72.850  1.00 60.55           C  
+ATOM   1492  CD2 LEU A 203      50.182   2.319  72.147  1.00 60.88           C  
+ATOM   1493  N   PRO A 204      53.594   5.467  73.701  1.00 60.19           N  
+ATOM   1494  CA  PRO A 204      54.427   6.664  73.866  1.00 60.30           C  
+ATOM   1495  C   PRO A 204      53.537   7.894  74.018  1.00 60.41           C  
+ATOM   1496  O   PRO A 204      52.481   7.977  73.395  1.00 60.34           O  
+ATOM   1497  CB  PRO A 204      55.237   6.703  72.570  1.00 60.07           C  
+ATOM   1498  CG  PRO A 204      55.349   5.254  72.197  1.00 60.33           C  
+ATOM   1499  CD  PRO A 204      53.954   4.742  72.470  1.00 60.03           C  
+ATOM   1500  N   ARG A 205      53.956   8.843  74.843  1.00 60.69           N  
+ATOM   1501  CA  ARG A 205      53.171  10.052  75.047  1.00 62.34           C  
+ATOM   1502  C   ARG A 205      52.963  10.758  73.706  1.00 61.75           C  
+ATOM   1503  O   ARG A 205      53.929  11.175  73.066  1.00 62.25           O  
+ATOM   1504  CB  ARG A 205      53.895  10.993  76.007  1.00 65.20           C  
+ATOM   1505  CG  ARG A 205      54.473  10.317  77.238  1.00 71.21           C  
+ATOM   1506  CD  ARG A 205      55.347  11.294  78.010  1.00 75.99           C  
+ATOM   1507  NE  ARG A 205      56.194  10.634  79.002  1.00 80.68           N  
+ATOM   1508  CZ  ARG A 205      57.146  11.250  79.701  1.00 82.80           C  
+ATOM   1509  NH1 ARG A 205      57.375  12.547  79.520  1.00 83.42           N  
+ATOM   1510  NH2 ARG A 205      57.876  10.569  80.578  1.00 83.44           N  
+ATOM   1511  N   GLY A 206      51.709  10.885  73.280  1.00 60.65           N  
+ATOM   1512  CA  GLY A 206      51.414  11.553  72.021  1.00 58.74           C  
+ATOM   1513  C   GLY A 206      51.039  10.648  70.858  1.00 57.72           C  
+ATOM   1514  O   GLY A 206      50.530  11.116  69.840  1.00 57.45           O  
+ATOM   1515  N   GLU A 207      51.288   9.353  71.005  1.00 56.61           N  
+ATOM   1516  CA  GLU A 207      50.983   8.390  69.957  1.00 56.75           C  
+ATOM   1517  C   GLU A 207      49.481   8.210  69.758  1.00 56.35           C  
+ATOM   1518  O   GLU A 207      49.008   8.095  68.630  1.00 56.37           O  
+ATOM   1519  CB  GLU A 207      51.619   7.035  70.289  1.00 58.24           C  
+ATOM   1520  CG  GLU A 207      51.245   5.907  69.328  1.00 61.56           C  
+ATOM   1521  CD  GLU A 207      51.943   6.005  67.978  1.00 63.92           C  
+ATOM   1522  OE1 GLU A 207      52.271   7.134  67.547  1.00 64.56           O  
+ATOM   1523  OE2 GLU A 207      52.148   4.946  67.340  1.00 64.66           O  
+ATOM   1524  N   LYS A 208      48.736   8.184  70.858  1.00 55.81           N  
+ATOM   1525  CA  LYS A 208      47.291   7.994  70.803  1.00 54.47           C  
+ATOM   1526  C   LYS A 208      46.591   9.054  69.968  1.00 54.10           C  
+ATOM   1527  O   LYS A 208      45.808   8.731  69.076  1.00 54.24           O  
+ATOM   1528  CB  LYS A 208      46.695   7.998  72.215  1.00 53.61           C  
+ATOM   1529  CG  LYS A 208      45.220   7.622  72.257  1.00 51.11           C  
+ATOM   1530  CD  LYS A 208      45.027   6.180  71.831  1.00 49.58           C  
+ATOM   1531  CE  LYS A 208      43.572   5.785  71.839  1.00 46.85           C  
+ATOM   1532  NZ  LYS A 208      43.441   4.340  71.534  1.00 46.61           N  
+ATOM   1533  N   LYS A 209      46.868  10.319  70.265  1.00 53.65           N  
+ATOM   1534  CA  LYS A 209      46.248  11.420  69.535  1.00 53.32           C  
+ATOM   1535  C   LYS A 209      46.620  11.367  68.062  1.00 54.50           C  
+ATOM   1536  O   LYS A 209      45.845  11.783  67.202  1.00 54.77           O  
+ATOM   1537  CB  LYS A 209      46.683  12.763  70.116  1.00 51.21           C  
+ATOM   1538  CG  LYS A 209      46.033  13.946  69.436  1.00 48.73           C  
+ATOM   1539  CD  LYS A 209      46.562  15.259  69.976  1.00 48.11           C  
+ATOM   1540  CE  LYS A 209      45.841  16.435  69.349  1.00 46.46           C  
+ATOM   1541  NZ  LYS A 209      46.410  17.738  69.771  1.00 47.55           N  
+ATOM   1542  N   ARG A 210      47.813  10.858  67.777  1.00 55.70           N  
+ATOM   1543  CA  ARG A 210      48.287  10.749  66.406  1.00 56.99           C  
+ATOM   1544  C   ARG A 210      47.528   9.641  65.680  1.00 56.95           C  
+ATOM   1545  O   ARG A 210      47.042   9.840  64.564  1.00 56.48           O  
+ATOM   1546  CB  ARG A 210      49.784  10.440  66.385  1.00 58.95           C  
+ATOM   1547  CG  ARG A 210      50.405  10.512  65.001  1.00 61.02           C  
+ATOM   1548  CD  ARG A 210      51.718   9.749  64.944  1.00 63.75           C  
+ATOM   1549  NE  ARG A 210      51.524   8.322  65.202  1.00 65.84           N  
+ATOM   1550  CZ  ARG A 210      50.788   7.512  64.442  1.00 66.16           C  
+ATOM   1551  NH1 ARG A 210      50.170   7.983  63.366  1.00 66.15           N  
+ATOM   1552  NH2 ARG A 210      50.667   6.228  64.759  1.00 65.33           N  
+ATOM   1553  N   GLN A 211      47.438   8.476  66.319  1.00 56.05           N  
+ATOM   1554  CA  GLN A 211      46.735   7.331  65.748  1.00 55.34           C  
+ATOM   1555  C   GLN A 211      45.298   7.708  65.427  1.00 53.74           C  
+ATOM   1556  O   GLN A 211      44.826   7.499  64.309  1.00 53.99           O  
+ATOM   1557  CB  GLN A 211      46.732   6.146  66.727  1.00 57.24           C  
+ATOM   1558  CG  GLN A 211      48.058   5.403  66.842  1.00 60.85           C  
+ATOM   1559  CD  GLN A 211      47.982   4.210  67.784  1.00 62.89           C  
+ATOM   1560  OE1 GLN A 211      47.139   3.324  67.620  1.00 63.24           O  
+ATOM   1561  NE2 GLN A 211      48.868   4.182  68.773  1.00 63.72           N  
+ATOM   1562  N   VAL A 212      44.615   8.273  66.419  1.00 51.56           N  
+ATOM   1563  CA  VAL A 212      43.216   8.679  66.295  1.00 48.04           C  
+ATOM   1564  C   VAL A 212      42.937   9.604  65.116  1.00 45.48           C  
+ATOM   1565  O   VAL A 212      42.021   9.362  64.334  1.00 43.48           O  
+ATOM   1566  CB  VAL A 212      42.735   9.375  67.585  1.00 46.87           C  
+ATOM   1567  CG1 VAL A 212      41.301   9.839  67.425  1.00 47.50           C  
+ATOM   1568  CG2 VAL A 212      42.853   8.419  68.756  1.00 45.84           C  
+ATOM   1569  N   GLY A 213      43.728  10.664  65.000  1.00 44.03           N  
+ATOM   1570  CA  GLY A 213      43.542  11.616  63.919  1.00 43.19           C  
+ATOM   1571  C   GLY A 213      43.835  11.061  62.538  1.00 42.50           C  
+ATOM   1572  O   GLY A 213      43.246  11.501  61.552  1.00 42.61           O  
+ATOM   1573  N   ALA A 214      44.744  10.093  62.468  1.00 41.63           N  
+ATOM   1574  CA  ALA A 214      45.119   9.474  61.203  1.00 39.58           C  
+ATOM   1575  C   ALA A 214      44.128   8.385  60.793  1.00 38.85           C  
+ATOM   1576  O   ALA A 214      44.039   8.032  59.619  1.00 39.86           O  
+ATOM   1577  CB  ALA A 214      46.525   8.886  61.313  1.00 39.82           C  
+ATOM   1578  N   ALA A 215      43.381   7.856  61.757  1.00 36.60           N  
+ATOM   1579  CA  ALA A 215      42.414   6.801  61.472  1.00 33.99           C  
+ATOM   1580  C   ALA A 215      41.119   7.352  60.886  1.00 32.84           C  
+ATOM   1581  O   ALA A 215      40.317   6.603  60.317  1.00 32.52           O  
+ATOM   1582  CB  ALA A 215      42.118   6.010  62.738  1.00 33.98           C  
+ATOM   1583  N   VAL A 216      40.911   8.658  61.033  1.00 31.30           N  
+ATOM   1584  CA  VAL A 216      39.713   9.302  60.498  1.00 30.33           C  
+ATOM   1585  C   VAL A 216      39.781   9.256  58.980  1.00 29.51           C  
+ATOM   1586  O   VAL A 216      40.721   9.778  58.388  1.00 29.59           O  
+ATOM   1587  CB  VAL A 216      39.629  10.780  60.920  1.00 30.17           C  
+ATOM   1588  CG1 VAL A 216      38.431  11.439  60.253  1.00 28.16           C  
+ATOM   1589  CG2 VAL A 216      39.532  10.885  62.433  1.00 29.30           C  
+ATOM   1590  N   PRO A 217      38.790   8.624  58.331  1.00 28.53           N  
+ATOM   1591  CA  PRO A 217      38.765   8.523  56.867  1.00 27.89           C  
+ATOM   1592  C   PRO A 217      39.094   9.848  56.183  1.00 26.79           C  
+ATOM   1593  O   PRO A 217      39.957   9.895  55.316  1.00 25.32           O  
+ATOM   1594  CB  PRO A 217      37.342   8.054  56.582  1.00 28.59           C  
+ATOM   1595  CG  PRO A 217      37.060   7.170  57.762  1.00 28.21           C  
+ATOM   1596  CD  PRO A 217      37.598   7.987  58.920  1.00 28.45           C  
+ATOM   1597  N   PHE A 218      38.410  10.916  56.589  1.00 26.23           N  
+ATOM   1598  CA  PHE A 218      38.634  12.243  56.020  1.00 26.96           C  
+ATOM   1599  C   PHE A 218      40.113  12.639  56.061  1.00 28.62           C  
+ATOM   1600  O   PHE A 218      40.557  13.473  55.273  1.00 29.39           O  
+ATOM   1601  CB  PHE A 218      37.813  13.294  56.771  1.00 25.34           C  
+ATOM   1602  CG  PHE A 218      37.843  14.663  56.135  1.00 26.10           C  
+ATOM   1603  CD1 PHE A 218      36.899  15.020  55.175  1.00 26.93           C  
+ATOM   1604  CD2 PHE A 218      38.807  15.600  56.501  1.00 26.10           C  
+ATOM   1605  CE1 PHE A 218      36.912  16.287  54.594  1.00 24.35           C  
+ATOM   1606  CE2 PHE A 218      38.828  16.870  55.925  1.00 25.01           C  
+ATOM   1607  CZ  PHE A 218      37.879  17.213  54.972  1.00 24.55           C  
+ATOM   1608  N   GLY A 219      40.870  12.068  56.992  1.00 29.98           N  
+ATOM   1609  CA  GLY A 219      42.286  12.383  57.062  1.00 31.28           C  
+ATOM   1610  C   GLY A 219      42.759  13.360  58.125  1.00 32.62           C  
+ATOM   1611  O   GLY A 219      43.926  13.766  58.115  1.00 32.48           O  
+ATOM   1612  N   ARG A 220      41.872  13.752  59.034  1.00 32.75           N  
+ATOM   1613  CA  ARG A 220      42.264  14.667  60.099  1.00 32.67           C  
+ATOM   1614  C   ARG A 220      41.242  14.715  61.222  1.00 33.39           C  
+ATOM   1615  O   ARG A 220      40.089  14.311  61.058  1.00 33.04           O  
+ATOM   1616  CB  ARG A 220      42.488  16.080  59.549  1.00 32.06           C  
+ATOM   1617  CG  ARG A 220      41.264  16.982  59.553  1.00 31.62           C  
+ATOM   1618  CD  ARG A 220      41.560  18.295  58.836  1.00 31.43           C  
+ATOM   1619  NE  ARG A 220      40.436  19.233  58.714  1.00 32.68           N  
+ATOM   1620  CZ  ARG A 220      39.176  18.996  59.067  1.00 34.77           C  
+ATOM   1621  NH1 ARG A 220      38.819  17.833  59.589  1.00 40.13           N  
+ATOM   1622  NH2 ARG A 220      38.260  19.936  58.887  1.00 33.56           N  
+ATOM   1623  N   MET A 221      41.685  15.210  62.369  1.00 34.46           N  
+ATOM   1624  CA  MET A 221      40.823  15.330  63.526  1.00 36.12           C  
+ATOM   1625  C   MET A 221      39.796  16.421  63.233  1.00 35.62           C  
+ATOM   1626  O   MET A 221      40.037  17.306  62.409  1.00 35.49           O  
+ATOM   1627  CB  MET A 221      41.665  15.687  64.752  1.00 39.51           C  
+ATOM   1628  CG  MET A 221      40.999  15.396  66.074  1.00 41.17           C  
+ATOM   1629  SD  MET A 221      42.254  15.072  67.311  1.00 48.07           S  
+ATOM   1630  CE  MET A 221      42.587  13.344  67.007  1.00 44.94           C  
+ATOM   1631  N   GLY A 222      38.651  16.349  63.903  1.00 35.13           N  
+ATOM   1632  CA  GLY A 222      37.597  17.323  63.689  1.00 34.04           C  
+ATOM   1633  C   GLY A 222      37.910  18.728  64.160  1.00 34.46           C  
+ATOM   1634  O   GLY A 222      38.894  18.968  64.856  1.00 32.50           O  
+ATOM   1635  N   ARG A 223      37.043  19.660  63.779  1.00 35.55           N  
+ATOM   1636  CA  ARG A 223      37.194  21.064  64.128  1.00 37.27           C  
+ATOM   1637  C   ARG A 223      35.792  21.624  64.353  1.00 37.14           C  
+ATOM   1638  O   ARG A 223      34.829  21.146  63.758  1.00 37.79           O  
+ATOM   1639  CB  ARG A 223      37.882  21.789  62.973  1.00 40.76           C  
+ATOM   1640  CG  ARG A 223      38.869  22.866  63.374  1.00 46.38           C  
+ATOM   1641  CD  ARG A 223      40.052  22.861  62.420  1.00 48.38           C  
+ATOM   1642  NE  ARG A 223      39.629  22.531  61.062  1.00 51.61           N  
+ATOM   1643  CZ  ARG A 223      40.445  22.473  60.012  1.00 52.89           C  
+ATOM   1644  NH1 ARG A 223      41.738  22.727  60.162  1.00 54.40           N  
+ATOM   1645  NH2 ARG A 223      39.969  22.155  58.813  1.00 52.64           N  
+ATOM   1646  N   ALA A 224      35.666  22.629  65.208  1.00 36.60           N  
+ATOM   1647  CA  ALA A 224      34.352  23.200  65.480  1.00 36.54           C  
+ATOM   1648  C   ALA A 224      33.659  23.649  64.195  1.00 36.01           C  
+ATOM   1649  O   ALA A 224      32.459  23.456  64.030  1.00 35.98           O  
+ATOM   1650  CB  ALA A 224      34.479  24.371  66.450  1.00 36.19           C  
+ATOM   1651  N   GLU A 225      34.427  24.239  63.285  1.00 36.54           N  
+ATOM   1652  CA  GLU A 225      33.897  24.725  62.015  1.00 36.13           C  
+ATOM   1653  C   GLU A 225      33.254  23.635  61.161  1.00 33.95           C  
+ATOM   1654  O   GLU A 225      32.456  23.929  60.276  1.00 33.83           O  
+ATOM   1655  CB  GLU A 225      35.006  25.414  61.213  1.00 38.60           C  
+ATOM   1656  CG  GLU A 225      35.567  26.663  61.881  1.00 43.71           C  
+ATOM   1657  CD  GLU A 225      36.398  26.357  63.118  1.00 46.36           C  
+ATOM   1658  OE1 GLU A 225      36.616  27.290  63.919  1.00 49.37           O  
+ATOM   1659  OE2 GLU A 225      36.842  25.199  63.285  1.00 46.89           O  
+ATOM   1660  N   ASP A 226      33.600  22.380  61.418  1.00 30.48           N  
+ATOM   1661  CA  ASP A 226      33.019  21.290  60.651  1.00 28.59           C  
+ATOM   1662  C   ASP A 226      31.594  21.013  61.090  1.00 27.55           C  
+ATOM   1663  O   ASP A 226      30.814  20.431  60.341  1.00 26.90           O  
+ATOM   1664  CB  ASP A 226      33.837  20.012  60.819  1.00 27.46           C  
+ATOM   1665  CG  ASP A 226      35.259  20.175  60.355  1.00 29.29           C  
+ATOM   1666  OD1 ASP A 226      35.484  20.992  59.431  1.00 33.27           O  
+ATOM   1667  OD2 ASP A 226      36.149  19.482  60.894  1.00 26.89           O  
+ATOM   1668  N   LEU A 227      31.260  21.451  62.301  1.00 26.95           N  
+ATOM   1669  CA  LEU A 227      29.941  21.213  62.888  1.00 25.55           C  
+ATOM   1670  C   LEU A 227      28.897  22.318  62.761  1.00 24.79           C  
+ATOM   1671  O   LEU A 227      27.705  22.033  62.713  1.00 25.55           O  
+ATOM   1672  CB  LEU A 227      30.111  20.860  64.373  1.00 24.60           C  
+ATOM   1673  CG  LEU A 227      30.508  19.435  64.795  1.00 25.02           C  
+ATOM   1674  CD1 LEU A 227      31.388  18.770  63.767  1.00 22.80           C  
+ATOM   1675  CD2 LEU A 227      31.224  19.509  66.133  1.00 25.24           C  
+ATOM   1676  N   THR A 228      29.334  23.571  62.708  1.00 25.33           N  
+ATOM   1677  CA  THR A 228      28.405  24.699  62.631  1.00 26.26           C  
+ATOM   1678  C   THR A 228      27.376  24.663  61.496  1.00 25.76           C  
+ATOM   1679  O   THR A 228      26.234  25.099  61.683  1.00 27.50           O  
+ATOM   1680  CB  THR A 228      29.172  26.033  62.583  1.00 27.39           C  
+ATOM   1681  OG1 THR A 228      30.023  26.063  61.432  1.00 29.26           O  
+ATOM   1682  CG2 THR A 228      30.029  26.186  63.838  1.00 27.87           C  
+ATOM   1683  N   GLY A 229      27.762  24.143  60.332  1.00 23.67           N  
+ATOM   1684  CA  GLY A 229      26.829  24.065  59.218  1.00 20.40           C  
+ATOM   1685  C   GLY A 229      25.595  23.251  59.573  1.00 19.34           C  
+ATOM   1686  O   GLY A 229      24.463  23.688  59.356  1.00 18.85           O  
+ATOM   1687  N   MET A 230      25.812  22.059  60.120  1.00 19.43           N  
+ATOM   1688  CA  MET A 230      24.717  21.176  60.517  1.00 20.56           C  
+ATOM   1689  C   MET A 230      23.919  21.779  61.690  1.00 20.54           C  
+ATOM   1690  O   MET A 230      22.688  21.683  61.736  1.00 19.43           O  
+ATOM   1691  CB  MET A 230      25.279  19.802  60.898  1.00 21.95           C  
+ATOM   1692  CG  MET A 230      24.234  18.778  61.285  1.00 22.84           C  
+ATOM   1693  SD  MET A 230      23.037  18.482  59.979  1.00 25.30           S  
+ATOM   1694  CE  MET A 230      23.893  17.232  59.046  1.00 23.83           C  
+ATOM   1695  N   ALA A 231      24.622  22.409  62.628  1.00 19.80           N  
+ATOM   1696  CA  ALA A 231      23.976  23.043  63.774  1.00 19.79           C  
+ATOM   1697  C   ALA A 231      22.955  24.077  63.285  1.00 20.62           C  
+ATOM   1698  O   ALA A 231      21.874  24.224  63.863  1.00 20.55           O  
+ATOM   1699  CB  ALA A 231      25.024  23.716  64.657  1.00 18.85           C  
+ATOM   1700  N   ILE A 232      23.308  24.790  62.218  1.00 21.65           N  
+ATOM   1701  CA  ILE A 232      22.429  25.804  61.622  1.00 22.41           C  
+ATOM   1702  C   ILE A 232      21.302  25.157  60.798  1.00 22.34           C  
+ATOM   1703  O   ILE A 232      20.125  25.508  60.938  1.00 22.23           O  
+ATOM   1704  CB  ILE A 232      23.233  26.760  60.690  1.00 22.14           C  
+ATOM   1705  CG1 ILE A 232      24.255  27.553  61.510  1.00 21.71           C  
+ATOM   1706  CG2 ILE A 232      22.293  27.711  59.970  1.00 20.73           C  
+ATOM   1707  CD1 ILE A 232      25.247  28.342  60.672  1.00 21.14           C  
+ATOM   1708  N   PHE A 233      21.669  24.206  59.942  1.00 21.98           N  
+ATOM   1709  CA  PHE A 233      20.696  23.536  59.094  1.00 20.26           C  
+ATOM   1710  C   PHE A 233      19.520  22.942  59.863  1.00 20.62           C  
+ATOM   1711  O   PHE A 233      18.363  23.154  59.495  1.00 21.09           O  
+ATOM   1712  CB  PHE A 233      21.366  22.430  58.284  1.00 19.22           C  
+ATOM   1713  CG  PHE A 233      20.426  21.720  57.347  1.00 19.57           C  
+ATOM   1714  CD1 PHE A 233      19.952  22.355  56.203  1.00 20.24           C  
+ATOM   1715  CD2 PHE A 233      19.993  20.430  57.622  1.00 19.07           C  
+ATOM   1716  CE1 PHE A 233      19.057  21.715  55.347  1.00 20.20           C  
+ATOM   1717  CE2 PHE A 233      19.097  19.779  56.773  1.00 20.60           C  
+ATOM   1718  CZ  PHE A 233      18.628  20.424  55.632  1.00 20.62           C  
+ATOM   1719  N   LEU A 234      19.813  22.191  60.921  1.00 19.98           N  
+ATOM   1720  CA  LEU A 234      18.761  21.559  61.715  1.00 20.60           C  
+ATOM   1721  C   LEU A 234      17.793  22.544  62.361  1.00 21.64           C  
+ATOM   1722  O   LEU A 234      16.700  22.160  62.771  1.00 21.11           O  
+ATOM   1723  CB  LEU A 234      19.375  20.668  62.798  1.00 18.60           C  
+ATOM   1724  CG  LEU A 234      19.938  19.333  62.308  1.00 17.74           C  
+ATOM   1725  CD1 LEU A 234      20.567  18.564  63.458  1.00 15.97           C  
+ATOM   1726  CD2 LEU A 234      18.812  18.524  61.682  1.00 17.93           C  
+ATOM   1727  N   ALA A 235      18.192  23.812  62.439  1.00 22.87           N  
+ATOM   1728  CA  ALA A 235      17.355  24.841  63.045  1.00 25.13           C  
+ATOM   1729  C   ALA A 235      16.507  25.610  62.037  1.00 26.81           C  
+ATOM   1730  O   ALA A 235      15.700  26.459  62.423  1.00 28.97           O  
+ATOM   1731  CB  ALA A 235      18.229  25.820  63.833  1.00 24.33           C  
+ATOM   1732  N   THR A 236      16.679  25.320  60.752  1.00 26.60           N  
+ATOM   1733  CA  THR A 236      15.925  26.025  59.716  1.00 26.35           C  
+ATOM   1734  C   THR A 236      14.688  25.260  59.259  1.00 25.67           C  
+ATOM   1735  O   THR A 236      14.532  24.071  59.542  1.00 26.18           O  
+ATOM   1736  CB  THR A 236      16.804  26.292  58.486  1.00 26.23           C  
+ATOM   1737  OG1 THR A 236      17.209  25.042  57.917  1.00 25.70           O  
+ATOM   1738  CG2 THR A 236      18.039  27.087  58.877  1.00 24.61           C  
+ATOM   1739  N   PRO A 237      13.778  25.941  58.551  1.00 24.86           N  
+ATOM   1740  CA  PRO A 237      12.575  25.249  58.086  1.00 24.52           C  
+ATOM   1741  C   PRO A 237      12.850  24.220  56.990  1.00 25.24           C  
+ATOM   1742  O   PRO A 237      11.963  23.448  56.627  1.00 25.86           O  
+ATOM   1743  CB  PRO A 237      11.670  26.392  57.627  1.00 22.45           C  
+ATOM   1744  CG  PRO A 237      12.629  27.458  57.243  1.00 23.42           C  
+ATOM   1745  CD  PRO A 237      13.675  27.391  58.319  1.00 24.22           C  
+ATOM   1746  N   GLU A 238      14.072  24.200  56.463  1.00 25.76           N  
+ATOM   1747  CA  GLU A 238      14.415  23.223  55.440  1.00 26.78           C  
+ATOM   1748  C   GLU A 238      14.594  21.862  56.098  1.00 27.45           C  
+ATOM   1749  O   GLU A 238      14.824  20.858  55.417  1.00 28.63           O  
+ATOM   1750  CB  GLU A 238      15.705  23.607  54.707  1.00 28.34           C  
+ATOM   1751  CG  GLU A 238      15.549  24.748  53.720  1.00 29.47           C  
+ATOM   1752  CD  GLU A 238      16.743  24.880  52.781  1.00 31.84           C  
+ATOM   1753  OE1 GLU A 238      17.884  25.016  53.266  1.00 32.42           O  
+ATOM   1754  OE2 GLU A 238      16.541  24.850  51.549  1.00 33.50           O  
+ATOM   1755  N   ALA A 239      14.476  21.836  57.425  1.00 26.09           N  
+ATOM   1756  CA  ALA A 239      14.619  20.605  58.196  1.00 24.01           C  
+ATOM   1757  C   ALA A 239      13.340  20.241  58.953  1.00 24.62           C  
+ATOM   1758  O   ALA A 239      13.337  19.321  59.780  1.00 25.04           O  
+ATOM   1759  CB  ALA A 239      15.778  20.741  59.175  1.00 23.04           C  
+ATOM   1760  N   ASP A 240      12.251  20.949  58.668  1.00 22.92           N  
+ATOM   1761  CA  ASP A 240      10.983  20.679  59.340  1.00 21.54           C  
+ATOM   1762  C   ASP A 240      10.523  19.235  59.247  1.00 21.09           C  
+ATOM   1763  O   ASP A 240       9.713  18.798  60.058  1.00 21.96           O  
+ATOM   1764  CB  ASP A 240       9.864  21.549  58.776  1.00 21.66           C  
+ATOM   1765  CG  ASP A 240       9.937  22.983  59.245  1.00 22.84           C  
+ATOM   1766  OD1 ASP A 240      10.857  23.337  60.015  1.00 23.30           O  
+ATOM   1767  OD2 ASP A 240       9.054  23.762  58.833  1.00 25.36           O  
+ATOM   1768  N   TYR A 241      11.009  18.494  58.260  1.00 19.28           N  
+ATOM   1769  CA  TYR A 241      10.574  17.113  58.113  1.00 18.03           C  
+ATOM   1770  C   TYR A 241      11.587  16.132  58.710  1.00 18.36           C  
+ATOM   1771  O   TYR A 241      11.430  14.915  58.583  1.00 18.99           O  
+ATOM   1772  CB  TYR A 241      10.320  16.795  56.629  1.00 16.72           C  
+ATOM   1773  CG  TYR A 241       9.357  15.646  56.381  1.00 14.84           C  
+ATOM   1774  CD1 TYR A 241       8.013  15.730  56.776  1.00 15.54           C  
+ATOM   1775  CD2 TYR A 241       9.787  14.472  55.761  1.00 12.80           C  
+ATOM   1776  CE1 TYR A 241       7.128  14.668  56.561  1.00 14.31           C  
+ATOM   1777  CE2 TYR A 241       8.912  13.410  55.539  1.00 12.47           C  
+ATOM   1778  CZ  TYR A 241       7.590  13.514  55.941  1.00 14.81           C  
+ATOM   1779  OH  TYR A 241       6.733  12.456  55.731  1.00 17.97           O  
+ATOM   1780  N   ILE A 242      12.624  16.659  59.360  1.00 18.06           N  
+ATOM   1781  CA  ILE A 242      13.632  15.802  59.990  1.00 18.59           C  
+ATOM   1782  C   ILE A 242      13.275  15.639  61.479  1.00 20.10           C  
+ATOM   1783  O   ILE A 242      13.363  16.584  62.262  1.00 18.52           O  
+ATOM   1784  CB  ILE A 242      15.044  16.401  59.828  1.00 16.72           C  
+ATOM   1785  CG1 ILE A 242      15.407  16.442  58.333  1.00 16.44           C  
+ATOM   1786  CG2 ILE A 242      16.056  15.562  60.591  1.00 15.55           C  
+ATOM   1787  CD1 ILE A 242      16.715  17.134  58.009  1.00 13.53           C  
+ATOM   1788  N   VAL A 243      12.864  14.430  61.854  1.00 20.04           N  
+ATOM   1789  CA  VAL A 243      12.441  14.145  63.225  1.00 18.99           C  
+ATOM   1790  C   VAL A 243      13.112  12.946  63.895  1.00 18.34           C  
+ATOM   1791  O   VAL A 243      13.210  11.873  63.303  1.00 18.35           O  
+ATOM   1792  CB  VAL A 243      10.923  13.896  63.262  1.00 18.93           C  
+ATOM   1793  CG1 VAL A 243      10.460  13.640  64.685  1.00 18.33           C  
+ATOM   1794  CG2 VAL A 243      10.198  15.083  62.658  1.00 17.52           C  
+ATOM   1795  N   ALA A 244      13.554  13.145  65.138  1.00 17.17           N  
+ATOM   1796  CA  ALA A 244      14.180  12.100  65.952  1.00 16.24           C  
+ATOM   1797  C   ALA A 244      15.363  11.404  65.300  1.00 15.92           C  
+ATOM   1798  O   ALA A 244      15.486  10.185  65.372  1.00 18.93           O  
+ATOM   1799  CB  ALA A 244      13.128  11.057  66.361  1.00 12.40           C  
+ATOM   1800  N   GLN A 245      16.247  12.179  64.689  1.00 15.76           N  
+ATOM   1801  CA  GLN A 245      17.418  11.619  64.031  1.00 14.89           C  
+ATOM   1802  C   GLN A 245      18.677  12.078  64.733  1.00 14.04           C  
+ATOM   1803  O   GLN A 245      18.679  13.107  65.421  1.00 13.19           O  
+ATOM   1804  CB  GLN A 245      17.496  12.098  62.566  1.00 16.43           C  
+ATOM   1805  CG  GLN A 245      16.248  11.831  61.733  1.00 14.23           C  
+ATOM   1806  CD  GLN A 245      15.967  10.355  61.600  1.00 13.84           C  
+ATOM   1807  OE1 GLN A 245      16.882   9.559  61.366  1.00 15.40           O  
+ATOM   1808  NE2 GLN A 245      14.700   9.975  61.740  1.00 12.98           N  
+ATOM   1809  N   THR A 246      19.746  11.311  64.532  1.00 13.90           N  
+ATOM   1810  CA  THR A 246      21.073  11.618  65.060  1.00 13.69           C  
+ATOM   1811  C   THR A 246      21.963  11.546  63.810  1.00 14.66           C  
+ATOM   1812  O   THR A 246      22.130  10.479  63.219  1.00 15.17           O  
+ATOM   1813  CB  THR A 246      21.543  10.573  66.112  1.00 13.15           C  
+ATOM   1814  OG1 THR A 246      20.665  10.607  67.247  1.00 14.80           O  
+ATOM   1815  CG2 THR A 246      22.958  10.882  66.581  1.00 10.43           C  
+ATOM   1816  N   TYR A 247      22.493  12.695  63.398  1.00 14.72           N  
+ATOM   1817  CA  TYR A 247      23.338  12.801  62.209  1.00 13.19           C  
+ATOM   1818  C   TYR A 247      24.814  12.835  62.562  1.00 14.07           C  
+ATOM   1819  O   TYR A 247      25.249  13.694  63.324  1.00 15.30           O  
+ATOM   1820  CB  TYR A 247      22.986  14.074  61.436  1.00 10.03           C  
+ATOM   1821  CG  TYR A 247      21.655  14.036  60.698  1.00 10.79           C  
+ATOM   1822  CD1 TYR A 247      21.058  15.210  60.240  1.00 10.59           C  
+ATOM   1823  CD2 TYR A 247      21.023  12.831  60.410  1.00  9.17           C  
+ATOM   1824  CE1 TYR A 247      19.871  15.181  59.514  1.00 11.19           C  
+ATOM   1825  CE2 TYR A 247      19.840  12.796  59.681  1.00  9.39           C  
+ATOM   1826  CZ  TYR A 247      19.274  13.973  59.238  1.00 10.28           C  
+ATOM   1827  OH  TYR A 247      18.108  13.938  58.506  1.00 16.71           O  
+ATOM   1828  N   ASN A 248      25.582  11.910  61.998  1.00 13.65           N  
+ATOM   1829  CA  ASN A 248      27.012  11.844  62.258  1.00 16.85           C  
+ATOM   1830  C   ASN A 248      27.802  12.808  61.380  1.00 18.74           C  
+ATOM   1831  O   ASN A 248      27.707  12.752  60.148  1.00 22.45           O  
+ATOM   1832  CB  ASN A 248      27.529  10.424  62.015  1.00 17.50           C  
+ATOM   1833  CG  ASN A 248      27.012   9.429  63.034  1.00 19.69           C  
+ATOM   1834  OD1 ASN A 248      26.091   9.720  63.800  1.00 18.80           O  
+ATOM   1835  ND2 ASN A 248      27.602   8.238  63.042  1.00 21.89           N  
+ATOM   1836  N   VAL A 249      28.572  13.690  62.014  1.00 18.57           N  
+ATOM   1837  CA  VAL A 249      29.420  14.646  61.301  1.00 18.70           C  
+ATOM   1838  C   VAL A 249      30.800  14.378  61.884  1.00 20.64           C  
+ATOM   1839  O   VAL A 249      31.308  15.149  62.698  1.00 22.16           O  
+ATOM   1840  CB  VAL A 249      28.997  16.110  61.576  1.00 18.65           C  
+ATOM   1841  CG1 VAL A 249      29.853  17.072  60.737  1.00 18.55           C  
+ATOM   1842  CG2 VAL A 249      27.526  16.300  61.236  1.00 15.89           C  
+ATOM   1843  N   ASP A 250      31.399  13.275  61.440  1.00 21.03           N  
+ATOM   1844  CA  ASP A 250      32.677  12.801  61.955  1.00 21.01           C  
+ATOM   1845  C   ASP A 250      33.738  12.428  60.914  1.00 21.15           C  
+ATOM   1846  O   ASP A 250      34.615  11.612  61.204  1.00 20.51           O  
+ATOM   1847  CB  ASP A 250      32.391  11.562  62.789  1.00 23.83           C  
+ATOM   1848  CG  ASP A 250      31.742  10.454  61.955  1.00 27.33           C  
+ATOM   1849  OD1 ASP A 250      31.203   9.479  62.526  1.00 28.60           O  
+ATOM   1850  OD2 ASP A 250      31.777  10.562  60.708  1.00 28.72           O  
+ATOM   1851  N   GLY A 251      33.659  12.986  59.709  1.00 20.11           N  
+ATOM   1852  CA  GLY A 251      34.647  12.657  58.691  1.00 17.10           C  
+ATOM   1853  C   GLY A 251      34.732  11.174  58.349  1.00 18.53           C  
+ATOM   1854  O   GLY A 251      35.765  10.691  57.867  1.00 17.43           O  
+ATOM   1855  N   GLY A 252      33.653  10.441  58.610  1.00 18.10           N  
+ATOM   1856  CA  GLY A 252      33.631   9.026  58.300  1.00 19.73           C  
+ATOM   1857  C   GLY A 252      33.998   8.089  59.440  1.00 23.83           C  
+ATOM   1858  O   GLY A 252      34.022   6.867  59.248  1.00 22.71           O  
+ATOM   1859  N   ASN A 253      34.276   8.640  60.623  1.00 25.53           N  
+ATOM   1860  CA  ASN A 253      34.653   7.820  61.778  1.00 25.63           C  
+ATOM   1861  C   ASN A 253      33.661   6.701  62.091  1.00 24.79           C  
+ATOM   1862  O   ASN A 253      34.053   5.594  62.456  1.00 25.09           O  
+ATOM   1863  CB  ASN A 253      34.850   8.707  63.001  1.00 27.95           C  
+ATOM   1864  CG  ASN A 253      36.241   8.580  63.574  1.00 32.16           C  
+ATOM   1865  OD1 ASN A 253      37.211   8.425  62.829  1.00 33.89           O  
+ATOM   1866  ND2 ASN A 253      36.355   8.652  64.898  1.00 33.82           N  
+ATOM   1867  N   TRP A 254      32.375   6.989  61.957  1.00 23.58           N  
+ATOM   1868  CA  TRP A 254      31.353   5.983  62.190  1.00 23.49           C  
+ATOM   1869  C   TRP A 254      30.267   6.167  61.134  1.00 24.70           C  
+ATOM   1870  O   TRP A 254      29.931   7.291  60.768  1.00 25.29           O  
+ATOM   1871  CB  TRP A 254      30.769   6.117  63.600  1.00 23.33           C  
+ATOM   1872  CG  TRP A 254      29.962   4.923  63.981  1.00 18.89           C  
+ATOM   1873  CD1 TRP A 254      28.604   4.811  63.964  1.00 19.59           C  
+ATOM   1874  CD2 TRP A 254      30.468   3.639  64.353  1.00 18.21           C  
+ATOM   1875  NE1 TRP A 254      28.229   3.532  64.301  1.00 18.41           N  
+ATOM   1876  CE2 TRP A 254      29.355   2.791  64.544  1.00 19.37           C  
+ATOM   1877  CE3 TRP A 254      31.756   3.121  64.540  1.00 17.89           C  
+ATOM   1878  CZ2 TRP A 254      29.489   1.449  64.921  1.00 19.13           C  
+ATOM   1879  CZ3 TRP A 254      31.890   1.790  64.912  1.00 19.67           C  
+ATOM   1880  CH2 TRP A 254      30.762   0.967  65.097  1.00 20.58           C  
+ATOM   1881  N   MET A 255      29.709   5.069  60.642  1.00 26.34           N  
+ATOM   1882  CA  MET A 255      28.701   5.164  59.592  1.00 27.93           C  
+ATOM   1883  C   MET A 255      27.302   4.748  60.005  1.00 27.64           C  
+ATOM   1884  O   MET A 255      27.057   3.586  60.326  1.00 29.54           O  
+ATOM   1885  CB  MET A 255      29.146   4.331  58.399  1.00 28.54           C  
+ATOM   1886  CG  MET A 255      30.558   4.642  57.948  1.00 30.99           C  
+ATOM   1887  SD  MET A 255      31.116   3.394  56.790  1.00 34.74           S  
+ATOM   1888  CE  MET A 255      31.526   2.062  57.912  1.00 35.45           C  
+ATOM   1889  N   SER A 256      26.376   5.699  59.965  1.00 26.90           N  
+ATOM   1890  CA  SER A 256      24.998   5.430  60.347  1.00 28.27           C  
+ATOM   1891  C   SER A 256      24.040   5.839  59.231  1.00 28.44           C  
+ATOM   1892  O   SER A 256      24.543   6.294  58.186  1.00 28.92           O  
+ATOM   1893  CB  SER A 256      24.664   6.188  61.642  1.00 28.64           C  
+ATOM   1894  OG  SER A 256      25.569   5.836  62.681  1.00 28.28           O  
+ATOM   1895  OXT SER A 256      22.811   5.701  59.408  1.00 27.92           O  
+TER    1896      SER A 256                                                      
+ATOM   1897  N   MET B   1      22.333 -31.975  81.215  1.00 44.89           N  
+ATOM   1898  CA  MET B   1      23.104 -30.998  82.028  1.00 43.40           C  
+ATOM   1899  C   MET B   1      24.121 -30.191  81.211  1.00 40.48           C  
+ATOM   1900  O   MET B   1      25.266 -30.614  81.040  1.00 38.97           O  
+ATOM   1901  CB  MET B   1      23.828 -31.727  83.164  1.00 48.82           C  
+ATOM   1902  CG  MET B   1      23.086 -31.723  84.500  1.00 55.57           C  
+ATOM   1903  SD  MET B   1      21.607 -32.746  84.539  1.00 63.93           S  
+ATOM   1904  CE  MET B   1      21.996 -33.836  85.950  1.00 64.69           C  
+ATOM   1905  N   ARG B   2      23.696 -29.028  80.719  1.00 36.83           N  
+ATOM   1906  CA  ARG B   2      24.559 -28.139  79.937  1.00 34.96           C  
+ATOM   1907  C   ARG B   2      25.364 -27.172  80.811  1.00 35.14           C  
+ATOM   1908  O   ARG B   2      26.395 -26.645  80.380  1.00 32.28           O  
+ATOM   1909  CB  ARG B   2      23.718 -27.336  78.940  1.00 33.73           C  
+ATOM   1910  CG  ARG B   2      23.238 -28.146  77.746  1.00 32.92           C  
+ATOM   1911  CD  ARG B   2      22.324 -27.336  76.844  1.00 31.91           C  
+ATOM   1912  NE  ARG B   2      20.948 -27.300  77.331  1.00 29.39           N  
+ATOM   1913  CZ  ARG B   2      19.974 -26.610  76.748  1.00 28.52           C  
+ATOM   1914  NH1 ARG B   2      20.230 -25.900  75.658  1.00 29.53           N  
+ATOM   1915  NH2 ARG B   2      18.748 -26.629  77.251  1.00 24.50           N  
+ATOM   1916  N   LEU B   3      24.879 -26.948  82.035  1.00 35.35           N  
+ATOM   1917  CA  LEU B   3      25.517 -26.051  83.001  1.00 35.96           C  
+ATOM   1918  C   LEU B   3      25.918 -26.814  84.257  1.00 36.30           C  
+ATOM   1919  O   LEU B   3      25.896 -26.269  85.363  1.00 36.22           O  
+ATOM   1920  CB  LEU B   3      24.552 -24.934  83.398  1.00 35.42           C  
+ATOM   1921  CG  LEU B   3      24.114 -23.986  82.292  1.00 35.29           C  
+ATOM   1922  CD1 LEU B   3      23.053 -23.030  82.818  1.00 34.67           C  
+ATOM   1923  CD2 LEU B   3      25.326 -23.232  81.782  1.00 36.28           C  
+ATOM   1924  N   ASP B   4      26.293 -28.071  84.073  1.00 36.90           N  
+ATOM   1925  CA  ASP B   4      26.676 -28.939  85.174  1.00 36.98           C  
+ATOM   1926  C   ASP B   4      27.895 -28.464  85.964  1.00 35.91           C  
+ATOM   1927  O   ASP B   4      28.965 -28.220  85.397  1.00 35.18           O  
+ATOM   1928  CB  ASP B   4      26.921 -30.348  84.631  1.00 40.30           C  
+ATOM   1929  CG  ASP B   4      26.710 -31.417  85.672  1.00 42.40           C  
+ATOM   1930  OD1 ASP B   4      27.611 -31.630  86.508  1.00 43.22           O  
+ATOM   1931  OD2 ASP B   4      25.630 -32.042  85.657  1.00 45.90           O  
+ATOM   1932  N   GLY B   5      27.712 -28.331  87.278  1.00 33.88           N  
+ATOM   1933  CA  GLY B   5      28.795 -27.922  88.158  1.00 32.44           C  
+ATOM   1934  C   GLY B   5      29.114 -26.440  88.192  1.00 31.59           C  
+ATOM   1935  O   GLY B   5      30.175 -26.035  88.671  1.00 30.27           O  
+ATOM   1936  N   LYS B   6      28.194 -25.621  87.701  1.00 29.73           N  
+ATOM   1937  CA  LYS B   6      28.425 -24.190  87.678  1.00 26.65           C  
+ATOM   1938  C   LYS B   6      27.518 -23.429  88.609  1.00 24.24           C  
+ATOM   1939  O   LYS B   6      26.453 -23.911  88.999  1.00 21.80           O  
+ATOM   1940  CB  LYS B   6      28.272 -23.674  86.250  1.00 28.36           C  
+ATOM   1941  CG  LYS B   6      29.349 -24.236  85.362  1.00 30.63           C  
+ATOM   1942  CD  LYS B   6      29.236 -23.799  83.936  1.00 30.62           C  
+ATOM   1943  CE  LYS B   6      30.451 -24.305  83.190  1.00 31.26           C  
+ATOM   1944  NZ  LYS B   6      31.699 -23.829  83.847  1.00 30.39           N  
+ATOM   1945  N   THR B   7      27.956 -22.227  88.962  1.00 22.81           N  
+ATOM   1946  CA  THR B   7      27.197 -21.370  89.858  1.00 22.54           C  
+ATOM   1947  C   THR B   7      26.767 -20.100  89.133  1.00 22.22           C  
+ATOM   1948  O   THR B   7      27.528 -19.531  88.344  1.00 21.28           O  
+ATOM   1949  CB  THR B   7      28.037 -20.980  91.090  1.00 22.52           C  
+ATOM   1950  OG1 THR B   7      29.159 -20.196  90.672  1.00 22.87           O  
+ATOM   1951  CG2 THR B   7      28.545 -22.224  91.804  1.00 18.96           C  
+ATOM   1952  N   ALA B   8      25.546 -19.658  89.406  1.00 20.36           N  
+ATOM   1953  CA  ALA B   8      25.024 -18.457  88.775  1.00 19.59           C  
+ATOM   1954  C   ALA B   8      24.261 -17.582  89.756  1.00 20.06           C  
+ATOM   1955  O   ALA B   8      23.399 -18.063  90.499  1.00 20.55           O  
+ATOM   1956  CB  ALA B   8      24.111 -18.833  87.608  1.00 15.64           C  
+ATOM   1957  N   LEU B   9      24.588 -16.295  89.747  1.00 19.16           N  
+ATOM   1958  CA  LEU B   9      23.926 -15.312  90.590  1.00 18.15           C  
+ATOM   1959  C   LEU B   9      22.953 -14.591  89.658  1.00 18.73           C  
+ATOM   1960  O   LEU B   9      23.372 -13.997  88.663  1.00 18.64           O  
+ATOM   1961  CB  LEU B   9      24.947 -14.304  91.132  1.00 17.78           C  
+ATOM   1962  CG  LEU B   9      24.555 -13.263  92.196  1.00 19.20           C  
+ATOM   1963  CD1 LEU B   9      25.601 -12.159  92.229  1.00 15.11           C  
+ATOM   1964  CD2 LEU B   9      23.215 -12.653  91.904  1.00 20.63           C  
+ATOM   1965  N   ILE B  10      21.665 -14.640  89.980  1.00 17.93           N  
+ATOM   1966  CA  ILE B  10      20.636 -13.984  89.176  1.00 17.19           C  
+ATOM   1967  C   ILE B  10      19.904 -12.944  90.025  1.00 18.44           C  
+ATOM   1968  O   ILE B  10      19.183 -13.293  90.962  1.00 19.83           O  
+ATOM   1969  CB  ILE B  10      19.604 -15.017  88.654  1.00 16.99           C  
+ATOM   1970  CG1 ILE B  10      20.332 -16.144  87.923  1.00 15.93           C  
+ATOM   1971  CG2 ILE B  10      18.590 -14.336  87.746  1.00 14.63           C  
+ATOM   1972  CD1 ILE B  10      19.466 -17.338  87.639  1.00 17.02           C  
+ATOM   1973  N   THR B  11      20.077 -11.669  89.685  1.00 19.15           N  
+ATOM   1974  CA  THR B  11      19.445 -10.585  90.428  1.00 19.20           C  
+ATOM   1975  C   THR B  11      17.965 -10.413  90.106  1.00 21.01           C  
+ATOM   1976  O   THR B  11      17.540 -10.555  88.961  1.00 22.16           O  
+ATOM   1977  CB  THR B  11      20.174  -9.255  90.177  1.00 19.26           C  
+ATOM   1978  OG1 THR B  11      19.923  -8.804  88.842  1.00 20.14           O  
+ATOM   1979  CG2 THR B  11      21.675  -9.442  90.360  1.00 18.23           C  
+ATOM   1980  N   GLY B  12      17.179 -10.103  91.131  1.00 21.33           N  
+ATOM   1981  CA  GLY B  12      15.751  -9.927  90.946  1.00 19.80           C  
+ATOM   1982  C   GLY B  12      15.078 -11.200  90.481  1.00 20.92           C  
+ATOM   1983  O   GLY B  12      14.114 -11.145  89.718  1.00 22.27           O  
+ATOM   1984  N   SER B  13      15.573 -12.346  90.946  1.00 21.37           N  
+ATOM   1985  CA  SER B  13      15.024 -13.643  90.549  1.00 21.26           C  
+ATOM   1986  C   SER B  13      13.969 -14.265  91.468  1.00 23.60           C  
+ATOM   1987  O   SER B  13      13.649 -15.449  91.340  1.00 23.89           O  
+ATOM   1988  CB  SER B  13      16.164 -14.644  90.350  1.00 20.11           C  
+ATOM   1989  OG  SER B  13      17.050 -14.647  91.454  1.00 19.93           O  
+ATOM   1990  N   ALA B  14      13.418 -13.488  92.390  1.00 24.69           N  
+ATOM   1991  CA  ALA B  14      12.398 -14.040  93.274  1.00 26.06           C  
+ATOM   1992  C   ALA B  14      11.129 -14.347  92.477  1.00 26.36           C  
+ATOM   1993  O   ALA B  14      10.396 -15.281  92.797  1.00 25.95           O  
+ATOM   1994  CB  ALA B  14      12.089 -13.062  94.410  1.00 26.92           C  
+ATOM   1995  N   ARG B  15      10.875 -13.558  91.437  1.00 28.20           N  
+ATOM   1996  CA  ARG B  15       9.692 -13.752  90.598  1.00 28.95           C  
+ATOM   1997  C   ARG B  15       9.992 -13.451  89.131  1.00 27.90           C  
+ATOM   1998  O   ARG B  15      11.118 -13.126  88.764  1.00 28.52           O  
+ATOM   1999  CB  ARG B  15       8.556 -12.832  91.065  1.00 30.38           C  
+ATOM   2000  CG  ARG B  15       8.137 -13.025  92.508  1.00 33.62           C  
+ATOM   2001  CD  ARG B  15       7.232 -11.897  92.978  1.00 35.09           C  
+ATOM   2002  NE  ARG B  15       7.046 -11.929  94.425  0.00 35.26           N  
+ATOM   2003  CZ  ARG B  15       6.444 -10.972  95.124  0.00 35.58           C  
+ATOM   2004  NH1 ARG B  15       6.321 -11.089  96.439  0.00 35.71           N  
+ATOM   2005  NH2 ARG B  15       5.969  -9.897  94.510  0.00 35.71           N  
+ATOM   2006  N   GLY B  16       8.963 -13.570  88.300  1.00 28.38           N  
+ATOM   2007  CA  GLY B  16       9.088 -13.272  86.883  1.00 27.70           C  
+ATOM   2008  C   GLY B  16      10.120 -14.022  86.065  1.00 26.50           C  
+ATOM   2009  O   GLY B  16      10.411 -15.197  86.306  1.00 26.60           O  
+ATOM   2010  N   ILE B  17      10.671 -13.317  85.083  1.00 24.92           N  
+ATOM   2011  CA  ILE B  17      11.663 -13.871  84.171  1.00 24.22           C  
+ATOM   2012  C   ILE B  17      12.906 -14.332  84.910  1.00 22.77           C  
+ATOM   2013  O   ILE B  17      13.517 -15.340  84.542  1.00 20.48           O  
+ATOM   2014  CB  ILE B  17      12.052 -12.823  83.095  1.00 25.86           C  
+ATOM   2015  CG1 ILE B  17      10.816 -12.466  82.262  1.00 26.75           C  
+ATOM   2016  CG2 ILE B  17      13.147 -13.365  82.192  1.00 26.68           C  
+ATOM   2017  CD1 ILE B  17      11.022 -11.286  81.334  1.00 29.46           C  
+ATOM   2018  N   GLY B  18      13.279 -13.586  85.949  1.00 22.63           N  
+ATOM   2019  CA  GLY B  18      14.445 -13.944  86.738  1.00 20.55           C  
+ATOM   2020  C   GLY B  18      14.283 -15.324  87.353  1.00 20.30           C  
+ATOM   2021  O   GLY B  18      15.242 -16.102  87.412  1.00 20.43           O  
+ATOM   2022  N   ARG B  19      13.072 -15.638  87.807  1.00 19.66           N  
+ATOM   2023  CA  ARG B  19      12.815 -16.941  88.403  1.00 21.57           C  
+ATOM   2024  C   ARG B  19      12.823 -18.055  87.357  1.00 22.14           C  
+ATOM   2025  O   ARG B  19      13.253 -19.174  87.642  1.00 21.61           O  
+ATOM   2026  CB  ARG B  19      11.479 -16.950  89.148  1.00 21.15           C  
+ATOM   2027  CG  ARG B  19      11.103 -18.342  89.628  1.00 22.88           C  
+ATOM   2028  CD  ARG B  19       9.922 -18.353  90.575  1.00 23.47           C  
+ATOM   2029  NE  ARG B  19       9.606 -19.731  90.946  1.00 27.34           N  
+ATOM   2030  CZ  ARG B  19       8.836 -20.083  91.971  1.00 25.27           C  
+ATOM   2031  NH1 ARG B  19       8.289 -19.157  92.749  1.00 24.67           N  
+ATOM   2032  NH2 ARG B  19       8.616 -21.368  92.213  1.00 22.11           N  
+ATOM   2033  N   ALA B  20      12.345 -17.752  86.152  1.00 23.22           N  
+ATOM   2034  CA  ALA B  20      12.327 -18.748  85.077  1.00 24.03           C  
+ATOM   2035  C   ALA B  20      13.762 -19.138  84.706  1.00 23.64           C  
+ATOM   2036  O   ALA B  20      14.050 -20.308  84.439  1.00 23.70           O  
+ATOM   2037  CB  ALA B  20      11.597 -18.201  83.860  1.00 24.34           C  
+ATOM   2038  N   PHE B  21      14.661 -18.158  84.688  1.00 22.59           N  
+ATOM   2039  CA  PHE B  21      16.061 -18.434  84.375  1.00 23.39           C  
+ATOM   2040  C   PHE B  21      16.659 -19.340  85.457  1.00 22.18           C  
+ATOM   2041  O   PHE B  21      17.356 -20.308  85.151  1.00 20.85           O  
+ATOM   2042  CB  PHE B  21      16.876 -17.133  84.302  1.00 25.80           C  
+ATOM   2043  CG  PHE B  21      16.602 -16.291  83.082  1.00 28.44           C  
+ATOM   2044  CD1 PHE B  21      17.211 -15.051  82.938  1.00 27.80           C  
+ATOM   2045  CD2 PHE B  21      15.734 -16.729  82.081  1.00 30.26           C  
+ATOM   2046  CE1 PHE B  21      16.963 -14.257  81.823  1.00 28.47           C  
+ATOM   2047  CE2 PHE B  21      15.482 -15.940  80.960  1.00 28.96           C  
+ATOM   2048  CZ  PHE B  21      16.096 -14.701  80.833  1.00 29.04           C  
+ATOM   2049  N   ALA B  22      16.388 -19.018  86.722  1.00 21.58           N  
+ATOM   2050  CA  ALA B  22      16.908 -19.807  87.842  1.00 19.55           C  
+ATOM   2051  C   ALA B  22      16.420 -21.251  87.776  1.00 18.43           C  
+ATOM   2052  O   ALA B  22      17.212 -22.182  87.902  1.00 16.52           O  
+ATOM   2053  CB  ALA B  22      16.502 -19.176  89.159  1.00 19.16           C  
+ATOM   2054  N   GLU B  23      15.122 -21.446  87.571  1.00 19.05           N  
+ATOM   2055  CA  GLU B  23      14.595 -22.806  87.481  1.00 21.77           C  
+ATOM   2056  C   GLU B  23      15.245 -23.546  86.305  1.00 22.05           C  
+ATOM   2057  O   GLU B  23      15.593 -24.727  86.417  1.00 22.62           O  
+ATOM   2058  CB  GLU B  23      13.070 -22.792  87.308  1.00 22.91           C  
+ATOM   2059  CG  GLU B  23      12.316 -22.076  88.418  1.00 28.47           C  
+ATOM   2060  CD  GLU B  23      10.799 -22.126  88.240  1.00 33.10           C  
+ATOM   2061  OE1 GLU B  23      10.323 -21.939  87.096  1.00 36.89           O  
+ATOM   2062  OE2 GLU B  23      10.080 -22.334  89.242  1.00 33.36           O  
+ATOM   2063  N   ALA B  24      15.428 -22.848  85.185  1.00 21.40           N  
+ATOM   2064  CA  ALA B  24      16.036 -23.464  84.003  1.00 22.63           C  
+ATOM   2065  C   ALA B  24      17.500 -23.829  84.234  1.00 21.75           C  
+ATOM   2066  O   ALA B  24      17.942 -24.915  83.852  1.00 23.64           O  
+ATOM   2067  CB  ALA B  24      15.907 -22.535  82.793  1.00 21.76           C  
+ATOM   2068  N   TYR B  25      18.253 -22.931  84.859  1.00 20.93           N  
+ATOM   2069  CA  TYR B  25      19.666 -23.189  85.135  1.00 22.36           C  
+ATOM   2070  C   TYR B  25      19.819 -24.361  86.096  1.00 23.70           C  
+ATOM   2071  O   TYR B  25      20.755 -25.150  85.984  1.00 24.29           O  
+ATOM   2072  CB  TYR B  25      20.337 -21.951  85.741  1.00 21.31           C  
+ATOM   2073  CG  TYR B  25      20.839 -20.912  84.747  1.00 22.24           C  
+ATOM   2074  CD1 TYR B  25      20.276 -20.784  83.467  1.00 20.54           C  
+ATOM   2075  CD2 TYR B  25      21.850 -20.022  85.111  1.00 20.72           C  
+ATOM   2076  CE1 TYR B  25      20.713 -19.795  82.584  1.00 18.84           C  
+ATOM   2077  CE2 TYR B  25      22.291 -19.033  84.242  1.00 21.60           C  
+ATOM   2078  CZ  TYR B  25      21.722 -18.921  82.980  1.00 21.84           C  
+ATOM   2079  OH  TYR B  25      22.174 -17.932  82.131  1.00 18.02           O  
+ATOM   2080  N   VAL B  26      18.900 -24.470  87.050  1.00 25.10           N  
+ATOM   2081  CA  VAL B  26      18.959 -25.558  88.014  1.00 25.83           C  
+ATOM   2082  C   VAL B  26      18.697 -26.875  87.294  1.00 27.16           C  
+ATOM   2083  O   VAL B  26      19.274 -27.906  87.636  1.00 27.40           O  
+ATOM   2084  CB  VAL B  26      17.919 -25.368  89.150  1.00 25.72           C  
+ATOM   2085  CG1 VAL B  26      17.880 -26.604  90.033  1.00 24.96           C  
+ATOM   2086  CG2 VAL B  26      18.286 -24.158  89.989  1.00 25.40           C  
+ATOM   2087  N   ARG B  27      17.830 -26.833  86.287  1.00 28.53           N  
+ATOM   2088  CA  ARG B  27      17.506 -28.026  85.516  1.00 27.91           C  
+ATOM   2089  C   ARG B  27      18.738 -28.486  84.723  1.00 26.84           C  
+ATOM   2090  O   ARG B  27      18.917 -29.676  84.471  1.00 25.84           O  
+ATOM   2091  CB  ARG B  27      16.354 -27.720  84.563  1.00 30.90           C  
+ATOM   2092  CG  ARG B  27      15.469 -28.901  84.212  1.00 35.78           C  
+ATOM   2093  CD  ARG B  27      14.486 -28.524  83.097  1.00 42.80           C  
+ATOM   2094  NE  ARG B  27      14.091 -27.111  83.132  1.00 48.12           N  
+ATOM   2095  CZ  ARG B  27      13.013 -26.622  83.749  1.00 50.43           C  
+ATOM   2096  NH1 ARG B  27      12.768 -25.316  83.711  1.00 49.33           N  
+ATOM   2097  NH2 ARG B  27      12.173 -27.428  84.390  1.00 51.54           N  
+ATOM   2098  N   GLU B  28      19.593 -27.544  84.335  1.00 25.59           N  
+ATOM   2099  CA  GLU B  28      20.790 -27.892  83.575  1.00 24.76           C  
+ATOM   2100  C   GLU B  28      21.961 -28.287  84.464  1.00 25.07           C  
+ATOM   2101  O   GLU B  28      23.103 -28.337  84.002  1.00 25.42           O  
+ATOM   2102  CB  GLU B  28      21.215 -26.732  82.667  1.00 25.33           C  
+ATOM   2103  CG  GLU B  28      20.206 -26.353  81.577  1.00 24.57           C  
+ATOM   2104  CD  GLU B  28      19.950 -27.467  80.571  1.00 24.49           C  
+ATOM   2105  OE1 GLU B  28      20.919 -28.130  80.129  1.00 21.01           O  
+ATOM   2106  OE2 GLU B  28      18.770 -27.668  80.212  1.00 25.76           O  
+ATOM   2107  N   GLY B  29      21.677 -28.547  85.740  1.00 25.37           N  
+ATOM   2108  CA  GLY B  29      22.711 -28.976  86.673  1.00 23.05           C  
+ATOM   2109  C   GLY B  29      23.549 -27.899  87.333  1.00 23.39           C  
+ATOM   2110  O   GLY B  29      24.701 -28.129  87.692  1.00 23.11           O  
+ATOM   2111  N   ALA B  30      22.982 -26.719  87.519  1.00 23.26           N  
+ATOM   2112  CA  ALA B  30      23.738 -25.644  88.135  1.00 23.66           C  
+ATOM   2113  C   ALA B  30      23.230 -25.268  89.527  1.00 24.47           C  
+ATOM   2114  O   ALA B  30      22.118 -25.636  89.928  1.00 22.22           O  
+ATOM   2115  CB  ALA B  30      23.703 -24.421  87.229  1.00 24.61           C  
+ATOM   2116  N   ARG B  31      24.071 -24.546  90.262  1.00 24.74           N  
+ATOM   2117  CA  ARG B  31      23.728 -24.052  91.591  1.00 26.57           C  
+ATOM   2118  C   ARG B  31      23.424 -22.583  91.381  1.00 25.17           C  
+ATOM   2119  O   ARG B  31      24.200 -21.875  90.744  1.00 27.00           O  
+ATOM   2120  CB  ARG B  31      24.903 -24.218  92.555  1.00 29.68           C  
+ATOM   2121  CG  ARG B  31      24.972 -25.596  93.174  1.00 35.53           C  
+ATOM   2122  CD  ARG B  31      26.380 -26.153  93.139  1.00 42.84           C  
+ATOM   2123  NE  ARG B  31      27.300 -25.435  94.015  1.00 49.08           N  
+ATOM   2124  CZ  ARG B  31      28.609 -25.672  94.076  1.00 52.51           C  
+ATOM   2125  NH1 ARG B  31      29.150 -26.607  93.306  1.00 55.10           N  
+ATOM   2126  NH2 ARG B  31      29.379 -24.979  94.909  1.00 53.63           N  
+ATOM   2127  N   VAL B  32      22.293 -22.125  91.897  1.00 24.47           N  
+ATOM   2128  CA  VAL B  32      21.908 -20.734  91.712  1.00 24.54           C  
+ATOM   2129  C   VAL B  32      21.646 -19.967  93.006  1.00 23.18           C  
+ATOM   2130  O   VAL B  32      21.415 -20.551  94.054  1.00 24.08           O  
+ATOM   2131  CB  VAL B  32      20.659 -20.642  90.811  1.00 23.56           C  
+ATOM   2132  CG1 VAL B  32      20.919 -21.385  89.508  1.00 25.77           C  
+ATOM   2133  CG2 VAL B  32      19.449 -21.228  91.523  1.00 22.64           C  
+ATOM   2134  N   ALA B  33      21.693 -18.644  92.909  1.00 23.50           N  
+ATOM   2135  CA  ALA B  33      21.455 -17.761  94.040  1.00 22.30           C  
+ATOM   2136  C   ALA B  33      20.263 -16.870  93.734  1.00 22.94           C  
+ATOM   2137  O   ALA B  33      20.312 -16.051  92.814  1.00 22.76           O  
+ATOM   2138  CB  ALA B  33      22.689 -16.899  94.304  1.00 19.92           C  
+ATOM   2139  N   ILE B  34      19.183 -17.041  94.488  1.00 23.37           N  
+ATOM   2140  CA  ILE B  34      18.005 -16.216  94.293  1.00 23.97           C  
+ATOM   2141  C   ILE B  34      18.243 -14.935  95.080  1.00 25.84           C  
+ATOM   2142  O   ILE B  34      17.995 -14.877  96.279  1.00 27.31           O  
+ATOM   2143  CB  ILE B  34      16.732 -16.910  94.811  1.00 22.92           C  
+ATOM   2144  CG1 ILE B  34      16.569 -18.274  94.131  1.00 23.22           C  
+ATOM   2145  CG2 ILE B  34      15.517 -16.038  94.533  1.00 19.65           C  
+ATOM   2146  CD1 ILE B  34      16.474 -18.211  92.601  1.00 22.45           C  
+ATOM   2147  N   ALA B  35      18.759 -13.918  94.402  1.00 27.21           N  
+ATOM   2148  CA  ALA B  35      19.040 -12.637  95.033  1.00 28.61           C  
+ATOM   2149  C   ALA B  35      17.872 -11.703  94.808  1.00 30.87           C  
+ATOM   2150  O   ALA B  35      17.390 -11.565  93.685  1.00 33.64           O  
+ATOM   2151  CB  ALA B  35      20.307 -12.032  94.447  1.00 27.10           C  
+ATOM   2152  N   ASP B  36      17.411 -11.059  95.872  1.00 31.94           N  
+ATOM   2153  CA  ASP B  36      16.291 -10.139  95.754  1.00 32.69           C  
+ATOM   2154  C   ASP B  36      16.371  -9.171  96.915  1.00 32.21           C  
+ATOM   2155  O   ASP B  36      17.035  -9.453  97.907  1.00 31.56           O  
+ATOM   2156  CB  ASP B  36      14.972 -10.911  95.802  1.00 35.02           C  
+ATOM   2157  CG  ASP B  36      13.849 -10.197  95.073  1.00 36.76           C  
+ATOM   2158  OD1 ASP B  36      13.867 -10.191  93.821  1.00 36.57           O  
+ATOM   2159  OD2 ASP B  36      12.954  -9.644  95.753  1.00 37.09           O  
+ATOM   2160  N   ILE B  37      15.703  -8.032  96.793  1.00 33.01           N  
+ATOM   2161  CA  ILE B  37      15.728  -7.051  97.865  1.00 36.39           C  
+ATOM   2162  C   ILE B  37      14.874  -7.527  99.042  1.00 38.31           C  
+ATOM   2163  O   ILE B  37      15.113  -7.143 100.194  1.00 38.62           O  
+ATOM   2164  CB  ILE B  37      15.238  -5.673  97.376  1.00 36.78           C  
+ATOM   2165  CG1 ILE B  37      15.509  -4.624  98.455  1.00 37.34           C  
+ATOM   2166  CG2 ILE B  37      13.762  -5.733  97.023  1.00 35.45           C  
+ATOM   2167  CD1 ILE B  37      15.404  -3.193  97.957  1.00 40.15           C  
+ATOM   2168  N   ASN B  38      13.885  -8.372  98.750  1.00 38.59           N  
+ATOM   2169  CA  ASN B  38      13.019  -8.926  99.788  1.00 39.38           C  
+ATOM   2170  C   ASN B  38      13.413 -10.371 100.091  1.00 37.56           C  
+ATOM   2171  O   ASN B  38      13.061 -11.286  99.348  1.00 36.79           O  
+ATOM   2172  CB  ASN B  38      11.553  -8.877  99.354  1.00 43.02           C  
+ATOM   2173  CG  ASN B  38      10.641  -9.646 100.299  1.00 46.46           C  
+ATOM   2174  OD1 ASN B  38      10.715  -9.492 101.521  1.00 47.86           O  
+ATOM   2175  ND2 ASN B  38       9.774 -10.477  99.736  1.00 47.66           N  
+ATOM   2176  N   LEU B  39      14.138 -10.566 101.190  1.00 36.36           N  
+ATOM   2177  CA  LEU B  39      14.605 -11.890 101.591  1.00 35.56           C  
+ATOM   2178  C   LEU B  39      13.477 -12.906 101.828  1.00 36.41           C  
+ATOM   2179  O   LEU B  39      13.660 -14.110 101.640  1.00 35.39           O  
+ATOM   2180  CB  LEU B  39      15.477 -11.763 102.841  1.00 33.92           C  
+ATOM   2181  CG  LEU B  39      16.226 -13.011 103.312  1.00 34.93           C  
+ATOM   2182  CD1 LEU B  39      17.059 -13.592 102.181  1.00 33.38           C  
+ATOM   2183  CD2 LEU B  39      17.114 -12.640 104.480  1.00 34.08           C  
+ATOM   2184  N   GLU B  40      12.310 -12.418 102.231  1.00 37.11           N  
+ATOM   2185  CA  GLU B  40      11.162 -13.287 102.475  1.00 37.39           C  
+ATOM   2186  C   GLU B  40      10.851 -14.045 101.181  1.00 35.36           C  
+ATOM   2187  O   GLU B  40      10.841 -15.276 101.146  1.00 34.64           O  
+ATOM   2188  CB  GLU B  40       9.951 -12.440 102.881  1.00 39.37           C  
+ATOM   2189  CG  GLU B  40       9.209 -12.911 104.114  0.00 39.68           C  
+ATOM   2190  CD  GLU B  40       8.082 -11.969 104.496  0.00 40.25           C  
+ATOM   2191  OE1 GLU B  40       6.918 -12.418 104.531  0.00 40.48           O  
+ATOM   2192  OE2 GLU B  40       8.360 -10.780 104.758  0.00 40.48           O  
+ATOM   2193  N   ALA B  41      10.606 -13.287 100.117  1.00 33.95           N  
+ATOM   2194  CA  ALA B  41      10.298 -13.856  98.808  1.00 31.20           C  
+ATOM   2195  C   ALA B  41      11.466 -14.681  98.295  1.00 27.51           C  
+ATOM   2196  O   ALA B  41      11.279 -15.765  97.748  1.00 27.50           O  
+ATOM   2197  CB  ALA B  41       9.973 -12.741  97.819  1.00 31.33           C  
+ATOM   2198  N   ALA B  42      12.672 -14.159  98.473  1.00 25.36           N  
+ATOM   2199  CA  ALA B  42      13.871 -14.854  98.030  1.00 25.75           C  
+ATOM   2200  C   ALA B  42      13.937 -16.249  98.635  1.00 25.80           C  
+ATOM   2201  O   ALA B  42      14.137 -17.231  97.918  1.00 25.78           O  
+ATOM   2202  CB  ALA B  42      15.115 -14.058  98.409  1.00 26.01           C  
+ATOM   2203  N   ARG B  43      13.765 -16.338  99.951  1.00 25.39           N  
+ATOM   2204  CA  ARG B  43      13.806 -17.630 100.630  1.00 23.77           C  
+ATOM   2205  C   ARG B  43      12.717 -18.555 100.097  1.00 22.22           C  
+ATOM   2206  O   ARG B  43      12.967 -19.730  99.817  1.00 19.94           O  
+ATOM   2207  CB  ARG B  43      13.615 -17.457 102.139  1.00 25.61           C  
+ATOM   2208  CG  ARG B  43      14.665 -16.601 102.831  1.00 27.52           C  
+ATOM   2209  CD  ARG B  43      15.122 -17.243 104.140  1.00 31.58           C  
+ATOM   2210  NE  ARG B  43      14.005 -17.700 104.968  1.00 32.09           N  
+ATOM   2211  CZ  ARG B  43      13.156 -16.893 105.595  1.00 33.64           C  
+ATOM   2212  NH1 ARG B  43      13.291 -15.574 105.502  1.00 35.77           N  
+ATOM   2213  NH2 ARG B  43      12.157 -17.406 106.298  1.00 32.05           N  
+ATOM   2214  N   ALA B  44      11.508 -18.015  99.964  1.00 20.81           N  
+ATOM   2215  CA  ALA B  44      10.368 -18.785  99.471  1.00 22.16           C  
+ATOM   2216  C   ALA B  44      10.644 -19.465  98.125  1.00 24.28           C  
+ATOM   2217  O   ALA B  44      10.371 -20.658  97.949  1.00 24.24           O  
+ATOM   2218  CB  ALA B  44       9.137 -17.879  99.358  1.00 21.07           C  
+ATOM   2219  N   THR B  45      11.182 -18.704  97.174  1.00 24.35           N  
+ATOM   2220  CA  THR B  45      11.480 -19.249  95.856  1.00 23.83           C  
+ATOM   2221  C   THR B  45      12.624 -20.255  95.922  1.00 22.06           C  
+ATOM   2222  O   THR B  45      12.583 -21.286  95.258  1.00 22.32           O  
+ATOM   2223  CB  THR B  45      11.825 -18.115  94.860  1.00 25.00           C  
+ATOM   2224  OG1 THR B  45      10.646 -17.338  94.603  1.00 23.08           O  
+ATOM   2225  CG2 THR B  45      12.356 -18.679  93.555  1.00 23.55           C  
+ATOM   2226  N   ALA B  46      13.640 -19.963  96.727  1.00 22.75           N  
+ATOM   2227  CA  ALA B  46      14.784 -20.871  96.874  1.00 23.64           C  
+ATOM   2228  C   ALA B  46      14.346 -22.223  97.441  1.00 24.53           C  
+ATOM   2229  O   ALA B  46      14.796 -23.270  96.991  1.00 24.93           O  
+ATOM   2230  CB  ALA B  46      15.838 -20.247  97.780  1.00 22.38           C  
+ATOM   2231  N   ALA B  47      13.464 -22.189  98.433  1.00 26.28           N  
+ATOM   2232  CA  ALA B  47      12.956 -23.406  99.051  1.00 27.22           C  
+ATOM   2233  C   ALA B  47      12.123 -24.175  98.037  1.00 28.08           C  
+ATOM   2234  O   ALA B  47      12.160 -25.405  97.986  1.00 28.55           O  
+ATOM   2235  CB  ALA B  47      12.094 -23.051 100.256  1.00 26.43           C  
+ATOM   2236  N   GLU B  48      11.367 -23.426  97.239  1.00 29.28           N  
+ATOM   2237  CA  GLU B  48      10.488 -23.979  96.216  1.00 30.61           C  
+ATOM   2238  C   GLU B  48      11.277 -24.678  95.098  1.00 29.87           C  
+ATOM   2239  O   GLU B  48      10.871 -25.733  94.609  1.00 27.86           O  
+ATOM   2240  CB  GLU B  48       9.625 -22.849  95.637  1.00 33.09           C  
+ATOM   2241  CG  GLU B  48       8.197 -23.240  95.309  1.00 39.45           C  
+ATOM   2242  CD  GLU B  48       7.268 -22.032  95.188  1.00 44.25           C  
+ATOM   2243  OE1 GLU B  48       7.190 -21.235  96.151  1.00 44.72           O  
+ATOM   2244  OE2 GLU B  48       6.607 -21.882  94.134  1.00 48.84           O  
+ATOM   2245  N   ILE B  49      12.406 -24.090  94.709  1.00 28.63           N  
+ATOM   2246  CA  ILE B  49      13.240 -24.651  93.652  1.00 27.66           C  
+ATOM   2247  C   ILE B  49      14.073 -25.845  94.120  1.00 28.83           C  
+ATOM   2248  O   ILE B  49      14.316 -26.771  93.345  1.00 30.78           O  
+ATOM   2249  CB  ILE B  49      14.174 -23.567  93.045  1.00 26.34           C  
+ATOM   2250  CG1 ILE B  49      13.340 -22.553  92.256  1.00 25.39           C  
+ATOM   2251  CG2 ILE B  49      15.204 -24.203  92.133  1.00 23.84           C  
+ATOM   2252  CD1 ILE B  49      14.124 -21.353  91.775  1.00 23.60           C  
+ATOM   2253  N   GLY B  50      14.528 -25.835  95.371  1.00 27.21           N  
+ATOM   2254  CA  GLY B  50      15.297 -26.973  95.846  1.00 26.07           C  
+ATOM   2255  C   GLY B  50      16.700 -26.744  96.389  1.00 25.55           C  
+ATOM   2256  O   GLY B  50      17.215 -25.629  96.385  1.00 24.65           O  
+ATOM   2257  N   PRO B  51      17.353 -27.819  96.856  1.00 25.51           N  
+ATOM   2258  CA  PRO B  51      18.704 -27.824  97.428  1.00 25.54           C  
+ATOM   2259  C   PRO B  51      19.773 -27.134  96.585  1.00 26.21           C  
+ATOM   2260  O   PRO B  51      20.834 -26.787  97.099  1.00 27.79           O  
+ATOM   2261  CB  PRO B  51      19.007 -29.314  97.590  1.00 24.96           C  
+ATOM   2262  CG  PRO B  51      17.674 -29.923  97.763  1.00 26.34           C  
+ATOM   2263  CD  PRO B  51      16.823 -29.189  96.768  1.00 23.65           C  
+ATOM   2264  N   ALA B  52      19.516 -26.948  95.293  1.00 26.16           N  
+ATOM   2265  CA  ALA B  52      20.514 -26.313  94.432  1.00 25.27           C  
+ATOM   2266  C   ALA B  52      20.468 -24.791  94.504  1.00 24.44           C  
+ATOM   2267  O   ALA B  52      21.460 -24.120  94.216  1.00 24.99           O  
+ATOM   2268  CB  ALA B  52      20.338 -26.779  92.986  1.00 24.01           C  
+ATOM   2269  N   ALA B  53      19.320 -24.256  94.907  1.00 22.34           N  
+ATOM   2270  CA  ALA B  53      19.126 -22.816  95.007  1.00 22.39           C  
+ATOM   2271  C   ALA B  53      19.167 -22.270  96.439  1.00 22.83           C  
+ATOM   2272  O   ALA B  53      18.587 -22.856  97.349  1.00 22.96           O  
+ATOM   2273  CB  ALA B  53      17.801 -22.451  94.362  1.00 19.59           C  
+ATOM   2274  N   CYS B  54      19.852 -21.145  96.634  1.00 22.97           N  
+ATOM   2275  CA  CYS B  54      19.927 -20.517  97.949  1.00 25.09           C  
+ATOM   2276  C   CYS B  54      19.461 -19.070  97.826  1.00 25.89           C  
+ATOM   2277  O   CYS B  54      19.558 -18.481  96.754  1.00 27.36           O  
+ATOM   2278  CB  CYS B  54      21.352 -20.592  98.526  1.00 24.07           C  
+ATOM   2279  SG  CYS B  54      22.669 -19.731  97.633  1.00 30.68           S  
+ATOM   2280  N   ALA B  55      18.936 -18.507  98.911  1.00 26.00           N  
+ATOM   2281  CA  ALA B  55      18.436 -17.133  98.894  1.00 25.48           C  
+ATOM   2282  C   ALA B  55      19.427 -16.162  99.518  1.00 25.52           C  
+ATOM   2283  O   ALA B  55      20.243 -16.552 100.348  1.00 27.47           O  
+ATOM   2284  CB  ALA B  55      17.105 -17.056  99.624  1.00 23.92           C  
+ATOM   2285  N   ILE B  56      19.358 -14.898  99.110  1.00 25.47           N  
+ATOM   2286  CA  ILE B  56      20.250 -13.872  99.636  1.00 25.34           C  
+ATOM   2287  C   ILE B  56      19.702 -12.488  99.328  1.00 25.82           C  
+ATOM   2288  O   ILE B  56      19.256 -12.223  98.217  1.00 25.75           O  
+ATOM   2289  CB  ILE B  56      21.667 -13.995  99.045  1.00 26.48           C  
+ATOM   2290  CG1 ILE B  56      22.590 -12.957  99.693  1.00 27.83           C  
+ATOM   2291  CG2 ILE B  56      21.625 -13.804  97.546  1.00 25.28           C  
+ATOM   2292  CD1 ILE B  56      24.067 -13.181  99.397  1.00 28.39           C  
+ATOM   2293  N   ALA B  57      19.733 -11.606 100.323  1.00 25.62           N  
+ATOM   2294  CA  ALA B  57      19.223 -10.257 100.151  1.00 24.70           C  
+ATOM   2295  C   ALA B  57      20.192  -9.427  99.338  1.00 24.32           C  
+ATOM   2296  O   ALA B  57      21.403  -9.472  99.566  1.00 24.02           O  
+ATOM   2297  CB  ALA B  57      18.993  -9.609 101.501  1.00 24.92           C  
+ATOM   2298  N   LEU B  58      19.650  -8.673  98.385  1.00 24.01           N  
+ATOM   2299  CA  LEU B  58      20.463  -7.815  97.528  1.00 23.73           C  
+ATOM   2300  C   LEU B  58      19.715  -6.576  97.055  1.00 24.08           C  
+ATOM   2301  O   LEU B  58      18.587  -6.660  96.574  1.00 24.10           O  
+ATOM   2302  CB  LEU B  58      20.949  -8.593  96.302  1.00 21.68           C  
+ATOM   2303  CG  LEU B  58      21.790  -7.797  95.295  1.00 19.77           C  
+ATOM   2304  CD1 LEU B  58      23.116  -7.395  95.933  1.00 15.95           C  
+ATOM   2305  CD2 LEU B  58      22.040  -8.647  94.058  1.00 14.69           C  
+ATOM   2306  N   ASP B  59      20.351  -5.423  97.220  1.00 25.28           N  
+ATOM   2307  CA  ASP B  59      19.791  -4.155  96.770  1.00 25.81           C  
+ATOM   2308  C   ASP B  59      20.864  -3.597  95.846  1.00 24.95           C  
+ATOM   2309  O   ASP B  59      21.820  -2.964  96.303  1.00 23.50           O  
+ATOM   2310  CB  ASP B  59      19.575  -3.188  97.933  1.00 27.37           C  
+ATOM   2311  CG  ASP B  59      19.025  -1.842  97.476  1.00 28.24           C  
+ATOM   2312  OD1 ASP B  59      19.362  -1.418  96.354  1.00 28.27           O  
+ATOM   2313  OD2 ASP B  59      18.270  -1.199  98.238  1.00 30.72           O  
+ATOM   2314  N   VAL B  60      20.703  -3.851  94.551  1.00 24.97           N  
+ATOM   2315  CA  VAL B  60      21.662  -3.412  93.536  1.00 22.87           C  
+ATOM   2316  C   VAL B  60      21.978  -1.915  93.512  1.00 22.57           C  
+ATOM   2317  O   VAL B  60      22.908  -1.495  92.822  1.00 22.46           O  
+ATOM   2318  CB  VAL B  60      21.202  -3.859  92.125  1.00 22.68           C  
+ATOM   2319  CG1 VAL B  60      21.265  -5.374  92.016  1.00 18.44           C  
+ATOM   2320  CG2 VAL B  60      19.779  -3.375  91.857  1.00 21.63           C  
+ATOM   2321  N   THR B  61      21.223  -1.113  94.260  1.00 22.05           N  
+ATOM   2322  CA  THR B  61      21.475   0.326  94.307  1.00 22.52           C  
+ATOM   2323  C   THR B  61      22.346   0.727  95.495  1.00 22.66           C  
+ATOM   2324  O   THR B  61      22.598   1.916  95.708  1.00 22.47           O  
+ATOM   2325  CB  THR B  61      20.176   1.141  94.418  1.00 24.16           C  
+ATOM   2326  OG1 THR B  61      19.622   0.975  95.730  1.00 22.40           O  
+ATOM   2327  CG2 THR B  61      19.168   0.695  93.372  1.00 23.65           C  
+ATOM   2328  N   ASP B  62      22.803  -0.254  96.267  1.00 23.85           N  
+ATOM   2329  CA  ASP B  62      23.638   0.022  97.438  1.00 23.58           C  
+ATOM   2330  C   ASP B  62      24.949  -0.727  97.348  1.00 22.37           C  
+ATOM   2331  O   ASP B  62      24.972  -1.954  97.380  1.00 22.85           O  
+ATOM   2332  CB  ASP B  62      22.913  -0.382  98.728  1.00 26.51           C  
+ATOM   2333  CG  ASP B  62      23.800  -0.254  99.960  1.00 27.97           C  
+ATOM   2334  OD1 ASP B  62      24.169   0.883 100.320  1.00 27.97           O  
+ATOM   2335  OD2 ASP B  62      24.140  -1.293 100.560  1.00 29.84           O  
+ATOM   2336  N   GLN B  63      26.046   0.012  97.242  1.00 21.31           N  
+ATOM   2337  CA  GLN B  63      27.353  -0.617  97.127  1.00 21.19           C  
+ATOM   2338  C   GLN B  63      27.613  -1.626  98.242  1.00 22.04           C  
+ATOM   2339  O   GLN B  63      28.148  -2.708  97.997  1.00 22.82           O  
+ATOM   2340  CB  GLN B  63      28.448   0.450  97.129  1.00 19.83           C  
+ATOM   2341  CG  GLN B  63      29.824  -0.075  96.746  1.00 18.65           C  
+ATOM   2342  CD  GLN B  63      29.831  -0.732  95.373  1.00 18.74           C  
+ATOM   2343  OE1 GLN B  63      29.308  -0.172  94.405  1.00 16.61           O  
+ATOM   2344  NE2 GLN B  63      30.428  -1.918  95.282  1.00 14.02           N  
+ATOM   2345  N   ALA B  64      27.231  -1.269  99.469  1.00 23.54           N  
+ATOM   2346  CA  ALA B  64      27.439  -2.142 100.626  1.00 21.32           C  
+ATOM   2347  C   ALA B  64      26.756  -3.482 100.409  1.00 19.75           C  
+ATOM   2348  O   ALA B  64      27.364  -4.537 100.593  1.00 19.11           O  
+ATOM   2349  CB  ALA B  64      26.904  -1.475 101.892  1.00 20.75           C  
+ATOM   2350  N   SER B  65      25.489  -3.433 100.012  1.00 18.59           N  
+ATOM   2351  CA  SER B  65      24.728  -4.646  99.758  1.00 19.89           C  
+ATOM   2352  C   SER B  65      25.381  -5.457  98.635  1.00 21.50           C  
+ATOM   2353  O   SER B  65      25.389  -6.686  98.671  1.00 21.86           O  
+ATOM   2354  CB  SER B  65      23.290  -4.293  99.382  1.00 18.17           C  
+ATOM   2355  OG  SER B  65      22.511  -5.466  99.222  1.00 16.77           O  
+ATOM   2356  N   ILE B  66      25.943  -4.761  97.650  1.00 22.00           N  
+ATOM   2357  CA  ILE B  66      26.596  -5.419  96.527  1.00 23.44           C  
+ATOM   2358  C   ILE B  66      27.833  -6.187  96.980  1.00 25.17           C  
+ATOM   2359  O   ILE B  66      27.987  -7.366  96.656  1.00 27.84           O  
+ATOM   2360  CB  ILE B  66      26.984  -4.383  95.427  1.00 22.96           C  
+ATOM   2361  CG1 ILE B  66      25.717  -3.887  94.724  1.00 20.97           C  
+ATOM   2362  CG2 ILE B  66      27.947  -5.003  94.413  1.00 21.20           C  
+ATOM   2363  CD1 ILE B  66      25.949  -2.755  93.755  1.00 20.97           C  
+ATOM   2364  N   ASP B  67      28.709  -5.529  97.731  1.00 26.27           N  
+ATOM   2365  CA  ASP B  67      29.926  -6.178  98.214  1.00 28.93           C  
+ATOM   2366  C   ASP B  67      29.637  -7.344  99.162  1.00 28.84           C  
+ATOM   2367  O   ASP B  67      30.335  -8.362  99.135  1.00 28.08           O  
+ATOM   2368  CB  ASP B  67      30.833  -5.159  98.911  1.00 32.12           C  
+ATOM   2369  CG  ASP B  67      31.293  -4.052  97.976  1.00 36.40           C  
+ATOM   2370  OD1 ASP B  67      31.662  -4.369  96.823  1.00 40.15           O  
+ATOM   2371  OD2 ASP B  67      31.298  -2.872  98.391  1.00 37.10           O  
+ATOM   2372  N   ARG B  68      28.613  -7.198  99.999  1.00 29.04           N  
+ATOM   2373  CA  ARG B  68      28.254  -8.260 100.930  1.00 30.81           C  
+ATOM   2374  C   ARG B  68      27.750  -9.485 100.202  1.00 29.73           C  
+ATOM   2375  O   ARG B  68      28.100 -10.610 100.563  1.00 30.58           O  
+ATOM   2376  CB  ARG B  68      27.177  -7.802 101.903  1.00 33.18           C  
+ATOM   2377  CG  ARG B  68      27.722  -7.238 103.192  1.00 38.38           C  
+ATOM   2378  CD  ARG B  68      26.645  -7.276 104.265  1.00 41.68           C  
+ATOM   2379  NE  ARG B  68      25.462  -6.516 103.872  1.00 44.19           N  
+ATOM   2380  CZ  ARG B  68      25.393  -5.187 103.866  1.00 45.09           C  
+ATOM   2381  NH1 ARG B  68      26.444  -4.461 104.238  1.00 45.47           N  
+ATOM   2382  NH2 ARG B  68      24.271  -4.582 103.489  1.00 44.53           N  
+ATOM   2383  N   CYS B  69      26.920  -9.266  99.185  1.00 27.69           N  
+ATOM   2384  CA  CYS B  69      26.374 -10.372  98.407  1.00 27.26           C  
+ATOM   2385  C   CYS B  69      27.470 -11.180  97.717  1.00 26.20           C  
+ATOM   2386  O   CYS B  69      27.477 -12.404  97.779  1.00 27.84           O  
+ATOM   2387  CB  CYS B  69      25.386  -9.858  97.358  1.00 27.37           C  
+ATOM   2388  SG  CYS B  69      24.907 -11.103  96.122  1.00 27.40           S  
+ATOM   2389  N   VAL B  70      28.398 -10.496  97.064  1.00 25.79           N  
+ATOM   2390  CA  VAL B  70      29.475 -11.187  96.367  1.00 24.75           C  
+ATOM   2391  C   VAL B  70      30.364 -11.955  97.341  1.00 24.23           C  
+ATOM   2392  O   VAL B  70      30.635 -13.144  97.142  1.00 24.56           O  
+ATOM   2393  CB  VAL B  70      30.334 -10.189  95.549  1.00 24.90           C  
+ATOM   2394  CG1 VAL B  70      31.486 -10.919  94.874  1.00 22.87           C  
+ATOM   2395  CG2 VAL B  70      29.467  -9.498  94.504  1.00 22.50           C  
+ATOM   2396  N   ALA B  71      30.814 -11.276  98.392  1.00 23.23           N  
+ATOM   2397  CA  ALA B  71      31.665 -11.904  99.403  1.00 24.27           C  
+ATOM   2398  C   ALA B  71      31.014 -13.156 100.004  1.00 23.55           C  
+ATOM   2399  O   ALA B  71      31.661 -14.195 100.146  1.00 21.52           O  
+ATOM   2400  CB  ALA B  71      31.981 -10.902 100.516  1.00 23.88           C  
+ATOM   2401  N   GLU B  72      29.736 -13.056 100.356  1.00 22.84           N  
+ATOM   2402  CA  GLU B  72      29.044 -14.191 100.938  1.00 26.18           C  
+ATOM   2403  C   GLU B  72      28.986 -15.374  99.986  1.00 26.89           C  
+ATOM   2404  O   GLU B  72      29.245 -16.513 100.385  1.00 26.97           O  
+ATOM   2405  CB  GLU B  72      27.627 -13.814 101.356  1.00 28.11           C  
+ATOM   2406  CG  GLU B  72      26.868 -15.006 101.923  1.00 33.57           C  
+ATOM   2407  CD  GLU B  72      25.582 -14.626 102.628  1.00 36.18           C  
+ATOM   2408  OE1 GLU B  72      24.825 -15.551 102.993  1.00 36.10           O  
+ATOM   2409  OE2 GLU B  72      25.328 -13.412 102.819  1.00 39.21           O  
+ATOM   2410  N   LEU B  73      28.641 -15.102  98.729  1.00 27.02           N  
+ATOM   2411  CA  LEU B  73      28.558 -16.151  97.721  1.00 25.80           C  
+ATOM   2412  C   LEU B  73      29.924 -16.760  97.449  1.00 25.40           C  
+ATOM   2413  O   LEU B  73      30.034 -17.958  97.181  1.00 24.34           O  
+ATOM   2414  CB  LEU B  73      27.960 -15.599  96.429  1.00 24.20           C  
+ATOM   2415  CG  LEU B  73      26.456 -15.369  96.540  1.00 24.33           C  
+ATOM   2416  CD1 LEU B  73      25.926 -14.704  95.270  1.00 24.51           C  
+ATOM   2417  CD2 LEU B  73      25.777 -16.707  96.794  1.00 20.33           C  
+ATOM   2418  N   LEU B  74      30.968 -15.941  97.522  1.00 25.86           N  
+ATOM   2419  CA  LEU B  74      32.307 -16.453  97.297  1.00 28.35           C  
+ATOM   2420  C   LEU B  74      32.698 -17.439  98.402  1.00 30.09           C  
+ATOM   2421  O   LEU B  74      33.427 -18.396  98.147  1.00 30.57           O  
+ATOM   2422  CB  LEU B  74      33.315 -15.304  97.204  1.00 27.89           C  
+ATOM   2423  CG  LEU B  74      33.440 -14.679  95.809  1.00 28.34           C  
+ATOM   2424  CD1 LEU B  74      34.458 -13.551  95.839  1.00 28.19           C  
+ATOM   2425  CD2 LEU B  74      33.867 -15.742  94.802  1.00 25.80           C  
+ATOM   2426  N   ASP B  75      32.207 -17.217  99.622  1.00 31.99           N  
+ATOM   2427  CA  ASP B  75      32.503 -18.131 100.725  1.00 34.52           C  
+ATOM   2428  C   ASP B  75      31.677 -19.402 100.598  1.00 33.26           C  
+ATOM   2429  O   ASP B  75      32.149 -20.495 100.911  1.00 33.83           O  
+ATOM   2430  CB  ASP B  75      32.205 -17.481 102.077  1.00 40.19           C  
+ATOM   2431  CG  ASP B  75      33.268 -16.485 102.492  1.00 45.68           C  
+ATOM   2432  OD1 ASP B  75      33.903 -16.694 103.550  1.00 48.50           O  
+ATOM   2433  OD2 ASP B  75      33.472 -15.496 101.758  1.00 48.96           O  
+ATOM   2434  N   ARG B  76      30.441 -19.254 100.136  1.00 30.91           N  
+ATOM   2435  CA  ARG B  76      29.557 -20.396  99.973  1.00 30.18           C  
+ATOM   2436  C   ARG B  76      29.900 -21.275  98.767  1.00 30.09           C  
+ATOM   2437  O   ARG B  76      29.826 -22.503  98.853  1.00 29.36           O  
+ATOM   2438  CB  ARG B  76      28.113 -19.923  99.854  1.00 30.20           C  
+ATOM   2439  CG  ARG B  76      27.531 -19.314 101.115  1.00 30.91           C  
+ATOM   2440  CD  ARG B  76      26.066 -18.974 100.905  1.00 33.29           C  
+ATOM   2441  NE  ARG B  76      25.424 -18.456 102.112  1.00 37.95           N  
+ATOM   2442  CZ  ARG B  76      25.277 -19.141 103.246  1.00 40.03           C  
+ATOM   2443  NH1 ARG B  76      25.728 -20.387 103.351  1.00 40.50           N  
+ATOM   2444  NH2 ARG B  76      24.669 -18.582 104.284  1.00 40.44           N  
+ATOM   2445  N   TRP B  77      30.276 -20.653  97.649  1.00 29.76           N  
+ATOM   2446  CA  TRP B  77      30.603 -21.405  96.432  1.00 29.47           C  
+ATOM   2447  C   TRP B  77      32.089 -21.520  96.088  1.00 30.25           C  
+ATOM   2448  O   TRP B  77      32.536 -22.547  95.568  1.00 30.65           O  
+ATOM   2449  CB  TRP B  77      29.896 -20.801  95.220  1.00 29.78           C  
+ATOM   2450  CG  TRP B  77      28.412 -20.873  95.257  1.00 29.33           C  
+ATOM   2451  CD1 TRP B  77      27.647 -21.805  95.899  1.00 28.49           C  
+ATOM   2452  CD2 TRP B  77      27.504 -20.023  94.552  1.00 28.69           C  
+ATOM   2453  NE1 TRP B  77      26.319 -21.589  95.633  1.00 28.29           N  
+ATOM   2454  CE2 TRP B  77      26.202 -20.501  94.807  1.00 29.02           C  
+ATOM   2455  CE3 TRP B  77      27.665 -18.904  93.724  1.00 29.88           C  
+ATOM   2456  CZ2 TRP B  77      25.061 -19.898  94.261  1.00 31.59           C  
+ATOM   2457  CZ3 TRP B  77      26.530 -18.302  93.180  1.00 30.49           C  
+ATOM   2458  CH2 TRP B  77      25.245 -18.802  93.452  1.00 31.51           C  
+ATOM   2459  N   GLY B  78      32.852 -20.469  96.364  1.00 29.47           N  
+ATOM   2460  CA  GLY B  78      34.263 -20.497  96.045  1.00 29.41           C  
+ATOM   2461  C   GLY B  78      34.509 -19.717  94.766  1.00 31.04           C  
+ATOM   2462  O   GLY B  78      35.633 -19.296  94.488  1.00 31.95           O  
+ATOM   2463  N   SER B  79      33.449 -19.520  93.985  1.00 30.19           N  
+ATOM   2464  CA  SER B  79      33.539 -18.778  92.731  1.00 29.27           C  
+ATOM   2465  C   SER B  79      32.168 -18.595  92.097  1.00 28.21           C  
+ATOM   2466  O   SER B  79      31.287 -19.444  92.246  1.00 28.29           O  
+ATOM   2467  CB  SER B  79      34.427 -19.518  91.735  1.00 31.60           C  
+ATOM   2468  OG  SER B  79      33.770 -20.682  91.259  1.00 32.83           O  
+ATOM   2469  N   ILE B  80      32.000 -17.482  91.391  1.00 26.65           N  
+ATOM   2470  CA  ILE B  80      30.755 -17.175  90.688  1.00 26.52           C  
+ATOM   2471  C   ILE B  80      31.034 -17.313  89.188  1.00 25.21           C  
+ATOM   2472  O   ILE B  80      31.724 -16.482  88.602  1.00 24.65           O  
+ATOM   2473  CB  ILE B  80      30.296 -15.736  90.967  1.00 26.80           C  
+ATOM   2474  CG1 ILE B  80      30.119 -15.522  92.473  1.00 26.83           C  
+ATOM   2475  CG2 ILE B  80      28.991 -15.466  90.250  1.00 27.12           C  
+ATOM   2476  CD1 ILE B  80      29.888 -14.067  92.856  1.00 23.61           C  
+ATOM   2477  N   ASP B  81      30.504 -18.360  88.567  1.00 24.46           N  
+ATOM   2478  CA  ASP B  81      30.745 -18.583  87.146  1.00 24.39           C  
+ATOM   2479  C   ASP B  81      29.876 -17.746  86.216  1.00 24.74           C  
+ATOM   2480  O   ASP B  81      30.334 -17.299  85.169  1.00 25.43           O  
+ATOM   2481  CB  ASP B  81      30.540 -20.059  86.796  1.00 24.37           C  
+ATOM   2482  CG  ASP B  81      31.357 -20.988  87.671  1.00 25.38           C  
+ATOM   2483  OD1 ASP B  81      32.566 -20.723  87.856  1.00 26.43           O  
+ATOM   2484  OD2 ASP B  81      30.789 -21.991  88.163  1.00 25.53           O  
+ATOM   2485  N   ILE B  82      28.623 -17.536  86.601  1.00 23.93           N  
+ATOM   2486  CA  ILE B  82      27.683 -16.792  85.772  1.00 21.60           C  
+ATOM   2487  C   ILE B  82      26.957 -15.698  86.554  1.00 22.34           C  
+ATOM   2488  O   ILE B  82      26.583 -15.898  87.704  1.00 22.43           O  
+ATOM   2489  CB  ILE B  82      26.612 -17.740  85.205  1.00 18.73           C  
+ATOM   2490  CG1 ILE B  82      27.274 -18.978  84.625  1.00 17.05           C  
+ATOM   2491  CG2 ILE B  82      25.791 -17.038  84.145  1.00 19.79           C  
+ATOM   2492  CD1 ILE B  82      26.296 -20.077  84.303  1.00 18.47           C  
+ATOM   2493  N   LEU B  83      26.747 -14.551  85.911  1.00 22.57           N  
+ATOM   2494  CA  LEU B  83      26.041 -13.435  86.525  1.00 21.18           C  
+ATOM   2495  C   LEU B  83      24.974 -12.917  85.558  1.00 21.01           C  
+ATOM   2496  O   LEU B  83      25.299 -12.461  84.467  1.00 23.64           O  
+ATOM   2497  CB  LEU B  83      27.027 -12.311  86.867  1.00 21.01           C  
+ATOM   2498  CG  LEU B  83      26.573 -11.020  87.578  1.00 21.35           C  
+ATOM   2499  CD1 LEU B  83      26.493  -9.891  86.598  1.00 19.17           C  
+ATOM   2500  CD2 LEU B  83      25.240 -11.222  88.288  1.00 20.83           C  
+ATOM   2501  N   VAL B  84      23.706 -12.998  85.948  1.00 17.93           N  
+ATOM   2502  CA  VAL B  84      22.629 -12.507  85.104  1.00 17.00           C  
+ATOM   2503  C   VAL B  84      21.988 -11.275  85.728  1.00 18.72           C  
+ATOM   2504  O   VAL B  84      21.257 -11.387  86.717  1.00 20.49           O  
+ATOM   2505  CB  VAL B  84      21.511 -13.569  84.892  1.00 15.76           C  
+ATOM   2506  CG1 VAL B  84      20.376 -12.965  84.077  1.00 13.04           C  
+ATOM   2507  CG2 VAL B  84      22.060 -14.787  84.170  1.00 12.13           C  
+ATOM   2508  N   ASN B  85      22.255 -10.103  85.157  1.00 17.74           N  
+ATOM   2509  CA  ASN B  85      21.669  -8.873  85.667  1.00 17.59           C  
+ATOM   2510  C   ASN B  85      20.222  -8.713  85.213  1.00 18.43           C  
+ATOM   2511  O   ASN B  85      19.945  -7.998  84.255  1.00 20.52           O  
+ATOM   2512  CB  ASN B  85      22.485  -7.666  85.212  1.00 19.96           C  
+ATOM   2513  CG  ASN B  85      23.784  -7.515  85.982  1.00 20.72           C  
+ATOM   2514  OD1 ASN B  85      23.793  -7.571  87.207  1.00 21.77           O  
+ATOM   2515  ND2 ASN B  85      24.884  -7.306  85.267  1.00 21.98           N  
+ATOM   2516  N   ASN B  86      19.298  -9.365  85.914  1.00 18.82           N  
+ATOM   2517  CA  ASN B  86      17.879  -9.306  85.569  1.00 20.37           C  
+ATOM   2518  C   ASN B  86      17.045  -8.235  86.294  1.00 21.88           C  
+ATOM   2519  O   ASN B  86      15.982  -7.833  85.806  1.00 23.37           O  
+ATOM   2520  CB  ASN B  86      17.242 -10.669  85.818  1.00 21.44           C  
+ATOM   2521  CG  ASN B  86      15.740 -10.649  85.640  1.00 24.23           C  
+ATOM   2522  OD1 ASN B  86      15.238 -10.580  84.523  1.00 27.01           O  
+ATOM   2523  ND2 ASN B  86      15.011 -10.696  86.750  1.00 28.11           N  
+ATOM   2524  N   ALA B  87      17.510  -7.782  87.453  1.00 20.24           N  
+ATOM   2525  CA  ALA B  87      16.778  -6.782  88.227  1.00 20.38           C  
+ATOM   2526  C   ALA B  87      16.534  -5.476  87.456  1.00 20.34           C  
+ATOM   2527  O   ALA B  87      17.457  -4.899  86.879  1.00 18.29           O  
+ATOM   2528  CB  ALA B  87      17.531  -6.491  89.530  1.00 19.62           C  
+ATOM   2529  N   ALA B  88      15.291  -5.001  87.458  1.00 21.38           N  
+ATOM   2530  CA  ALA B  88      14.964  -3.761  86.751  1.00 23.92           C  
+ATOM   2531  C   ALA B  88      13.566  -3.233  87.067  1.00 24.82           C  
+ATOM   2532  O   ALA B  88      12.708  -3.969  87.549  1.00 26.22           O  
+ATOM   2533  CB  ALA B  88      15.102  -3.975  85.243  1.00 22.81           C  
+ATOM   2534  N   LEU B  89      13.348  -1.951  86.788  1.00 26.09           N  
+ATOM   2535  CA  LEU B  89      12.053  -1.314  87.008  1.00 28.25           C  
+ATOM   2536  C   LEU B  89      11.531  -0.698  85.720  1.00 28.98           C  
+ATOM   2537  O   LEU B  89      12.308  -0.239  84.883  1.00 28.20           O  
+ATOM   2538  CB  LEU B  89      12.156  -0.213  88.060  1.00 31.55           C  
+ATOM   2539  CG  LEU B  89      12.031  -0.642  89.519  1.00 35.98           C  
+ATOM   2540  CD1 LEU B  89      12.190   0.578  90.422  1.00 36.17           C  
+ATOM   2541  CD2 LEU B  89      10.678  -1.317  89.732  1.00 34.89           C  
+ATOM   2542  N   PHE B  90      10.211  -0.680  85.572  1.00 28.92           N  
+ATOM   2543  CA  PHE B  90       9.589  -0.109  84.386  1.00 30.19           C  
+ATOM   2544  C   PHE B  90       8.722   1.072  84.779  1.00 31.05           C  
+ATOM   2545  O   PHE B  90       8.181   1.108  85.879  1.00 33.06           O  
+ATOM   2546  CB  PHE B  90       8.742  -1.169  83.673  1.00 30.00           C  
+ATOM   2547  CG  PHE B  90       7.941  -0.632  82.522  1.00 30.62           C  
+ATOM   2548  CD1 PHE B  90       6.633  -0.192  82.709  1.00 30.23           C  
+ATOM   2549  CD2 PHE B  90       8.506  -0.532  81.255  1.00 30.79           C  
+ATOM   2550  CE1 PHE B  90       5.897   0.344  81.649  1.00 29.95           C  
+ATOM   2551  CE2 PHE B  90       7.782   0.001  80.190  1.00 30.56           C  
+ATOM   2552  CZ  PHE B  90       6.475   0.441  80.388  1.00 30.53           C  
+ATOM   2553  N   ASP B  91       8.594   2.042  83.885  1.00 30.81           N  
+ATOM   2554  CA  ASP B  91       7.777   3.214  84.163  1.00 31.47           C  
+ATOM   2555  C   ASP B  91       7.533   3.968  82.857  1.00 32.99           C  
+ATOM   2556  O   ASP B  91       8.304   3.838  81.902  1.00 33.34           O  
+ATOM   2557  CB  ASP B  91       8.491   4.114  85.173  1.00 32.21           C  
+ATOM   2558  CG  ASP B  91       7.540   5.063  85.897  1.00 34.44           C  
+ATOM   2559  OD1 ASP B  91       8.035   5.932  86.649  1.00 34.19           O  
+ATOM   2560  OD2 ASP B  91       6.304   4.939  85.724  1.00 31.85           O  
+ATOM   2561  N   LEU B  92       6.455   4.744  82.801  1.00 33.27           N  
+ATOM   2562  CA  LEU B  92       6.155   5.495  81.595  1.00 32.93           C  
+ATOM   2563  C   LEU B  92       5.484   6.828  81.867  1.00 31.45           C  
+ATOM   2564  O   LEU B  92       4.758   6.983  82.842  1.00 31.93           O  
+ATOM   2565  CB  LEU B  92       5.307   4.646  80.638  1.00 35.41           C  
+ATOM   2566  CG  LEU B  92       4.068   3.901  81.137  1.00 37.67           C  
+ATOM   2567  CD1 LEU B  92       2.898   4.847  81.224  1.00 39.67           C  
+ATOM   2568  CD2 LEU B  92       3.730   2.781  80.170  1.00 38.88           C  
+ATOM   2569  N   ALA B  93       5.756   7.793  80.994  1.00 30.81           N  
+ATOM   2570  CA  ALA B  93       5.202   9.138  81.098  1.00 29.23           C  
+ATOM   2571  C   ALA B  93       5.763  10.025  79.986  1.00 28.02           C  
+ATOM   2572  O   ALA B  93       6.919   9.884  79.592  1.00 26.12           O  
+ATOM   2573  CB  ALA B  93       5.544   9.746  82.453  1.00 27.08           C  
+ATOM   2574  N   PRO B  94       4.939  10.942  79.461  1.00 26.67           N  
+ATOM   2575  CA  PRO B  94       5.383  11.845  78.400  1.00 26.91           C  
+ATOM   2576  C   PRO B  94       6.555  12.667  78.923  1.00 27.53           C  
+ATOM   2577  O   PRO B  94       6.814  12.706  80.128  1.00 26.43           O  
+ATOM   2578  CB  PRO B  94       4.152  12.712  78.146  1.00 27.05           C  
+ATOM   2579  CG  PRO B  94       3.021  11.802  78.488  1.00 27.57           C  
+ATOM   2580  CD  PRO B  94       3.508  11.133  79.748  1.00 26.64           C  
+ATOM   2581  N   ILE B  95       7.252  13.330  78.013  1.00 27.51           N  
+ATOM   2582  CA  ILE B  95       8.397  14.146  78.376  1.00 27.66           C  
+ATOM   2583  C   ILE B  95       8.036  15.206  79.414  1.00 27.98           C  
+ATOM   2584  O   ILE B  95       8.672  15.300  80.459  1.00 27.66           O  
+ATOM   2585  CB  ILE B  95       8.991  14.842  77.119  1.00 28.16           C  
+ATOM   2586  CG1 ILE B  95       9.500  13.782  76.131  1.00 27.81           C  
+ATOM   2587  CG2 ILE B  95      10.124  15.789  77.517  1.00 26.99           C  
+ATOM   2588  CD1 ILE B  95      10.700  12.997  76.617  1.00 22.85           C  
+ATOM   2589  N   VAL B  96       7.009  15.998  79.127  1.00 28.66           N  
+ATOM   2590  CA  VAL B  96       6.603  17.070  80.029  1.00 30.17           C  
+ATOM   2591  C   VAL B  96       6.074  16.602  81.384  1.00 30.39           C  
+ATOM   2592  O   VAL B  96       5.785  17.417  82.252  1.00 29.52           O  
+ATOM   2593  CB  VAL B  96       5.545  17.981  79.359  1.00 30.04           C  
+ATOM   2594  CG1 VAL B  96       6.086  18.507  78.048  1.00 31.22           C  
+ATOM   2595  CG2 VAL B  96       4.267  17.215  79.115  1.00 29.69           C  
+ATOM   2596  N   GLU B  97       5.959  15.293  81.571  1.00 31.45           N  
+ATOM   2597  CA  GLU B  97       5.460  14.759  82.833  1.00 31.22           C  
+ATOM   2598  C   GLU B  97       6.464  13.881  83.569  1.00 30.63           C  
+ATOM   2599  O   GLU B  97       6.137  13.293  84.601  1.00 33.54           O  
+ATOM   2600  CB  GLU B  97       4.175  13.966  82.599  1.00 32.15           C  
+ATOM   2601  CG  GLU B  97       2.940  14.823  82.399  1.00 34.52           C  
+ATOM   2602  CD  GLU B  97       1.703  13.982  82.148  1.00 37.03           C  
+ATOM   2603  OE1 GLU B  97       1.551  12.939  82.820  1.00 39.62           O  
+ATOM   2604  OE2 GLU B  97       0.879  14.363  81.288  1.00 38.29           O  
+ATOM   2605  N   ILE B  98       7.683  13.789  83.053  1.00 27.60           N  
+ATOM   2606  CA  ILE B  98       8.701  12.970  83.700  1.00 25.34           C  
+ATOM   2607  C   ILE B  98       9.149  13.622  85.009  1.00 25.66           C  
+ATOM   2608  O   ILE B  98       9.461  14.813  85.041  1.00 24.48           O  
+ATOM   2609  CB  ILE B  98       9.922  12.772  82.773  1.00 23.13           C  
+ATOM   2610  CG1 ILE B  98       9.511  11.945  81.548  1.00 21.81           C  
+ATOM   2611  CG2 ILE B  98      11.052  12.091  83.533  1.00 22.68           C  
+ATOM   2612  CD1 ILE B  98      10.624  11.741  80.535  1.00 17.95           C  
+ATOM   2613  N   THR B  99       9.173  12.842  86.088  1.00 26.22           N  
+ATOM   2614  CA  THR B  99       9.580  13.360  87.398  1.00 26.13           C  
+ATOM   2615  C   THR B  99      11.010  12.955  87.717  1.00 27.11           C  
+ATOM   2616  O   THR B  99      11.498  11.924  87.242  1.00 27.77           O  
+ATOM   2617  CB  THR B  99       8.679  12.828  88.546  1.00 25.46           C  
+ATOM   2618  OG1 THR B  99       8.806  11.403  88.636  1.00 25.04           O  
+ATOM   2619  CG2 THR B  99       7.224  13.181  88.302  1.00 21.48           C  
+ATOM   2620  N   ARG B 100      11.681  13.770  88.523  1.00 27.26           N  
+ATOM   2621  CA  ARG B 100      13.053  13.481  88.924  1.00 29.26           C  
+ATOM   2622  C   ARG B 100      13.046  12.168  89.664  1.00 30.24           C  
+ATOM   2623  O   ARG B 100      13.992  11.377  89.627  1.00 30.47           O  
+ATOM   2624  CB  ARG B 100      13.563  14.546  89.884  1.00 29.17           C  
+ATOM   2625  CG  ARG B 100      13.764  15.893  89.265  1.00 30.31           C  
+ATOM   2626  CD  ARG B 100      15.226  16.212  89.253  1.00 29.58           C  
+ATOM   2627  NE  ARG B 100      15.501  17.398  88.463  1.00 30.62           N  
+ATOM   2628  CZ  ARG B 100      16.716  17.748  88.072  1.00 29.67           C  
+ATOM   2629  NH1 ARG B 100      16.887  18.844  87.353  1.00 31.99           N  
+ATOM   2630  NH2 ARG B 100      17.758  16.999  88.402  1.00 28.57           N  
+ATOM   2631  N   GLU B 101      11.956  11.927  90.356  1.00 31.97           N  
+ATOM   2632  CA  GLU B 101      11.854  10.745  91.161  1.00 34.22           C  
+ATOM   2633  C   GLU B 101      11.839   9.536  90.258  1.00 31.44           C  
+ATOM   2634  O   GLU B 101      12.512   8.524  90.523  1.00 31.10           O  
+ATOM   2635  CB  GLU B 101      10.613  10.908  92.033  1.00 40.52           C  
+ATOM   2636  CG  GLU B 101      10.399  12.396  92.527  1.00 50.10           C  
+ATOM   2637  CD  GLU B 101      11.699  13.248  92.737  1.00 56.02           C  
+ATOM   2638  OE1 GLU B 101      12.793  12.835  92.309  1.00 61.23           O  
+ATOM   2639  OE2 GLU B 101      11.621  14.365  93.319  1.00 57.13           O  
+ATOM   2640  N   SER B 102      11.081   9.611  89.170  1.00 29.97           N  
+ATOM   2641  CA  SER B 102      11.031   8.475  88.250  1.00 28.47           C  
+ATOM   2642  C   SER B 102      12.412   8.252  87.649  1.00 26.04           C  
+ATOM   2643  O   SER B 102      12.894   7.127  87.652  1.00 25.10           O  
+ATOM   2644  CB  SER B 102       9.989   8.653  87.106  1.00 31.00           C  
+ATOM   2645  OG  SER B 102      10.016   7.512  86.232  1.00 36.70           O  
+ATOM   2646  N   TYR B 103      13.028   9.309  87.121  1.00 23.82           N  
+ATOM   2647  CA  TYR B 103      14.359   9.221  86.545  1.00 22.22           C  
+ATOM   2648  C   TYR B 103      15.373   8.573  87.505  1.00 21.92           C  
+ATOM   2649  O   TYR B 103      16.052   7.622  87.137  1.00 21.08           O  
+ATOM   2650  CB  TYR B 103      14.866  10.615  86.162  1.00 20.27           C  
+ATOM   2651  CG  TYR B 103      16.339  10.687  85.786  1.00 20.21           C  
+ATOM   2652  CD1 TYR B 103      16.778  10.359  84.498  1.00 22.77           C  
+ATOM   2653  CD2 TYR B 103      17.306  11.046  86.729  1.00 22.35           C  
+ATOM   2654  CE1 TYR B 103      18.149  10.384  84.162  1.00 23.06           C  
+ATOM   2655  CE2 TYR B 103      18.677  11.069  86.401  1.00 22.43           C  
+ATOM   2656  CZ  TYR B 103      19.087  10.733  85.119  1.00 25.32           C  
+ATOM   2657  OH  TYR B 103      20.429  10.712  84.795  1.00 25.61           O  
+ATOM   2658  N   ASP B 104      15.487   9.123  88.716  1.00 23.77           N  
+ATOM   2659  CA  ASP B 104      16.427   8.652  89.750  1.00 23.05           C  
+ATOM   2660  C   ASP B 104      16.433   7.141  90.029  1.00 22.60           C  
+ATOM   2661  O   ASP B 104      17.494   6.533  90.093  1.00 21.81           O  
+ATOM   2662  CB  ASP B 104      16.162   9.407  91.056  1.00 26.31           C  
+ATOM   2663  CG  ASP B 104      16.664  10.846  91.026  1.00 28.27           C  
+ATOM   2664  OD1 ASP B 104      16.451  11.555  92.026  1.00 33.48           O  
+ATOM   2665  OD2 ASP B 104      17.275  11.276  90.021  1.00 32.58           O  
+ATOM   2666  N   ARG B 105      15.247   6.563  90.201  1.00 24.33           N  
+ATOM   2667  CA  ARG B 105      15.072   5.125  90.481  1.00 28.07           C  
+ATOM   2668  C   ARG B 105      15.499   4.202  89.341  1.00 28.14           C  
+ATOM   2669  O   ARG B 105      16.391   3.354  89.515  1.00 29.78           O  
+ATOM   2670  CB  ARG B 105      13.605   4.816  90.760  1.00 31.94           C  
+ATOM   2671  CG  ARG B 105      13.206   4.693  92.198  1.00 38.12           C  
+ATOM   2672  CD  ARG B 105      11.863   3.981  92.260  1.00 43.51           C  
+ATOM   2673  NE  ARG B 105      10.722   4.876  92.063  1.00 50.43           N  
+ATOM   2674  CZ  ARG B 105      10.322   5.766  92.968  1.00 53.44           C  
+ATOM   2675  NH1 ARG B 105      10.976   5.867  94.118  1.00 53.99           N  
+ATOM   2676  NH2 ARG B 105       9.273   6.552  92.736  1.00 54.85           N  
+ATOM   2677  N   LEU B 106      14.860   4.396  88.190  1.00 26.67           N  
+ATOM   2678  CA  LEU B 106      15.138   3.610  87.021  1.00 24.60           C  
+ATOM   2679  C   LEU B 106      16.612   3.592  86.682  1.00 22.14           C  
+ATOM   2680  O   LEU B 106      17.179   2.544  86.407  1.00 24.24           O  
+ATOM   2681  CB  LEU B 106      14.324   4.146  85.846  1.00 25.18           C  
+ATOM   2682  CG  LEU B 106      12.802   4.137  85.945  1.00 27.37           C  
+ATOM   2683  CD1 LEU B 106      12.263   3.918  84.549  1.00 29.98           C  
+ATOM   2684  CD2 LEU B 106      12.342   3.009  86.859  1.00 26.50           C  
+ATOM   2685  N   PHE B 107      17.249   4.751  86.720  1.00 20.70           N  
+ATOM   2686  CA  PHE B 107      18.675   4.758  86.399  1.00 20.59           C  
+ATOM   2687  C   PHE B 107      19.487   4.098  87.509  1.00 20.12           C  
+ATOM   2688  O   PHE B 107      20.477   3.380  87.254  1.00 18.46           O  
+ATOM   2689  CB  PHE B 107      19.202   6.182  86.098  1.00 20.24           C  
+ATOM   2690  CG  PHE B 107      19.092   6.575  84.635  1.00 22.27           C  
+ATOM   2691  CD1 PHE B 107      17.875   6.982  84.086  1.00 21.87           C  
+ATOM   2692  CD2 PHE B 107      20.194   6.471  83.798  1.00 22.37           C  
+ATOM   2693  CE1 PHE B 107      17.766   7.274  82.725  1.00 21.47           C  
+ATOM   2694  CE2 PHE B 107      20.091   6.758  82.440  1.00 22.43           C  
+ATOM   2695  CZ  PHE B 107      18.877   7.159  81.906  1.00 20.01           C  
+ATOM   2696  N   ALA B 108      19.024   4.301  88.740  1.00 18.94           N  
+ATOM   2697  CA  ALA B 108      19.677   3.720  89.908  1.00 17.94           C  
+ATOM   2698  C   ALA B 108      19.663   2.196  89.852  1.00 16.95           C  
+ATOM   2699  O   ALA B 108      20.687   1.551  90.077  1.00 17.89           O  
+ATOM   2700  CB  ALA B 108      18.984   4.195  91.195  1.00 19.04           C  
+ATOM   2701  N   ILE B 109      18.504   1.626  89.542  1.00 16.19           N  
+ATOM   2702  CA  ILE B 109      18.365   0.176  89.475  1.00 17.64           C  
+ATOM   2703  C   ILE B 109      18.748  -0.448  88.128  1.00 17.10           C  
+ATOM   2704  O   ILE B 109      19.561  -1.378  88.091  1.00 16.49           O  
+ATOM   2705  CB  ILE B 109      16.924  -0.242  89.845  1.00 18.13           C  
+ATOM   2706  CG1 ILE B 109      16.669   0.088  91.319  1.00 18.34           C  
+ATOM   2707  CG2 ILE B 109      16.716  -1.734  89.593  1.00 15.67           C  
+ATOM   2708  CD1 ILE B 109      15.255  -0.219  91.790  1.00 19.09           C  
+ATOM   2709  N   ASN B 110      18.178   0.061  87.034  1.00 17.66           N  
+ATOM   2710  CA  ASN B 110      18.456  -0.475  85.691  1.00 18.19           C  
+ATOM   2711  C   ASN B 110      19.877  -0.283  85.169  1.00 17.17           C  
+ATOM   2712  O   ASN B 110      20.442  -1.192  84.563  1.00 17.15           O  
+ATOM   2713  CB  ASN B 110      17.485   0.117  84.671  1.00 18.31           C  
+ATOM   2714  CG  ASN B 110      16.041  -0.220  84.976  1.00 20.74           C  
+ATOM   2715  OD1 ASN B 110      15.746  -1.016  85.877  1.00 23.05           O  
+ATOM   2716  ND2 ASN B 110      15.129   0.380  84.224  1.00 19.57           N  
+ATOM   2717  N   VAL B 111      20.453   0.892  85.402  1.00 17.00           N  
+ATOM   2718  CA  VAL B 111      21.801   1.179  84.922  1.00 15.28           C  
+ATOM   2719  C   VAL B 111      22.866   1.020  85.995  1.00 17.90           C  
+ATOM   2720  O   VAL B 111      23.760   0.178  85.873  1.00 19.15           O  
+ATOM   2721  CB  VAL B 111      21.903   2.608  84.363  1.00 13.21           C  
+ATOM   2722  CG1 VAL B 111      23.259   2.809  83.714  1.00 12.84           C  
+ATOM   2723  CG2 VAL B 111      20.783   2.865  83.375  1.00 12.05           C  
+ATOM   2724  N   SER B 112      22.780   1.837  87.041  1.00 18.36           N  
+ATOM   2725  CA  SER B 112      23.748   1.780  88.132  1.00 19.64           C  
+ATOM   2726  C   SER B 112      23.885   0.355  88.687  1.00 18.94           C  
+ATOM   2727  O   SER B 112      24.998  -0.172  88.841  1.00 17.94           O  
+ATOM   2728  CB  SER B 112      23.322   2.734  89.246  1.00 21.80           C  
+ATOM   2729  OG  SER B 112      24.242   2.680  90.314  1.00 28.43           O  
+ATOM   2730  N   GLY B 113      22.746  -0.264  88.980  1.00 17.85           N  
+ATOM   2731  CA  GLY B 113      22.758  -1.619  89.493  1.00 17.71           C  
+ATOM   2732  C   GLY B 113      23.492  -2.595  88.586  1.00 18.57           C  
+ATOM   2733  O   GLY B 113      24.285  -3.406  89.063  1.00 19.29           O  
+ATOM   2734  N   THR B 114      23.248  -2.523  87.278  1.00 17.20           N  
+ATOM   2735  CA  THR B 114      23.902  -3.436  86.342  1.00 16.24           C  
+ATOM   2736  C   THR B 114      25.409  -3.189  86.265  1.00 14.79           C  
+ATOM   2737  O   THR B 114      26.206  -4.127  86.283  1.00 14.42           O  
+ATOM   2738  CB  THR B 114      23.261  -3.333  84.913  1.00 18.11           C  
+ATOM   2739  OG1 THR B 114      21.918  -3.843  84.952  1.00 14.24           O  
+ATOM   2740  CG2 THR B 114      24.070  -4.134  83.883  1.00 14.85           C  
+ATOM   2741  N   LEU B 115      25.802  -1.924  86.203  1.00 14.67           N  
+ATOM   2742  CA  LEU B 115      27.218  -1.582  86.114  1.00 15.55           C  
+ATOM   2743  C   LEU B 115      28.047  -2.047  87.313  1.00 16.25           C  
+ATOM   2744  O   LEU B 115      28.971  -2.847  87.174  1.00 15.59           O  
+ATOM   2745  CB  LEU B 115      27.379  -0.070  85.939  1.00 14.22           C  
+ATOM   2746  CG  LEU B 115      28.798   0.514  85.892  1.00 14.05           C  
+ATOM   2747  CD1 LEU B 115      29.658  -0.228  84.881  1.00 11.31           C  
+ATOM   2748  CD2 LEU B 115      28.706   1.992  85.543  1.00 12.48           C  
+ATOM   2749  N   PHE B 116      27.717  -1.551  88.496  1.00 17.84           N  
+ATOM   2750  CA  PHE B 116      28.477  -1.928  89.682  1.00 18.67           C  
+ATOM   2751  C   PHE B 116      28.359  -3.413  90.043  1.00 17.90           C  
+ATOM   2752  O   PHE B 116      29.293  -4.005  90.587  1.00 17.62           O  
+ATOM   2753  CB  PHE B 116      28.087  -0.991  90.831  1.00 17.76           C  
+ATOM   2754  CG  PHE B 116      28.430   0.444  90.539  1.00 16.87           C  
+ATOM   2755  CD1 PHE B 116      29.763   0.833  90.421  1.00 18.19           C  
+ATOM   2756  CD2 PHE B 116      27.438   1.371  90.255  1.00 15.94           C  
+ATOM   2757  CE1 PHE B 116      30.102   2.118  90.015  1.00 18.47           C  
+ATOM   2758  CE2 PHE B 116      27.767   2.660  89.846  1.00 18.33           C  
+ATOM   2759  CZ  PHE B 116      29.103   3.034  89.724  1.00 17.25           C  
+ATOM   2760  N   MET B 117      27.231  -4.029  89.710  1.00 18.04           N  
+ATOM   2761  CA  MET B 117      27.070  -5.450  89.980  1.00 18.53           C  
+ATOM   2762  C   MET B 117      28.039  -6.194  89.051  1.00 18.50           C  
+ATOM   2763  O   MET B 117      28.626  -7.208  89.438  1.00 20.66           O  
+ATOM   2764  CB  MET B 117      25.628  -5.868  89.709  1.00 20.82           C  
+ATOM   2765  CG  MET B 117      25.200  -7.150  90.378  1.00 25.65           C  
+ATOM   2766  SD  MET B 117      25.284  -7.066  92.183  1.00 31.09           S  
+ATOM   2767  CE  MET B 117      26.372  -8.407  92.502  1.00 28.42           C  
+ATOM   2768  N   MET B 118      28.212  -5.678  87.830  1.00 17.59           N  
+ATOM   2769  CA  MET B 118      29.131  -6.267  86.841  1.00 17.19           C  
+ATOM   2770  C   MET B 118      30.578  -6.145  87.319  1.00 15.33           C  
+ATOM   2771  O   MET B 118      31.376  -7.091  87.238  1.00 14.04           O  
+ATOM   2772  CB  MET B 118      29.023  -5.544  85.486  1.00 17.97           C  
+ATOM   2773  CG  MET B 118      28.343  -6.328  84.365  1.00 20.09           C  
+ATOM   2774  SD  MET B 118      28.773  -5.713  82.688  1.00 18.06           S  
+ATOM   2775  CE  MET B 118      28.195  -4.056  82.753  1.00 10.37           C  
+ATOM   2776  N   GLN B 119      30.911  -4.952  87.794  1.00 14.53           N  
+ATOM   2777  CA  GLN B 119      32.246  -4.655  88.283  1.00 16.86           C  
+ATOM   2778  C   GLN B 119      32.645  -5.548  89.461  1.00 17.40           C  
+ATOM   2779  O   GLN B 119      33.763  -6.062  89.512  1.00 16.78           O  
+ATOM   2780  CB  GLN B 119      32.306  -3.189  88.703  1.00 17.76           C  
+ATOM   2781  CG  GLN B 119      33.679  -2.708  89.119  1.00 19.12           C  
+ATOM   2782  CD  GLN B 119      33.609  -1.340  89.747  1.00 20.67           C  
+ATOM   2783  OE1 GLN B 119      32.991  -1.164  90.803  1.00 23.16           O  
+ATOM   2784  NE2 GLN B 119      34.229  -0.357  89.104  1.00 20.22           N  
+ATOM   2785  N   ALA B 120      31.721  -5.731  90.402  1.00 17.66           N  
+ATOM   2786  CA  ALA B 120      31.979  -6.547  91.583  1.00 18.10           C  
+ATOM   2787  C   ALA B 120      32.296  -7.988  91.218  1.00 19.17           C  
+ATOM   2788  O   ALA B 120      33.295  -8.549  91.673  1.00 19.42           O  
+ATOM   2789  CB  ALA B 120      30.782  -6.501  92.502  1.00 17.70           C  
+ATOM   2790  N   VAL B 121      31.444  -8.580  90.385  1.00 21.10           N  
+ATOM   2791  CA  VAL B 121      31.610  -9.965  89.958  1.00 20.64           C  
+ATOM   2792  C   VAL B 121      32.780 -10.141  88.990  1.00 23.03           C  
+ATOM   2793  O   VAL B 121      33.456 -11.181  88.995  1.00 23.79           O  
+ATOM   2794  CB  VAL B 121      30.314 -10.484  89.315  1.00 19.82           C  
+ATOM   2795  CG1 VAL B 121      30.493 -11.899  88.830  1.00 20.19           C  
+ATOM   2796  CG2 VAL B 121      29.186 -10.424  90.324  1.00 21.01           C  
+ATOM   2797  N   ALA B 122      33.024  -9.134  88.158  1.00 23.76           N  
+ATOM   2798  CA  ALA B 122      34.137  -9.210  87.216  1.00 24.52           C  
+ATOM   2799  C   ALA B 122      35.413  -9.304  88.036  1.00 24.80           C  
+ATOM   2800  O   ALA B 122      36.255 -10.167  87.789  1.00 24.75           O  
+ATOM   2801  CB  ALA B 122      34.169  -7.966  86.319  1.00 25.31           C  
+ATOM   2802  N   ARG B 123      35.546  -8.413  89.018  1.00 25.93           N  
+ATOM   2803  CA  ARG B 123      36.716  -8.401  89.890  1.00 28.03           C  
+ATOM   2804  C   ARG B 123      36.962  -9.793  90.461  1.00 27.25           C  
+ATOM   2805  O   ARG B 123      38.089 -10.291  90.445  1.00 28.11           O  
+ATOM   2806  CB  ARG B 123      36.522  -7.402  91.037  1.00 30.50           C  
+ATOM   2807  CG  ARG B 123      36.670  -5.951  90.623  1.00 35.47           C  
+ATOM   2808  CD  ARG B 123      37.683  -5.227  91.504  1.00 40.24           C  
+ATOM   2809  NE  ARG B 123      37.231  -5.113  92.887  1.00 44.36           N  
+ATOM   2810  CZ  ARG B 123      36.197  -4.370  93.274  1.00 47.50           C  
+ATOM   2811  NH1 ARG B 123      35.505  -3.668  92.379  1.00 47.47           N  
+ATOM   2812  NH2 ARG B 123      35.852  -4.329  94.555  1.00 47.51           N  
+ATOM   2813  N   ALA B 124      35.902 -10.422  90.956  1.00 25.79           N  
+ATOM   2814  CA  ALA B 124      36.021 -11.757  91.519  1.00 25.52           C  
+ATOM   2815  C   ALA B 124      36.461 -12.753  90.452  1.00 27.01           C  
+ATOM   2816  O   ALA B 124      37.356 -13.566  90.689  1.00 25.97           O  
+ATOM   2817  CB  ALA B 124      34.697 -12.186  92.125  1.00 25.79           C  
+ATOM   2818  N   MET B 125      35.836 -12.690  89.275  1.00 28.07           N  
+ATOM   2819  CA  MET B 125      36.198 -13.595  88.184  1.00 28.97           C  
+ATOM   2820  C   MET B 125      37.649 -13.416  87.760  1.00 29.69           C  
+ATOM   2821  O   MET B 125      38.355 -14.398  87.552  1.00 30.94           O  
+ATOM   2822  CB  MET B 125      35.281 -13.390  86.980  1.00 28.91           C  
+ATOM   2823  CG  MET B 125      33.857 -13.819  87.244  1.00 28.91           C  
+ATOM   2824  SD  MET B 125      32.754 -13.319  85.934  1.00 30.10           S  
+ATOM   2825  CE  MET B 125      31.431 -14.503  86.111  1.00 25.08           C  
+ATOM   2826  N   ILE B 126      38.103 -12.172  87.636  1.00 29.78           N  
+ATOM   2827  CA  ILE B 126      39.487 -11.943  87.245  1.00 31.12           C  
+ATOM   2828  C   ILE B 126      40.420 -12.551  88.293  1.00 33.62           C  
+ATOM   2829  O   ILE B 126      41.419 -13.190  87.953  1.00 34.26           O  
+ATOM   2830  CB  ILE B 126      39.786 -10.442  87.081  1.00 29.76           C  
+ATOM   2831  CG1 ILE B 126      38.974  -9.888  85.908  1.00 28.59           C  
+ATOM   2832  CG2 ILE B 126      41.270 -10.226  86.817  1.00 29.28           C  
+ATOM   2833  CD1 ILE B 126      39.197  -8.419  85.652  1.00 28.05           C  
+ATOM   2834  N   ALA B 127      40.084 -12.366  89.567  1.00 35.16           N  
+ATOM   2835  CA  ALA B 127      40.896 -12.917  90.652  1.00 35.66           C  
+ATOM   2836  C   ALA B 127      40.798 -14.439  90.640  1.00 35.46           C  
+ATOM   2837  O   ALA B 127      41.742 -15.131  91.004  1.00 35.97           O  
+ATOM   2838  CB  ALA B 127      40.424 -12.367  92.000  1.00 33.45           C  
+ATOM   2839  N   GLY B 128      39.646 -14.952  90.218  1.00 36.75           N  
+ATOM   2840  CA  GLY B 128      39.445 -16.389  90.155  1.00 36.42           C  
+ATOM   2841  C   GLY B 128      40.402 -17.034  89.173  1.00 37.02           C  
+ATOM   2842  O   GLY B 128      40.810 -18.176  89.358  1.00 37.19           O  
+ATOM   2843  N   GLY B 129      40.744 -16.303  88.116  1.00 38.14           N  
+ATOM   2844  CA  GLY B 129      41.678 -16.812  87.128  1.00 38.10           C  
+ATOM   2845  C   GLY B 129      41.122 -17.775  86.101  1.00 38.78           C  
+ATOM   2846  O   GLY B 129      41.878 -18.337  85.309  1.00 39.67           O  
+ATOM   2847  N   ARG B 130      39.813 -17.986  86.096  1.00 39.46           N  
+ATOM   2848  CA  ARG B 130      39.238 -18.894  85.115  1.00 40.73           C  
+ATOM   2849  C   ARG B 130      38.037 -18.309  84.378  1.00 38.98           C  
+ATOM   2850  O   ARG B 130      37.140 -19.035  83.943  1.00 38.75           O  
+ATOM   2851  CB  ARG B 130      38.881 -20.227  85.776  1.00 44.97           C  
+ATOM   2852  CG  ARG B 130      37.966 -20.135  86.974  1.00 49.80           C  
+ATOM   2853  CD  ARG B 130      38.324 -21.225  87.973  1.00 55.25           C  
+ATOM   2854  NE  ARG B 130      37.211 -21.563  88.853  1.00 60.12           N  
+ATOM   2855  CZ  ARG B 130      36.150 -22.270  88.475  1.00 62.56           C  
+ATOM   2856  NH1 ARG B 130      36.058 -22.719  87.230  1.00 63.15           N  
+ATOM   2857  NH2 ARG B 130      35.182 -22.533  89.343  1.00 65.26           N  
+ATOM   2858  N   GLY B 131      38.035 -16.985  84.247  1.00 35.09           N  
+ATOM   2859  CA  GLY B 131      36.973 -16.297  83.538  1.00 33.85           C  
+ATOM   2860  C   GLY B 131      35.553 -16.527  84.008  1.00 32.12           C  
+ATOM   2861  O   GLY B 131      35.321 -16.879  85.162  1.00 33.29           O  
+ATOM   2862  N   GLY B 132      34.601 -16.313  83.101  1.00 30.38           N  
+ATOM   2863  CA  GLY B 132      33.199 -16.482  83.429  1.00 26.76           C  
+ATOM   2864  C   GLY B 132      32.258 -15.932  82.373  1.00 25.57           C  
+ATOM   2865  O   GLY B 132      32.690 -15.485  81.314  1.00 26.37           O  
+ATOM   2866  N   LYS B 133      30.966 -15.958  82.684  1.00 24.46           N  
+ATOM   2867  CA  LYS B 133      29.911 -15.497  81.792  1.00 22.99           C  
+ATOM   2868  C   LYS B 133      29.013 -14.446  82.443  1.00 23.36           C  
+ATOM   2869  O   LYS B 133      28.475 -14.665  83.530  1.00 26.10           O  
+ATOM   2870  CB  LYS B 133      29.026 -16.678  81.386  1.00 22.72           C  
+ATOM   2871  CG  LYS B 133      29.746 -17.821  80.695  1.00 23.16           C  
+ATOM   2872  CD  LYS B 133      30.197 -17.444  79.302  1.00 20.39           C  
+ATOM   2873  CE  LYS B 133      30.870 -18.628  78.627  1.00 22.52           C  
+ATOM   2874  NZ  LYS B 133      31.426 -18.250  77.301  1.00 23.90           N  
+ATOM   2875  N   ILE B 134      28.847 -13.309  81.775  1.00 21.94           N  
+ATOM   2876  CA  ILE B 134      27.976 -12.248  82.270  1.00 20.45           C  
+ATOM   2877  C   ILE B 134      26.905 -11.987  81.214  1.00 20.97           C  
+ATOM   2878  O   ILE B 134      27.220 -11.817  80.034  1.00 24.32           O  
+ATOM   2879  CB  ILE B 134      28.745 -10.938  82.545  1.00 17.42           C  
+ATOM   2880  CG1 ILE B 134      29.712 -11.131  83.714  1.00 17.98           C  
+ATOM   2881  CG2 ILE B 134      27.768  -9.834  82.895  1.00 15.93           C  
+ATOM   2882  CD1 ILE B 134      30.520  -9.889  84.062  1.00 14.84           C  
+ATOM   2883  N   ILE B 135      25.646 -11.965  81.646  1.00 18.32           N  
+ATOM   2884  CA  ILE B 135      24.513 -11.748  80.765  1.00 13.96           C  
+ATOM   2885  C   ILE B 135      23.648 -10.622  81.295  1.00 16.69           C  
+ATOM   2886  O   ILE B 135      23.099 -10.730  82.392  1.00 18.09           O  
+ATOM   2887  CB  ILE B 135      23.640 -13.005  80.682  1.00 13.51           C  
+ATOM   2888  CG1 ILE B 135      24.445 -14.161  80.091  1.00 11.69           C  
+ATOM   2889  CG2 ILE B 135      22.397 -12.723  79.856  1.00 13.39           C  
+ATOM   2890  CD1 ILE B 135      23.678 -15.461  80.021  1.00  9.93           C  
+ATOM   2891  N   ASN B 136      23.519  -9.545  80.522  1.00 15.42           N  
+ATOM   2892  CA  ASN B 136      22.700  -8.419  80.935  1.00 15.26           C  
+ATOM   2893  C   ASN B 136      21.348  -8.520  80.266  1.00 17.30           C  
+ATOM   2894  O   ASN B 136      21.212  -9.136  79.214  1.00 17.77           O  
+ATOM   2895  CB  ASN B 136      23.355  -7.087  80.559  1.00 14.91           C  
+ATOM   2896  CG  ASN B 136      24.725  -6.918  81.187  1.00 18.67           C  
+ATOM   2897  OD1 ASN B 136      24.929  -7.280  82.342  1.00 19.20           O  
+ATOM   2898  ND2 ASN B 136      25.667  -6.356  80.434  1.00 15.78           N  
+ATOM   2899  N   MET B 137      20.340  -7.926  80.887  1.00 18.96           N  
+ATOM   2900  CA  MET B 137      19.010  -7.953  80.327  1.00 19.92           C  
+ATOM   2901  C   MET B 137      18.715  -6.599  79.755  1.00 22.28           C  
+ATOM   2902  O   MET B 137      18.592  -5.612  80.486  1.00 22.16           O  
+ATOM   2903  CB  MET B 137      17.977  -8.304  81.392  1.00 19.46           C  
+ATOM   2904  CG  MET B 137      18.075  -9.743  81.858  1.00 21.29           C  
+ATOM   2905  SD  MET B 137      17.881 -10.917  80.489  1.00 22.94           S  
+ATOM   2906  CE  MET B 137      16.103 -11.037  80.435  1.00 17.97           C  
+ATOM   2907  N   ALA B 138      18.623  -6.558  78.431  1.00 24.30           N  
+ATOM   2908  CA  ALA B 138      18.326  -5.329  77.724  1.00 24.69           C  
+ATOM   2909  C   ALA B 138      16.827  -5.334  77.459  1.00 25.28           C  
+ATOM   2910  O   ALA B 138      16.046  -5.789  78.297  1.00 25.48           O  
+ATOM   2911  CB  ALA B 138      19.106  -5.277  76.424  1.00 23.00           C  
+ATOM   2912  N   SER B 139      16.426  -4.848  76.291  1.00 25.17           N  
+ATOM   2913  CA  SER B 139      15.015  -4.795  75.939  1.00 24.47           C  
+ATOM   2914  C   SER B 139      14.868  -4.112  74.586  1.00 24.65           C  
+ATOM   2915  O   SER B 139      15.739  -3.343  74.179  1.00 21.99           O  
+ATOM   2916  CB  SER B 139      14.250  -3.997  77.001  1.00 23.52           C  
+ATOM   2917  OG  SER B 139      12.912  -3.756  76.600  1.00 24.45           O  
+ATOM   2918  N   GLN B 140      13.770  -4.389  73.888  1.00 24.49           N  
+ATOM   2919  CA  GLN B 140      13.560  -3.750  72.602  1.00 25.89           C  
+ATOM   2920  C   GLN B 140      13.554  -2.245  72.827  1.00 23.93           C  
+ATOM   2921  O   GLN B 140      13.946  -1.470  71.950  1.00 24.37           O  
+ATOM   2922  CB  GLN B 140      12.233  -4.193  71.976  1.00 28.95           C  
+ATOM   2923  CG  GLN B 140      11.027  -4.098  72.893  1.00 32.22           C  
+ATOM   2924  CD  GLN B 140       9.710  -4.202  72.129  1.00 34.46           C  
+ATOM   2925  OE1 GLN B 140       9.517  -5.111  71.314  1.00 34.39           O  
+ATOM   2926  NE2 GLN B 140       8.795  -3.268  72.394  1.00 34.07           N  
+ATOM   2927  N   ALA B 141      13.129  -1.839  74.020  1.00 21.78           N  
+ATOM   2928  CA  ALA B 141      13.066  -0.427  74.365  1.00 18.21           C  
+ATOM   2929  C   ALA B 141      14.449   0.201  74.276  1.00 17.76           C  
+ATOM   2930  O   ALA B 141      14.576   1.416  74.150  1.00 17.87           O  
+ATOM   2931  CB  ALA B 141      12.491  -0.257  75.753  1.00 17.44           C  
+ATOM   2932  N   GLY B 142      15.483  -0.632  74.342  1.00 17.97           N  
+ATOM   2933  CA  GLY B 142      16.843  -0.133  74.237  1.00 20.43           C  
+ATOM   2934  C   GLY B 142      17.304   0.056  72.790  1.00 23.36           C  
+ATOM   2935  O   GLY B 142      18.336   0.683  72.539  1.00 22.85           O  
+ATOM   2936  N   ARG B 143      16.542  -0.481  71.835  1.00 22.94           N  
+ATOM   2937  CA  ARG B 143      16.878  -0.371  70.414  1.00 23.96           C  
+ATOM   2938  C   ARG B 143      16.369   0.931  69.788  1.00 24.95           C  
+ATOM   2939  O   ARG B 143      17.008   1.487  68.895  1.00 27.01           O  
+ATOM   2940  CB  ARG B 143      16.294  -1.553  69.639  1.00 22.02           C  
+ATOM   2941  CG  ARG B 143      16.832  -2.908  70.053  1.00 18.76           C  
+ATOM   2942  CD  ARG B 143      18.297  -3.067  69.698  1.00 14.41           C  
+ATOM   2943  NE  ARG B 143      18.693  -4.466  69.824  1.00 14.09           N  
+ATOM   2944  CZ  ARG B 143      19.918  -4.928  69.594  1.00 12.40           C  
+ATOM   2945  NH1 ARG B 143      20.175  -6.221  69.736  1.00 11.71           N  
+ATOM   2946  NH2 ARG B 143      20.884  -4.100  69.229  1.00 10.18           N  
+ATOM   2947  N   ARG B 144      15.212   1.402  70.244  1.00 24.39           N  
+ATOM   2948  CA  ARG B 144      14.637   2.639  69.726  1.00 23.26           C  
+ATOM   2949  C   ARG B 144      13.756   3.267  70.798  1.00 21.28           C  
+ATOM   2950  O   ARG B 144      13.117   2.561  71.571  1.00 17.90           O  
+ATOM   2951  CB  ARG B 144      13.800   2.368  68.457  1.00 24.50           C  
+ATOM   2952  CG  ARG B 144      12.427   1.731  68.698  1.00 22.97           C  
+ATOM   2953  CD  ARG B 144      12.543   0.327  69.281  1.00 26.39           C  
+ATOM   2954  NE  ARG B 144      11.249  -0.233  69.681  1.00 27.80           N  
+ATOM   2955  CZ  ARG B 144      10.463   0.289  70.621  1.00 29.70           C  
+ATOM   2956  NH1 ARG B 144      10.834   1.392  71.264  1.00 30.92           N  
+ATOM   2957  NH2 ARG B 144       9.310  -0.294  70.925  1.00 27.28           N  
+ATOM   2958  N   GLY B 145      13.722   4.594  70.826  1.00 21.06           N  
+ATOM   2959  CA  GLY B 145      12.918   5.299  71.804  1.00 22.90           C  
+ATOM   2960  C   GLY B 145      11.429   5.264  71.524  1.00 23.90           C  
+ATOM   2961  O   GLY B 145      11.007   4.890  70.438  1.00 26.77           O  
+ATOM   2962  N   GLU B 146      10.638   5.650  72.519  1.00 25.06           N  
+ATOM   2963  CA  GLU B 146       9.183   5.684  72.417  1.00 25.12           C  
+ATOM   2964  C   GLU B 146       8.686   6.955  73.074  1.00 25.83           C  
+ATOM   2965  O   GLU B 146       9.246   7.397  74.079  1.00 27.33           O  
+ATOM   2966  CB  GLU B 146       8.552   4.501  73.139  1.00 25.49           C  
+ATOM   2967  CG  GLU B 146       8.809   3.170  72.512  1.00 29.63           C  
+ATOM   2968  CD  GLU B 146       7.891   2.110  73.072  1.00 31.74           C  
+ATOM   2969  OE1 GLU B 146       6.668   2.382  73.154  1.00 33.38           O  
+ATOM   2970  OE2 GLU B 146       8.384   1.015  73.425  1.00 32.21           O  
+ATOM   2971  N   ALA B 147       7.621   7.522  72.524  1.00 24.61           N  
+ATOM   2972  CA  ALA B 147       7.053   8.760  73.041  1.00 26.70           C  
+ATOM   2973  C   ALA B 147       6.781   8.774  74.544  1.00 27.67           C  
+ATOM   2974  O   ALA B 147       7.174   9.713  75.234  1.00 29.15           O  
+ATOM   2975  CB  ALA B 147       5.765   9.090  72.294  1.00 26.54           C  
+ATOM   2976  N   LEU B 148       6.109   7.741  75.047  1.00 26.72           N  
+ATOM   2977  CA  LEU B 148       5.754   7.678  76.463  1.00 25.88           C  
+ATOM   2978  C   LEU B 148       6.650   6.793  77.326  1.00 25.10           C  
+ATOM   2979  O   LEU B 148       6.263   6.433  78.436  1.00 25.39           O  
+ATOM   2980  CB  LEU B 148       4.310   7.183  76.612  1.00 24.01           C  
+ATOM   2981  CG  LEU B 148       3.204   7.871  75.807  1.00 24.39           C  
+ATOM   2982  CD1 LEU B 148       1.890   7.136  76.013  1.00 23.43           C  
+ATOM   2983  CD2 LEU B 148       3.080   9.312  76.232  1.00 23.94           C  
+ATOM   2984  N   VAL B 149       7.838   6.445  76.844  1.00 23.19           N  
+ATOM   2985  CA  VAL B 149       8.711   5.563  77.623  1.00 21.24           C  
+ATOM   2986  C   VAL B 149      10.150   6.078  77.637  1.00 19.48           C  
+ATOM   2987  O   VAL B 149      11.109   5.305  77.704  1.00 19.09           O  
+ATOM   2988  CB  VAL B 149       8.667   4.117  77.038  1.00 21.93           C  
+ATOM   2989  CG1 VAL B 149       9.218   3.110  78.038  1.00 21.67           C  
+ATOM   2990  CG2 VAL B 149       7.241   3.753  76.662  1.00 19.57           C  
+ATOM   2991  N   GLY B 150      10.288   7.397  77.588  1.00 17.99           N  
+ATOM   2992  CA  GLY B 150      11.602   8.008  77.569  1.00 19.18           C  
+ATOM   2993  C   GLY B 150      12.597   7.490  78.590  1.00 20.32           C  
+ATOM   2994  O   GLY B 150      13.695   7.056  78.233  1.00 20.88           O  
+ATOM   2995  N   VAL B 151      12.222   7.533  79.865  1.00 18.99           N  
+ATOM   2996  CA  VAL B 151      13.117   7.087  80.920  1.00 17.25           C  
+ATOM   2997  C   VAL B 151      13.544   5.631  80.748  1.00 16.51           C  
+ATOM   2998  O   VAL B 151      14.731   5.334  80.657  1.00 16.38           O  
+ATOM   2999  CB  VAL B 151      12.469   7.276  82.319  1.00 18.31           C  
+ATOM   3000  CG1 VAL B 151      13.419   6.788  83.403  1.00 19.16           C  
+ATOM   3001  CG2 VAL B 151      12.143   8.744  82.552  1.00 16.84           C  
+ATOM   3002  N   TYR B 152      12.579   4.724  80.688  1.00 16.69           N  
+ATOM   3003  CA  TYR B 152      12.887   3.305  80.549  1.00 18.24           C  
+ATOM   3004  C   TYR B 152      13.747   2.990  79.322  1.00 18.08           C  
+ATOM   3005  O   TYR B 152      14.700   2.216  79.419  1.00 17.85           O  
+ATOM   3006  CB  TYR B 152      11.589   2.489  80.501  1.00 19.87           C  
+ATOM   3007  CG  TYR B 152      11.812   0.997  80.455  1.00 21.36           C  
+ATOM   3008  CD1 TYR B 152      12.193   0.291  81.591  1.00 21.51           C  
+ATOM   3009  CD2 TYR B 152      11.663   0.291  79.261  1.00 23.54           C  
+ATOM   3010  CE1 TYR B 152      12.420  -1.087  81.540  1.00 22.88           C  
+ATOM   3011  CE2 TYR B 152      11.885  -1.082  79.199  1.00 22.68           C  
+ATOM   3012  CZ  TYR B 152      12.261  -1.764  80.337  1.00 23.80           C  
+ATOM   3013  OH  TYR B 152      12.456  -3.128  80.270  1.00 25.75           O  
+ATOM   3014  N   CYS B 153      13.413   3.582  78.175  1.00 17.25           N  
+ATOM   3015  CA  CYS B 153      14.180   3.349  76.952  1.00 16.40           C  
+ATOM   3016  C   CYS B 153      15.626   3.791  77.129  1.00 14.82           C  
+ATOM   3017  O   CYS B 153      16.560   3.079  76.744  1.00 14.52           O  
+ATOM   3018  CB  CYS B 153      13.554   4.092  75.762  1.00 17.92           C  
+ATOM   3019  SG  CYS B 153      12.035   3.336  75.119  1.00 21.12           S  
+ATOM   3020  N   ALA B 154      15.815   4.966  77.714  1.00 14.14           N  
+ATOM   3021  CA  ALA B 154      17.163   5.482  77.942  1.00 16.11           C  
+ATOM   3022  C   ALA B 154      18.001   4.520  78.789  1.00 15.92           C  
+ATOM   3023  O   ALA B 154      19.170   4.280  78.486  1.00 17.46           O  
+ATOM   3024  CB  ALA B 154      17.095   6.855  78.615  1.00 14.83           C  
+ATOM   3025  N   THR B 155      17.408   3.957  79.841  1.00 16.64           N  
+ATOM   3026  CA  THR B 155      18.158   3.045  80.702  1.00 17.54           C  
+ATOM   3027  C   THR B 155      18.580   1.790  79.945  1.00 16.86           C  
+ATOM   3028  O   THR B 155      19.703   1.315  80.104  1.00 18.15           O  
+ATOM   3029  CB  THR B 155      17.355   2.636  81.995  1.00 17.66           C  
+ATOM   3030  OG1 THR B 155      16.264   1.768  81.656  1.00 15.77           O  
+ATOM   3031  CG2 THR B 155      16.814   3.881  82.709  1.00 14.89           C  
+ATOM   3032  N   LYS B 156      17.694   1.256  79.114  1.00 15.98           N  
+ATOM   3033  CA  LYS B 156      18.036   0.061  78.356  1.00 17.40           C  
+ATOM   3034  C   LYS B 156      19.043   0.352  77.238  1.00 17.38           C  
+ATOM   3035  O   LYS B 156      19.832  -0.520  76.857  1.00 18.02           O  
+ATOM   3036  CB  LYS B 156      16.768  -0.598  77.807  1.00 18.62           C  
+ATOM   3037  CG  LYS B 156      15.902  -1.213  78.903  1.00 20.38           C  
+ATOM   3038  CD  LYS B 156      16.713  -2.184  79.768  1.00 19.26           C  
+ATOM   3039  CE  LYS B 156      15.846  -2.885  80.819  1.00 21.56           C  
+ATOM   3040  NZ  LYS B 156      16.616  -3.928  81.573  1.00 18.38           N  
+ATOM   3041  N   ALA B 157      19.038   1.577  76.725  1.00 16.25           N  
+ATOM   3042  CA  ALA B 157      20.007   1.932  75.696  1.00 17.23           C  
+ATOM   3043  C   ALA B 157      21.390   1.949  76.358  1.00 17.74           C  
+ATOM   3044  O   ALA B 157      22.386   1.506  75.769  1.00 17.92           O  
+ATOM   3045  CB  ALA B 157      19.685   3.299  75.117  1.00 14.49           C  
+ATOM   3046  N   ALA B 158      21.442   2.447  77.595  1.00 15.62           N  
+ATOM   3047  CA  ALA B 158      22.706   2.524  78.331  1.00 14.03           C  
+ATOM   3048  C   ALA B 158      23.222   1.130  78.667  1.00 11.84           C  
+ATOM   3049  O   ALA B 158      24.426   0.909  78.717  1.00 10.17           O  
+ATOM   3050  CB  ALA B 158      22.529   3.349  79.599  1.00 14.04           C  
+ATOM   3051  N   VAL B 159      22.307   0.188  78.876  1.00 12.73           N  
+ATOM   3052  CA  VAL B 159      22.681  -1.195  79.179  1.00 14.42           C  
+ATOM   3053  C   VAL B 159      23.384  -1.827  77.976  1.00 15.78           C  
+ATOM   3054  O   VAL B 159      24.432  -2.479  78.108  1.00 16.95           O  
+ATOM   3055  CB  VAL B 159      21.440  -2.055  79.505  1.00 15.83           C  
+ATOM   3056  CG1 VAL B 159      21.820  -3.534  79.494  1.00 13.24           C  
+ATOM   3057  CG2 VAL B 159      20.867  -1.653  80.854  1.00 14.21           C  
+ATOM   3058  N   ILE B 160      22.783  -1.655  76.802  1.00 15.69           N  
+ATOM   3059  CA  ILE B 160      23.354  -2.185  75.572  1.00 12.82           C  
+ATOM   3060  C   ILE B 160      24.756  -1.595  75.394  1.00 12.12           C  
+ATOM   3061  O   ILE B 160      25.686  -2.287  74.998  1.00 10.90           O  
+ATOM   3062  CB  ILE B 160      22.455  -1.812  74.379  1.00 13.82           C  
+ATOM   3063  CG1 ILE B 160      21.170  -2.634  74.448  1.00 13.16           C  
+ATOM   3064  CG2 ILE B 160      23.189  -2.023  73.073  1.00 12.13           C  
+ATOM   3065  CD1 ILE B 160      20.089  -2.155  73.541  1.00 14.64           C  
+ATOM   3066  N   SER B 161      24.907  -0.313  75.705  1.00 11.16           N  
+ATOM   3067  CA  SER B 161      26.201   0.343  75.582  1.00 11.80           C  
+ATOM   3068  C   SER B 161      27.206  -0.244  76.573  1.00 13.59           C  
+ATOM   3069  O   SER B 161      28.354  -0.548  76.205  1.00 13.32           O  
+ATOM   3070  CB  SER B 161      26.051   1.848  75.826  1.00 13.02           C  
+ATOM   3071  OG  SER B 161      27.315   2.490  75.835  1.00 15.59           O  
+ATOM   3072  N   LEU B 162      26.773  -0.410  77.828  1.00 12.32           N  
+ATOM   3073  CA  LEU B 162      27.651  -0.960  78.856  1.00 14.71           C  
+ATOM   3074  C   LEU B 162      28.035  -2.395  78.520  1.00 13.57           C  
+ATOM   3075  O   LEU B 162      29.155  -2.826  78.803  1.00 13.72           O  
+ATOM   3076  CB  LEU B 162      26.989  -0.883  80.242  1.00 16.43           C  
+ATOM   3077  CG  LEU B 162      26.892   0.545  80.807  1.00 17.24           C  
+ATOM   3078  CD1 LEU B 162      26.027   0.554  82.053  1.00 20.88           C  
+ATOM   3079  CD2 LEU B 162      28.281   1.078  81.110  1.00 14.56           C  
+ATOM   3080  N   THR B 163      27.112  -3.134  77.912  1.00 13.55           N  
+ATOM   3081  CA  THR B 163      27.402  -4.511  77.519  1.00 13.79           C  
+ATOM   3082  C   THR B 163      28.536  -4.553  76.484  1.00 14.13           C  
+ATOM   3083  O   THR B 163      29.362  -5.471  76.486  1.00 14.28           O  
+ATOM   3084  CB  THR B 163      26.173  -5.179  76.916  1.00 14.02           C  
+ATOM   3085  OG1 THR B 163      25.135  -5.225  77.896  1.00 14.46           O  
+ATOM   3086  CG2 THR B 163      26.504  -6.591  76.455  1.00 15.11           C  
+ATOM   3087  N   GLN B 164      28.585  -3.555  75.604  1.00 14.37           N  
+ATOM   3088  CA  GLN B 164      29.626  -3.521  74.584  1.00 13.44           C  
+ATOM   3089  C   GLN B 164      30.960  -3.127  75.191  1.00 12.98           C  
+ATOM   3090  O   GLN B 164      31.969  -3.780  74.937  1.00 13.14           O  
+ATOM   3091  CB  GLN B 164      29.242  -2.550  73.463  1.00 13.02           C  
+ATOM   3092  CG  GLN B 164      27.901  -2.878  72.854  1.00 14.35           C  
+ATOM   3093  CD  GLN B 164      27.456  -1.873  71.813  1.00 19.25           C  
+ATOM   3094  OE1 GLN B 164      27.726  -0.666  71.926  1.00 22.11           O  
+ATOM   3095  NE2 GLN B 164      26.745  -2.358  70.799  1.00 16.52           N  
+ATOM   3096  N   SER B 165      30.961  -2.064  75.997  1.00 13.49           N  
+ATOM   3097  CA  SER B 165      32.183  -1.591  76.646  1.00 13.49           C  
+ATOM   3098  C   SER B 165      32.809  -2.668  77.543  1.00 14.04           C  
+ATOM   3099  O   SER B 165      34.029  -2.874  77.534  1.00 14.00           O  
+ATOM   3100  CB  SER B 165      31.888  -0.349  77.487  1.00 14.84           C  
+ATOM   3101  OG  SER B 165      31.414   0.723  76.688  1.00 13.35           O  
+ATOM   3102  N   ALA B 166      31.973  -3.363  78.307  1.00 11.90           N  
+ATOM   3103  CA  ALA B 166      32.465  -4.403  79.197  1.00 11.42           C  
+ATOM   3104  C   ALA B 166      32.925  -5.592  78.376  1.00 12.32           C  
+ATOM   3105  O   ALA B 166      33.992  -6.163  78.629  1.00 12.81           O  
+ATOM   3106  CB  ALA B 166      31.367  -4.823  80.174  1.00 13.14           C  
+ATOM   3107  N   GLY B 167      32.117  -5.961  77.385  1.00 13.03           N  
+ATOM   3108  CA  GLY B 167      32.464  -7.077  76.529  1.00 12.96           C  
+ATOM   3109  C   GLY B 167      33.858  -6.917  75.949  1.00 14.80           C  
+ATOM   3110  O   GLY B 167      34.679  -7.827  76.044  1.00 16.17           O  
+ATOM   3111  N   LEU B 168      34.135  -5.756  75.362  1.00 14.77           N  
+ATOM   3112  CA  LEU B 168      35.439  -5.496  74.757  1.00 16.45           C  
+ATOM   3113  C   LEU B 168      36.566  -5.404  75.773  1.00 18.39           C  
+ATOM   3114  O   LEU B 168      37.698  -5.800  75.496  1.00 18.94           O  
+ATOM   3115  CB  LEU B 168      35.401  -4.197  73.953  1.00 16.69           C  
+ATOM   3116  CG  LEU B 168      34.456  -4.153  72.746  1.00 16.82           C  
+ATOM   3117  CD1 LEU B 168      34.454  -2.755  72.146  1.00 17.25           C  
+ATOM   3118  CD2 LEU B 168      34.893  -5.177  71.712  1.00 15.76           C  
+ATOM   3119  N   ASN B 169      36.262  -4.872  76.950  1.00 20.40           N  
+ATOM   3120  CA  ASN B 169      37.278  -4.717  77.976  1.00 20.61           C  
+ATOM   3121  C   ASN B 169      37.563  -6.004  78.736  1.00 19.64           C  
+ATOM   3122  O   ASN B 169      38.707  -6.287  79.054  1.00 19.18           O  
+ATOM   3123  CB  ASN B 169      36.874  -3.607  78.958  1.00 21.53           C  
+ATOM   3124  CG  ASN B 169      37.963  -3.302  79.981  1.00 22.86           C  
+ATOM   3125  OD1 ASN B 169      39.147  -3.264  79.649  1.00 23.09           O  
+ATOM   3126  ND2 ASN B 169      37.563  -3.065  81.223  1.00 21.30           N  
+ATOM   3127  N   LEU B 170      36.534  -6.799  78.997  1.00 20.24           N  
+ATOM   3128  CA  LEU B 170      36.719  -8.023  79.771  1.00 21.02           C  
+ATOM   3129  C   LEU B 170      37.020  -9.309  79.013  1.00 21.98           C  
+ATOM   3130  O   LEU B 170      37.427 -10.299  79.620  1.00 22.14           O  
+ATOM   3131  CB  LEU B 170      35.499  -8.241  80.676  1.00 20.48           C  
+ATOM   3132  CG  LEU B 170      35.225  -7.131  81.702  1.00 18.58           C  
+ATOM   3133  CD1 LEU B 170      33.921  -7.393  82.436  1.00 16.78           C  
+ATOM   3134  CD2 LEU B 170      36.379  -7.050  82.679  1.00 19.97           C  
+ATOM   3135  N   ILE B 171      36.841  -9.310  77.696  1.00 22.60           N  
+ATOM   3136  CA  ILE B 171      37.093 -10.529  76.939  1.00 21.87           C  
+ATOM   3137  C   ILE B 171      38.544 -10.992  77.084  1.00 23.51           C  
+ATOM   3138  O   ILE B 171      38.834 -12.178  76.969  1.00 23.30           O  
+ATOM   3139  CB  ILE B 171      36.731 -10.356  75.416  1.00 20.03           C  
+ATOM   3140  CG1 ILE B 171      36.818 -11.709  74.702  1.00 14.25           C  
+ATOM   3141  CG2 ILE B 171      37.663  -9.365  74.744  1.00 18.19           C  
+ATOM   3142  CD1 ILE B 171      35.806 -12.732  75.205  1.00  9.88           C  
+ATOM   3143  N   ARG B 172      39.450 -10.055  77.347  1.00 26.68           N  
+ATOM   3144  CA  ARG B 172      40.865 -10.386  77.497  1.00 30.84           C  
+ATOM   3145  C   ARG B 172      41.113 -11.245  78.741  1.00 31.32           C  
+ATOM   3146  O   ARG B 172      42.121 -11.941  78.820  1.00 31.95           O  
+ATOM   3147  CB  ARG B 172      41.719  -9.098  77.539  1.00 35.83           C  
+ATOM   3148  CG  ARG B 172      41.232  -8.021  78.535  1.00 43.50           C  
+ATOM   3149  CD  ARG B 172      41.997  -6.671  78.443  1.00 46.99           C  
+ATOM   3150  NE  ARG B 172      41.626  -5.850  77.282  1.00 52.34           N  
+ATOM   3151  CZ  ARG B 172      41.335  -4.545  77.332  1.00 54.33           C  
+ATOM   3152  NH1 ARG B 172      41.366  -3.895  78.488  1.00 55.39           N  
+ATOM   3153  NH2 ARG B 172      41.016  -3.878  76.224  1.00 55.25           N  
+ATOM   3154  N   HIS B 173      40.189 -11.205  79.702  1.00 30.43           N  
+ATOM   3155  CA  HIS B 173      40.318 -11.995  80.926  1.00 27.92           C  
+ATOM   3156  C   HIS B 173      39.519 -13.285  80.877  1.00 27.25           C  
+ATOM   3157  O   HIS B 173      39.392 -13.979  81.887  1.00 27.97           O  
+ATOM   3158  CB  HIS B 173      39.867 -11.190  82.144  1.00 28.39           C  
+ATOM   3159  CG  HIS B 173      40.752 -10.027  82.455  1.00 30.18           C  
+ATOM   3160  ND1 HIS B 173      40.354  -8.721  82.268  1.00 32.26           N  
+ATOM   3161  CD2 HIS B 173      42.029  -9.972  82.900  1.00 29.53           C  
+ATOM   3162  CE1 HIS B 173      41.350  -7.910  82.581  1.00 31.93           C  
+ATOM   3163  NE2 HIS B 173      42.377  -8.644  82.966  1.00 32.11           N  
+ATOM   3164  N   GLY B 174      38.974 -13.608  79.710  1.00 24.62           N  
+ATOM   3165  CA  GLY B 174      38.197 -14.825  79.581  1.00 20.62           C  
+ATOM   3166  C   GLY B 174      36.771 -14.660  80.068  1.00 19.90           C  
+ATOM   3167  O   GLY B 174      36.105 -15.637  80.407  1.00 19.97           O  
+ATOM   3168  N   ILE B 175      36.293 -13.422  80.105  1.00 19.49           N  
+ATOM   3169  CA  ILE B 175      34.927 -13.153  80.541  1.00 19.48           C  
+ATOM   3170  C   ILE B 175      34.077 -12.678  79.371  1.00 19.83           C  
+ATOM   3171  O   ILE B 175      34.361 -11.636  78.782  1.00 19.65           O  
+ATOM   3172  CB  ILE B 175      34.881 -12.057  81.626  1.00 18.82           C  
+ATOM   3173  CG1 ILE B 175      35.697 -12.490  82.851  1.00 18.89           C  
+ATOM   3174  CG2 ILE B 175      33.428 -11.768  82.005  1.00 16.28           C  
+ATOM   3175  CD1 ILE B 175      35.859 -11.385  83.890  1.00 16.51           C  
+ATOM   3176  N   ASN B 176      33.036 -13.438  79.045  1.00 20.28           N  
+ATOM   3177  CA  ASN B 176      32.131 -13.075  77.957  1.00 19.87           C  
+ATOM   3178  C   ASN B 176      30.975 -12.246  78.487  1.00 20.40           C  
+ATOM   3179  O   ASN B 176      30.266 -12.665  79.397  1.00 20.18           O  
+ATOM   3180  CB  ASN B 176      31.543 -14.323  77.280  1.00 22.17           C  
+ATOM   3181  CG  ASN B 176      32.591 -15.164  76.564  1.00 21.82           C  
+ATOM   3182  OD1 ASN B 176      33.378 -15.863  77.197  1.00 22.72           O  
+ATOM   3183  ND2 ASN B 176      32.602 -15.094  75.232  1.00 17.83           N  
+ATOM   3184  N   VAL B 177      30.773 -11.076  77.902  1.00 21.26           N  
+ATOM   3185  CA  VAL B 177      29.677 -10.211  78.312  1.00 20.52           C  
+ATOM   3186  C   VAL B 177      28.743  -9.995  77.116  1.00 21.21           C  
+ATOM   3187  O   VAL B 177      29.165  -9.495  76.076  1.00 21.70           O  
+ATOM   3188  CB  VAL B 177      30.205  -8.841  78.806  1.00 20.00           C  
+ATOM   3189  CG1 VAL B 177      29.064  -8.000  79.358  1.00 17.89           C  
+ATOM   3190  CG2 VAL B 177      31.264  -9.049  79.857  1.00 19.15           C  
+ATOM   3191  N   ASN B 178      27.481 -10.387  77.269  1.00 19.88           N  
+ATOM   3192  CA  ASN B 178      26.485 -10.225  76.214  1.00 19.36           C  
+ATOM   3193  C   ASN B 178      25.152  -9.891  76.860  1.00 19.68           C  
+ATOM   3194  O   ASN B 178      25.019  -9.967  78.079  1.00 19.82           O  
+ATOM   3195  CB  ASN B 178      26.348 -11.515  75.388  1.00 19.01           C  
+ATOM   3196  CG  ASN B 178      27.605 -11.838  74.599  1.00 16.91           C  
+ATOM   3197  OD1 ASN B 178      28.015 -11.078  73.726  1.00 17.19           O  
+ATOM   3198  ND2 ASN B 178      28.222 -12.964  74.910  1.00 15.93           N  
+ATOM   3199  N   ALA B 179      24.167  -9.530  76.048  1.00 19.47           N  
+ATOM   3200  CA  ALA B 179      22.848  -9.194  76.569  1.00 21.08           C  
+ATOM   3201  C   ALA B 179      21.711  -9.799  75.746  1.00 22.05           C  
+ATOM   3202  O   ALA B 179      21.876 -10.115  74.567  1.00 21.84           O  
+ATOM   3203  CB  ALA B 179      22.687  -7.681  76.641  1.00 19.90           C  
+ATOM   3204  N   ILE B 180      20.565  -9.977  76.397  1.00 22.69           N  
+ATOM   3205  CA  ILE B 180      19.369 -10.510  75.759  1.00 21.62           C  
+ATOM   3206  C   ILE B 180      18.368  -9.373  75.746  1.00 22.34           C  
+ATOM   3207  O   ILE B 180      18.224  -8.657  76.737  1.00 24.00           O  
+ATOM   3208  CB  ILE B 180      18.765 -11.690  76.552  1.00 20.46           C  
+ATOM   3209  CG1 ILE B 180      19.731 -12.875  76.551  1.00 20.73           C  
+ATOM   3210  CG2 ILE B 180      17.437 -12.108  75.932  1.00 21.33           C  
+ATOM   3211  CD1 ILE B 180      19.237 -14.075  77.339  1.00 20.70           C  
+ATOM   3212  N   ALA B 181      17.685  -9.186  74.625  1.00 23.26           N  
+ATOM   3213  CA  ALA B 181      16.710  -8.111  74.534  1.00 24.71           C  
+ATOM   3214  C   ALA B 181      15.337  -8.678  74.219  1.00 26.50           C  
+ATOM   3215  O   ALA B 181      15.031  -8.989  73.071  1.00 26.56           O  
+ATOM   3216  CB  ALA B 181      17.128  -7.109  73.467  1.00 23.31           C  
+ATOM   3217  N   PRO B 182      14.497  -8.846  75.253  1.00 28.00           N  
+ATOM   3218  CA  PRO B 182      13.145  -9.380  75.075  1.00 28.32           C  
+ATOM   3219  C   PRO B 182      12.251  -8.331  74.430  1.00 29.15           C  
+ATOM   3220  O   PRO B 182      12.586  -7.147  74.405  1.00 29.18           O  
+ATOM   3221  CB  PRO B 182      12.702  -9.694  76.509  1.00 28.00           C  
+ATOM   3222  CG  PRO B 182      13.991  -9.855  77.259  1.00 27.89           C  
+ATOM   3223  CD  PRO B 182      14.833  -8.755  76.683  1.00 26.53           C  
+ATOM   3224  N   GLY B 183      11.114  -8.767  73.906  1.00 31.77           N  
+ATOM   3225  CA  GLY B 183      10.190  -7.834  73.294  1.00 35.56           C  
+ATOM   3226  C   GLY B 183       9.144  -7.485  74.331  1.00 38.70           C  
+ATOM   3227  O   GLY B 183       9.456  -6.899  75.368  1.00 38.72           O  
+ATOM   3228  N   VAL B 184       7.897  -7.842  74.050  1.00 41.18           N  
+ATOM   3229  CA  VAL B 184       6.819  -7.595  74.987  1.00 43.10           C  
+ATOM   3230  C   VAL B 184       6.512  -8.916  75.674  1.00 46.08           C  
+ATOM   3231  O   VAL B 184       5.971  -9.830  75.062  1.00 47.04           O  
+ATOM   3232  CB  VAL B 184       5.551  -7.082  74.280  1.00 41.85           C  
+ATOM   3233  CG1 VAL B 184       5.744  -5.646  73.848  1.00 40.91           C  
+ATOM   3234  CG2 VAL B 184       5.236  -7.954  73.079  1.00 41.44           C  
+ATOM   3235  N   VAL B 185       6.897  -9.029  76.938  1.00 49.51           N  
+ATOM   3236  CA  VAL B 185       6.634 -10.245  77.683  1.00 52.83           C  
+ATOM   3237  C   VAL B 185       5.373 -10.014  78.502  1.00 56.81           C  
+ATOM   3238  O   VAL B 185       5.212  -8.970  79.143  1.00 57.80           O  
+ATOM   3239  CB  VAL B 185       7.788 -10.593  78.638  1.00 50.90           C  
+ATOM   3240  CG1 VAL B 185       7.473 -11.864  79.404  1.00 51.05           C  
+ATOM   3241  CG2 VAL B 185       9.068 -10.766  77.848  1.00 50.41           C  
+ATOM   3242  N   ASP B 186       4.474 -10.992  78.464  1.00 60.55           N  
+ATOM   3243  CA  ASP B 186       3.224 -10.921  79.191  1.00 64.52           C  
+ATOM   3244  C   ASP B 186       3.440 -10.916  80.687  1.00 66.67           C  
+ATOM   3245  O   ASP B 186       4.360 -11.555  81.208  1.00 66.08           O  
+ATOM   3246  CB  ASP B 186       2.310 -12.095  78.824  1.00 66.53           C  
+ATOM   3247  CG  ASP B 186       0.907 -11.644  78.478  1.00 69.55           C  
+ATOM   3248  OD1 ASP B 186       0.432 -12.012  77.381  1.00 71.69           O  
+ATOM   3249  OD2 ASP B 186       0.279 -10.933  79.292  1.00 70.03           O  
+ATOM   3250  N   GLY B 187       2.602 -10.163  81.380  1.00 68.91           N  
+ATOM   3251  CA  GLY B 187       2.673 -10.081  82.817  1.00 71.23           C  
+ATOM   3252  C   GLY B 187       1.392  -9.513  83.374  1.00 73.42           C  
+ATOM   3253  O   GLY B 187       0.522  -9.020  82.654  1.00 73.53           O  
+ATOM   3254  N   GLU B 188       1.292  -9.583  84.688  1.00 75.15           N  
+ATOM   3255  CA  GLU B 188       0.135  -9.069  85.370  1.00 76.44           C  
+ATOM   3256  C   GLU B 188       0.304  -7.560  85.299  1.00 76.27           C  
+ATOM   3257  O   GLU B 188      -0.642  -6.832  84.998  1.00 76.44           O  
+ATOM   3258  CB  GLU B 188       0.139  -9.558  86.816  1.00 77.91           C  
+ATOM   3259  CG  GLU B 188       1.505  -9.437  87.460  1.00 79.66           C  
+ATOM   3260  CD  GLU B 188       1.468  -9.635  88.956  1.00 80.35           C  
+ATOM   3261  OE1 GLU B 188       1.298 -10.790  89.401  1.00 80.39           O  
+ATOM   3262  OE2 GLU B 188       1.603  -8.628  89.687  1.00 80.20           O  
+ATOM   3263  N   HIS B 189       1.539  -7.115  85.522  1.00 75.44           N  
+ATOM   3264  CA  HIS B 189       1.892  -5.701  85.475  1.00 74.50           C  
+ATOM   3265  C   HIS B 189       1.283  -5.008  84.262  1.00 73.37           C  
+ATOM   3266  O   HIS B 189       1.162  -3.782  84.233  1.00 73.07           O  
+ATOM   3267  CB  HIS B 189       3.409  -5.546  85.421  1.00 75.06           C  
+ATOM   3268  CG  HIS B 189       4.025  -6.097  84.172  1.00 76.04           C  
+ATOM   3269  ND1 HIS B 189       4.465  -5.297  83.137  1.00 76.53           N  
+ATOM   3270  CD2 HIS B 189       4.242  -7.372  83.774  1.00 76.49           C  
+ATOM   3271  CE1 HIS B 189       4.923  -6.055  82.158  1.00 76.08           C  
+ATOM   3272  NE2 HIS B 189       4.797  -7.322  82.520  1.00 76.23           N  
+ATOM   3273  N   TRP B 190       0.923  -5.799  83.257  1.00 72.24           N  
+ATOM   3274  CA  TRP B 190       0.313  -5.279  82.047  1.00 71.62           C  
+ATOM   3275  C   TRP B 190      -1.064  -4.709  82.343  1.00 71.76           C  
+ATOM   3276  O   TRP B 190      -1.609  -3.948  81.548  1.00 71.30           O  
+ATOM   3277  CB  TRP B 190       0.198  -6.382  80.991  1.00 71.07           C  
+ATOM   3278  CG  TRP B 190       1.231  -6.264  79.918  1.00 69.94           C  
+ATOM   3279  CD1 TRP B 190       2.364  -7.015  79.775  1.00 69.83           C  
+ATOM   3280  CD2 TRP B 190       1.252  -5.299  78.862  1.00 68.94           C  
+ATOM   3281  NE1 TRP B 190       3.090  -6.574  78.693  1.00 69.80           N  
+ATOM   3282  CE2 TRP B 190       2.430  -5.521  78.116  1.00 69.18           C  
+ATOM   3283  CE3 TRP B 190       0.389  -4.265  78.475  1.00 67.85           C  
+ATOM   3284  CZ2 TRP B 190       2.768  -4.745  77.003  1.00 68.37           C  
+ATOM   3285  CZ3 TRP B 190       0.726  -3.493  77.369  1.00 67.68           C  
+ATOM   3286  CH2 TRP B 190       1.906  -3.739  76.647  1.00 67.79           C  
+ATOM   3287  N   ASP B 191      -1.627  -5.085  83.486  1.00 72.15           N  
+ATOM   3288  CA  ASP B 191      -2.939  -4.592  83.882  1.00 72.44           C  
+ATOM   3289  C   ASP B 191      -2.879  -3.080  84.063  1.00 71.41           C  
+ATOM   3290  O   ASP B 191      -3.710  -2.346  83.526  1.00 71.11           O  
+ATOM   3291  CB  ASP B 191      -3.380  -5.255  85.190  1.00 74.22           C  
+ATOM   3292  CG  ASP B 191      -4.489  -6.270  84.986  1.00 76.05           C  
+ATOM   3293  OD1 ASP B 191      -4.804  -6.584  83.818  1.00 76.42           O  
+ATOM   3294  OD2 ASP B 191      -5.044  -6.756  85.996  1.00 78.03           O  
+ATOM   3295  N   GLY B 192      -1.885  -2.625  84.819  1.00 70.34           N  
+ATOM   3296  CA  GLY B 192      -1.726  -1.204  85.061  1.00 68.71           C  
+ATOM   3297  C   GLY B 192      -1.154  -0.491  83.854  1.00 67.74           C  
+ATOM   3298  O   GLY B 192      -1.609   0.594  83.497  1.00 67.26           O  
+ATOM   3299  N   VAL B 193      -0.155  -1.101  83.224  1.00 67.33           N  
+ATOM   3300  CA  VAL B 193       0.483  -0.517  82.048  1.00 66.28           C  
+ATOM   3301  C   VAL B 193      -0.552  -0.217  80.963  1.00 66.02           C  
+ATOM   3302  O   VAL B 193      -0.506   0.837  80.327  1.00 65.75           O  
+ATOM   3303  CB  VAL B 193       1.565  -1.462  81.469  1.00 66.13           C  
+ATOM   3304  CG1 VAL B 193       2.241  -0.810  80.267  1.00 64.79           C  
+ATOM   3305  CG2 VAL B 193       2.590  -1.796  82.543  1.00 64.72           C  
+ATOM   3306  N   ASP B 194      -1.480  -1.148  80.756  1.00 65.29           N  
+ATOM   3307  CA  ASP B 194      -2.534  -0.976  79.760  1.00 64.71           C  
+ATOM   3308  C   ASP B 194      -3.417   0.201  80.147  1.00 64.07           C  
+ATOM   3309  O   ASP B 194      -3.833   0.988  79.300  1.00 62.56           O  
+ATOM   3310  CB  ASP B 194      -3.399  -2.235  79.668  1.00 65.78           C  
+ATOM   3311  CG  ASP B 194      -4.621  -2.040  78.785  1.00 66.59           C  
+ATOM   3312  OD1 ASP B 194      -4.460  -1.958  77.547  1.00 67.25           O  
+ATOM   3313  OD2 ASP B 194      -5.743  -1.958  79.333  1.00 66.18           O  
+ATOM   3314  N   ALA B 195      -3.707   0.304  81.439  1.00 64.56           N  
+ATOM   3315  CA  ALA B 195      -4.536   1.384  81.956  1.00 64.99           C  
+ATOM   3316  C   ALA B 195      -3.869   2.717  81.650  1.00 64.97           C  
+ATOM   3317  O   ALA B 195      -4.523   3.671  81.221  1.00 64.41           O  
+ATOM   3318  CB  ALA B 195      -4.723   1.220  83.461  1.00 65.23           C  
+ATOM   3319  N   LYS B 196      -2.559   2.764  81.875  1.00 65.84           N  
+ATOM   3320  CA  LYS B 196      -1.759   3.961  81.630  1.00 66.88           C  
+ATOM   3321  C   LYS B 196      -1.912   4.436  80.193  1.00 66.12           C  
+ATOM   3322  O   LYS B 196      -2.289   5.580  79.949  1.00 65.02           O  
+ATOM   3323  CB  LYS B 196      -0.284   3.673  81.911  1.00 68.85           C  
+ATOM   3324  CG  LYS B 196       0.058   3.513  83.379  1.00 71.50           C  
+ATOM   3325  CD  LYS B 196      -0.034   4.843  84.105  1.00 73.53           C  
+ATOM   3326  CE  LYS B 196       0.473   4.717  85.531  1.00 75.80           C  
+ATOM   3327  NZ  LYS B 196       0.535   6.043  86.207  1.00 78.00           N  
+ATOM   3328  N   PHE B 197      -1.604   3.552  79.248  1.00 65.71           N  
+ATOM   3329  CA  PHE B 197      -1.718   3.881  77.833  1.00 65.93           C  
+ATOM   3330  C   PHE B 197      -3.156   4.232  77.466  1.00 66.65           C  
+ATOM   3331  O   PHE B 197      -3.400   5.175  76.713  1.00 66.50           O  
+ATOM   3332  CB  PHE B 197      -1.258   2.708  76.964  1.00 64.58           C  
+ATOM   3333  CG  PHE B 197       0.231   2.546  76.895  1.00 62.86           C  
+ATOM   3334  CD1 PHE B 197       0.865   1.518  77.584  1.00 62.43           C  
+ATOM   3335  CD2 PHE B 197       1.000   3.413  76.125  1.00 61.34           C  
+ATOM   3336  CE1 PHE B 197       2.244   1.354  77.505  1.00 61.38           C  
+ATOM   3337  CE2 PHE B 197       2.376   3.258  76.040  1.00 60.74           C  
+ATOM   3338  CZ  PHE B 197       3.000   2.225  76.730  1.00 60.40           C  
+ATOM   3339  N   ALA B 198      -4.104   3.464  77.994  1.00 67.83           N  
+ATOM   3340  CA  ALA B 198      -5.516   3.699  77.715  1.00 68.71           C  
+ATOM   3341  C   ALA B 198      -5.881   5.127  78.091  1.00 69.34           C  
+ATOM   3342  O   ALA B 198      -6.622   5.802  77.376  1.00 69.21           O  
+ATOM   3343  CB  ALA B 198      -6.375   2.715  78.498  1.00 68.56           C  
+ATOM   3344  N   ASP B 199      -5.339   5.585  79.214  1.00 70.38           N  
+ATOM   3345  CA  ASP B 199      -5.608   6.930  79.702  1.00 71.33           C  
+ATOM   3346  C   ASP B 199      -4.825   7.998  78.937  1.00 70.85           C  
+ATOM   3347  O   ASP B 199      -5.344   9.077  78.658  1.00 69.98           O  
+ATOM   3348  CB  ASP B 199      -5.277   7.011  81.194  1.00 73.24           C  
+ATOM   3349  CG  ASP B 199      -5.775   8.291  81.830  1.00 75.53           C  
+ATOM   3350  OD1 ASP B 199      -7.003   8.529  81.794  1.00 76.91           O  
+ATOM   3351  OD2 ASP B 199      -4.944   9.057  82.364  1.00 76.23           O  
+ATOM   3352  N   TYR B 200      -3.578   7.687  78.596  1.00 70.98           N  
+ATOM   3353  CA  TYR B 200      -2.709   8.617  77.879  1.00 71.09           C  
+ATOM   3354  C   TYR B 200      -3.040   8.808  76.402  1.00 71.65           C  
+ATOM   3355  O   TYR B 200      -2.731   9.851  75.829  1.00 71.29           O  
+ATOM   3356  CB  TYR B 200      -1.247   8.167  77.987  1.00 70.62           C  
+ATOM   3357  CG  TYR B 200      -0.548   8.536  79.280  1.00 70.15           C  
+ATOM   3358  CD1 TYR B 200       0.005   7.553  80.099  1.00 70.25           C  
+ATOM   3359  CD2 TYR B 200      -0.401   9.870  79.662  1.00 69.44           C  
+ATOM   3360  CE1 TYR B 200       0.689   7.885  81.262  1.00 70.33           C  
+ATOM   3361  CE2 TYR B 200       0.283  10.215  80.826  1.00 69.32           C  
+ATOM   3362  CZ  TYR B 200       0.827   9.217  81.621  1.00 70.17           C  
+ATOM   3363  OH  TYR B 200       1.518   9.547  82.768  1.00 70.76           O  
+ATOM   3364  N   GLU B 201      -3.670   7.814  75.785  1.00 72.74           N  
+ATOM   3365  CA  GLU B 201      -3.977   7.902  74.358  1.00 73.51           C  
+ATOM   3366  C   GLU B 201      -5.458   7.779  73.996  1.00 73.32           C  
+ATOM   3367  O   GLU B 201      -5.788   7.563  72.830  1.00 73.28           O  
+ATOM   3368  CB  GLU B 201      -3.187   6.830  73.593  1.00 74.84           C  
+ATOM   3369  CG  GLU B 201      -1.817   6.519  74.185  1.00 76.63           C  
+ATOM   3370  CD  GLU B 201      -1.122   5.350  73.501  1.00 77.03           C  
+ATOM   3371  OE1 GLU B 201      -0.248   5.590  72.643  1.00 76.76           O  
+ATOM   3372  OE2 GLU B 201      -1.453   4.186  73.817  1.00 77.57           O  
+ATOM   3373  N   ASN B 202      -6.344   7.908  74.980  1.00 72.41           N  
+ATOM   3374  CA  ASN B 202      -7.779   7.812  74.722  1.00 71.24           C  
+ATOM   3375  C   ASN B 202      -8.117   6.474  74.062  1.00 69.78           C  
+ATOM   3376  O   ASN B 202      -8.616   6.431  72.938  1.00 69.17           O  
+ATOM   3377  CB  ASN B 202      -8.218   8.978  73.822  1.00 72.75           C  
+ATOM   3378  CG  ASN B 202      -9.723   9.025  73.603  1.00 74.35           C  
+ATOM   3379  OD1 ASN B 202     -10.500   9.037  74.557  1.00 75.59           O  
+ATOM   3380  ND2 ASN B 202     -10.138   9.068  72.340  1.00 74.19           N  
+ATOM   3381  N   LEU B 203      -7.840   5.383  74.772  1.00 68.67           N  
+ATOM   3382  CA  LEU B 203      -8.105   4.038  74.264  1.00 68.10           C  
+ATOM   3383  C   LEU B 203      -8.940   3.218  75.252  1.00 67.53           C  
+ATOM   3384  O   LEU B 203      -8.814   3.378  76.465  1.00 67.55           O  
+ATOM   3385  CB  LEU B 203      -6.784   3.300  74.003  1.00 67.77           C  
+ATOM   3386  CG  LEU B 203      -5.777   3.850  72.987  1.00 67.47           C  
+ATOM   3387  CD1 LEU B 203      -4.498   3.037  73.082  1.00 67.38           C  
+ATOM   3388  CD2 LEU B 203      -6.346   3.788  71.574  1.00 67.21           C  
+ATOM   3389  N   PRO B 204      -9.810   2.329  74.740  1.00 66.97           N  
+ATOM   3390  CA  PRO B 204     -10.645   1.495  75.613  1.00 66.44           C  
+ATOM   3391  C   PRO B 204      -9.768   0.653  76.541  1.00 66.14           C  
+ATOM   3392  O   PRO B 204      -8.720   0.163  76.129  1.00 66.23           O  
+ATOM   3393  CB  PRO B 204     -11.419   0.631  74.621  1.00 66.23           C  
+ATOM   3394  CG  PRO B 204     -11.563   1.533  73.436  1.00 65.94           C  
+ATOM   3395  CD  PRO B 204     -10.184   2.141  73.326  1.00 66.87           C  
+ATOM   3396  N   ARG B 205     -10.190   0.488  77.789  1.00 66.21           N  
+ATOM   3397  CA  ARG B 205      -9.413  -0.300  78.740  1.00 67.58           C  
+ATOM   3398  C   ARG B 205      -9.165  -1.701  78.174  1.00 66.78           C  
+ATOM   3399  O   ARG B 205     -10.111  -2.454  77.935  1.00 67.07           O  
+ATOM   3400  CB  ARG B 205     -10.161  -0.426  80.069  1.00 69.85           C  
+ATOM   3401  CG  ARG B 205     -10.723   0.877  80.622  1.00 74.11           C  
+ATOM   3402  CD  ARG B 205     -11.655   0.591  81.799  1.00 77.50           C  
+ATOM   3403  NE  ARG B 205     -12.439   1.755  82.210  1.00 80.59           N  
+ATOM   3404  CZ  ARG B 205     -13.404   1.721  83.129  1.00 81.87           C  
+ATOM   3405  NH1 ARG B 205     -13.708   0.580  83.739  1.00 81.83           N  
+ATOM   3406  NH2 ARG B 205     -14.068   2.828  83.440  1.00 82.30           N  
+ATOM   3407  N   GLY B 206      -7.898  -2.044  77.953  1.00 64.88           N  
+ATOM   3408  CA  GLY B 206      -7.570  -3.362  77.435  1.00 62.82           C  
+ATOM   3409  C   GLY B 206      -7.254  -3.426  75.952  1.00 61.37           C  
+ATOM   3410  O   GLY B 206      -6.824  -4.464  75.451  1.00 61.15           O  
+ATOM   3411  N   GLU B 207      -7.468  -2.325  75.243  1.00 60.86           N  
+ATOM   3412  CA  GLU B 207      -7.191  -2.282  73.813  1.00 60.53           C  
+ATOM   3413  C   GLU B 207      -5.685  -2.258  73.553  1.00 60.57           C  
+ATOM   3414  O   GLU B 207      -5.197  -2.893  72.620  1.00 61.42           O  
+ATOM   3415  CB  GLU B 207      -7.842  -1.045  73.183  1.00 60.50           C  
+ATOM   3416  CG  GLU B 207      -7.462  -0.806  71.723  1.00 61.68           C  
+ATOM   3417  CD  GLU B 207      -8.139  -1.765  70.758  1.00 62.01           C  
+ATOM   3418  OE1 GLU B 207      -8.559  -2.864  71.184  1.00 62.29           O  
+ATOM   3419  OE2 GLU B 207      -8.238  -1.417  69.563  1.00 63.04           O  
+ATOM   3420  N   LYS B 208      -4.953  -1.526  74.387  1.00 59.82           N  
+ATOM   3421  CA  LYS B 208      -3.508  -1.413  74.240  1.00 58.47           C  
+ATOM   3422  C   LYS B 208      -2.803  -2.764  74.333  1.00 57.65           C  
+ATOM   3423  O   LYS B 208      -1.989  -3.104  73.473  1.00 57.78           O  
+ATOM   3424  CB  LYS B 208      -2.943  -0.468  75.303  1.00 58.69           C  
+ATOM   3425  CG  LYS B 208      -1.468  -0.148  75.119  1.00 58.26           C  
+ATOM   3426  CD  LYS B 208      -1.234   0.593  73.814  1.00 57.23           C  
+ATOM   3427  CE  LYS B 208       0.230   0.938  73.629  1.00 56.42           C  
+ATOM   3428  NZ  LYS B 208       0.447   1.695  72.368  1.00 56.15           N  
+ATOM   3429  N   LYS B 209      -3.105  -3.531  75.375  1.00 55.68           N  
+ATOM   3430  CA  LYS B 209      -2.473  -4.833  75.534  1.00 55.00           C  
+ATOM   3431  C   LYS B 209      -2.818  -5.730  74.353  1.00 54.53           C  
+ATOM   3432  O   LYS B 209      -2.030  -6.589  73.962  1.00 53.24           O  
+ATOM   3433  CB  LYS B 209      -2.925  -5.503  76.831  1.00 55.21           C  
+ATOM   3434  CG  LYS B 209      -2.248  -6.844  77.076  1.00 55.37           C  
+ATOM   3435  CD  LYS B 209      -2.799  -7.548  78.302  1.00 56.19           C  
+ATOM   3436  CE  LYS B 209      -2.108  -8.886  78.511  1.00 56.55           C  
+ATOM   3437  NZ  LYS B 209      -2.657  -9.625  79.680  1.00 56.81           N  
+ATOM   3438  N   ARG B 210      -4.003  -5.526  73.789  1.00 55.20           N  
+ATOM   3439  CA  ARG B 210      -4.447  -6.322  72.652  1.00 56.00           C  
+ATOM   3440  C   ARG B 210      -3.658  -5.938  71.401  1.00 55.59           C  
+ATOM   3441  O   ARG B 210      -3.102  -6.802  70.722  1.00 56.61           O  
+ATOM   3442  CB  ARG B 210      -5.943  -6.107  72.404  1.00 57.46           C  
+ATOM   3443  CG  ARG B 210      -6.560  -7.094  71.420  1.00 58.86           C  
+ATOM   3444  CD  ARG B 210      -7.897  -6.592  70.899  1.00 59.39           C  
+ATOM   3445  NE  ARG B 210      -7.737  -5.361  70.130  1.00 61.46           N  
+ATOM   3446  CZ  ARG B 210      -7.023  -5.263  69.011  1.00 62.93           C  
+ATOM   3447  NH1 ARG B 210      -6.397  -6.328  68.520  1.00 62.98           N  
+ATOM   3448  NH2 ARG B 210      -6.926  -4.096  68.382  1.00 63.59           N  
+ATOM   3449  N   GLN B 211      -3.614  -4.640  71.103  1.00 54.82           N  
+ATOM   3450  CA  GLN B 211      -2.892  -4.138  69.937  1.00 53.85           C  
+ATOM   3451  C   GLN B 211      -1.438  -4.597  69.926  1.00 52.49           C  
+ATOM   3452  O   GLN B 211      -0.957  -5.128  68.925  1.00 52.30           O  
+ATOM   3453  CB  GLN B 211      -2.933  -2.607  69.893  1.00 55.17           C  
+ATOM   3454  CG  GLN B 211      -4.265  -2.019  69.458  1.00 57.86           C  
+ATOM   3455  CD  GLN B 211      -4.221  -0.501  69.327  1.00 59.38           C  
+ATOM   3456  OE1 GLN B 211      -3.377   0.049  68.616  1.00 58.85           O  
+ATOM   3457  NE2 GLN B 211      -5.137   0.180  70.011  1.00 59.61           N  
+ATOM   3458  N   VAL B 212      -0.743  -4.385  71.042  1.00 50.48           N  
+ATOM   3459  CA  VAL B 212       0.659  -4.775  71.162  1.00 48.20           C  
+ATOM   3460  C   VAL B 212       0.854  -6.263  70.878  1.00 47.04           C  
+ATOM   3461  O   VAL B 212       1.764  -6.649  70.143  1.00 47.47           O  
+ATOM   3462  CB  VAL B 212       1.211  -4.462  72.571  1.00 47.69           C  
+ATOM   3463  CG1 VAL B 212       2.673  -4.864  72.658  1.00 48.12           C  
+ATOM   3464  CG2 VAL B 212       1.056  -2.985  72.873  1.00 47.66           C  
+ATOM   3465  N   GLY B 213       0.000  -7.099  71.455  1.00 44.40           N  
+ATOM   3466  CA  GLY B 213       0.127  -8.526  71.227  1.00 44.63           C  
+ATOM   3467  C   GLY B 213      -0.072  -8.910  69.771  1.00 43.50           C  
+ATOM   3468  O   GLY B 213       0.663  -9.734  69.223  1.00 43.48           O  
+ATOM   3469  N   ALA B 214      -1.065  -8.298  69.135  1.00 42.10           N  
+ATOM   3470  CA  ALA B 214      -1.376  -8.591  67.745  1.00 41.27           C  
+ATOM   3471  C   ALA B 214      -0.335  -8.074  66.755  1.00 40.01           C  
+ATOM   3472  O   ALA B 214      -0.246  -8.566  65.633  1.00 40.01           O  
+ATOM   3473  CB  ALA B 214      -2.740  -8.026  67.403  1.00 42.33           C  
+ATOM   3474  N   ALA B 215       0.453  -7.091  67.171  1.00 38.55           N  
+ATOM   3475  CA  ALA B 215       1.476  -6.515  66.304  1.00 37.36           C  
+ATOM   3476  C   ALA B 215       2.757  -7.346  66.222  1.00 36.96           C  
+ATOM   3477  O   ALA B 215       3.555  -7.170  65.301  1.00 38.37           O  
+ATOM   3478  CB  ALA B 215       1.808  -5.102  66.763  1.00 37.49           C  
+ATOM   3479  N   VAL B 216       2.967  -8.239  67.183  1.00 34.88           N  
+ATOM   3480  CA  VAL B 216       4.163  -9.071  67.168  1.00 32.52           C  
+ATOM   3481  C   VAL B 216       4.079 -10.016  65.968  1.00 31.88           C  
+ATOM   3482  O   VAL B 216       3.113 -10.761  65.823  1.00 30.81           O  
+ATOM   3483  CB  VAL B 216       4.287  -9.892  68.477  1.00 32.02           C  
+ATOM   3484  CG1 VAL B 216       5.458 -10.858  68.384  1.00 29.57           C  
+ATOM   3485  CG2 VAL B 216       4.475  -8.949  69.663  1.00 31.56           C  
+ATOM   3486  N   PRO B 217       5.094  -9.992  65.088  1.00 31.47           N  
+ATOM   3487  CA  PRO B 217       5.099 -10.858  63.909  1.00 30.94           C  
+ATOM   3488  C   PRO B 217       4.713 -12.297  64.232  1.00 30.48           C  
+ATOM   3489  O   PRO B 217       3.820 -12.859  63.601  1.00 31.40           O  
+ATOM   3490  CB  PRO B 217       6.535 -10.735  63.408  1.00 30.38           C  
+ATOM   3491  CG  PRO B 217       6.877  -9.328  63.751  1.00 29.06           C  
+ATOM   3492  CD  PRO B 217       6.343  -9.211  65.159  1.00 31.31           C  
+ATOM   3493  N   PHE B 218       5.390 -12.880  65.218  1.00 29.48           N  
+ATOM   3494  CA  PHE B 218       5.141 -14.259  65.645  1.00 27.96           C  
+ATOM   3495  C   PHE B 218       3.657 -14.551  65.867  1.00 28.32           C  
+ATOM   3496  O   PHE B 218       3.208 -15.679  65.669  1.00 28.47           O  
+ATOM   3497  CB  PHE B 218       5.904 -14.553  66.942  1.00 24.99           C  
+ATOM   3498  CG  PHE B 218       5.898 -16.006  67.340  1.00 20.92           C  
+ATOM   3499  CD1 PHE B 218       6.879 -16.872  66.864  1.00 17.35           C  
+ATOM   3500  CD2 PHE B 218       4.921 -16.504  68.200  1.00 18.07           C  
+ATOM   3501  CE1 PHE B 218       6.894 -18.209  67.238  1.00 18.38           C  
+ATOM   3502  CE2 PHE B 218       4.923 -17.844  68.585  1.00 19.03           C  
+ATOM   3503  CZ  PHE B 218       5.914 -18.702  68.104  1.00 19.47           C  
+ATOM   3504  N   GLY B 219       2.907 -13.544  66.304  1.00 29.32           N  
+ATOM   3505  CA  GLY B 219       1.485 -13.732  66.530  1.00 32.45           C  
+ATOM   3506  C   GLY B 219       0.992 -13.738  67.971  1.00 35.48           C  
+ATOM   3507  O   GLY B 219      -0.183 -14.005  68.220  1.00 36.93           O  
+ATOM   3508  N   ARG B 220       1.868 -13.450  68.928  1.00 36.17           N  
+ATOM   3509  CA  ARG B 220       1.463 -13.436  70.329  1.00 35.97           C  
+ATOM   3510  C   ARG B 220       2.510 -12.747  71.189  1.00 37.07           C  
+ATOM   3511  O   ARG B 220       3.649 -12.538  70.763  1.00 36.00           O  
+ATOM   3512  CB  ARG B 220       1.256 -14.864  70.851  1.00 34.24           C  
+ATOM   3513  CG  ARG B 220       2.550 -15.598  71.181  1.00 34.48           C  
+ATOM   3514  CD  ARG B 220       2.281 -17.008  71.685  1.00 36.23           C  
+ATOM   3515  NE  ARG B 220       3.467 -17.742  72.146  1.00 35.68           N  
+ATOM   3516  CZ  ARG B 220       4.535 -17.200  72.728  1.00 36.21           C  
+ATOM   3517  NH1 ARG B 220       4.614 -15.890  72.924  1.00 35.83           N  
+ATOM   3518  NH2 ARG B 220       5.516 -17.981  73.161  1.00 36.23           N  
+ATOM   3519  N   MET B 221       2.109 -12.420  72.414  1.00 39.02           N  
+ATOM   3520  CA  MET B 221       2.970 -11.756  73.385  1.00 38.94           C  
+ATOM   3521  C   MET B 221       3.994 -12.745  73.957  1.00 37.85           C  
+ATOM   3522  O   MET B 221       3.741 -13.944  74.019  1.00 37.07           O  
+ATOM   3523  CB  MET B 221       2.096 -11.173  74.494  1.00 41.73           C  
+ATOM   3524  CG  MET B 221       2.722 -10.034  75.264  1.00 45.46           C  
+ATOM   3525  SD  MET B 221       1.452  -9.055  76.097  1.00 50.60           S  
+ATOM   3526  CE  MET B 221       1.045  -7.846  74.824  1.00 48.06           C  
+ATOM   3527  N   GLY B 222       5.145 -12.231  74.375  1.00 37.03           N  
+ATOM   3528  CA  GLY B 222       6.201 -13.075  74.908  1.00 39.07           C  
+ATOM   3529  C   GLY B 222       5.920 -13.856  76.181  1.00 40.41           C  
+ATOM   3530  O   GLY B 222       5.018 -13.527  76.942  1.00 40.87           O  
+ATOM   3531  N   ARG B 223       6.715 -14.898  76.407  1.00 41.90           N  
+ATOM   3532  CA  ARG B 223       6.585 -15.755  77.581  1.00 43.80           C  
+ATOM   3533  C   ARG B 223       7.996 -16.051  78.094  1.00 42.24           C  
+ATOM   3534  O   ARG B 223       8.945 -16.101  77.312  1.00 42.05           O  
+ATOM   3535  CB  ARG B 223       5.875 -17.058  77.194  1.00 48.50           C  
+ATOM   3536  CG  ARG B 223       4.904 -17.584  78.248  1.00 56.28           C  
+ATOM   3537  CD  ARG B 223       4.155 -18.829  77.763  1.00 61.40           C  
+ATOM   3538  NE  ARG B 223       3.343 -18.555  76.578  1.00 66.72           N  
+ATOM   3539  CZ  ARG B 223       2.278 -17.757  76.562  1.00 68.88           C  
+ATOM   3540  NH1 ARG B 223       1.883 -17.145  77.673  1.00 69.26           N  
+ATOM   3541  NH2 ARG B 223       1.613 -17.563  75.429  1.00 70.37           N  
+ATOM   3542  N   ALA B 224       8.136 -16.241  79.402  1.00 40.24           N  
+ATOM   3543  CA  ALA B 224       9.443 -16.520  79.997  1.00 38.15           C  
+ATOM   3544  C   ALA B 224      10.121 -17.750  79.383  1.00 36.83           C  
+ATOM   3545  O   ALA B 224      11.349 -17.809  79.281  1.00 36.14           O  
+ATOM   3546  CB  ALA B 224       9.300 -16.696  81.504  1.00 37.54           C  
+ATOM   3547  N   GLU B 225       9.325 -18.727  78.967  1.00 35.08           N  
+ATOM   3548  CA  GLU B 225       9.872 -19.936  78.367  1.00 35.91           C  
+ATOM   3549  C   GLU B 225      10.564 -19.650  77.032  1.00 33.45           C  
+ATOM   3550  O   GLU B 225      11.424 -20.416  76.595  1.00 32.99           O  
+ATOM   3551  CB  GLU B 225       8.767 -20.979  78.169  1.00 39.68           C  
+ATOM   3552  CG  GLU B 225       8.182 -21.503  79.478  1.00 46.28           C  
+ATOM   3553  CD  GLU B 225       7.350 -20.464  80.220  1.00 49.95           C  
+ATOM   3554  OE1 GLU B 225       7.080 -20.662  81.426  1.00 51.33           O  
+ATOM   3555  OE2 GLU B 225       6.957 -19.453  79.597  1.00 52.23           O  
+ATOM   3556  N   ASP B 226      10.189 -18.546  76.393  1.00 29.25           N  
+ATOM   3557  CA  ASP B 226      10.786 -18.173  75.118  1.00 26.16           C  
+ATOM   3558  C   ASP B 226      12.227 -17.735  75.277  1.00 25.60           C  
+ATOM   3559  O   ASP B 226      13.029 -17.876  74.354  1.00 26.08           O  
+ATOM   3560  CB  ASP B 226      10.014 -17.022  74.466  1.00 24.74           C  
+ATOM   3561  CG  ASP B 226       8.586 -17.388  74.127  1.00 23.25           C  
+ATOM   3562  OD1 ASP B 226       8.321 -18.558  73.779  1.00 24.35           O  
+ATOM   3563  OD2 ASP B 226       7.724 -16.492  74.188  1.00 24.43           O  
+ATOM   3564  N   LEU B 227      12.550 -17.207  76.455  1.00 24.33           N  
+ATOM   3565  CA  LEU B 227      13.887 -16.686  76.746  1.00 23.06           C  
+ATOM   3566  C   LEU B 227      14.912 -17.623  77.369  1.00 22.64           C  
+ATOM   3567  O   LEU B 227      16.115 -17.391  77.232  1.00 23.14           O  
+ATOM   3568  CB  LEU B 227      13.769 -15.469  77.660  1.00 21.40           C  
+ATOM   3569  CG  LEU B 227      13.301 -14.108  77.153  1.00 21.06           C  
+ATOM   3570  CD1 LEU B 227      12.477 -14.237  75.896  1.00 24.29           C  
+ATOM   3571  CD2 LEU B 227      12.510 -13.436  78.271  1.00 20.39           C  
+ATOM   3572  N   THR B 228      14.457 -18.667  78.056  1.00 23.28           N  
+ATOM   3573  CA  THR B 228      15.390 -19.570  78.736  1.00 22.66           C  
+ATOM   3574  C   THR B 228      16.430 -20.234  77.841  1.00 21.99           C  
+ATOM   3575  O   THR B 228      17.581 -20.421  78.250  1.00 21.88           O  
+ATOM   3576  CB  THR B 228      14.634 -20.655  79.544  1.00 22.96           C  
+ATOM   3577  OG1 THR B 228      13.877 -21.493  78.660  1.00 23.74           O  
+ATOM   3578  CG2 THR B 228      13.691 -19.995  80.548  1.00 22.52           C  
+ATOM   3579  N   GLY B 229      16.028 -20.579  76.621  1.00 21.11           N  
+ATOM   3580  CA  GLY B 229      16.944 -21.220  75.693  1.00 18.97           C  
+ATOM   3581  C   GLY B 229      18.161 -20.363  75.411  1.00 18.10           C  
+ATOM   3582  O   GLY B 229      19.293 -20.840  75.440  1.00 17.03           O  
+ATOM   3583  N   MET B 230      17.934 -19.087  75.136  1.00 17.13           N  
+ATOM   3584  CA  MET B 230      19.044 -18.186  74.860  1.00 17.90           C  
+ATOM   3585  C   MET B 230      19.874 -17.966  76.138  1.00 16.84           C  
+ATOM   3586  O   MET B 230      21.104 -17.913  76.085  1.00 14.48           O  
+ATOM   3587  CB  MET B 230      18.507 -16.856  74.314  1.00 17.50           C  
+ATOM   3588  CG  MET B 230      19.569 -15.857  73.890  1.00 19.83           C  
+ATOM   3589  SD  MET B 230      20.712 -16.508  72.655  1.00 23.81           S  
+ATOM   3590  CE  MET B 230      19.698 -16.419  71.199  1.00 25.03           C  
+ATOM   3591  N   ALA B 231      19.200 -17.849  77.284  1.00 17.91           N  
+ATOM   3592  CA  ALA B 231      19.899 -17.644  78.562  1.00 18.27           C  
+ATOM   3593  C   ALA B 231      20.910 -18.762  78.841  1.00 17.92           C  
+ATOM   3594  O   ALA B 231      22.035 -18.502  79.280  1.00 17.90           O  
+ATOM   3595  CB  ALA B 231      18.898 -17.557  79.698  1.00 18.92           C  
+ATOM   3596  N   ILE B 232      20.506 -20.003  78.580  1.00 17.16           N  
+ATOM   3597  CA  ILE B 232      21.383 -21.151  78.782  1.00 17.09           C  
+ATOM   3598  C   ILE B 232      22.536 -21.116  77.782  1.00 17.24           C  
+ATOM   3599  O   ILE B 232      23.713 -21.137  78.168  1.00 15.33           O  
+ATOM   3600  CB  ILE B 232      20.617 -22.476  78.582  1.00 18.77           C  
+ATOM   3601  CG1 ILE B 232      19.506 -22.598  79.628  1.00 20.08           C  
+ATOM   3602  CG2 ILE B 232      21.576 -23.660  78.679  1.00 16.99           C  
+ATOM   3603  CD1 ILE B 232      18.632 -23.811  79.433  1.00 19.05           C  
+ATOM   3604  N   PHE B 233      22.181 -21.067  76.494  1.00 17.27           N  
+ATOM   3605  CA  PHE B 233      23.157 -21.039  75.408  1.00 15.99           C  
+ATOM   3606  C   PHE B 233      24.308 -20.064  75.629  1.00 15.01           C  
+ATOM   3607  O   PHE B 233      25.469 -20.441  75.514  1.00 12.79           O  
+ATOM   3608  CB  PHE B 233      22.486 -20.691  74.076  1.00 18.86           C  
+ATOM   3609  CG  PHE B 233      23.442 -20.679  72.910  1.00 19.95           C  
+ATOM   3610  CD1 PHE B 233      23.914 -21.873  72.373  1.00 21.48           C  
+ATOM   3611  CD2 PHE B 233      23.907 -19.478  72.383  1.00 19.13           C  
+ATOM   3612  CE1 PHE B 233      24.839 -21.875  71.326  1.00 22.51           C  
+ATOM   3613  CE2 PHE B 233      24.831 -19.468  71.338  1.00 21.99           C  
+ATOM   3614  CZ  PHE B 233      25.299 -20.670  70.808  1.00 21.99           C  
+ATOM   3615  N   LEU B 234      23.993 -18.809  75.932  1.00 14.86           N  
+ATOM   3616  CA  LEU B 234      25.039 -17.811  76.146  1.00 17.21           C  
+ATOM   3617  C   LEU B 234      25.989 -18.099  77.303  1.00 18.37           C  
+ATOM   3618  O   LEU B 234      27.019 -17.428  77.439  1.00 21.02           O  
+ATOM   3619  CB  LEU B 234      24.427 -16.421  76.330  1.00 15.31           C  
+ATOM   3620  CG  LEU B 234      23.780 -15.844  75.066  1.00 18.90           C  
+ATOM   3621  CD1 LEU B 234      23.115 -14.499  75.370  1.00 17.84           C  
+ATOM   3622  CD2 LEU B 234      24.846 -15.691  73.983  1.00 14.46           C  
+ATOM   3623  N   ALA B 235      25.665 -19.090  78.130  1.00 19.19           N  
+ATOM   3624  CA  ALA B 235      26.522 -19.430  79.266  1.00 20.68           C  
+ATOM   3625  C   ALA B 235      27.323 -20.709  79.028  1.00 22.11           C  
+ATOM   3626  O   ALA B 235      28.109 -21.129  79.880  1.00 21.90           O  
+ATOM   3627  CB  ALA B 235      25.680 -19.572  80.534  1.00 21.07           C  
+ATOM   3628  N   THR B 236      27.120 -21.333  77.871  1.00 22.79           N  
+ATOM   3629  CA  THR B 236      27.841 -22.558  77.540  1.00 22.36           C  
+ATOM   3630  C   THR B 236      29.069 -22.220  76.713  1.00 23.07           C  
+ATOM   3631  O   THR B 236      29.221 -21.093  76.238  1.00 23.70           O  
+ATOM   3632  CB  THR B 236      26.960 -23.527  76.736  1.00 22.29           C  
+ATOM   3633  OG1 THR B 236      26.556 -22.900  75.511  1.00 23.93           O  
+ATOM   3634  CG2 THR B 236      25.726 -23.917  77.538  1.00 18.81           C  
+ATOM   3635  N   PRO B 237      29.978 -23.186  76.545  1.00 24.51           N  
+ATOM   3636  CA  PRO B 237      31.185 -22.925  75.754  1.00 25.99           C  
+ATOM   3637  C   PRO B 237      30.936 -22.808  74.244  1.00 26.94           C  
+ATOM   3638  O   PRO B 237      31.818 -22.389  73.496  1.00 27.58           O  
+ATOM   3639  CB  PRO B 237      32.111 -24.086  76.127  1.00 24.90           C  
+ATOM   3640  CG  PRO B 237      31.167 -25.171  76.528  1.00 26.75           C  
+ATOM   3641  CD  PRO B 237      30.096 -24.447  77.295  1.00 25.09           C  
+ATOM   3642  N   GLU B 238      29.738 -23.164  73.795  1.00 27.16           N  
+ATOM   3643  CA  GLU B 238      29.425 -23.041  72.373  1.00 27.02           C  
+ATOM   3644  C   GLU B 238      29.227 -21.567  72.030  1.00 27.47           C  
+ATOM   3645  O   GLU B 238      28.994 -21.214  70.873  1.00 27.45           O  
+ATOM   3646  CB  GLU B 238      28.152 -23.805  72.018  1.00 26.67           C  
+ATOM   3647  CG  GLU B 238      28.272 -25.312  72.105  1.00 28.94           C  
+ATOM   3648  CD  GLU B 238      27.080 -26.014  71.484  1.00 30.85           C  
+ATOM   3649  OE1 GLU B 238      25.933 -25.679  71.848  1.00 29.77           O  
+ATOM   3650  OE2 GLU B 238      27.288 -26.900  70.628  1.00 34.04           O  
+ATOM   3651  N   ALA B 239      29.319 -20.706  73.041  1.00 25.40           N  
+ATOM   3652  CA  ALA B 239      29.137 -19.276  72.834  1.00 22.82           C  
+ATOM   3653  C   ALA B 239      30.379 -18.505  73.226  1.00 21.42           C  
+ATOM   3654  O   ALA B 239      30.329 -17.296  73.423  1.00 20.84           O  
+ATOM   3655  CB  ALA B 239      27.941 -18.780  73.633  1.00 21.90           C  
+ATOM   3656  N   ASP B 240      31.498 -19.209  73.331  1.00 21.89           N  
+ATOM   3657  CA  ASP B 240      32.751 -18.579  73.710  1.00 23.25           C  
+ATOM   3658  C   ASP B 240      33.246 -17.508  72.754  1.00 24.05           C  
+ATOM   3659  O   ASP B 240      34.018 -16.634  73.152  1.00 23.28           O  
+ATOM   3660  CB  ASP B 240      33.849 -19.628  73.862  1.00 26.46           C  
+ATOM   3661  CG  ASP B 240      33.798 -20.333  75.200  1.00 28.78           C  
+ATOM   3662  OD1 ASP B 240      33.101 -19.832  76.109  1.00 30.60           O  
+ATOM   3663  OD2 ASP B 240      34.467 -21.377  75.344  1.00 28.91           O  
+ATOM   3664  N   TYR B 241      32.818 -17.575  71.496  1.00 23.34           N  
+ATOM   3665  CA  TYR B 241      33.273 -16.610  70.500  1.00 22.33           C  
+ATOM   3666  C   TYR B 241      32.294 -15.449  70.341  1.00 20.62           C  
+ATOM   3667  O   TYR B 241      32.511 -14.542  69.546  1.00 18.68           O  
+ATOM   3668  CB  TYR B 241      33.494 -17.319  69.158  1.00 22.92           C  
+ATOM   3669  CG  TYR B 241      34.482 -16.626  68.241  1.00 23.95           C  
+ATOM   3670  CD1 TYR B 241      35.810 -16.443  68.627  1.00 23.18           C  
+ATOM   3671  CD2 TYR B 241      34.091 -16.159  66.980  1.00 26.16           C  
+ATOM   3672  CE1 TYR B 241      36.728 -15.814  67.785  1.00 24.39           C  
+ATOM   3673  CE2 TYR B 241      35.006 -15.527  66.124  1.00 25.36           C  
+ATOM   3674  CZ  TYR B 241      36.321 -15.359  66.535  1.00 25.95           C  
+ATOM   3675  OH  TYR B 241      37.233 -14.743  65.704  1.00 26.48           O  
+ATOM   3676  N   ILE B 242      31.219 -15.481  71.118  1.00 21.52           N  
+ATOM   3677  CA  ILE B 242      30.210 -14.429  71.078  1.00 19.87           C  
+ATOM   3678  C   ILE B 242      30.569 -13.350  72.116  1.00 20.09           C  
+ATOM   3679  O   ILE B 242      30.525 -13.587  73.323  1.00 21.14           O  
+ATOM   3680  CB  ILE B 242      28.825 -15.047  71.332  1.00 17.59           C  
+ATOM   3681  CG1 ILE B 242      28.603 -16.172  70.305  1.00 13.57           C  
+ATOM   3682  CG2 ILE B 242      27.730 -13.986  71.223  1.00 16.06           C  
+ATOM   3683  CD1 ILE B 242      27.196 -16.758  70.294  1.00 13.12           C  
+ATOM   3684  N   VAL B 243      30.937 -12.169  71.624  1.00 18.87           N  
+ATOM   3685  CA  VAL B 243      31.367 -11.067  72.474  1.00 18.00           C  
+ATOM   3686  C   VAL B 243      30.664  -9.732  72.221  1.00 18.88           C  
+ATOM   3687  O   VAL B 243      30.522  -9.304  71.080  1.00 21.17           O  
+ATOM   3688  CB  VAL B 243      32.886 -10.834  72.300  1.00 15.97           C  
+ATOM   3689  CG1 VAL B 243      33.367  -9.725  73.215  1.00 13.64           C  
+ATOM   3690  CG2 VAL B 243      33.635 -12.121  72.554  1.00 14.31           C  
+ATOM   3691  N   ALA B 244      30.250  -9.075  73.301  1.00 16.24           N  
+ATOM   3692  CA  ALA B 244      29.599  -7.768  73.241  1.00 15.18           C  
+ATOM   3693  C   ALA B 244      28.338  -7.684  72.381  1.00 14.63           C  
+ATOM   3694  O   ALA B 244      28.024  -6.633  71.820  1.00 15.18           O  
+ATOM   3695  CB  ALA B 244      30.614  -6.710  72.791  1.00 10.85           C  
+ATOM   3696  N   GLN B 245      27.587  -8.769  72.301  1.00 13.92           N  
+ATOM   3697  CA  GLN B 245      26.379  -8.743  71.492  1.00 14.43           C  
+ATOM   3698  C   GLN B 245      25.104  -8.605  72.306  1.00 15.84           C  
+ATOM   3699  O   GLN B 245      25.064  -8.926  73.487  1.00 18.49           O  
+ATOM   3700  CB  GLN B 245      26.271 -10.019  70.651  1.00 12.12           C  
+ATOM   3701  CG  GLN B 245      27.471 -10.293  69.750  1.00 16.91           C  
+ATOM   3702  CD  GLN B 245      27.778  -9.131  68.832  1.00 17.13           C  
+ATOM   3703  OE1 GLN B 245      26.891  -8.621  68.140  1.00 20.22           O  
+ATOM   3704  NE2 GLN B 245      29.034  -8.701  68.820  1.00 14.81           N  
+ATOM   3705  N   THR B 246      24.060  -8.117  71.653  1.00 14.87           N  
+ATOM   3706  CA  THR B 246      22.755  -8.001  72.265  1.00 15.33           C  
+ATOM   3707  C   THR B 246      21.861  -8.756  71.292  1.00 16.60           C  
+ATOM   3708  O   THR B 246      21.657  -8.320  70.157  1.00 16.93           O  
+ATOM   3709  CB  THR B 246      22.290  -6.549  72.365  1.00 15.11           C  
+ATOM   3710  OG1 THR B 246      23.169  -5.834  73.238  1.00 16.56           O  
+ATOM   3711  CG2 THR B 246      20.870  -6.483  72.906  1.00 13.13           C  
+ATOM   3712  N   TYR B 247      21.359  -9.904  71.729  1.00 15.98           N  
+ATOM   3713  CA  TYR B 247      20.502 -10.731  70.893  1.00 16.75           C  
+ATOM   3714  C   TYR B 247      19.027 -10.506  71.203  1.00 18.07           C  
+ATOM   3715  O   TYR B 247      18.593 -10.662  72.345  1.00 19.74           O  
+ATOM   3716  CB  TYR B 247      20.842 -12.210  71.094  1.00 13.41           C  
+ATOM   3717  CG  TYR B 247      22.152 -12.662  70.480  1.00 11.49           C  
+ATOM   3718  CD1 TYR B 247      22.651 -13.936  70.738  1.00 12.03           C  
+ATOM   3719  CD2 TYR B 247      22.871 -11.839  69.609  1.00 13.13           C  
+ATOM   3720  CE1 TYR B 247      23.828 -14.391  70.149  1.00 12.61           C  
+ATOM   3721  CE2 TYR B 247      24.059 -12.287  69.002  1.00 12.16           C  
+ATOM   3722  CZ  TYR B 247      24.524 -13.567  69.279  1.00 14.83           C  
+ATOM   3723  OH  TYR B 247      25.667 -14.046  68.674  1.00 17.52           O  
+ATOM   3724  N   ASN B 248      18.258 -10.140  70.181  1.00 18.83           N  
+ATOM   3725  CA  ASN B 248      16.830  -9.916  70.351  1.00 18.71           C  
+ATOM   3726  C   ASN B 248      16.080 -11.240  70.271  1.00 19.23           C  
+ATOM   3727  O   ASN B 248      16.264 -12.005  69.326  1.00 21.09           O  
+ATOM   3728  CB  ASN B 248      16.284  -8.991  69.258  1.00 19.85           C  
+ATOM   3729  CG  ASN B 248      16.881  -7.594  69.304  1.00 23.28           C  
+ATOM   3730  OD1 ASN B 248      17.669  -7.259  70.189  1.00 25.29           O  
+ATOM   3731  ND2 ASN B 248      16.502  -6.767  68.337  1.00 24.75           N  
+ATOM   3732  N   VAL B 249      15.253 -11.514  71.276  1.00 18.13           N  
+ATOM   3733  CA  VAL B 249      14.418 -12.715  71.317  1.00 16.63           C  
+ATOM   3734  C   VAL B 249      13.047 -12.100  71.580  1.00 18.82           C  
+ATOM   3735  O   VAL B 249      12.550 -12.098  72.709  1.00 20.96           O  
+ATOM   3736  CB  VAL B 249      14.816 -13.649  72.480  1.00 14.50           C  
+ATOM   3737  CG1 VAL B 249      13.929 -14.879  72.492  1.00 13.76           C  
+ATOM   3738  CG2 VAL B 249      16.271 -14.062  72.340  1.00 10.65           C  
+ATOM   3739  N   ASP B 250      12.448 -11.572  70.518  1.00 17.80           N  
+ATOM   3740  CA  ASP B 250      11.185 -10.858  70.613  1.00 17.75           C  
+ATOM   3741  C   ASP B 250      10.095 -11.260  69.622  1.00 18.08           C  
+ATOM   3742  O   ASP B 250       9.141 -10.511  69.420  1.00 16.16           O  
+ATOM   3743  CB  ASP B 250      11.482  -9.373  70.426  1.00 17.93           C  
+ATOM   3744  CG  ASP B 250      12.183  -9.089  69.092  1.00 18.76           C  
+ATOM   3745  OD1 ASP B 250      12.701  -7.966  68.912  1.00 16.59           O  
+ATOM   3746  OD2 ASP B 250      12.212  -9.993  68.222  1.00 13.07           O  
+ATOM   3747  N   GLY B 251      10.223 -12.422  68.997  1.00 18.98           N  
+ATOM   3748  CA  GLY B 251       9.206 -12.814  68.037  1.00 20.23           C  
+ATOM   3749  C   GLY B 251       9.133 -11.884  66.826  1.00 21.79           C  
+ATOM   3750  O   GLY B 251       8.109 -11.822  66.144  1.00 23.86           O  
+ATOM   3751  N   GLY B 252      10.209 -11.149  66.560  1.00 21.43           N  
+ATOM   3752  CA  GLY B 252      10.226 -10.255  65.416  1.00 21.54           C  
+ATOM   3753  C   GLY B 252       9.843  -8.809  65.670  1.00 23.84           C  
+ATOM   3754  O   GLY B 252       9.842  -7.999  64.744  1.00 23.16           O  
+ATOM   3755  N   ASN B 253       9.524  -8.464  66.914  1.00 26.13           N  
+ATOM   3756  CA  ASN B 253       9.131  -7.091  67.224  1.00 26.72           C  
+ATOM   3757  C   ASN B 253      10.157  -6.064  66.767  1.00 25.25           C  
+ATOM   3758  O   ASN B 253       9.800  -4.957  66.372  1.00 22.22           O  
+ATOM   3759  CB  ASN B 253       8.862  -6.935  68.716  1.00 30.08           C  
+ATOM   3760  CG  ASN B 253       7.473  -6.409  68.988  1.00 33.97           C  
+ATOM   3761  OD1 ASN B 253       6.514  -6.778  68.300  1.00 34.72           O  
+ATOM   3762  ND2 ASN B 253       7.348  -5.551  69.997  1.00 34.75           N  
+ATOM   3763  N   TRP B 254      11.432  -6.429  66.826  1.00 24.84           N  
+ATOM   3764  CA  TRP B 254      12.490  -5.532  66.379  1.00 25.04           C  
+ATOM   3765  C   TRP B 254      13.578  -6.362  65.719  1.00 25.15           C  
+ATOM   3766  O   TRP B 254      13.864  -7.482  66.152  1.00 24.91           O  
+ATOM   3767  CB  TRP B 254      13.068  -4.716  67.542  1.00 22.70           C  
+ATOM   3768  CG  TRP B 254      13.872  -3.548  67.057  1.00 20.34           C  
+ATOM   3769  CD1 TRP B 254      15.229  -3.468  66.959  1.00 22.21           C  
+ATOM   3770  CD2 TRP B 254      13.358  -2.320  66.527  1.00 19.87           C  
+ATOM   3771  NE1 TRP B 254      15.597  -2.263  66.396  1.00 21.06           N  
+ATOM   3772  CE2 TRP B 254      14.465  -1.542  66.122  1.00 21.41           C  
+ATOM   3773  CE3 TRP B 254      12.067  -1.802  66.350  1.00 20.88           C  
+ATOM   3774  CZ2 TRP B 254      14.320  -0.270  65.550  1.00 22.97           C  
+ATOM   3775  CZ3 TRP B 254      11.922  -0.534  65.779  1.00 19.60           C  
+ATOM   3776  CH2 TRP B 254      13.042   0.213  65.387  1.00 22.11           C  
+ATOM   3777  N   MET B 255      14.186  -5.809  64.673  1.00 25.64           N  
+ATOM   3778  CA  MET B 255      15.212  -6.529  63.930  1.00 25.91           C  
+ATOM   3779  C   MET B 255      16.598  -5.911  64.041  1.00 24.50           C  
+ATOM   3780  O   MET B 255      16.786  -4.723  63.784  1.00 24.96           O  
+ATOM   3781  CB  MET B 255      14.784  -6.625  62.466  1.00 26.73           C  
+ATOM   3782  CG  MET B 255      13.402  -7.240  62.301  1.00 28.57           C  
+ATOM   3783  SD  MET B 255      12.681  -6.986  60.664  1.00 34.13           S  
+ATOM   3784  CE  MET B 255      12.256  -5.258  60.755  1.00 30.06           C  
+ATOM   3785  N   SER B 256      17.566  -6.734  64.432  1.00 23.90           N  
+ATOM   3786  CA  SER B 256      18.942  -6.278  64.584  1.00 23.46           C  
+ATOM   3787  C   SER B 256      19.884  -7.335  64.032  1.00 23.50           C  
+ATOM   3788  O   SER B 256      19.390  -8.439  63.723  1.00 25.09           O  
+ATOM   3789  CB  SER B 256      19.253  -6.025  66.064  1.00 22.10           C  
+ATOM   3790  OG  SER B 256      18.279  -5.173  66.635  1.00 18.70           O  
+ATOM   3791  OXT SER B 256      21.095  -7.051  63.923  1.00 22.97           O  
+TER    3792      SER B 256                                                      
+END                                                                             
diff --git a/examples/demos/data/sh2.aln b/examples/demos/data/sh2.aln
new file mode 100644
index 0000000000000000000000000000000000000000..7a18486a077f360b5522ed8b9c65523a716f9277
--- /dev/null
+++ b/examples/demos/data/sh2.aln
@@ -0,0 +1,210 @@
+CLUSTAL 2.0.12 multiple sequence alignment
+
+
+SH2                         -------------------------KP-HPWFFGKIPRAKAEEMLSKQR- 23
+UniRef90_UPI0000EB201F      KAELNGKDGFIPKN-------YIEMKP-HPWFFGKIPRAKAEEMLSKQR- 45
+UniRef90_P62993             KAELNGKDGFIPKN-------YIEMKP-HPWFFGKIPRAKAEEMLSKQR- 78
+UniRef90_P87379             KAELNGKDGFIPKN-------YIEMKA-HPWFFGKIPRAKAEEMLGKQR- 78
+UniRef90_UPI00016E653C      KAELRGKDGFIPKN-------YIEMKA-HPWFYGKIPRAKAEEILNKQR- 78
+UniRef90_UPI00016E653B      KAELRGKDGFIPKN-------YIEMKA-HPWFYGKIPRAKAEEILNKQR- 78
+UniRef90_Q4T656             DQALS-FASLLPVS-------FSAC---CRWFYGKIPRAKAEEILNKQR- 75
+UniRef90_UPI0001555716      KAELNGKDGFIPKN-------YIEMKP-HLWFFGKIPRAYAEEMLGKQL- 388
+UniRef90_UPI000180AF26      KAEQDGKEGLVPMN-------YIQMKP-CEWFARNMTRANAELRL-KNA- 52
+UniRef90_UPI000180AF37      KAEQDGKEGLVPMN-------YIEIKE-CEWFARNMTRANAELRL-KNT- 77
+UniRef90_A8XPY6             KAELDGTEGFIPSN-------YIRMGD-CSWYLGKITRNDAEVLLKKSNV 79
+UniRef90_P29355             KAELDGNEGFIPSN-------YIRMTE-CNWYLGKITRNDAEVLLKKPTV 79
+UniRef90_UPI000186E6C5      RAELDSKEGLIPSN-------YIEMKN-HDWYYGRITRADAEKLLMNK-- 77
+UniRef90_Q08012             RAELDGKEGLIPSN-------YIEMKN-HDWYYGRITRADAEKLLSNK-- 77
+UniRef90_B7P0R2             RAELDSKEGLIPSN-------YIEMKK-HDWYYGRITRADAEKLLSNK-- 77
+UniRef90_D3PIQ8             RAESGGKEGLIPSN-------YIDMKP-HDWYYSRMTRATAEKLLSNK-- 77
+UniRef90_C4WWT7             RAEFEGKEGLIPSN-------YIEMKN-HDWYYGKITRADAEKLLDQQ-- 77
+UniRef90_UPI0000586DB6      -------------------------------------RDGAEELLKND-- 40
+UniRef90_UPI0001CBA623      KAELDGREGFIPKN-------YITMRP-HDWFHGKISRAKAEELLQLQP- 78
+UniRef90_UPI0001CBA624      NAELDGREGLIPKN-------YIEMKP-HEWFHGKISREKAEELLQLQS- 77
+UniRef90_UPI000192619C      KAEQNGKEGFVPKN-------YIQMKP-HSWYYGKIRRSEAEQLLLQEP- 52
+UniRef90_UPI0000521DDC      RAEIDGRMGLVPKN-------YIELKA-HDWYHGKISRVKAEQSLNKPHY 79
+UniRef90_C1LZF7             LAEQEGRTGLIPCN-------YITMRP-HPWYIRHCSRMEAEERLQEIDQ 79
+UniRef90_UPI0000E478D2      LAHQGAKQGLVPEN-------YLKIEKSHPWYVGKISRKVAEEYLMSMP- 80
+UniRef90_UPI0000E49A1C      ----------MGPK-------HTYPEIAMAWFFPTITRKNAELLLMQE-- 31
+UniRef90_A8E5T1             KAELFGREGYIPKN-------YIKVKP-HPWYAGRISRQVAEEILLKRNF 79
+UniRef90_C1C3T6             KAELKGQEGYIPKN-------YIKVKP-HPWYAGRISRQVAEEILLKKRF 79
+UniRef90_Q13588             KAELRGVEGFIPKN-------YIRVKP-HPWYSGRISRQLAEEILMKRNH 79
+UniRef90_UPI0001C606E3      KAELRGAEGFVPKN-------YIHIKP-HPWYSGRISRQLAEEILMKRNQ 79
+UniRef90_Q9CX99             KAELRGAEGFVPKN-------YIRVKP-HPWYSGRISRQLAEETLMKRNH 79
+UniRef90_UPI0000DA3575      GVGLKPIEGMRPTNRTXRIPADIVPSP-HRWYSGRISRQLAEETLMKRNH 86
+UniRef90_UPI0000D9440A      KAELRGAEGFIPKN-------YIQVKP-HPWFAGRISRQFAEEILLRRNH 79
+UniRef90_UPI000155C0E1      RTSLLGGESFFYKN-------IQKLSP-SPWYAGRISRQLAEEVLLKRNH 79
+UniRef90_UPI0000E80FCB      KAELYGCEGFVPKN-------YIKVKP-HPWYAGRISRHVAEELLLKRRY 79
+UniRef90_UPI00016E4BE7      TAELHNRKGFVPKN-------YINLRP-HAWFAGRISRSVAESRLRQRE- 78
+UniRef90_Q503S8             TAEFVNRKGYVPKN-------YISLRP-HAWFAGRISRHVAENRLHQRD- 78
+UniRef90_Q4V9Q1             TAELLGRRGYVPKN-------YINVRP-HTWFVGGISRQAAENRLRPLE- 78
+UniRef90_UPI00017B202F      TAEIQGKRGYIPQN-------YISLLP-YPWFVGRVSRLEAEKRLRWQD- 78
+UniRef90_UPI0000E25B42      KAELGSQEGYVPKN-------FIDIQF-PEWFHEGLSRHQAENLLMGKE- 149
+UniRef90_O75791             KAELGSQEGYVPKN-------FIDIQF-PKWFHEGLSRHQAENLLMGKE- 76
+UniRef90_B7Z8F8             RHKLNP---FSSK----------------RWFHEGLSRHQAENLLMGKE- 50
+UniRef90_UPI00005BC6B6      KAELGSQEGYVPKN-------FIEIEF-PEWFHEGLSRHQAESLLMGKE- 76
+UniRef90_O89100             KAELGSQEGYVPKN-------FIDIEF-PEWFHEGLSRHQAENLLMGKD- 76
+UniRef90_UPI0000EDE7DF      KAELKSHEGYVPKN-------FIDIHI-PGWFHEGISRHEAESLLMGKE- 76
+UniRef90_UPI0000F2E19C      KAELGSQEGYVPKN-------FIDIQF-PSWFHEDISRHDAESLLMGKD- 241
+UniRef90_UPI0000E7F8B9      KAELRSQEGYVPKN-------FIDFHV-PPWFDEKISRHEAESILMNKG- 76
+UniRef90_UPI0000ECD2B7      KAELRSQEGYVPKN-------FIDFHV-PPWFDEKISRHEAESILMNKG- 76
+UniRef90_UPI000194E163      KAELRSHEGYVPKN-------FIDFHV-PHWFDEKISRHEAENLLMSKG- 91
+UniRef90_B5X487             KAELHGQEGFVPQN-------YIERQT-PSWFKETASRSSAEELLMSRE- 76
+UniRef90_Q567F1             KAELHGHEGYVPKN-------YVDRQI-PSWFKESASRGSAEETLMSRE- 76
+                                                                              
+
+SH2                         -------HDGAFLIRESESA--PGDFSL----SVKFGNDVQHFKVLR--D 58
+UniRef90_UPI0000EB201F      -------HDGAFLIRESESA--PGDFSL----SVKFGNDVQHFKVLR--D 80
+UniRef90_P62993             -------HDGAFLIRESESA--PGDFSL----SVKFGNDVQHFKVLR--D 113
+UniRef90_P87379             -------HDGAFLIRESESA--PGDFSL----SVKFGNDVQHFKVLR--D 113
+UniRef90_UPI00016E653C      -------RDGAFLIRESESA--PGDFSL----SVKYGNDVQHFKVLR--D 113
+UniRef90_UPI00016E653B      -------RDGAFLIRESESA--PGDFSL----SVKYGNDVQHFKVLR--D 113
+UniRef90_Q4T656             -------RDGAFLIRESESA--PGDFSL----SVKYGNDVQHFKVLR--D 110
+UniRef90_UPI0001555716      -------NYGSFFILXXXXP--PGDALTGARSTPRFGNDVQHFKVLR--D 427
+UniRef90_UPI000180AF26      -------LDESFLVRESEST--PGDFSL----SVKTNSGVQHFKVLR--D 87
+UniRef90_UPI000180AF37      -------LDGSFLVRESEST--PGEFSV----SVKTNSGVQHFKVLR--D 112
+UniRef90_A8XPY6             -------RDGHFLVRQCESS--PGEFSI----SVRFQDSVQHFKVLR--D 114
+UniRef90_P29355             -------RDGHFLVRQCESS--PGEFSI----SVRFQDSVQHFKVLR--D 114
+UniRef90_UPI000186E6C5      -------HEGAFLIRVSESS--PGDFSL----SVKCSDGVQHFKVLR--D 112
+UniRef90_Q08012             -------HEGAFLIRISESS--PGDFSL----SVKCPDGVQHFKVLR--D 112
+UniRef90_B7P0R2             -------HEGAFLIRVSESS--PGDFSL----SVRCGDGVQHFKVLR--D 112
+UniRef90_D3PIQ8             -------HEGAFVIRVSESS--PGDFSL----SVKCGDGVQHFKVLR--D 112
+UniRef90_C4WWT7             -------PEGCFLVRISESS--PGDFSL----SVKCGDGVQHFKVLR--D 112
+UniRef90_UPI0000586DB6      -------GDGAFLIRESEGT--PGDYSL----SVKFVDGVQHFKVLR--D 75
+UniRef90_UPI0001CBA623      -------HDGAFLIRESESA--PGDFSL----SVKFKDEVQHFKVLR--D 113
+UniRef90_UPI0001CBA624      -------YDGAFLIRESEST--PGDFSL----SVKFKDGVQNFKILR--D 112
+UniRef90_UPI000192619C      -------HDGAYLIRDSEST--AGDFSL----SVKFNNQVQHFKVLR--D 87
+UniRef90_UPI0000521DDC      -------PDGAFLIRESESS--PGDFSL----SVKYGSAVQHFKVLR--D 114
+UniRef90_C1LZF7             ETAQHLQPDGAFILRQSEAD--GKGFSL----SVKQGCEVLHFKVLQ--D 121
+UniRef90_UPI0000E478D2      -------SDGAFMIRDSESNPDSGNFSL----SVKFRDQVQHFKILT--D 117
+UniRef90_UPI0000E49A1C      -------RNGAFLVRRSESS--EGLYSL----SVKYNESVQHFRILQ--D 66
+UniRef90_A8E5T1             --------VGAFLIRDSESS--PGDFSI----SVNYGHHVQHFKVLRDTE 115
+UniRef90_C1C3T6             --------LGAFLIRDSESS--PGEFSI----SVNYGHHVQHFKVLR--E 113
+UniRef90_Q13588             --------LGAFLIRESESS--PGEFSV----SVNYGDQVQHFKVLR--E 113
+UniRef90_UPI0001C606E3      --------LGAFLIRESESS--PGEFSV----SVNYGDQVQHFKVLR--E 113
+UniRef90_Q9CX99             --------LGAFLIRESESS--PGEFSV----SVNYGDQVQHFKVLR--E 113
+UniRef90_UPI0000DA3575      --------LGAFLIRESESS--PGEFSV----SVNYGDQVQHFKVLR--E 120
+UniRef90_UPI0000D9440A      --------LGAFLIRESESS--PGEFSV----SVNYGNQVQHFKVLR--E 113
+UniRef90_UPI000155C0E1      --------LGAFLIRESESS--PGEFSV----SVNYGDQVQHFKVLR--E 113
+UniRef90_UPI0000E80FCB      --------VGAFLIRESESA--PGEFSI----SVNYGQHVQHFKVLR--E 113
+UniRef90_UPI00016E4BE7      --------CGAFLVRESESA--PGEFSM----SVSYGDHVQHFKVLQD-- 112
+UniRef90_Q503S8             --------CGSFLVRESESA--PGEFSM----SVSYGDHVQHFKVLKD-- 112
+UniRef90_Q4V9Q1             --------CGAFLIRESEST--PGEFSV----SVSYGDHVQHFKVLKD-- 112
+UniRef90_UPI00017B202F      --------PGVFLVRESESA--PGEFSV----SVSYGNRVEHFRVLE--- 111
+UniRef90_UPI0000E25B42      --------VGFFIIRASQSS--PGDFSI----SVRHEDDVQHFKVMR--D 183
+UniRef90_O75791             --------VGFFIIRASQSS--PGDFSI----SVRHEDDVQHFKVMR--D 110
+UniRef90_B7Z8F8             --------VGFFIIRASQSS--PGDFSI----SVRHEDDVQHFKVMR--D 84
+UniRef90_UPI00005BC6B6      --------LGCFIIRASQSS--PGDFSI----SVRHEDDVQHFKVMR--D 110
+UniRef90_O89100             --------IGFFIIRASQSS--PGDFSI----SVRHEDDVQHFKVMR--D 110
+UniRef90_UPI0000EDE7DF      --------VGSFIIRASQSS--PGDFSI----SVRHEDDVQHFKVMR--D 110
+UniRef90_UPI0000F2E19C      --------VGSFIIRASQSS--PGDFSI----SVRHEDDVQHFKVMR--D 275
+UniRef90_UPI0000E7F8B9      --------VGSFIVRASQNS--HGDFSI----SVRHEDDVQHFKVMR--D 110
+UniRef90_UPI0000ECD2B7      --------VGSFIVRASQNS--HGDFSI----SVRHEDDVQHFKVMR--D 110
+UniRef90_UPI000194E163      --------VGCFVVRASQNS--HGDFSI----SVRHEDDVQHFKVMR--D 125
+UniRef90_B5X487             --------VGGFLIRGSQSS--PGEFSI----SVRHEFDVQHFKVMK--D 110
+UniRef90_Q567F1             --------VGAFLIRGSQSS--PGDFSI----SVRHDYDVQHFKVMK--D 110
+                                                                   * :*:::    
+
+SH2                         GAGKYFLWVVKFNSLNELVDYHRSTSVSR---------------NQQIFL 93
+UniRef90_UPI0000EB201F      GAGKYFLWVVKFNSLNELVDYHRSTSVSR---------------NQQIFL 115
+UniRef90_P62993             GAGKYFLWVVKFNSLNELVDYHRSTSVSR---------------NQQIFL 148
+UniRef90_P87379             GAGKYFLWVVKFNSLNELVDYHRSTSVSR---------------NQQIFL 148
+UniRef90_UPI00016E653C      GAGKYFLWVVKFNSLNELVEYHRTTSVSR---------------NQQIFL 148
+UniRef90_UPI00016E653B      GAGKYFLWVVKFNSLNELVEYHRTTSVSR---------------NQQIFL 148
+UniRef90_Q4T656             GAGKYFLWVVKFTSLNELVEYHRTTSVSR---------------NQQIFL 145
+UniRef90_UPI0001555716      GAGKYFLWVVKFNSLNELVDYHRSTSVSR---------------NQQIFL 462
+UniRef90_UPI000180AF26      GAGKYFIWLVKFKSLNQLVDYHRTSSVSR---------------SEQILL 122
+UniRef90_UPI000180AF37      GAGKYFIWVVKFSSLNELVVYHRVMTVSG---------------SERIFL 147
+UniRef90_A8XPY6             QNGKYYLWAVKFNSLNELVAYHRTASVSR---------------THTILL 149
+UniRef90_P29355             QNGKYYLWAVKFNSLNELVAYHRTASVSR---------------THTILL 149
+UniRef90_UPI000186E6C5      AQGKFFLWVVKFSSLNELVEYHRTSSVSR---------------SQHVKL 147
+UniRef90_Q08012             AQSKFFLWVVKFNSLNELVEYHRTASVSR---------------SQDVKL 147
+UniRef90_B7P0R2             TLGKFFLWVVKFASLNELVEYHRSASVSR---------------SQDIKL 147
+UniRef90_D3PIQ8             GQGKFFLWVVKFNSLNELVEYHHSASVSR---------------SQDIKL 147
+UniRef90_C4WWT7             AQAKFFLWVVKFDSLNELVDYHRESSVSR---------------SQDVRL 147
+UniRef90_UPI0000586DB6      GAGKYFLWVVKFNSLNQLVEYHRTSSVSR---------------SQTIYL 110
+UniRef90_UPI0001CBA623      GAGKYFLWVVKFNSLNELVEYHRSSSVSR---------------TQTIYL 148
+UniRef90_UPI0001CBA624      GAGKYFLWVVKFNSLNQLVDYHRTSSVSR---------------SEQIFL 147
+UniRef90_UPI000192619C      GAGKYFLWVVKFNSLNQLVEYHRAASVSR---------------SQTIYL 122
+UniRef90_UPI0000521DDC      GAGKYFLWVVKFSSLNELIKYHREQSISR---------------TQQIML 149
+UniRef90_C1LZF7             EAGKYFFWLSKFDSINQLIDHHRKTSISR---------------NRLLTL 156
+UniRef90_UPI0000E478D2      LAGKYFLWVVKFTSINDLVDYHKDNSVSRTQEIVLNEPCVPIEDANQRPQ 167
+UniRef90_UPI0000E49A1C      TAGKFHLWIVKFPSLDALVDYYRTTSVTR---------------ENQVST 101
+UniRef90_A8E5T1             SNGKYYLWEAKFNSLNELVDYYRRHSIAK---------------FHEVFL 150
+UniRef90_C1C3T6             KSGTYFLWETKFGSLNELVEFYRSSSIAK---------------THPVLL 148
+UniRef90_Q13588             ASGKYFLWEEKFNSLNELVDFYRTTTIAK---------------KRQIFL 148
+UniRef90_UPI0001C606E3      ASGKYFLWEEKFNSLNELVDFYRTTTIAK---------------KRQIFL 148
+UniRef90_Q9CX99             ASGKYFLWEEKFNSLNELVDFYRTTTIAK---------------RRQIFL 148
+UniRef90_UPI0000DA3575      ASGKYFLWEEKFNSLNELVDFYRTTTIAK---------------RRQIFL 155
+UniRef90_UPI0000D9440A      NMGKYFLWEEKFNSLNELVDFYRTTTIAK---------------KKQIFL 148
+UniRef90_UPI000155C0E1      RIGKYYLWEEKFNSLNELVDFYRTTTIAK---------------KKQIFL 148
+UniRef90_UPI0000E80FCB      RNGKYFLWEEKFNSLNELVDFYRTTTIAK---------------KQQIFL 148
+UniRef90_UPI00016E4BE7      RGGQYYVWDELFPSLNELVEFYHCNSIAR---------------ERTVLL 147
+UniRef90_Q503S8             REGYYFVWEEIFPSLNQLVDFYKTNSIAK---------------ERTVFL 147
+UniRef90_Q4V9Q1             GLGQYFIWDEVFSSLNQLVDFYRINSIAK---------------ERTVFL 147
+UniRef90_UPI00017B202F      GGGQYCIWEESFCSLNRLVDFYRTHSIAM---------------DKVVCL 146
+UniRef90_UPI0000E25B42      NKGNYFLWTEKFPSLNKLVDYYRTNSISR---------------QKQIFL 218
+UniRef90_O75791             NKGNYFLWTEKFPSLNKLVDYYRTNSISR---------------QKQIFL 145
+UniRef90_B7Z8F8             NKGNYFLWTEKFPSLNKLVDYYRTNSISR---------------QKQIFL 119
+UniRef90_UPI00005BC6B6      NKGNYFLWTEKFPSLNKLVDYYRKNSISK---------------QKQIFL 145
+UniRef90_O89100             TKGNYFLWTEKFPSLNKLVDYYRTTSISK---------------QKQVFL 145
+UniRef90_UPI0000EDE7DF      AKGHYFLWTEKFQSLNRLVEFYKTSSISR---------------QKQIFL 145
+UniRef90_UPI0000F2E19C      AKGHYFLWTEKFQSLNQLVNFYRTSSISK---------------QKQIYL 310
+UniRef90_UPI0000E7F8B9      SKGNYYLWTEKFYSLNKLVDYYRTSTISR---------------QKQILL 145
+UniRef90_UPI0000ECD2B7      SKGNYYLWTEKFYSLNKLVDYYRTSTISR---------------QKQILL 145
+UniRef90_UPI000194E163      SKGSYYLWTEKFHSLNKLVDYYKTSSISR---------------QKQIFL 160
+UniRef90_B5X487             SKGHYFLWSEKFTSLNKLVDFYKNTSISK---------------QRDIYL 145
+UniRef90_Q567F1             KSGHYYLWTEKFTSLNKLVDFYKTTSISK---------------QKEIFL 145
+                              . : .*   * *:: *: .::  :::                 .    
+
+SH2                         RDIEQVP------------------------------------------- 100
+UniRef90_UPI0000EB201F      RDIEQVPQQNSIFSLCQR----TSLTLCSIVSLEASEEENPVVREWSPHS 161
+UniRef90_P62993             RDIEQVP------------------------------------------- 155
+UniRef90_P87379             RDIEQVPQVHGGDRATS--------------------------------- 165
+UniRef90_UPI00016E653C      REIEQ--------------------------------------------- 153
+UniRef90_UPI00016E653B      REIEQVTQVNVGTHYIN--------------------------------- 165
+UniRef90_Q4T656             RDIEQVTQV----------------------------------------- 154
+UniRef90_UPI0001555716      RDIEQMPQQKSPVCDRLS----FLFCAVNCRACSDGVFHG---------- 498
+UniRef90_UPI000180AF26      RHPIIS-------------------------------------------- 128
+UniRef90_UPI000180AF37      LHPIS--------------------------------------------- 152
+UniRef90_A8XPY6             ADMNV--------------------------------------------- 154
+UniRef90_P29355             SDMNV--------------------------------------------- 154
+UniRef90_UPI000186E6C5      RDMVP--------------------------------------------- 152
+UniRef90_Q08012             RDMIP--------------------------------------------- 152
+UniRef90_B7P0R2             RDMHP--------------------------------------------- 152
+UniRef90_D3PIQ8             KEIIC--------------------------------------------- 152
+UniRef90_C4WWT7             RDMPAATQNG---------------------------------------- 157
+UniRef90_UPI0000586DB6      KDRKS--------------------------------------------- 115
+UniRef90_UPI0001CBA623      LKMHV--------------------------------------------- 153
+UniRef90_UPI0001CBA624      KDKQ---------------------------------------------- 151
+UniRef90_UPI000192619C      KDMTN--------------------------------------------- 127
+UniRef90_UPI0000521DDC      VDLPV--------------------------------------------- 154
+UniRef90_C1LZF7             VDLVPSKRFPTN-------------------------------------- 168
+UniRef90_UPI0000E478D2      PAMQQSR------------------------------------------- 174
+UniRef90_UPI0000E49A1C      QSVEQWS------------------------------------------- 108
+UniRef90_A8E5T1             CDEEQ--------------------------------------------- 155
+UniRef90_C1C3T6             RDEEE--------------------------------------------- 153
+UniRef90_Q13588             RDEEP--------------------------------------------- 153
+UniRef90_UPI0001C606E3      RDEEP--------------------------------------------- 153
+UniRef90_Q9CX99             CDEQP--------------------------------------------- 153
+UniRef90_UPI0000DA3575      CDEQP--------------------------------------------- 160
+UniRef90_UPI0000D9440A      RDEEP--------------------------------------------- 153
+UniRef90_UPI000155C0E1      RDEEQ--------------------------------------------- 153
+UniRef90_UPI0000E80FCB      RDDEQ--------------------------------------------- 153
+UniRef90_UPI00016E4BE7      RDPEQ--------------------------------------------- 152
+UniRef90_Q503S8             RDLDH--------------------------------------------- 152
+UniRef90_Q4V9Q1             RDPEG--------------------------------------------- 152
+UniRef90_UPI00017B202F      RDPPS--------------------------------------------- 151
+UniRef90_UPI0000E25B42      RDRTREDQGHRGNSLDR---RSQGGPHLSGAVGEEIRPSMNRKLSDHPPT 265
+UniRef90_O75791             RDRTREDQGHRGNSLDR---RSQGGPHLSGAVGEEIRPSMNRKLSDHPPT 192
+UniRef90_B7Z8F8             RDRTREDQGHRGNSLDR---RSQGGPHLSGAVGEEIRPSMNRKLSDHPPT 166
+UniRef90_UPI00005BC6B6      RDRTREEQGQRGNSLDR---RSQGGHPLSGAVGEEIRPSMNRKPSDHP-L 191
+UniRef90_O89100             RDGTQ-DQGHRGNSLDR---RSQGGPHPSGTVGEEIRPSVNRKLSDHLPL 191
+UniRef90_UPI0000EDE7DF      RDGTREDQERRGGSLDR---RAQEGLGLGGACGEEIRVPMNRKMSDLHPP 192
+UniRef90_UPI0000F2E19C      RDGGREEQDRWGGSLER---RLQEGLHISGGVGEETRPSTNRKQSDHPPA 357
+UniRef90_UPI0000E7F8B9      RDDSREEKERRGGSLER---MSRDGLHVGGAAAEAHS-SMSKRYVDHP-- 189
+UniRef90_UPI0000ECD2B7      RDDSREEKERRGGSLER---MSRDGLHVGGAAAEAHS-SMSKRYVDHPVP 191
+UniRef90_UPI000194E163      RDNSQEEKERHGGSLER---IGREGFHMGGAAGEDHS-SISKRYVEYPIP 206
+UniRef90_B5X487             RDGSRDDQSPSTPQPLKRGSLPEERS-----YGAPTAATSHRRASDLP-- 188
+UniRef90_Q567F1             RDGSGDE--PRAPPPIK--SQPEVRPPPGGGYGSPQTSSQNRSTTDPT-- 189
+                                                                              
diff --git a/examples/demos/data/sh2.face b/examples/demos/data/sh2.face
new file mode 100644
index 0000000000000000000000000000000000000000..5b13977c39763b5ee1a524d004e177c41f031acb
--- /dev/null
+++ b/examples/demos/data/sh2.face
@@ -0,0 +1,47483 @@
+# MSMS solvent excluded surface faces for /tmp/tmpNakzL3/entity
+#faces  #sphere density probe_r
+  47480     832  5.00  1.50
+     1   3337      2  3      3
+     2   3337   3338  3      3
+  3337   3339   3338  3      3
+  3338   3339   3340  3      3
+  3339   3341   3340  3      3
+  3340   3341   3342  3      3
+  3341   3343   3342  3      3
+  3342   3343   3344  3      3
+  3343   3345   3344  3      3
+  3344   3345   3346  3      3
+  3345   3347   3346  3      3
+  3346   3347   3348  3      3
+  3347   3349   3348  3      3
+  3348   3349   3350  3      3
+  3349   3351   3350  3      3
+  3350   3351   3352  3      3
+  3351   3353   3352  3      3
+  3352   3353   3354  3      3
+  3353      5   3354  3      3
+  3354      5      4  3      3
+     5      8      6  3      5
+     6      8      7  3      5
+     8   3357   3355  3      7
+  3355   3357   3358  3      7
+  3355   3358   3356  3      7
+  3356   3358   3359  3      7
+  3356   3359      9  3      7
+     9   3359   3360  3      7
+  3357   3361   3358  3      7
+  3358   3361   3362  3      7
+  3358   3362   3359  3      7
+  3359   3362   3363  3      7
+  3359   3363   3360  3      7
+  3360   3363   3364  3      7
+  3361   3365   3362  3      7
+  3362   3365   3366  3      7
+  3362   3366   3363  3      7
+  3363   3366   3367  3      7
+  3363   3367   3364  3      7
+  3364   3367   3368  3      7
+  3365   3369   3366  3      7
+  3366   3369   3370  3      7
+  3366   3370   3367  3      7
+  3367   3370   3371  3      7
+  3367   3371   3368  3      7
+  3368   3371   3372  3      7
+  3369   3373   3370  3      7
+  3370   3373   3374  3      7
+  3370   3374   3371  3      7
+  3371   3374   3375  3      7
+  3371   3375   3372  3      7
+  3372   3375   3376  3      7
+  3373     11   3374  3      7
+  3374     11   3377  3      7
+  3374   3377   3375  3      7
+  3375   3377   3378  3      7
+  3375   3378   3376  3      7
+  3376   3378     10  3      7
+    11   3384   3379  3      9
+  3379   3384   3385  3      9
+  3379   3385   3380  3      9
+  3380   3385   3386  3      9
+  3380   3386   3381  3      9
+  3381   3386   3387  3      9
+  3381   3387   3382  3      9
+  3382   3387   3388  3      9
+  3382   3388   3383  3      9
+  3383   3388   3389  3      9
+  3383   3389     12  3      9
+    12   3389   3390  3      9
+  3384     14   3385  3      9
+  3385     14   3391  3      9
+  3385   3391   3386  3      9
+  3386   3391   3392  3      9
+  3386   3392   3387  3      9
+  3387   3392   3393  3      9
+  3387   3393   3388  3      9
+  3388   3393   3394  3      9
+  3388   3394   3389  3      9
+  3389   3394   3395  3      9
+  3389   3395   3390  3      9
+  3390   3395     13  3      9
+    14   3400   3396  3     11
+  3396   3400   3401  3     11
+  3396   3401   3397  3     11
+  3397   3401   3402  3     11
+  3397   3402   3398  3     11
+  3398   3402   3403  3     11
+  3398   3403   3399  3     11
+  3399   3403   3404  3     11
+  3399   3404     15  3     11
+    15   3404   3405  3     11
+  3400     17   3401  3     11
+  3401     17   3406  3     11
+  3401   3406   3402  3     11
+  3402   3406   3407  3     11
+  3402   3407   3403  3     11
+  3403   3407   3408  3     11
+  3403   3408   3404  3     11
+  3404   3408   3409  3     11
+  3404   3409   3405  3     11
+  3405   3409     16  3     11
+    17      1   3410  3     12
+  3410      1   3416  3     12
+  3410   3416   3411  3     12
+  3411   3416   3417  3     12
+  3411   3417   3412  3     12
+  3412   3417   3418  3     12
+  3412   3418   3413  3     12
+  3413   3418   3419  3     12
+  3413   3419   3414  3     12
+  3414   3419   3420  3     12
+  3414   3420   3415  3     12
+  3415   3420   3421  3     12
+  3415   3421     18  3     12
+    18   3421      3  3     12
+    18     20   3422  3     14
+  3422     20   3425  3     14
+  3422   3425   3423  3     14
+  3423   3425   3426  3     14
+  3423   3426   3424  3     14
+  3424   3426   3427  3     14
+  3424   3427     16  3     14
+    16   3427     19  3     14
+    20   3430   3428  3     16
+  3428   3430   3431  3     16
+  3428   3431   3429  3     16
+  3429   3431   3432  3     16
+  3429   3432     21  3     16
+    21   3432   3433  3     16
+  3430     23   3431  3     16
+  3431     23   3434  3     16
+  3431   3434   3432  3     16
+  3432   3434   3435  3     16
+  3432   3435   3433  3     16
+  3433   3435     22  3     16
+    23     26     24  3     18
+    24     26     25  3     18
+    26   3438   3436  3     20
+  3436   3438   3439  3     20
+  3436   3439   3437  3     20
+  3437   3439   3440  3     20
+  3437   3440     27  3     20
+    27   3440   3441  3     20
+  3438   3442   3439  3     20
+  3439   3442   3443  3     20
+  3439   3443   3440  3     20
+  3440   3443   3444  3     20
+  3440   3444   3441  3     20
+  3441   3444   3445  3     20
+  3442     29   3443  3     20
+  3443     29   3446  3     20
+  3443   3446   3444  3     20
+  3444   3446   3447  3     20
+  3444   3447   3445  3     20
+  3445   3447     28  3     20
+    29     32   3448  3     22
+  3448     32   3451  3     22
+  3448   3451   3449  3     22
+  3449   3451   3452  3     22
+  3449   3452   3450  3     22
+  3450   3452   3453  3     22
+  3450   3453     30  3     22
+    30   3453     31  3     22
+    32     35   3454  3     24
+  3454     35   3456  3     24
+  3454   3456   3455  3     24
+  3455   3456   3457  3     24
+  3455   3457     33  3     24
+    33   3457     34  3     24
+    35      3   3458  3     25
+  3458      3   3464  3     25
+  3458   3464   3459  3     25
+  3459   3464   3465  3     25
+  3459   3465   3460  3     25
+  3460   3465   3466  3     25
+  3460   3466   3461  3     25
+  3461   3466   3467  3     25
+  3461   3467   3462  3     25
+  3462   3467   3468  3     25
+  3462   3468   3463  3     25
+  3463   3468   3469  3     25
+  3463   3469     36  3     25
+    36   3469      2  3     25
+    36   3474   3470  3     27
+  3470   3474   3475  3     27
+  3470   3475   3471  3     27
+  3471   3475   3476  3     27
+  3471   3476   3472  3     27
+  3472   3476   3477  3     27
+  3472   3477   3473  3     27
+  3473   3477   3478  3     27
+  3473   3478     34  3     27
+    34   3478   3479  3     27
+  3474   3480   3475  3     27
+  3475   3480   3481  3     27
+  3475   3481   3476  3     27
+  3476   3481   3482  3     27
+  3476   3482   3477  3     27
+  3477   3482   3483  3     27
+  3477   3483   3478  3     27
+  3478   3483   3484  3     27
+  3478   3484   3479  3     27
+  3479   3484   3485  3     27
+  3480     38   3481  3     27
+  3481     38   3486  3     27
+  3481   3486   3482  3     27
+  3482   3486   3487  3     27
+  3482   3487   3483  3     27
+  3483   3487   3488  3     27
+  3483   3488   3484  3     27
+  3484   3488   3489  3     27
+  3484   3489   3485  3     27
+  3485   3489     37  3     27
+    38   3493   3490  3     29
+  3490   3493   3494  3     29
+  3490   3494   3491  3     29
+  3491   3494   3495  3     29
+  3491   3495   3492  3     29
+  3492   3495   3496  3     29
+  3492   3496     39  3     29
+    39   3496   3497  3     29
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+  3494   3499   3495  3     29
+  3495   3499   3500  3     29
+  3495   3500   3496  3     29
+  3496   3500   3501  3     29
+  3496   3501   3497  3     29
+  3497   3501   3502  3     29
+  3498   3503   3499  3     29
+  3499   3503   3504  3     29
+  3499   3504   3500  3     29
+  3500   3504   3505  3     29
+  3500   3505   3501  3     29
+  3501   3505   3506  3     29
+  3501   3506   3502  3     29
+  3502   3506   3507  3     29
+  3503     41   3504  3     29
+  3504     41   3508  3     29
+  3504   3508   3505  3     29
+  3505   3508   3509  3     29
+  3505   3509   3506  3     29
+  3506   3509   3510  3     29
+  3506   3510   3507  3     29
+  3507   3510     40  3     29
+    41      4   3511  3     30
+  3511      4   3512  3     30
+  3511   3512     42  3     30
+    42   3512      6  3     30
+    42     44   3513  3     32
+  3513     44   3515  3     32
+  3513   3515   3514  3     32
+  3514   3515   3516  3     32
+  3514   3516     40  3     32
+    40   3516     43  3     32
+    44     47   3517  3     34
+  3517     47   3520  3     34
+  3517   3520   3518  3     34
+  3518   3520   3521  3     34
+  3518   3521   3519  3     34
+  3519   3521   3522  3     34
+  3519   3522     45  3     34
+    45   3522     46  3     34
+    47     50   3523  3     36
+  3523     50   3527  3     36
+  3523   3527   3524  3     36
+  3524   3527   3528  3     36
+  3524   3528   3525  3     36
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+  3525   3529   3526  3     36
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+  3526   3530     48  3     36
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+    50      7   3531  3     37
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+  3531   3532     51  3     37
+    51   3532      9  3     37
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+    68     71   3625  3     52
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diff --git a/examples/demos/data/sh2.pdb b/examples/demos/data/sh2.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..e254cf039a75bdfc8a4cbde99216dde4a5418bbf
--- /dev/null
+++ b/examples/demos/data/sh2.pdb
@@ -0,0 +1,888 @@
+HELIX    1   1 PRO A   66  LYS A   76  1                                  11    
+HELIX    2   2 SER A  127  HIS A  135  1                                   9    
+SHEET    1   A 4 PHE A  83  GLU A  87  0                                        
+SHEET    2   A 4 PHE A  95  PHE A 101 -1  O  SER A  96   N  ARG A  86           
+SHEET    3   A 4 ASP A 104  ARG A 112 -1  O  PHE A 108   N  LEU A  97           
+SHEET    4   A 4 TYR A 118  PHE A 119 -1  O  PHE A 119   N  LEU A 111
+ATOM      1  N   MET A  55     -11.301  11.863  12.812  1.00 46.35           N  
+ATOM      2  CA  MET A  55     -10.174  12.241  13.713  1.00 45.84           C  
+ATOM      3  C   MET A  55      -9.595  11.051  14.465  1.00 44.35           C  
+ATOM      4  O   MET A  55     -10.219   9.989  14.526  1.00 46.54           O  
+ATOM      5  CB  MET A  55     -10.591  13.367  14.670  1.00 48.03           C  
+ATOM      6  CG  MET A  55     -11.911  13.150  15.404  1.00 49.20           C  
+ATOM      7  SD  MET A  55     -12.173  14.422  16.660  1.00 55.85           S  
+ATOM      8  CE  MET A  55     -10.955  13.907  17.875  1.00 52.51           C  
+ATOM      9  N   LYS A  56      -8.383  11.240  14.995  1.00 42.02           N  
+ATOM     10  CA  LYS A  56      -7.611  10.243  15.755  1.00 39.04           C  
+ATOM     11  C   LYS A  56      -7.093   9.042  14.960  1.00 35.73           C  
+ATOM     12  O   LYS A  56      -7.875   8.322  14.336  1.00 35.25           O  
+ATOM     13  CB  LYS A  56      -8.367   9.735  16.999  1.00 40.07           C  
+ATOM     14  CG  LYS A  56      -8.392  10.697  18.162  1.00 41.30           C  
+ATOM     15  CD  LYS A  56      -9.261  10.144  19.283  1.00 43.06           C  
+ATOM     16  CE  LYS A  56      -9.291  11.093  20.474  1.00 43.02           C  
+ATOM     17  NZ  LYS A  56      -7.941  11.318  21.057  1.00 42.52           N  
+ATOM     18  N   PRO A  57      -5.757   8.838  14.934  1.00 32.59           N  
+ATOM     19  CA  PRO A  57      -5.167   7.704  14.210  1.00 30.22           C  
+ATOM     20  C   PRO A  57      -5.475   6.389  14.924  1.00 28.03           C  
+ATOM     21  O   PRO A  57      -5.774   6.389  16.125  1.00 25.91           O  
+ATOM     22  CB  PRO A  57      -3.678   8.017  14.254  1.00 30.30           C  
+ATOM     23  CG  PRO A  57      -3.518   8.821  15.511  1.00 30.21           C  
+ATOM     24  CD  PRO A  57      -4.694   9.727  15.450  1.00 32.07           C  
+ATOM     25  N   HIS A  58      -5.434   5.288  14.176  1.00 26.73           N  
+ATOM     26  CA  HIS A  58      -5.705   3.960  14.726  1.00 26.95           C  
+ATOM     27  C   HIS A  58      -4.622   3.524  15.706  1.00 27.12           C  
+ATOM     28  O   HIS A  58      -3.426   3.545  15.366  1.00 27.18           O  
+ATOM     29  CB  HIS A  58      -5.849   2.928  13.607  1.00 26.98           C  
+ATOM     30  CG  HIS A  58      -7.149   3.014  12.872  1.00 27.32           C  
+ATOM     31  ND1 HIS A  58      -8.359   3.179  13.510  1.00 28.47           N  
+ATOM     32  CD2 HIS A  58      -7.428   2.948  11.552  1.00 26.86           C  
+ATOM     33  CE1 HIS A  58      -9.327   3.211  12.613  1.00 28.81           C  
+ATOM     34  NE2 HIS A  58      -8.789   3.073  11.416  1.00 28.59           N  
+ATOM     35  N   PRO A  59      -5.020   3.161  16.948  1.00 27.05           N  
+ATOM     36  CA  PRO A  59      -4.064   2.725  17.976  1.00 26.49           C  
+ATOM     37  C   PRO A  59      -3.515   1.307  17.792  1.00 25.98           C  
+ATOM     38  O   PRO A  59      -2.801   0.795  18.659  1.00 26.77           O  
+ATOM     39  CB  PRO A  59      -4.874   2.858  19.268  1.00 26.70           C  
+ATOM     40  CG  PRO A  59      -6.258   2.507  18.822  1.00 27.23           C  
+ATOM     41  CD  PRO A  59      -6.384   3.262  17.517  1.00 27.94           C  
+ATOM     42  N   TRP A  60      -3.807   0.705  16.641  1.00 23.73           N  
+ATOM     43  CA  TRP A  60      -3.371  -0.650  16.363  1.00 22.05           C  
+ATOM     44  C   TRP A  60      -2.311  -0.858  15.292  1.00 21.12           C  
+ATOM     45  O   TRP A  60      -1.814  -1.970  15.124  1.00 19.47           O  
+ATOM     46  CB  TRP A  60      -4.578  -1.549  16.094  1.00 20.73           C  
+ATOM     47  CG  TRP A  60      -5.636  -1.027  15.135  1.00 19.95           C  
+ATOM     48  CD1 TRP A  60      -6.839  -0.471  15.475  1.00 18.34           C  
+ATOM     49  CD2 TRP A  60      -5.634  -1.125  13.701  1.00 21.37           C  
+ATOM     50  NE1 TRP A  60      -7.590  -0.230  14.350  1.00 19.38           N  
+ATOM     51  CE2 TRP A  60      -6.883  -0.623  13.246  1.00 19.29           C  
+ATOM     52  CE3 TRP A  60      -4.704  -1.594  12.751  1.00 20.18           C  
+ATOM     53  CZ2 TRP A  60      -7.231  -0.581  11.877  1.00 20.26           C  
+ATOM     54  CZ3 TRP A  60      -5.045  -1.554  11.379  1.00 20.05           C  
+ATOM     55  CH2 TRP A  60      -6.306  -1.049  10.963  1.00 19.97           C  
+ATOM     56  N   PHE A  61      -1.980   0.191  14.544  1.00 22.58           N  
+ATOM     57  CA  PHE A  61      -0.962   0.055  13.501  1.00 20.39           C  
+ATOM     58  C   PHE A  61       0.393   0.457  14.047  1.00 22.27           C  
+ATOM     59  O   PHE A  61       0.645   1.639  14.340  1.00 22.00           O  
+ATOM     60  CB  PHE A  61      -1.304   0.881  12.267  1.00 20.45           C  
+ATOM     61  CG  PHE A  61      -0.504   0.510  11.044  1.00 18.86           C  
+ATOM     62  CD1 PHE A  61      -0.892  -0.580  10.251  1.00 20.04           C  
+ATOM     63  CD2 PHE A  61       0.650   1.234  10.689  1.00 19.96           C  
+ATOM     64  CE1 PHE A  61      -0.138  -0.957   9.112  1.00 20.03           C  
+ATOM     65  CE2 PHE A  61       1.416   0.874   9.556  1.00 19.76           C  
+ATOM     66  CZ  PHE A  61       1.024  -0.224   8.763  1.00 19.54           C  
+ATOM     67  N   PHE A  62       1.271  -0.539  14.140  1.00 21.40           N  
+ATOM     68  CA  PHE A  62       2.612  -0.344  14.678  1.00 21.91           C  
+ATOM     69  C   PHE A  62       3.734  -0.393  13.645  1.00 22.34           C  
+ATOM     70  O   PHE A  62       4.910  -0.258  13.998  1.00 24.21           O  
+ATOM     71  CB  PHE A  62       2.873  -1.363  15.786  1.00 22.58           C  
+ATOM     72  CG  PHE A  62       2.242  -1.023  17.100  1.00 22.20           C  
+ATOM     73  CD1 PHE A  62       0.841  -0.954  17.238  1.00 21.95           C  
+ATOM     74  CD2 PHE A  62       3.042  -0.820  18.232  1.00 22.73           C  
+ATOM     75  CE1 PHE A  62       0.235  -0.692  18.488  1.00 21.77           C  
+ATOM     76  CE2 PHE A  62       2.453  -0.557  19.496  1.00 25.91           C  
+ATOM     77  CZ  PHE A  62       1.043  -0.494  19.621  1.00 25.11           C  
+ATOM     78  N   GLY A  63       3.365  -0.539  12.371  1.00 20.22           N  
+ATOM     79  CA  GLY A  63       4.342  -0.585  11.293  1.00 20.67           C  
+ATOM     80  C   GLY A  63       5.264  -1.780  11.345  1.00 20.79           C  
+ATOM     81  O   GLY A  63       4.834  -2.874  11.700  1.00 19.22           O  
+ATOM     82  N   LYS A  64       6.545  -1.555  11.072  1.00 20.29           N  
+ATOM     83  CA  LYS A  64       7.521  -2.635  11.071  1.00 22.16           C  
+ATOM     84  C   LYS A  64       8.055  -3.014  12.464  1.00 23.01           C  
+ATOM     85  O   LYS A  64       9.266  -3.098  12.676  1.00 23.84           O  
+ATOM     86  CB  LYS A  64       8.662  -2.326  10.087  1.00 22.60           C  
+ATOM     87  CG  LYS A  64       9.244  -3.559   9.417  1.00 26.28           C  
+ATOM     88  CD  LYS A  64      10.508  -3.211   8.641  1.00 27.71           C  
+ATOM     89  CE  LYS A  64      10.985  -4.388   7.812  1.00 30.37           C  
+ATOM     90  NZ  LYS A  64      12.229  -4.043   7.053  1.00 30.90           N  
+ATOM     91  N   ILE A  65       7.141  -3.248  13.409  1.00 24.30           N  
+ATOM     92  CA  ILE A  65       7.527  -3.666  14.757  1.00 23.54           C  
+ATOM     93  C   ILE A  65       7.811  -5.171  14.643  1.00 23.07           C  
+ATOM     94  O   ILE A  65       7.027  -5.913  14.030  1.00 23.44           O  
+ATOM     95  CB  ILE A  65       6.423  -3.339  15.851  1.00 25.59           C  
+ATOM     96  CG1 ILE A  65       6.962  -3.595  17.271  1.00 26.04           C  
+ATOM     97  CG2 ILE A  65       5.173  -4.174  15.650  1.00 21.66           C  
+ATOM     98  CD1 ILE A  65       6.029  -3.211  18.423  1.00 25.92           C  
+ATOM     99  N   PRO A  66       9.005  -5.608  15.082  1.00 23.03           N  
+ATOM    100  CA  PRO A  66       9.328  -7.039  15.000  1.00 23.30           C  
+ATOM    101  C   PRO A  66       8.373  -7.936  15.805  1.00 22.52           C  
+ATOM    102  O   PRO A  66       7.733  -7.476  16.760  1.00 21.80           O  
+ATOM    103  CB  PRO A  66      10.731  -7.092  15.577  1.00 22.47           C  
+ATOM    104  CG  PRO A  66      11.321  -5.780  15.171  1.00 23.62           C  
+ATOM    105  CD  PRO A  66      10.202  -4.821  15.455  1.00 22.54           C  
+ATOM    106  N   ARG A  67       8.271  -9.196  15.382  1.00 22.06           N  
+ATOM    107  CA  ARG A  67       7.433 -10.219  16.020  1.00 22.83           C  
+ATOM    108  C   ARG A  67       7.699 -10.347  17.529  1.00 24.10           C  
+ATOM    109  O   ARG A  67       6.768 -10.261  18.334  1.00 23.86           O  
+ATOM    110  CB  ARG A  67       7.674 -11.560  15.316  1.00 23.94           C  
+ATOM    111  CG  ARG A  67       6.907 -12.774  15.864  1.00 24.62           C  
+ATOM    112  CD  ARG A  67       7.324 -14.023  15.112  1.00 23.47           C  
+ATOM    113  NE  ARG A  67       6.867 -15.262  15.739  1.00 22.04           N  
+ATOM    114  CZ  ARG A  67       5.894 -16.036  15.262  1.00 20.66           C  
+ATOM    115  NH1 ARG A  67       5.240 -15.700  14.155  1.00 19.53           N  
+ATOM    116  NH2 ARG A  67       5.607 -17.184  15.863  1.00 23.22           N  
+ATOM    117  N   ALA A  68       8.974 -10.480  17.898  1.00 22.59           N  
+ATOM    118  CA  ALA A  68       9.386 -10.612  19.299  1.00 23.66           C  
+ATOM    119  C   ALA A  68       9.109  -9.356  20.121  1.00 23.97           C  
+ATOM    120  O   ALA A  68       8.824  -9.445  21.320  1.00 21.85           O  
+ATOM    121  CB  ALA A  68      10.850 -10.990  19.384  1.00 24.34           C  
+ATOM    122  N   LYS A  69       9.149  -8.199  19.455  1.00 23.41           N  
+ATOM    123  CA  LYS A  69       8.880  -6.917  20.103  1.00 25.09           C  
+ATOM    124  C   LYS A  69       7.378  -6.717  20.320  1.00 23.56           C  
+ATOM    125  O   LYS A  69       6.968  -6.064  21.278  1.00 23.45           O  
+ATOM    126  CB  LYS A  69       9.470  -5.764  19.296  1.00 28.16           C  
+ATOM    127  CG  LYS A  69      10.376  -4.839  20.098  1.00 34.10           C  
+ATOM    128  CD  LYS A  69      11.700  -5.504  20.427  1.00 35.59           C  
+ATOM    129  CE  LYS A  69      12.617  -4.610  21.248  1.00 38.56           C  
+ATOM    130  NZ  LYS A  69      13.031  -3.384  20.500  1.00 40.78           N  
+ATOM    131  N   ALA A  70       6.569  -7.318  19.442  1.00 21.80           N  
+ATOM    132  CA  ALA A  70       5.106  -7.272  19.532  1.00 20.39           C  
+ATOM    133  C   ALA A  70       4.711  -8.157  20.718  1.00 20.37           C  
+ATOM    134  O   ALA A  70       3.856  -7.788  21.511  1.00 18.06           O  
+ATOM    135  CB  ALA A  70       4.477  -7.795  18.247  1.00 20.76           C  
+ATOM    136  N   GLU A  71       5.429  -9.273  20.876  1.00 20.11           N  
+ATOM    137  CA  GLU A  71       5.215 -10.213  21.983  1.00 21.59           C  
+ATOM    138  C   GLU A  71       5.492  -9.561  23.332  1.00 22.42           C  
+ATOM    139  O   GLU A  71       4.665  -9.622  24.238  1.00 23.01           O  
+ATOM    140  CB  GLU A  71       6.103 -11.453  21.844  1.00 20.77           C  
+ATOM    141  CG  GLU A  71       5.676 -12.404  20.752  1.00 20.33           C  
+ATOM    142  CD  GLU A  71       6.580 -13.621  20.589  1.00 23.37           C  
+ATOM    143  OE1 GLU A  71       7.586 -13.757  21.325  1.00 24.10           O  
+ATOM    144  OE2 GLU A  71       6.275 -14.452  19.703  1.00 22.08           O  
+ATOM    145  N   GLU A  72       6.639  -8.890  23.414  1.00 24.69           N  
+ATOM    146  CA  GLU A  72       7.114  -8.182  24.603  1.00 26.91           C  
+ATOM    147  C   GLU A  72       6.147  -7.077  25.056  1.00 26.71           C  
+ATOM    148  O   GLU A  72       5.800  -7.000  26.231  1.00 27.59           O  
+ATOM    149  CB  GLU A  72       8.487  -7.585  24.281  1.00 29.90           C  
+ATOM    150  CG  GLU A  72       9.259  -6.984  25.439  1.00 35.72           C  
+ATOM    151  CD  GLU A  72      10.634  -6.502  25.009  1.00 38.18           C  
+ATOM    152  OE1 GLU A  72      11.515  -7.357  24.771  1.00 41.23           O  
+ATOM    153  OE2 GLU A  72      10.827  -5.272  24.900  1.00 40.41           O  
+ATOM    154  N   MET A  73       5.683  -6.273  24.099  1.00 25.69           N  
+ATOM    155  CA  MET A  73       4.764  -5.161  24.348  1.00 25.99           C  
+ATOM    156  C   MET A  73       3.375  -5.643  24.772  1.00 23.81           C  
+ATOM    157  O   MET A  73       2.828  -5.155  25.769  1.00 24.09           O  
+ATOM    158  CB  MET A  73       4.675  -4.265  23.093  1.00 29.48           C  
+ATOM    159  CG  MET A  73       3.816  -2.985  23.205  1.00 33.88           C  
+ATOM    160  SD  MET A  73       2.045  -3.236  22.891  1.00 40.73           S  
+ATOM    161  CE  MET A  73       1.356  -1.829  23.696  1.00 40.37           C  
+ATOM    162  N   LEU A  74       2.830  -6.601  24.019  1.00 19.41           N  
+ATOM    163  CA  LEU A  74       1.496  -7.148  24.282  1.00 21.16           C  
+ATOM    164  C   LEU A  74       1.366  -8.006  25.540  1.00 20.66           C  
+ATOM    165  O   LEU A  74       0.301  -8.035  26.151  1.00 20.51           O  
+ATOM    166  CB  LEU A  74       0.951  -7.895  23.059  1.00 18.35           C  
+ATOM    167  CG  LEU A  74       0.681  -7.041  21.812  1.00 18.12           C  
+ATOM    168  CD1 LEU A  74       0.294  -7.950  20.684  1.00 16.60           C  
+ATOM    169  CD2 LEU A  74      -0.402  -6.006  22.047  1.00 16.44           C  
+ATOM    170  N   SER A  75       2.447  -8.677  25.939  1.00 21.80           N  
+ATOM    171  CA  SER A  75       2.456  -9.511  27.159  1.00 25.20           C  
+ATOM    172  C   SER A  75       2.269  -8.632  28.411  1.00 25.97           C  
+ATOM    173  O   SER A  75       1.759  -9.099  29.433  1.00 28.52           O  
+ATOM    174  CB  SER A  75       3.775 -10.286  27.278  1.00 23.60           C  
+ATOM    175  OG  SER A  75       4.885  -9.397  27.275  1.00 26.10           O  
+ATOM    176  N   LYS A  76       2.668  -7.361  28.293  1.00 25.99           N  
+ATOM    177  CA  LYS A  76       2.553  -6.363  29.360  1.00 27.23           C  
+ATOM    178  C   LYS A  76       1.156  -5.735  29.416  1.00 25.74           C  
+ATOM    179  O   LYS A  76       0.802  -5.100  30.401  1.00 24.43           O  
+ATOM    180  CB  LYS A  76       3.613  -5.267  29.209  1.00 30.60           C  
+ATOM    181  CG  LYS A  76       5.036  -5.752  29.442  1.00 33.98           C  
+ATOM    182  CD  LYS A  76       6.011  -4.579  29.425  1.00 40.37           C  
+ATOM    183  CE  LYS A  76       7.436  -5.038  29.716  1.00 41.35           C  
+ATOM    184  NZ  LYS A  76       7.962  -5.994  28.697  1.00 43.77           N  
+ATOM    185  N   GLN A  77       0.360  -5.934  28.366  1.00 24.14           N  
+ATOM    186  CA  GLN A  77      -1.015  -5.418  28.316  1.00 23.22           C  
+ATOM    187  C   GLN A  77      -1.864  -6.227  29.291  1.00 22.39           C  
+ATOM    188  O   GLN A  77      -1.605  -7.409  29.499  1.00 21.05           O  
+ATOM    189  CB  GLN A  77      -1.578  -5.514  26.899  1.00 22.91           C  
+ATOM    190  CG  GLN A  77      -1.026  -4.488  25.925  1.00 19.40           C  
+ATOM    191  CD  GLN A  77      -1.510  -3.085  26.220  1.00 21.60           C  
+ATOM    192  OE1 GLN A  77      -2.715  -2.821  26.205  1.00 21.35           O  
+ATOM    193  NE2 GLN A  77      -0.578  -2.178  26.500  1.00 20.89           N  
+ATOM    194  N  AARG A  78      -2.851  -5.608  29.934  0.50 23.71           N  
+ATOM    194  N  BARG A  78      -2.833  -5.548  29.881  0.50 23.71           N  
+ATOM    195  CA AARG A  78      -3.679  -6.371  30.876  0.50 24.25           C  
+ATOM    195  CA BARG A  78      -3.736  -6.099  30.882  0.50 24.25           C  
+ATOM    196  C  AARG A  78      -4.796  -7.173  30.240  0.50 24.10           C  
+ATOM    196  C  BARG A  78      -4.834  -7.024  30.341  0.50 24.10           C  
+ATOM    197  O  AARG A  78      -5.000  -8.339  30.597  0.50 26.14           O  
+ATOM    197  O  BARG A  78      -5.070  -8.106  30.884  0.50 26.14           O  
+ATOM    198  CB AARG A  78      -4.249  -5.512  32.015  0.50 26.10           C  
+ATOM    198  CB BARG A  78      -4.381  -4.923  31.620  0.50 26.10           C  
+ATOM    199  CG AARG A  78      -4.735  -6.393  33.187  0.50 26.78           C  
+ATOM    199  CG BARG A  78      -5.189  -5.307  32.831  0.50 26.78           C  
+ATOM    200  CD AARG A  78      -5.396  -5.623  34.306  0.50 28.73           C  
+ATOM    200  CD BARG A  78      -6.058  -4.173  33.250  0.50 28.73           C  
+ATOM    201  NE AARG A  78      -5.728  -6.434  35.489  0.50 29.50           N  
+ATOM    201  NE BARG A  78      -6.914  -4.592  34.350  0.50 29.50           N  
+ATOM    202  CZ AARG A  78      -4.857  -7.074  36.277  0.50 30.52           C  
+ATOM    202  CZ BARG A  78      -7.687  -3.785  35.065  0.50 30.52           C  
+ATOM    203  NH1AARG A  78      -3.549  -7.043  36.041  0.50 29.29           N  
+ATOM    203  NH1BARG A  78      -7.726  -2.481  34.810  0.50 29.29           N  
+ATOM    204  NH2AARG A  78      -5.302  -7.727  37.342  0.50 31.57           N  
+ATOM    204  NH2BARG A  78      -8.428  -4.294  36.038  0.50 31.57           N  
+ATOM    205  N   HIS A  79      -5.502  -6.582  29.287  1.00 25.37           N  
+ATOM    206  CA  HIS A  79      -6.623  -7.268  28.651  1.00 24.14           C  
+ATOM    207  C   HIS A  79      -6.342  -8.257  27.535  1.00 26.02           C  
+ATOM    208  O   HIS A  79      -5.534  -7.989  26.632  1.00 25.31           O  
+ATOM    209  CB  HIS A  79      -7.629  -6.234  28.157  1.00 25.31           C  
+ATOM    210  CG  HIS A  79      -8.133  -5.311  29.226  1.00 27.99           C  
+ATOM    211  ND1 HIS A  79      -8.925  -5.739  30.270  1.00 29.47           N  
+ATOM    212  CD2 HIS A  79      -7.952  -3.982  29.412  1.00 28.40           C  
+ATOM    213  CE1 HIS A  79      -9.209  -4.713  31.054  1.00 29.32           C  
+ATOM    214  NE2 HIS A  79      -8.629  -3.634  30.556  1.00 28.66           N  
+ATOM    215  N   ASP A  80      -7.037  -9.402  27.609  1.00 25.33           N  
+ATOM    216  CA  ASP A  80      -6.962 -10.446  26.591  1.00 25.36           C  
+ATOM    217  C   ASP A  80      -7.614  -9.840  25.348  1.00 24.85           C  
+ATOM    218  O   ASP A  80      -8.646  -9.169  25.453  1.00 23.39           O  
+ATOM    219  CB  ASP A  80      -7.768 -11.679  27.006  1.00 26.93           C  
+ATOM    220  CG  ASP A  80      -7.090 -12.502  28.085  1.00 30.53           C  
+ATOM    221  OD1 ASP A  80      -5.839 -12.525  28.149  1.00 29.14           O  
+ATOM    222  OD2 ASP A  80      -7.829 -13.142  28.866  1.00 32.00           O  
+ATOM    223  N   GLY A  81      -6.974 -10.015  24.197  1.00 23.06           N  
+ATOM    224  CA  GLY A  81      -7.504  -9.450  22.970  1.00 21.59           C  
+ATOM    225  C   GLY A  81      -6.759  -8.203  22.530  1.00 20.69           C  
+ATOM    226  O   GLY A  81      -6.999  -7.711  21.422  1.00 21.71           O  
+ATOM    227  N   ALA A  82      -5.878  -7.677  23.392  1.00 19.57           N  
+ATOM    228  CA  ALA A  82      -5.071  -6.490  23.067  1.00 19.24           C  
+ATOM    229  C   ALA A  82      -4.201  -6.896  21.880  1.00 18.50           C  
+ATOM    230  O   ALA A  82      -3.520  -7.921  21.911  1.00 18.78           O  
+ATOM    231  CB  ALA A  82      -4.232  -6.062  24.236  1.00 18.27           C  
+ATOM    232  N   PHE A  83      -4.290  -6.114  20.816  1.00 19.38           N  
+ATOM    233  CA  PHE A  83      -3.607  -6.453  19.584  1.00 18.96           C  
+ATOM    234  C   PHE A  83      -2.881  -5.337  18.864  1.00 19.03           C  
+ATOM    235  O   PHE A  83      -2.975  -4.174  19.225  1.00 21.27           O  
+ATOM    236  CB  PHE A  83      -4.653  -7.063  18.621  1.00 18.84           C  
+ATOM    237  CG  PHE A  83      -5.593  -6.043  18.010  1.00 18.07           C  
+ATOM    238  CD1 PHE A  83      -5.482  -5.698  16.650  1.00 19.08           C  
+ATOM    239  CD2 PHE A  83      -6.535  -5.368  18.807  1.00 19.15           C  
+ATOM    240  CE1 PHE A  83      -6.296  -4.686  16.092  1.00 19.28           C  
+ATOM    241  CE2 PHE A  83      -7.356  -4.353  18.266  1.00 19.03           C  
+ATOM    242  CZ  PHE A  83      -7.237  -4.011  16.911  1.00 19.82           C  
+ATOM    243  N   LEU A  84      -2.284  -5.727  17.741  1.00 18.10           N  
+ATOM    244  CA  LEU A  84      -1.602  -4.820  16.848  1.00 18.21           C  
+ATOM    245  C   LEU A  84      -1.459  -5.454  15.474  1.00 17.25           C  
+ATOM    246  O   LEU A  84      -1.461  -6.677  15.340  1.00 15.82           O  
+ATOM    247  CB  LEU A  84      -0.227  -4.403  17.399  1.00 18.70           C  
+ATOM    248  CG  LEU A  84       0.963  -5.324  17.689  1.00 18.94           C  
+ATOM    249  CD1 LEU A  84       1.757  -5.641  16.439  1.00 18.83           C  
+ATOM    250  CD2 LEU A  84       1.868  -4.612  18.680  1.00 16.70           C  
+ATOM    251  N   ILE A  85      -1.376  -4.598  14.459  1.00 16.48           N  
+ATOM    252  CA  ILE A  85      -1.141  -5.025  13.087  1.00 15.71           C  
+ATOM    253  C   ILE A  85       0.276  -4.538  12.829  1.00 16.26           C  
+ATOM    254  O   ILE A  85       0.622  -3.392  13.138  1.00 16.71           O  
+ATOM    255  CB  ILE A  85      -2.132  -4.387  12.055  1.00 16.64           C  
+ATOM    256  CG1 ILE A  85      -3.531  -5.011  12.185  1.00 16.82           C  
+ATOM    257  CG2 ILE A  85      -1.611  -4.543  10.610  1.00 16.76           C  
+ATOM    258  CD1 ILE A  85      -3.705  -6.426  11.628  1.00 20.48           C  
+ATOM    259  N   ARG A  86       1.095  -5.430  12.291  1.00 16.77           N  
+ATOM    260  CA  ARG A  86       2.473  -5.100  11.988  1.00 15.66           C  
+ATOM    261  C   ARG A  86       2.843  -5.530  10.590  1.00 17.95           C  
+ATOM    262  O   ARG A  86       2.173  -6.376   9.996  1.00 16.74           O  
+ATOM    263  CB  ARG A  86       3.409  -5.767  12.995  1.00 13.47           C  
+ATOM    264  CG  ARG A  86       3.247  -7.261  13.115  1.00 13.70           C  
+ATOM    265  CD  ARG A  86       4.097  -7.815  14.236  1.00 18.81           C  
+ATOM    266  NE  ARG A  86       3.818  -9.229  14.434  1.00 19.30           N  
+ATOM    267  CZ  ARG A  86       4.414 -10.216  13.778  1.00 19.86           C  
+ATOM    268  NH1 ARG A  86       5.351  -9.959  12.873  1.00 18.77           N  
+ATOM    269  NH2 ARG A  86       4.036 -11.463  14.002  1.00 19.36           N  
+ATOM    270  N   GLU A  87       3.919  -4.940  10.078  1.00 18.67           N  
+ATOM    271  CA  GLU A  87       4.430  -5.268   8.754  1.00 22.01           C  
+ATOM    272  C   GLU A  87       5.506  -6.319   8.983  1.00 23.29           C  
+ATOM    273  O   GLU A  87       6.443  -6.106   9.754  1.00 21.72           O  
+ATOM    274  CB  GLU A  87       4.961  -4.016   8.060  1.00 20.74           C  
+ATOM    275  CG  GLU A  87       3.910  -2.916   8.034  1.00 20.53           C  
+ATOM    276  CD  GLU A  87       4.221  -1.805   7.079  1.00 20.48           C  
+ATOM    277  OE1 GLU A  87       4.115  -2.030   5.854  1.00 18.78           O  
+ATOM    278  OE2 GLU A  87       4.572  -0.702   7.548  1.00 21.44           O  
+ATOM    279  N   SER A  88       5.278  -7.490   8.394  1.00 25.14           N  
+ATOM    280  CA  SER A  88       6.146  -8.658   8.522  1.00 30.16           C  
+ATOM    281  C   SER A  88       7.572  -8.475   8.016  1.00 31.78           C  
+ATOM    282  O   SER A  88       7.830  -7.691   7.102  1.00 31.34           O  
+ATOM    283  CB  SER A  88       5.487  -9.858   7.824  1.00 31.22           C  
+ATOM    284  OG  SER A  88       6.158 -11.083   8.098  1.00 33.79           O  
+ATOM    285  N   GLU A  89       8.496  -9.161   8.684  1.00 34.33           N  
+ATOM    286  CA  GLU A  89       9.910  -9.147   8.331  1.00 34.28           C  
+ATOM    287  C   GLU A  89      10.238 -10.449   7.589  1.00 34.91           C  
+ATOM    288  O   GLU A  89      11.142 -10.479   6.750  1.00 35.79           O  
+ATOM    289  CB  GLU A  89      10.785  -9.016   9.579  1.00 33.80           C  
+ATOM    290  CG  GLU A  89      10.685  -7.680  10.296  1.00 33.89           C  
+ATOM    291  CD  GLU A  89      11.669  -7.561  11.447  1.00 33.72           C  
+ATOM    292  OE1 GLU A  89      11.614  -8.402  12.373  1.00 30.65           O  
+ATOM    293  OE2 GLU A  89      12.507  -6.630  11.423  1.00 35.73           O  
+ATOM    294  N   SER A  90       9.485 -11.513   7.891  1.00 36.32           N  
+ATOM    295  CA  SER A  90       9.675 -12.824   7.252  1.00 36.13           C  
+ATOM    296  C   SER A  90       9.063 -12.840   5.850  1.00 37.21           C  
+ATOM    297  O   SER A  90       9.502 -13.592   4.974  1.00 38.74           O  
+ATOM    298  CB  SER A  90       9.075 -13.955   8.104  1.00 35.59           C  
+ATOM    299  OG  SER A  90       7.653 -13.935   8.131  1.00 36.25           O  
+ATOM    300  N   ALA A  91       8.055 -11.993   5.650  1.00 36.12           N  
+ATOM    301  CA  ALA A  91       7.375 -11.866   4.363  1.00 35.07           C  
+ATOM    302  C   ALA A  91       7.188 -10.374   4.057  1.00 34.44           C  
+ATOM    303  O   ALA A  91       6.166  -9.783   4.434  1.00 33.06           O  
+ATOM    304  CB  ALA A  91       6.023 -12.601   4.393  1.00 36.10           C  
+ATOM    305  N   PRO A  92       8.189  -9.734   3.398  1.00 33.85           N  
+ATOM    306  CA  PRO A  92       8.141  -8.307   3.044  1.00 32.72           C  
+ATOM    307  C   PRO A  92       6.960  -7.947   2.155  1.00 31.39           C  
+ATOM    308  O   PRO A  92       6.740  -8.573   1.115  1.00 32.49           O  
+ATOM    309  CB  PRO A  92       9.468  -8.090   2.310  1.00 33.92           C  
+ATOM    310  CG  PRO A  92      10.375  -9.092   2.945  1.00 34.25           C  
+ATOM    311  CD  PRO A  92       9.484 -10.309   2.981  1.00 34.10           C  
+ATOM    312  N   GLY A  93       6.197  -6.950   2.596  1.00 30.52           N  
+ATOM    313  CA  GLY A  93       5.028  -6.501   1.863  1.00 28.53           C  
+ATOM    314  C   GLY A  93       3.742  -7.026   2.469  1.00 28.38           C  
+ATOM    315  O   GLY A  93       2.644  -6.621   2.073  1.00 29.12           O  
+ATOM    316  N   ASP A  94       3.877  -7.943   3.423  1.00 27.73           N  
+ATOM    317  CA  ASP A  94       2.724  -8.538   4.092  1.00 26.63           C  
+ATOM    318  C   ASP A  94       2.536  -8.030   5.510  1.00 24.96           C  
+ATOM    319  O   ASP A  94       3.453  -7.470   6.106  1.00 25.62           O  
+ATOM    320  CB  ASP A  94       2.838 -10.066   4.109  1.00 29.22           C  
+ATOM    321  CG  ASP A  94       2.751 -10.684   2.723  1.00 29.78           C  
+ATOM    322  OD1 ASP A  94       2.202 -10.050   1.789  1.00 32.78           O  
+ATOM    323  OD2 ASP A  94       3.225 -11.825   2.575  1.00 35.13           O  
+ATOM    324  N   PHE A  95       1.322  -8.201   6.022  1.00 22.36           N  
+ATOM    325  CA  PHE A  95       0.986  -7.799   7.377  1.00 20.72           C  
+ATOM    326  C   PHE A  95       0.767  -9.033   8.230  1.00 20.75           C  
+ATOM    327  O   PHE A  95       0.498 -10.121   7.715  1.00 19.54           O  
+ATOM    328  CB  PHE A  95      -0.279  -6.931   7.408  1.00 18.96           C  
+ATOM    329  CG  PHE A  95      -0.164  -5.668   6.612  1.00 19.08           C  
+ATOM    330  CD1 PHE A  95      -0.610  -5.628   5.276  1.00 16.88           C  
+ATOM    331  CD2 PHE A  95       0.436  -4.525   7.172  1.00 16.90           C  
+ATOM    332  CE1 PHE A  95      -0.452  -4.459   4.496  1.00 20.33           C  
+ATOM    333  CE2 PHE A  95       0.600  -3.349   6.408  1.00 17.78           C  
+ATOM    334  CZ  PHE A  95       0.158  -3.315   5.069  1.00 19.53           C  
+ATOM    335  N   SER A  96       0.876  -8.841   9.538  1.00 21.05           N  
+ATOM    336  CA  SER A  96       0.674  -9.902  10.515  1.00 20.51           C  
+ATOM    337  C   SER A  96      -0.116  -9.299  11.661  1.00 19.95           C  
+ATOM    338  O   SER A  96      -0.022  -8.095  11.907  1.00 19.30           O  
+ATOM    339  CB  SER A  96       2.013 -10.432  11.028  1.00 19.60           C  
+ATOM    340  OG  SER A  96       2.790 -10.958   9.972  1.00 22.71           O  
+ATOM    341  N   LEU A  97      -0.901 -10.141  12.335  1.00 17.57           N  
+ATOM    342  CA  LEU A  97      -1.735  -9.735  13.461  1.00 19.49           C  
+ATOM    343  C   LEU A  97      -1.203 -10.447  14.704  1.00 17.42           C  
+ATOM    344  O   LEU A  97      -1.111 -11.670  14.721  1.00 18.24           O  
+ATOM    345  CB  LEU A  97      -3.195 -10.159  13.210  1.00 19.00           C  
+ATOM    346  CG  LEU A  97      -4.464  -9.532  13.818  1.00 23.13           C  
+ATOM    347  CD1 LEU A  97      -5.459 -10.631  14.128  1.00 22.15           C  
+ATOM    348  CD2 LEU A  97      -4.224  -8.690  15.049  1.00 21.59           C  
+ATOM    349  N   SER A  98      -0.901  -9.672  15.743  1.00 17.13           N  
+ATOM    350  CA  SER A  98      -0.383 -10.202  17.008  1.00 18.39           C  
+ATOM    351  C   SER A  98      -1.398  -9.866  18.089  1.00 17.34           C  
+ATOM    352  O   SER A  98      -1.794  -8.720  18.217  1.00 17.34           O  
+ATOM    353  CB  SER A  98       0.987  -9.608  17.309  1.00 16.78           C  
+ATOM    354  OG  SER A  98       1.921 -10.006  16.316  1.00 18.56           O  
+ATOM    355  N   VAL A  99      -1.864 -10.883  18.812  1.00 17.69           N  
+ATOM    356  CA  VAL A  99      -2.911 -10.719  19.828  1.00 19.80           C  
+ATOM    357  C   VAL A  99      -2.540 -11.362  21.158  1.00 19.64           C  
+ATOM    358  O   VAL A  99      -2.083 -12.499  21.189  1.00 18.25           O  
+ATOM    359  CB  VAL A  99      -4.249 -11.418  19.386  1.00 19.72           C  
+ATOM    360  CG1 VAL A  99      -5.410 -10.940  20.248  1.00 19.01           C  
+ATOM    361  CG2 VAL A  99      -4.553 -11.198  17.928  1.00 19.34           C  
+ATOM    362  N   LYS A 100      -2.821 -10.658  22.254  1.00 20.64           N  
+ATOM    363  CA  LYS A 100      -2.558 -11.185  23.591  1.00 20.57           C  
+ATOM    364  C   LYS A 100      -3.720 -12.093  23.996  1.00 20.04           C  
+ATOM    365  O   LYS A 100      -4.876 -11.785  23.720  1.00 20.70           O  
+ATOM    366  CB  LYS A 100      -2.429 -10.052  24.620  1.00 22.10           C  
+ATOM    367  CG  LYS A 100      -2.080 -10.532  26.032  1.00 23.82           C  
+ATOM    368  CD  LYS A 100      -2.568  -9.580  27.096  1.00 27.01           C  
+ATOM    369  CE  LYS A 100      -2.560 -10.240  28.469  1.00 30.35           C  
+ATOM    370  NZ  LYS A 100      -1.181 -10.539  28.929  1.00 28.75           N  
+ATOM    371  N   PHE A 101      -3.384 -13.221  24.619  1.00 21.21           N  
+ATOM    372  CA  PHE A 101      -4.368 -14.178  25.125  1.00 23.43           C  
+ATOM    373  C   PHE A 101      -3.734 -15.012  26.231  1.00 23.74           C  
+ATOM    374  O   PHE A 101      -3.093 -16.037  25.969  1.00 23.68           O  
+ATOM    375  CB  PHE A 101      -4.914 -15.087  24.022  1.00 24.24           C  
+ATOM    376  CG  PHE A 101      -6.243 -15.699  24.357  1.00 25.11           C  
+ATOM    377  CD1 PHE A 101      -6.390 -17.094  24.419  1.00 25.75           C  
+ATOM    378  CD2 PHE A 101      -7.376 -14.880  24.577  1.00 25.07           C  
+ATOM    379  CE1 PHE A 101      -7.664 -17.681  24.689  1.00 25.98           C  
+ATOM    380  CE2 PHE A 101      -8.648 -15.443  24.847  1.00 24.21           C  
+ATOM    381  CZ  PHE A 101      -8.791 -16.849  24.899  1.00 25.48           C  
+ATOM    382  N   GLY A 102      -3.930 -14.564  27.469  1.00 25.15           N  
+ATOM    383  CA  GLY A 102      -3.361 -15.245  28.625  1.00 26.29           C  
+ATOM    384  C   GLY A 102      -1.877 -14.993  28.739  1.00 26.64           C  
+ATOM    385  O   GLY A 102      -1.451 -13.846  28.668  1.00 28.01           O  
+ATOM    386  N   ASN A 103      -1.100 -16.072  28.841  1.00 27.82           N  
+ATOM    387  CA  ASN A 103       0.354 -16.001  28.956  1.00 30.45           C  
+ATOM    388  C   ASN A 103       1.042 -15.990  27.588  1.00 29.43           C  
+ATOM    389  O   ASN A 103       2.270 -15.902  27.508  1.00 30.46           O  
+ATOM    390  CB  ASN A 103       0.876 -17.178  29.792  1.00 32.42           C  
+ATOM    391  CG  ASN A 103       2.229 -16.890  30.435  1.00 34.84           C  
+ATOM    392  OD1 ASN A 103       2.363 -15.956  31.226  1.00 40.34           O  
+ATOM    393  ND2 ASN A 103       3.236 -17.683  30.087  1.00 36.08           N  
+ATOM    394  N   ASP A 104       0.242 -16.071  26.523  1.00 29.06           N  
+ATOM    395  CA  ASP A 104       0.757 -16.085  25.150  1.00 27.63           C  
+ATOM    396  C   ASP A 104       0.333 -14.891  24.306  1.00 25.19           C  
+ATOM    397  O   ASP A 104      -0.638 -14.193  24.608  1.00 21.61           O  
+ATOM    398  CB  ASP A 104       0.280 -17.333  24.386  1.00 30.34           C  
+ATOM    399  CG  ASP A 104       0.624 -18.631  25.080  1.00 33.41           C  
+ATOM    400  OD1 ASP A 104       1.772 -18.782  25.555  1.00 36.30           O  
+ATOM    401  OD2 ASP A 104      -0.269 -19.502  25.139  1.00 35.42           O  
+ATOM    402  N   VAL A 105       1.125 -14.652  23.264  1.00 22.89           N  
+ATOM    403  CA  VAL A 105       0.848 -13.629  22.275  1.00 22.71           C  
+ATOM    404  C   VAL A 105       0.847 -14.436  20.977  1.00 23.77           C  
+ATOM    405  O   VAL A 105       1.885 -14.951  20.523  1.00 25.15           O  
+ATOM    406  CB  VAL A 105       1.877 -12.491  22.254  1.00 21.47           C  
+ATOM    407  CG1 VAL A 105       1.562 -11.527  21.108  1.00 18.79           C  
+ATOM    408  CG2 VAL A 105       1.843 -11.724  23.573  1.00 19.83           C  
+ATOM    409  N   GLN A 106      -0.354 -14.596  20.439  1.00 20.59           N  
+ATOM    410  CA  GLN A 106      -0.593 -15.366  19.228  1.00 20.74           C  
+ATOM    411  C   GLN A 106      -0.429 -14.543  17.961  1.00 20.58           C  
+ATOM    412  O   GLN A 106      -0.813 -13.374  17.916  1.00 20.07           O  
+ATOM    413  CB  GLN A 106      -1.991 -15.978  19.287  1.00 19.27           C  
+ATOM    414  CG  GLN A 106      -2.180 -16.941  20.450  1.00 21.40           C  
+ATOM    415  CD  GLN A 106      -3.531 -17.626  20.445  1.00 22.38           C  
+ATOM    416  OE1 GLN A 106      -4.254 -17.593  19.447  1.00 22.11           O  
+ATOM    417  NE2 GLN A 106      -3.878 -18.258  21.567  1.00 21.46           N  
+ATOM    418  N   HIS A 107       0.173 -15.161  16.947  1.00 18.73           N  
+ATOM    419  CA  HIS A 107       0.406 -14.508  15.669  1.00 18.21           C  
+ATOM    420  C   HIS A 107      -0.423 -15.125  14.559  1.00 19.67           C  
+ATOM    421  O   HIS A 107      -0.617 -16.343  14.511  1.00 19.27           O  
+ATOM    422  CB  HIS A 107       1.896 -14.527  15.310  1.00 19.88           C  
+ATOM    423  CG  HIS A 107       2.768 -13.937  16.371  1.00 19.85           C  
+ATOM    424  ND1 HIS A 107       2.836 -12.583  16.612  1.00 18.40           N  
+ATOM    425  CD2 HIS A 107       3.566 -14.524  17.294  1.00 19.69           C  
+ATOM    426  CE1 HIS A 107       3.636 -12.361  17.639  1.00 18.28           C  
+ATOM    427  NE2 HIS A 107       4.093 -13.522  18.070  1.00 18.09           N  
+ATOM    428  N   PHE A 108      -0.974 -14.247  13.720  1.00 17.84           N  
+ATOM    429  CA  PHE A 108      -1.807 -14.619  12.580  1.00 18.06           C  
+ATOM    430  C   PHE A 108      -1.235 -13.935  11.340  1.00 19.95           C  
+ATOM    431  O   PHE A 108      -0.778 -12.792  11.411  1.00 19.39           O  
+ATOM    432  CB  PHE A 108      -3.261 -14.127  12.766  1.00 18.60           C  
+ATOM    433  CG  PHE A 108      -3.966 -14.685  13.982  1.00 19.40           C  
+ATOM    434  CD1 PHE A 108      -3.724 -14.152  15.266  1.00 20.90           C  
+ATOM    435  CD2 PHE A 108      -4.872 -15.752  13.855  1.00 21.09           C  
+ATOM    436  CE1 PHE A 108      -4.369 -14.680  16.413  1.00 19.57           C  
+ATOM    437  CE2 PHE A 108      -5.526 -16.290  14.994  1.00 20.88           C  
+ATOM    438  CZ  PHE A 108      -5.272 -15.753  16.275  1.00 21.10           C  
+ATOM    439  N   LYS A 109      -1.230 -14.637  10.213  1.00 19.66           N  
+ATOM    440  CA  LYS A 109      -0.750 -14.041   8.975  1.00 21.58           C  
+ATOM    441  C   LYS A 109      -1.942 -13.431   8.242  1.00 20.96           C  
+ATOM    442  O   LYS A 109      -2.975 -14.075   8.108  1.00 21.08           O  
+ATOM    443  CB  LYS A 109      -0.034 -15.087   8.098  1.00 24.16           C  
+ATOM    444  CG  LYS A 109       0.463 -14.587   6.724  1.00 26.38           C  
+ATOM    445  CD  LYS A 109       1.565 -13.499   6.811  1.00 31.48           C  
+ATOM    446  CE  LYS A 109       2.941 -14.086   7.063  1.00 31.64           C  
+ATOM    447  NZ  LYS A 109       3.391 -14.983   5.958  1.00 35.14           N  
+ATOM    448  N   VAL A 110      -1.815 -12.163   7.851  1.00 20.32           N  
+ATOM    449  CA  VAL A 110      -2.869 -11.494   7.092  1.00 19.85           C  
+ATOM    450  C   VAL A 110      -2.601 -11.848   5.628  1.00 21.71           C  
+ATOM    451  O   VAL A 110      -1.586 -11.459   5.041  1.00 21.82           O  
+ATOM    452  CB  VAL A 110      -2.889  -9.958   7.300  1.00 20.05           C  
+ATOM    453  CG1 VAL A 110      -4.014  -9.326   6.496  1.00 21.04           C  
+ATOM    454  CG2 VAL A 110      -3.069  -9.617   8.778  1.00 20.52           C  
+ATOM    455  N   LEU A 111      -3.497 -12.661   5.083  1.00 21.59           N  
+ATOM    456  CA  LEU A 111      -3.411 -13.139   3.711  1.00 25.08           C  
+ATOM    457  C   LEU A 111      -4.077 -12.150   2.750  1.00 26.75           C  
+ATOM    458  O   LEU A 111      -4.857 -11.298   3.175  1.00 25.91           O  
+ATOM    459  CB  LEU A 111      -4.064 -14.518   3.634  1.00 24.66           C  
+ATOM    460  CG  LEU A 111      -3.540 -15.538   4.653  1.00 25.88           C  
+ATOM    461  CD1 LEU A 111      -4.564 -16.610   4.929  1.00 25.09           C  
+ATOM    462  CD2 LEU A 111      -2.211 -16.125   4.194  1.00 23.16           C  
+ATOM    463  N   ARG A 112      -3.731 -12.246   1.468  1.00 28.17           N  
+ATOM    464  CA  ARG A 112      -4.279 -11.363   0.440  1.00 29.55           C  
+ATOM    465  C   ARG A 112      -4.500 -12.149  -0.857  1.00 30.76           C  
+ATOM    466  O   ARG A 112      -3.568 -12.796  -1.356  1.00 31.83           O  
+ATOM    467  CB  ARG A 112      -3.322 -10.184   0.204  1.00 31.79           C  
+ATOM    468  CG  ARG A 112      -4.004  -8.914  -0.312  1.00 33.58           C  
+ATOM    469  CD  ARG A 112      -3.014  -7.787  -0.548  1.00 35.40           C  
+ATOM    470  NE  ARG A 112      -3.642  -6.690  -1.284  1.00 33.58           N  
+ATOM    471  CZ  ARG A 112      -3.042  -5.953  -2.216  1.00 33.96           C  
+ATOM    472  NH1 ARG A 112      -1.769  -6.170  -2.546  1.00 34.06           N  
+ATOM    473  NH2 ARG A 112      -3.740  -5.025  -2.862  1.00 31.88           N  
+ATOM    474  N   ASP A 113      -5.735 -12.126  -1.377  1.00 29.94           N  
+ATOM    475  CA  ASP A 113      -6.067 -12.849  -2.617  1.00 31.10           C  
+ATOM    476  C   ASP A 113      -5.719 -12.076  -3.896  1.00 31.83           C  
+ATOM    477  O   ASP A 113      -5.267 -10.931  -3.821  1.00 31.04           O  
+ATOM    478  CB  ASP A 113      -7.543 -13.343  -2.633  1.00 28.48           C  
+ATOM    479  CG  ASP A 113      -8.593 -12.213  -2.677  1.00 27.85           C  
+ATOM    480  OD1 ASP A 113      -8.312 -11.057  -3.054  1.00 24.93           O  
+ATOM    481  OD2 ASP A 113      -9.762 -12.512  -2.359  1.00 29.99           O  
+ATOM    482  N   GLY A 114      -5.991 -12.693  -5.052  1.00 32.39           N  
+ATOM    483  CA  GLY A 114      -5.725 -12.078  -6.351  1.00 33.30           C  
+ATOM    484  C   GLY A 114      -6.502 -10.802  -6.658  1.00 32.74           C  
+ATOM    485  O   GLY A 114      -6.091 -10.019  -7.522  1.00 34.46           O  
+ATOM    486  N   ALA A 115      -7.617 -10.596  -5.951  1.00 31.14           N  
+ATOM    487  CA  ALA A 115      -8.458  -9.406  -6.112  1.00 31.26           C  
+ATOM    488  C   ALA A 115      -8.036  -8.307  -5.121  1.00 31.35           C  
+ATOM    489  O   ALA A 115      -8.659  -7.244  -5.046  1.00 32.95           O  
+ATOM    490  CB  ALA A 115      -9.939  -9.773  -5.925  1.00 30.37           C  
+ATOM    491  N   GLY A 116      -6.979  -8.591  -4.360  1.00 31.39           N  
+ATOM    492  CA  GLY A 116      -6.446  -7.658  -3.379  1.00 31.28           C  
+ATOM    493  C   GLY A 116      -7.150  -7.603  -2.033  1.00 30.27           C  
+ATOM    494  O   GLY A 116      -6.840  -6.719  -1.225  1.00 30.71           O  
+ATOM    495  N   LYS A 117      -8.048  -8.553  -1.769  1.00 27.52           N  
+ATOM    496  CA  LYS A 117      -8.796  -8.588  -0.509  1.00 27.94           C  
+ATOM    497  C   LYS A 117      -8.033  -9.294   0.611  1.00 28.55           C  
+ATOM    498  O   LYS A 117      -7.399 -10.320   0.380  1.00 29.10           O  
+ATOM    499  CB  LYS A 117     -10.165  -9.250  -0.699  1.00 27.80           C  
+ATOM    500  CG  LYS A 117     -11.016  -8.636  -1.805  1.00 29.42           C  
+ATOM    501  CD  LYS A 117     -12.476  -9.022  -1.652  1.00 32.12           C  
+ATOM    502  CE  LYS A 117     -13.289  -8.647  -2.881  1.00 32.61           C  
+ATOM    503  NZ  LYS A 117     -13.227  -7.188  -3.188  1.00 36.13           N  
+ATOM    504  N   TYR A 118      -8.113  -8.740   1.822  1.00 27.58           N  
+ATOM    505  CA  TYR A 118      -7.430  -9.299   2.989  1.00 25.78           C  
+ATOM    506  C   TYR A 118      -8.291 -10.320   3.723  1.00 23.95           C  
+ATOM    507  O   TYR A 118      -9.511 -10.206   3.738  1.00 23.82           O  
+ATOM    508  CB  TYR A 118      -7.037  -8.193   3.973  1.00 27.31           C  
+ATOM    509  CG  TYR A 118      -6.130  -7.114   3.433  1.00 26.26           C  
+ATOM    510  CD1 TYR A 118      -6.664  -5.903   2.965  1.00 29.67           C  
+ATOM    511  CD2 TYR A 118      -4.731  -7.266   3.439  1.00 27.54           C  
+ATOM    512  CE1 TYR A 118      -5.825  -4.848   2.515  1.00 28.14           C  
+ATOM    513  CE2 TYR A 118      -3.877  -6.221   2.991  1.00 28.07           C  
+ATOM    514  CZ  TYR A 118      -4.439  -5.017   2.535  1.00 28.37           C  
+ATOM    515  OH  TYR A 118      -3.624  -3.995   2.124  1.00 29.05           O  
+ATOM    516  N   PHE A 119      -7.642 -11.327   4.308  1.00 23.31           N  
+ATOM    517  CA  PHE A 119      -8.319 -12.377   5.071  1.00 22.41           C  
+ATOM    518  C   PHE A 119      -7.412 -13.130   6.044  1.00 22.49           C  
+ATOM    519  O   PHE A 119      -6.188 -13.002   6.008  1.00 20.93           O  
+ATOM    520  CB  PHE A 119      -9.080 -13.375   4.153  1.00 22.17           C  
+ATOM    521  CG  PHE A 119      -8.204 -14.208   3.233  1.00 23.41           C  
+ATOM    522  CD1 PHE A 119      -8.070 -15.597   3.449  1.00 22.49           C  
+ATOM    523  CD2 PHE A 119      -7.599 -13.639   2.091  1.00 22.41           C  
+ATOM    524  CE1 PHE A 119      -7.353 -16.419   2.539  1.00 21.73           C  
+ATOM    525  CE2 PHE A 119      -6.876 -14.448   1.169  1.00 23.75           C  
+ATOM    526  CZ  PHE A 119      -6.754 -15.842   1.393  1.00 23.54           C  
+ATOM    527  N   LEU A 120      -8.040 -13.861   6.962  1.00 20.71           N  
+ATOM    528  CA  LEU A 120      -7.312 -14.671   7.934  1.00 20.22           C  
+ATOM    529  C   LEU A 120      -7.722 -16.123   7.730  1.00 20.80           C  
+ATOM    530  O   LEU A 120      -6.891 -17.030   7.825  1.00 20.37           O  
+ATOM    531  CB  LEU A 120      -7.624 -14.248   9.379  1.00 17.72           C  
+ATOM    532  CG  LEU A 120      -7.230 -12.879   9.955  1.00 18.59           C  
+ATOM    533  CD1 LEU A 120      -7.651 -12.821  11.418  1.00 16.20           C  
+ATOM    534  CD2 LEU A 120      -5.743 -12.625   9.831  1.00 17.54           C  
+ATOM    535  N   TRP A 121      -9.017 -16.331   7.474  1.00 19.35           N  
+ATOM    536  CA  TRP A 121      -9.578 -17.672   7.278  1.00 21.67           C  
+ATOM    537  C   TRP A 121     -10.322 -17.817   5.945  1.00 22.63           C  
+ATOM    538  O   TRP A 121      -9.702 -18.177   4.951  1.00 22.48           O  
+ATOM    539  CB  TRP A 121     -10.479 -18.066   8.466  1.00 21.50           C  
+ATOM    540  CG  TRP A 121      -9.840 -17.857   9.826  1.00 22.71           C  
+ATOM    541  CD1 TRP A 121     -10.021 -16.782  10.649  1.00 23.55           C  
+ATOM    542  CD2 TRP A 121      -8.896 -18.712  10.487  1.00 22.56           C  
+ATOM    543  NE1 TRP A 121      -9.246 -16.909  11.776  1.00 23.70           N  
+ATOM    544  CE2 TRP A 121      -8.548 -18.083  11.709  1.00 23.21           C  
+ATOM    545  CE3 TRP A 121      -8.307 -19.952  10.171  1.00 22.60           C  
+ATOM    546  CZ2 TRP A 121      -7.634 -18.655  12.630  1.00 24.69           C  
+ATOM    547  CZ3 TRP A 121      -7.390 -20.530  11.095  1.00 23.39           C  
+ATOM    548  CH2 TRP A 121      -7.072 -19.873  12.308  1.00 24.38           C  
+ATOM    549  N   VAL A 122     -11.639 -17.574   5.925  1.00 24.03           N  
+ATOM    550  CA  VAL A 122     -12.433 -17.678   4.689  1.00 25.97           C  
+ATOM    551  C   VAL A 122     -13.082 -16.363   4.239  1.00 25.58           C  
+ATOM    552  O   VAL A 122     -13.046 -16.032   3.051  1.00 25.87           O  
+ATOM    553  CB  VAL A 122     -13.506 -18.841   4.724  1.00 27.57           C  
+ATOM    554  CG1 VAL A 122     -12.831 -20.190   4.931  1.00 28.62           C  
+ATOM    555  CG2 VAL A 122     -14.560 -18.624   5.800  1.00 31.28           C  
+ATOM    556  N   VAL A 123     -13.629 -15.605   5.196  1.00 26.29           N  
+ATOM    557  CA  VAL A 123     -14.291 -14.315   4.938  1.00 26.93           C  
+ATOM    558  C   VAL A 123     -13.268 -13.282   4.437  1.00 26.58           C  
+ATOM    559  O   VAL A 123     -12.199 -13.127   5.030  1.00 25.72           O  
+ATOM    560  CB  VAL A 123     -15.032 -13.785   6.216  1.00 26.70           C  
+ATOM    561  CG1 VAL A 123     -15.834 -12.521   5.902  1.00 26.68           C  
+ATOM    562  CG2 VAL A 123     -15.973 -14.852   6.768  1.00 27.83           C  
+ATOM    563  N   LYS A 124     -13.601 -12.642   3.314  1.00 24.92           N  
+ATOM    564  CA  LYS A 124     -12.753 -11.642   2.657  1.00 26.49           C  
+ATOM    565  C   LYS A 124     -13.144 -10.211   3.035  1.00 26.65           C  
+ATOM    566  O   LYS A 124     -14.321  -9.917   3.263  1.00 25.54           O  
+ATOM    567  CB  LYS A 124     -12.828 -11.787   1.123  1.00 25.22           C  
+ATOM    568  CG  LYS A 124     -12.547 -13.175   0.542  1.00 26.89           C  
+ATOM    569  CD  LYS A 124     -11.125 -13.628   0.770  1.00 24.05           C  
+ATOM    570  CE  LYS A 124     -10.843 -14.989   0.144  1.00 26.07           C  
+ATOM    571  NZ  LYS A 124     -10.574 -14.908  -1.319  1.00 22.78           N  
+ATOM    572  N   PHE A 125     -12.138  -9.335   3.118  1.00 26.75           N  
+ATOM    573  CA  PHE A 125     -12.331  -7.917   3.469  1.00 28.50           C  
+ATOM    574  C   PHE A 125     -11.594  -7.018   2.500  1.00 28.84           C  
+ATOM    575  O   PHE A 125     -10.461  -7.308   2.119  1.00 30.12           O  
+ATOM    576  CB  PHE A 125     -11.804  -7.622   4.877  1.00 26.65           C  
+ATOM    577  CG  PHE A 125     -12.308  -8.562   5.912  1.00 25.82           C  
+ATOM    578  CD1 PHE A 125     -11.582  -9.731   6.220  1.00 25.73           C  
+ATOM    579  CD2 PHE A 125     -13.540  -8.332   6.541  1.00 25.77           C  
+ATOM    580  CE1 PHE A 125     -12.079 -10.669   7.142  1.00 26.40           C  
+ATOM    581  CE2 PHE A 125     -14.050  -9.257   7.460  1.00 25.82           C  
+ATOM    582  CZ  PHE A 125     -13.315 -10.434   7.764  1.00 27.06           C  
+ATOM    583  N   ASN A 126     -12.203  -5.874   2.192  1.00 29.97           N  
+ATOM    584  CA  ASN A 126     -11.618  -4.889   1.280  1.00 29.53           C  
+ATOM    585  C   ASN A 126     -10.474  -4.077   1.881  1.00 28.46           C  
+ATOM    586  O   ASN A 126      -9.731  -3.409   1.152  1.00 27.57           O  
+ATOM    587  CB  ASN A 126     -12.696  -3.934   0.765  1.00 31.52           C  
+ATOM    588  CG  ASN A 126     -13.705  -4.624  -0.137  1.00 35.20           C  
+ATOM    589  OD1 ASN A 126     -13.335  -5.290  -1.107  1.00 34.80           O  
+ATOM    590  ND2 ASN A 126     -14.989  -4.464   0.179  1.00 35.33           N  
+ATOM    591  N   SER A 127     -10.337  -4.138   3.207  1.00 26.39           N  
+ATOM    592  CA  SER A 127      -9.290  -3.402   3.914  1.00 22.78           C  
+ATOM    593  C   SER A 127      -8.875  -4.049   5.239  1.00 22.54           C  
+ATOM    594  O   SER A 127      -9.570  -4.919   5.759  1.00 23.05           O  
+ATOM    595  CB  SER A 127      -9.756  -1.972   4.190  1.00 22.76           C  
+ATOM    596  OG  SER A 127     -10.808  -1.953   5.136  1.00 21.05           O  
+ATOM    597  N   LEU A 128      -7.730  -3.609   5.767  1.00 21.37           N  
+ATOM    598  CA  LEU A 128      -7.203  -4.062   7.056  1.00 21.58           C  
+ATOM    599  C   LEU A 128      -8.122  -3.546   8.155  1.00 20.84           C  
+ATOM    600  O   LEU A 128      -8.379  -4.256   9.115  1.00 19.67           O  
+ATOM    601  CB  LEU A 128      -5.792  -3.509   7.305  1.00 22.90           C  
+ATOM    602  CG  LEU A 128      -4.557  -4.084   6.607  1.00 25.32           C  
+ATOM    603  CD1 LEU A 128      -3.357  -3.203   6.934  1.00 22.55           C  
+ATOM    604  CD2 LEU A 128      -4.302  -5.521   7.069  1.00 27.12           C  
+ATOM    605  N   ASN A 129      -8.657  -2.334   7.948  1.00 19.42           N  
+ATOM    606  CA  ASN A 129      -9.568  -1.653   8.880  1.00 20.11           C  
+ATOM    607  C   ASN A 129     -10.851  -2.469   9.100  1.00 20.71           C  
+ATOM    608  O   ASN A 129     -11.305  -2.615  10.229  1.00 20.76           O  
+ATOM    609  CB  ASN A 129      -9.909  -0.245   8.347  1.00 18.00           C  
+ATOM    610  CG  ASN A 129     -10.371   0.733   9.443  1.00 18.48           C  
+ATOM    611  OD1 ASN A 129     -10.391   1.941   9.215  1.00 17.08           O  
+ATOM    612  ND2 ASN A 129     -10.754   0.215  10.617  1.00 16.45           N  
+ATOM    613  N   GLU A 130     -11.389  -3.029   8.017  1.00 21.12           N  
+ATOM    614  CA  GLU A 130     -12.604  -3.845   8.054  1.00 20.91           C  
+ATOM    615  C   GLU A 130     -12.335  -5.218   8.664  1.00 21.09           C  
+ATOM    616  O   GLU A 130     -13.199  -5.764   9.342  1.00 19.15           O  
+ATOM    617  CB  GLU A 130     -13.197  -3.977   6.646  1.00 23.33           C  
+ATOM    618  CG  GLU A 130     -13.766  -2.673   6.105  1.00 24.89           C  
+ATOM    619  CD  GLU A 130     -14.000  -2.708   4.606  1.00 25.07           C  
+ATOM    620  OE1 GLU A 130     -15.134  -3.002   4.186  1.00 26.47           O  
+ATOM    621  OE2 GLU A 130     -13.047  -2.438   3.845  1.00 27.33           O  
+ATOM    622  N   LEU A 131     -11.126  -5.747   8.446  1.00 20.16           N  
+ATOM    623  CA  LEU A 131     -10.707  -7.042   8.997  1.00 19.98           C  
+ATOM    624  C   LEU A 131     -10.618  -6.930  10.512  1.00 19.57           C  
+ATOM    625  O   LEU A 131     -11.118  -7.788  11.235  1.00 18.89           O  
+ATOM    626  CB  LEU A 131      -9.343  -7.464   8.416  1.00 20.26           C  
+ATOM    627  CG  LEU A 131      -8.713  -8.818   8.784  1.00 19.37           C  
+ATOM    628  CD1 LEU A 131      -7.996  -9.362   7.572  1.00 19.38           C  
+ATOM    629  CD2 LEU A 131      -7.762  -8.708   9.954  1.00 20.20           C  
+ATOM    630  N   VAL A 132      -9.955  -5.865  10.960  1.00 17.41           N  
+ATOM    631  CA  VAL A 132      -9.758  -5.562  12.371  1.00 18.29           C  
+ATOM    632  C   VAL A 132     -11.111  -5.349  13.071  1.00 17.07           C  
+ATOM    633  O   VAL A 132     -11.404  -6.020  14.058  1.00 17.71           O  
+ATOM    634  CB  VAL A 132      -8.837  -4.311  12.512  1.00 16.87           C  
+ATOM    635  CG1 VAL A 132      -8.968  -3.656  13.880  1.00 18.20           C  
+ATOM    636  CG2 VAL A 132      -7.393  -4.697  12.239  1.00 16.97           C  
+ATOM    637  N   ASP A 133     -11.945  -4.479  12.501  1.00 16.17           N  
+ATOM    638  CA  ASP A 133     -13.259  -4.158  13.065  1.00 19.73           C  
+ATOM    639  C   ASP A 133     -14.204  -5.336  13.200  1.00 19.14           C  
+ATOM    640  O   ASP A 133     -14.866  -5.478  14.224  1.00 21.64           O  
+ATOM    641  CB  ASP A 133     -13.919  -3.001  12.308  1.00 17.72           C  
+ATOM    642  CG  ASP A 133     -13.240  -1.666  12.580  1.00 21.83           C  
+ATOM    643  OD1 ASP A 133     -12.381  -1.595  13.495  1.00 20.87           O  
+ATOM    644  OD2 ASP A 133     -13.550  -0.687  11.865  1.00 22.47           O  
+ATOM    645  N   TYR A 134     -14.199  -6.210  12.196  1.00 19.30           N  
+ATOM    646  CA  TYR A 134     -15.034  -7.411  12.183  1.00 21.13           C  
+ATOM    647  C   TYR A 134     -14.611  -8.309  13.330  1.00 21.29           C  
+ATOM    648  O   TYR A 134     -15.444  -8.803  14.086  1.00 22.53           O  
+ATOM    649  CB  TYR A 134     -14.841  -8.161  10.858  1.00 21.62           C  
+ATOM    650  CG  TYR A 134     -15.520  -9.521  10.735  1.00 23.52           C  
+ATOM    651  CD1 TYR A 134     -16.893  -9.625  10.426  1.00 24.22           C  
+ATOM    652  CD2 TYR A 134     -14.774 -10.716  10.866  1.00 22.18           C  
+ATOM    653  CE1 TYR A 134     -17.513 -10.904  10.246  1.00 24.11           C  
+ATOM    654  CE2 TYR A 134     -15.374 -11.990  10.680  1.00 21.44           C  
+ATOM    655  CZ  TYR A 134     -16.741 -12.070  10.374  1.00 22.71           C  
+ATOM    656  OH  TYR A 134     -17.324 -13.303  10.225  1.00 25.11           O  
+ATOM    657  N   HIS A 135     -13.297  -8.459  13.469  1.00 20.34           N  
+ATOM    658  CA  HIS A 135     -12.720  -9.305  14.491  1.00 20.81           C  
+ATOM    659  C   HIS A 135     -12.758  -8.810  15.937  1.00 20.26           C  
+ATOM    660  O   HIS A 135     -12.248  -9.472  16.845  1.00 19.83           O  
+ATOM    661  CB  HIS A 135     -11.351  -9.795  14.043  1.00 19.83           C  
+ATOM    662  CG  HIS A 135     -11.422 -10.863  12.998  1.00 20.16           C  
+ATOM    663  ND1 HIS A 135     -11.950 -12.112  13.253  1.00 21.03           N  
+ATOM    664  CD2 HIS A 135     -11.056 -10.868  11.695  1.00 19.22           C  
+ATOM    665  CE1 HIS A 135     -11.902 -12.838  12.152  1.00 20.12           C  
+ATOM    666  NE2 HIS A 135     -11.365 -12.108  11.193  1.00 18.30           N  
+ATOM    667  N   ARG A 136     -13.447  -7.689  16.146  1.00 19.91           N  
+ATOM    668  CA  ARG A 136     -13.660  -7.125  17.478  1.00 22.49           C  
+ATOM    669  C   ARG A 136     -14.880  -7.814  18.093  1.00 22.68           C  
+ATOM    670  O   ARG A 136     -15.063  -7.789  19.302  1.00 23.55           O  
+ATOM    671  CB  ARG A 136     -13.924  -5.617  17.413  1.00 21.94           C  
+ATOM    672  CG  ARG A 136     -12.716  -4.780  17.067  1.00 20.26           C  
+ATOM    673  CD  ARG A 136     -13.104  -3.307  16.970  1.00 22.93           C  
+ATOM    674  NE  ARG A 136     -12.001  -2.476  16.487  1.00 20.56           N  
+ATOM    675  CZ  ARG A 136     -11.003  -2.024  17.244  1.00 22.88           C  
+ATOM    676  NH1 ARG A 136     -10.949  -2.315  18.542  1.00 21.22           N  
+ATOM    677  NH2 ARG A 136     -10.052  -1.273  16.702  1.00 20.45           N  
+ATOM    678  N   SER A 137     -15.695  -8.445  17.246  1.00 23.28           N  
+ATOM    679  CA  SER A 137     -16.901  -9.137  17.702  1.00 23.91           C  
+ATOM    680  C   SER A 137     -17.078 -10.563  17.191  1.00 23.12           C  
+ATOM    681  O   SER A 137     -18.079 -11.221  17.499  1.00 24.37           O  
+ATOM    682  CB  SER A 137     -18.132  -8.310  17.380  1.00 23.72           C  
+ATOM    683  OG  SER A 137     -18.100  -7.056  18.034  1.00 26.54           O  
+ATOM    684  N   THR A 138     -16.134 -11.017  16.370  1.00 23.28           N  
+ATOM    685  CA  THR A 138     -16.121 -12.384  15.854  1.00 21.21           C  
+ATOM    686  C   THR A 138     -14.689 -12.830  16.123  1.00 21.98           C  
+ATOM    687  O   THR A 138     -13.742 -12.115  15.794  1.00 20.52           O  
+ATOM    688  CB  THR A 138     -16.453 -12.461  14.340  1.00 22.06           C  
+ATOM    689  OG1 THR A 138     -17.783 -11.974  14.118  1.00 22.19           O  
+ATOM    690  CG2 THR A 138     -16.371 -13.907  13.824  1.00 23.42           C  
+ATOM    691  N   SER A 139     -14.538 -14.006  16.726  1.00 20.73           N  
+ATOM    692  CA  SER A 139     -13.226 -14.538  17.078  1.00 20.97           C  
+ATOM    693  C   SER A 139     -12.190 -14.660  15.965  1.00 20.35           C  
+ATOM    694  O   SER A 139     -12.499 -15.126  14.865  1.00 21.60           O  
+ATOM    695  CB  SER A 139     -13.381 -15.883  17.775  1.00 21.71           C  
+ATOM    696  OG  SER A 139     -12.118 -16.413  18.145  1.00 23.49           O  
+ATOM    697  N   VAL A 140     -10.960 -14.238  16.269  1.00 21.02           N  
+ATOM    698  CA  VAL A 140      -9.844 -14.335  15.316  1.00 21.99           C  
+ATOM    699  C   VAL A 140      -9.338 -15.766  15.215  1.00 22.42           C  
+ATOM    700  O   VAL A 140      -8.619 -16.109  14.281  1.00 21.90           O  
+ATOM    701  CB  VAL A 140      -8.621 -13.442  15.684  1.00 21.07           C  
+ATOM    702  CG1 VAL A 140      -8.880 -12.049  15.325  1.00 23.61           C  
+ATOM    703  CG2 VAL A 140      -8.283 -13.532  17.149  1.00 19.28           C  
+ATOM    704  N   SER A 141      -9.710 -16.579  16.200  1.00 23.82           N  
+ATOM    705  CA  SER A 141      -9.300 -17.976  16.272  1.00 25.41           C  
+ATOM    706  C   SER A 141     -10.499 -18.913  16.141  1.00 27.82           C  
+ATOM    707  O   SER A 141     -11.617 -18.575  16.538  1.00 27.29           O  
+ATOM    708  CB  SER A 141      -8.590 -18.222  17.605  1.00 24.04           C  
+ATOM    709  OG  SER A 141      -8.123 -19.552  17.726  1.00 25.85           O  
+ATOM    710  N   ARG A 142     -10.244 -20.102  15.603  1.00 31.60           N  
+ATOM    711  CA  ARG A 142     -11.278 -21.120  15.431  1.00 33.71           C  
+ATOM    712  C   ARG A 142     -11.369 -22.015  16.662  1.00 34.10           C  
+ATOM    713  O   ARG A 142     -12.461 -22.423  17.057  1.00 34.78           O  
+ATOM    714  CB  ARG A 142     -10.970 -21.996  14.224  1.00 36.79           C  
+ATOM    715  CG  ARG A 142     -10.892 -21.281  12.890  1.00 39.27           C  
+ATOM    716  CD  ARG A 142     -10.683 -22.297  11.774  1.00 44.43           C  
+ATOM    717  NE  ARG A 142      -9.473 -23.093  11.993  1.00 45.39           N  
+ATOM    718  CZ  ARG A 142      -9.432 -24.421  11.971  1.00 46.90           C  
+ATOM    719  NH1 ARG A 142     -10.535 -25.123  11.724  1.00 48.89           N  
+ATOM    720  NH2 ARG A 142      -8.306 -25.051  12.285  1.00 48.76           N  
+ATOM    721  N   ASN A 143     -10.211 -22.304  17.259  1.00 34.97           N  
+ATOM    722  CA  ASN A 143     -10.095 -23.169  18.441  1.00 35.41           C  
+ATOM    723  C   ASN A 143     -10.477 -22.491  19.755  1.00 34.85           C  
+ATOM    724  O   ASN A 143     -10.878 -23.159  20.714  1.00 35.46           O  
+ATOM    725  CB  ASN A 143      -8.661 -23.706  18.562  1.00 37.97           C  
+ATOM    726  CG  ASN A 143      -8.246 -24.553  17.378  1.00 40.37           C  
+ATOM    727  OD1 ASN A 143      -8.949 -25.492  16.987  1.00 42.11           O  
+ATOM    728  ND2 ASN A 143      -7.091 -24.227  16.796  1.00 41.15           N  
+ATOM    729  N   GLN A 144     -10.276 -21.176  19.819  1.00 33.24           N  
+ATOM    730  CA  GLN A 144     -10.573 -20.380  21.014  1.00 32.51           C  
+ATOM    731  C   GLN A 144     -11.378 -19.136  20.653  1.00 31.86           C  
+ATOM    732  O   GLN A 144     -11.368 -18.696  19.497  1.00 31.23           O  
+ATOM    733  CB  GLN A 144      -9.266 -19.934  21.691  1.00 31.99           C  
+ATOM    734  CG  GLN A 144      -8.363 -21.062  22.192  1.00 33.51           C  
+ATOM    735  CD  GLN A 144      -6.966 -20.590  22.526  1.00 35.05           C  
+ATOM    736  OE1 GLN A 144      -6.270 -20.004  21.688  1.00 34.10           O  
+ATOM    737  NE2 GLN A 144      -6.536 -20.856  23.751  1.00 33.43           N  
+ATOM    738  N   GLN A 145     -12.067 -18.570  21.645  1.00 30.23           N  
+ATOM    739  CA  GLN A 145     -12.847 -17.355  21.439  1.00 30.26           C  
+ATOM    740  C   GLN A 145     -12.024 -16.141  21.873  1.00 28.21           C  
+ATOM    741  O   GLN A 145     -11.955 -15.805  23.060  1.00 30.32           O  
+ATOM    742  CB  GLN A 145     -14.200 -17.421  22.168  1.00 31.31           C  
+ATOM    743  CG  GLN A 145     -15.154 -18.522  21.672  1.00 35.74           C  
+ATOM    744  CD  GLN A 145     -15.483 -18.428  20.177  1.00 39.42           C  
+ATOM    745  OE1 GLN A 145     -16.085 -17.451  19.710  1.00 38.32           O  
+ATOM    746  NE2 GLN A 145     -15.084 -19.451  19.423  1.00 38.80           N  
+ATOM    747  N   ILE A 146     -11.317 -15.560  20.900  1.00 25.66           N  
+ATOM    748  CA  ILE A 146     -10.450 -14.395  21.112  1.00 23.43           C  
+ATOM    749  C   ILE A 146     -10.995 -13.189  20.343  1.00 22.82           C  
+ATOM    750  O   ILE A 146     -11.016 -13.185  19.109  1.00 22.93           O  
+ATOM    751  CB  ILE A 146      -8.983 -14.666  20.636  1.00 22.36           C  
+ATOM    752  CG1 ILE A 146      -8.491 -16.043  21.109  1.00 22.20           C  
+ATOM    753  CG2 ILE A 146      -8.052 -13.539  21.114  1.00 22.36           C  
+ATOM    754  CD1 ILE A 146      -7.118 -16.438  20.623  1.00 23.55           C  
+ATOM    755  N   PHE A 147     -11.381 -12.154  21.083  1.00 21.92           N  
+ATOM    756  CA  PHE A 147     -11.935 -10.939  20.497  1.00 22.35           C  
+ATOM    757  C   PHE A 147     -10.938  -9.786  20.596  1.00 22.81           C  
+ATOM    758  O   PHE A 147     -10.404  -9.507  21.672  1.00 22.21           O  
+ATOM    759  CB  PHE A 147     -13.248 -10.564  21.200  1.00 25.62           C  
+ATOM    760  CG  PHE A 147     -14.297 -11.641  21.155  1.00 28.77           C  
+ATOM    761  CD1 PHE A 147     -14.512 -12.474  22.275  1.00 31.16           C  
+ATOM    762  CD2 PHE A 147     -15.081 -11.834  20.000  1.00 29.72           C  
+ATOM    763  CE1 PHE A 147     -15.506 -13.498  22.246  1.00 31.49           C  
+ATOM    764  CE2 PHE A 147     -16.077 -12.850  19.951  1.00 30.08           C  
+ATOM    765  CZ  PHE A 147     -16.288 -13.683  21.080  1.00 32.10           C  
+ATOM    766  N   LEU A 148     -10.734  -9.084  19.482  1.00 20.63           N  
+ATOM    767  CA  LEU A 148      -9.800  -7.956  19.434  1.00 22.54           C  
+ATOM    768  C   LEU A 148     -10.291  -6.697  20.130  1.00 23.59           C  
+ATOM    769  O   LEU A 148     -11.424  -6.266  19.915  1.00 22.14           O  
+ATOM    770  CB  LEU A 148      -9.474  -7.572  17.986  1.00 21.74           C  
+ATOM    771  CG  LEU A 148      -8.877  -8.570  17.008  1.00 21.44           C  
+ATOM    772  CD1 LEU A 148      -8.507  -7.857  15.703  1.00 19.29           C  
+ATOM    773  CD2 LEU A 148      -7.674  -9.244  17.609  1.00 20.25           C  
+ATOM    774  N   ARG A 149      -9.442  -6.130  20.982  1.00 23.79           N  
+ATOM    775  CA  ARG A 149      -9.756  -4.880  21.663  1.00 25.57           C  
+ATOM    776  C   ARG A 149      -8.502  -4.020  21.705  1.00 24.79           C  
+ATOM    777  O   ARG A 149      -7.402  -4.535  21.879  1.00 25.69           O  
+ATOM    778  CB  ARG A 149     -10.366  -5.107  23.054  1.00 30.11           C  
+ATOM    779  CG  ARG A 149      -9.527  -5.865  24.063  1.00 34.12           C  
+ATOM    780  CD  ARG A 149     -10.291  -6.020  25.363  1.00 35.74           C  
+ATOM    781  NE  ARG A 149     -10.657  -4.727  25.938  1.00 39.28           N  
+ATOM    782  CZ  ARG A 149     -11.128  -4.554  27.172  1.00 40.01           C  
+ATOM    783  NH1 ARG A 149     -11.295  -5.593  27.985  1.00 38.81           N  
+ATOM    784  NH2 ARG A 149     -11.430  -3.335  27.596  1.00 40.58           N  
+ATOM    785  N   ASP A 150      -8.662  -2.721  21.463  1.00 23.60           N  
+ATOM    786  CA  ASP A 150      -7.546  -1.768  21.451  1.00 24.45           C  
+ATOM    787  C   ASP A 150      -6.606  -1.853  22.647  1.00 25.46           C  
+ATOM    788  O   ASP A 150      -7.029  -2.173  23.759  1.00 26.40           O  
+ATOM    789  CB  ASP A 150      -8.066  -0.331  21.327  1.00 24.39           C  
+ATOM    790  CG  ASP A 150      -8.757  -0.062  20.000  1.00 24.29           C  
+ATOM    791  OD1 ASP A 150      -8.497  -0.778  19.009  1.00 23.90           O  
+ATOM    792  OD2 ASP A 150      -9.546   0.900  19.946  1.00 27.60           O  
+ATOM    793  N   ILE A 151      -5.320  -1.624  22.391  1.00 26.29           N  
+ATOM    794  CA  ILE A 151      -4.304  -1.629  23.441  1.00 26.99           C  
+ATOM    795  C   ILE A 151      -4.560  -0.470  24.407  1.00 28.61           C  
+ATOM    796  O   ILE A 151      -5.149   0.550  24.018  1.00 26.09           O  
+ATOM    797  CB  ILE A 151      -2.861  -1.494  22.875  1.00 27.96           C  
+ATOM    798  CG1 ILE A 151      -2.769  -0.374  21.829  1.00 29.06           C  
+ATOM    799  CG2 ILE A 151      -2.395  -2.815  22.333  1.00 27.78           C  
+ATOM    800  CD1 ILE A 151      -1.557   0.501  21.997  1.00 29.36           C  
+ATOM    801  N   GLU A 152      -4.214  -0.674  25.676  1.00 29.81           N  
+ATOM    802  CA  GLU A 152      -4.385   0.354  26.695  1.00 33.50           C  
+ATOM    803  C   GLU A 152      -3.187   1.284  26.620  1.00 35.21           C  
+ATOM    804  O   GLU A 152      -2.074   0.931  27.014  1.00 35.73           O  
+ATOM    805  CB  GLU A 152      -4.504  -0.260  28.087  1.00 35.54           C  
+ATOM    806  CG  GLU A 152      -5.839  -0.937  28.360  1.00 38.01           C  
+ATOM    807  CD  GLU A 152      -6.617  -0.299  29.503  1.00 41.18           C  
+ATOM    808  OE1 GLU A 152      -6.027  -0.053  30.581  1.00 40.22           O  
+ATOM    809  OE2 GLU A 152      -7.829  -0.057  29.320  1.00 44.38           O  
+ATOM    810  N   GLN A 153      -3.429   2.445  26.027  1.00 36.81           N  
+ATOM    811  CA  GLN A 153      -2.418   3.472  25.843  1.00 39.68           C  
+ATOM    812  C   GLN A 153      -2.648   4.645  26.792  1.00 40.16           C  
+ATOM    813  O   GLN A 153      -3.772   4.904  27.228  1.00 41.16           O  
+ATOM    814  CB  GLN A 153      -2.410   3.948  24.370  1.00 41.39           C  
+ATOM    815  CG  GLN A 153      -3.628   4.779  23.879  1.00 42.78           C  
+ATOM    816  CD  GLN A 153      -4.953   4.030  23.922  1.00 45.15           C  
+ATOM    817  OE1 GLN A 153      -5.703   4.125  24.905  1.00 46.32           O  
+ATOM    818  NE2 GLN A 153      -5.253   3.283  22.853  1.00 42.56           N  
+ATOM    819  N   VAL A 154      -1.558   5.322  27.121  1.00 40.20           N  
+ATOM    820  CA  VAL A 154      -1.569   6.490  27.988  1.00 40.79           C  
+ATOM    821  C   VAL A 154      -1.331   7.688  27.052  1.00 40.93           C  
+ATOM    822  O   VAL A 154      -0.487   7.595  26.156  1.00 40.96           O  
+ATOM    823  CB  VAL A 154      -0.435   6.363  29.067  1.00 40.84           C  
+ATOM    824  CG1 VAL A 154      -0.185   7.673  29.754  1.00 41.51           C  
+ATOM    825  CG2 VAL A 154      -0.818   5.320  30.120  1.00 41.19           C  
+ATOM    826  N   PRO A 155      -2.113   8.789  27.194  1.00 41.47           N  
+ATOM    827  CA  PRO A 155      -1.905   9.957  26.319  1.00 42.60           C  
+ATOM    828  C   PRO A 155      -0.535  10.645  26.489  1.00 42.98           C  
+ATOM    829  O   PRO A 155      -0.264  11.200  27.576  1.00 43.40           O  
+ATOM    830  CB  PRO A 155      -3.078  10.879  26.686  1.00 42.83           C  
+ATOM    831  CG  PRO A 155      -3.438  10.461  28.097  1.00 42.81           C  
+ATOM    832  CD  PRO A 155      -3.337   8.969  28.002  1.00 42.03           C  
+HETATM  833  C   AYI A   1      -3.059 -20.043   9.725  1.00 22.23           C  
+HETATM  834  N   AYI A   1      -3.255 -19.243  12.043  1.00 22.20           N  
+HETATM  835  O   AYI A   1      -3.396 -20.048   8.542  1.00 21.84           O  
+HETATM  836  CA  AYI A   1      -4.003 -19.519  10.808  1.00 21.59           C  
+HETATM  837  CB  AYI A   1      -4.723 -18.261  10.316  1.00 21.51           C  
+HETATM  838  CG  AYI A   1      -3.746 -17.157   9.909  1.00 19.80           C  
+HETATM  839  NAE AYI A   1      -1.888 -20.486  10.172  1.00 20.26           N  
+HETATM  840  OD1 AYI A   1      -2.672 -17.013  10.490  1.00 20.94           O  
+HETATM  841  ND2 AYI A   1      -4.160 -16.386   8.906  1.00 19.94           N  
+HETATM  842  CAA AYI A   1      -2.119 -19.695  17.244  1.00 26.11           C  
+HETATM  843  OAI AYI A   1      -3.808 -21.224  12.970  1.00 20.09           O  
+HETATM  844  CAR AYI A   1      -2.544 -18.466  16.439  1.00 21.49           C  
+HETATM  845  CAC AYI A   1      -4.602 -19.587  15.525  1.00 20.39           C  
+HETATM  846  NAV AYI A   1      -1.169 -19.072  13.956  1.00 22.56           N  
+HETATM  847  CBA AYI A   1      -3.223 -20.142  13.023  1.00 22.21           C  
+HETATM  848  CBE AYI A   1      -3.297 -18.870  15.169  1.00 22.75           C  
+HETATM  849  CBG AYI A   1      -2.431 -19.756  14.273  1.00 20.42           C  
+HETATM  850  CAB AYI A   1       5.955 -19.410  13.421  1.00 32.64           C  
+HETATM  851  OAH AYI A   1       3.642 -18.092  13.918  1.00 26.67           O  
+HETATM  852  OAJ AYI A   1      -0.350 -20.706  12.625  1.00 24.62           O  
+HETATM  853  OAK AYI A   1       6.600 -14.261  10.518  1.00 26.03           O  
+HETATM  854  OAL AYI A   1       5.770 -11.840  10.648  1.00 26.28           O  
+HETATM  855  OAM AYI A   1       5.271 -13.466  12.568  1.00 25.20           O  
+HETATM  856  CAN AYI A   1       2.318 -14.918  11.347  1.00 24.37           C  
+HETATM  857  CAO AYI A   1       4.164 -16.101  10.364  1.00 27.23           C  
+HETATM  858  CAP AYI A   1       1.699 -16.129  11.636  1.00 25.20           C  
+HETATM  859  CAQ AYI A   1       3.544 -17.312  10.653  1.00 28.17           C  
+HETATM  860  NAT AYI A   1       4.660 -19.811  12.854  1.00 31.47           N  
+HETATM  861  OAW AYI A   1       4.071 -13.712  10.290  1.00 25.65           O  
+HETATM  862  CAZ AYI A   1       3.598 -19.081  13.188  1.00 28.62           C  
+HETATM  863  CBB AYI A   1      -0.235 -19.615  13.180  1.00 24.38           C  
+HETATM  864  CBC AYI A   1       3.551 -14.900  10.705  1.00 25.82           C  
+HETATM  865  CBD AYI A   1       2.307 -17.330  11.288  1.00 26.35           C  
+HETATM  866  CBH AYI A   1       2.272 -19.572  12.607  1.00 26.80           C  
+HETATM  867  CBI AYI A   1       1.032 -18.772  13.005  1.00 25.64           C  
+HETATM  868  CBJ AYI A   1       1.594 -18.653  11.586  1.00 26.69           C  
+HETATM  869  PBK AYI A   1       5.493 -13.391  10.976  1.00 25.47           P  
+TER     870      AYI A   1                                                      
+END   
\ No newline at end of file
diff --git a/examples/demos/data/sh2.vert b/examples/demos/data/sh2.vert
new file mode 100644
index 0000000000000000000000000000000000000000..6d1ac0c2b8f1ed3a774a061c27b4203df2c79511
--- /dev/null
+++ b/examples/demos/data/sh2.vert
@@ -0,0 +1,23745 @@
+# MSMS solvent excluded surface vertices for /tmp/tmpNakzL3/entity
+#vertex #sphere density probe_r
+  23742     832  5.00  1.50
+  -17.880    -6.992    16.257     0.144     0.753    -0.642       0     682  1 
+  -17.880    -6.455    16.655     0.144     0.396    -0.907       0     683  1 
+  -16.274    -5.671    14.763    -0.926    -0.127     0.355       0     640  1 
+  -18.176    -7.843    19.332    -0.050    -0.518     0.854       0     683  1 
+  -18.196    -8.477    19.121    -0.036    -0.095     0.995       0     682  1 
+  -17.628    -8.859    19.269    -0.415     0.159     0.896       0     679  1 
+  -18.022    -9.559    18.978    -0.641    -0.241     0.729       0     679  1 
+  -18.590    -9.178    18.829    -0.262    -0.496     0.828       0     682  1 
+  -18.534   -10.567    18.793    -0.299     0.430     0.852       0     681  1 
+  -18.973   -10.673    16.399    -0.588     0.361    -0.724       0     681  1 
+  -19.060    -9.291    16.267    -0.531    -0.561    -0.636       0     682  1 
+  -18.826   -11.047    14.720    -0.686     0.610     0.396       0     689  1 
+  -18.120   -10.493    14.173    -0.222     0.974     0.036       0     689  1 
+  -18.304    -8.698    15.682    -0.098    -0.222    -0.970       0     682  1 
+  -16.958    -8.918    14.157    -0.996    -0.076     0.047       0     648  1 
+  -16.523    -7.763    14.339    -0.710     0.685     0.167       0     648  1 
+  -17.839    -7.462    15.877     0.168     0.484    -0.859       0     682  1 
+  -16.236    -6.111    14.408    -0.901    -0.416     0.121       0     640  1 
+  -16.538    -7.748    14.055    -0.720     0.694    -0.020       0     648  1 
+  -16.251    -6.097    14.124    -0.911    -0.407    -0.066       0     640  1 
+  -16.425    -7.032    13.175    -0.795     0.217     0.567       0     646  1 
+  -16.305    -6.229    12.404    -0.726     0.676     0.126       0     646  1 
+  -16.139    -5.346    13.404    -0.837     0.087    -0.540       0     640  1 
+  -15.922    -5.271    12.874    -0.982     0.037    -0.186       0     639  1 
+  -15.712    -4.452    13.123    -0.862     0.505    -0.044       0     639  1 
+  -15.942    -4.580    13.637    -0.708     0.591    -0.386       0     640  1 
+  -15.581    -3.374    12.711    -0.949    -0.213     0.230       0     641  1 
+  -14.848    -2.827    13.781    -0.531     0.100     0.842       0     641  1 
+  -15.258    -4.068    14.636    -0.258     0.927     0.271       0     640  1 
+  -14.472    -2.968    15.932    -0.782     0.194    -0.593       0     673  1 
+  -14.795    -3.507    16.566    -0.966    -0.114    -0.231       0     673  1 
+  -15.560    -4.573    15.229    -0.456     0.596     0.661       0     640  1 
+  -15.173    -4.574    16.771    -0.714     0.596    -0.367       0     671  1 
+  -15.527    -5.201    16.848    -0.916     0.238    -0.323       0     671  1 
+  -15.890    -5.159    15.301    -0.674     0.210     0.708       0     640  1 
+  -17.497    -5.943    17.193     0.397     0.732    -0.553       0     683  1 
+  -15.235    -5.321    18.534    -0.749     0.169     0.641       0     671  1 
+  -17.223    -6.055    18.769     0.577     0.658     0.484       0     683  1 
+  -15.715    -6.419    19.399    -0.429     0.901     0.064       0     670  1 
+  -16.372    -8.048    20.031    -0.861    -0.170     0.479       0     670  1 
+  -17.880    -7.684    19.401     0.145    -0.413     0.899       0     683  1 
+  -17.311    -8.688    19.343    -0.235     0.256     0.938       0     679  1 
+  -16.049    -8.601    20.126    -0.649    -0.534     0.542       0     670  1 
+  -16.966    -9.280    19.445    -0.037    -0.082     0.996       0     679  1 
+  -16.126   -10.525    20.506    -0.597     0.748     0.289       0     762  1 
+  -16.550   -10.948    20.345    -0.839     0.507     0.197       0     762  1 
+  -17.390    -9.703    19.284    -0.279    -0.323     0.904       0     679  1 
+  -17.010   -11.417    20.322    -0.533     0.819     0.212       0     764  1 
+  -17.207   -11.537    20.196    -0.646     0.751     0.140       0     764  1 
+  -17.587    -9.823    19.158    -0.392    -0.392     0.832       0     679  1 
+  -18.128   -10.813    18.962    -0.032     0.268     0.963       0     681  1 
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+   -0.277   -16.734    13.082     0.224    -0.257    -0.940   -1932     421  1 
+   -0.514   -16.399    12.856     0.382    -0.481    -0.789    1932     421  1 
+   -0.695   -16.134    12.515     0.502    -0.657    -0.562    1932     429  1 
+   -0.802   -15.966    12.091     0.574    -0.770    -0.279   -1932     429  1 
+   -0.723   -16.982    13.136    -0.070    -0.420    -0.905   -1932     421  1 
+   -0.924   -16.627    12.906     0.064    -0.657    -0.751    1932     421  1 
+   -1.116   -16.368    12.566     0.192    -0.830    -0.524    1932     429  1 
+   -1.280   -16.231    12.149     0.301    -0.921    -0.246   -1932     429  1 
+   -1.188   -17.096    13.321    -0.376    -0.496    -0.783   -1932     421  1 
+   -1.352   -16.732    13.076    -0.266    -0.738    -0.620    1932     421  1 
+   -1.555   -16.476    12.740    -0.131    -0.909    -0.396    1932     429  1 
+   -1.777   -16.353    12.346     0.017    -0.991    -0.134   -1932     429  1 
+   -1.740   -16.700    13.343    -0.566    -0.713    -0.413   -1932     421  1 
+   -1.953   -16.443    13.015    -0.424    -0.885    -0.194   -1932     429  1 
+   -1.985   -16.822    13.717    -0.403    -0.632    -0.662   -1933     421  1 
+   -2.416   -16.671    13.730    -0.115    -0.733    -0.671   -1933     421  1 
+   -2.864   -16.622    13.649     0.183    -0.765    -0.617   -1933     435  1 
+   -3.286   -16.680    13.483     0.464    -0.727    -0.506   -1933     435  1 
+   -1.713   -17.298    14.068    -0.721    -0.629    -0.291   -1933     421  1 
+   -2.066   -17.007    14.074    -0.486    -0.823    -0.295    1933     421  1 
+   -2.486   -16.831    14.038    -0.206    -0.940    -0.271    1933     421  1 
+   -2.935   -16.786    13.964     0.094    -0.970    -0.222    1933     435  1 
+   -3.371   -16.876    13.860     0.384    -0.910    -0.153    1933     435  1 
+   -3.753   -17.092    13.734     0.639    -0.766    -0.069   -1933     435  1 
+   -2.129   -17.011    14.479    -0.551    -0.826     0.121   -1933     421  1 
+   -2.540   -16.834    14.388    -0.276    -0.944     0.182   -1933     421  1 
+   -2.991   -16.788    14.322     0.024    -0.974     0.226   -1933     435  1 
+   -3.437   -16.879    14.288     0.322    -0.914     0.248   -1933     435  1 
+   -3.353   -16.547    13.137     0.509    -0.816    -0.275   -1935     435  1 
+   -3.001   -16.353    12.995     0.274    -0.945    -0.180   -1935     429  1 
+   -2.615   -16.274    12.830     0.017    -0.997    -0.071   -1935     429  1 
+   -3.901   -16.699    12.749     0.555    -0.541    -0.632   -1935     435  1 
+   -3.580   -16.424    12.700     0.341    -0.725    -0.599    1935     435  1 
+   -3.217   -16.236    12.578     0.099    -0.850    -0.517    1935     429  1 
+   -2.843   -16.151    12.393    -0.151    -0.907    -0.394    1935     429  1 
+   -2.486   -16.176    12.161    -0.388    -0.890    -0.239   -1935     429  1 
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+   -3.452   -15.958    12.259    -0.091    -0.625    -0.775   -1935     429  1 
+   -3.089   -15.860    12.059    -0.333    -0.691    -0.642   -1935     429  1 
+   -3.829   -15.915    12.206     0.159    -0.654    -0.740   -1936     432  1 
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+   -4.197   -15.676    12.019    -0.087    -0.494    -0.865    1936     432  1 
+   -3.835   -15.360    11.665    -0.328    -0.704    -0.629   -1936     432  1 
+   -4.551   -15.362    11.963    -0.325    -0.283    -0.903   -1936     432  1 
+   -2.986   -15.345    11.298    -0.369    -0.824    -0.431   -1939     432  1 
+   -2.634   -15.406    10.883    -0.603    -0.783    -0.153   -1939     439  1 
+   -3.174   -15.086    11.097    -0.519    -0.617    -0.591   -1939     432  1 
+   -2.818   -15.153    10.686    -0.757    -0.572    -0.317   -1939     439  1 
+   -2.491   -15.572    11.017    -0.699    -0.672    -0.243   -1941     429  1 
+   -2.033   -15.924    10.529    -0.518    -0.831     0.204   -1941     439  1 
+   -2.138   -15.857    11.106    -0.448    -0.875    -0.181    1941     429  1 
+   -2.348   -15.993    11.640    -0.309    -0.785    -0.537   -1941     429  1 
+   -1.588   -16.084    10.639    -0.231    -0.933     0.275   -1941     439  1 
+   -1.715   -16.009    11.210    -0.147    -0.983    -0.106    1941     429  1 
+   -1.876   -16.162    11.756    -0.039    -0.881    -0.471   -1941     429  1 
+   -1.117   -16.085    10.754     0.073    -0.934     0.349   -1941     439  1 
+   -1.267   -16.010    11.319     0.173    -0.985    -0.028    1941     429  1 
+   -1.376   -16.163    11.878     0.246    -0.882    -0.401   -1941     429  1 
+   -0.670   -15.929    10.861     0.361    -0.833     0.418   -1941     439  1 
+   -0.842   -15.861    11.422     0.476    -0.879     0.045    1941     429  1 
+   -0.903   -15.997    11.992     0.517    -0.788    -0.336   -1941     429  1 
+   -0.487   -15.578    11.506     0.729    -0.677     0.105   -1941     429  1 
+    0.038   -15.335    10.767     0.818    -0.450     0.357   -1942     439  1 
+    0.112   -15.052    11.320     0.769    -0.639    -0.012   -1942     430  1 
+   -0.161   -15.284    12.037     0.634    -0.762    -0.132   -1946     430  1 
+   -0.100   -15.385    12.449     0.593    -0.695    -0.407   -1946     420  1 
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+    0.276   -14.640    12.165     0.958    -0.284    -0.037   -1946     430  1 
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+    0.471   -14.927    12.940     0.828    -0.093    -0.553   -1946     420  1 
+    0.345   -14.456    12.194     0.912    -0.407    -0.056   -1948     430  1 
+    0.460   -14.422    12.626     0.835    -0.429    -0.344   -1948     430  1 
+    0.687   -14.446    13.012     0.684    -0.413    -0.601   -1948     422  1 
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+    1.387   -14.653    13.515     0.217    -0.275    -0.936   -1948     422  1 
+    0.426   -14.023    12.195     0.997     0.049    -0.055   -1948     430  1 
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+    0.741   -14.158    13.012     0.788     0.139    -0.600   -1948     422  1 
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+    0.493   -13.934    10.460     0.979     0.035     0.199   -1951     440  1 
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+    0.521   -13.470    10.656     0.978    -0.204     0.032   -1953     431  1 
+    0.831   -13.493     9.795     0.772    -0.189     0.607   -1955     440  1 
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+    1.316   -12.784     9.802     0.448    -0.661     0.602   -1955     340  1 
+    1.655   -12.541     9.921     0.222    -0.823     0.522   -1955     340  1 
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+    0.930   -13.548     9.610     0.876    -0.246     0.415   -1955     440  1 
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+    1.382   -12.820     9.682     0.575    -0.731     0.368   -1955     340  1 
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+    2.116   -12.453     9.934     0.086    -0.976     0.200   -1955     340  1 
+    1.143   -13.994     9.218     0.734     0.052     0.677   -1956     440  1 
+    1.555   -14.005     8.904     0.460     0.059     0.886   -1956     446  1 
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+    1.554   -14.112     8.905     0.459    -0.049     0.887   -1956     446  1 
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+    2.639   -12.807     9.304    -0.263    -0.740     0.620   -1958     340  1 
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+    3.311   -13.958     8.769     0.211     0.073     0.975   -1958     446  1 
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+    3.122   -12.783     9.303     0.337    -0.710     0.619    1958     340  1 
+    3.145   -12.540     9.678     0.322    -0.872     0.369    1958     340  1 
+    3.212   -12.413    10.102     0.277    -0.957     0.086   -1958     340  1 
+    3.674   -13.273     8.579     0.704     0.016     0.710   -1958     446  1 
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+    3.507   -12.574     9.098     0.816    -0.450     0.364   -1958     340  1 
+    3.586   -12.300     9.443     0.763    -0.632     0.134   -1958     340  1 
+    4.161   -13.280     8.256     0.379     0.020     0.925   -1960     446  1 
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+    4.818   -12.596     8.297    -0.058    -0.436     0.898   -1960     284  1 
+    5.150   -12.338     8.529    -0.280    -0.608     0.743   -1960     284  1 
+    4.269   -13.376     8.201     0.488    -0.077     0.870   -1960     446  1 
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+    4.903   -12.672     8.253     0.065    -0.546     0.835   -1960     284  1 
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+    4.426   -13.834     8.163     0.383     0.229     0.895   -1962     446  1 
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+    5.288   -13.880     8.086    -0.192     0.259     0.947   -1962     299  1 
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+    6.055   -13.795     8.482    -0.703     0.203     0.682   -1962     299  1 
+    4.069   -14.345     8.375     0.645    -0.148     0.750   -1962     446  1 
+    4.440   -14.250     8.161     0.398    -0.211     0.893    1962     446  1 
+    4.861   -14.182     8.061     0.117    -0.257     0.959    1962     446  1 
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+    5.711   -14.147     8.228    -0.450    -0.280     0.848    1962     299  1 
+    6.068   -14.184     8.481    -0.688    -0.255     0.680    1962     299  1 
+    6.336   -14.253     8.820    -0.866    -0.209     0.453   -1962     299  1 
+    4.152   -14.836     8.079     0.692    -0.429     0.581   -1962     446  1 
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+    4.905   -14.443     7.903     0.190    -0.690     0.698    1962     446  1 
+    5.335   -14.373     7.948    -0.097    -0.737     0.669    1962     299  1 
+    5.753   -14.397     8.078    -0.375    -0.721     0.582    1962     299  1 
+    6.123   -14.513     8.282    -0.622    -0.644     0.446    1962     299  1 
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+    4.587   -14.789     7.588     0.554    -0.782     0.286   -1962     446  1 
+    4.970   -14.582     7.635     0.298    -0.920     0.254   -1962     446  1 
+    5.392   -14.493     7.716     0.017    -0.980     0.200   -1962     299  1 
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+    6.205   -14.688     7.944    -0.525    -0.850     0.048   -1962     299  1 
+    3.933   -15.391     7.676     0.567    -0.746     0.350   -1963     446  1 
+    4.099   -15.758     7.098     0.457    -0.500     0.736   -1963     447  1 
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+    3.716   -15.966     7.111     0.210    -0.634     0.744   -1963     447  1 
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+    3.303   -16.088     7.042    -0.057    -0.713     0.699   -1963     447  1 
+    4.731   -15.132     6.973     0.458    -0.554     0.696   -1965     447  1 
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+    5.514   -14.703     7.208    -0.064    -0.840     0.539   -1965     299  1 
+    5.911   -14.663     7.451    -0.329    -0.866     0.377   -1965     299  1 
+    6.260   -14.751     7.749    -0.562    -0.808     0.178   -1965     299  1 
+    4.737   -15.586     6.435     0.868    -0.389     0.308   -1965     447  1 
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+    5.235   -14.906     6.813     0.537    -0.842     0.055    1965     447  1 
+    5.615   -14.736     7.025     0.283    -0.955    -0.086    1965     299  1 
+    6.037   -14.706     7.223     0.002    -0.976    -0.218    1965     299  1 
+    6.460   -14.817     7.390    -0.280    -0.902    -0.330    1965     299  1 
+    6.841   -15.060     7.509    -0.534    -0.740    -0.409   -1965     299  1 
+    5.048   -14.975     6.274     0.900    -0.335    -0.278   -1965     447  1 
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+    5.674   -14.623     6.855     0.483    -0.570    -0.665   -1965     299  1 
+    6.110   -14.565     7.013     0.192    -0.608    -0.770   -1965     299  1 
+    6.575   -14.595     7.058    -0.117    -0.588    -0.800   -1965     299  1 
+    5.062   -14.822     5.674     0.891    -0.437     0.123   -1967     447  1 
+    5.351   -14.481     5.460     0.699    -0.664     0.265   -1967     304  1 
+    5.753   -14.249     5.290     0.431    -0.819     0.378   -1967     304  1 
+    4.776   -15.406     5.404     0.893    -0.273    -0.357   -1967     447  1 
+    4.943   -14.964     5.258     0.782    -0.567    -0.260    1967     447  1 
+    5.239   -14.614     5.069     0.585    -0.800    -0.134    1967     304  1 
+    5.629   -14.396     4.859     0.324    -0.946     0.007    1967     304  1 
+    6.073   -14.331     4.649     0.029    -0.989     0.146   -1967     304  1 
+    4.484   -15.390     4.938     0.705    -0.263    -0.658   -1967     447  1 
+    4.703   -14.951     4.872     0.560    -0.556    -0.614    1967     447  1 
+    5.012   -14.603     4.706     0.354    -0.788    -0.504    1967     304  1 
+    5.379   -14.383     4.458     0.109    -0.935    -0.338    1967     304  1 
+    5.764   -14.315     4.155    -0.148    -0.980    -0.136   -1967     304  1 
+    4.102   -15.192     4.596     0.458    -0.135    -0.878   -1967     447  1 
+    4.386   -14.787     4.590     0.269    -0.404    -0.874    1967     447  1 
+    4.714   -14.448     4.441     0.050    -0.630    -0.775    1967     304  1 
+    5.051   -14.212     4.165    -0.174    -0.788    -0.591    1967     304  1 
+    5.359   -14.105     3.793    -0.380    -0.859    -0.343   -1967     304  1 
+    4.054   -14.502     4.465    -0.037    -0.143    -0.989   -1967     447  1 
+    4.402   -14.180     4.323    -0.269    -0.357    -0.895   -1967     304  1 
+    4.706   -13.916     4.035    -0.471    -0.533    -0.703   -1967     304  1 
+    3.587   -14.433     4.395     0.275    -0.189    -0.943   -1969     447  1 
+    3.508   -14.042     4.228     0.327    -0.449    -0.831   -1969     447  1 
+    3.470   -13.707     3.957     0.352    -0.673    -0.651   -1969     323  1 
+    3.476   -13.456     3.605     0.348    -0.840    -0.416   -1969     323  1 
+    3.526   -13.309     3.202     0.315    -0.938    -0.147   -1969     323  1 
+    3.013   -14.868     4.459    -0.244     0.074    -0.967   -1969     447  1 
+    3.098   -14.448     4.405    -0.301    -0.206    -0.931    1969     447  1 
+    3.146   -14.053     4.236    -0.332    -0.470    -0.818    1969     447  1 
+    3.152   -13.717     3.964    -0.337    -0.694    -0.637    1969     323  1 
+    3.116   -13.467     3.613    -0.313    -0.860    -0.403    1969     323  1 
+    3.042   -13.324     3.211    -0.263    -0.955    -0.135    1969     323  1 
+    2.934   -13.301     2.793    -0.191    -0.971     0.144   -1969     323  1 
+    2.723   -14.228     4.629    -0.742     0.052    -0.668   -1969     447  1 
+    2.867   -13.890     4.401    -0.839    -0.173    -0.516   -1969     447  1 
+    2.908   -13.574     4.110    -0.866    -0.384    -0.322   -1969     323  1 
+    2.840   -13.305     3.777    -0.820    -0.563    -0.100   -1969     323  1 
+    2.670   -13.107     3.433    -0.707    -0.695     0.129   -1969     323  1 
+    2.075   -14.209     5.052    -0.311     0.040    -0.950   -1971     445  1 
+    2.026   -14.279     5.068    -0.346    -0.010    -0.938   -1971     445  1 
+    2.001   -14.596     5.044    -0.329     0.201    -0.922   -1972     447  1 
+    1.514   -14.526     5.142    -0.004     0.154    -0.988   -1972     444  1 
+    2.372   -15.102     4.796    -0.658    -0.077    -0.750   -1972     447  1 
+    1.946   -15.019     5.049    -0.373    -0.132    -0.918    1972     447  1 
+    1.457   -14.958     5.148    -0.047    -0.172    -0.984    1972     444  1 
+    0.960   -14.926     5.081     0.284    -0.194    -0.939   -1972     444  1 
+    2.353   -15.547     4.954    -0.670    -0.364    -0.647   -1972     447  1 
+    1.929   -15.420     5.192    -0.387    -0.449    -0.806    1972     447  1 
+    1.439   -15.368     5.293    -0.061    -0.483    -0.874    1972     444  1 
+    0.940   -15.398     5.248     0.272    -0.463    -0.843   -1972     444  1 
+    2.379   -15.917     5.247    -0.653    -0.603    -0.459   -1972     447  1 
+    1.952   -15.754     5.455    -0.368    -0.712    -0.598    1972     447  1 
+    1.464   -15.710     5.563    -0.042    -0.741    -0.670    1972     444  1 
+    0.968   -15.790     5.558     0.288    -0.688    -0.666   -1972     444  1 
+    2.448   -16.171     5.640    -0.608    -0.767    -0.205   -1972     447  1 
+    2.014   -15.982     5.809    -0.319    -0.893    -0.318    1972     447  1 
+    1.527   -15.943     5.925     0.006    -0.918    -0.396    1972     444  1 
+    1.040   -16.059     5.974     0.330    -0.841    -0.428   -1972     444  1 
+    2.551   -16.279     6.088    -0.542    -0.836     0.084   -1972     447  1 
+    2.107   -16.079     6.213    -0.246    -0.969     0.001    1972     447  1 
+    1.622   -16.043     6.339     0.077    -0.994    -0.083    1972     444  1 
+    1.149   -16.173     6.450     0.392    -0.906    -0.157   -1972     444  1 
+    2.220   -16.034     6.622    -0.157    -0.933     0.323   -1972     447  1 
+    1.737   -15.996     6.756     0.165    -0.958     0.233   -1972     444  1 
+    0.109   -13.486     5.196     0.244     0.153    -0.958   -1975     444  1 
+   -0.205   -13.072     5.083     0.453    -0.123    -0.883   -1975     451  1 
+   -0.434   -12.682     4.805     0.606    -0.383    -0.697   -1975     451  1 
+   -0.136   -13.671     5.151     0.014    -0.020    -1.000   -1975     444  1 
+   -0.422   -13.236     5.044     0.204    -0.310    -0.928   -1975     451  1 
+   -0.668   -12.859     4.762     0.369    -0.562    -0.741   -1975     451  1 
+   -0.325   -12.465     4.751     0.533    -0.528    -0.661   -1977     451  1 
+   -0.035   -12.632     5.024     0.340    -0.416    -0.843   -1977     451  1 
+    0.298   -12.851     5.192     0.118    -0.270    -0.956   -1977     445  1 
+    0.645   -13.103     5.241    -0.113    -0.102    -0.988   -1977     445  1 
+   -0.243   -12.349     4.739     0.612    -0.416    -0.673   -1977     451  1 
+    0.038   -12.529     5.014     0.424    -0.296    -0.856   -1977     451  1 
+    0.372   -12.745     5.181     0.202    -0.152    -0.968   -1977     445  1 
+    0.731   -12.981     5.229    -0.038     0.005    -0.999   -1977     445  1 
+   -0.188   -11.866     4.259     0.575    -0.738    -0.353   -1979     451  1 
+    0.151   -11.613     4.088     0.349    -0.906    -0.238   -1979     451  1 
+    0.539   -11.487     3.883     0.090    -0.991    -0.102   -1979     321  1 
+    0.940   -11.498     3.665    -0.177    -0.983     0.044   -1979     321  1 
+    1.316   -11.646     3.452    -0.428    -0.885     0.185   -1979     321  1 
+   -0.736   -12.017     3.911     0.559    -0.367    -0.743   -1979     451  1 
+   -0.384   -11.727     3.939     0.325    -0.560    -0.762    1979     451  1 
+    0.013   -11.515     3.861     0.060    -0.701    -0.710    1979     451  1 
+    0.418   -11.400     3.685    -0.210    -0.778    -0.593    1979     321  1 
+    0.794   -11.394     3.426    -0.461    -0.782    -0.420    1979     321  1 
+    1.106   -11.496     3.108    -0.669    -0.714    -0.208    1979     321  1 
+    1.325   -11.698     2.762    -0.815    -0.579     0.022   -1979     321  1 
+   -0.534   -11.398     3.768     0.132    -0.139    -0.981   -1979     451  1 
+   -0.094   -11.282     3.740    -0.162    -0.216    -0.963   -1979     451  1 
+    0.325   -11.196     3.579    -0.440    -0.273    -0.855   -1979     321  1 
+    0.682   -11.149     3.298    -0.679    -0.305    -0.668   -1979     321  1 
+    0.945   -11.143     2.925    -0.854    -0.309    -0.419   -1979     321  1 
+   -0.611   -11.269     3.731     0.183    -0.225    -0.957   -1981     451  1 
+   -0.241   -11.035     3.679    -0.063    -0.381    -0.922   -1981     451  1 
+    0.121   -10.849     3.508    -0.304    -0.505    -0.808   -1981     451  1 
+    0.443   -10.729     3.231    -0.519    -0.585    -0.623   -1981     322  1 
+    0.698   -10.685     2.874    -0.689    -0.614    -0.385   -1981     322  1 
+    0.863   -10.721     2.466    -0.799    -0.590    -0.114   -1981     322  1 
+   -0.606   -10.631     4.013     0.191     0.856    -0.480   -1981     451  1 
+   -0.239   -10.755     3.803    -0.054     0.939    -0.340   -1981     451  1 
+    0.121   -10.757     3.548    -0.295     0.940    -0.170   -1981     451  1 
+    0.443   -10.637     3.272    -0.509     0.860     0.014   -1981     322  1 
+    0.699   -10.406     2.997    -0.680     0.706     0.197   -1981     322  1 
+    0.867   -10.083     2.748    -0.792     0.491     0.363   -1981     322  1 
+   -0.501   -10.364     4.380     0.120     0.678    -0.725   -1983     451  1 
+   -0.033   -10.218     4.479    -0.192     0.581    -0.791   -1983     451  1 
+    0.403    -9.976     4.446    -0.483     0.420    -0.769   -1983     317  1 
+    0.759    -9.665     4.284    -0.720     0.212    -0.661   -1983     317  1 
+    0.995    -9.317     4.013    -0.877    -0.019    -0.480   -1983     317  1 
+   -0.543   -10.265     4.493     0.051     0.841    -0.538   -1983     451  1 
+   -0.055   -10.167     4.538    -0.275     0.776    -0.568   -1983     451  1 
+    0.387    -9.940     4.488    -0.569     0.624    -0.535   -1983     317  1 
+    0.735    -9.608     4.349    -0.801     0.403    -0.442   -1983     317  1 
+    0.949    -9.210     4.136    -0.944     0.138    -0.300   -1983     317  1 
+   -0.721   -10.062     4.717     0.169     0.706    -0.688   -1985     451  1 
+   -0.391    -9.786     4.963    -0.050     0.522    -0.851   -1985     451  1 
+   -0.070    -9.425     5.069    -0.265     0.281    -0.922   -1985     324  1 
+    0.208    -9.018     5.025    -0.450     0.010    -0.893   -1985     324  1 
+   -0.919    -9.933     4.872    -0.070     0.863    -0.500   -1985     451  1 
+   -0.546    -9.685     5.084    -0.318     0.698    -0.641   -1985     451  1 
+   -0.225    -9.323     5.191    -0.532     0.457    -0.713   -1985     324  1 
+    0.009    -8.887     5.181    -0.688     0.166    -0.706   -1985     324  1 
+   -2.004    -9.868     4.942     0.183     0.893    -0.410   -1990     451  1 
+   -2.325    -9.633     5.148     0.397     0.737    -0.547   -1990     453  1 
+   -2.593    -9.299     5.281     0.576     0.514    -0.636   -1990     453  1 
+   -2.057    -9.888     4.882     0.137     0.876    -0.462   -1990     451  1 
+   -2.376    -9.652     5.090     0.350     0.719    -0.601   -1990     453  1 
+   -2.649    -9.320     5.218     0.531     0.497    -0.686   -1990     453  1 
+   -2.169    -9.995     4.550     0.212     0.947    -0.240   -1992     451  1 
+   -2.590    -9.853     4.454     0.492     0.853    -0.177   -1992     451  1 
+   -2.942    -9.594     4.334     0.727     0.680    -0.097   -1992     451  1 
+   -3.195    -9.241     4.201     0.896     0.445    -0.008   -1992     511  1 
+   -3.325    -8.827     4.066     0.982     0.169     0.082   -1992     511  1 
+   -3.320    -8.390     3.943     0.979    -0.122     0.164   -1992     511  1 
+   -2.254   -10.173     4.251     0.059     0.629    -0.775   -1992     451  1 
+   -2.623    -9.922     4.337     0.305     0.462    -0.833   -1992     451  1 
+   -2.949    -9.608     4.309     0.523     0.252    -0.814   -1992     451  1 
+   -3.204    -9.260     4.169     0.693     0.020    -0.721   -1992     511  1 
+   -3.364    -8.908     3.930     0.799    -0.214    -0.562   -1992     511  1 
+   -3.414    -8.586     3.614     0.832    -0.429    -0.351   -1992     511  1 
+   -2.043   -10.607     3.670    -0.082     0.918    -0.388   -1994     451  1 
+   -2.222   -10.723     3.218     0.038     0.995    -0.087   -1994     451  1 
+   -2.395   -10.674     2.751     0.153     0.962     0.224   -1994     467  1 
+   -2.542   -10.463     2.322     0.251     0.822     0.511   -1994     467  1 
+   -2.648   -10.116     1.977     0.321     0.591     0.740   -1994     467  1 
+   -1.316   -10.675     3.767     0.178     0.516    -0.838   -1994     451  1 
+   -1.723   -10.799     3.505     0.450     0.598    -0.663    1994     451  1 
+   -2.056   -10.823     3.132     0.671     0.614    -0.415    1994     451  1 
+   -2.277   -10.745     2.690     0.818     0.562    -0.120    1994     467  1 
+   -2.361   -10.573     2.228     0.874     0.447     0.188    1994     467  1 
+   -2.299   -10.326     1.797     0.833     0.283     0.475    1994     467  1 
+   -2.098   -10.032     1.446     0.699     0.087     0.709   -1994     467  1 
+   -1.685   -11.189     3.388     0.513    -0.049    -0.857   -1994     451  1 
+   -2.036   -11.026     3.071     0.747    -0.157    -0.645   -1994     451  1 
+   -2.262   -10.889     2.647     0.898    -0.248    -0.362   -1994     467  1 
+   -2.339   -10.794     2.162     0.949    -0.312    -0.039   -1994     467  1 
+   -2.257   -10.751     1.670     0.895    -0.341     0.289   -1994     467  1 
+   -1.652   -11.502     3.387     0.491     0.160    -0.856   -1996     451  1 
+   -1.985   -11.621     3.090     0.714     0.240    -0.658   -1996     451  1 
+   -2.217   -11.706     2.700     0.868     0.296    -0.398   -1996     463  1 
+   -2.326   -11.749     2.252     0.940     0.325    -0.099   -1996     463  1 
+   -1.599   -11.785     3.418     0.549    -0.147    -0.823   -1996     451  1 
+   -1.941   -11.857     3.116     0.777    -0.099    -0.622   -1996     451  1 
+   -2.173   -11.943     2.725     0.932    -0.042    -0.361   -1996     463  1 
+   -2.272   -12.035     2.283     0.998     0.019    -0.066   -1996     463  1 
+   -1.530   -12.008     3.480     0.503     0.002    -0.864   -1997     451  1 
+   -1.810   -12.281     3.234     0.690     0.184    -0.700   -1997     456  1 
+   -0.955   -12.181     3.861     0.415    -0.475    -0.776   -1997     451  1 
+   -1.324   -12.420     3.718     0.661    -0.315    -0.681    1997     451  1 
+   -1.599   -12.704     3.479     0.844    -0.126    -0.521    1997     456  1 
+   -1.754   -13.006     3.165     0.947     0.076    -0.312   -1997     456  1 
+   -1.267   -12.777     4.091     0.705    -0.589    -0.395   -1997     451  1 
+   -1.541   -13.070     3.861     0.887    -0.393    -0.242   -1997     456  1 
+   -2.222   -12.353     2.375     0.964     0.232    -0.128   -1998     463  1 
+   -1.996   -13.040     2.685     0.808     0.057    -0.586   -1998     456  1 
+   -2.226   -12.812     2.193     0.962    -0.095    -0.257    1998     463  1 
+   -2.233   -12.606     1.640     0.966    -0.233     0.111   -1998     463  1 
+   -2.190   -13.528     2.519     0.698    -0.222    -0.681   -1998     456  1 
+   -2.400   -13.250     2.043     0.838    -0.407    -0.364    1998     463  1 
+   -2.416   -13.067     1.483     0.848    -0.529     0.010   -1998     463  1 
+   -2.722   -13.611     1.945     0.608    -0.665    -0.434   -1998     463  1 
+   -2.269   -11.255     1.458     0.903    -0.005     0.430   -1999     467  1 
+   -2.200   -12.063     1.305     0.987     0.118    -0.105   -1999     463  1 
+   -2.175   -11.556     0.996     0.970    -0.220     0.100    1999     467  1 
+   -1.921   -11.101     0.712     0.801    -0.524     0.290   -1999     467  1 
+   -2.301   -11.823     0.521     0.880    -0.411    -0.239   -1999     467  1 
+   -3.036    -9.369     1.874     0.581     0.093     0.809   -2000     467  1 
+   -3.289    -9.054     2.109     0.749    -0.117     0.652   -2000     467  1 
+   -3.433    -8.757     2.439     0.845    -0.315     0.432   -2000     511  1 
+   -3.454    -8.505     2.832     0.859    -0.483     0.170   -2000     511  1 
+   -2.947    -9.203     1.763     0.663     0.246     0.707   -2000     467  1 
+   -3.212    -8.913     2.015     0.841     0.053     0.539   -2000     467  1 
+   -3.356    -8.615     2.345     0.936    -0.146     0.319   -2000     511  1 
+   -3.364    -8.339     2.721     0.941    -0.330     0.068   -2000     511  1 
+   -3.297    -8.175     4.238     0.963    -0.266    -0.033   -2002     511  1 
+   -3.277    -8.417     4.629     0.950    -0.105    -0.293   -2002     453  1 
+   -3.123    -8.674     4.979     0.848     0.066    -0.526   -2002     453  1 
+   -3.284    -8.125     4.269     0.974    -0.227    -0.009   -2002     511  1 
+   -3.265    -8.370     4.658     0.961    -0.064    -0.268   -2002     453  1 
+   -3.110    -8.623     5.009     0.858     0.105    -0.503   -2002     453  1 
+   -2.948    -7.497     4.042     0.750    -0.646     0.142   -2003     511  1 
+   -2.608    -7.187     4.229     0.523    -0.852     0.017   -2003     511  1 
+   -2.182    -7.018     4.419     0.240    -0.965    -0.109   -2003     330  1 
+   -1.717    -7.007     4.591    -0.071    -0.972    -0.224   -2003     330  1 
+   -2.928    -7.483     3.984     0.771    -0.632     0.083   -2003     511  1 
+   -2.591    -7.176     4.182     0.547    -0.836    -0.049   -2003     511  1 
+   -2.165    -7.007     4.372     0.263    -0.949    -0.175   -2003     330  1 
+   -1.696    -6.993     4.533    -0.050    -0.958    -0.283   -2003     330  1 
+   -1.559    -7.232     5.068    -0.176    -0.822    -0.542   -2004     330  1 
+   -1.880    -7.424     5.333     0.038    -0.695    -0.718   -2004     330  1 
+   -2.196    -7.712     5.498     0.249    -0.502    -0.828   -2004     453  1 
+   -2.476    -8.071     5.547     0.436    -0.263    -0.861   -2004     453  1 
+   -2.696    -8.467     5.475     0.582     0.001    -0.813   -2004     453  1 
+   -1.524    -7.256     5.095    -0.137    -0.848    -0.512   -2004     330  1 
+   -1.854    -7.441     5.353     0.084    -0.725    -0.684   -2004     330  1 
+   -2.173    -7.727     5.515     0.296    -0.534    -0.792   -2004     453  1 
+   -2.451    -8.088     5.566     0.481    -0.293    -0.826   -2004     453  1 
+   -2.661    -8.491     5.502     0.621    -0.025    -0.783   -2004     453  1 
+   -0.416    -7.508     4.898    -0.405    -0.754    -0.518   -2006     330  1 
+   -0.080    -7.917     5.038    -0.629    -0.480    -0.611   -2006     324  1 
+   -0.168    -7.395     4.647    -0.208    -0.664    -0.719   -2006     330  1 
+    0.162    -7.807     4.793    -0.428    -0.389    -0.816   -2006     324  1 
+   -0.082    -7.201     4.391    -0.266    -0.793    -0.548   -2007     330  1 
+    0.338    -7.402     4.346    -0.545    -0.659    -0.518   -2007     330  1 
+    0.678    -7.699     4.225    -0.772    -0.461    -0.438   -2007     317  1 
+    0.905    -8.063     4.041    -0.924    -0.218    -0.315   -2007     317  1 
+    0.074    -6.887     4.058    -0.122    -0.504    -0.855   -2007     330  1 
+    0.470    -7.135     4.062    -0.386    -0.339    -0.858   -2007     330  1 
+    0.810    -7.432     3.942    -0.613    -0.141    -0.777   -2007     317  1 
+    1.061    -7.749     3.708    -0.780     0.071    -0.621   -2007     317  1 
+    0.799    -8.377     4.352    -0.853    -0.009    -0.522   -2008     324  1 
+    0.806    -8.674     4.408    -0.848    -0.220    -0.482   -2008     324  1 
+    1.173    -9.209     3.276    -0.996    -0.092     0.011   -2009     317  1 
+    1.121    -9.458     2.892    -0.961     0.074     0.267   -2009     322  1 
+    1.329    -8.596     2.838    -0.882     0.357    -0.309   -2009     317  1 
+    1.273    -8.860     2.465    -0.844     0.533    -0.060   -2009     322  1 
+    1.146   -11.140     1.706    -0.695    -0.717    -0.055   -2011     322  1 
+    1.326   -11.509     2.131    -0.815    -0.471    -0.338   -2011     321  1 
+    1.811   -11.707     1.618    -0.687    -0.586    -0.429   -2013     323  1 
+    1.884   -11.283     0.960    -0.209    -0.811    -0.546   -2013     322  1 
+    2.179   -11.667     1.229    -0.407    -0.556    -0.725    2013     323  1 
+    2.392   -12.165     1.350    -0.548    -0.224    -0.806   -2013     323  1 
+    2.378   -11.108     0.712     0.116    -0.696    -0.708   -2013     322  1 
+    2.638   -11.505     1.000    -0.058    -0.432    -0.900    2013     323  1 
+    2.886   -11.990     1.103    -0.223    -0.109    -0.969   -2013     323  1 
+    2.885   -10.831     0.678     0.449    -0.514    -0.731   -2013     322  1 
+    3.108   -11.247     0.968     0.301    -0.236    -0.924    2013     323  1 
+    3.393   -11.712     1.069     0.111     0.074    -0.991   -2013     323  1 
+    3.513   -10.938     1.140     0.609    -0.000    -0.793   -2013     323  1 
+    3.717    -9.971     1.130     0.629    -0.362    -0.687   -2017     322  1 
+    4.084    -9.709     1.225     0.385    -0.537    -0.751   -2017     322  1 
+    4.505    -9.523     1.214     0.105    -0.661    -0.743   -2017     308  1 
+    4.940    -9.430     1.098    -0.186    -0.723    -0.666   -2017     308  1 
+    5.349    -9.440     0.888    -0.458    -0.717    -0.526   -2017     308  1 
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+    4.024     0.601     9.831     0.309     0.836    -0.453    1772      79  2 
+    4.024     0.448     9.387     0.309     0.938    -0.157    1772      79  2 
+    4.024     0.448     8.917     0.309     0.938     0.157    1772     278  2 
+    3.606     0.734     9.616     0.588     0.747    -0.310    1772      65  2 
+    3.606     0.642     9.152     0.588     0.809     0.000    1772      65  2 
+    5.955    -0.331     9.978     0.309     0.836    -0.453    1775      82  2 
+    5.537    -0.197     9.764     0.588     0.747    -0.310    1775      79  2 
+    5.537    -0.290     9.299     0.588     0.809     0.000    1775     278  2 
+    5.973     0.031    12.243     0.588     0.809     0.000    1777      79  2 
+    4.839    -2.494    20.223     0.309     0.836     0.453    1804      98  2 
+    4.839    -2.205    19.852     0.309     0.644     0.700    1804      98  2 
+    4.421    -2.360    21.366     0.588     0.747    -0.310    1804     159  2 
+    4.421    -2.452    20.902     0.588     0.809     0.000    1804     159  2 
+    4.421    -2.360    20.438     0.588     0.747     0.310    1804      98  2 
+    4.421    -2.097    20.044     0.588     0.572     0.572    1804      98  2 
+    4.089    -2.002    21.343     0.809     0.509    -0.294    1804     159  2 
+    4.089    -2.121    20.902     0.809     0.588     0.000    1804     159  2 
+    4.089    -2.002    20.461     0.809     0.509     0.294    1804      76  2 
+    4.089    -1.680    20.139     0.809     0.294     0.509    1804      76  2 
+    3.876    -1.702    20.902     0.951     0.309     0.000    1804      76  2 
+    3.876    -1.471    20.501     0.951     0.155     0.268    1804      76  2 
+    4.738    -4.559    27.064     0.000     0.989    -0.149    1814     157  2 
+    4.738    -4.559    26.617     0.000     0.989     0.149    1814     157  2 
+    4.738    -4.427    26.190     0.000     0.901     0.434    1814     155  2 
+    4.274    -4.482    26.606     0.309     0.938     0.157    1814     157  2 
+    4.274    -4.330    26.161     0.309     0.836     0.453    1814     157  2 
+    2.194    -4.315    27.815     0.000     0.989    -0.149    1818     180  2 
+    2.194    -4.315    27.368     0.000     0.989     0.149    1818     157  2 
+    2.194    -4.183    26.940     0.000     0.901     0.434    1818     157  2 
+    1.731    -4.239    27.826     0.309     0.938    -0.157    1818     157  2 
+    1.731    -4.239    27.356     0.309     0.938     0.157    1818     157  2 
+    1.731    -4.086    26.912     0.309     0.836     0.453    1818     157  2 
+    1.313    -4.045    27.591     0.588     0.809     0.000    1818     157  2 
+    1.313    -3.953    27.127     0.588     0.747     0.310    1818     157  2 
+    1.313    -3.690    26.733     0.588     0.572     0.572    1818     157  2 
+    0.981    -3.595    27.150     0.809     0.509     0.294    1818     193  2 
+    0.981    -3.272    26.828     0.809     0.294     0.509    1818     193  2 
+    1.775    -4.207    28.585     0.000     0.989    -0.149    1821     178  2 
+    1.312    -4.131    28.127     0.309     0.938     0.157    1821     178  2 
+    0.894    -3.845    27.897     0.588     0.747     0.310    1821     178  2 
+   -0.396    -3.819    28.880     0.000     0.901     0.434    1826     186  2 
+   -0.396    -3.567    28.510     0.000     0.733     0.680    1826     186  2 
+    1.463   -10.626    28.472     0.000    -0.956     0.295    1854     173  2 
+    1.140   -11.386    25.380    -0.309    -0.520     0.796    1860     408  2 
+    1.140   -11.041    25.698    -0.309    -0.751     0.584    1860     408  2 
+    1.140   -10.817    26.111    -0.309    -0.900     0.309    1860     171  2 
+    0.676   -11.231    25.401     0.000    -0.623     0.782    1860     408  2 
+    0.676   -10.927    25.729     0.000    -0.826     0.563    1860     408  2 
+    0.676   -10.733    26.132     0.000    -0.956     0.295    1860     171  2 
+    0.213   -11.041    25.698     0.309    -0.751     0.584    1860     367  2 
+    0.213   -10.817    26.111     0.309    -0.900     0.309    1860     367  2 
+   -0.205   -11.046    26.109     0.588    -0.747     0.310    1860     367  2 
+    0.099   -10.722    27.013     0.309    -0.951     0.000    1862     370  2 
+    0.099   -10.799    27.477     0.309    -0.900    -0.309    1862     370  2 
+   -0.319   -10.935    27.013     0.588    -0.809     0.000    1862     367  2 
+   -0.319   -11.028    27.478     0.588    -0.747    -0.310    1862     370  2 
+    0.631   -12.139    25.046     0.000    -0.075     0.997    1866     408  2 
+    0.167   -12.369    25.120     0.309     0.079     0.948    1866     397  2 
+    0.167   -11.901    25.159     0.309    -0.233     0.922    1866     408  2 
+   -0.251   -12.715    25.421     0.588     0.310     0.747    1866     397  2 
+   -0.251   -12.251    25.328     0.588    -0.000     0.809    1866     397  2 
+   -0.251   -11.787    25.421     0.588    -0.310     0.747    1866     367  2 
+   -0.583   -11.810    25.778     0.809    -0.294     0.509    1866     367  2 
+    1.982   -14.960    29.163     0.309     0.938     0.157    1887     389  2 
+    1.998   -18.372    28.362     0.000    -1.000     0.000    1896     390  2 
+    1.998   -18.439    28.804     0.000    -0.956    -0.295    1896     393  2 
+    1.998   -18.633    27.517     0.000    -0.826     0.563    1896     400  2 
+    1.998   -18.439    27.920     0.000    -0.956     0.295    1896     400  2 
+    0.882   -16.214    21.215     0.000    -1.000     0.000    1913     405  2 
+    0.882   -16.281    21.657     0.000    -0.956    -0.295    1913     405  2 
+    0.419   -16.288    21.215     0.309    -0.951     0.000    1913     405  2 
+    0.419   -16.365    21.678     0.309    -0.900    -0.309    1913     405  2 
+    0.419   -16.589    22.091     0.309    -0.751    -0.584    1913     398  2 
+    0.419   -16.934    22.409     0.309    -0.520    -0.796    1913     398  2 
+    0.001   -16.501    21.215     0.588    -0.809     0.000    1913     414  2 
+    0.001   -16.593    21.680     0.588    -0.747    -0.310    1913     414  2 
+    0.001   -16.856    22.073     0.588    -0.572    -0.572    1913     398  2 
+   -0.331   -16.833    21.215     0.809    -0.588     0.000    1913     414  2 
+   -0.331   -16.951    21.656     0.809    -0.509    -0.294    1913     414  2 
+   -0.892   -16.518    17.009     0.000    -1.000     0.000    1922     418  2 
+    0.740   -16.563    15.567     0.588    -0.747     0.310    1925     421  2 
+   -2.126   -16.421    13.187    -0.309    -0.900    -0.309    1931     429  2 
+   -2.589   -16.337    13.166     0.000    -0.956    -0.295    1931     429  2 
+    1.525   -12.427    10.242     0.309    -0.900     0.309    1952     340  2 
+    1.107   -12.655    10.241     0.588    -0.747     0.310    1952     431  2 
+    0.775   -13.012    10.264     0.809    -0.509     0.294    1952     431  2 
+    2.244   -13.369     8.837     0.000    -0.365     0.931    1954     446  2 
+    2.244   -12.982     9.060     0.000    -0.623     0.782    1954     340  2 
+    2.244   -12.677     9.388     0.000    -0.826     0.563    1954     340  2 
+    1.781   -13.567     8.850     0.309    -0.233     0.922    1954     446  2 
+    1.781   -13.137     9.039     0.309    -0.520     0.796    1954     446  2 
+    1.781   -12.791     9.357     0.309    -0.751     0.584    1954     340  2 
+    1.362   -13.452     9.112     0.588    -0.310     0.747    1954     440  2 
+    1.362   -13.059     9.375     0.588    -0.572     0.572    1954     440  2 
+    4.730   -12.314     8.471     0.000    -0.623     0.782    1957     284  2 
+    4.730   -12.010     8.799     0.000    -0.826     0.563    1957     284  2 
+    4.267   -12.469     8.450     0.309    -0.520     0.796    1957     284  2 
+    4.267   -12.123     8.768     0.309    -0.751     0.584    1957     340  2 
+    3.848   -12.785     8.523     0.588    -0.310     0.747    1957     446  2 
+    3.848   -12.391     8.786     0.588    -0.572     0.572    1957     340  2 
+    3.848   -12.128     9.180     0.588    -0.747     0.310    1957     340  2 
+    5.882   -13.491     8.292    -0.588    -0.000     0.809    1959     299  2 
+    5.882   -13.027     8.384    -0.588    -0.310     0.747    1959     284  2 
+    5.464   -13.609     8.084    -0.309     0.079     0.948    1959     299  2 
+    5.464   -13.141     8.123    -0.309    -0.233     0.922    1959     284  2 
+    5.464   -12.711     8.311    -0.309    -0.520     0.796    1959     284  2 
+    5.001   -13.379     8.010     0.000    -0.075     0.997    1959     446  2 
+    5.001   -12.943     8.109     0.000    -0.365     0.931    1959     284  2 
+    4.537   -13.609     8.084     0.309     0.079     0.948    1959     446  2 
+    4.536   -15.104     7.158     0.588    -0.572     0.572    1961     447  2 
+    6.399   -14.044     6.300     0.000    -0.956    -0.295    1964     299  2 
+    6.399   -14.238     6.703     0.000    -0.826    -0.563    1964     299  2 
+    5.935   -14.051     5.858     0.309    -0.951     0.000    1964     304  2 
+    5.935   -14.128     6.321     0.309    -0.900    -0.309    1964     304  2 
+    5.935   -14.352     6.734     0.309    -0.751    -0.584    1964     299  2 
+    5.517   -14.264     5.858     0.588    -0.809     0.000    1964     447  2 
+    5.517   -14.357     6.322     0.588    -0.747    -0.310    1964     447  2 
+    5.185   -14.596     5.858     0.809    -0.588     0.000    1964     447  2 
+    4.462   -13.590     3.857    -0.309    -0.751    -0.584    1966     304  2 
+    3.999   -13.282     3.423     0.000    -0.956    -0.295    1966     323  2 
+    3.999   -13.476     3.826     0.000    -0.826    -0.563    1966     323  2 
+    3.999   -13.781     4.154     0.000    -0.623    -0.782    1966     447  2 
+    3.999   -14.168     4.377     0.000    -0.365    -0.931    1966     447  2 
+    2.491   -13.291     4.485    -0.588    -0.572    -0.572    1968     447  2 
+    2.491   -13.685     4.748    -0.588    -0.310    -0.747    1968     447  2 
+    2.491   -14.149     4.841    -0.588     0.000    -0.809    1968     447  2 
+    2.073   -13.799     5.010    -0.309    -0.233    -0.922    1968     445  2 
+    1.556   -11.759     3.730    -0.588    -0.809     0.000    1976     321  2 
+    1.556   -11.851     4.194    -0.588    -0.747    -0.310    1976     321  2 
+    1.556   -12.114     4.588    -0.588    -0.572    -0.572    1976     445  2 
+    1.138   -11.623     4.193    -0.309    -0.900    -0.309    1976     321  2 
+    1.138   -11.847     4.606    -0.309    -0.751    -0.584    1976     321  2 
+    1.138   -12.192     4.924    -0.309    -0.520    -0.796    1976     445  2 
+    1.138   -12.622     5.113    -0.309    -0.233    -0.922    1976     445  2 
+    0.675   -11.539     4.172     0.000    -0.956    -0.295    1976     451  2 
+    0.675   -11.733     4.575     0.000    -0.826    -0.563    1976     451  2 
+    0.675   -12.037     4.903     0.000    -0.623    -0.782    1976     451  2 
+    0.675   -12.425     5.126     0.000    -0.365    -0.931    1976     445  2 
+    0.211   -11.847     4.606     0.309    -0.751    -0.584    1976     451  2 
+    0.211   -12.192     4.924     0.309    -0.520    -0.796    1976     451  2 
+    1.106    -9.578     3.694    -0.951     0.155    -0.268    1980     317  2 
+    1.106    -9.810     3.293    -0.951     0.309     0.000    1980     322  2 
+    0.893    -9.787     4.056    -0.809     0.294    -0.509    1980     317  2 
+    0.893   -10.110     3.734    -0.809     0.509    -0.294    1980     322  2 
+    0.893   -10.228     3.293    -0.809     0.588     0.000    1980     322  2 
+    0.561   -10.204     4.151    -0.588     0.572    -0.572    1980     451  2 
+    0.561   -10.468     3.757    -0.588     0.747    -0.310    1980     322  2 
+    0.143   -10.601     3.972    -0.309     0.836    -0.453    1980     451  2 
+    0.747    -9.003     4.567    -0.809     0.000    -0.588    1982     324  2 
+    0.415    -9.468     4.807    -0.588     0.310    -0.747    1982     324  2 
+   -0.003    -9.970     4.735    -0.309     0.644    -0.700    1982     451  2 
+   -0.142    -8.173     5.243    -0.588    -0.310    -0.747    1984     324  2 
+   -0.142    -8.638     5.335    -0.588     0.000    -0.809    1984     324  2 
+   -0.560    -7.858     5.316    -0.309    -0.520    -0.796    1984     324  2 
+   -0.560    -8.288     5.505    -0.309    -0.233    -0.922    1984     324  2 
+   -0.560    -8.756     5.543    -0.309     0.079    -0.948    1984     324  2 
+   -0.560    -9.211     5.428    -0.309     0.382    -0.871    1984     324  2 
+   -1.023    -9.737     5.142     0.000     0.733    -0.680    1984     451  2 
+   -1.265    -7.402     5.203    -0.309    -0.751    -0.584    1986     330  2 
+   -1.265    -7.748     5.521    -0.309    -0.520    -0.796    1986     330  2 
+   -1.265    -8.178     5.710    -0.309    -0.233    -0.922    1986     330  2 
+   -1.265    -8.646     5.749    -0.309     0.079    -0.948    1986     451  2 
+   -1.265    -9.101     5.634    -0.309     0.382    -0.871    1986     451  2 
+   -1.729    -7.593     5.500     0.000    -0.623    -0.782    1986     330  2 
+   -1.729    -7.980     5.723     0.000    -0.365    -0.931    1986     330  2 
+   -1.729    -8.416     5.823     0.000    -0.075    -0.997    1986     453  2 
+   -1.729    -8.862     5.790     0.000     0.223    -0.975    1986     453  2 
+   -1.729    -9.278     5.626     0.000     0.500    -0.866    1986     451  2 
+   -1.729    -9.628     5.347     0.000     0.733    -0.680    1986     451  2 
+   -2.192    -8.178     5.710     0.309    -0.233    -0.922    1986     453  2 
+   -2.192    -8.646     5.749     0.309     0.079    -0.948    1986     453  2 
+   -2.192    -9.101     5.634     0.309     0.382    -0.871    1986     453  2 
+   -2.192    -9.494     5.377     0.309     0.644    -0.700    1986     451  2 
+   -2.734    -9.695     4.653     0.588     0.747    -0.310    1989     451  2 
+   -3.065    -9.015     4.953     0.809     0.294    -0.509    1989     453  2 
+   -3.065    -9.337     4.630     0.809     0.509    -0.294    1989     453  2 
+   -3.278    -8.806     4.590     0.951     0.155    -0.268    1989     453  2 
+   -2.629   -10.196     4.137     0.309     0.644    -0.700    1991     451  2 
+   -2.629   -10.485     3.767     0.309     0.836    -0.453    1991     451  2 
+   -2.629   -10.637     3.322     0.309     0.938    -0.157    1991     451  2 
+   -2.629   -10.637     2.853     0.309     0.938     0.157    1991     451  2 
+   -3.047   -10.088     3.946     0.588     0.572    -0.572    1991     451  2 
+   -3.047   -10.351     3.552     0.588     0.747    -0.310    1991     451  2 
+   -3.047   -10.443     3.088     0.588     0.809     0.000    1991     451  2 
+   -3.047   -10.351     2.623     0.588     0.747     0.310    1991     467  2 
+   -3.047   -10.088     2.229     0.588     0.572     0.572    1991     467  2 
+   -3.047    -9.694     1.966     0.588     0.310     0.747    1991     467  2 
+   -3.379    -9.671     3.851     0.809     0.294    -0.509    1991     511  2 
+   -3.379    -9.994     3.528     0.809     0.509    -0.294    1991     451  2 
+   -3.379   -10.112     3.088     0.809     0.588     0.000    1991     467  2 
+   -3.379    -9.994     2.647     0.809     0.509     0.294    1991     467  2 
+   -3.379    -9.671     2.324     0.809     0.294     0.509    1991     467  2 
+   -3.592    -8.766     3.088     0.951    -0.309     0.000    1991     511  2 
+   -3.592    -8.998     3.489     0.951    -0.155    -0.268    1991     511  2 
+   -3.592    -9.462     3.489     0.951     0.155    -0.268    1991     511  2 
+   -3.592    -9.693     3.088     0.951     0.309     0.000    1991     511  2 
+   -3.592    -9.462     2.686     0.951     0.155     0.268    1991     511  2 
+   -3.592    -8.998     2.686     0.951    -0.155     0.268    1991     511  2 
+   -3.665    -9.230     3.088     1.000     0.000     0.000    1991     511  2 
+   -2.128   -11.262     2.985     0.809     0.000    -0.588    1993     451  2 
+   -2.341   -11.494     2.505     0.951     0.155    -0.268    1993     463  2 
+   -2.341   -11.030     1.702     0.951    -0.155     0.268    1993     463  2 
+   -2.415   -11.262     2.103     1.000     0.000     0.000    1993     463  2 
+   -2.286    -7.116     4.719     0.309    -0.900    -0.309    2001     330  2 
+   -2.286    -7.339     5.132     0.309    -0.751    -0.584    2001     330  2 
+   -2.704    -7.344     4.720     0.588    -0.747    -0.310    2001     511  2 
+   -2.704    -7.607     5.114     0.588    -0.572    -0.572    2001     453  2 
+   -2.704    -8.001     5.377     0.588    -0.310    -0.747    2001     453  2 
+   -3.036    -7.584     4.255     0.809    -0.588     0.000    2001     511  2 
+   -3.036    -7.702     4.696     0.809    -0.509    -0.294    2001     511  2 
+   -3.036    -8.024     5.019     0.809    -0.294    -0.509    2001     453  2 
+    4.514    -8.443     1.142    -0.309    -0.233    -0.922    2016     314  2 
+    4.514    -8.911     1.180    -0.309     0.079    -0.948    2016     308  2 
+    4.051    -8.245     1.155     0.000    -0.365    -0.931    2016     314  2 
+    4.051    -8.681     1.254     0.000    -0.075    -0.997    2016     314  2 
+    3.587    -8.911     1.180     0.309     0.079    -0.948    2016     322  2 
+    5.071    -6.344     3.840     0.000     0.733     0.680    2026     312  2 
+    6.446    -7.203     6.148    -0.309     0.836    -0.453    2032     282  2 
+    6.446    -7.355     5.703    -0.309     0.938    -0.157    2032     282  2 
+    6.446    -7.355     5.234    -0.309     0.938     0.157    2032     282  2 
+    6.446    -7.203     4.790    -0.309     0.836     0.453    2032     312  2 
+    5.982    -7.299     6.119     0.000     0.901    -0.434    2032     282  2 
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+   -8.420    11.196    22.526    -0.309    -0.079     0.948    3287      17  1 
diff --git a/examples/demos/entity_to_density.py b/examples/demos/entity_to_density.py
new file mode 100644
index 0000000000000000000000000000000000000000..71a9e9a50386821bfb91169c824e0f58d2e7b883
--- /dev/null
+++ b/examples/demos/entity_to_density.py
@@ -0,0 +1,35 @@
+from ost.mol import alg
+# tabula rasa first
+scene.RemoveAll()
+
+# load the fragment
+frag=io.LoadPDB('data/1crn.pdb')
+
+# now let's calculate the size of the map by taking the bounding box of
+# the fragment and adding 5 Angstrom on each side.
+frag_bounds=frag.bounds
+real_size=frag_bounds.max-frag_bounds.min+geom.Vec3(10,10,10)
+# We use 2 pixels per Angstroem, so we have to multiply the size by 2.
+map_size=img.Size(int(real_size.x)*2, int(real_size.y)*2, int(real_size.z)*2)
+den_map=img.CreateImage(map_size)
+# we use 2 pixels per Angstrom
+den_map.SetSpatialSampling(2)
+den_map.SetAbsoluteOrigin(frag_bounds.min-geom.Vec3(5, 5, 5))
+
+
+# Calculate a density map from the fragment using a simple real-space method:
+#
+# This function is based on Dimaio et al.,J. Mol. Biol(2009)
+# In essence every atom gives rise to a Gaussian centered at the atom's
+# position. Sigma and Magnitude of the Gaussian are calculated from the
+# atomic mass.
+alg.EntityToDensityRosetta(frag.CreateFullView(), den_map,
+                           alg.HIGH_RESOLUTION, 5.0)
+
+# Create Graphical Representations and add to the Scene
+gfx_frag=gfx.Entity('Fragment', gfx.HSC, frag)
+gfx_frag.SetColor(gfx.YELLOW)
+gfx_map=gfx.MapIso('Density', den_map, 250.0)
+scene.Add(gfx_frag)
+scene.Add(gfx_map)
+scene.CenterOn(gfx_frag)
diff --git a/examples/map/gfx_mapslab.py b/examples/demos/gfx_mapslab.py
similarity index 91%
rename from examples/map/gfx_mapslab.py
rename to examples/demos/gfx_mapslab.py
index 54ec25a73c2c965ddb9f90cd6a8e1fca0ff5d38b..de59b2e5d1df8ee8386ae75921543139bddefde6 100644
--- a/examples/map/gfx_mapslab.py
+++ b/examples/demos/gfx_mapslab.py
@@ -1,5 +1,9 @@
 import math,random
 from ost import img
+
+# remove all objects from scene, just in case
+scene.RemoveAll()
+
 vmax=-10000.0
 vmin=+10000.0
 mh=img.CreateMap(img.Size(32,32,32))
@@ -45,6 +49,9 @@ go1.SetLineWidth(1.5)
 scene.Add(go1)
 scene.SetCenter(go1.GetCenter())
 
+
 go2 = gfx.MapSlab("slab",mh,geom.Plane(go1.GetCenter(),geom.Vec3(0.0,0.0,1.0)))
 scene.Add(go2)
 go2.ColorBy(gfx.YELLOW,gfx.GREEN,0.2,0.8)
+
+print 'Demo 4: Projecting the density of a map onto a plane...' 
diff --git a/examples/entity/load_and_display.py b/examples/demos/load_and_display.py
similarity index 71%
rename from examples/entity/load_and_display.py
rename to examples/demos/load_and_display.py
index 8ee89b89fd242279ec9e22a53cd97b1c6fe6fdbd..be2783a00f0a7c6c048580ccd0200f95d4c0d919 100644
--- a/examples/entity/load_and_display.py
+++ b/examples/demos/load_and_display.py
@@ -1,5 +1,7 @@
+# remove all objects from scene, just in case
+scene.RemoveAll()
 # Load chain A of SDH
-ent=io.LoadPDB('sdh.pdb', restrict_chains='A')
+ent=io.LoadPDB('data/sdh.pdb', restrict_chains='A')
 
 # create graphics object
 go=gfx.Entity('SDH', ent)
@@ -14,4 +16,6 @@ go.SetRenderMode(gfx.SIMPLE, sidechains)
 scene.Add(go)
 
 # center the scene on the geometric center of the SDH
-scene.CenterOn(go)
\ No newline at end of file
+scene.CenterOn(go)
+
+print 'Demo 1: loading and displaying a pdb file'
diff --git a/examples/entity/rendermodes.py b/examples/demos/rendermodes.py
similarity index 52%
rename from examples/entity/rendermodes.py
rename to examples/demos/rendermodes.py
index 58087b0a58fa39adbb61a0df2456290a294408cc..a7d08937dbf14f950349f6f68b50222a51c5649e 100644
--- a/examples/entity/rendermodes.py
+++ b/examples/demos/rendermodes.py
@@ -1,5 +1,12 @@
-# load pdb file
-eh=io.LoadEntity("sdh.pdb")
+# This script shows how to switch between different render modes 
+# programmatically and change render options.
+
+
+# remove all objects from scene, just in case
+scene.RemoveAll()
+
+# load pdb structure
+eh=io.LoadPDB("data/sdh.pdb")
 
 
 sdh_go=gfx.Entity("SDH2", eh.Select("cname=A"))
@@ -9,7 +16,7 @@ scene.CenterOn(sdh_go)
 
 def Tube():
   sdh_go.SetRenderMode(gfx.TUBE)
-  sdh_go.GetOptions(gfx.TUBE).SetTubeRadius(0.8)
+  sdh_go.tube_options.SetTubeRadius(0.8)
   # apply color gradient for the atomic bfactors
   sdh_go.ColorBy("abfac",gfx.BLUE,gfx.RED)
   # and apply radius gradient as well 
@@ -32,15 +39,15 @@ def Cartoon():
   sdh_go.SetColor(gfx.Color(1,0,0),"rtype=E")
   sdh_go.SetDetailColor(gfx.Color(1.0,0.8,0.2),"rtype=E")
   # these are the default params for the rendering
-  #sdh_go.GetOptions(gfx.HSC).SetArcDetail(4)    # circular profile detail
-  #sdh_go.GetOptions(gfx.HSC).SetSphereDetail(4) # sphere detail
-  #sdh_go.GetOptions(gfx.HSC).SetSplineDetail(8) # segments between backbone atoms
-  #sdh_go.GetOptions(gfx.HSC).SetTubeRadius(0.4) # coil radius 
-  #sdh_go.GetOptions(gfx.HSC).SetTubeRatio(1.0)  # coil axial ratio
-  #sdh_go.GetOptions(gfx.HSC).SetHelixWidth(1.1)   # helical width
-  #sdh_go.GetOptions(gfx.HSC).SetHelixThickness(0.2)   # helical thickness
-  #sdh_go.GetOptions(gfx.HSC).SetStrandWidth(1.2)  # strand width
-  #sdh_go.GetOptions(gfx.HSC).SetStrandThickness(0.2)  # strand thickness
+  #sdh_go.cartoon_options.SetArcDetail(4)    # circular profile detail
+  #sdh_go.cartoon_options.SetSphereDetail(4) # sphere detail
+  #sdh_go.cartoon_options.SetSplineDetail(8) # segments between backbone atoms
+  #sdh_go.cartoon_options.SetTubeRadius(0.4) # coil radius 
+  #sdh_go.cartoon_options.SetTubeRatio(1.0)  # coil axial ratio
+  #sdh_go.cartoon_options.SetHelixWidth(1.1)   # helical width
+  #sdh_go.cartoon_options.SetHelixThickness(0.2)   # helical thickness
+  #sdh_go.cartoon_options.SetStrandWidth(1.2)  # strand width
+  #sdh_go.cartoon_options.SetStrandThickness(0.2)  # strand thickness
 
 Cartoon()
-print 'Type Spheres(), Tube(), Trace(), or Cartoon()\n to switch render modes'
+
diff --git a/examples/misc/the_hammer.py b/examples/demos/the_hammer.py
similarity index 95%
rename from examples/misc/the_hammer.py
rename to examples/demos/the_hammer.py
index 11689000889b8c7289b9bad18e338784ef03f400..f6c77ebca38b663fd03b5e922604ccb3a3ef73e8 100644
--- a/examples/misc/the_hammer.py
+++ b/examples/demos/the_hammer.py
@@ -1,6 +1,10 @@
 from PyQt4 import QtCore
 import math
 from ost import qa
+
+# remove all objects from scene, just in case
+scene.RemoveAll()
+
 class Anim(QtCore.QTimer):
     def __init__(self, a, b):
         QtCore.QTimer.__init__(self)
@@ -82,3 +86,5 @@ grad.SetColorAt(0.0, gfx.Color(0.0, 1.0, 0.0))
 grad.SetColorAt(0.5, gfx.Color(1.0, 0.0, 1.0))
 grad.SetColorAt(1.0, gfx.Color(1.0, 0.0, 0.0))
 b_go.ColorBy('clash', gfx.Color(0,1,0), gfx.Color(1,0,0), 0.0, 10.0, mol.Prop.Level.ATOM)
+scene.CenterOn(b_go)
+print 'Demo 7: Illustrating a clash score'
diff --git a/examples/entity/bbox.py b/examples/entity/bbox.py
deleted file mode 100644
index f1a3593cda1da3b5ca32bec085e80423460fec05..0000000000000000000000000000000000000000
--- a/examples/entity/bbox.py
+++ /dev/null
@@ -1,16 +0,0 @@
-sdh=io.LoadPDB('sdh.pdb')
-helix=sdh.Select('rnum=99:128 and cname=A and aname=CA,C,N,O')
-go=gfx.Entity('helix', gfx.SIMPLE, helix)
-scene.Add(go)
-
-bbox=mol.BoundingBoxFromEntity(helix)
-
-def RenderBBox(bbox):
-  bb=gfx.Cuboid('xxx', bbox)
-  bb.SetFillColor(gfx.Color(0.5, 0.8, 0.5, 0.2))
-  scene.Add(bb)
-
-print 'C1:',(helix.GetGeometricStart()+helix.GetGeometricEnd())*.5
-  
-RenderBBox(bbox)
-scene.center=go.center
\ No newline at end of file
diff --git a/examples/img/circle.png b/examples/img/circle.png
deleted file mode 100644
index 87e380ffaf4071286584078d1461f6c9414fca1b..0000000000000000000000000000000000000000
Binary files a/examples/img/circle.png and /dev/null differ
diff --git a/examples/img/fft_li.py b/examples/img/fft_li.py
deleted file mode 100644
index f272d4c22f52cd0746db2bb4d4e4e07d1468c0e3..0000000000000000000000000000000000000000
--- a/examples/img/fft_li.py
+++ /dev/null
@@ -1,13 +0,0 @@
-import sys
-import ost.img.alg
-
-images=io.LoadImageList(sys.argv[1:])
-viewers=[]
-i=1
-for im in images:
-   im.CenterSpatialOrigin()
-   im.ApplyIP(img.alg.DFT()) 
-   v=gui.CreateDataViewer(im)
-   v.SetName(sys.argv[i])
-   viewers.append(v)
-   i+=1
diff --git a/examples/misc/ambient_occlusion.py b/examples/misc/ambient_occlusion.py
deleted file mode 100644
index 3ed9da4e8c072a70a20e7d02489064c0f0b511fe..0000000000000000000000000000000000000000
--- a/examples/misc/ambient_occlusion.py
+++ /dev/null
@@ -1,53 +0,0 @@
-def test1():
-    global surf
-    prot=io.LoadPDB("fragment.pdb")
-    surf=io.LoadSurface("fragment","msms")
-    surf.Attach(prot,5.0)
-    scene.Add(gfx.Surface("surf",surf))
-    scene["surf"].SetColor(gfx.RED,"ele=O")
-    scene["surf"].SetColor(gfx.BLUE,"ele=N")
-    scene.CenterOn("surf")
-    scene.SetFog(False)
-    # turn on full contribution from light
-    scene.SetLightProp(1,1,1)
-    
-    # use a material with 10% global ambient light,
-    # 90% diffuse light, and full specular with small
-    # hilights
-    scene["surf"].SetMat(0.1,0.9,1,128)
-
-    # turn on ambient occlusion
-    # this may take seconds to calculate
-    scene["surf"].AmbientOcclusion(True)
-
-    # blend the ambient occlusion 100% into the surface,
-    # reducing the color intensity
-    scene["surf"].AmbientOcclusionWeight(1)
-    # blend the local color 30% percent into the surface
-    scene["surf"].AmbientLocalWeight(0.3)
-
-    scene.AutoAutoslab(False)
-    scene.Autoslab()
-
-def test2():
-    global plist
-    plist=gfx.PrimList("t")
-    plist.AddPoint(geom.Vec3(-1,-1,0), gfx.RED)
-    plist.AddPoint(geom.Vec3(1,-1,0), gfx.GREEN)
-    plist.AddPoint(geom.Vec3(1,1,0), gfx.YELLOW)
-    plist.AddPoint(geom.Vec3(-1,1,0), gfx.BLUE)
-    plist.AddPoint(geom.Vec3(0,0,4), gfx.MAGENTA)
-    plist.SetMat(1,1,1,64)
-    scene.SetLightProp(0,1,0)
-    plist.SetRadius(1.5)
-    plist.SetSphereDetail(4)
-    plist.SetRenderMode(gfx.CUSTOM)
-    plist.AmbientOcclusion(True)
-    scene.Add(plist)
-    scene.CenterOn(plist)
-    scene.AutoAutoslab(False)
-    scene.Autoslab()
-    plist.AmbientOcclusion(True)
-
-
-test1()
diff --git a/examples/trj/test_trj_blur.py b/examples/trj/test_trj_blur.py
deleted file mode 100644
index dbbab5f8d1676c3febd75beed47b5b849fe3cf44..0000000000000000000000000000000000000000
--- a/examples/trj/test_trj_blur.py
+++ /dev/null
@@ -1,34 +0,0 @@
-# trajectory generated by Raimund Dutzler
-from PyQt4 import QtCore
-
-class Anim(QtCore.QTimer):
-    def __init__(self,cg,go):
-        QtCore.QTimer.__init__(self)
-        self.cg_=cg
-        self.go_=go
-        self.frame_=0
-        QtCore.QObject.connect(self, QtCore.SIGNAL("timeout()"), self.OnTimer)
-        
-    def OnTimer(self):
-        self.step()
-        
-    def step(self):
-        self.frame_=(self.frame_+1)%self.cg_.GetFrameCount()
-        go.BlurSnapshot()
-        self.cg_.CopyFrame(self.frame_)
-        go.UpdatePositions()
-
-cg = io.LoadCHARMMTraj("sample.pdb","sample.dcd")
-eh=cg.GetEntity()
-ev=eh.Select("not ele=H")
-go=gfx.Entity("mol",gfx.SIMPLE, ev)
-go.SetBlur(True)
-
-scene.Add(go)
-scene.SetCenter(go.GetCenter())
-scene.AutoAutoslab(True)
-
-anim=Anim(cg,go)
-
-print "enter anim.start(10) to start trajectory animation; use anim.stop() to turn it off again."
-
diff --git a/graphics/favicon.ico b/graphics/favicon.ico
new file mode 100644
index 0000000000000000000000000000000000000000..4c6795c6a77acd5b919daa4f4cb3dc7a0ad54e22
Binary files /dev/null and b/graphics/favicon.ico differ
diff --git a/modules/CMakeLists.txt b/modules/CMakeLists.txt
index dd418e1c256f3c9dcf0c17d24cd732a693db1c05..20e102235b323e0a3b32e531beef75808129b535 100644
--- a/modules/CMakeLists.txt
+++ b/modules/CMakeLists.txt
@@ -3,7 +3,8 @@ file(GLOB ALL_FILES *)
 foreach(fname ${ALL_FILES})
   if(NOT ${fname} MATCHES ".*.svn" 
      AND NOT ${fname} MATCHES ".*CMakeFiles" 
-     AND NOT ${fname} MATCHES ".*main")
+     AND NOT ${fname} MATCHES ".*main"
+     AND NOT ${fname} MATCHES "doc")
       if(IS_DIRECTORY ${fname})
         add_subdirectory(${fname})
       endif()
diff --git a/modules/base/doc/base.rst b/modules/base/doc/base.rst
new file mode 100644
index 0000000000000000000000000000000000000000..6e0a6caf5f16b2367498e4284a98a1f067be92dd
--- /dev/null
+++ b/modules/base/doc/base.rst
@@ -0,0 +1,7 @@
+:mod:`ost` - OpenStructure Base Module
+================================================================================
+
+.. toctree::
+
+  logging
+  settings
diff --git a/modules/base/doc/generic.rst b/modules/base/doc/generic.rst
new file mode 100644
index 0000000000000000000000000000000000000000..919497f390775a68deee2fcc973a22f29beace75
--- /dev/null
+++ b/modules/base/doc/generic.rst
@@ -0,0 +1,168 @@
+Storing Custom Data
+================================================================================
+
+Introduction
+--------------------------------------------------------------------------------
+
+.. currentmodule:: ost
+
+It is often very convenient to store any arbitrary data inside an Entity. A few 
+examples are: 
+
+  * calculated properties of atoms
+  * sequence conservation of a residue
+  * interaction energy of a substructure with its surrounding
+  * fit of a fragment inside an electron density map
+
+In OpenStructure this is supported by the use of generic properties. Most 
+building blocks are derived from :class:`~ost.GenericPropertyContainer`, meaning 
+that arbitrary key-value pairs can be stored in them. In essence, the following 
+classes support generic properties:
+
+  * :class:`~ost.mol.EntityHandle` and :class:`~ost.mol.EntityView`
+  * :class:`~ost.mol.ChainHandle` and :class:`~ost.mol.ChainView`
+  * :class:`~ost.mol.ResidueHandle` and :class:`~ost.mol.ResidueView`
+  * :class:`~ost.mol.AtomHandle` and :class:`~ost.mol.AtomView`
+  * :class:`~ost.mol.BondHandle`
+  * :class:`~ost.seq.SequenceHandle` and :class:`~ost.seq.AlignmentHandle`
+
+The view variants will reflect the generic properties of the handle variants.
+
+A generic property key is always a string, and a value can be one of string, 
+float, int or bool. For each of these data types, methods to retrieve and store 
+values are available both in Python and C++.
+
+Storing and Accessing Data
+--------------------------------------------------------------------------------
+
+All OpenStructure building blocks that are :class:`~ost.GenericPropContainers`, 
+have four different methods to store generic data, depending on the data type 
+(i.e. string, float, int or bool).
+
+To store a float value with the key 'myfloatprop' in all atoms of an entity:
+
+.. code-block:: python
+  
+  import math
+  for atom in entity.GetAtomList(): 
+    val=5*math.sin(0.4*atom.GetPos().x)
+    atom.SetFloatProp("myfloatprop", val)
+  
+If a GenericProp at a given level (i.e. atom, bond, residue, chain or entity) 
+already exists, it will be overwritten. To check if it exists, use:
+
+.. code-block:: python
+  
+  exists=atom.HasProp("myfloatprop")
+  print exists
+    
+To access the value of a generic property, we first check if the property exists
+and then access it, using the method suitable for the data type of the property. 
+For the previously set property `myfloatprop` of the data type real, at the atom 
+level:
+
+.. code-block:: python
+  
+  for atom in entity.GetAtomList(): 
+    if atom.HasProp("myfloatprop"):
+      print atom.GetFloatProp("myfloatprop")
+        
+When trying to access a property that has not been set, or one that has been 
+set, but at a different level, an error is thrown. The same is true when trying 
+to access a property of a different data type, e.g.:
+
+.. code-block:: python
+
+  # all of the following lines will throw errors
+  # error because the property does not exist 
+  print atom.GetFloatProp("unknownprop")
+  
+  # error because the property was set at another level
+  print entity.GetFloatProp("myfloatprop")
+  
+  # error because the data type of the property is different
+  print atom.GetStringProp("myfloatprop")
+      
+
+Use of Generic Properties in Queries
+--------------------------------------------------------------------------------
+
+The :doc:`../mol/base/query` can also be used for numeric generic properties 
+(i.e. bool, int, float), but the syntax is slightly different. To access any 
+generic properties, it needs to be specified that they are generic and at which 
+level (chain, residue, atom) they are defined. Therefore, all generic properties 
+start with a 'g', followed by an 'a', 'r' or 'c' for atom, residue or chain 
+level respectively. For more details see :doc:`../mol/base/query`. 
+
+
+API documentation
+--------------------------------------------------------------------------------
+
+.. class:: GenericPropertyContainer
+
+  .. method:: HasProp(key)
+  
+    checks existence of property. Returns true, if the the class contains a
+    property with the given name, false if not.
+  
+  .. method:: GetPropAsString(key)
+  
+    Returns the string representation of a property, or the empty String if 
+    the property addressed by key does not exist. Note that this is not the 
+    same as trying to get a generic float/int/bool property as a string type; 
+    the latter will result in a boost:get exception. Use this method to obtain 
+    a representation suitable for output.
+    
+  .. method:: GetStringProp(key)
+              GetStringProp(key, default_value)
+  
+    Get string property. The first signature raises a GenericPropError error if
+    the property does not exist, the second returns the default value.
+  
+  
+  .. method:: GetFloatProp(key)
+              GetFloatProp(key, default_value)
+   
+    Get float property. The first signature raises a GenericPropError error if
+    the property does not exist, the second returns the default value.
+
+
+  .. method:: GetIntProp(key)
+              GetIntProp(key, default_value)
+
+    Get int property. The first signature raises a GenericPropError error if
+    the property does not exist, the second returns the default value.
+
+  .. method:: GetBoolProp(key)
+              GetBoolProp(key, default_value)
+
+    Get bool property. The first signature raises a GenericPropError error if
+    the property does not exist, the second returns the default value.
+        
+  .. method:: ClearProps()
+    
+    Remove all generic properties
+  
+ 
+  .. method:: SetStringProp(key, value)
+    
+    Set string property, overriding an existing property with the same name
+    
+  .. method:: SetFloatProp(key, value)
+    
+    Set float property, overriding an existing property with the same name
+
+  .. method:: SetIntProp(key, value)
+  
+    Set int property, overriding an existing property with the same name
+  
+  .. method:: SetBoolProp(key, value)
+  
+    Set bool property, overriding a property with the same name
+    
+  .. method:: RemoveProp(key)
+  
+    Removes the property with given key, regardless of its type. If the property 
+    does not exist, the method has no effect.
+    
+
diff --git a/modules/base/doc/logging.rst b/modules/base/doc/logging.rst
new file mode 100644
index 0000000000000000000000000000000000000000..1a81d479490ced8accd47006543a4c9c247b6749
--- /dev/null
+++ b/modules/base/doc/logging.rst
@@ -0,0 +1,193 @@
+Logging
+================================================================================
+
+.. currentmodule:: ost
+
+OpenStructure has a logging system going beyond what print statements can offer. Messages can be logged to the terminal to the graphical user interface or a file. Depending on the needs, groups of messages can be turned and off.
+
+.. function:: LogError(message)  
+              LogWarning(message)      
+              LogInfo(message)
+              LogVerbose(message)
+  
+  Add a message to the log. For the choice of the appropriate logging level, 
+  see :ref:`picking-logging-level`.
+  
+  :param message: The message to be logged
+  :type  message: str
+  
+.. note::
+
+  In C++, the logging facility is implemented as a set of macros, called
+  `LOG_ERROR`, `LOG_WARNING`, `LOG_SCRIPT`, `LOG_INFO`, `LOG_VERBOSE`,
+  `LOG_DEBUG` and `LOG_TRACE`. The last two are only active when compiling with 
+  debugging symbols. When debugging symbols are off, they expand to an empty 
+  macro and thus don't create any overhead.
+
+
+Verbosity Level
+--------------------------------------------------------------------------------
+
+You can change the verbosity level  with the following two methods:
+
+.. function:: PushVerbosityLevel(verbosity)
+
+  Change the verbosity level to the given integer value. All log events 
+  which have a severity above verbosity will be ignored. By default, the log 
+  level is 2, meaning that errors, warnings and script logging events are 
+  visible.
+
+  :type  verbosity: :class:`int`
+
+.. function:: PopVerbosityLevel()
+
+  Change the log level back to the previous verbosity level. It is an error to 
+  pop the verbosity level without a matching call to 
+  :func:`PushVerbosityLevel`.
+         
+Log sinks
+--------------------------------------------------------------------------------
+
+When running OpenStructure from the command-line, the log messages are by 
+default output to stderr. When running DNG, the log messages are additionally 
+logged to the messages widget. However, it is also possible to log into a file 
+or theoretically even to a remote computer. All these are instances of so-called 
+log sinks: classes that derive from LogSink and implement the LogMessage method.
+
+
+.. class:: LogSink
+
+  .. method:: LogMessage(message, severity)
+
+     This method is called whenever something gets logged. This method must be 
+     implemented by all subclasses.
+     
+     :param message: The logged message
+    
+     :type  message: :class:`str`
+     
+     :param severity: Marks how severe the logged message is. Errors have 
+          severity 0, warnings 1 etc.
+    
+     :type  severity: :data:`int`
+
+For convenience, there are 3 LogSink implementations available in OpenStructure that are sufficient for most use cases.
+
+.. class:: FileLogSink(filename)
+
+  The FileLogSink logs all messages into the given file.
+  
+  :param filename: The filename
+  :type filename: :class:`str`
+
+.. class:: StreamLogSink(stream)
+
+  The stream log sink writes all log messages to the stream. stream must have a 
+  write method that accepts a string. To write messages to stderr, use
+  
+  .. code-block:: python
+  
+    stderr_sink=ost.StreamLogSink(sys.stderr)
+    ost.PushLogSink(stderr_sink)
+    ost.LogInfo('Welcome, master')
+  
+.. class:: MultiLogSink
+
+     A LogSink for multiplexing the log messages into multiple sinks at the same 
+     time, e.g. the terminal and the messages widget.
+     
+  .. method:: AddSink(sink)
+  
+    Add a new sink. The sink's :meth:`LogSink.LogMessage` method will be called 
+    every time something gets logged.
+    
+    :type sink: :class:`~ost.LogSink`
+    :param sink: the log sink to be added
+
+  .. method:: RemoveSink(sink)
+  
+    Remove the given sink. If the doesn't exist, this method has no effect.
+    
+    :type sink: :class:`~ost.LogSink`
+    :param sink: the log sink to be removed
+    
+
+To change the current log sink you can use the following methods:
+
+.. method:: PushLogSink(sink)
+
+   Push the new sink onto the log sink stack. All of the messages will now be 
+   logged to the new sink. To switch back to the previous log sink, use 
+   :func:`PopLogSink`.
+
+.. method:: PopLogSink()
+
+   Change the log sink back to the previous one. It is an error to pop the log 
+   sink when there is only one log sink on the stack.
+
+.. _picking-logging-level:
+
+Guidelines for picking logging level
+--------------------------------------------------------------------------------
+
+Each logging event has an associated level that marks its importance. For example, users should always see errors, but they do not need to see detailed information on the loading process. Here is a list of guidelines that we use in the code. We encourage developers to adhere to these guidelines as closely as possible.
+
+ERROR: 
+  Cannot be silenced, very important message to the user, some command did not
+  complete as expected or was aborted. 
+
+WARNING:
+  Diagnose potential problems that do not abort the execution, but may 
+  point to a misconfiguration/misuse. This level is turned on by default.
+
+SCRIPT: 
+  Logging level that should be used from scripts, e.g. to report progress. These 
+  logging messages are turned on by default.
+
+INFO: 
+  Informative and important messages that summarize a complex command, such as 
+  information on a loaded file, or results from an algorithm. These logging 
+  messages are not turned on by default.
+
+VERBOSE: 
+  Grey-zone between user and developer need, and perhaps the hardest to get
+  right. This is the lowest logging level users will be able to see when they 
+  use an optimized build. An example for this is the OpenGL setup/info in gfx, 
+  or the path search during startup, or more detailed info on file IO. These 
+  messages are not turned on by default.
+
+DEBUG: 
+  For developers, but not quite at the trace level. This level is turned off by 
+  default, not available in Python and only enabled when compiling with 
+  debugging symbols.
+
+TRACE:
+  Used to debug inner loops. Once turned on, you will probably get more debug 
+  output that you will be able to handle. This  level is turned off by default, 
+  not available in python and only enabled when compiling with debugging 
+  symbols.
+
+
+Example
+--------------------------------------------------------------------------------
+
+The following snippet explains how to create a custom log sink which logs to the 
+terminal (or the python shell in DNG). The logger also prints the current time.
+
+.. code-block:: python
+
+  import datetime
+  class PyLogger(ost.LogSink):
+    def __init__(self):
+      ost.LogSink.__init__(self)
+
+    def LogMessage(self, message, severity):
+      levels=['ERROR', 'WARNING', 'SCRIPT', 'INFO', 
+              'VERBOSE', 'DEBUG', 'TRACE']
+      level=levels[severity]
+      print '%s[%s]: %s' % (level, str(datetime.datetime.now()), message),
+
+  py_logger=PyLogger()
+  ost.PushLogSink(py_logger)
+
+  ost.LogInfo("amazing logging system")
\ No newline at end of file
diff --git a/modules/base/doc/settings.rst b/modules/base/doc/settings.rst
new file mode 100644
index 0000000000000000000000000000000000000000..8ba0ffc3786c1be74b85077fde007b696a85f50d
--- /dev/null
+++ b/modules/base/doc/settings.rst
@@ -0,0 +1,6 @@
+:mod:`ost.settings` - Locate Files and Retrieve Preferences
+================================================================================
+
+.. automodule:: ost.settings
+  :synopsis: Helper Functions to Locate Files and Retrieve Preferences
+  :members:
diff --git a/modules/base/pymod/CMakeLists.txt b/modules/base/pymod/CMakeLists.txt
index 4eb36a9147d7d83b081d05f4abeb3ca0a2868467..22700288ae061f64b45fb741e13b5044b2bf8977 100644
--- a/modules/base/pymod/CMakeLists.txt
+++ b/modules/base/pymod/CMakeLists.txt
@@ -7,4 +7,4 @@ set(OST_BASE_PYMOD_SOURCES
 
 pymod(NAME base OUTPUT_DIR ost 
       CPP ${OST_BASE_PYMOD_SOURCES} 
-      PY __init__.py settings.py)
+      PY __init__.py settings.py stutil.py)
diff --git a/modules/base/pymod/__init__.py b/modules/base/pymod/__init__.py
index 3d2137f7e76f6a66a8cf2041319d801742fafedf..c6d7a8ec17b8085fb4412236f0bfbbf5f6cc648f 100644
--- a/modules/base/pymod/__init__.py
+++ b/modules/base/pymod/__init__.py
@@ -17,6 +17,7 @@
 # 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #------------------------------------------------------------------------------
 from _base import *
+from stutil import *
 
 from ost import geom
 from ost import io
@@ -35,3 +36,10 @@ try:
 except ImportError:
   pass
 
+
+class StreamLogSink(LogSink):
+  def __init__(self, stream):
+    LogSink.__init__(self)
+    self._stream=stream
+  def LogMessage(self, message, level):
+    self._stream.write(message)
diff --git a/modules/base/pymod/export_logger.cc b/modules/base/pymod/export_logger.cc
index b385742e744fea3f056ec84db24317ac1038d748..4c2b79b20f3b95dcdf8f0576a3bd166c49916a37 100644
--- a/modules/base/pymod/export_logger.cc
+++ b/modules/base/pymod/export_logger.cc
@@ -20,11 +20,32 @@
 using namespace boost::python;
 
 #include <ost/log.hh>
+#include <ost/log_sink.hh>
+#include <ost/dyn_cast.hh>
+
 using namespace ost;
 
 
 namespace {
 
+struct WrappedLogSink : public LogSink {
+  WrappedLogSink(PyObject* self): self_(self)
+  { }
+  virtual void LogMessage(const String& message , int severity) 
+  {
+    call_method<void>(self_, "LogMessage", message, severity);
+  }
+  
+  void LogMessageDefault(const String& message, int severity)
+  {
+  }
+  PyObject* self_;
+};
+
+
+
+typedef boost::shared_ptr<WrappedLogSink> WrappedLogSinkPtr;
+
 void push_verb(int n) 
 {
  if(n<0){
@@ -39,21 +60,66 @@ void pop_verb()
   Logger::Instance().PopVerbosityLevel();
 }
 
-void log_error(const String& m) {LOGN_MESSAGE(m);}
-void log_message(const String& m) {LOGN_MESSAGE(m);}
-void log_verbose(const String& m) {LOGN_VERBOSE(m);}
-void log_debug(const String& m) {LOGN_DEBUG(m);}
+void push_log_sink(LogSinkPtr sink)
+{
+  Logger::Instance().PushSink(sink);
+}
 
+void pop_log_sink()
+{
+  Logger::Instance().PopSink();
+}
+
+
+void log_error(const String& m) {LOG_ERROR(m);}
+void log_warning(const String& m) {LOG_WARNING(m);}
+void log_script(const String& m) {LOG_SCRIPT(m);}
+void log_info(const String& m) {LOG_INFO(m);}
+void log_verbose(const String& m) {LOG_VERBOSE(m);}
+
+
+void reset_sinks()
+{
+  Logger::Instance().ResetSinks();
+}
 }
 
 void export_Logger()
 {
-  
+  class_<LogSink, WrappedLogSinkPtr, 
+         boost::noncopyable>("LogSink")
+    .def("LogMessage", &WrappedLogSink::LogMessageDefault)
+  ;
+
+  class_<MultiLogSink, MultiLogSinkPtr, bases<LogSink>, 
+         boost::noncopyable >("MultiLogSink", init<>())
+    .def("AddSink",&MultiLogSink::AddSink)
+    .def("RemoveSink",&MultiLogSink::RemoveSink)
+    .def("LogMessage", &MultiLogSink::LogMessage)
+  ;
+
+  class_<FileLogSink, FileLogSinkPtr, bases<LogSink>, 
+         boost::noncopyable >("FileLogSink", init<const String&>())
+    .def("LogMessage", &FileLogSink::LogMessage)
+  ;
+
   def("PushVerbosityLevel",push_verb);
   def("PopVerbosityLevel",pop_verb);
-
+  def("PushLogSink",push_log_sink);
+  def("PopLogSink",pop_log_sink);
   def("LogError",log_error);
-  def("LogMessage",log_message);
-  def("LogVerbose",log_verbose);
-  def("LogDebug",log_debug);
+  def("LogWarning",log_warning);
+  def("LogInfo",log_info);
+  def("LogScript", log_script);
+  def("LogVerbose", log_verbose);
+  
+  // this relatively ugly construct is required to work around a problem with
+  // the "ost" command-line interpreter. If we don't remove all the sinks from
+  // the sink stack, we will get "Fatal Python error: PyEval_SaveThread: 
+  // NULL tstate" upon exiting ost. I don't completely understand why, though.
+  scope().attr("__dict__")["atexit"]=import("atexit");
+
+  def("_reset_sinks", &reset_sinks);
+  object r=scope().attr("_reset_sinks");
+  scope().attr("atexit").attr("register")(r);
 }
diff --git a/modules/base/pymod/settings.py b/modules/base/pymod/settings.py
index 1740c3287dace8d503aa93f801c763ba9384dfa5..56bf46b4aeedf36cfcd471390cf361860608682e 100644
--- a/modules/base/pymod/settings.py
+++ b/modules/base/pymod/settings.py
@@ -1,14 +1,15 @@
-import os
+import os, platform
 import __main__
  
 
 def GetValue(val_key,val_default=None,prefix='OST'):
-  '''
+  """
   Returns the value of the variable val_key if defined, otherwise returns the 
   default value provided by the user (if provided). Search order: 
-  1) environment variable called $prefix_$val_key 
-  2) variable called val_key in .dngrc file
-  '''
+  
+   * environment variable called $prefix_$val_key 
+   * variable called val_key in .ostrc file
+  """
   if prefix:
     env_var_name='%s_%s' % (prefix, val_key)
   else:
@@ -24,6 +25,12 @@ def GetValue(val_key,val_default=None,prefix='OST'):
       return val_default
 
 class FileNotFound(RuntimeError):
+  """
+  Raised when :func:`Locate` is unable to locate a file. The exception contains
+  detailed information on what was tried to locate the file, i.e. search paths, 
+  environment variables and also provides useful hints on how to let Locate know
+  where to find the file.
+  """
   def __init__(self, name, reason):
     self.name=name
     self.reason=reason
@@ -33,22 +40,26 @@ class FileNotFound(RuntimeError):
 def Locate(file_name, explicit_file_name=None, search_paths=[],
            env_name=None, search_system_paths=True):
   """
-  Helper function to locate files. To get the full name of 
-  an executable, let's say qmake, use
+  Helper function to locate files. To get the full name of an executable, let's 
+  say qmake, use
+  
+  .. code-block:: python
 
-  abs_qmake_path=Locate('qmake', env_name='QMAKE_EXECUTABLE')
+    abs_qmake_path=Locate('qmake', env_name='QMAKE_EXECUTABLE')
 
-  First the function checks if an environment variable with the
-  name QMAKE_EXECUTABLE is set. If so, the value of this variable
-  is returned. Next, each directory listed in search_paths is 
-  searched. If the executable could still not be found and
-  search_system_paths is set to True, the binary search paths are
-  searched.
+  First the function checks if an environment variable with the name 
+  QMAKE_EXECUTABLE is set. If so, the value of this variable is returned. Next, 
+  each directory listed in search_paths is searched. If the executable could 
+  still not be found and search_system_paths is set to True, the binary search 
+  paths are searched.
 
-  If the file could not be located, a FileNotFound exception will be raised
-  containing a detail description why Locate failed. The error message is
-  formatted in such a way that it can directly be presented to the user.
+  If the file could not be located, a :exc:`~ost.settings.FileNotFound` 
+  exception will be raised containing a detail description why Locate failed. The 
+  error message is formatted in such a way that it can directly be presented to 
+  the user.
   """
+  def _is_executable(filename):
+    return os.path.exists(filename) and os.access(filename, os.X_OK)
   if type(file_name) is str:
     file_names=[file_name]
   else:
@@ -57,14 +68,14 @@ def Locate(file_name, explicit_file_name=None, search_paths=[],
   epxl_inexistent='explicitly set file "%s" does not exist'
   set_env_var='set the environment variable %s to the absolute path to %s or '
   if explicit_file_name:
-    if os.path.exists(explicit_file_name):
+    if _is_executable(explicit_file_name):
       return explicit_file_name
     else:
       raise FileNotFound(file_name, epxl_inexistent % explicit_file_name)
   if env_name:
     file_env_name=os.getenv(env_name, None)
     if file_env_name:
-      if os.path.exists(file_env_name):
+      if _is_executable(file_env_name):
         return file_env_name
       else:
         raise FileNotFound(file_name, 
@@ -73,16 +84,19 @@ def Locate(file_name, explicit_file_name=None, search_paths=[],
   for search_path in search_paths:
     for file_name in file_names:
       full_file_name=os.path.join(search_path, file_name)
-      if os.path.exists(full_file_name):
+      if _is_executable(full_file_name):
         return full_file_name
 
   if search_system_paths:
     paths=os.getenv('PATH')
-    searched+=paths.split(':')
+    if platform.system() == "Windows":
+      searched+=paths.split(';')
+    else:
+      searched+=paths.split(':')
     for path in searched:
       for file_name in file_names:
         full_file_name=os.path.join(path, file_name)
-        if os.path.exists(full_file_name):
+        if _is_executable(full_file_name):
           return full_file_name
   msg=''        
   if len(searched)>0:
diff --git a/modules/base/pymod/stutil.py b/modules/base/pymod/stutil.py
new file mode 100644
index 0000000000000000000000000000000000000000..75bb922485ac2239d0158b3ba80a33cc05976990
--- /dev/null
+++ b/modules/base/pymod/stutil.py
@@ -0,0 +1,105 @@
+import math
+from ost import mol
+
+def FloatValueExtract(func):
+  """
+  Decorator to wrap functions that take a list of float values. In addition to 
+  passing in a list of float values directly, it is possible to extract the 
+  values from attributes or generic properties.
+  """
+  def _dec(xs, prop=None, attr=None):
+    if prop!=None:
+      if len(xs)==0:
+        return func([])
+      assert attr==None
+      level=mol.Prop.Level.UNSPECIFIED
+      if isinstance(xs[0], mol.AtomBase):
+        level=mol.Prop.Level.ATOM
+      elif isinstance(xs[0], mol.ResidueBase):
+        level=mol.Prop.Level.RESIDUE
+      elif isinstance(xs[0], mol.ChainBase):
+        level=mol.Prop.Level.CHAIN
+      epm=mol.EntityPropertyMapper(prop, level)
+      vals=[]
+      for x in xs:
+        try:
+          vals.append(epm.Get(x))
+        except:
+          pass
+      return func(vals)
+    if attr!=None:
+      vals=[]
+      for x in xs:
+        try:
+          vals.append(getattr(x, attr))
+        except:
+          pass
+      return func(vals)
+    return func(xs)
+  return _dec
+
+@FloatValueExtract  
+def Mean(xs):
+  """
+  Calculate mean of dataset
+  """
+  if len(xs)==0:
+    raise RuntimeError("Can't calculate mean of empty sequence")
+  return sum(xs)/len(xs)
+
+@FloatValueExtract
+def StdDev(xs):
+  """
+  Calculate standard-deviation of dataset
+  
+            | sum[xi-<x>]^2 |
+  sigma=sqrt|---------------|
+            |       n       |
+  """
+  mean=Mean(xs)
+  return math.sqrt(sum([(x-mean)**2 for x in xs])/len(xs))
+
+@FloatValueExtract
+def Min(xs):
+  return min(xs)
+
+@FloatValueExtract
+def Max(xs):
+  return max(xs)
+
+def Correl(xs, ys):
+  """
+  Calculates the correlation coefficient between xs and ys as
+  
+    sum[(xi-<x>)*(yi-<y>)]
+  r=----------------------
+          (n-1)*sx*sy
+          
+  where <x>, <y> are the mean of dataset xs and ys, and, sx and sy are the 
+  standard deviations.
+  """
+  if len(xs)!=len(ys):
+    raise RuntimeError("Can't calculate correl. Sequence lengths do not match.")
+  if len(xs)==1:
+    raise RuntimeError("Can't calculate correl of sequences with length 1.")
+  mean_x=Mean(xs)
+  mean_y=Mean(ys)
+  sigma_x, sigma_y=(0.0, 0.0)
+  cross_term=0.0
+  for x, y in zip(xs, ys):
+    cross_term+=(x-mean_x)*(y-mean_y)
+    sigma_x+=(x-mean_x)**2
+    sigma_y+=(y-mean_y)**2
+  sigma_x=math.sqrt(sigma_x/len(xs))
+  sigma_y=math.sqrt(sigma_y/len(ys))  
+  return cross_term/((len(xs)-1)*sigma_x*sigma_y)
+
+def Histogram(xs, bounds, num_bins):
+  bins=[0 for i in range(num_bins)]
+  d=1.0*num_bins/(bounds[1]-bounds[0])
+  for x in xs:
+    index=int((x-bounds[0])*d)
+    if index>num_bins-1 or index<0:
+      continue
+    bins[index]+=1
+  return bins
diff --git a/modules/base/pymod/wrap_base.cc b/modules/base/pymod/wrap_base.cc
index c3dd609ecfcaca8ba873cf6d83a49f30c27c12cc..20a6668cbedd99e9137d31c51ccf6de0ac2c515e 100644
--- a/modules/base/pymod/wrap_base.cc
+++ b/modules/base/pymod/wrap_base.cc
@@ -16,12 +16,13 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#include <vector>
-
 #include <boost/python.hpp>
 #include <boost/python/suite/indexing/vector_indexing_suite.hpp>
+#include <vector>
+#include <ost/export_helper/vector.hh>
 #include <ost/base.hh>
 #include <ost/platform.hh>
+#include <ost/message.hh>
 
 using namespace boost::python;
 
@@ -30,16 +31,35 @@ void export_GenericProp();
 void export_Range();
 void export_Units();
 
+// exception translator
+void translator(const ost::Error& x) {
+  PyErr_SetString(PyExc_Exception, x.what() );
+}
+
+
 BOOST_PYTHON_MODULE(_base)
 {
+  register_exception_translator<ost::Error>(&translator);
+
   def("SetPrefixPath", &ost::SetPrefixPath);
   def("GetPrefixPath", &ost::GetPrefixPath);
   def("GetSharedDataPath", &ost::GetSharedDataPath);  
   export_Logger();
   export_Range();
   export_Units();
+  typedef std::vector<Real> FloatList;
+  class_<FloatList>("FloatList", init<>())
+    .def(vector_indexing_suite<FloatList>())
+    .def(ost::VectorAdditions<FloatList>())
+  ;
   
   class_<std::vector<String> >("StringList", init<>())
     .def(vector_indexing_suite<std::vector<String> >())
+  ;
+  
+  typedef std::vector<int> IntList;
+  class_<std::vector<int> >("IntList", init<>())
+    .def(vector_indexing_suite<std::vector<int> >())
+    .def(ost::VectorAdditions<IntList>())
   ;  
 }
diff --git a/modules/base/src/CMakeLists.txt b/modules/base/src/CMakeLists.txt
index 386e9d920a5f23f59dd187bc0d25e6db7d3faac2..4836b0896db66c48a37069196cd3fab6a8ff0393 100644
--- a/modules/base/src/CMakeLists.txt
+++ b/modules/base/src/CMakeLists.txt
@@ -1,6 +1,7 @@
 set(OST_BASE_SOURCES 
 generic_property.cc
 log.cc
+log_sink.cc
 profile.cc
 units.cc
 string_ref.cc
@@ -15,6 +16,7 @@ integrity_error.hh
 invalid_handle.hh
 ptr_observer.hh
 log.hh
+log_sink.hh
 profile.hh
 dyn_cast.hh
 stdint.hh
@@ -33,6 +35,7 @@ tri_matrix.hh
 set(OST_EXPORT_HELPERS
 generic_property_def.hh 
 pair_to_tuple_conv.hh 
+vector.hh
 )
 module(NAME base SOURCES ${OST_BASE_SOURCES} 
        HEADERS ${OST_EXPORT_HELPERS} IN_DIR export_helper 
diff --git a/modules/base/src/export_helper/generic_property_def.hh b/modules/base/src/export_helper/generic_property_def.hh
index 3203bc19876f70e349032f78581d34843756aaa0..785bcce900b6ab8ee2f5eca3aeb68d5c87923695 100644
--- a/modules/base/src/export_helper/generic_property_def.hh
+++ b/modules/base/src/export_helper/generic_property_def.hh
@@ -28,105 +28,105 @@
 template <typename C>
 String depr_get_string_a(C& c, const String& k, const String& v)
 {
-  LOGN_MESSAGE("GetGenericStringProperty is deprecated. Use GetStringProp");
+  WARN_DEPRECATED("GetGenericStringProperty is deprecated. Use GetStringProp");
   return c.GetStringProp(k, v);
 }
 
 template <typename C>
 String depr_get_string_b(C& c, const String& k)
 {
-  LOGN_MESSAGE("GetGenericStringProperty is deprecated. Use GetStringProp");
+  WARN_DEPRECATED("GetGenericStringProperty is deprecated. Use GetStringProp");
   return c.GetStringProp(k);
 }
 
 template <typename C>
 void depr_set_string(C& c, const String& k, const String& v)
 {
-  LOGN_MESSAGE("SetGenericStringProperty is deprecated. Use SetStringProp");
+  WARN_DEPRECATED("SetGenericStringProperty is deprecated. Use SetStringProp");
   return c.SetStringProp(k, v);
 }
 
 template <typename C>
 int depr_get_int_a(C& c, const String& k, const int& v)
 {
-  LOGN_MESSAGE("GetGenericIntProperty is deprecated. Use GetIntProp");
+  WARN_DEPRECATED("GetGenericIntProperty is deprecated. Use GetIntProp");
   return c.GetIntProp(k, v);
 }
 
 template <typename C>
 int depr_get_int_b(C& c, const String& k)
 {
-  LOGN_MESSAGE("GetGenericIntProperty is deprecated. Use GetIntProp");
+  WARN_DEPRECATED("GetGenericIntProperty is deprecated. Use GetIntProp");
   return c.GetIntProp(k);
 }
 
 template <typename C>
 void depr_set_int(C& c, const String& k, const int& v)
 {
-  LOGN_MESSAGE("SetGenericIntProperty is deprecated. Use SetIntProp");
+  WARN_DEPRECATED("SetGenericIntProperty is deprecated. Use SetIntProp");
   return c.SetIntProp(k, v);
 }
 
 template <typename C>
 bool depr_get_bool_a(C& c, const String& k, const bool& v)
 {
-  LOGN_MESSAGE("GetGenericBoolProperty is deprecated. Use GetBoolProp");
+  WARN_DEPRECATED("GetGenericBoolProperty is deprecated. Use GetBoolProp");
   return c.GetBoolProp(k, v);
 }
 
 template <typename C>
 bool depr_get_bool_b(C& c, const String& k)
 {
-  LOGN_MESSAGE("GetGenericBoolProperty is deprecated. Use GetBoolProp");
+  WARN_DEPRECATED("GetGenericBoolProperty is deprecated. Use GetBoolProp");
   return c.GetBoolProp(k);
 }
 
 template <typename C>
 void depr_set_bool(C& c, const String& k, const bool& v)
 {
-  LOGN_MESSAGE("SetGenericBoolProperty is deprecated. Use SetBoolProp");
+  WARN_DEPRECATED("SetGenericBoolProperty is deprecated. Use SetBoolProp");
   return c.SetBoolProp(k, v);
 }
 
 template <typename C>
 Real depr_get_float_a(C& c, const String& k, const float& v)
 {
-  LOGN_MESSAGE("GetGenericFloatProperty is deprecated. Use GetFloatProp");
+  WARN_DEPRECATED("GetGenericFloatProperty is deprecated. Use GetFloatProp");
   return c.GetFloatProp(k, v);
 }
 
 template <typename C>
 Real depr_get_float_b(C& c, const String& k)
 {
-  LOGN_MESSAGE("GetGenericFloatProperty is deprecated. Use GetFloatProp");
+  WARN_DEPRECATED("GetGenericFloatProperty is deprecated. Use GetFloatProp");
   return c.GetFloatProp(k);
 }
 
 template <typename C>
 void depr_set_float(C& c, const String& k, const Real& v)
 {
-  LOGN_MESSAGE("SetGenericFloatProperty is deprecated. Use SetFloatProp");
+  WARN_DEPRECATED("SetGenericFloatProperty is deprecated. Use SetFloatProp");
   return c.SetFloatProp(k, v);
 }
 
 template <typename C>
 void depr_clear_props(C& c)
 {
-  LOGN_MESSAGE("ClearGenericProperties is deprecated. Use ClearProps");
+  WARN_DEPRECATED("ClearGenericProperties is deprecated. Use ClearProps");
   c.ClearProps();  
 }
 
 template <typename C>
 bool depr_has_prop(C& c, const String& k)
 {
-  LOGN_MESSAGE("HasGenericProperty is deprecated. Use HasProp");
+  WARN_DEPRECATED("HasGenericProperty is deprecated. Use HasProp");
   return c.HasProp(k);  
 }
 
 template <typename C>
 String depr_prop_as_string(C& c, const String& k)
 {
-  LOGN_MESSAGE("GetGenericPropertyStringRepresentation is deprecated. Use GetPropAsString");
+  WARN_DEPRECATED("GetGenericPropertyStringRepresentation is deprecated. Use GetPropAsString");
   return c.GetPropAsString(k);  
 }
 
@@ -185,6 +185,7 @@ void generic_prop_def(O& bp_class)
     .def("SetGenericFloatProperty", &depr_set_float<C>)
     .def("SetGenericBoolProperty", &depr_set_bool<C>)
     .def("SetGenericStringProperty", &depr_set_string<C>)
+    .def("RemoveProp", &C::RemoveProp)
   ;
 }
 
diff --git a/modules/base/src/export_helper/vector.hh b/modules/base/src/export_helper/vector.hh
new file mode 100644
index 0000000000000000000000000000000000000000..0b262bf5561aac5523112c0ad34cd2c4b4e0e776
--- /dev/null
+++ b/modules/base/src/export_helper/vector.hh
@@ -0,0 +1,46 @@
+#ifndef OST_EXPORT_HELPER_VECTOR_HH
+#define OST_EXPORT_HELPER_VECTOR_HH
+
+# include <boost/python/def_visitor.hpp>
+
+/*
+  Author: Marco Biasini
+ */
+
+namespace ost {
+
+
+template <typename Container>
+class VectorAdditions : 
+  public boost::python::def_visitor<VectorAdditions<Container> > {
+public:
+ template <class Class>
+ void visit(Class& cl) const
+ {
+   cl
+     .def("__str__", &to_string)
+   ;
+ }
+private:
+  static std::string to_string(Container& cl)
+  {
+    std::stringstream ss;
+    ss << "[";
+    bool first=true;
+    for (typename Container::const_iterator
+         i=cl.begin(), e=cl.end(); i!=e; ++i) {
+      if (first) {
+        first=false;
+      } else {
+        ss << ", ";
+      }
+      ss << (*i);
+    }
+    ss << "]";
+    return ss.str();
+  }
+};
+
+}
+
+#endif
diff --git a/modules/base/src/generic_property.hh b/modules/base/src/generic_property.hh
index 4ea8d3253cf16236f69e47c84e91d5732f48c987..12e53932e1ad7217bb50d7eefdded0733cc7e5c3 100644
--- a/modules/base/src/generic_property.hh
+++ b/modules/base/src/generic_property.hh
@@ -34,6 +34,7 @@
 #include <boost/variant.hpp>
 
 #include <ost/module_config.hh>
+#include <ost/invalid_handle.hh>
 
 namespace ost {
 
@@ -102,6 +103,12 @@ public:
     }
   }
   
+  void RemoveProp(const String& key)
+  {
+    if (map_) {
+      map_->erase(key);
+    }
+  }
   void Assign(const GenericPropContainerImpl& impl)
   {
     if (impl.map_) {
@@ -159,9 +166,11 @@ protected:
   {
     return static_cast<const H*>(this)->GpImpl();
   }  
+  
 public:
   /// \brief checks existence of property
   bool HasProp(const String& key) const {
+    CheckHandleValidity(*static_cast<const H*>(this));
     return this->GetImpl()->HasProp(key);
   }
     
@@ -174,6 +183,7 @@ public:
   /// a representation suitable for output.
   String GetPropAsString(const String& key) const
   {
+    CheckHandleValidity(*static_cast<const H*>(this));    
     if(!HasProp(key)) return "";
     std::ostringstream rep("");
     rep << this->GetImpl()->GenericProp(key);
@@ -182,6 +192,7 @@ public:
     /// \brief returns String property, raises an exception if it does not exist
     String GetStringProp(const String& key) const
     {
+      CheckHandleValidity(*static_cast<const H*>(this));      
       return this->gp_get<String>(key);
     }
 
@@ -189,6 +200,7 @@ public:
   ///     not exist
   Real GetFloatProp(const String& key) const
   {
+    CheckHandleValidity(*static_cast<const H*>(this));    
     if(HasProp(key)) {
       GenericPropValue value=this->GetImpl()->GenericProp(key);
       if (value.which()==1) {
@@ -210,18 +222,21 @@ public:
   /// \brief returns integer property, raises an exception if it does not exist
   int GetIntProp(const String& key) const
   {
+    CheckHandleValidity(*static_cast<const H*>(this));    
     return this->gp_get<int>(key);
   }
 
   /// \brief returns boolean property, raises an exception if it does not exist
   bool GetBoolProp(const String& key) const
   {
+    CheckHandleValidity(*static_cast<const H*>(this));    
     return this->gp_get<bool>(key);
   }
 
   /// \brief returns String property, or the given default if it does not exist
   String GetStringProp(const String& key, const String& def) const
   {
+    CheckHandleValidity(*static_cast<const H*>(this));    
     return this->gp_get<String>(key,def);
   }
 
@@ -229,6 +244,7 @@ public:
   ///     not exist
   Real GetFloatProp(const String& key, Real def) const
   {
+    CheckHandleValidity(*static_cast<const H*>(this));    
     if(this->HasProp(key)) {
       GenericPropValue value=GetImpl()->GenericProp(key);
       if (value.which()==1) {
@@ -247,17 +263,20 @@ public:
   /// \brief returns integer property, or the given default if it does not exist
   int GetIntProp(const String& key, int def) const
   {
+    CheckHandleValidity(*static_cast<const H*>(this));    
     return this->gp_get<int>(key, def);
   }
 
   /// \brief returns boolean property, or the given default if it does not exist
   bool GetBoolProp(const String& key, bool def) const
   {
+    CheckHandleValidity(*static_cast<const H*>(this));    
     return this->gp_get<bool>(key, def);
   }
 
   std::map<String,GenericPropValue> GetPropMap() const
   {
+    CheckHandleValidity(*static_cast<const H*>(this));    
     return this->GetImpl()->GetPropMap();
   }  
 };
@@ -270,32 +289,43 @@ class  TEMPLATE_EXPORT GenericPropContainer :
 public:
   void ClearProps()
   {
+    CheckHandleValidity(*static_cast<const H*>(this));    
     this->GetImpl()->ClearProps();
   }
   
   /// \brief sets String property
   void SetStringProp(const String& key, const String& value)
   {
+    CheckHandleValidity(*static_cast<const H*>(this));    
     this->GetImpl()->GenericProp(key)=value;
   }
 
   /// \brief sets floating point property
   void SetFloatProp(const String& key, Real value)
   {
+    CheckHandleValidity(*static_cast<const H*>(this));    
     this->GetImpl()->GenericProp(key)=value;
   }
 
   /// \brief sets integer property
   void SetIntProp(const String& key, int value)
   {
+    CheckHandleValidity(*static_cast<const H*>(this));    
     this->GetImpl()->GenericProp(key)=value;
   }
 
   /// \ brief sets boolean property
   void SetBoolProp(const String& key, bool value)
   {
+    CheckHandleValidity(*static_cast<const H*>(this));    
     this->GetImpl()->GenericProp(key)=value;
   }
+  
+  void RemoveProp(const String& key)
+  {
+    CheckHandleValidity(*static_cast<const H*>(this));
+    this->GetImpl()->RemoveProp(key);
+  }
 };
 
 
diff --git a/modules/base/src/log.cc b/modules/base/src/log.cc
index ec77c8525bcdf7d17fa82dd05a8f13acbe722e4c..55d348b75f4f5ade2edd349e3ee780ccffcd7cbc 100644
--- a/modules/base/src/log.cc
+++ b/modules/base/src/log.cc
@@ -16,26 +16,13 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#include <iostream>
-
-
+#include <ost/log_sink.hh>
 #include <ost/log.hh>
 
 namespace ost {
 
 Logger& Log = Logger::Instance();
 
-namespace {
-
-  class DevNull: public std::streambuf {
-  protected:
-    virtual int_type overflow(int_type c) {return c;}
-    virtual std::streamsize xsputn(const char* s, std::streamsize num) {return num;}
-  };
-
-} // anon ns
-
-
 Logger& Logger::Instance()
 {
   static Logger inst;
@@ -45,15 +32,18 @@ Logger& Logger::Instance()
 Logger::Logger():
   level_(0),
   level_stack_(),
-  null_(new DevNull())
+  sink_stack_()
 {
+  sink_stack_.push(LogSinkPtr(new StreamLogSink(std::cerr)));
 }
 
 Logger::Logger(const Logger&):
   level_(0),
   level_stack_(),
-  null_(0)
-{}
+  sink_stack_()
+{
+  sink_stack_.push(LogSinkPtr(new StreamLogSink(std::cerr)));
+}
 
 Logger& Logger::operator=(const Logger&)
 {
@@ -78,15 +68,30 @@ void Logger::PopVerbosityLevel()
   }
 }
 
-std::ostream& Logger::operator()(enum LogLevel l)
+void Logger::PushFile(const String& fn)
 {
-  if(l<=level_) {
-    return std::cout;
-  }
-  return null_;
+  sink_stack_.push(LogSinkPtr(new FileLogSink(fn)));
 }
 
+void Logger::PopFile()
+{
+  WARN_DEPRECATED("Logger::PopFile is deprecated. Use Logger::PopSink instead");
+  this->PopSink();
+}
+
+void Logger::PushSink(LogSinkPtr& sink)
+{
+  sink_stack_.push(sink);
+}
 
+void Logger::PopSink()
+{
+  if(sink_stack_.size()>1) {
+    sink_stack_.pop();
+  } else {
+    LOG_ERROR("Can't pop sink. There is only one sink left on the stack");
+  }
+}
 
 } // ns
 
diff --git a/modules/base/src/log.hh b/modules/base/src/log.hh
index ac86280a2159f650f5c36ab326afa4bbd83cc21d..b535346f3caeae6f56c2809d5453a0ca78ef3ff6 100644
--- a/modules/base/src/log.hh
+++ b/modules/base/src/log.hh
@@ -22,73 +22,76 @@
 #include <ostream>
 #include <stack>
 
+#include <ost/log_sink.hh>
 #include <ost/module_config.hh>
 
 namespace ost {
 
+typedef std::stack<LogSinkPtr> LogSinkStack;
+
   // singleton
 class DLLEXPORT_OST_BASE Logger {
 public:
   enum LogLevel {
-    QUIET=0,
-    NORMAL,
-    VERBOSE,
-    DEBUG,
-    DUMP,
-    TRACE
+    QUIET   =0,
+    WARNING =1,
+    SCRIPT  =2,
+    INFO    =3,
+    VERBOSE =4,
+    DEBUG   =5,
+    TRACE   =6
   };
-  
+
   void PushVerbosityLevel(int level);
   void PopVerbosityLevel();
-
-  std::ostream& operator()(enum LogLevel);
+  void PushSink(LogSinkPtr& sink);
+  void PushFile(const String& filename);
+  //! DEPRECATED use PopSink() instead
+  void PopFile();
+  void PopSink();
 
   static Logger& Instance();
-
+  LogSinkPtr GetCurrentSink() { return sink_stack_.top(); }
   int GetLogLevel() const {return level_;}
   
+  void ResetSinks() {
+    while (sink_stack_.size()>1) {
+      sink_stack_.pop();
+    }
+  }
 protected:
   Logger();
   Logger(const Logger&);
   Logger& operator=(const Logger&);
-
+  
 private:
   int level_;
   std::stack<int> level_stack_;
-  std::ostream null_;
+  LogSinkStack sink_stack_;
 };
 
-#define PUSH_VERBOSITY(n) ::ost::Logger::Instance().PushVerbosityLevel(n)
-#define POP_VERBOSITY(n) ::ost::Logger::Instance().PopVerbosityLevel()
-
-#define LOG_ERROR(m) ::ost::Logger::Instance()(::ost::Logger::QUIET) << m;
-#define LOGN_ERROR(m) ::ost::Logger::Instance()(::ost::Logger::QUIET) << m << std::endl;
 
-#define LOG_MESSAGE(m) if(::ost::Logger::Instance().GetLogLevel()>=::ost::Logger::NORMAL) {(::ost::Logger::Instance()(::ost::Logger::NORMAL)) << m ;}
-#define LOGN_MESSAGE(m) if(::ost::Logger::Instance().GetLogLevel()>=::ost::Logger::NORMAL) {(::ost::Logger::Instance()(::ost::Logger::NORMAL)) << m << std::endl;}
+#define OST_DO_LOGGING_(m, l) if (::ost::Logger::Instance().GetLogLevel()>=l) {\
+    std::stringstream tmp_s__;                                                 \
+    tmp_s__ << m << std::endl;                                                 \
+    ::ost::Logger::Instance().GetCurrentSink()->LogMessage(tmp_s__.str(), l);  \
+  }
 
-#define LOG_VERBOSE(m) if(::ost::Logger::Instance().GetLogLevel()>=::ost::Logger::VERBOSE) {(::ost::Logger::Instance()(::ost::Logger::VERBOSE)) << m ;}
-#define LOGN_VERBOSE(m) if(::ost::Logger::Instance().GetLogLevel()>=::ost::Logger::VERBOSE) {(::ost::Logger::Instance()(::ost::Logger::VERBOSE)) << m << std::endl;}
-
-#define LOG_DEBUG(m) if(::ost::Logger::Instance().GetLogLevel()>=::ost::Logger::DEBUG) {(::ost::Logger::Instance()(::ost::Logger::DEBUG)) << m ;}
-#define LOGN_DEBUG(m) if(::ost::Logger::Instance().GetLogLevel()>=::ost::Logger::DEBUG) {(::ost::Logger::Instance()(::ost::Logger::DEBUG)) << m << std::endl;}
+#define WARN_DEPRECATED(m) OST_DO_LOGGING_(m, ::ost::Logger::WARNING)
+#define PUSH_VERBOSITY(n) ::ost::Logger::Instance().PushVerbosityLevel(n)
+#define POP_VERBOSITY(n) ::ost::Logger::Instance().PopVerbosityLevel()
 
+#define LOG_ERROR(m) OST_DO_LOGGING_(m, ::ost::Logger::QUIET)
+#define LOG_WARNING(m) OST_DO_LOGGING_(m, ::ost::Logger::WARNING)
+#define LOG_SCRIPT(m) OST_DO_LOGGING_(m, ::ost::Logger::SCRIPT)
+#define LOG_INFO(m) OST_DO_LOGGING_(m, ::ost::Logger::INFO)
+#define LOG_VERBOSE(m) OST_DO_LOGGING_(m, ::ost::Logger::VERBOSE)
 #ifdef NDEBUG
-
-#  define LOG_DUMP(m)
-#  define LOGN_DUMP(m)
-
+#  define LOG_DEBUG(m)
 #  define LOG_TRACE(m)
-#  define LOGN_TRACE(m)
-
 #else
-
-#  define LOG_DUMP(m) if(::ost::Logger::Instance().GetLogLevel()>=::ost::Logger::DUMP) {(::ost::Logger::Instance()(::ost::Logger::DUMP)) << m ;}
-#  define LOGN_DUMP(m) if(::ost::Logger::Instance().GetLogLevel()>=::ost::Logger::DUMP) {(::ost::Logger::Instance()(::ost::Logger::DUMP)) << m << std::endl;}
-
-#  define LOG_TRACE(m) if(::ost::Logger::Instance().GetLogLevel()>=::ost::Logger::TRACE) {(::ost::Logger::Instance()(::ost::Logger::TRACE)) << m ;}
-#  define LOGN_TRACE(m) if(::ost::Logger::Instance().GetLogLevel()>=::ost::Logger::TRACE) {(::ost::Logger::Instance()(::ost::Logger::TRACE)) << m << std::endl;}
-
+#  define LOG_DEBUG(m) OST_DO_LOGGING_(m, ::ost::Logger::DEBUG)
+#  define LOG_TRACE(m) OST_DO_LOGGING_(m, ::ost::Logger::TRACE)
 #endif
 
 }
diff --git a/modules/gui/src/plot_viewer/plot_function_info.cc b/modules/base/src/log_sink.cc
similarity index 56%
rename from modules/gui/src/plot_viewer/plot_function_info.cc
rename to modules/base/src/log_sink.cc
index e991e0c9cdedba2a6cbf06474a5ff04c89465d12..9dad7e5e2361ccec498c18a1ba24a7c37703bfc7 100644
--- a/modules/gui/src/plot_viewer/plot_function_info.cc
+++ b/modules/base/src/log_sink.cc
@@ -16,35 +16,37 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-/*
-  Author: Andreas Schenk
-*/
+#include <ost/log.hh>
+#include <ost/log_sink.hh>
+#include <iostream>
+namespace ost {
 
-#include "plot_function_info.hh"
-#include "plot_viewer_panel.hh"
+MultiLogSink::MultiLogSink(){}
 
-namespace ost{namespace gui{
-
-PlotFunctionInfo::PlotFunctionInfo(PlotViewerPanel * viewer):
-  PlotInfoBase(viewer),
-  start(0.0),
-  end(1.0),
-  delta(1.0)
-{
-  name="Function";
-  connect(viewer,SIGNAL(rangeChanged(Real,Real,Real)),this,SLOT(OnRangeChange(Real,Real,Real)));
+bool MultiLogSink::AddSink(LogSinkPtr& sink) {
+  if ((std::find( sinks_.begin(), sinks_.end(), sink))==sinks_.end()) {
+    sinks_.push_back(sink);
+    return true;
+  }
+  return false;
 }
 
-PlotFunctionInfo::~PlotFunctionInfo()
-{
+bool MultiLogSink::RemoveSink(LogSinkPtr& sink){
+  std::vector<LogSinkPtr>::iterator found=std::find(sinks_.begin(), 
+                                                    sinks_.end(), sink);
+  if (found!=sinks_.end() ){
+    sinks_.erase(found);
+    return true;
+  }
+  return false;
 }
 
-void PlotFunctionInfo::OnRangeChange(Real s,Real e,Real d)
-{
-  start=s;
-  end=e;
-  delta=d;
-  emit appearanceChanged();
+void MultiLogSink::LogMessage(const String& message, int severity){
+  for (std::vector<LogSinkPtr>::const_iterator 
+       i=sinks_.begin(), e=sinks_.end(); i!=e; ++i) {
+    (*i)->LogMessage(message, severity);        
+  }
 }
 
-}}//ns
+} // ns
+
diff --git a/modules/base/src/log_sink.hh b/modules/base/src/log_sink.hh
new file mode 100644
index 0000000000000000000000000000000000000000..4878d7f4a4e9e721691f6aa6415defe3374f0955
--- /dev/null
+++ b/modules/base/src/log_sink.hh
@@ -0,0 +1,87 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+//------------------------------------------------------------------------------
+#ifndef OST_LOG_SINK_HH
+#define OST_LOG_SINK_HH
+
+#include <ostream>
+#include <iostream>
+#include <fstream>
+#include <stack>
+#include <vector>
+
+#include <boost/shared_ptr.hpp>
+
+#include <ost/module_config.hh>
+
+namespace ost {
+
+class DLLEXPORT LogSink {
+public:
+  LogSink(){};
+  virtual ~LogSink() { }
+  virtual void LogMessage(const String& message, int severity=0)=0;
+};
+
+typedef boost::shared_ptr<LogSink> LogSinkPtr;
+
+class DLLEXPORT StreamLogSink : public LogSink {
+public:
+  StreamLogSink(std::ostream& stream):stream_(stream){}
+  virtual void LogMessage(const String& message, int severity){
+    stream_ << message;
+  }
+
+private:
+  std::ostream& stream_;
+};
+
+class DLLEXPORT FileLogSink : public LogSink {
+public:
+  FileLogSink(const String& file_name):stream_(file_name.c_str(), std::ios::out){}
+  virtual void LogMessage(const String& message, int severity){
+    if (stream_.is_open()){
+      stream_ << message;
+      stream_.flush();
+    }
+  }
+
+  ~FileLogSink(){
+    stream_.flush();
+  }
+private:
+  std::ofstream stream_;
+};
+
+typedef boost::shared_ptr<FileLogSink> FileLogSinkPtr;
+
+
+class DLLEXPORT_OST_BASE MultiLogSink : public LogSink {
+public:
+  MultiLogSink();
+  bool AddSink(LogSinkPtr& observer);
+  bool RemoveSink(LogSinkPtr& observer);
+  void LogMessage(const String& message, int severity);
+private:
+  std::vector<LogSinkPtr> sinks_;
+};
+
+typedef boost::shared_ptr<MultiLogSink> MultiLogSinkPtr;
+
+}
+#endif
diff --git a/modules/base/src/message.cc b/modules/base/src/message.cc
index 7a53deb15384cf3648bf203a7815076d01d485ce..401ff1fb8755fb39fa322bf503e2c4f69677c733 100644
--- a/modules/base/src/message.cc
+++ b/modules/base/src/message.cc
@@ -1,17 +1,43 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 by the OpenStructure authors
+// Copyright (C) 2003-2010 by the IPLT authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+//------------------------------------------------------------------------------
+/*
+  messages and logs
+
+  Authors: Ansgar Philippsen, Andteas Schenk
+*/
+
 #include "message.hh"
 
 namespace ost {
- 
-Message::Message(const String& mesg,const String& prefix):
-  _prefix(prefix), _mesg(mesg) {}
 
-Message::~Message() throw() {}
+Error::Error(const String& m):
+  mesg_(m)
+{}
 
-const char* Message::what() const throw() {
-  String msg = _prefix + ": " +_mesg;
-  return msg.c_str();
+Error::~Error() throw()
+{
 }
 
-Error::Error(const String& m): Message(m,"Error") {}
+const char* Error::what() const throw()
+{
+  return mesg_.c_str();
+}
 
 }
\ No newline at end of file
diff --git a/modules/base/src/message.hh b/modules/base/src/message.hh
index 6b51a9891709800d0ff749ada92239e5c4d2a46b..aca6387f6be79fbc618acdf2454eb5468584d5c0 100644
--- a/modules/base/src/message.hh
+++ b/modules/base/src/message.hh
@@ -20,7 +20,7 @@
 /*
   messages and logs
 
-  Author: Ansgar Philippsen
+  Authors: Ansgar Philippsen, Andteas Schenk
 */
 
 #ifndef OST_MESSAGE_HH
@@ -31,18 +31,14 @@
 
 namespace ost {
 
-struct DLLEXPORT Message: public std::exception {
-  Message(const String& mesg,const String& prefix="");
-  virtual ~Message() throw();
-  // exception interface
-  virtual const char* what() const throw();
-
-  String _prefix;
-  String _mesg;
-};
 
-struct DLLEXPORT Error: public Message {
+class DLLEXPORT Error: virtual public std::exception {
+public:
   Error(const String& m);
+  ~Error() throw();
+  virtual const char* what() const throw();
+protected:
+  String mesg_;
 };
 
 } // namespace
diff --git a/modules/base/src/pod_vector.hh b/modules/base/src/pod_vector.hh
index a4da274b7f3d77da393fd803e74242a5986146e5..46b05bef7a01bd9343aed777fe91b8442b606f26 100644
--- a/modules/base/src/pod_vector.hh
+++ b/modules/base/src/pod_vector.hh
@@ -25,10 +25,11 @@
 
 #include <ost/module_config.hh>
 
+#include <cassert>
 #include <memory>
 #include <iterator>
 #include <string>
-
+#include <iostream>
 namespace ost {
 
 /// \brief vector container that treats its data as POD - even if it isn't in 
@@ -37,6 +38,17 @@ template <typename T>
 class TEMPLATE_DEF_EXPORT PodVector {
 public:
   PodVector(): begin_(NULL), end_(NULL), capacity_(NULL) {}
+  PodVector(const PodVector<T>& rhs)
+  {
+    this->do_reserve(rhs.capacity());
+    this->raw_set(rhs.data(), rhs.size());
+  }
+  ~PodVector()
+  {
+    if (begin_) {
+      free(begin_);
+    }
+  }
   typedef T value_type;
   typedef T& reference;
   typedef const T& const_reference;
@@ -75,7 +87,7 @@ public:
   
   void push_back(const_reference val)
   {
-    if (end_<=capacity_) {
+    if (end_>=capacity_) {
       this->do_reserve(this->capacity()*2);
     }
     memcpy(end_, &val, sizeof(value_type));
@@ -87,7 +99,11 @@ public:
     --end_;
   }
   
-  void clear() { return this->do_reserve(0); }
+  void clear()
+  {
+    this->do_reserve(0);
+    end_=begin_;
+  }
   
   void reserve(size_t n)
   {
@@ -102,6 +118,16 @@ public:
   {
     return begin_[index];
   }
+  T* data() { return begin_; }
+
+  const T* data() const { return begin_; }
+
+  void raw_set(T* data, size_t n)
+  {
+    this->do_reserve(n);
+    memcpy(begin_, data, sizeof(T)*n);
+    end_=begin_+n;
+  }
 private:
   void do_reserve(size_t n);
   value_type*    begin_;
diff --git a/modules/base/src/string_ref.cc b/modules/base/src/string_ref.cc
index 547c38deefdfed9219c359e0a7544742bd8e9c04..af19d7b8fafe5e2e632f955cc3a46b9625d34703 100644
--- a/modules/base/src/string_ref.cc
+++ b/modules/base/src/string_ref.cc
@@ -93,4 +93,24 @@ std::ostream& operator<<(std::ostream& stream, const StringRef& strref)
   return stream;
 }
 
+std::vector<StringRef> StringRef::split(char p) const
+{
+  std::vector<StringRef> result;
+  const char* s=begin_;
+  const char* l=begin_;
+  while (s!=end_) {
+    if (*s==p) {
+      if (l!=s) {
+        result.push_back(StringRef(l, s-l));
+      }
+      l=s+1;
+    }
+    ++s;
+  }
+  if (l!=s) {
+    result.push_back(StringRef(l, s-l));
+  }
+  return result;
+}
+
 }
diff --git a/modules/base/src/string_ref.hh b/modules/base/src/string_ref.hh
index b1a38dcf0dba2767454084e83c8c03e405ed3486..c6150b9224d65f606c344e50ea1c19be16aa6012 100644
--- a/modules/base/src/string_ref.hh
+++ b/modules/base/src/string_ref.hh
@@ -27,6 +27,7 @@
 #include <iostream>
 #include <ost/base.hh>
 #include <string.h>
+#include <vector>
 #include <ost/module_config.hh>
 
 
@@ -133,6 +134,8 @@ public:
   
   bool empty() const { return begin_==end_; }
 
+  /// \brief split string into chunks delimited by \p p
+  std::vector<StringRef> split(char p) const;
 private:
   const char* begin_;
   const char* end_;  
diff --git a/modules/bindings/pymod/clustalw.py b/modules/bindings/pymod/clustalw.py
index fdf024ebc0c2acaeb7825371e53af56ff65ecf74..a1327ee7e3d8611dd86a0adea70026502201dca2 100644
--- a/modules/bindings/pymod/clustalw.py
+++ b/modules/bindings/pymod/clustalw.py
@@ -1,14 +1,32 @@
 from ost.bindings import utils
-from ost import settings, io, seq
+from ost import settings, io, seq, LogError
 import os
 import subprocess
 
-def ClustalW(seq1, seq2, clustalw=None):
+def ClustalW(seq1, seq2=None, clustalw=None, keep_files=False):
   clustalw_path=settings.Locate(('clustalw', 'clustalw2'), 
                                 explicit_file_name=clustalw)
-  seq_list=seq.CreateSequenceList()
-  seq_list.AddSequence(seq1)
-  seq_list.AddSequence(seq2)  
+  
+  if seq2!=None:
+    if isinstance(seq1, seq.SequenceHandle) and isinstance(seq2, seq.SequenceHandle):
+      seq_list=seq.CreateSequenceList()
+      seq_list.AddSequence(seq1)
+      seq_list.AddSequence(seq2)
+    elif isinstance(seq1, str) and isinstance(seq2, str):
+      seqh1=CreateSequence("seq1", seq1)
+      seqh2=CreateSequence("seq2", seq2)
+      seq_list=seq.CreateSequenceList()
+      seq_list.AddSequence(seqh1)
+      seq_list.AddSequence(seqh2)
+    else:
+      LogError("WARNING: Specify at least two Sequences")
+      return
+  elif isinstance(seq1, seq.SequenceList):
+    seq_list=seq1
+  else:
+    LogError("WARNING: Specify either two SequenceHandles or one SequenceList")
+    return
+  
   temp_dir=utils.TempDirWithFiles((seq_list,))
   out=os.path.join(temp_dir.dirname, 'out.fasta')
   command='%s -infile="%s" -output=fasta -outfile="%s"' % (clustalw_path,
@@ -17,15 +35,17 @@ def ClustalW(seq1, seq2, clustalw=None):
   ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
   ps.stdout.readlines()
   aln=io.LoadAlignment(out)
-  aln.SetSequenceOffset(0,seq1.GetSequenceOffset())
-  aln.SetSequenceOffset(1,seq2.GetSequenceOffset())
-  if seq1.HasAttachedView():
-    aln.AttachView(0,seq1.GetAttachedView().Copy())
-  if seq2.HasAttachedView():
-    aln.AttachView(1,seq2.GetAttachedView().Copy())
+  
 
+  for sequence in seq_list:
+    for seq_num,aln_seq in enumerate(aln.sequences):
+      if aln_seq.GetName()==sequence.GetName():
+        break
+    aln.SetSequenceOffset(seq_num,sequence.GetSequenceOffset())
+    if sequence.HasAttachedView():
+      aln.AttachView(seq_num,sequence.GetAttachedView().Copy())
 
-  #~ temp_dir.Cleanup()
+  if not keep_files:
+    temp_dir.Cleanup()
   
   return aln
-  
diff --git a/modules/bindings/pymod/msms.py b/modules/bindings/pymod/msms.py
index a7a3dd13eb2be594c69f0fb368c941ce403dfd7a..dc3b8590626aad471534d47ce660220d616800d9 100644
--- a/modules/bindings/pymod/msms.py
+++ b/modules/bindings/pymod/msms.py
@@ -24,6 +24,20 @@ from ost import mol
 from ost import settings
 from ost import geom
 
+
+
+## \brief custom exception that substitutes CalledProcessError
+#
+# Python 2.4 does not include the CalledProcessError exception.
+# This one substitutes it 
+class MsmsProcessError(Exception):
+  def __init__(self, returncode,command):
+    self.returncode = returncode
+    self.command = command
+  def __str__(self):
+    return repr(self.returncode)
+
+
 ## \brief Method to check if MSMS executable is present
 #
 # \param msms_exe Explicit path to msms executable
@@ -106,7 +120,7 @@ def _RunMSMS(command):
   #check for successful completion of msms
   if proc.returncode!=0:
     print "WARNING: msms error\n", stdout_value
-    raise subprocess.CalledProcessError(proc.returncode, command)
+    raise subprocess.MsmsProcessError(proc.returncode, command)
 
   return stdout_value
   
@@ -134,7 +148,8 @@ def _RunMSMS(command):
 # \param attach_esa    Attaches per atom SESA to specified FloatProp at atom level
 # \return              Touplet of lists for (SES, SAS)
 def CalculateSurfaceArea(entity, density=1.0, radius=1.5,  all_surf=False,
-                         no_hydrogens=False, selection="",
+                         no_hydrogens=False, no_hetatoms=False, no_waters=False,
+                         selection='',
                          msms_exe=None, msms_env=None, keep_files=False, 
                          attach_asa=None, attach_esa=None):
   import re 
@@ -144,7 +159,19 @@ def CalculateSurfaceArea(entity, density=1.0, radius=1.5,  all_surf=False,
 
   # parse selection
   if no_hydrogens:
-    selection+=" and ele!=H"
+    if selection!='':
+      selection+=" and "
+    selection+="ele!=H"
+  
+  if no_hetatoms:
+    if selection!='':
+      selection+=" and "
+    selection+="ishetatm=False"
+  
+  if no_waters:
+    if selection!='':
+      selection+=" and "
+    selection+="rname!=HOH"
 
   # setup files for msms
   (msms_data_dir, msms_data_file)=_SetupFiles(entity, selection)
@@ -205,8 +232,10 @@ def CalculateSurfaceArea(entity, density=1.0, radius=1.5,  all_surf=False,
 # \param keep_files    Do not delete temporary files
 # \return list of OST SurfaceHandle objects
 def CalculateSurface(entity, density=1.0, radius=1.5, all_surf=False,
-                     no_hydrogens=False, selection="",
+                     no_hydrogens=False, no_hetatoms=False, no_waters=False,
+                     selection='',
                      msms_exe=None, msms_env=None, keep_files=False):
+  
   import os
   import re
 
@@ -215,10 +244,21 @@ def CalculateSurface(entity, density=1.0, radius=1.5, all_surf=False,
 
   # parse selection
   if no_hydrogens:
-    selection+=" and ele!=H"
+    if selection!='':
+      selection+=" and "
+    selection+="ele!=H"
+      
+  if no_hetatoms:
+    if selection!='':
+      selection+=" and "
+    selection+="ishetatm=False"
+      
+  if no_waters:
+    if selection!='':
+      selection+=" and "
+    selection+="rname!=HOH"
 
   # setup files for msms
-  
   (msms_data_dir, msms_data_file)=_SetupFiles(entity, selection)
 
   # set command line
diff --git a/modules/bindings/pymod/naccess.py b/modules/bindings/pymod/naccess.py
new file mode 100644
index 0000000000000000000000000000000000000000..f18d8e9a6029ffd824393e8eb00239a7452d1c6f
--- /dev/null
+++ b/modules/bindings/pymod/naccess.py
@@ -0,0 +1,231 @@
+'''
+Naccess module
+
+Author: Florian Kiefer
+
+This module is for calculating surface areas
+from OpenStructure using the external program naccess
+
+How To Use This Module:
+ 1. Import it (e.g. as "from ost.bindings import naccess")
+ 2. Use it (e.g. as "sasa = naccess.CalculateSurfaceArea(entity)")
+
+Requirement:
+ - naccess installed
+'''
+
+import tempfile
+import subprocess
+import os
+import re
+from ost import io
+from ost import mol
+from ost import settings
+from ost import geom
+
+## \brief Method to check if naccess executable is present
+#
+# \param naccess Explicit path to msms executable
+# \return         Path to the executable
+# \exception      FileNotFound if executable is not found
+def _GetExecutable(naccess_exe):
+  return settings.Locate('naccess', explicit_file_name=naccess_exe)
+
+## \brief Setup files for naccess calculation in temporary directory
+#
+# \param entity      EntityHandle or EntityView to calculate surface
+# \param selection   Calculate surface for subset of entity 
+# \return            array containing temporary directory, input filename for naccess and directory of the input file
+# \exception         RuntimeError if selection is not valid
+def _SetupFiles(entity, selection):
+  # create temporary directory
+  tmp_dir_name=tempfile.mkdtemp()
+
+  # select only heavy atoms if no_hydrogens is true
+  entity_view=entity.Select(selection)
+  if len(entity_view.atoms) > 50000:
+    raise RuntimeError, "Too much atoms for NACCESS (> 50 000)"
+  if not entity_view.IsValid():
+    raise RuntimeError, "Could not create view for selection (%s)"%(selection)
+  
+  # write entity to tmp file
+  tmp_file_name=os.path.join(tmp_dir_name,"entity.pdb")
+  tmp_file_base = os.path.join(tmp_dir_name,"entity")
+  io.SavePDB(entity_view, tmp_file_name)
+  return (tmp_dir_name, tmp_file_name, tmp_file_base)
+
+## \brief Reads Area file (.asa) and attach asa per atom to an entitiy
+#
+# \param entity   EntityHandle or EntityView for attaching sasa on atom level
+# \param file     Filename of area file
+# \param asa_atom Name of the float property for SASA
+ 
+
+def _ParseAsaFile(entity, file, asa_atom):
+  
+  asa_fh = open(file)
+  asa_lines = asa_fh.readlines()
+  asa_fh.close()
+  
+  for l in  asa_lines:
+    if l.startswith("ATOM"):
+      # get res_number, chain_id and atom name
+      atom_name = l[12:16]
+      chain_id = l[21]
+      res_number = l[22:27]
+      asa = l[54:63]
+      atom_name = atom_name.strip()
+      chain_id = chain_id.strip()
+      res_number = res_number.strip()
+      asa = asa.strip()
+      #print "res_number:", res_number
+      m=re.match(r'(?P<num>-?\d+)(?P<ins>\w)?', res_number)
+      di = m.groupdict()
+      
+      if di["ins"] == None:
+        resNum = mol.ResNum(int(di["num"]))
+      else:
+        resNum = mol.ResNum(int(di["num"]), di["ins"])
+      #print res_number, resNum.num, resNum.ins
+      a = entity.FindAtom(chain_id, resNum, atom_name)
+      a.SetFloatProp(asa_atom, float(asa))
+      
+## \brief Reads Area file (.rsa) and attach asa (absolute + relative) per residue to an entitiy
+#
+# \param entity   EntityHandle or EntityView for attaching sasa on atom level
+# \param file     Filename of .rsa file
+# \param asa_atom Name of the float property for absolute SASA
+# \param asa_atom Name of the float property for relative SASA
+# \exception         RuntimeError if residue names are not the same  
+
+def _ParseRsaFile(enti,file, asa_abs, asa_rel):
+  area_fh = open(file)
+  area_lines = area_fh.readlines()
+  area_fh.close()
+  # shift first line
+  area_lines = area_lines[4:]
+  
+  
+  for l in area_lines:
+    if l.startswith("RES"):
+      p = re.compile(r'\s+')
+      t = p.split(l)
+      #res_name, chain_id , res_number, abs_all, rel_all = t[1:6]
+      res_name = l[3:8]
+      res_name = res_name.strip()
+      chain_id = l[8:9]
+      res_number = l[9:14]
+      res_number= res_number.strip()
+      #print l[15:30]
+      abs_all, rel_all =l[15:28].strip().split()
+      m=re.match(r'(?P<num>-?\d+)(?P<ins>\w)?', res_number)
+      di = m.groupdict()
+      if di["ins"] == None:
+        resNum = mol.ResNum(int(di["num"]))
+      else:
+        resNum = mol.ResNum(int(di["num"]), di["ins"])
+      
+      res = enti.handle.FindResidue(chain_id, resNum)
+      #res = entity.FindResidue(chain_id, mol.ResNum(int(res_number)))
+      #print res_name, chain_id, res_number
+      if res_name == res.name:
+        res.SetFloatProp(asa_rel, float(rel_all) )
+        res.SetFloatProp(asa_abs, float(abs_all) )
+      else:
+        raise RuntimeError, "Residue Names are not the same for ResNumb: %s (%s vs %s)" % (res_number, res.name, res_name)
+      
+## \brief Method which recursively deletes a directory
+#
+# \warning This method removes also non-empty directories without asking, so
+#          be careful!
+def __CleanupFiles(dir_name):
+  import shutil
+  shutil.rmtree(dir_name)
+
+## \brief Method to run the MSMS surface calculation
+#
+# This method starts the external MSMS executable and returns the stdout of MSMS
+#
+# \param command          Command to execute
+# \return                 stdout of MSMS
+# \exception              CalledProcessError for non-zero return value
+def _RunNACCESS(command, temp_dir):
+  proc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, cwd = temp_dir)
+  stdout_value, stderr_value = proc.communicate()
+
+  #check for successful completion of msms
+  if proc.returncode!=0:
+    print "WARNING: naccess error\n", stdout_value
+    raise subprocess.CalledProcessError(proc.returncode, command)
+
+  return stdout_value
+  
+
+## \brief Calculates analytical the solvent accessible surface
+#  area by using the external naccess program
+#
+# This method calculates the molecular surface areas by invoking the external
+# program naccess. First, it is checked if the naccess executable is present, then, 
+# the necessary files are prepared in a temporary directory and naccess is
+# executed. The last step is to remove the temporary directory.
+# 
+#
+# \param entity             OST entity to calculate surface
+# \param radius             Surface probe radius
+# \param include_hydrogens  Calculate surface including hydrogens
+# \param include_hetatm     Calculate surface including hetatms
+# \param include_water      Calculate surface including water
+# \param selection          Calculate surface for subset of entity
+# \param naccess  _exe      msms executable (full path to executable)
+# \param keep_files         Do not delete temporary files
+# \param asa_abs            Attaches per residue absolute SASA to specified FloatProp on residue level
+# \param asa_rel            Attaches per residue relative SASA to specified FloatProp on residue level
+# \param asa_atom           Attaches per atom SASA to specified FloatProp at atom level
+# \return                   absolute SASA calculated using asa_atom 
+def CalculateSurfaceArea(entity,  radius=1.4,  
+                         include_hydrogens=False, include_hetatm = False, 
+                         include_water = False, selection="",
+                         naccess_exe=None, keep_files=False , asa_abs= "asaAbs", asa_rel="asaRel", asa_atom="asaAtom"):
+  import re 
+  
+  # check if msms executable is specified
+  naccess_executable=_GetExecutable(naccess_exe)
+  # parse selection
+  
+  # setup files for msms
+  (naccess_data_dir, naccess_data_file,naccess_data_base )=_SetupFiles(entity, selection)
+
+  # set command line
+  command="%s %s -p %f " % \
+          (naccess_executable, naccess_data_file, radius)
+  if include_hydrogens:
+    command = "%s -w" % command
+  if include_water:
+    command = "%s -y" % command
+  if include_hetatm:
+    command = "%s -h" % command
+  #print command
+  stdout_value=_RunNACCESS(command, naccess_data_dir)
+  
+  new_asa= os.path.join(naccess_data_dir, "%s.asa" % naccess_data_base) 
+  _ParseAsaFile(entity, new_asa, asa_atom)
+    
+  new_rsa = os.path.join(naccess_data_dir, "%s.rsa" % naccess_data_base) 
+  _ParseRsaFile(entity, new_rsa, asa_abs, asa_rel)
+  
+  # Calculate Asa for all atoms:
+  sasa = 0.0 
+  for a in entity.atoms:
+    sasa += a.GetFloatProp(asa_atom, 0.0)
+    
+  
+  # first read in result_file
+  
+  # parse MSMS output
+  
+  # clean up
+  if not keep_files:
+    __CleanupFiles(naccess_data_dir)
+
+  return sasa
+  
diff --git a/modules/bindings/pymod/tmtools.py b/modules/bindings/pymod/tmtools.py
index b8ab2a26104692ce681fccfb80ddfe30c19fd104..9405a31df86e42656ac449db07679968af097928 100644
--- a/modules/bindings/pymod/tmtools.py
+++ b/modules/bindings/pymod/tmtools.py
@@ -28,8 +28,8 @@ tmalign: Y. Zhang and J. Skolnick, Nucl. Acids Res. 2005 33, 2302-9
 Authors: Pascal Benkert, Marco Biasini
 """
 
-import subprocess, os, tempfile
-from ost import settings, io, geom
+import subprocess, os, tempfile, platform
+from ost import settings, io, geom, seq
 
 def _SetupFiles(models):
   # create temporary directory
@@ -43,11 +43,13 @@ def _CleanupFiles(dir_name):
   shutil.rmtree(dir_name)
 
 class TMAlignResult:
-  def __init__(self, rmsd, tm_score, aligned_length, transform):
+  def __init__(self, rmsd, tm_score, aligned_length, transform, ref_sequence, alignment):
     self.rmsd=rmsd
     self.tm_score=tm_score    
     self.aligned_length=aligned_length
     self.transform=transform
+    self.ref_sequence =ref_sequence
+    self.alignment=alignment
 
 def _ParseTmAlign(lines):
   info_line=lines[11].split(',')
@@ -61,14 +63,24 @@ def _ParseTmAlign(lines):
                 tf2[4], tf3[2], tf3[3], tf3[4])
   tf=geom.Mat4(rot)
   tf.PasteTranslation(geom.Vec3(tf1[1], tf2[1], tf3[1]))
-  return TMAlignResult(rmsd, aln_length, tm_score, tf)
+  seq1 = seq.CreateSequence("1",lines[20].strip())
+  seq2 = seq.CreateSequence("2",lines[22].strip())
+  alignment = seq.CreateAlignment()
+  alignment.AddSequence(seq2)
+  alignment.AddSequence(seq1)
+  return TMAlignResult(rmsd, aln_length, tm_score, tf, seq2, alignment)
 
 def _RunTmAlign(tmalign, tmp_dir):
-  tmalign_path=settings.Locate('tmalign', explicit_file_name=tmalign)
   model1_filename=os.path.join(tmp_dir, 'model01.pdb')
-  model2_filename=os.path.join(tmp_dir, 'model02.pdb')  
-  command="%s '%s' '%s'" %(tmalign_path, model1_filename, model2_filename)
+  model2_filename=os.path.join(tmp_dir, 'model02.pdb')
+  if platform.system() == "Windows":
+    tmalign_path=settings.Locate('tmalign.exe', explicit_file_name=tmalign)
+    command="\"%s\" %s %s" %(os.path.normpath(tmalign_path), model1_filename, model2_filename)
+  else:
+    tmalign_path=settings.Locate('tmalign', explicit_file_name=tmalign)  
+    command="\"%s\" \"%s\" \"%s\"" %(tmalign_path, model1_filename, model2_filename)
   ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
+  ps.wait()
   lines=ps.stdout.readlines()
   if (len(lines))<22:
     raise RuntimeError("tmalign superposition failed")
@@ -104,11 +116,16 @@ def _ParseTmScore(lines):
 
 
 def _RunTmScore(tmscore, tmp_dir):
-  tmscore_path=settings.Locate('tmscore', explicit_file_name=tmscore)
   model1_filename=os.path.join(tmp_dir, 'model01.pdb')
   model2_filename=os.path.join(tmp_dir, 'model02.pdb')  
-  command="%s '%s' '%s'" %(tmscore_path, model1_filename, model2_filename)
+  if platform.system() == "Windows":
+    tmscore_path=settings.Locate('tmscore.exe', explicit_file_name=tmscore)
+    command="\"%s\" %s %s" %(os.path.normpath(tmscore_path), model1_filename, model2_filename)
+  else:
+    tmscore_path=settings.Locate('tmscore', explicit_file_name=tmscore)
+    command="\"%s\" \"%s\" \"%s\"" %(tmscore_path, model1_filename, model2_filename)
   ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
+  ps.wait()
   lines=ps.stdout.readlines()
   if (len(lines))<22:
     raise RuntimeError("tmscore superposition failed")
@@ -131,4 +148,4 @@ def TMScore(model1, model2, tmscore=None):
   result=_RunTmScore(tmscore, tmp_dir_name)
   model1.handle.RequestXCSEditor().ApplyTransform(result.transform)  
   _CleanupFiles(tmp_dir_name)
-  return result
\ No newline at end of file
+  return result
diff --git a/modules/bindings/tests/CMakeLists.txt b/modules/bindings/tests/CMakeLists.txt
index 0c89630581708b409e4ba1d428ef4630554fe001..5a3f44e3d827f7571b5aaed58fde891abc8543bb 100644
--- a/modules/bindings/tests/CMakeLists.txt
+++ b/modules/bindings/tests/CMakeLists.txt
@@ -1,5 +1,6 @@
 set(OST_BINDINGS_UNIT_TESTS
   test_msms.py
+  test_clustalw.py
 )
 
 ost_unittest(bindings "${OST_BINDINGS_UNIT_TESTS}")
diff --git a/modules/bindings/tests/test_clustalw.py b/modules/bindings/tests/test_clustalw.py
new file mode 100644
index 0000000000000000000000000000000000000000..fc93a19b6d4c270d46f1c79a3554077e8295f908
--- /dev/null
+++ b/modules/bindings/tests/test_clustalw.py
@@ -0,0 +1,44 @@
+import unittest
+from ost import *
+from ost import settings
+from ost.bindings import clustalw
+
+class TestClustalWBindings(unittest.TestCase):
+  
+  def setUp(self):
+    self.protein = io.LoadEntity("testfiles/testprotein.pdb").Select("cname=A")
+
+    self.targetseq = io.LoadSequence("testfiles/test.fasta")
+    self.targetseq.AttachView(self.protein)
+    self.templseq = io.LoadSequence("testfiles/similar.fasta")
+    self.multseq = io.LoadSequenceList("testfiles/multiple.fasta")
+    self.pw_alignment = io.LoadAlignment("testfiles/pairwise_aln.fasta")
+    self.mult_alignment = io.LoadAlignment("testfiles/multiple_aln.fasta")
+    
+  def testPairwiseClustalW(self):
+    aln=clustalw.ClustalW(self.targetseq, self.templseq)
+    assert self.pw_alignment.ToString(80) == aln.ToString(80), \
+           "Pairwise alignment differs from precomputed one"
+  
+  def testAttachedViewClustalW(self):
+    aln=clustalw.ClustalW(self.targetseq, self.templseq)
+    assert aln.FindSequence("testseq").HasAttachedView(), \
+           "Aligned sequence doesn't have an attached view"
+    
+  def testMultipleClustalW(self):
+    aln=clustalw.ClustalW(self.multseq)
+    assert self.mult_alignment.ToString(80) == aln.ToString(80), \
+           "Multiple alignment differs from precomputed one"
+
+
+if __name__ == "__main__":
+  # test if clustalw package is available on system, otherwise ignore tests
+  try:
+    clustalw_path=settings.Locate(('clustalw', 'clustalw2'))
+  except(settings.FileNotFound):
+    print "Could not find clustalw executable: ignoring unit tests"
+    exit(0)
+  try:
+    unittest.main()
+  except Exception, e:
+    print e
\ No newline at end of file
diff --git a/modules/bindings/tests/test_msms.py b/modules/bindings/tests/test_msms.py
index 8cd56ee5a5b8577ba2c82a39e408bc01c60a4617..61810be5576058d45cbe6b929052eb9522ca1531 100755
--- a/modules/bindings/tests/test_msms.py
+++ b/modules/bindings/tests/test_msms.py
@@ -16,13 +16,13 @@ class TestMSMSBindings(unittest.TestCase):
     surf=msms.CalculateSurface(self.protein, msms_env='MSMSSERVER')[0]
     assert self.num_vert==len(surf.GetVertexIDList()) \
        and self.num_tri==len(surf.GetTriIDList()), \
-       "Number of surface vertices or triangles do not match precalculated values"
+       "Number of surface vertices (%i) or triangles (%i) do not match precalculated values (%i/%i)"%(len(surf.GetVertexIDList()),len(surf.GetTriIDList()),self.num_vert,self.num_tri)
   
   def testCalculateSurfaceAres(self):
      (msms_ases, msms_asas)=msms.CalculateSurfaceArea(self.protein, \
                                                       msms_env='MSMSSERVER')
      assert self.ases==msms_ases[0] and self.asas==msms_asas[0], \
-     "SASA or SESA do not match precalculated values"
+     "SASA (%f) or SESA (%f) do not match precalculated values (%f/%f)"%(msms_asas[0],msms_ases[0],self.asas,self.ases)
 
 
 if __name__ == "__main__":
diff --git a/modules/bindings/tests/testfiles/multiple.fasta b/modules/bindings/tests/testfiles/multiple.fasta
new file mode 100644
index 0000000000000000000000000000000000000000..56895f50475694418d7f7c4dab0cb5d0a0dc737f
--- /dev/null
+++ b/modules/bindings/tests/testfiles/multiple.fasta
@@ -0,0 +1,58 @@
+>P50198.1
+MANRLAGKVALITGGASGLGAAQAKRFAEEGAKVVIGDLNEEMAKGVVAEIRAAGGDALFIRLDVTDAASWNNAIAAAVDGFGGLTTLSNTAGIIHPGGFEEESIEGWNKMVAVNQTAIFLGIKAAIPELVKSGNGSIINISSLIGMFPTAGNASYCATKAAVRIMSKAAALEFVDRGVRVNTIVPGGMNTPITANVPPDVLKQQTSQIPMGKLGDPIDIANGALFLASDEAKYITGVDLPIDGGWSVGV
+>Q9WYG0.1
+MNFQGKVVLITGAGSGIGKKAAVMFAERGAKVAINDISEEKGKETVELIKSMGGEAAFIFGDVAKDAEQIVKKTVETFGRLDILVNNAGIVPYGNIEETSEEDFDKTMAVNVKGPFLLSKYAVEQMKKQGGGVIVNVSSEAGLIGIPRRCVYSVSKAALLGLTRSLAVDYVDYGIRVNAVCPGTTQSEGLMARVKASPNPEELLKKMTSRIPMKRLGKEEEIAFAILFAACDEAGFMTGSIINIDGGSTAV
+>Q8KWT4.1
+MNLTDKTVLITGGASGIGYAAVQAFLNQQANVVVADIDEAQGEAMIRKENNDRLHFVHTDITDEPACQNAIRSAVDKFGGLDVLINNAGIEIVAPIHEMELSNWNKVLNVNLTGMFLMSKHALKYMLKSGKGNIINTCSVGGVVAWPDIPAYNASKGGVLQLTRSMAVDYAKHNIRVNCVCPGIIDTPLNEKSFLENNEGTLEEIKKEKAKVNPLLRLGKPEEIANVMLFLASDLSSYMTGSAITADGGYTAQ
+>P39640.2
+MNLTDKTVLITGGASGIGYAAVQAFLGQQANVVVADIDEAQGEAMVRKENNDRLHFVQTDITDEAACQHAVESAVHTFGGLDVLINNAGIEIVAPIHEMELSDWNKVLQVNLTGMFLMSKHALKHMLAAGKGNIINTCSVGGLVAWPDIPAYNASKGGVLQLTKSMAVDYAKHQIRVNCVCPGIIDTPLNEKSFLENNEGTLEEIKKEKAKVNPLLRLGKPEEIANVMLFLASDLSSYMTGSAITADGGYTAQ
+>P46331.2
+MGRLENKTAVITGAATGIGQATAEVFANEGARVIIGDINKDQMEETVDAIRKNGGQAESFHLDVSDENSVKAFADQIKDACGTIDILFNNAGVDQEGGKVHEYPVDLFDRIIAVDLRGTFLCSKYLIPLMLENGGSIINTSSMSGRAADLDRSGYNAAKGGITNLTKAMAIDYARNGIRVNSISPGTIETPLIDKLAGTKEQEMGEQFREANKWITPLGRLGQPKEMATVALFLASDDSSYVTGEDITADGGIMAYTWPGKMLIEEKWKEETK
+>P50197.1
+MSDLSGKTIIVTGGGSGIGRATVELLVASGANVPVADINDEAGEAVVATSGGKAAYFRCDIAQEEDVKALVAQTLAAFGGLDGSFNNAAIPQAGLPLAEVSLERFRQSMDINVTGTFLCMKYQILAMIERGTKGSIVNTASAAGVVGVPMHGEYVGAKHAVVGLTRVAAADYGKHGIRVNALVPGAVRTPMLQRAMDNDAGLEPYLNSIHPIGRFSEPHEQAQAAVWLLSDAASFVTGSCLAADGGFTAI
+>P42317.2
+MRKQVALVTGAAGGIGFEIAREFAREGASVIVSDLRPEACEKAASKLAEEGFDAAAIPYDVTKEAQVADTVNVIQKQYGRLDILVNNAGIQHVAPIEEFPTDTFEQLIKVMLTAPFIAMKHVFPIMKKQQFGRIINIASVNGLVGFAGKSAYNSAKHGVIGLTKVGALEGAPHGITVNALCPGYVDTQLVRNQLSDLSKTRNVPYDSVLEQVIFPLVPQKRLLSVKEIADYAVFLASEKAKGVTGQAVVLDGGYTAQ
+>target
+MRLDGKTALITGSARGIGRAFAEAYVREGARVAIADINLEAARATAAEIGPAACAIALDVTDQASIDRCVAELLDRWGSIDILVNNAALFDLAPIVEITRESYDRLFAINVSGTLFMMQAVARAMIAGGRGGKIINMASQAGRRGEALVGVYCATKAAVISLTQSAGLNLIRHGINVNAIAPGVVDGEHWDGVDAKFADYENLPRGEKKRQVGAAVPFGRMGRAEDLTGMAIFLATPEADYIVAQTYNVDGGNWMS
+>Q59787.1
+MRLDGKTALITGSARGIGRAFAEAYVREGARVAIADINLEAARATAAEIGPAACAIALDVTDQASIDRCVAELLDRWGSIDILVNNAALFDLAPIVEITRESYDRLFAINVSGTLFMMQAVARAMIAGGRGGKIINMASQAGRRGEALVGVYCATKAAVISLTQSAGLNLIRHGINVNAIAPGVVDGEHWDGVDAKFADYENLPRGEKKRQVGAAVPFGRMGRAEDLTGMAIFLATPEADYIVAQTYNVDGGNWMS
+>Q48436.2
+MKKVALVTGAGQGIGKAIALRLVKDGFAVAIADYNDATAKAVASEINQAGGRAMAVKVDVSDRDQVFAAVEQARKTLGGFDVIVNNAGVAPSTPIESITPEIVDKVYNINVKGVIWGIQAAVEAFKKEGHGGKIINACSQAGHVGNPELAVYSSSKFAVRGLTQTAARDLAPLGITVNGYCPGIVKTPMWAEIDRQVSEAAGKPLGYGTAEFAKRITLGRLSEPEDVAACVSYLASPDSDYMTGQSLLIDGGMVFN
+>Q04520.1
+MQKVALVTGAGQGIGKAIALRLVKDGFAVAIADYNDATATAVAAEINQAGGRAVAIKVDVSRRDQVFAAVEQARKALGGFNVIVNNAGIAPSTPIESITEEIVDRVYNINVKGVIWGMQAAVEAFKKEGHGGKIVNACSQAGHVGNPELAVYSSSKFAVRGLTQTAARDLAPLGITVNGFCPGIVKTPMWAEIDRQCRKRRANRWATARLNLPNASPLAACRSLKTSPPACRSSPARIPTI
+>P66776.1
+MTNNKVALVTGGAQGIGFKIAERLVEDGFKVAVVDFNEEGAKAAALKLSSDGTKAIAIKADVSNRDDVFNAVRQTAAQFGDFHVMVNNAGLGPTTPIDTITEEQFKTVYGVNVAGVLWGIQAAHEQFKKFNHGGKIINATSQAGVEGNPGLSLYCSTKFAVRGLTQVAAQDLASEGITVNAFAPGIVQTPMMESIAVATAEEAGKPEAWGWEQFTSQIALGRVSQPEDVSNVVSFLAGKDSDYITGQTIIVDGGMRFR
+>Q5HKG6.1
+MSKTAIITGSAGGLGKGIAERLANDGFNIVLQDINEALLLETEKEFKEKGYQAVAFKSDVSKKKEQEELVQFAVTEFGQLDVMVNNAGVDAVTPILEIGEEELSKLFNINVFGTLFGIQAAANQFIKQKSKGKIINACSIAGHESYEVLGTYSATKHSVRSFTQTAAKELADKGITVNAYCPGVAKTEMWDRIDEEMVKLDDSLEIGDAFEAFSSEIKLGRYQEPSDVANLVSFLASNDSDYITGQSILTDGGLVYR
+>Q8CQD2.1
+MSKTAIITGAAGGLGKGIAERLANDGFNIVLQDINEALLLETEKEFKEKGYQAVAYKSDVSKKKEQEELVQFAVTEFGQLDVMVNNAGVDAVTPILEIGEEELSKLFNINVFGTLFGIQAAANQFIKQKSKGKIINACSIAGHESYEVLGTYSATKHSVRSFTQTAAKELADKGITVNAYCPGVAKTEMWDRIDEEMVKLDDSLEIGDAFEAFSSEIKLGRYQEPSDVANLVSFLASNDSDYITGQSILTDGGLVYR
+>P50199.1
+MSHPDLFSLSGARALVTGASRGIGLTLAKGLARYGAEVVLNGRNAESLDSAQSGFEAEGLKASTAVFDVTDQDAVIDGVAAIERDMGPIDILINNAGIQRRAPLEEFSRKDWDDLMSTNVNAVFFVGQAVARHMIPRGRGKIVNICSVQSELARPGIAPYTATKGAVKNLTKGMATDWGRHGLQINGLAPGYFATEMTERLVADEEFTDWLCKRTPAGRWGQVEELVGAAVFLSSRASSFVNGQVLMVDGGITVSL
+>P0A9Q0.1
+MNDLFSLAGKNILITGSAQGIGFLLATGLGKYGAQIIINDITAERAELAVEKLHQEGIQAVAAPFNVTHKHEIDAAVEHIEKDIGPIDVLVNNAGIQRRHPFTEFPEQEWNDVIAVNQTAVFLVSQAVTRHMVERKAGKVINICSMQSELGRDTITPYAASKGAVKMLTRGMCVELARHNIQVNGIAPGYFKTEMTKALVEDEAFTAWLCKRTPAARWGDPQELIGAAVFLSSKASDFVNGHLLFVDGGMLVAV
+>Q05528.1
+MILNTFNLQGKVALITGCDTGLGQGMAVGLAEAGCDIVGVNIVEPKETIEKVTAVGRRFLSLTADMSDISGHAALVEKAVAEFGKVDILVNNAGIIRREDAIEFSEKNWDDVMNLNIKSVFFMSQTVARQFIKQGHGGKIINIASMLSFQGGIPVPSYTASKKRVMGITRIVANEWAKHNINVNAIAPGYMATNNTQHVRADQDRSKEILDRIPAGRWGLPQDLQGPAVFLASSASDYVNGYTIAVDGGWLAR
+>P37769.2
+MILSAFSLEGKVAVVTGCDTGLGQGMALGLAQAGCDIVGINIVEPTETIEQVTALGRRFLSLTADLRKIDGIPALLDRAVAEFGHIDILVNNAGLIRREDALEFSEKDWDDVMNLNIKSVFFMSQAAAKHFIAQGNGGKIINIASMLSFQGGIRVPSYTASKSGVMGVTRLMANEWAKHNINVNAIAPGYMATNNTQQLRADEQRSAEILDRIPAGRWGLPSDLMGPIVFLASSASDYVNGYTIAVDGGWLAR
+>P50842.1
+MGYLHDAFSLKGKTALVTGPGTGIGQGIAKALAGAGADIIGTSHTSSLSETQQLVEQEGRIFTSFTLDMSKPEAIKDSAAELFENRQIDILVNNAGIIHREKAEDFPEENWQHVLNVNLNSLFILTQLAGRHMLKRGHGKIINIASLLSFQGGILVPAYTASKHAVAGLTKSFANEWAASGIQVNAIAPGYISTANTKPIRDDEKRNEDILKRIPAGRWGQADDIGGTAVFLASRASDYVNGHILAVDGGWLSR
+>Q1JP75.1
+MDLRLAGRRALVTGAGKGIGRSIVKALHAAGARVVAVSRTQADLDSLVRECPGVETVCVDLADWEATEQALGGVGPVDLLVNNAAVAFLQPFLEVTKEAYDMSFSVNLRAVIQVSQIVARGLIARGAPGVIVNVSSQASQRGLTNHSVYCSTKGALDTLTKVMAVELGPHKIRVNAVNPTVVMTPMGQAAWSDPQKAKAMLDRIPLGRFAEVENVVDTILFLLSDRSSMTTGSTVPVDGGFLAT
+>Q91XV4.1
+MDLGLAGRRALVTGAGKGIGRSTVLALQAAGAHVVAVSRTQADLDSLVSECPGVETVCVDLADWEATEQALSSVGPVDLLVNNAAVALLQPFLEVTKEAFDMSFNVNLRAVIQVSQIVARGMIARGAPGAIVNVSSQASQRALANHSVYCSTKGALDMLTKMMALELGPHKIRVNAVNPTVVMTSMGRTNWSDPHKAKVMLDRIPLGKFAEVENVVDAILFLLSHRSNMTTGSTLPVDGGFLVT
+>Q7Z4W1.2
+MELFLAGRRVLVTGAGKGIGRGTVQALHATGARVVAVSRTQADLDSLVRECPGIEPVCVDLGDWEATERALGSVGPVDLLVNNAAVALLQPFLEVTKEAFDRSFEVNLRAVIQVSQIVARGLIARGVPGAIVNVSSQCSQRAVTNHSVYCSTKGALDMLTKVMALELGPHKIRVNAVNPTVVMTSMGQATWSDPHKAKTMLNRIPLGKFAEVEHVVNAILFLLSDRSGMTTGSTLPVEGGFWAC
+>P40397.2
+MANQKKKTLPPQHQNQQPGFEYLMDPRPVFDKPKKAKKLEGKTAIITGGDSGIGRAVSVLFAKEGANVVIVYLNEHQDAEETKQYVEKEGVKCLLIAGDVGDEAFCNDVVGQASQVFPSIDILVNNAAEQHVQPSIEKITSHQLIRTFQTNIFSMFYLTKAVLPHLKKGSSIINTASITAYKGNKTLIDYSATKGAIVTFTRSLSQSLVQQGIRVNAVAPGPIWTPLIPASFAAKDVEVFGSDVPMERPGQPVEVAPSYLYLASDDSTYVTGQTIHVNGGTIVNG
+>O07575.1
+MNPMDRQTEGQEPQHQDRQPGIESKMNPLPLSEDEDYRGSGKLKGKVAIITGGDSGIGRAAAIAFAKEGADISILYLDEHSDAEETRKRIEKENVRCLLIPGDVGDENHCEQAVQQTVDHFGKLDILVNNAAEQHPQDSILNISTEQLEKTFRTNIFSMFHMTKKALPHLQEGCAIINTTSITAYEGDTALIDYSSTKGAIVSFTRSMAKSLADKGIRVNAVAPGPIWTPLIPATFPEEKVKQHGLDTPMGRPGQPVEHAGAYVLLASDESSYMTGQTIHVNGGRFIST
+>Q5KTS5.1
+MASGGQFPPQKQESQPGKEHLMDPSPQHASPHYKPANKLQGKVALVTGGDSGIGRSVCYHFALEGATVAFTFVKGHEDKDANETLELLRKAKSSDAKDPIAIAADLGFDDNCKKVVDQVVNAFGSIDVLVNNAAEQYKASTVEDIDEERLERVFRTNIFAYFFMARHALKHMREGSTIINTTSINAYKGNAKLLDYTATKGAIVAFTRGLSLQLISKGIRVNGVAPGPVWTPLIPSSFDEEEVKQFGSEVPMKRAGQPYEIATAYVFLASCDSSYYSGQVLHPNGGAIVNG
+>Q49117.2
+MSKLEGKVAVVTGASKGIGAAIAKALAKDGAAVVVNYASSKAGADAVVEAITAAGGKAIAVQADVSQAVQARGLVEAAVQQFGRLDVLVNNSGVYEFAAIEEVTEEHYRRIFDVNVLGVLLATQAASKHLGEGGSIINISSVVTDVLMPTSAVYSGTKGALNAISGVLANELAPRKIRVNVVSPGYVVTEGTHTAGIAGSEMEAGLVAQTPLGRSGQPDDIAGVVAFLASDDARWVTGEVINASGGVR
+>Q9KQH7.2
+MNLEGKVALVTGASRGIGKAIAELLAERGAKVIGTATSESGAQAISDYLGDNGKGMALNVTNPESIEAVLKAITDEFGGVDILVNNAGITRDNLLMRMKEEEWSDIMETNLTSIFRLSKAVLRGMMKKRQGRIINVGSVVGTMGNAGQANYAAAKAGVIGFTKSMAREVASRGVTVNTVAPGFIETDMTKALNDEQRTATLAQVPAGRLGDPREIASAVAFLASPEAAYITGETLHVNGGMYMI
+>P55336.1
+MNLEGKIALVTGASRGIGRAIAELLVERGATVIGTATSEGGAAAISEYLGENGKGLALNVTDVESIEATLKTINDECGAIDILVNNAGITRDNLLMRMKDDEWNDIINTNLTPIYRMSKAVLRGMMKKRAGRIINVGSVVGTMGNAGQTNYAAAKAGVIGFTKSMAREVASRGVTVNTVAPGFIETDMTKALNDDQRAATLSNVPAGRLGDPREIASAVVFLASPEAAYITGETLHVNGGMYMV
+>P0A2C9.1
+MSFEGKIALVTGASRGIGRAIAETLVARGAKVIGTATSENGAKNISDYLGANGKGLMLNVTDPASIESVLENIRAEFGEVDILVNNAGITRDNLLMRMKDDEWNDIIETNLSSVFRLSKAVMRAMMKKRCGRIITIGSVVGTMGNAGQANYAAAKAGLIGFSKSLAREVASRGITVNVVAPGFIETDMTRALSDDQRAGILAQVPAGRLGGAQEIASAVAFLASDEASYITGETLHVNGGMYMV
diff --git a/modules/bindings/tests/testfiles/multiple_aln.fasta b/modules/bindings/tests/testfiles/multiple_aln.fasta
new file mode 100644
index 0000000000000000000000000000000000000000..45aff7ddb88fb44399b02de678e51844b550c6a4
--- /dev/null
+++ b/modules/bindings/tests/testfiles/multiple_aln.fasta
@@ -0,0 +1,58 @@
+>P50198.1
+--------------------------------------MANRLAGKVALITGGASGLGAAQAKRFAEEGAKVVIGDLNEEMAKGVVAEIRAAGGD-------ALFIRLDVTDAASWNNAIAAAVDGFG--GLTTLSNTAGIIHPGG-FEEESIEGWNKMVAVNQTAIFLGIKAAIPELVKSGN-GSIINISSLIGMFPTAGNASYCATKAAVRIMSKAAALEFVDRGVRVNTIVPG-----GMNTP--ITAN-----VPPDVLKQQTSQIPMGKLGDPIDIANGALFLASDEAKYITGVDLPIDGGWSVGV----------------
+>Q9WYG0.1
+--------------------------------------MN--FQGKVVLITGAGSGIGKKAAVMFAERGAKVAINDISEEKGKETVELIKSMGGE-------AAFIFGDVAKDA--EQIVKKTVETFG--RLDILVNNAGIVPYGN-IEETSEEDFDKTMAVNVKGPFLLSKYAVEQMKKQGG-GVIVNVSSEAGLIGIPRRCVYSVSKAALLGLTRSLAVDYVDYGIRVNAVCPGTTQSEGLMAR--VKASP----NPEELLKKMTSRIPMKRLGKEEEIAFAILFAACDEAGFMTGSIINIDGG-STAV----------------
+>Q8KWT4.1
+--------------------------------------MN--LTDKTVLITGGASGIGYAAVQAFLNQQANVVVADIDEAQGEAMIR--KENNDR-------LHFVHTDITDEPACQNAIRSAVDKFG--GLDVLINNAGIEIVAP-IHEMELSNWNKVLNVNLTGMFLMSKHALKYMLKSGK-GNIINTCSVGGVVAWPDIPAYNASKGGVLQLTRSMAVDYAKHNIRVNCVCPGIIDTPLNEKSFLENNEG----TLEEIKKEKAKVNPLLRLGKPEEIANVMLFLASDLSSYMTGSAITADGGYTAQ-----------------
+>P39640.2
+--------------------------------------MN--LTDKTVLITGGASGIGYAAVQAFLGQQANVVVADIDEAQGEAMVR--KENNDR-------LHFVQTDITDEAACQHAVESAVHTFG--GLDVLINNAGIEIVAP-IHEMELSDWNKVLQVNLTGMFLMSKHALKHMLAAGK-GNIINTCSVGGLVAWPDIPAYNASKGGVLQLTKSMAVDYAKHQIRVNCVCPGIIDTPLNEKSFLENNEG----TLEEIKKEKAKVNPLLRLGKPEEIANVMLFLASDLSSYMTGSAITADGGYTAQ-----------------
+>P46331.2
+--------------------------------------MGR-LENKTAVITGAATGIGQATAEVFANEGARVIIGDINKDQMEETVDAIRKNGGQ-------AESFHLDVSDENSVKAFADQIKDACG--TIDILFNNAGVDQEGGKVHEYPVDLFDRIIAVDLRGTFLCSKYLIPLMLENG--GSIINTSSMSGRAADLDRSGYNAAKGGITNLTKAMAIDYARNGIRVNSISPGTIETPLIDKLAGTKEQE----MGEQFREANKWITPLGRLGQPKEMATVALFLASDDSSYVTGEDITADGGIMAYTWPGKMLIEEKWKEETK
+>P50197.1
+--------------------------------------MSD-LSGKTIIVTGGGSGIGRATVELLVASGANVPVADINDEAGEAVVA---TSGGK-------AAYFRCDIAQEEDVKALVAQTLAAFG--GLDGSFNNAAIPQAGLPLAEVSLERFRQSMDINVTGTFLCMKYQILAMIERGTKGSIVNTASAAGVVGVPMHGEYVGAKHAVVGLTRVAAADYGKHGIRVNALVPGAVRTPMLQR--AMDNDA----GLEPYLNS---IHPIGRFSEPHEQAQAAVWLLSDAASFVTGSCLAADGGFTAI-----------------
+>P50199.1
+----------------------------------MSHPDLFSLSGARALVTGASRGIGLTLAKGLARYGAEVVLNGRNAESLDSAQSGFEAEGLK-------ASTAVFDVTDQDAVIDGVAAIERDMG--PIDILINNAGIQRRAP-LEEFSRKDWDDLMSTNVNAVFFVGQAVARHMIPRGRG-KIVNICSVQSELARPGIAPYTATKGAVKNLTKGMATDWGRHGLQINGLAPGYFATEMTERLVADEEFT----------DWLCKRTPAGRWGQVEELVGAAVFLSSRASSFVNGQVLMVDGGITVSL----------------
+>P0A9Q0.1
+----------------------------------MN--DLFSLAGKNILITGSAQGIGFLLATGLGKYGAQIIINDITAERAELAVEKLHQEGIQ-------AVAAPFNVTHKHEIDAAVEHIEKDIG--PIDVLVNNAGIQRRHP-FTEFPEQEWNDVIAVNQTAVFLVSQAVTRHMVERKAG-KVINICSMQSELGRDTITPYAASKGAVKMLTRGMCVELARHNIQVNGIAPGYFKTEMTKALVEDEAFT----------AWLCKRTPAARWGDPQELIGAAVFLSSKASDFVNGHLLFVDGGMLVAV----------------
+>Q05528.1
+-----------------------------------MILNTFNLQGKVALITGCDTGLGQGMAVGLAEAGCDIVGVN-IVE-PKETIEKVTAVGRR-------FLSLTADMSDISGHAALVEKAVAEFG--KVDILVNNAGIIRRED-AIEFSEKNWDDVMNLNIKSVFFMSQTVARQFIKQGHGGKIINIASMLSFQGGIPVPSYTASKKRVMGITRIVANEWAKHNINVNAIAPGYMATNNTQHVRADQDRS----------KEILDRIPAGRWGLPQDLQGPAVFLASSASDYVNGYTIAVDGGWLAR-----------------
+>P37769.2
+-----------------------------------MILSAFSLEGKVAVVTGCDTGLGQGMALGLAQAGCDIVGIN-IVE-PTETIEQVTALGRR-------FLSLTADLRKIDGIPALLDRAVAEFG--HIDILVNNAGLIRRED-ALEFSEKDWDDVMNLNIKSVFFMSQAAAKHFIAQGNGGKIINIASMLSFQGGIRVPSYTASKSGVMGVTRLMANEWAKHNINVNAIAPGYMATNNTQQLRADEQRS----------AEILDRIPAGRWGLPSDLMGPIVFLASSASDYVNGYTIAVDGGWLAR-----------------
+>P50842.1
+---------------------------------MGYLHDAFSLKGKTALVTGPGTGIGQGIAKALAGAGADIIGTS-HTSSLSETQQLVEQEGRI-------FTSFTLDMSKPE---AIKDSAAELFENRQIDILVNNAGIIHREK-AEDFPEENWQHVLNVNLNSLFILTQLAGRHMLKRGHG-KIINIASLLSFQGGILVPAYTASKHAVAGLTKSFANEWAASGIQVNAIAPGYISTANTKPIRDDEKRN----------EDILKRIPAGRWGQADDIGGTAVFLASRASDYVNGHILAVDGGWLSR-----------------
+>Q9KQH7.2
+----------------------------------------MNLEGKVALVTGASRGIGKAIAELLAERGAKVIGTATSESGAQAISDYLGDNG----------KGMALNVTNPESIEAVLKAITDEFG--GVDILVNNAGITRDNL-LMRMKEEEWSDIMETNLTSIFRLSKAVLRGMMKKRQG-RIINVGSVVGTMGNAGQANYAAAKAGVIGFTKSMAREVASRGVTVNTVAPGFIETDMTKALNDEQR------------TATLAQVPAGRLGDPREIASAVAFLASPEAAYITGETLHVNGGMYMI-----------------
+>P55336.1
+----------------------------------------MNLEGKIALVTGASRGIGRAIAELLVERGATVIGTATSEGGAAAISEYLGENG----------KGLALNVTDVESIEATLKTINDECG--AIDILVNNAGITRDNL-LMRMKDDEWNDIINTNLTPIYRMSKAVLRGMMKKRAG-RIINVGSVVGTMGNAGQTNYAAAKAGVIGFTKSMAREVASRGVTVNTVAPGFIETDMTKALNDDQR------------AATLSNVPAGRLGDPREIASAVVFLASPEAAYITGETLHVNGGMYMV-----------------
+>P0A2C9.1
+----------------------------------------MSFEGKIALVTGASRGIGRAIAETLVARGAKVIGTATSENGAKNISDYLGANG----------KGLMLNVTDPASIESVLENIRAEFG--EVDILVNNAGITRDNL-LMRMKDDEWNDIIETNLSSVFRLSKAVMRAMMKKRCG-RIITIGSVVGTMGNAGQANYAAAKAGLIGFSKSLAREVASRGITVNVVAPGFIETDMTRALSDDQR------------AGILAQVPAGRLGGAQEIASAVAFLASDEASYITGETLHVNGGMYMV-----------------
+>P42317.2
+------------------------------------------MRKQVALVTGAAGGIGFEIAREFAREGASVIVSDLRPEACEKAASKLAEEGFD-------AAAIPYDVTKEAQVADTVNVIQKQYG--RLDILVNNAGIQHVAP-IEEFPTDTFEQLIKVMLTAPFIAMKHVFPIMKKQQFG-RIINIASVNGLVGFAGKSAYNSAKHGVIGLTKVGALEGAPHGITVNALCPGYVDTQLVRNQLSDLSKTRNVPYDSVLEQVIFPLVPQKRLLSVKEIADYAVFLASEKAKGVTGQAVVLDGGYTAQ-----------------
+>P40397.2
+MANQKKKT--LPPQHQNQQPGFEYLMDPRPVFDKP--KKAKKLEGKTAIITGGDSGIGRAVSVLFAKEGANVVIVYLN--EHQDAEETKQYVEKE----GVKCLLIAGDVGDEAFCNDVVGQASQVFP--SIDILVNNAAEQHVQPSIEKITSHQLIRTFQTNIFSMFYLTKAVLPHLKKGSS---IINTASITAYKGNKTLIDYSATKGAIVTFTRSLSQSLVQQGIRVNAVAPGPIWTP--LIPASFAAKD---------VEVFGSDVPMERPGQPVEVAPSYLYLASDDSTYVTGQTIHVNGGTIVNG----------------
+>O07575.1
+MNPMDRQTEGQEPQHQDRQPGIESKMNPLPLSEDEDYRGSGKLKGKVAIITGGDSGIGRAAAIAFAKEGADISILYLD--EHSDAEETRKRIEKE----NVRCLLIPGDVGDENHCEQAVQQTVDHFG--KLDILVNNAAEQHPQDSILNISTEQLEKTFRTNIFSMFHMTKKALPHLQEGCA---IINTTSITAYEGDTALIDYSSTKGAIVSFTRSMAKSLADKGIRVNAVAPGPIWTP--LIPATFPEEK---------VKQHGLDTPMGRPGQPVEHAGAYVLLASDESSYMTGQTIHVNGGRFIST----------------
+>Q5KTS5.1
+MASGGQFP----PQKQESQPGKEHLMDPSPQHASPHYKPANKLQGKVALVTGGDSGIGRSVCYHFALEGATVAFTFVKGHEDKDANETLELLRKAKSSDAKDPIAIAADLGFDDNCKKVVDQVVNAFG--SIDVLVNNAAEQYKASTVEDIDEERLERVFRTNIFAYFFMARHALKHMREGST---IINTTSINAYKGNAKLLDYTATKGAIVAFTRGLSLQLISKGIRVNGVAPGPVWTP--LIPSSFDEEE---------VKQFGSEVPMKRAGQPYEIATAYVFLASCDSSYYSGQVLHPNGGAIVNG----------------
+>Q49117.2
+---------------------------------------MSKLEGKVAVVTGASKGIGAAIAKALAKDGAAVVVNYAS--SKAGADAVVEAITAA----GGKAIAVQADVSQAVQARGLVEAAVQQFG--RLDVLVN-NSGVYEFAAIEEVTEEHYRRIFDVNVLGVLLATQAASKHLGEGGS---IINISSVVTDVLMPTSAVYSGTKGALNAISGVLANELAPRKIRVNVVSPGYVVTEGTHTAGIAGSEM---------EAGLVAQTPLGRSGQPDDIAGVVAFLASDDARWVTGEVINASGGVR-------------------
+>target
+----------------------------------------MRLDGKTALITGSARGIGRAFAEAYVREGARVAIADINLEAARATAAEI---GP-------AACAIALDVTDQASIDRCVAELLDRWG--SIDILVNNAALFDLAP-IVEITRESYDRLFAINVSGTLFMMQAVARAMIAGGRGGKIINMASQAGRRGEALVGVYCATKAAVISLTQSAGLNLIRHGINVNAIAPGVVDGEHWDGVDAKFAD-YENLPRGEKKRQVGAAVPFGRMGRAEDLTGMAIFLATPEADYIVAQTYNVDGGNWMS-----------------
+>Q59787.1
+----------------------------------------MRLDGKTALITGSARGIGRAFAEAYVREGARVAIADINLEAARATAAEI---GP-------AACAIALDVTDQASIDRCVAELLDRWG--SIDILVNNAALFDLAP-IVEITRESYDRLFAINVSGTLFMMQAVARAMIAGGRGGKIINMASQAGRRGEALVGVYCATKAAVISLTQSAGLNLIRHGINVNAIAPGVVDGEHWDGVDAKFAD-YENLPRGEKKRQVGAAVPFGRMGRAEDLTGMAIFLATPEADYIVAQTYNVDGGNWMS-----------------
+>Q48436.2
+-------------------------------------------MKKVALVTGAGQGIGKAIALRLVKDGFAVAIADYNDATAKAVASEINQAGG-------RAMAVKVDVSDRDQVFAAVEQARKTLG--GFDVIVNNAGVAPSTP-IESITPEIVDKVYNINVKGVIWGIQAAVEAFKKEGHGGKIINACSQAGHVGNPELAVYSSSKFAVRGLTQTAARDLAPLGITVNGYCPGIVKTPMWAEIDRQVSE-AAGKPLGYGTAEFAKRITLGRLSEPEDVAACVSYLASPDSDYMTGQSLLIDGGMVFN-----------------
+>Q04520.1
+-------------------------------------------MQKVALVTGAGQGIGKAIALRLVKDGFAVAIADYNDATATAVAAEINQAGG-------RAVAIKVDVSRRDQVFAAVEQARKALG--GFNVIVNNAGIAPSTP-IESITEEIVDRVYNINVKGVIWGMQAAVEAFKKEGHGGKIVNACSQAGHVGNPELAVYSSSKFAVRGLTQTAARDLAPLGITVNGFCPGIVKTPMWAEIDRQCRK-RRAN--RWATARLN-------LPNASPLAACRSLKTSPPACRSSPARIPTI-----------------------
+>P66776.1
+-----------------------------------------MTNNKVALVTGGAQGIGFKIAERLVEDGFKVAVVDFNEEGAKAAALKLSSDGT-------KAIAIKADVSNRDDVFNAVRQTAAQFG--DFHVMVNNAGLGPTTP-IDTITEEQFKTVYGVNVAGVLWGIQAAHEQFKKFNHGGKIINATSQAGVEGNPGLSLYCSTKFAVRGLTQVAAQDLASEGITVNAFAPGIVQTPMMESIAVATAE-EAGKPEAWGWEQFTSQIALGRVSQPEDVSNVVSFLAGKDSDYITGQTIIVDGGMRFR-----------------
+>Q5HKG6.1
+-------------------------------------------MSKTAIITGSAGGLGKGIAERLANDGFNIVLQDINEALLLETEKEFKEKGY-------QAVAFKSDVSKKKEQEELVQFAVTEFG--QLDVMVNNAGVDAVTP-ILEIGEEELSKLFNINVFGTLFGIQAAANQFIKQKSKGKIINACSIAGHESYEVLGTYSATKHSVRSFTQTAAKELADKGITVNAYCPGVAKTEMWDRIDEEMVKLDDSLEIGDAFEAFSSEIKLGRYQEPSDVANLVSFLASNDSDYITGQSILTDGGLVYR-----------------
+>Q8CQD2.1
+-------------------------------------------MSKTAIITGAAGGLGKGIAERLANDGFNIVLQDINEALLLETEKEFKEKGY-------QAVAYKSDVSKKKEQEELVQFAVTEFG--QLDVMVNNAGVDAVTP-ILEIGEEELSKLFNINVFGTLFGIQAAANQFIKQKSKGKIINACSIAGHESYEVLGTYSATKHSVRSFTQTAAKELADKGITVNAYCPGVAKTEMWDRIDEEMVKLDDSLEIGDAFEAFSSEIKLGRYQEPSDVANLVSFLASNDSDYITGQSILTDGGLVYR-----------------
+>Q1JP75.1
+--------------------------------------MDLRLAGRRALVTGAGKGIGRSIVKALHAAGARVVAVSRTQADLDSLVRECP-----------GVETVCVDLAD----WEATEQALGGVG--PVDLLVNNAAVAFLQP-FLEVTKEAYDMSFSVNLRAVIQVSQIVARGLIARGAPGVIVNVSSQASQRGLTNHSVYCSTKGALDTLTKVMAVELGPHKIRVNAVNPTVVMTPMGQAAWSDPQK----------AKAMLDRIPLGRFAEVENVVDTILFLLSDRSSMTTGSTVPVDGGFLAT-----------------
+>Q91XV4.1
+--------------------------------------MDLGLAGRRALVTGAGKGIGRSTVLALQAAGAHVVAVSRTQADLDSLVSECP-----------GVETVCVDLAD----WEATEQALSSVG--PVDLLVNNAAVALLQP-FLEVTKEAFDMSFNVNLRAVIQVSQIVARGMIARGAPGAIVNVSSQASQRALANHSVYCSTKGALDMLTKMMALELGPHKIRVNAVNPTVVMTSMGRTNWSDPHK----------AKVMLDRIPLGKFAEVENVVDAILFLLSHRSNMTTGSTLPVDGGFLVT-----------------
+>Q7Z4W1.2
+--------------------------------------MELFLAGRRVLVTGAGKGIGRGTVQALHATGARVVAVSRTQADLDSLVRECP-----------GIEPVCVDLGD----WEATERALGSVG--PVDLLVNNAAVALLQP-FLEVTKEAFDRSFEVNLRAVIQVSQIVARGLIARGVPGAIVNVSSQCSQRAVTNHSVYCSTKGALDMLTKVMALELGPHKIRVNAVNPTVVMTSMGQATWSDPHK----------AKTMLNRIPLGKFAEVEHVVNAILFLLSDRSGMTTGSTLPVEGGFWAC-----------------
diff --git a/modules/bindings/tests/testfiles/pairwise_aln.fasta b/modules/bindings/tests/testfiles/pairwise_aln.fasta
new file mode 100644
index 0000000000000000000000000000000000000000..b6fe766c1208cde1071a4f7144f7f4407c76fb63
--- /dev/null
+++ b/modules/bindings/tests/testfiles/pairwise_aln.fasta
@@ -0,0 +1,4 @@
+>testseq
+------MRLDGKTALITGSARGIGRAFAEAYVREGARVAIADIN---LEAARATAAEIGPAACAIALDVTDQASIDRCVAELLDRWGSIDILVNNAALFDLAPIVEITRESYDRLFAINVSGTLFMMQAVARAMIAGGRGGKIINMASQAGRRGEALVGVYCATKAAVISLTQSAGLNLIRHGINVNAIAPGVVDGEHWDGVDAKFADYENLPRGEKKRQVGAAVPFGRMGRAEDLTGMAIFLATPEADYIVAQTYNVDGGNWMS-
+>P50199.1
+MSHPDLFSLSGARALVTGASRGIGLTLAKGLARYGAEVVLNGRNAESLDSAQSGFEAEGLKASTAVFDVTDQDAVIDGVAAIERDMGPIDILINNAGIQRRAPLEEFSRKDWDDLMSTNVNAVFFVGQAVARHMIPRGRG-KIVNICSVQSELARPGIAPYTATKGAVKNLTKGMATDWGRHGLQINGLAPGYFATEMTE----RLVADEEFTDWLCKR-----TPAGRWGQVEELVGAAVFLSSRASSFVNGQVLMVDGGITVSL
diff --git a/modules/bindings/tests/testfiles/similar.fasta b/modules/bindings/tests/testfiles/similar.fasta
new file mode 100644
index 0000000000000000000000000000000000000000..af6487c81676327376422a7c17485c5bf99db926
--- /dev/null
+++ b/modules/bindings/tests/testfiles/similar.fasta
@@ -0,0 +1,2 @@
+>P50199.1
+MSHPDLFSLSGARALVTGASRGIGLTLAKGLARYGAEVVLNGRNAESLDSAQSGFEAEGLKASTAVFDVTDQDAVIDGVAAIERDMGPIDILINNAGIQRRAPLEEFSRKDWDDLMSTNVNAVFFVGQAVARHMIPRGRGKIVNICSVQSELARPGIAPYTATKGAVKNLTKGMATDWGRHGLQINGLAPGYFATEMTERLVADEEFTDWLCKRTPAGRWGQVEELVGAAVFLSSRASSFVNGQVLMVDGGITVSL
diff --git a/modules/bindings/tests/testfiles/test.fasta b/modules/bindings/tests/testfiles/test.fasta
new file mode 100644
index 0000000000000000000000000000000000000000..38da1518cab1d2c60452b96b401b8b251454574e
--- /dev/null
+++ b/modules/bindings/tests/testfiles/test.fasta
@@ -0,0 +1,2 @@
+>testseq
+MRLDGKTALITGSARGIGRAFAEAYVREGARVAIADINLEAARATAAEIGPAACAIALDVTDQASIDRCVAELLDRWGSIDILVNNAALFDLAPIVEITRESYDRLFAINVSGTLFMMQAVARAMIAGGRGGKIINMASQAGRRGEALVGVYCATKAAVISLTQSAGLNLIRHGINVNAIAPGVVDGEHWDGVDAKFADYENLPRGEKKRQVGAAVPFGRMGRAEDLTGMAIFLATPEADYIVAQTYNVDGGNWMS
diff --git a/modules/conop/data/charmm.cif b/modules/conop/data/charmm.cif
new file mode 100644
index 0000000000000000000000000000000000000000..ced6449d30ad68b02a4026cf8e752a479637d445
--- /dev/null
+++ b/modules/conop/data/charmm.cif
@@ -0,0 +1,2247 @@
+data_ALA
+_chem_comp.id                                    ALA 
+_chem_comp.type                                  "L-PEPTIDE-LINKING" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "C3 H11 N O3" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       A
+_chem_comp.three_letter_code                     ALA 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+ALA N N N 0 N N N N ALA 1
+ALA CA CA C 0 N N N CA ALA 2
+ALA C C C 0 N N N C ALA 3
+ALA O O O 0 N Y N O ALA 4
+ALA CB CB C 0 N N N CB ALA 5
+ALA HA HA H 0 N N N HA ALA 6
+ALA HN HN H 0 N N N HN ALA 7
+ALA HB1 HB1 H 0 N N N HB1 ALA 8
+ALA HB2 HB2 H 0 N N N HB2 ALA 9
+ALA HB3 HB3 H 0 N N N HB3 ALA 10
+ALA OT1 OT1 O 0 N Y N OT1 ALA 11
+ALA OT2 OT2 O 0 N Y N OT2 ALA 12
+ALA HT1 HT1 H 0 N N N HT1 ALA 13
+ALA HT2 HT2 H 0 N N N HT2 ALA 14
+ALA HT3 HT3 H 0 N N N HT3 ALA 15
+ALA HT1 HT1 H 0 N N N HT1 ALA 16
+ALA HT2 HT2 H 0 N N N HT2 ALA 17
+ALA HT3 HT3 H 0 N N N HT3 ALA 18
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+ALA CB CA SING N N 1
+ALA N HN SING N N 2
+ALA N CA SING N N 3
+ALA C CA SING N N 4
+ALA CA HA SING N N 5
+ALA CB HB1 SING N N 6
+ALA CB HB2 SING N N 7
+ALA CB HB3 SING N N 8
+ALA O C SING N N 9
+ALA OT1 C SING N N 10
+ALA OT2 C SING N N 11
+ALA HT1 NH SING N N 12
+ALA HT2 NH SING N N 13
+ALA HT3 NH SING N N 14
+data_ARG
+_chem_comp.id                                    ARG 
+_chem_comp.type                                  "L-PEPTIDE-LINKING" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "C6 H16 N4 O3" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       R
+_chem_comp.three_letter_code                     ARG 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+ARG N N N 0 N N N N ARG 1
+ARG CA CA C 0 N N N CA ARG 2
+ARG C C C 0 N N N C ARG 3
+ARG O O O 0 N Y N O ARG 4
+ARG CB CB C 0 N N N CB ARG 5
+ARG CG CG C 0 N N N CG ARG 6
+ARG CD CD C 0 N N N CD ARG 7
+ARG NE NE N 0 N N N NE ARG 8
+ARG CZ CZ C 0 N N N CZ ARG 9
+ARG NH1 NH1 N 0 N N N NH1 ARG 10
+ARG NH2 NH2 N 0 N N N NH2 ARG 11
+ARG HN HN H 0 N N N HN ARG 12
+ARG HB1 HB1 H 0 N N N HB1 ARG 13
+ARG HB2 HB2 H 0 N N N HB2 ARG 14
+ARG HA HA H 0 N N N HA ARG 15
+ARG HG1 HG1 H 0 N N N HG1 ARG 16
+ARG HG2 HG2 H 0 N N N HG2 ARG 17
+ARG HD1 HD1 H 0 N N N HD1 ARG 18
+ARG HD2 HD2 H 0 N N N HD2 ARG 19
+ARG HH11 HH11 H 0 N N N HH11 ARG 20
+ARG HH12 HH12 H 0 N N N HH12 ARG 21
+ARG HH21 HH21 H 0 N N N HH21 ARG 22
+ARG HH22 HH22 H 0 N N N HH22 ARG 23
+ARG HE HE H 0 N N N HE ARG 24
+ARG OT1 OT1 O 0 N Y N OT1 ARG 25
+ARG OT2 OT2 O 0 N Y N OT2 ARG 26
+ARG HT1 HT1 H 0 N N N HT1 ARG 27
+ARG HT2 HT2 H 0 N N N HT2 ARG 28
+ARG HT3 HT3 H 0 N N N HT3 ARG 29
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+ARG CB CA SING N N 1
+ARG CG CB SING N N 2
+ARG CD CG SING N N 3
+ARG NE CD SING N N 4
+ARG CZ NE SING N N 5
+ARG NH2 CZ SING N N 6
+ARG N HN SING N N 7
+ARG N CA SING N N 8
+ARG C CA SING N N 9
+ARG CA HA SING N N 10
+ARG CB HB1 SING N N 11
+ARG CB HB2 SING N N 12
+ARG CG HG1 SING N N 13
+ARG CG HG2 SING N N 14
+ARG CD HD1 SING N N 15
+ARG CD HD2 SING N N 16
+ARG NE HE SING N N 17
+ARG NH1 HH11 SING N N 18
+ARG NH1 HH12 SING N N 19
+ARG NH2 HH21 SING N N 20
+ARG NH2 HH22 SING N N 21
+ARG O C SING N N 22
+ARG CZ NH1 SING N N 23
+ARG OT1 C SING N N 24
+ARG OT2 C SING N N 25
+ARG HT1 NH SING N N 26
+ARG HT2 NH SING N N 27
+ARG HT3 NH SING N N 28
+data_ASN
+_chem_comp.id                                    ASN 
+_chem_comp.type                                  "L-PEPTIDE-LINKING" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "C4 H9 N2 O4" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       N
+_chem_comp.three_letter_code                     ASN 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+ASN N N N 0 N N N N ASN 1
+ASN CA CA C 0 N N N CA ASN 2
+ASN C C C 0 N N N C ASN 3
+ASN O O O 0 N Y N O ASN 4
+ASN CB CB C 0 N N N CB ASN 5
+ASN CG CG C 0 N N N CG ASN 6
+ASN OD1 OD1 O 0 N N N OD1 ASN 7
+ASN ND2 ND2 N 0 N N N ND2 ASN 8
+ASN HN HN H 0 N N N HN ASN 9
+ASN HA HA H 0 N N N HA ASN 10
+ASN HB1 HB1 H 0 N N N HB1 ASN 11
+ASN HB2 HB2 H 0 N N N HB2 ASN 12
+ASN HD21 HD21 H 0 N N N HD21 ASN 13
+ASN HD22 HD22 H 0 N N N HD22 ASN 14
+ASN OT1 OT1 O 0 N Y N OT1 ASN 15
+ASN OT2 OT2 O 0 N Y N OT2 ASN 16
+ASN HT1 HT1 H 0 N N N HT1 ASN 17
+ASN HT2 HT2 H 0 N N N HT2 ASN 18
+ASN HT3 HT3 H 0 N N N HT3 ASN 19
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+ASN CB CA SING N N 1
+ASN CG CB SING N N 2
+ASN ND2 CG SING N N 3
+ASN N HN SING N N 4
+ASN N CA SING N N 5
+ASN C CA SING N N 6
+ASN CA HA SING N N 7
+ASN CB HB1 SING N N 8
+ASN CB HB2 SING N N 9
+ASN ND2 HD21 SING N N 10
+ASN ND2 HD22 SING N N 11
+ASN C O SING N N 12
+ASN CG OD1 SING N N 13
+ASN OT1 C SING N N 14
+ASN OT2 C SING N N 15
+ASN HT1 NH SING N N 16
+ASN HT2 NH SING N N 17
+ASN HT3 NH SING N N 18
+data_ASP
+_chem_comp.id                                    ASP 
+_chem_comp.type                                  "L-PEPTIDE-LINKING" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "C4 H7 N O5" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       D
+_chem_comp.three_letter_code                     ASP 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+ASP N N N 0 N N N N ASP 1
+ASP CA CA C 0 N N N CA ASP 2
+ASP C C C 0 N N N C ASP 3
+ASP O O O 0 N Y N O ASP 4
+ASP CB CB C 0 N N N CB ASP 5
+ASP CG CG C 0 N N N CG ASP 6
+ASP OD1 OD1 O 0 N N N OD1 ASP 7
+ASP OD2 OD2 O 0 N N N OD2 ASP 8
+ASP HA HA H 0 N N N HA ASP 9
+ASP HB1 HB1 H 0 N N N HB1 ASP 10
+ASP HB2 HB2 H 0 N N N HB2 ASP 11
+ASP HN HN H 0 N N N HN ASP 12
+ASP OT1 OT1 O 0 N Y N OT1 ASP 13
+ASP OT2 OT2 O 0 N Y N OT2 ASP 14
+ASP HT1 HT1 H 0 N N N HT1 ASP 15
+ASP HT2 HT2 H 0 N N N HT2 ASP 16
+ASP HT3 HT3 H 0 N N N HT3 ASP 17
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+ASP CB CA SING N N 1
+ASP CG CB SING N N 2
+ASP OD2 CG SING N N 3
+ASP N HN SING N N 4
+ASP N CA SING N N 5
+ASP C CA SING N N 6
+ASP CA HA SING N N 7
+ASP CB HB1 SING N N 8
+ASP CB HB2 SING N N 9
+ASP O C SING N N 10
+ASP CG OD1 SING N N 11
+ASP OT1 C SING N N 12
+ASP OT2 C SING N N 13
+ASP HT1 NH SING N N 14
+ASP HT2 NH SING N N 15
+ASP HT3 NH SING N N 16
+data_ASPP
+_chem_comp.id                                    ASPP 
+_chem_comp.type                                  "L-PEPTIDE-LINKING" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "C4 H8 N O5" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       D
+_chem_comp.three_letter_code                     ASPP 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+ASPP N N N 0 N N N N ASPP 1
+ASPP CA CA C 0 N N N CA ASPP 2
+ASPP C C C 0 N N N C ASPP 3
+ASPP O O O 0 N Y N O ASPP 4
+ASPP CB CB C 0 N N N CB ASPP 5
+ASPP CG CG C 0 N N N CG ASPP 6
+ASPP OD1 OD1 O 0 N N N OD1 ASPP 7
+ASPP OD2 OD2 O 0 N N N OD2 ASPP 8
+ASPP HN HN H 0 N N N HN ASPP 9
+ASPP HA HA H 0 N N N HA ASPP 10
+ASPP HB1 HB1 H 0 N N N HB1 ASPP 11
+ASPP HB2 HB2 H 0 N N N HB2 ASPP 12
+ASPP HD2 HD2 H 0 N N N HD2 ASPP 13
+ASPP OT1 OT1 O 0 N Y N OT1 ASPP 14
+ASPP OT2 OT2 O 0 N Y N OT2 ASPP 15
+ASPP HT1 HT1 H 0 N N N HT1 ASPP 16
+ASPP HT2 HT2 H 0 N N N HT2 ASPP 17
+ASPP HT3 HT3 H 0 N N N HT3 ASPP 18
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+ASPP CB CA SING N N 1
+ASPP CG CB SING N N 2
+ASPP OD2 CG SING N N 3
+ASPP OD2 HD2 SING N N 4
+ASPP N HN SING N N 5
+ASPP N CA SING N N 6
+ASPP C CA SING N N 7
+ASPP CA HA SING N N 8
+ASPP CB HB1 SING N N 9
+ASPP CB HB2 SING N N 10
+ASPP O C SING N N 11
+ASPP CG OD1 SING N N 12
+ASPP OT1 C SING N N 13
+ASPP OT2 C SING N N 14
+ASPP HT1 NH SING N N 15
+ASPP HT2 NH SING N N 16
+ASPP HT3 NH SING N N 17
+data_CYS
+_chem_comp.id                                    CYS 
+_chem_comp.type                                  "L-PEPTIDE-LINKING" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "C3 H8 N O3 S" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       C
+_chem_comp.three_letter_code                     CYS 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+CYS N N N 0 N N N N CYS 1
+CYS CA CA C 0 N N N CA CYS 2
+CYS C C C 0 N N N C CYS 3
+CYS O O O 0 N Y N O CYS 4
+CYS CB CB C 0 N N N CB CYS 5
+CYS SG SG S 0 N N N SG CYS 6
+CYS HA HA H 0 N N N HA CYS 7
+CYS HN HN H 0 N N N HN CYS 8
+CYS HB1 HB1 H 0 N N N HB1 CYS 9
+CYS HB2 HB2 H 0 N N N HB2 CYS 10
+CYS HG1 HG1 H 0 N N N HG1 CYS 11
+CYS OT1 OT1 O 0 N Y N OT1 CYS 12
+CYS OT2 OT2 O 0 N Y N OT2 CYS 13
+CYS HT1 HT1 H 0 N N N HT1 CYS 14
+CYS HT2 HT2 H 0 N N N HT2 CYS 15
+CYS HT3 HT3 H 0 N N N HT3 CYS 16
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+CYS CB CA SING N N 1
+CYS SG CB SING N N 2
+CYS N HN SING N N 3
+CYS N CA SING N N 4
+CYS C CA SING N N 5
+CYS CA HA SING N N 6
+CYS CB HB1 SING N N 7
+CYS CB HB2 SING N N 8
+CYS SG HG1 SING N N 9
+CYS O C SING N N 10
+CYS OT1 C SING N N 11
+CYS OT2 C SING N N 12
+CYS HT1 NH SING N N 13
+CYS HT2 NH SING N N 14
+CYS HT3 NH SING N N 15
+data_CYS2
+_chem_comp.id                                    CYS2 
+_chem_comp.type                                  "L-PEPTIDE-LINKING" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "C3 H7 N O3 S" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       C
+_chem_comp.three_letter_code                     CYS2 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+CYS2 N N N 0 N N N N CYS2 1
+CYS2 CA CA C 0 N N N CA CYS2 2
+CYS2 C C C 0 N N N C CYS2 3
+CYS2 O O O 0 N Y N O CYS2 4
+CYS2 CB CB C 0 N N N CB CYS2 5
+CYS2 SG SG S 0 N N N SG CYS2 6
+CYS2 HN HN H 0 N N N HN CYS2 7
+CYS2 HA HA H 0 N N N HA CYS2 8
+CYS2 HB1 HB1 H 0 N N N HB1 CYS2 9
+CYS2 HB2 HB2 H 0 N N N HB2 CYS2 10
+CYS2 OT1 OT1 O 0 N Y N OT1 CYS2 11
+CYS2 OT2 OT2 O 0 N Y N OT2 CYS2 12
+CYS2 HT1 HT1 H 0 N N N HT1 CYS2 13
+CYS2 HT2 HT2 H 0 N N N HT2 CYS2 14
+CYS2 HT3 HT3 H 0 N N N HT3 CYS2 15
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+CYS2 CB CA SING N N 1
+CYS2 SG CB SING N N 2
+CYS2 N HN SING N N 3
+CYS2 N CA SING N N 4
+CYS2 C CA SING N N 5
+CYS2 CA HA SING N N 6
+CYS2 CB HB1 SING N N 7
+CYS2 CB HB2 SING N N 8
+CYS2 O C SING N N 9
+CYS2 OT1 C SING N N 10
+CYS2 OT2 C SING N N 11
+CYS2 HT1 NH SING N N 12
+CYS2 HT2 NH SING N N 13
+CYS2 HT3 NH SING N N 14
+data_GLN
+_chem_comp.id                                    GLN 
+_chem_comp.type                                  "L-PEPTIDE-LINKING" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "C5 H11 N2 O4" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       N
+_chem_comp.three_letter_code                     GLN 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+GLN N N N 0 N N N N GLN 1
+GLN CA CA C 0 N N N CA GLN 2
+GLN C C C 0 N N N C GLN 3
+GLN O O O 0 N Y N O GLN 4
+GLN CB CB C 0 N N N CB GLN 5
+GLN CG CG C 0 N N N CG GLN 6
+GLN CD CD C 0 N N N CD GLN 7
+GLN OE1 OE1 O 0 N N N OE1 GLN 8
+GLN NE2 NE2 N 0 N N N NE2 GLN 9
+GLN HN HN H 0 N N N HN GLN 10
+GLN HA HA H 0 N N N HA GLN 11
+GLN HB1 HB1 H 0 N N N HB1 GLN 12
+GLN HB2 HB2 H 0 N N N HB2 GLN 13
+GLN HG1 HG1 H 0 N N N HG1 GLN 14
+GLN HG2 HG2 H 0 N N N HG2 GLN 15
+GLN HE21 HE21 H 0 N N N HE21 GLN 16
+GLN HE22 HE22 H 0 N N N HE22 GLN 17
+GLN OT1 OT1 O 0 N Y N OT1 GLN 18
+GLN OT2 OT2 O 0 N Y N OT2 GLN 19
+GLN HT1 HT1 H 0 N N N HT1 GLN 20
+GLN HT2 HT2 H 0 N N N HT2 GLN 21
+GLN HT3 HT3 H 0 N N N HT3 GLN 22
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+GLN CB CA SING N N 1
+GLN CG CB SING N N 2
+GLN CD CG SING N N 3
+GLN NE2 CD SING N N 4
+GLN N HN SING N N 5
+GLN N CA SING N N 6
+GLN C CA SING N N 7
+GLN CA HA SING N N 8
+GLN CB HB1 SING N N 9
+GLN CB HB2 SING N N 10
+GLN CG HG1 SING N N 11
+GLN CG HG2 SING N N 12
+GLN NE2 HE21 SING N N 13
+GLN NE2 HE22 SING N N 14
+GLN O C SING N N 15
+GLN CD OE1 SING N N 16
+GLN OT1 C SING N N 17
+GLN OT2 C SING N N 18
+GLN HT1 NH SING N N 19
+GLN HT2 NH SING N N 20
+GLN HT3 NH SING N N 21
+data_GLU
+_chem_comp.id                                    GLU 
+_chem_comp.type                                  "L-PEPTIDE-LINKING" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "C5 H9 N O5" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       E
+_chem_comp.three_letter_code                     GLU 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+GLU N N N 0 N N N N GLU 1
+GLU CA CA C 0 N N N CA GLU 2
+GLU C C C 0 N N N C GLU 3
+GLU O O O 0 N Y N O GLU 4
+GLU CB CB C 0 N N N CB GLU 5
+GLU CG CG C 0 N N N CG GLU 6
+GLU CD CD C 0 N N N CD GLU 7
+GLU OE1 OE1 O 0 N N N OE1 GLU 8
+GLU OE2 OE2 O 0 N N N OE2 GLU 9
+GLU HN HN H 0 N N N HN GLU 10
+GLU HA HA H 0 N N N HA GLU 11
+GLU HB1 HB1 H 0 N N N HB1 GLU 12
+GLU HB2 HB2 H 0 N N N HB2 GLU 13
+GLU HG1 HG1 H 0 N N N HG1 GLU 14
+GLU HG2 HG2 H 0 N N N HG2 GLU 15
+GLU OT1 OT1 O 0 N Y N OT1 GLU 16
+GLU OT2 OT2 O 0 N Y N OT2 GLU 17
+GLU HT1 HT1 H 0 N N N HT1 GLU 18
+GLU HT2 HT2 H 0 N N N HT2 GLU 19
+GLU HT3 HT3 H 0 N N N HT3 GLU 20
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+GLU CB CA SING N N 1
+GLU CG CB SING N N 2
+GLU CD CG SING N N 3
+GLU OE2 CD SING N N 4
+GLU N HN SING N N 5
+GLU N CA SING N N 6
+GLU C CA SING N N 7
+GLU CA HA SING N N 8
+GLU CB HB1 SING N N 9
+GLU CB HB2 SING N N 10
+GLU CG HG1 SING N N 11
+GLU CG HG2 SING N N 12
+GLU O C SING N N 13
+GLU CD OE1 SING N N 14
+GLU OT1 C SING N N 15
+GLU OT2 C SING N N 16
+GLU HT1 NH SING N N 17
+GLU HT2 NH SING N N 18
+GLU HT3 NH SING N N 19
+data_GLUP
+_chem_comp.id                                    GLUP 
+_chem_comp.type                                  "L-PEPTIDE-LINKING" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "C5 H10 N O5" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       E
+_chem_comp.three_letter_code                     GLUP 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+GLUP N N N 0 N N N N GLUP 1
+GLUP CA CA C 0 N N N CA GLUP 2
+GLUP C C C 0 N N N C GLUP 3
+GLUP O O O 0 N Y N O GLUP 4
+GLUP CB CB C 0 N N N CB GLUP 5
+GLUP CG CG C 0 N N N CG GLUP 6
+GLUP CD CD C 0 N N N CD GLUP 7
+GLUP OE1 OE1 O 0 N N N OE1 GLUP 8
+GLUP OE2 OE2 O 0 N N N OE2 GLUP 9
+GLUP HN HN H 0 N N N HN GLUP 10
+GLUP HA HA H 0 N N N HA GLUP 11
+GLUP HB1 HB1 H 0 N N N HB1 GLUP 12
+GLUP HB2 HB2 H 0 N N N HB2 GLUP 13
+GLUP HG1 HG1 H 0 N N N HG1 GLUP 14
+GLUP HG2 HG2 H 0 N N N HG2 GLUP 15
+GLUP HE2 HE2 H 0 N N N HE2 GLUP 16
+GLUP OT1 OT1 O 0 N Y N OT1 GLUP 17
+GLUP OT2 OT2 O 0 N Y N OT2 GLUP 18
+GLUP HT1 HT1 H 0 N N N HT1 GLUP 19
+GLUP HT2 HT2 H 0 N N N HT2 GLUP 20
+GLUP HT3 HT3 H 0 N N N HT3 GLUP 21
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+GLUP CB CA SING N N 1
+GLUP CG CB SING N N 2
+GLUP CD CG SING N N 3
+GLUP OE2 CD SING N N 4
+GLUP OE2 HE2 SING N N 5
+GLUP N HN SING N N 6
+GLUP N CA SING N N 7
+GLUP C CA SING N N 8
+GLUP CA HA SING N N 9
+GLUP CB HB1 SING N N 10
+GLUP CB HB2 SING N N 11
+GLUP CG HG1 SING N N 12
+GLUP CG HG2 SING N N 13
+GLUP O C SING N N 14
+GLUP CD OE1 SING N N 15
+GLUP OT1 C SING N N 16
+GLUP OT2 C SING N N 17
+GLUP HT1 NH SING N N 18
+GLUP HT2 NH SING N N 19
+GLUP HT3 NH SING N N 20
+data_GLY
+_chem_comp.id                                    GLY 
+_chem_comp.type                                  "L-PEPTIDE-LINKING" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "C2 H6 N O3" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       G
+_chem_comp.three_letter_code                     GLY 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+GLY N N N 0 N N N N GLY 1
+GLY HN HN H 0 N N N HN GLY 2
+GLY CA CA C 0 N N N CA GLY 3
+GLY HA1 HA1 H 0 N N N HA1 GLY 4
+GLY HA2 HA2 H 0 N N N HA2 GLY 5
+GLY C C C 0 N N N C GLY 6
+GLY O O O 0 N Y N O GLY 7
+GLY OT1 OT1 O 0 N Y N OT1 GLY 8
+GLY OT2 OT2 O 0 N Y N OT2 GLY 9
+GLY HT1 HT1 H 0 N N N HT1 GLY 10
+GLY HT2 HT2 H 0 N N N HT2 GLY 11
+GLY HT3 HT3 H 0 N N N HT3 GLY 12
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+GLY N HN SING N N 1
+GLY N CA SING N N 2
+GLY C CA SING N N 3
+GLY CA HA1 SING N N 4
+GLY CA HA2 SING N N 5
+GLY O C SING N N 6
+GLY OT1 C SING N N 7
+GLY OT2 C SING N N 8
+GLY HT1 NH SING N N 9
+GLY HT2 NH SING N N 10
+GLY HT3 NH SING N N 11
+data_HSD
+_chem_comp.id                                    HSD 
+_chem_comp.type                                  "L-PEPTIDE-LINKING" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "C6 H10 N3 O3" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       H
+_chem_comp.three_letter_code                     HSD 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+HSD N N N 0 N N N N HSD 1
+HSD CA CA C 0 N N N CA HSD 2
+HSD C C C 0 N N N C HSD 3
+HSD O O O 0 N Y N O HSD 4
+HSD CB CB C 0 N N N CB HSD 5
+HSD ND1 ND1 N 0 N N N ND1 HSD 6
+HSD CG CG C 0 N N N CG HSD 7
+HSD CE1 CE1 C 0 N N N CE1 HSD 8
+HSD NE2 NE2 N 0 N N N NE2 HSD 9
+HSD CD2 CD2 C 0 N N N CD2 HSD 10
+HSD HA HA H 0 N N N HA HSD 11
+HSD HN HN H 0 N N N HN HSD 12
+HSD HB1 HB1 H 0 N N N HB1 HSD 13
+HSD HB2 HB2 H 0 N N N HB2 HSD 14
+HSD HD1 HD1 H 0 N N N HD1 HSD 15
+HSD HE1 HE1 H 0 N N N HE1 HSD 16
+HSD HD2 HD2 H 0 N N N HD2 HSD 17
+HSD OT1 OT1 O 0 N Y N OT1 HSD 18
+HSD OT2 OT2 O 0 N Y N OT2 HSD 19
+HSD HT1 HT1 H 0 N N N HT1 HSD 20
+HSD HT2 HT2 H 0 N N N HT2 HSD 21
+HSD HT3 HT3 H 0 N N N HT3 HSD 22
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+HSD CB CA SING N N 1
+HSD CG CB SING N N 2
+HSD ND1 CG SING N N 3
+HSD CE1 ND1 SING N N 4
+HSD NE2 CD2 SING N N 5
+HSD N HN SING N N 6
+HSD N CA SING N N 7
+HSD C CA SING N N 8
+HSD CA HA SING N N 9
+HSD CB HB1 SING N N 10
+HSD CB HB2 SING N N 11
+HSD ND1 HD1 SING N N 12
+HSD CD2 HD2 SING N N 13
+HSD CE1 HE1 SING N N 14
+HSD O C SING N N 15
+HSD CG CD2 SING N N 16
+HSD CE1 NE2 SING N N 17
+HSD OT1 C SING N N 18
+HSD OT2 C SING N N 19
+HSD HT1 NH SING N N 20
+HSD HT2 NH SING N N 21
+HSD HT3 NH SING N N 22
+data_HSE
+_chem_comp.id                                    HSE 
+_chem_comp.type                                  "L-PEPTIDE-LINKING" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "C6 H10 N3 O3" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       H
+_chem_comp.three_letter_code                     HSE 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+HSE N N N 0 N N N N HSE 1
+HSE CA CA C 0 N N N CA HSE 2
+HSE C C C 0 N N N C HSE 3
+HSE O O O 0 N Y N O HSE 4
+HSE HA HA H 0 N N N HA HSE 5
+HSE CB CB C 0 N N N CB HSE 6
+HSE CG CG C 0 N N N CG HSE 7
+HSE ND1 ND1 N 0 N N N ND1 HSE 8
+HSE CE1 CE1 C 0 N N N CE1 HSE 9
+HSE NE2 NE2 N 0 N N N NE2 HSE 10
+HSE CD2 CD2 C 0 N N N CD2 HSE 11
+HSE HB1 HB1 H 0 N N N HB1 HSE 12
+HSE HB2 HB2 H 0 N N N HB2 HSE 13
+HSE HN HN H 0 N N N HN HSE 14
+HSE HE1 HE1 H 0 N N N HE1 HSE 15
+HSE HE2 HE2 H 0 N N N HE2 HSE 16
+HSE HD2 HD2 H 0 N N N HD2 HSE 17
+HSE OT1 OT1 O 0 N Y N OT1 HSE 18
+HSE OT2 OT2 O 0 N Y N OT2 HSE 19
+HSE HT1 HT1 H 0 N N N HT1 HSE 20
+HSE HT2 HT2 H 0 N N N HT2 HSE 21
+HSE HT3 HT3 H 0 N N N HT3 HSE 22
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+HSE CB CA SING N N 1
+HSE CG CB SING N N 2
+HSE ND1 CG SING N N 3
+HSE NE2 CD2 SING N N 4
+HSE N HN SING N N 5
+HSE N CA SING N N 6
+HSE C CA SING N N 7
+HSE NE2 CE1 SING N N 8
+HSE CA HA SING N N 9
+HSE CB HB1 SING N N 10
+HSE CB HB2 SING N N 11
+HSE NE2 HE2 SING N N 12
+HSE CD2 HD2 SING N N 13
+HSE CE1 HE1 SING N N 14
+HSE O C SING N N 15
+HSE CD2 CG SING N N 16
+HSE CE1 ND1 SING N N 17
+HSE OT1 C SING N N 18
+HSE OT2 C SING N N 19
+HSE HT1 NH SING N N 20
+HSE HT2 NH SING N N 21
+HSE HT3 NH SING N N 22
+data_HSP
+_chem_comp.id                                    HSP 
+_chem_comp.type                                  "L-PEPTIDE-LINKING" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "C6 H11 N3 O3" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       H
+_chem_comp.three_letter_code                     HSP 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+HSP N N N 0 N N N N HSP 1
+HSP CA CA C 0 N N N CA HSP 2
+HSP C C C 0 N N N C HSP 3
+HSP O O O 0 N Y N O HSP 4
+HSP CB CB C 0 N N N CB HSP 5
+HSP CD2 CD2 C 0 N N N CD2 HSP 6
+HSP CG CG C 0 N N N CG HSP 7
+HSP NE2 NE2 N 0 N N N NE2 HSP 8
+HSP ND1 ND1 N 0 N N N ND1 HSP 9
+HSP CE1 CE1 C 0 N N N CE1 HSP 10
+HSP HB1 HB1 H 0 N N N HB1 HSP 11
+HSP HB2 HB2 H 0 N N N HB2 HSP 12
+HSP HA HA H 0 N N N HA HSP 13
+HSP HD2 HD2 H 0 N N N HD2 HSP 14
+HSP HE2 HE2 H 0 N N N HE2 HSP 15
+HSP HD1 HD1 H 0 N N N HD1 HSP 16
+HSP HE1 HE1 H 0 N N N HE1 HSP 17
+HSP HN HN H 0 N N N HN HSP 18
+HSP OT1 OT1 O 0 N Y N OT1 HSP 19
+HSP OT2 OT2 O 0 N Y N OT2 HSP 20
+HSP HT1 HT1 H 0 N N N HT1 HSP 21
+HSP HT2 HT2 H 0 N N N HT2 HSP 22
+HSP HT3 HT3 H 0 N N N HT3 HSP 23
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+HSP CB CA SING N N 1
+HSP CG CB SING N N 2
+HSP ND1 CG SING N N 3
+HSP CE1 ND1 SING N N 4
+HSP NE2 CD2 SING N N 5
+HSP N HN SING N N 6
+HSP N CA SING N N 7
+HSP C CA SING N N 8
+HSP CA HA SING N N 9
+HSP CB HB1 SING N N 10
+HSP CB HB2 SING N N 11
+HSP ND1 HD1 SING N N 12
+HSP NE2 HE2 SING N N 13
+HSP CD2 HD2 SING N N 14
+HSP CE1 HE1 SING N N 15
+HSP O C SING N N 16
+HSP CD2 CG SING N N 17
+HSP NE2 CE1 SING N N 18
+HSP OT1 C SING N N 19
+HSP OT2 C SING N N 20
+HSP HT1 NH SING N N 21
+HSP HT2 NH SING N N 22
+HSP HT3 NH SING N N 23
+data_ILE
+_chem_comp.id                                    ILE 
+_chem_comp.type                                  "L-PEPTIDE-LINKING" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "C6 H14 N O3" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       I
+_chem_comp.three_letter_code                     ILE 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+ILE N N N 0 N N N N ILE 1
+ILE CA CA C 0 N N N CA ILE 2
+ILE C C C 0 N N N C ILE 3
+ILE O O O 0 N Y N O ILE 4
+ILE CB CB C 0 N N N CB ILE 5
+ILE CG2 CG2 C 0 N N N CG2 ILE 6
+ILE CG1 CG1 C 0 N N N CG1 ILE 7
+ILE CD CD C 0 N N N CD ILE 8
+ILE HA HA H 0 N N N HA ILE 9
+ILE HB HB H 0 N N N HB ILE 10
+ILE HG21 HG21 H 0 N N N HG21 ILE 11
+ILE HG22 HG22 H 0 N N N HG22 ILE 12
+ILE HG23 HG23 H 0 N N N HG23 ILE 13
+ILE HG11 HG11 H 0 N N N HG11 ILE 14
+ILE HG12 HG12 H 0 N N N HG12 ILE 15
+ILE HD1 HD1 H 0 N N N HD1 ILE 16
+ILE HD2 HD2 H 0 N N N HD2 ILE 17
+ILE HD3 HD3 H 0 N N N HD3 ILE 18
+ILE HN HN H 0 N N N HN ILE 19
+ILE OT1 OT1 O 0 N Y N OT1 ILE 20
+ILE OT2 OT2 O 0 N Y N OT2 ILE 21
+ILE HT1 HT1 H 0 N N N HT1 ILE 22
+ILE HT2 HT2 H 0 N N N HT2 ILE 23
+ILE HT3 HT3 H 0 N N N HT3 ILE 24
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+ILE CB CA SING N N 1
+ILE CG1 CB SING N N 2
+ILE CG2 CB SING N N 3
+ILE CD CG1 SING N N 4
+ILE N HN SING N N 5
+ILE N CA SING N N 6
+ILE C CA SING N N 7
+ILE CA HA SING N N 8
+ILE CB HB SING N N 9
+ILE CG1 HG11 SING N N 10
+ILE CG1 HG12 SING N N 11
+ILE CG2 HG21 SING N N 12
+ILE CG2 HG22 SING N N 13
+ILE CG2 HG23 SING N N 14
+ILE CD HD1 SING N N 15
+ILE CD HD2 SING N N 16
+ILE CD HD3 SING N N 17
+ILE O C SING N N 18
+ILE OT1 C SING N N 19
+ILE OT2 C SING N N 20
+ILE HT1 NH SING N N 21
+ILE HT2 NH SING N N 22
+ILE HT3 NH SING N N 23
+data_LEU
+_chem_comp.id                                    LEU 
+_chem_comp.type                                  "L-PEPTIDE-LINKING" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "C6 H14 N O3" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       L
+_chem_comp.three_letter_code                     LEU 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+LEU N N N 0 N N N N LEU 1
+LEU CA CA C 0 N N N CA LEU 2
+LEU C C C 0 N N N C LEU 3
+LEU O O O 0 N Y N O LEU 4
+LEU CB CB C 0 N N N CB LEU 5
+LEU CG CG C 0 N N N CG LEU 6
+LEU CD1 CD1 C 0 N N N CD1 LEU 7
+LEU CD2 CD2 C 0 N N N CD2 LEU 8
+LEU HB1 HB1 H 0 N N N HB1 LEU 9
+LEU HB2 HB2 H 0 N N N HB2 LEU 10
+LEU HA HA H 0 N N N HA LEU 11
+LEU HG HG H 0 N N N HG LEU 12
+LEU HD11 HD11 H 0 N N N HD11 LEU 13
+LEU HD12 HD12 H 0 N N N HD12 LEU 14
+LEU HD13 HD13 H 0 N N N HD13 LEU 15
+LEU HD21 HD21 H 0 N N N HD21 LEU 16
+LEU HD22 HD22 H 0 N N N HD22 LEU 17
+LEU HD23 HD23 H 0 N N N HD23 LEU 18
+LEU HN HN H 0 N N N HN LEU 19
+LEU OT1 OT1 O 0 N Y N OT1 LEU 20
+LEU OT2 OT2 O 0 N Y N OT2 LEU 21
+LEU HT1 HT1 H 0 N N N HT1 LEU 22
+LEU HT2 HT2 H 0 N N N HT2 LEU 23
+LEU HT3 HT3 H 0 N N N HT3 LEU 24
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+LEU CB CA SING N N 1
+LEU CG CB SING N N 2
+LEU CD1 CG SING N N 3
+LEU CD2 CG SING N N 4
+LEU N HN SING N N 5
+LEU N CA SING N N 6
+LEU C CA SING N N 7
+LEU CA HA SING N N 8
+LEU CB HB1 SING N N 9
+LEU CB HB2 SING N N 10
+LEU CG HG SING N N 11
+LEU CD1 HD11 SING N N 12
+LEU CD1 HD12 SING N N 13
+LEU CD1 HD13 SING N N 14
+LEU CD2 HD21 SING N N 15
+LEU CD2 HD22 SING N N 16
+LEU CD2 HD23 SING N N 17
+LEU O C SING N N 18
+LEU OT1 C SING N N 19
+LEU OT2 C SING N N 20
+LEU HT1 NH SING N N 21
+LEU HT2 NH SING N N 22
+LEU HT3 NH SING N N 23
+data_LYS
+_chem_comp.id                                    LYS 
+_chem_comp.type                                  "L-PEPTIDE-LINKING" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "C6 H16 N2 O3" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       K
+_chem_comp.three_letter_code                     LYS 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+LYS N N N 0 N N N N LYS 1
+LYS CA CA C 0 N N N CA LYS 2
+LYS C C C 0 N N N C LYS 3
+LYS O O O 0 N Y N O LYS 4
+LYS CB CB C 0 N N N CB LYS 5
+LYS CG CG C 0 N N N CG LYS 6
+LYS CD CD C 0 N N N CD LYS 7
+LYS CE CE C 0 N N N CE LYS 8
+LYS NZ NZ N 0 N N N NZ LYS 9
+LYS HA HA H 0 N N N HA LYS 10
+LYS HB1 HB1 H 0 N N N HB1 LYS 11
+LYS HB2 HB2 H 0 N N N HB2 LYS 12
+LYS HG1 HG1 H 0 N N N HG1 LYS 13
+LYS HG2 HG2 H 0 N N N HG2 LYS 14
+LYS HD1 HD1 H 0 N N N HD1 LYS 15
+LYS HD2 HD2 H 0 N N N HD2 LYS 16
+LYS HE1 HE1 H 0 N N N HE1 LYS 17
+LYS HE2 HE2 H 0 N N N HE2 LYS 18
+LYS HZ1 HZ1 H 0 N N N HZ1 LYS 19
+LYS HZ2 HZ2 H 0 N N N HZ2 LYS 20
+LYS HZ3 HZ3 H 0 N N N HZ3 LYS 21
+LYS HN HN H 0 N N N HN LYS 22
+LYS OT1 OT1 O 0 N Y N OT1 LYS 23
+LYS OT2 OT2 O 0 N Y N OT2 LYS 24
+LYS HT1 HT1 H 0 N N N HT1 LYS 25
+LYS HT2 HT2 H 0 N N N HT2 LYS 26
+LYS HT3 HT3 H 0 N N N HT3 LYS 27
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+LYS CB CA SING N N 1
+LYS CG CB SING N N 2
+LYS CD CG SING N N 3
+LYS CE CD SING N N 4
+LYS NZ CE SING N N 5
+LYS N HN SING N N 6
+LYS N CA SING N N 7
+LYS C CA SING N N 8
+LYS CA HA SING N N 9
+LYS CB HB1 SING N N 10
+LYS CB HB2 SING N N 11
+LYS CG HG1 SING N N 12
+LYS CG HG2 SING N N 13
+LYS CD HD1 SING N N 14
+LYS CD HD2 SING N N 15
+LYS CE HE1 SING N N 16
+LYS CE HE2 SING N N 17
+LYS O C SING N N 18
+LYS NZ HZ1 SING N N 19
+LYS NZ HZ2 SING N N 20
+LYS NZ HZ3 SING N N 21
+LYS OT1 C SING N N 22
+LYS OT2 C SING N N 23
+LYS HT1 NH SING N N 24
+LYS HT2 NH SING N N 25
+LYS HT3 NH SING N N 26
+data_LSN
+_chem_comp.id                                    LSN 
+_chem_comp.type                                  "L-PEPTIDE-LINKING" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "C6 H15 N2 O3" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       L
+_chem_comp.three_letter_code                     LSN 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+LSN N N N 0 N N N N LSN 1
+LSN CA CA C 0 N N N CA LSN 2
+LSN C C C 0 N N N C LSN 3
+LSN O O O 0 N Y N O LSN 4
+LSN CB CB C 0 N N N CB LSN 5
+LSN CG CG C 0 N N N CG LSN 6
+LSN CD CD C 0 N N N CD LSN 7
+LSN CE CE C 0 N N N CE LSN 8
+LSN NZ NZ N 0 N N N NZ LSN 9
+LSN HA HA H 0 N N N HA LSN 10
+LSN HB1 HB1 H 0 N N N HB1 LSN 11
+LSN HB2 HB2 H 0 N N N HB2 LSN 12
+LSN HG1 HG1 H 0 N N N HG1 LSN 13
+LSN HG2 HG2 H 0 N N N HG2 LSN 14
+LSN HD1 HD1 H 0 N N N HD1 LSN 15
+LSN HD2 HD2 H 0 N N N HD2 LSN 16
+LSN HE1 HE1 H 0 N N N HE1 LSN 17
+LSN HE2 HE2 H 0 N N N HE2 LSN 18
+LSN HZ1 HZ1 H 0 N N N HZ1 LSN 19
+LSN HZ2 HZ2 H 0 N N N HZ2 LSN 20
+LSN HN HN H 0 N N N HN LSN 21
+LSN OT1 OT1 O 0 N Y N OT1 LSN 22
+LSN OT2 OT2 O 0 N Y N OT2 LSN 23
+LSN HT1 HT1 H 0 N N N HT1 LSN 24
+LSN HT2 HT2 H 0 N N N HT2 LSN 25
+LSN HT3 HT3 H 0 N N N HT3 LSN 26
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+LSN CB CA SING N N 1
+LSN CG CB SING N N 2
+LSN CD CG SING N N 3
+LSN CE CD SING N N 4
+LSN NZ CE SING N N 5
+LSN N HN SING N N 6
+LSN N CA SING N N 7
+LSN C CA SING N N 8
+LSN CA HA SING N N 9
+LSN CB HB1 SING N N 10
+LSN CB HB2 SING N N 11
+LSN CG HG1 SING N N 12
+LSN CG HG2 SING N N 13
+LSN CD HD1 SING N N 14
+LSN CD HD2 SING N N 15
+LSN CE HE1 SING N N 16
+LSN CE HE2 SING N N 17
+LSN O C SING N N 18
+LSN NZ HZ1 SING N N 19
+LSN NZ HZ2 SING N N 20
+LSN OT1 C SING N N 21
+LSN OT2 C SING N N 22
+LSN HT1 NH SING N N 23
+LSN HT2 NH SING N N 24
+LSN HT3 NH SING N N 25
+data_MET
+_chem_comp.id                                    MET 
+_chem_comp.type                                  "L-PEPTIDE-LINKING" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "C5 H12 N O3 S" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       M
+_chem_comp.three_letter_code                     MET 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+MET N N N 0 N N N N MET 1
+MET CA CA C 0 N N N CA MET 2
+MET C C C 0 N N N C MET 3
+MET O O O 0 N Y N O MET 4
+MET CB CB C 0 N N N CB MET 5
+MET CG CG C 0 N N N CG MET 6
+MET SD SD S 0 N N N SD MET 7
+MET CE CE C 0 N N N CE MET 8
+MET HA HA H 0 N N N HA MET 9
+MET HB1 HB1 H 0 N N N HB1 MET 10
+MET HB2 HB2 H 0 N N N HB2 MET 11
+MET HG1 HG1 H 0 N N N HG1 MET 12
+MET HG2 HG2 H 0 N N N HG2 MET 13
+MET HE1 HE1 H 0 N N N HE1 MET 14
+MET HE2 HE2 H 0 N N N HE2 MET 15
+MET HE3 HE3 H 0 N N N HE3 MET 16
+MET HN HN H 0 N N N HN MET 17
+MET OT1 OT1 O 0 N Y N OT1 MET 18
+MET OT2 OT2 O 0 N Y N OT2 MET 19
+MET HT1 HT1 H 0 N N N HT1 MET 20
+MET HT2 HT2 H 0 N N N HT2 MET 21
+MET HT3 HT3 H 0 N N N HT3 MET 22
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+MET CB CA SING N N 1
+MET CG CB SING N N 2
+MET SD CG SING N N 3
+MET CE SD SING N N 4
+MET N HN SING N N 5
+MET N CA SING N N 6
+MET C CA SING N N 7
+MET CA HA SING N N 8
+MET CB HB1 SING N N 9
+MET CB HB2 SING N N 10
+MET CG HG1 SING N N 11
+MET CG HG2 SING N N 12
+MET CE HE1 SING N N 13
+MET CE HE2 SING N N 14
+MET CE HE3 SING N N 15
+MET O C SING N N 16
+MET OT1 C SING N N 17
+MET OT2 C SING N N 18
+MET HT1 NH SING N N 19
+MET HT2 NH SING N N 20
+MET HT3 NH SING N N 21
+data_PHE
+_chem_comp.id                                    PHE 
+_chem_comp.type                                  "L-PEPTIDE-LINKING" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "C9 H12 N O3" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       F
+_chem_comp.three_letter_code                     PHE 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+PHE N N N 0 N N N N PHE 1
+PHE CA CA C 0 N N N CA PHE 2
+PHE C C C 0 N N N C PHE 3
+PHE O O O 0 N Y N O PHE 4
+PHE CB CB C 0 N N N CB PHE 5
+PHE CG CG C 0 N N N CG PHE 6
+PHE CD1 CD1 C 0 N N N CD1 PHE 7
+PHE CE1 CE1 C 0 N N N CE1 PHE 8
+PHE CZ CZ C 0 N N N CZ PHE 9
+PHE CD2 CD2 C 0 N N N CD2 PHE 10
+PHE CE2 CE2 C 0 N N N CE2 PHE 11
+PHE HA HA H 0 N N N HA PHE 12
+PHE HB1 HB1 H 0 N N N HB1 PHE 13
+PHE HB2 HB2 H 0 N N N HB2 PHE 14
+PHE HD1 HD1 H 0 N N N HD1 PHE 15
+PHE HE1 HE1 H 0 N N N HE1 PHE 16
+PHE HZ HZ H 0 N N N HZ PHE 17
+PHE HD2 HD2 H 0 N N N HD2 PHE 18
+PHE HE2 HE2 H 0 N N N HE2 PHE 19
+PHE HN HN H 0 N N N HN PHE 20
+PHE OT1 OT1 O 0 N Y N OT1 PHE 21
+PHE OT2 OT2 O 0 N Y N OT2 PHE 22
+PHE HT1 HT1 H 0 N N N HT1 PHE 23
+PHE HT2 HT2 H 0 N N N HT2 PHE 24
+PHE HT3 HT3 H 0 N N N HT3 PHE 25
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+PHE CB CA SING N N 1
+PHE CG CB SING N N 2
+PHE CD2 CG SING N N 3
+PHE CE1 CD1 SING N N 4
+PHE CZ CE2 SING N N 5
+PHE N HN SING N N 6
+PHE N CA SING N N 7
+PHE C CA SING N N 8
+PHE CA HA SING N N 9
+PHE CB HB1 SING N N 10
+PHE CB HB2 SING N N 11
+PHE CD1 HD1 SING N N 12
+PHE CD2 HD2 SING N N 13
+PHE CE1 HE1 SING N N 14
+PHE O C SING N N 15
+PHE CD1 CG SING N N 16
+PHE CZ CE1 SING N N 17
+PHE CE2 CD2 SING N N 18
+PHE CE2 HE2 SING N N 19
+PHE CZ HZ SING N N 20
+PHE OT1 C SING N N 21
+PHE OT2 C SING N N 22
+PHE HT1 NH SING N N 23
+PHE HT2 NH SING N N 24
+PHE HT3 NH SING N N 25
+data_PRO
+_chem_comp.id                                    PRO 
+_chem_comp.type                                  "L-PEPTIDE-LINKING" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "C5 H10 N O3" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       P
+_chem_comp.three_letter_code                     PRO 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+PRO N N N 0 N N N N PRO 1
+PRO CD CD C 0 N N N CD PRO 2
+PRO CA CA C 0 N N N CA PRO 3
+PRO C C C 0 N N N C PRO 4
+PRO O O O 0 N Y N O PRO 5
+PRO CB CB C 0 N N N CB PRO 6
+PRO CG CG C 0 N N N CG PRO 7
+PRO HA HA H 0 N N N HA PRO 8
+PRO HB1 HB1 H 0 N N N HB1 PRO 9
+PRO HB2 HB2 H 0 N N N HB2 PRO 10
+PRO HG1 HG1 H 0 N N N HG1 PRO 11
+PRO HG2 HG2 H 0 N N N HG2 PRO 12
+PRO HD1 HD1 H 0 N N N HD1 PRO 13
+PRO HD2 HD2 H 0 N N N HD2 PRO 14
+PRO OT1 OT1 O 0 N Y N OT1 PRO 15
+PRO OT2 OT2 O 0 N Y N OT2 PRO 16
+PRO HT1 HT1 H 0 N N N HT1 PRO 17
+PRO HT2 HT2 H 0 N N N HT2 PRO 18
+PRO HT3 HT3 H 0 N N N HT3 PRO 19
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+PRO C CA SING N N 1
+PRO N CA SING N N 2
+PRO CA CB SING N N 3
+PRO CB CG SING N N 4
+PRO CG CD SING N N 5
+PRO N CD SING N N 6
+PRO HA CA SING N N 7
+PRO HG1 CG SING N N 8
+PRO HG2 CG SING N N 9
+PRO HD1 CD SING N N 10
+PRO HD2 CD SING N N 11
+PRO HB1 CB SING N N 12
+PRO HB2 CB SING N N 13
+PRO O C SING N N 14
+PRO OT1 C SING N N 15
+PRO OT2 C SING N N 16
+PRO HT1 NH SING N N 17
+PRO HT2 NH SING N N 18
+PRO HT3 NH SING N N 19
+data_SER
+_chem_comp.id                                    SER 
+_chem_comp.type                                  "L-PEPTIDE-LINKING" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "C3 H8 N O4" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       S
+_chem_comp.three_letter_code                     SER 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+SER N N N 0 N N N N SER 1
+SER CA CA C 0 N N N CA SER 2
+SER C C C 0 N N N C SER 3
+SER O O O 0 N Y N O SER 4
+SER CB CB C 0 N N N CB SER 5
+SER OG OG O 0 N N N OG SER 6
+SER HA HA H 0 N N N HA SER 7
+SER HB1 HB1 H 0 N N N HB1 SER 8
+SER HB2 HB2 H 0 N N N HB2 SER 9
+SER HG1 HG1 H 0 N N N HG1 SER 10
+SER HN HN H 0 N N N HN SER 11
+SER OT1 OT1 O 0 N Y N OT1 SER 12
+SER OT2 OT2 O 0 N Y N OT2 SER 13
+SER HT1 HT1 H 0 N N N HT1 SER 14
+SER HT2 HT2 H 0 N N N HT2 SER 15
+SER HT3 HT3 H 0 N N N HT3 SER 16
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+SER CB CA SING N N 1
+SER OG CB SING N N 2
+SER N HN SING N N 3
+SER N CA SING N N 4
+SER C CA SING N N 5
+SER CA HA SING N N 6
+SER CB HB1 SING N N 7
+SER CB HB2 SING N N 8
+SER OG HG1 SING N N 9
+SER O C SING N N 10
+SER OT1 C SING N N 11
+SER OT2 C SING N N 12
+SER HT1 NH SING N N 13
+SER HT2 NH SING N N 14
+SER HT3 NH SING N N 15
+data_THR
+_chem_comp.id                                    THR 
+_chem_comp.type                                  "L-PEPTIDE-LINKING" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "C4 H10 N O4" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       T
+_chem_comp.three_letter_code                     THR 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+THR N N N 0 N N N N THR 1
+THR CA CA C 0 N N N CA THR 2
+THR C C C 0 N N N C THR 3
+THR O O O 0 N Y N O THR 4
+THR CB CB C 0 N N N CB THR 5
+THR OG1 OG1 O 0 N N N OG1 THR 6
+THR CG2 CG2 C 0 N N N CG2 THR 7
+THR HA HA H 0 N N N HA THR 8
+THR HB HB H 0 N N N HB THR 9
+THR HG1 HG1 H 0 N N N HG1 THR 10
+THR HG21 HG21 H 0 N N N HG21 THR 11
+THR HG22 HG22 H 0 N N N HG22 THR 12
+THR HG23 HG23 H 0 N N N HG23 THR 13
+THR HN HN H 0 N N N HN THR 14
+THR OT1 OT1 O 0 N Y N OT1 THR 15
+THR OT2 OT2 O 0 N Y N OT2 THR 16
+THR HT1 HT1 H 0 N N N HT1 THR 17
+THR HT2 HT2 H 0 N N N HT2 THR 18
+THR HT3 HT3 H 0 N N N HT3 THR 19
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+THR CB CA SING N N 1
+THR OG1 CB SING N N 2
+THR CG2 CB SING N N 3
+THR N HN SING N N 4
+THR N CA SING N N 5
+THR C CA SING N N 6
+THR CA HA SING N N 7
+THR CB HB SING N N 8
+THR OG1 HG1 SING N N 9
+THR CG2 HG21 SING N N 10
+THR CG2 HG22 SING N N 11
+THR CG2 HG23 SING N N 12
+THR O C SING N N 13
+THR OT1 C SING N N 14
+THR OT2 C SING N N 15
+THR HT1 NH SING N N 16
+THR HT2 NH SING N N 17
+THR HT3 NH SING N N 18
+data_TRP
+_chem_comp.id                                    TRP 
+_chem_comp.type                                  "L-PEPTIDE-LINKING" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "C11 H13 N2 O3" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       W
+_chem_comp.three_letter_code                     TRP 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+TRP N N N 0 N N N N TRP 1
+TRP CA CA C 0 N N N CA TRP 2
+TRP C C C 0 N N N C TRP 3
+TRP O O O 0 N Y N O TRP 4
+TRP HA HA H 0 N N N HA TRP 5
+TRP CB CB C 0 N N N CB TRP 6
+TRP CG CG C 0 N N N CG TRP 7
+TRP CD1 CD1 C 0 N N N CD1 TRP 8
+TRP NE1 NE1 N 0 N N N NE1 TRP 9
+TRP CE2 CE2 C 0 N N N CE2 TRP 10
+TRP CD2 CD2 C 0 N N N CD2 TRP 11
+TRP CE3 CE3 C 0 N N N CE3 TRP 12
+TRP CZ3 CZ3 C 0 N N N CZ3 TRP 13
+TRP CZ2 CZ2 C 0 N N N CZ2 TRP 14
+TRP CH2 CH2 C 0 N N N CH2 TRP 15
+TRP HB1 HB1 H 0 N N N HB1 TRP 16
+TRP HB2 HB2 H 0 N N N HB2 TRP 17
+TRP HD1 HD1 H 0 N N N HD1 TRP 18
+TRP HE1 HE1 H 0 N N N HE1 TRP 19
+TRP HE3 HE3 H 0 N N N HE3 TRP 20
+TRP HZ3 HZ3 H 0 N N N HZ3 TRP 21
+TRP HZ2 HZ2 H 0 N N N HZ2 TRP 22
+TRP HH2 HH2 H 0 N N N HH2 TRP 23
+TRP HN HN H 0 N N N HN TRP 24
+TRP OT1 OT1 O 0 N Y N OT1 TRP 25
+TRP OT2 OT2 O 0 N Y N OT2 TRP 26
+TRP HT1 HT1 H 0 N N N HT1 TRP 27
+TRP HT2 HT2 H 0 N N N HT2 TRP 28
+TRP HT3 HT3 H 0 N N N HT3 TRP 29
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+TRP CB CA SING N N 1
+TRP CG CB SING N N 2
+TRP CD2 CG SING N N 3
+TRP NE1 CD1 SING N N 4
+TRP CZ2 CE2 SING N N 5
+TRP N HN SING N N 6
+TRP N CA SING N N 7
+TRP C CA SING N N 8
+TRP CZ3 CH2 SING N N 9
+TRP CD2 CE3 SING N N 10
+TRP NE1 CE2 SING N N 11
+TRP CA HA SING N N 12
+TRP CB HB1 SING N N 13
+TRP CB HB2 SING N N 14
+TRP CD1 HD1 SING N N 15
+TRP NE1 HE1 SING N N 16
+TRP CE3 HE3 SING N N 17
+TRP CZ2 HZ2 SING N N 18
+TRP CZ3 HZ3 SING N N 19
+TRP CH2 HH2 SING N N 20
+TRP O C SING N N 21
+TRP CD1 CG SING N N 22
+TRP CE2 CD2 SING N N 23
+TRP CZ3 CE3 SING N N 24
+TRP CH2 CZ2 SING N N 25
+TRP OT1 C SING N N 26
+TRP OT2 C SING N N 27
+TRP HT1 NH SING N N 28
+TRP HT2 NH SING N N 29
+TRP HT3 NH SING N N 30
+data_TYR
+_chem_comp.id                                    TYR 
+_chem_comp.type                                  "L-PEPTIDE-LINKING" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "C9 H12 N O4" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       Y
+_chem_comp.three_letter_code                     TYR 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+TYR N N N 0 N N N N TYR 1
+TYR CA CA C 0 N N N CA TYR 2
+TYR C C C 0 N N N C TYR 3
+TYR O O O 0 N Y N O TYR 4
+TYR HA HA H 0 N N N HA TYR 5
+TYR CB CB C 0 N N N CB TYR 6
+TYR CG CG C 0 N N N CG TYR 7
+TYR CD1 CD1 C 0 N N N CD1 TYR 8
+TYR CE1 CE1 C 0 N N N CE1 TYR 9
+TYR CZ CZ C 0 N N N CZ TYR 10
+TYR OH OH O 0 N N N OH TYR 11
+TYR CD2 CD2 C 0 N N N CD2 TYR 12
+TYR CE2 CE2 C 0 N N N CE2 TYR 13
+TYR HB1 HB1 H 0 N N N HB1 TYR 14
+TYR HB2 HB2 H 0 N N N HB2 TYR 15
+TYR HD1 HD1 H 0 N N N HD1 TYR 16
+TYR HE1 HE1 H 0 N N N HE1 TYR 17
+TYR HH HH H 0 N N N HH TYR 18
+TYR HD2 HD2 H 0 N N N HD2 TYR 19
+TYR HE2 HE2 H 0 N N N HE2 TYR 20
+TYR HN HN H 0 N N N HN TYR 21
+TYR OT1 OT1 O 0 N Y N OT1 TYR 22
+TYR OT2 OT2 O 0 N Y N OT2 TYR 23
+TYR HT1 HT1 H 0 N N N HT1 TYR 24
+TYR HT2 HT2 H 0 N N N HT2 TYR 25
+TYR HT3 HT3 H 0 N N N HT3 TYR 26
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+TYR CB CA SING N N 1
+TYR CG CB SING N N 2
+TYR CD2 CG SING N N 3
+TYR CE1 CD1 SING N N 4
+TYR CZ CE2 SING N N 5
+TYR OH CZ SING N N 6
+TYR N HN SING N N 7
+TYR N CA SING N N 8
+TYR C CA SING N N 9
+TYR CA HA SING N N 10
+TYR CB HB1 SING N N 11
+TYR CB HB2 SING N N 12
+TYR CD1 HD1 SING N N 13
+TYR CD2 HD2 SING N N 14
+TYR CE1 HE1 SING N N 15
+TYR CE2 HE2 SING N N 16
+TYR OH HH SING N N 17
+TYR O C SING N N 18
+TYR CD1 CG SING N N 19
+TYR CE1 CZ SING N N 20
+TYR CE2 CD2 SING N N 21
+TYR OT1 C SING N N 22
+TYR OT2 C SING N N 23
+TYR HT1 NH SING N N 24
+TYR HT2 NH SING N N 25
+TYR HT3 NH SING N N 26
+TYR HT1 NH SING N N 27
+TYR HT2 NH SING N N 28
+TYR HT3 NH SING N N 29
+data_VAL
+_chem_comp.id                                    VAL 
+_chem_comp.type                                  "L-PEPTIDE-LINKING" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "C5 H12 N O3" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       V
+_chem_comp.three_letter_code                     VAL 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+VAL N N N 0 N N N N VAL 1
+VAL CA CA C 0 N N N CA VAL 2
+VAL C C C 0 N N N C VAL 3
+VAL O O O 0 N Y N O VAL 4
+VAL CB CB C 0 N N N CB VAL 5
+VAL CG1 CG1 C 0 N N N CG1 VAL 6
+VAL CG2 CG2 C 0 N N N CG2 VAL 7
+VAL HN HN H 0 N N N HN VAL 8
+VAL HA HA H 0 N N N HA VAL 9
+VAL HB HB H 0 N N N HB VAL 10
+VAL HG11 HG11 H 0 N N N HG11 VAL 11
+VAL HG12 HG12 H 0 N N N HG12 VAL 12
+VAL HG13 HG13 H 0 N N N HG13 VAL 13
+VAL HG21 HG21 H 0 N N N HG21 VAL 14
+VAL HG22 HG22 H 0 N N N HG22 VAL 15
+VAL HG23 HG23 H 0 N N N HG23 VAL 16
+VAL OT1 OT1 O 0 N Y N OT1 VAL 17
+VAL OT2 OT2 O 0 N Y N OT2 VAL 18
+VAL HT1 HT1 H 0 N N N HT1 VAL 19
+VAL HT2 HT2 H 0 N N N HT2 VAL 20
+VAL HT3 HT3 H 0 N N N HT3 VAL 21
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+VAL CB CA SING N N 1
+VAL CG1 CB SING N N 2
+VAL CG2 CB SING N N 3
+VAL N HN SING N N 4
+VAL N CA SING N N 5
+VAL C CA SING N N 6
+VAL CA HA SING N N 7
+VAL CB HB SING N N 8
+VAL CG1 HG11 SING N N 9
+VAL CG1 HG12 SING N N 10
+VAL CG1 HG13 SING N N 11
+VAL CG2 HG21 SING N N 12
+VAL CG2 HG22 SING N N 13
+VAL CG2 HG23 SING N N 14
+VAL O C SING N N 15
+VAL OT1 C SING N N 16
+VAL OT2 C SING N N 17
+VAL HT1 NH SING N N 18
+VAL HT2 NH SING N N 19
+VAL HT3 NH SING N N 20
+
+
+data_HOH
+_chem_comp.id                                    HOH 
+_chem_comp.type                                  "NON-POLYMER" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "H2 O" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       .
+_chem_comp.three_letter_code                     HOH 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+HOH OW OW O 0 N N N OW HOH 1
+HOH HW1 HW1 H 0 N N N HW1 HOH 2
+HOH HW2 HW2 H 0 N N N HW2 HOH 3
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+HOH OW HW1 SING N N 1
+HOH OW HW2 SING N N 2
+HOH HW1 HW2 SING N N 3
+data_TIP3
+_chem_comp.id                                    TIP3 
+_chem_comp.type                                  "NON-POLYMER" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "H2 O" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       .
+_chem_comp.three_letter_code                     TIP3 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+TIP3 OH2 OH2 O 0 N N N OH2 TIP3 1
+TIP3 H1 H1 H 0 N N N H1 TIP3 2
+TIP3 H2 H2 H 0 N N N H2 TIP3 3
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+TIP3 OH2 H1 SING N N 1
+TIP3 OH2 H2 SING N N 2
+TIP3 H1 H2 SING N N 3
+data_TP3M
+_chem_comp.id                                    TP3M 
+_chem_comp.type                                  "NON-POLYMER" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "H2 O" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       .
+_chem_comp.three_letter_code                     TP3M 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+TP3M OH2 OH2 O 0 N N N OH2 TP3M 1
+TP3M H1 H1 H 0 N N N H1 TP3M 2
+TP3M H2 H2 H 0 N N N H2 TP3M 3
+#
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal
+TP3M OH2 H1 SING N N 1
+TP3M OH2 H2 SING N N 2
+data_SOD
+_chem_comp.id                                    SOD 
+_chem_comp.type                                  "NON-POLYMER" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "NA" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       ?
+_chem_comp.three_letter_code                     SOD 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+SOD SOD SOD NA 0 N N N SOD SOD 1
+data_MG
+_chem_comp.id                                    MG 
+_chem_comp.type                                  "NON-POLYMER" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "MG" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       ?
+_chem_comp.three_letter_code                     MG 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+MG MG MG MG 0 N N N MG MG 1
+data_POT
+_chem_comp.id                                    POT 
+_chem_comp.type                                  "NON-POLYMER" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "K" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       ?
+_chem_comp.three_letter_code                     POT 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+POT POT POT K 0 N N N POT POT 1
+data_CAL
+_chem_comp.id                                    CAL 
+_chem_comp.type                                  "NON-POLYMER" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "CA" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       ?
+_chem_comp.three_letter_code                     CAL 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+CAL CAL CAL CA 0 N N N CAL CAL 1
+data_CLA
+_chem_comp.id                                    CLA 
+_chem_comp.type                                  "NON-POLYMER" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "CA" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       ?
+_chem_comp.three_letter_code                     CLA 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+CLA CLA CLA CL 0 N N N CLA CLA 1
+data_ZN2
+_chem_comp.id                                    ZN2 
+_chem_comp.type                                  "NON-POLYMER" 
+_chem_comp.pdbx_type                             ATOMP 
+_chem_comp.formula                               "ZN" 
+_chem_comp.mon_nstd_parent_comp_id               ?
+_chem_comp.pdbx_initial_date                     2010-09-20 
+_chem_comp.pdbx_modified_date                    2010-09-20 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.one_letter_code                       ?
+_chem_comp.three_letter_code                     ZN2 
+#
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal  
+ZN2 ZN ZN ZN 0 N N N ZN ZN2 1
diff --git a/modules/conop/doc/conop.rst b/modules/conop/doc/conop.rst
index fb65ee1ad4e33a27ecf0ba0b9e50851531b8be72..6e8443558c8345033692c55e3d84c302d200b93d 100644
--- a/modules/conop/doc/conop.rst
+++ b/modules/conop/doc/conop.rst
@@ -1,7 +1,7 @@
-:mod:`conop` -- Connectivity and Topology of Molecules
+:mod:`~ost.conop` -- Connectivity and Topology of Molecules
 ================================================================================
 
-.. module:: conop
+.. module:: ost.conop
    :synopsis: The conop modules implement different strategies to derive
                connectivity information of molecules.
 
@@ -63,7 +63,7 @@ be achieved with
   conop.Conopology.Instance().RegisterBuilder(rbb,'rbb')
   conop.Conopology.Instance().SetDefaultBuilder('rbb')
 
-All subsequent calls to :func:`io.LoadEntity` will make use of the
+All subsequent calls to :func:`ost.io.LoadEntity` will make use of the
 RuleBasedBuilder  instead of the heuristic builder. See 
 :ref:`here <mmcif-convert>` for more  information on how to create the necessary 
 files to use the rule-based builder.
@@ -225,18 +225,20 @@ files to use the rule-based builder.
 Connecting atoms
 --------------------------------------------------------------------------------
 
-The high level interface is exposed by the Conopoloy singleton instance:
+A single function call to :func:`ConnectAll` is sufficient to assign residue and atoms properties as well as to connect atoms with bonds.
+
 
 .. code-block:: python
-  
-  import conop
-  
-  cc=conop.Conopology.Instance()
-  
+
+  # Suppose that BuildRawModel is a function that returns a protein structure
+  # with no atom properties assigned and no bonds formed.
   ent=BuildRawModel(...)
-  cc.ConnectAll(cc.GetBuilder(), ent)
+  print ent.bonds  # will return an empty list
+  # Call ConnectAll() to assign properties/connect atoms
+  conop.ConnectAll(ent)
+  print ent.bonds  # will print a list containing many bonds
 
-For fine grained control, the builder interface may be used directly.
+For fine grained control, the :class:`Builder` interface may be used directly.
 
 
 .. _mmcif-convert:
diff --git a/modules/conop/pymod/CMakeLists.txt b/modules/conop/pymod/CMakeLists.txt
index 9d38418097bcc8df02ffb148e96ffc9659483bb5..57eeb82c986e9b2220fa1e1c188b65d07ca6886b 100644
--- a/modules/conop/pymod/CMakeLists.txt
+++ b/modules/conop/pymod/CMakeLists.txt
@@ -2,7 +2,6 @@ set(OST_CONOP_PYMOD_SOURCES
   wrap_conop.cc
   export_builder.cc
   export_compound.cc
-  export_sanitizer.cc
   export_conop.cc
   export_ring_finder.cc
 )
diff --git a/modules/conop/pymod/export_builder.cc b/modules/conop/pymod/export_builder.cc
index 1e070a04e88b3abe64fd57caf856ea1496850d45..9e23e05698fa91f3d5568e46e5885fb4879c4f70 100644
--- a/modules/conop/pymod/export_builder.cc
+++ b/modules/conop/pymod/export_builder.cc
@@ -25,8 +25,19 @@ using namespace boost::python;
 using namespace ost::conop;
 
 void export_Builder() {
+  
+  enum_<Dialect>("Dialect")
+    .value("PDB_DIALECT", PDB_DIALECT)
+    .value("CHARMM_DIALECT", CHARMM_DIALECT)
+    .export_values()
+  ;
   //TODO Export virtual calls as Default* (see export_visitor.cc)
   class_<Builder>("Builder", no_init)
+    .add_property("dialect", &Builder::GetDialect, &Builder::SetDialect)
+    .add_property("strict_hydrogens", &Builder::GetStrictHydrogenMode, 
+                  &Builder::SetStrictHydrogenMode)
+    .def("GetDialect", &Builder::GetDialect)
+    .def("SetDialect", &Builder::SetDialect)
     .def("CompleteAtoms", &Builder::CompleteAtoms)
     .def("CheckResidueCompleteness", &Builder::CheckResidueCompleteness)
     .def("IdentifyResidue", &Builder::IdentifyResidue)
diff --git a/modules/conop/pymod/export_sanitizer.cc b/modules/conop/pymod/export_sanitizer.cc
deleted file mode 100644
index 3ed3810c5176de7a83c4e9b8d11aec79c247a741..0000000000000000000000000000000000000000
--- a/modules/conop/pymod/export_sanitizer.cc
+++ /dev/null
@@ -1,61 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#include <boost/python.hpp>
-#include <boost/python/register_ptr_to_python.hpp>
-#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
-using namespace boost::python;
-#include <ost/conop/sanitizer.hh>
-using namespace ost;
-using namespace ost::conop;
-
-namespace {
-struct WrappedSanitizer : Sanitizer
-{
-    WrappedSanitizer(PyObject *p)
-        : Sanitizer(CompoundLibPtr()), self(p) {
-    }
-
-    WrappedSanitizer(PyObject *p, const Sanitizer& s)
-        : Sanitizer(s), self(p) {}
-
-    virtual void OnUnknownAtom(const mol::AtomHandle& atom) {
-      call_method<void, mol::AtomHandle>(self, "OnUnknownAtom", atom);
-    }
-    void OnUnknownAtomDefault(const mol::AtomHandle& atom) {
-    }
-    virtual void OnMissingAtom(const mol::ResidueHandle& residue,
-                               const String& atom) {
-      call_method<void, mol::ResidueHandle, String>(self, "OnMissingAtom",
-                                               residue, atom);
-    }
-    void OnMissingAtomDefault(const mol::ResidueHandle& residue,
-                              const String& atom) {
-    }
- private:
-    PyObject* self;
-};
-
-}
-
-void export_Sanitizer() {
-  class_<Sanitizer, WrappedSanitizer, bases<mol::EntityVisitor>,boost::noncopyable >("Sanitizer", init<CompoundLibPtr>())
-    .def("OnUnknownAtom", &WrappedSanitizer::OnUnknownAtomDefault)
-    .def("OnMissingAtom", &WrappedSanitizer::OnMissingAtomDefault)
-  ;
-}
diff --git a/modules/conop/pymod/wrap_conop.cc b/modules/conop/pymod/wrap_conop.cc
index cb7915c94b004355131618118a9b049b77e40817..a7bcd1cb074f543ebfeee81969c3544017003511 100644
--- a/modules/conop/pymod/wrap_conop.cc
+++ b/modules/conop/pymod/wrap_conop.cc
@@ -29,6 +29,5 @@ BOOST_PYTHON_MODULE(_conop)
   export_Builder();
   export_Conop();
   export_Compound();
-  export_Sanitizer();
   export_RingFinder();
 }
diff --git a/modules/conop/src/CMakeLists.txt b/modules/conop/src/CMakeLists.txt
index fbf0a48be9b3aa69946da25925ad0f702af9f533..4d0840ea34d18bbe4f983c24f17d8ad8603769fd 100644
--- a/modules/conop/src/CMakeLists.txt
+++ b/modules/conop/src/CMakeLists.txt
@@ -4,7 +4,6 @@ builder_fw.hh
 conop.hh
 heuristic_builder.hh
 compound.hh
-sanitizer.hh
 compound_lib.hh
 module_config.hh
 rule_based_builder.hh
@@ -16,7 +15,6 @@ builder.cc
 conop.cc
 heuristic_builder.cc
 compound.cc
-sanitizer.cc
 compound_lib.cc
 rule_based_builder.cc
 ring_finder.cc
diff --git a/modules/conop/src/builder.cc b/modules/conop/src/builder.cc
index 14c103e55d29f8a69758663b38cefb99b498c06f..b53a146445c70fae93d0dc98d8b70af3a56b43b2 100644
--- a/modules/conop/src/builder.cc
+++ b/modules/conop/src/builder.cc
@@ -26,7 +26,7 @@ namespace ost { namespace conop {
 
 Builder::~Builder() {}
 
-void Builder::CompleteAtoms(const mol::ResidueHandle& rh) {}
+void Builder::CompleteAtoms(mol::ResidueHandle rh) {}
 
 void Builder::CheckResidueCompleteness(const mol::ResidueHandle& rh) {}
 
@@ -34,10 +34,10 @@ mol::ResidueKey Builder::IdentifyResidue(const mol::ResidueHandle& rh) {
   return mol::ResidueKey();
 }
 void Builder::FillResidueProps(mol::ResidueHandle residue){};
-void Builder::ConnectAtomsOfResidue(const mol::ResidueHandle& rh) {}
+void Builder::ConnectAtomsOfResidue(mol::ResidueHandle rh) {}
 
-void Builder::ConnectResidueToPrev(const mol::ResidueHandle& rh, 
-                                   const mol::ResidueHandle& p) {
+void Builder::ConnectResidueToPrev(mol::ResidueHandle rh, 
+                                   mol::ResidueHandle p) {
   this->ConnectResidueToNext(p, rh);
 }
 
@@ -46,11 +46,11 @@ bool Builder::IsResidueComplete(const mol::ResidueHandle& rh)
   return true;
 }
 
-void Builder::ConnectResidueToNext(const mol::ResidueHandle& rh, 
-                                   const mol::ResidueHandle& n) {}
+void Builder::ConnectResidueToNext(mol::ResidueHandle rh, 
+                                   mol::ResidueHandle n) {}
 
-void Builder::AssignTorsions(const mol::ChainHandle& ch) {}
-void Builder::AssignTorsionsToResidue(const mol::ResidueHandle& rh) {}
+void Builder::AssignTorsions(mol::ChainHandle ch) {}
+void Builder::AssignTorsionsToResidue(mol::ResidueHandle rh) {}
 
 void Builder::FillAtomProps(mol::AtomHandle atom) {}
 
@@ -159,7 +159,7 @@ bool Builder::AreResiduesConsecutive(const mol::ResidueHandle& r1,
          r2.GetNumber().GetInsCode()==r1.GetNumber().NextInsertionCode().GetInsCode();
 }
 
-void Builder::AssignBackBoneTorsionsToResidue(const mol::ResidueHandle& res)
+void Builder::AssignBackBoneTorsionsToResidue(mol::ResidueHandle res)
 {
 
   mol::ResidueHandle prev=res.GetPrev();
@@ -202,7 +202,7 @@ void Builder::AssignBackBoneTorsionsToResidue(const mol::ResidueHandle& res)
 
 
 
-void Builder::DistanceBasedConnect(const mol::AtomHandle& atom)
+void Builder::DistanceBasedConnect(mol::AtomHandle atom)
 {
   mol::EntityHandle ent=atom.GetEntity();
   mol::XCSEditor editor=ent.RequestXCSEditor(mol::BUFFERED_EDIT);
diff --git a/modules/conop/src/builder.hh b/modules/conop/src/builder.hh
index b47e432ac1b2b0dafef45f9052d0c81eea753dd4..5312d80e9e455293b16d6568a8d66971934b8718 100644
--- a/modules/conop/src/builder.hh
+++ b/modules/conop/src/builder.hh
@@ -29,6 +29,10 @@
 
 namespace ost { namespace conop {
 
+typedef enum {
+  PDB_DIALECT,
+  CHARMM_DIALECT
+} Dialect;
 /// \brief  abstract builder interface
 /// 
 /// A builder serves several purposes: \li knows how to connect atoms of
@@ -49,14 +53,20 @@ namespace ost { namespace conop {
 ///  behaviour.
 class DLLEXPORT_OST_CONOP Builder {
 public:
-public:
+  
+  Builder(): dialect_(PDB_DIALECT), strict_(false) { }
   virtual ~Builder();
   
   ///  \brief add any missing atoms to the residue based on its key,
   ///      with coordinates set to zero
-  virtual void CompleteAtoms(const mol::ResidueHandle& rh);
-
+  virtual void CompleteAtoms(mol::ResidueHandle rh);
 
+  virtual void SetDialect(Dialect dialect) { dialect_=dialect; }
+  
+  virtual void SetStrictHydrogenMode(bool strict) { strict_=strict; }
+  bool GetStrictHydrogenMode() const { return strict_; }
+  
+  Dialect GetDialect() const { return dialect_; }
   /// \brief verify that the given residue has all atoms it
   ///     is supposed to have based on its key
   virtual void CheckResidueCompleteness(const mol::ResidueHandle& rh);
@@ -80,27 +90,27 @@ public:
   /// Connects atoms of residue based on residue and atom name. This method does
   /// not establish inter-residue bonds. To connect atoms that belong to 
   /// different residues, use ConnectResidueToPrev(), or ConnectResidueToNext().
-  virtual void ConnectAtomsOfResidue(const mol::ResidueHandle& rh);
+  virtual void ConnectAtomsOfResidue(mol::ResidueHandle rh);
   /// \brief connect atoms of residue to previous
   /// 
   /// The order of the parameters is important. In case of a polypeptide chain,
   /// the residues are thought to be ordered from N- to C- terminus.
   /// 
   /// \sa ConnectResidueToNext
-  virtual void ConnectResidueToPrev(const mol::ResidueHandle& rh,
-                                    const mol::ResidueHandle& prev);
+  virtual void ConnectResidueToPrev(mol::ResidueHandle rh,
+                                    mol::ResidueHandle prev);
   /// \sa ConnectResidueToPrev                                    
-  virtual void ConnectResidueToNext(const mol::ResidueHandle& rh,
-                                    const mol::ResidueHandle& next);
+  virtual void ConnectResidueToNext(mol::ResidueHandle rh, 
+                                    mol::ResidueHandle next);
 
   /// \brief assign named torsions to a complete chain
-  virtual void AssignTorsions(const mol::ChainHandle& ch);
+  virtual void AssignTorsions(mol::ChainHandle ch);
   
   /// \brief assign named torsions to single residue
-  virtual void AssignTorsionsToResidue(const mol::ResidueHandle& residue);
+  virtual void AssignTorsionsToResidue(mol::ResidueHandle residue);
   
   /// \brief assign Backbone torsions to single residue  
-  void AssignBackBoneTorsionsToResidue(const mol::ResidueHandle& res);
+  void AssignBackBoneTorsionsToResidue(mol::ResidueHandle res);
   
   /// \brief  Check if peptide bond is formed between the two atoms.
   /// 
@@ -130,7 +140,10 @@ public:
 
   /// |brief Connect \p atom with all atoms for whith IsBondFeasible() and 
   ///    AreResiduesConsecutive() returns true
-  void DistanceBasedConnect(const mol::AtomHandle& atom);
+  void DistanceBasedConnect(mol::AtomHandle atom);
+private:
+  Dialect dialect_;
+  bool    strict_;
 };
 
 
diff --git a/modules/conop/src/chemdict_tool.cc b/modules/conop/src/chemdict_tool.cc
index 865425d8c75a7b3a9437f38d0bd753dc783ee465..65fca93101c8cfe07c3ac999fb32d701bb0e4a60 100644
--- a/modules/conop/src/chemdict_tool.cc
+++ b/modules/conop/src/chemdict_tool.cc
@@ -28,204 +28,14 @@
 #include <boost/iostreams/filtering_stream.hpp>
 #include <boost/iostreams/filter/gzip.hpp>
 
-#include <ost/mol/mol.hh>
-#include <ost/io/mol/star_parser.hh>
-#include <ost/conop/compound_lib.hh>
 
-using namespace ost;
-
-
-typedef enum {
-  ATOM_SPEC,
-  BOND_SPEC,
-  DONT_KNOW
-} LoopType;
-
-class ChemDictParser : public io::StarParser {
-public:
-  ChemDictParser(std::istream& stream): 
-    io::StarParser(stream),
-    compound_(new conop::Compound("UNK")), last_(0), loop_type_(DONT_KNOW)
-  {
-    this->InitTypeMap();
-  }
-  
-  virtual bool OnBeginData(const StringRef& data_name) 
-  {    
-    compound_.reset(new conop::Compound(data_name.str()));
-    if (last_!=data_name[0]) {
-      last_=data_name[0];
-      std::cout << last_ << std::flush;
-    }
-    atom_map_.clear();
-    insert_=true;
-    return true; 
-  }
-  
-  virtual bool OnBeginLoop(const io::StarLoopDesc& header) 
-  { 
-    if (header.GetCategory()=="chem_comp_atom") {
-      loop_type_=ATOM_SPEC;
-      indices_[ATOM_NAME]=header.GetIndex("atom_id");
-      indices_[ALT_ATOM_NAME]=header.GetIndex("alt_atom_id");
-      indices_[ELE]=header.GetIndex("type_symbol");      
-      indices_[IS_LEAVING]=header.GetIndex("pdbx_leaving_atom_flag");
-      indices_[IS_AROMATIC]=header.GetIndex("pdbx_aromatic_flag");
-      indices_[ORDINAL]=header.GetIndex("pdbx_ordinal");      
-      return true;
-    } else if (header.GetCategory()=="chem_comp_bond") {
-      loop_type_=BOND_SPEC;
-      indices_[ATOM_ID1]=header.GetIndex("atom_id_1");
-      indices_[ATOM_ID2]=header.GetIndex("atom_id_2");
-      indices_[BOND_ORDER]=header.GetIndex("value_order");
-      return true;
-    }
-    loop_type_=DONT_KNOW;
-    return false;
-  }
-  
-  virtual void OnDataRow(const io::StarLoopDesc& header, 
-                         const std::vector<StringRef>& columns) 
-  {                        
-    if (loop_type_==ATOM_SPEC) {
-      // compound_->AddBond()
-      conop::AtomSpec atom;
-      atom.is_leaving=columns[indices_[IS_LEAVING]][0]=='Y';
-      atom.name=columns[indices_[ATOM_NAME]].str();
-      atom.alt_name=columns[indices_[ALT_ATOM_NAME]].str();
-      atom.ordinal=columns[indices_[ORDINAL]].to_int().second-1;
-      atom.element=columns[indices_[ELE]].str();
-      atom.is_aromatic=columns[indices_[IS_AROMATIC]][0]=='Y';
-      compound_->AddAtom(atom);
-      atom_map_[atom.name]=atom.ordinal;
-    } else if (loop_type_==BOND_SPEC) {
-      conop::BondSpec bond;
-      String atom_one=columns[indices_[ATOM_ID1]].str();
-      String atom_two=columns[indices_[ATOM_ID2]].str();      
-      bond.atom_one=atom_map_[atom_one];
-      bond.atom_two=atom_map_[atom_two];
-      char b=columns[indices_[BOND_ORDER]][0];
-      bond.order=b=='D' ? 2 : (b=='S' ? 1 : 3);
-      if (bond.atom_one>bond.atom_two) {
-        std::swap(bond.atom_one, bond.atom_two);
-      }
-      compound_->AddBond(bond);
-    }
-  }
-  
-  virtual void OnDataItem(const io::StarDataItem& item)
-  {
-    if (item.GetCategory()==StringRef("chem_comp", 9)) {
-      if (item.GetName()==StringRef("type", 4)) {
-        // convert type to uppercase
-        String type=item.GetValue().str();
-        for (String::iterator i=type.begin(), e=type.end(); i!=e; ++i) {
-          *i=toupper(*i);
-        }
-        std::map<String, mol::ChemClass>::iterator i=tm_.find(type);
-        if (i!=tm_.end()) {
-          compound_->SetChemClass(i->second);          
-        } else {
-          std::cout << "unknown type '" << type << "' for compound " 
-                    << compound_->GetID() << std::endl;
-        }
-      } else if (item.GetName()==StringRef("formula", 7)) {
-        compound_->SetFormula(item.GetValue().str());
-      } else if (item.GetName()==StringRef("one_letter_code", 15)) {
-        if (item.GetValue().length()==1) {
-          compound_->SetOneLetterCode(item.GetValue()[0]);   
-        }
-      } else if (item.GetName()==StringRef("pdbx_initial_date", 17)) {        
-        compound_->SetCreationDate(conop::Date::FromString(item.GetValue()));
-      } else if (item.GetName()==StringRef("pdbx_modified_date", 18)) {
-        compound_->SetModificationDate(conop::Date::FromString(item.GetValue()));
-      }
-    } else if (item.GetName()==StringRef("atom_id", 7)) {
-      atom_.name=item.GetValue().str();
-    } else if (item.GetName()==StringRef("alt_atom_id", 11)) {
-      atom_.alt_name=item.GetValue().str();
-    } else if (item.GetName()==StringRef("type_symbol", 11)) {
-      atom_.element=item.GetValue().str();
-    } else if (item.GetName()==StringRef("pdbx_ordinal", 12)) {
-      atom_.ordinal=item.GetValue().to_int().second-1;
-    }
-  }
-  
-  virtual void OnEndData()
-  {
-    if (insert_) {
-      if (compound_->GetAtomSpecs().empty()) {
-        compound_->AddAtom(atom_);
-      }
-      lib_->AddCompound(compound_);      
-    }
-  }
-  
-  void SetCompoundLib(const conop::CompoundLibPtr& lib) 
-  {
-    lib_=lib;
-  }
-private:
-  void InitTypeMap();  
-  conop::CompoundLibPtr                   lib_;
-  conop::CompoundPtr                      compound_;
-  typedef enum {
-    ATOM_NAME=0,
-    ALT_ATOM_NAME=1,
-    IS_AROMATIC=2,
-    ORDINAL=3,
-    IS_LEAVING=4,
-    ELE=5,
-    STEREO_CONF=6,
-    ATOM_ID1=0,
-    ATOM_ID2=1,
-    BOND_ORDER=2,
-  } PropIndex;
-  char                                    last_;
-  int                                     indices_[10];
-  bool                                    insert_;
-  static std::map<String, mol::ChemClass> tm_;  
-  std::map<String, int>                   atom_map_;
-  LoopType                                loop_type_;  
-  conop::AtomSpec                         atom_;
-};
-
-std::map<String, mol::ChemClass> ChemDictParser::tm_=std::map<String, mol::ChemClass>();
+#include <ost/io/mol/chemdict_parser.hh>
 
-void ChemDictParser::InitTypeMap()
-{
-  if (!tm_.empty())
-    return;
-  tm_["L-PEPTIDE COOH CARBOXY TERMINUS"]=mol::ChemClass(mol::ChemClass::LPeptideLinking);
-  tm_["L-PEPTIDE NH3 AMINO TERMINUS"]=mol::ChemClass(mol::ChemClass::LPeptideLinking);   
-  tm_["D-PEPTIDE NH3 AMINO TERMINUS"]=mol::ChemClass(mol::ChemClass::DPeptideLinking);
-  tm_["L-SACCHARIDE 1,4 AND 1,4 LINKING"]=mol::ChemClass(mol::ChemClass::LSaccharide);
-  tm_["D-SACCHARIDE 1,4 AND 1,4 LINKING"]=mol::ChemClass(mol::ChemClass::DSaccharide);
-  tm_["L-SACCHARIDE"]=mol::ChemClass(mol::ChemClass::LSaccharide);
-  tm_["D-SACCHARIDE"]=mol::ChemClass(mol::ChemClass::DSaccharide);
-  tm_["SACCHARIDE"]=mol::ChemClass(mol::ChemClass::Saccharide);
-  tm_["D-PEPTIDE LINKING"]=mol::ChemClass(mol::ChemClass::DPeptideLinking);
-  tm_["L-PEPTIDE LINKING"]=mol::ChemClass(mol::ChemClass::LPeptideLinking);
-  tm_["L-PEPTIDE-LINKING"]=mol::ChemClass(mol::ChemClass::LPeptideLinking);
-  tm_["DNA LINKING"]=mol::ChemClass(mol::ChemClass::DNALinking);
-  tm_["RNA LINKING"]=mol::ChemClass(mol::ChemClass::RNALinking);
-  tm_["L-DNA LINKING"]=mol::ChemClass(mol::ChemClass::DNALinking);
-  tm_["L-RNA LINKING"]=mol::ChemClass(mol::ChemClass::RNALinking);  
-  tm_["R-DNA LINKING"]=mol::ChemClass(mol::ChemClass::DNALinking);
-  tm_["R-RNA LINKING"]=mol::ChemClass(mol::ChemClass::RNALinking);  
-  tm_["DNA OH 3 PRIME TERMINUS"]=mol::ChemClass(mol::ChemClass::DNALinking);
-  tm_["PEPTIDE-LIKE"]=mol::ChemClass(mol::ChemClass::PeptideLinking);
-  tm_["PEPTIDE LINKING"]=mol::ChemClass(mol::ChemClass::PeptideLinking);
-  tm_["PEPTIDE-LINKING"]=mol::ChemClass(mol::ChemClass::PeptideLinking);  
-  tm_["NON-POLYMER"]=mol::ChemClass(mol::ChemClass::NonPolymer);
-  tm_["RNA OH 3 PRIME TERMINUS"]=mol::ChemClass(mol::ChemClass::RNALinking);
-  tm_["?"]=mol::ChemClass(mol::ChemClass::Unknown);  
-  
-}
+using namespace ost;
 
 void PrintUsage()
 {
-  std::cout << "usage: chemdict_tool action compound-dict db" << std::endl;
+  std::cout << "usage: chemdict_tool action <compound-dict> <db> (pdb|charmm|amber|opls)" << std::endl;
   std::cout << "supported actions are:" << std::endl;
   std::cout << "  create  - creates a new db " << std::endl;
   std::cout << "  update  - update existing db" << std::endl;
@@ -233,17 +43,34 @@ void PrintUsage()
 
 int main(int argc, char const *argv[])
 {
-  if (argc!=4) {
+  if (argc!=4 && argc!=5) {
     PrintUsage();
     return 0;
   }
+  conop::Compound::Dialect dialect=conop::Compound::PDB;
+  if (argc==5) {
+    String format=argv[4];
+
+    if (format=="charmm") {
+      dialect=conop::Compound::CHARMM;
+    } else if (format=="pdb") {
+      dialect=conop::Compound::PDB;
+    } else if (format=="opls") {
+      dialect=conop::Compound::OPLS;
+    } else if (format=="amber") {
+      dialect=conop::Compound::AMBER;
+    } else {
+      PrintUsage();
+      return 0;
+    }
+  }
   boost::iostreams::filtering_stream<boost::iostreams::input>  filtered_istream;  
   std::ifstream istream(argv[2]);
   if (boost::iequals(".gz", boost::filesystem::extension(argv[2]))) {
     filtered_istream.push(boost::iostreams::gzip_decompressor());
   }
   filtered_istream.push(istream);  
-  ChemDictParser cdp(filtered_istream);
+  io::ChemdictParser cdp(filtered_istream, dialect);
   conop::CompoundLibPtr compound_lib;
   if (!strcmp(argv[1], "create")) {
     compound_lib=conop::CompoundLib::Create(argv[3]);
@@ -261,4 +88,4 @@ int main(int argc, char const *argv[])
   cdp.Parse();
   in_mem_lib->Copy(argv[3]);  
   return 0;
-}
+}
\ No newline at end of file
diff --git a/modules/conop/src/compound.hh b/modules/conop/src/compound.hh
index 6df62c8567e14acc00cbd45f0cdb8153ae081ea5..f381649ab30a3a77fe4ff06f6cf6b87a600faaff 100644
--- a/modules/conop/src/compound.hh
+++ b/modules/conop/src/compound.hh
@@ -112,15 +112,39 @@ typedef boost::shared_ptr<Compound> CompoundPtr;
 /// \brief Knows about the atoms and bonds of a chemical compounds
 class DLLEXPORT_OST_CONOP Compound {
 public:
+  typedef enum {
+    PDB    ='P',
+    CHARMM ='C',
+    OPLS   ='O',
+    AMBER  ='A',
+  } Dialect;
+  
   Compound(const String& id)
-    : olc_('?'), tlc_(id), chem_class_() {
+    : olc_('?'), tlc_(id), chem_class_(), dialect_(Compound::PDB) {
   }
 
   /// \brief three-letter code that is unique for every compound 
   const String& GetID() const {
     return tlc_;
   }
-
+  Dialect GetDialect() const { return dialect_; }
+  
+  String GetDialectAsString() const { 
+    switch (dialect_) {
+      case CHARMM:
+        return "CHARMM";
+      case PDB:
+        return "PDB";
+      case OPLS:
+        return "OPLS";
+      case AMBER:
+        return "AMBER";
+      default:
+        return "";
+    }
+  }
+  void SetDialect(Dialect dialect) { dialect_=dialect; }
+  
   void SetOneLetterCode(char olc) {
     olc_=olc;
   }
@@ -192,10 +216,11 @@ private:
   AtomSpecList                 atom_specs_;
   BondSpecList                 bond_specs_;
   mol::ChemClass               chem_class_;
+  Dialect                      dialect_;  
   Date                         creation_date_;
   Date                         mod_date_;
 };
 
 }}
 
-#endif
+#endif
\ No newline at end of file
diff --git a/modules/conop/src/compound_lib.cc b/modules/conop/src/compound_lib.cc
index a5c9ad1a77455341a3e466cf0447a0d8bd1cccac..10e46b16ba0dabe90274699accd01d8c832c548b 100644
--- a/modules/conop/src/compound_lib.cc
+++ b/modules/conop/src/compound_lib.cc
@@ -37,13 +37,16 @@ namespace {
 const char* CREATE_CMD[]={                                                         
 "CREATE TABLE IF NOT EXISTS chem_compounds (                                    "
 "  id              INTEGER PRIMARY KEY AUTOINCREMENT,                           "
-"  tlc             VARCHAR(3) UNIQUE NOT NULL,                                  "
+"  tlc             VARCHAR(3) NOT NULL,                                         "
 "  olc             VARCHAR(1) NOT NULL,                                         "
+"  dialect         VARCHAR(1) NOT NULL,                                         "
 "  chem_class      VARCHAR(1),                                                  "
 "  formula         VARCHAR(64) NOT NULL,                                        "
 "  pdb_initial     TIMESTAMP,                                                   "
 "  pdb_modified    TIMESTAMP                                                    "
 ");",
+" CREATE UNIQUE INDEX IF NOT EXISTS commpound_tlc_index ON chem_compounds       "
+"                                  (tlc, dialect)",
 "CREATE TABLE IF NOT EXISTS atoms (                                             "
 " id              INTEGER PRIMARY KEY AUTOINCREMENT,                            "
 " compound_id     INTEGER REFERENCES chem_compounds (id) ON DELETE CASCADE,     "
@@ -76,8 +79,8 @@ const char* CREATE_CMD[]={
 
 
 const char* INSERT_COMPOUND_STATEMENT="INSERT INTO chem_compounds               "
-"        (tlc, olc, chem_class, formula, pdb_initial, pdb_modified)             "
-" VALUES (?, ?, ?, ?, DATE(?), DATE(?))";
+"        (tlc, olc, dialect, chem_class, formula, pdb_initial, pdb_modified)    "
+" VALUES (?, ?, ?, ?, ?, DATE(?), DATE(?))";
 
 const char* INSERT_ATOM_STATEMENT="INSERT INTO atoms                            "
 "        (compound_id, name, alt_name, element, is_aromatic, stereo_conf,       "
@@ -104,8 +107,10 @@ void CompoundLib::AddCompound(const CompoundPtr& compound)
     char olc=compound->GetOneLetterCode();
     sqlite3_bind_text(stmt, 2, &olc, 1, NULL);
     char chem_type=compound->GetChemClass();
-    sqlite3_bind_text(stmt, 3, &chem_type, 1, NULL);
-    sqlite3_bind_text(stmt, 4, compound->GetFormula().c_str(), 
+    char dialect=compound->GetDialect();
+    sqlite3_bind_text(stmt, 3, &dialect, 1, NULL);
+    sqlite3_bind_text(stmt, 4, &chem_type, 1, NULL);
+    sqlite3_bind_text(stmt, 5, compound->GetFormula().c_str(), 
                       compound->GetFormula().length(), NULL);
     std::stringstream ss;
     ss << compound->GetCreationDate().year << "-" 
@@ -116,20 +121,21 @@ void CompoundLib::AddCompound(const CompoundPtr& compound)
     ss << compound->GetModificationDate().year << "-" 
        << compound->GetModificationDate().month << "-" 
        << compound->GetModificationDate().day;
-    sqlite3_bind_text(stmt, 5, date.c_str(), date.length(), NULL);
+    sqlite3_bind_text(stmt, 6, date.c_str(), date.length(), NULL);
     date=ss.str();
-    sqlite3_bind_text(stmt, 6, date.c_str(), date.length(), NULL);        
+    sqlite3_bind_text(stmt, 7, date.c_str(), date.length(), NULL);        
   } else {
-    LOGN_ERROR(sqlite3_errmsg(conn_));
+    LOG_ERROR(sqlite3_errmsg(conn_));
     sqlite3_finalize(stmt);    
     return;
   }
   retval=sqlite3_step(stmt);
   if (SQLITE_DONE!=retval) {
     if (sqlite3_errcode(conn_)==SQLITE_CONSTRAINT) {
-      LOGN_ERROR("Compound '" << compound->GetID() << "' already exists.");
+      LOG_ERROR("Compound '" << compound->GetID() << "' already exists for the "
+                << compound->GetDialectAsString() << " dialect.");
     } else {
-      LOGN_ERROR(sqlite3_errmsg(conn_));
+      LOG_ERROR(sqlite3_errmsg(conn_));
     }
   }
   sqlite3_finalize(stmt);  
@@ -155,7 +161,7 @@ void CompoundLib::AddCompound(const CompoundPtr& compound)
       assert(retval==SQLITE_DONE);
       atom_ids[i-al.begin()]=sqlite3_last_insert_rowid(conn_);
     } else {
-      std::cout << sqlite3_errmsg(conn_) << std::endl;
+      LOG_ERROR(sqlite3_errmsg(conn_));
     }
     sqlite3_finalize(stmt);
   }
@@ -173,7 +179,7 @@ void CompoundLib::AddCompound(const CompoundPtr& compound)
       retval=sqlite3_step(stmt);
       assert(retval==SQLITE_DONE);
     } else {
-      std::cout << sqlite3_errmsg(conn_) << std::endl;
+      LOG_ERROR(sqlite3_errmsg(conn_));
     }
     sqlite3_finalize(stmt);    
   }
@@ -193,12 +199,12 @@ CompoundLibPtr CompoundLib::Copy(const String& filename) const
     }
     int rc=sqlite3_errcode(clone->conn_);
     if (rc!=SQLITE_OK) {
-      std::cout << sqlite3_errmsg(clone->conn_) << std::endl;        
+      LOG_ERROR(sqlite3_errmsg(clone->conn_));
       return CompoundLibPtr();
     }
     return clone;      
   }
-  std::cout << sqlite3_errmsg(clone->conn_) << std::endl;
+  LOG_ERROR(sqlite3_errmsg(clone->conn_));
   return CompoundLibPtr();
 }
 
@@ -218,7 +224,7 @@ CompoundLibPtr CompoundLib::Create(const String& database)
         sqlite3_finalize(stmt);        
         assert(SQLITE_DONE==retval);
       } else {
-        std::cout << sqlite3_errmsg(lib->conn_) << std::endl;
+        LOG_ERROR(sqlite3_errmsg(lib->conn_));
         sqlite3_finalize(stmt);
         return CompoundLibPtr();
       }      
@@ -226,7 +232,7 @@ CompoundLibPtr CompoundLib::Create(const String& database)
     }
     return lib;
   }
-  std::cout << sqlite3_errmsg(lib->conn_) << std::endl;
+  LOG_ERROR(sqlite3_errmsg(lib->conn_));
   return CompoundLibPtr();  
 }
 
@@ -238,12 +244,14 @@ CompoundLibPtr CompoundLib::Load(const String& database)
   if (SQLITE_OK==retval) {
     return lib;
   }
-  std::cout << sqlite3_errmsg(lib->conn_) << std::endl;
+  LOG_ERROR(sqlite3_errmsg(lib->conn_));
   return CompoundLibPtr();
 }
 
 void CompoundLib::LoadAtomsFromDB(CompoundPtr comp, int pk) {
-  String aq=str(format("SELECT name, alt_name, element, ordinal, is_leaving FROM atoms WHERE compound_id=%d ORDER BY ordinal ASC") % pk);  
+  String aq=str(format("SELECT name, alt_name, element, ordinal, is_leaving "
+                       "FROM atoms WHERE compound_id=%d "
+                       "ORDER BY ordinal ASC") % pk);  
   sqlite3_stmt* stmt;
   int retval=sqlite3_prepare_v2(conn_, aq.c_str(), 
                                 static_cast<int>(aq.length()),
@@ -259,6 +267,8 @@ void CompoundLib::LoadAtomsFromDB(CompoundPtr comp, int pk) {
         atom_sp.is_leaving=bool(sqlite3_column_int(stmt, 4)!=0);
         comp->AddAtom(atom_sp);
       }
+  } else {
+    LOG_ERROR(sqlite3_errmsg(conn_));
   }
   sqlite3_finalize(stmt);
 }
@@ -285,16 +295,20 @@ void CompoundLib::LoadBondsFromDB(CompoundPtr comp, int pk) {
         bond_sp.order=sqlite3_column_int(stmt, 2);
         comp->AddBond(bond_sp);
       }
-  }       
+  } else {
+    LOG_ERROR(sqlite3_errmsg(conn_));
+  } 
   sqlite3_finalize(stmt);  
 }
 
-CompoundPtr CompoundLib::FindCompound(const String& id) {
+CompoundPtr CompoundLib::FindCompound(const String& id, 
+                                      Compound::Dialect dialect) {
   CompoundMap::iterator i=compound_cache_.find(id);
   if (i!=compound_cache_.end()) {
     return i->second;
   }
-  String query="select id, tlc, olc, chem_class from chem_compounds where tlc='"+id+"'";
+  String query="SELECT id, tlc, olc, chem_class, dialect FROM chem_compounds"
+               " WHERE tlc='"+id+"' AND dialect='"+String(1, char(dialect))+"'";
   sqlite3_stmt* stmt;
   int retval=sqlite3_prepare_v2(conn_, query.c_str(), 
                                 static_cast<int>(query.length()),
@@ -311,6 +325,7 @@ CompoundPtr CompoundLib::FindCompound(const String& id) {
       CompoundPtr compound(new Compound(id));
       compound->SetOneLetterCode((sqlite3_column_text(stmt, 2))[0]);
       compound->SetChemClass(mol::ChemClass(sqlite3_column_text(stmt, 3)[0]));
+      compound->SetDialect(Compound::Dialect(sqlite3_column_text(stmt, 4)[0]));
       // Load atoms and bonds      
       this->LoadAtomsFromDB(compound, pk);
       this->LoadBondsFromDB(compound, pk);
@@ -320,7 +335,7 @@ CompoundPtr CompoundLib::FindCompound(const String& id) {
     }
     assert(SQLITE_DONE==sqlite3_step(stmt));
   } else {
-    std::cout << "ERROR: " << sqlite3_errmsg(conn_) << std::endl;
+    LOG_ERROR("ERROR: " << sqlite3_errmsg(conn_));
     sqlite3_finalize(stmt);      
     return CompoundPtr();
   }
diff --git a/modules/conop/src/compound_lib.hh b/modules/conop/src/compound_lib.hh
index f8d1b6c2e82163def3472176046903627da3c92e..8948e3479585f61e0fd9fa3d8b4b5c747fa97ccf 100644
--- a/modules/conop/src/compound_lib.hh
+++ b/modules/conop/src/compound_lib.hh
@@ -41,7 +41,7 @@ public:
   static CompoundLibPtr Create(const String& database);
   ~CompoundLib();
   
-  CompoundPtr FindCompound(const String& id);
+  CompoundPtr FindCompound(const String& id, Compound::Dialect dialect);
   void AddCompound(const CompoundPtr& compound);
   CompoundLibPtr Copy(const String& filename) const;
   void ClearCache();
diff --git a/modules/conop/src/conop.cc b/modules/conop/src/conop.cc
index 3267e83e059ecffbeb3490ea18a01994ad5d8599..d7edd9aa8ef5b451128a45b742d1b74ffb45b954 100644
--- a/modules/conop/src/conop.cc
+++ b/modules/conop/src/conop.cc
@@ -42,7 +42,7 @@ Conopology::Conopology():
 
   ele_rad_map_["H"]  = 1.09;
                  
-  ele_rad_map_["C"]  = 1.75;
+  ele_rad_map_["C"]  = 1.70;  //was 1.75
   ele_rad_map_["N"]  = 1.55;
   ele_rad_map_["O"]  = 1.52;
   ele_rad_map_["F"]  = 1.47;
@@ -214,10 +214,13 @@ namespace {
 class PropAssigner: public mol::EntityVisitor {
 public:
   PropAssigner(const BuilderP& builder): builder_(builder) {}
+  
   virtual bool VisitResidue(const mol::ResidueHandle& res)
   {
     String key=builder_->IdentifyResidue(res);
-    builder_->CheckResidueCompleteness(res);
+    if (key=="UNK") {
+      unk_res_[res.GetKey()]+=1;
+    }
     builder_->FillResidueProps(res);
     return true;
   }
@@ -227,8 +230,23 @@ public:
     builder_->FillAtomProps(atom);
     return false;
   }
+  
+  virtual void OnExit()
+  {
+    for (std::map<String, int>::iterator i=unk_res_.begin(), 
+         e=unk_res_.end(); i!=e; ++i) {
+      if (i->second>1) {
+        LOG_WARNING("structure contains unknown residues with name " << i->first 
+                    << " ("<< i->second << "x)");
+      } else {        
+        LOG_WARNING("structure contains unknown residue with name " << i->first);
+      }
+
+    }
+  }
 private:
   BuilderP builder_;
+  std::map<String, int>  unk_res_;  
 };
 
 
@@ -247,8 +265,8 @@ public:
 
   virtual bool VisitResidue(const mol::ResidueHandle& res) {
     builder_->ConnectAtomsOfResidue(res);
-    if(prev_) {
-        builder_->ConnectResidueToPrev(res,prev_);
+    if (prev_) {
+      builder_->ConnectResidueToPrev(res,prev_);
     }
     prev_=res;
     return false;
@@ -279,15 +297,15 @@ private:
 void Conopology::ConnectAll(const BuilderP& b, mol::EntityHandle eh, int flag)
 {
   Profile profile_connect("ConnectAll");
-  LOGN_DEBUG("Conopology: ConnectAll: building internal coordinate system");
+  LOG_DEBUG("Conopology: ConnectAll: building internal coordinate system");
   mol::XCSEditor xcs_e=eh.RequestXCSEditor(mol::BUFFERED_EDIT);
   PropAssigner a(b);
   eh.Apply(a);
-  LOGN_DUMP("Conopology: ConnectAll: connecting all bonds");
+  LOG_DEBUG("Conopology: ConnectAll: connecting all bonds");
   Connector connector(b);
   eh.Apply(connector);
 
-  LOGN_DUMP("Conopology: ConnectAll: assigning all torsions");
+  LOG_DEBUG("Conopology: ConnectAll: assigning all torsions");
   TorsionMaker tmaker(b);
   eh.Apply(tmaker);
 }
@@ -300,6 +318,15 @@ Real Conopology::GetDefaultAtomRadius(const String& element) const
   return it==ele_rad_map_.end() ? 1.5 : it->second;
 }
 
+bool Conopology::IsValidElement(const String& element) const
+{
+  String upper_ele=element;
+  std::transform(upper_ele.begin(),upper_ele.end(),upper_ele.begin(),toupper);  
+  
+  std::map<String,Real>::const_iterator it = ele_mass_map_.find(upper_ele);
+  return it!=ele_mass_map_.end();
+}
+
 Real Conopology::GetDefaultAtomMass(const String& element) const
 {
   String upper_ele=element;
diff --git a/modules/conop/src/conop.hh b/modules/conop/src/conop.hh
index f8133a0781289326cc66a2d1021a68a9275f44ce..e8ad4bc0b7034942a446a0726c3cb2949ba76d36 100644
--- a/modules/conop/src/conop.hh
+++ b/modules/conop/src/conop.hh
@@ -53,6 +53,8 @@ public:
 
   void RegisterBuilder(const BuilderP& b, const String& name);
   void SetDefaultBuilder(const String& default_name);
+  
+  bool IsValidElement(const String& element) const;
 private:
   Conopology();
   Conopology(const Conopology&) {}
diff --git a/modules/conop/src/heuristic_builder.cc b/modules/conop/src/heuristic_builder.cc
index 644771764b9325a8601cf56e54615c711e12cea1..bb4a63a229bfdc5b270b447538115df02a8b9659 100644
--- a/modules/conop/src/heuristic_builder.cc
+++ b/modules/conop/src/heuristic_builder.cc
@@ -113,13 +113,13 @@ HeuristicBuilder::HeuristicBuilder():
 {
   int def_entry_count = sizeof(heuristic_connect::def_entry_table)/sizeof(heuristic_connect::CONN_DEF_ENTRY);
 
-  LOGN_DEBUG("importing internal connectivity tables");
+  LOG_DEBUG("importing internal connectivity tables");
   for(int ec=0;ec<def_entry_count;++ec) {
     heuristic_connect::CONN_DEF_ENTRY& def_entry = heuristic_connect::def_entry_table[ec];
     detail::ConnResEntry entry(def_entry.abbrev, def_entry.single,
                                def_entry.chem_class);
-    LOGN_DUMP("creating table entry for " << def_entry.abbrev);
-    LOGN_DUMP("working on bond entries");
+    LOG_DEBUG("creating table entry for " << def_entry.abbrev);
+    LOG_DEBUG("working on bond entries");
     for (int xx=0;xx<def_entry.name_count;++xx) {
       String name=def_entry.name_list[xx];
       if (name!="OXT")
@@ -151,14 +151,14 @@ HeuristicBuilder::HeuristicBuilder():
         else if(conn_nam[1]==String("-")) { entry.SetPrev(conn_nam[0]);}
         else if(conn_nam[0]==String("+")) { entry.SetNext(conn_nam[1]);}
         else if(conn_nam[1]==String("+")) { entry.SetNext(conn_nam[0]);}
-        LOGN_DUMP(" " << conn_nam[0] << " " << conn_nam[1]);
+        LOG_DEBUG(" " << conn_nam[0] << " " << conn_nam[1]);
             } else {
-        LOGN_DUMP(" " << conn_nam[0] << " " << conn_nam[1]);
+        LOG_DEBUG(" " << conn_nam[0] << " " << conn_nam[1]);
         entry.AddConn(conn_nam[0],conn_nam[1]);
       }
     }
     // then the torsion entries
-    LOGN_DUMP("working on torsion entries");
+    LOG_DEBUG("working on torsion entries");
     for(int cc=0;cc<def_entry.tor_count;++cc) {
       int tor_id[] = {def_entry.tor_list[cc].n1,
                       def_entry.tor_list[cc].n2,
@@ -183,7 +183,7 @@ HeuristicBuilder::HeuristicBuilder():
 
     emap_[def_entry.abbrev]=entry;
   }
-  LOGN_DUMP("done importing internal tables");
+  LOG_DEBUG("done importing internal tables");
 }
 
 HeuristicBuilder::~HeuristicBuilder()
@@ -201,18 +201,18 @@ void HeuristicBuilder::ConnectivityFromAtomNames(const mol::ResidueHandle& res,
      mol::AtomHandleList::iterator it2=it1;
      ++it2;
      for (;it2!=atomlist.end();++it2) {
-       LOG_DUMP("checking for atom pair (" << it1->GetName() << ","
+       LOG_DEBUG("checking for atom pair (" << it1->GetName() << ","
                 << it2->GetName() << ") in connectivity table of "
                 << res.GetKey() << "... ");
        int conn=centry.Check(it1->GetName(),it2->GetName());
        if (conn==1 && this->IsBondFeasible(*it1, *it2)) {
-         LOGN_DUMP( "found");
+         LOG_DEBUG( "found");
          editor.Connect(*it1,*it2);
        } else if(conn==2 && this->IsBondFeasible(*it2, *it1)) {
-         LOGN_DUMP( "found (reversed)");
+         LOG_DEBUG( "found (reversed)");
          editor.Connect(*it2,*it1);
        } else {
-         LOGN_DUMP( "not found");
+         LOG_DEBUG( "not found");
        }
      }
    } else {
@@ -221,17 +221,20 @@ void HeuristicBuilder::ConnectivityFromAtomNames(const mol::ResidueHandle& res,
  }
 }
 
-void HeuristicBuilder::ConnectAtomsOfResidue(const mol::ResidueHandle& res)
+void HeuristicBuilder::ConnectAtomsOfResidue(mol::ResidueHandle res)
 {
-  LOGN_DUMP("HeuristicBuilder: ConnectAtomsOfResidue on " << res.GetKey() << " " << res.GetNumber());
+  LOG_DEBUG("HeuristicBuilder: ConnectAtomsOfResidue on " << res.GetKey() << " " << res.GetNumber());
 
   mol::AtomHandleList atomlist = res.GetAtomList();
   mol::AtomHandleList unk_atomlist;
-  LOGN_DUMP( "using atom list:");
+#if !defined(NDEBUG)
+  std::stringstream ss;
+  ss << "using atom list:";
   for(mol::AtomHandleList::iterator it=atomlist.begin();it!=atomlist.end();++it) {
-    LOGN_DUMP( " " << it->GetName() << " @" << it->GetPos());
+    ss << " " << it->GetName() << " @" << it->GetPos();
   }
-
+  LOG_DEBUG(ss.str());
+#endif
   std::pair<detail::ConnResEntry,bool> ret = LookupResEntry(res.GetKey());
 
   if(ret.second) {
@@ -241,11 +244,11 @@ void HeuristicBuilder::ConnectAtomsOfResidue(const mol::ResidueHandle& res)
     for(mol::AtomHandleList::iterator it1=unk_atomlist.begin();
         it1!=unk_atomlist.end();
         ++it1) {
-      LOGN_DUMP( "atom " << it1->GetName() << " not found, using distance based connect");
+      LOG_DEBUG( "atom " << it1->GetName() << " not found, using distance based connect");
       Builder::DistanceBasedConnect(*it1);
     }
   } else {
-    LOGN_DUMP("no residue entry found, using distance based connect");
+    LOG_DEBUG("no residue entry found, using distance based connect");
     for(mol::AtomHandleList::iterator it1=atomlist.begin();
         it1!=atomlist.end();
         ++it1) {
@@ -263,16 +266,16 @@ void ConnectPrevNext(HeuristicBuilder* builder,mol::ResidueHandle res0,
   static String fname=flag ? "HeuristicBuilder: ConnectNextXCS" : "HeuristicBuilder: ConnectPrevXCS";
   if(!res0) return; // return if invalid
   mol::XCSEditor editor=res0.GetEntity().RequestXCSEditor(mol::BUFFERED_EDIT);
-  LOGN_DUMP(fname << " on " << res0.GetKey() << " " << res0.GetNumber());
+  LOG_DEBUG(fname << " on " << res0.GetKey() << " " << res0.GetNumber());
 
   if(!res1) {
     // auto-detect prev or next residue in chain
     // and perform sequence check
     if(flag) {
-      LOGN_DUMP(fname << " autodecting next residue");
+      LOG_DEBUG(fname << " autodecting next residue");
       res1 = res0.GetChain().GetNext(res0);
     } else {
-      LOGN_DUMP(fname << " autodecting next residue");
+      LOG_DEBUG(fname << " autodecting next residue");
       res1 = res0.GetChain().GetPrev(res0);
     }
   } else {
@@ -285,7 +288,8 @@ void ConnectPrevNext(HeuristicBuilder* builder,mol::ResidueHandle res0,
   }
 
   if(!res1) return; // ignore if prev/next residue is invalid
-  LOGN_DUMP(fname << " found second residue " << res1.GetKey() << " " << res1.GetNumber());
+  LOG_DEBUG(fname << " found second residue " << res1.GetKey() 
+            << " " << res1.GetNumber());
 
   std::pair<detail::ConnResEntry,bool> res0_ret = builder->LookupResEntry(res0.GetKey());
   std::pair<detail::ConnResEntry,bool> res1_ret = builder->LookupResEntry(res1.GetKey());
@@ -297,19 +301,26 @@ void ConnectPrevNext(HeuristicBuilder* builder,mol::ResidueHandle res0,
     String res1_atom_name = res1_centry.GetNext();
 
     if(res0_atom_name.empty() || res1_atom_name.empty()) return;
-    LOGN_DUMP(fname << ": looking up atom names " << res0_atom_name << " " << res1_atom_name);
+    LOG_DEBUG(fname << ": looking up atom names " << res0_atom_name << " " << res1_atom_name);
 
     // lookup both atoms in their respective residues
     mol::AtomHandle res0_atom = res0.FindAtom(res0_atom_name);
     mol::AtomHandle res1_atom = res1.FindAtom(res1_atom_name);
     if(res0_atom && res1_atom) {
-      LOGN_DUMP(fname << ": found atoms, connecting");
+      LOG_DEBUG(fname << ": found atoms, connecting");
       if(flag) {
-        if (builder->DoesPeptideBondExist(res0_atom, res1_atom))
+        if (builder->DoesPeptideBondExist(res0_atom, res1_atom)) {
           editor.Connect(res0_atom,res1_atom);
+          res0.SetIsProtein(true);
+          res1.SetIsProtein(true);
+        }
       } else {
-        if (builder->DoesPeptideBondExist(res1_atom, res0_atom))
+        if (builder->DoesPeptideBondExist(res1_atom, res0_atom)) {
           editor.Connect(res1_atom, res0_atom);
+          res0.SetIsProtein(true);
+          res1.SetIsProtein(true);
+        }
+
       }
     }
   } else {
@@ -319,7 +330,7 @@ void ConnectPrevNext(HeuristicBuilder* builder,mol::ResidueHandle res0,
 
 }
 
-void HeuristicBuilder::AssignTorsionsToResidue(const mol::ResidueHandle& res)
+void HeuristicBuilder::AssignTorsionsToResidue(mol::ResidueHandle res)
 {
 
   mol::XCSEditor editor=res.GetEntity().RequestXCSEditor(mol::BUFFERED_EDIT);
@@ -374,11 +385,11 @@ void HeuristicBuilder::AssignTorsionsToResidue(const mol::ResidueHandle& res)
         mol::TorsionHandle th = editor.AddTorsion(tel[ti].name, ah[0], ah[1],
                                              ah[2], ah[3]);
         if(th) {
-          LOGN_DUMP("added torsion entry for " << tel[ti].a[0] << " "
+          LOG_DEBUG("added torsion entry for " << tel[ti].a[0] << " "
                     << tel[ti].a[1] << " " << tel[ti].a[2] << " "
                     << tel[ti].a[3]);
         } else {
-          LOGN_DUMP("no torsion entry for " << tel[ti].a[0] << " "
+          LOG_DEBUG("no torsion entry for " << tel[ti].a[0] << " "
                     << tel[ti].a[1] << " " << tel[ti].a[2]
                     << " " << tel[ti].a[3]);
         }
@@ -387,7 +398,7 @@ void HeuristicBuilder::AssignTorsionsToResidue(const mol::ResidueHandle& res)
   }
 }
 
-void HeuristicBuilder::AssignTorsions(const mol::ChainHandle& chain)
+void HeuristicBuilder::AssignTorsions(mol::ChainHandle chain)
 {
   if (chain.GetResidueCount()==0)
     return;
@@ -402,13 +413,13 @@ void HeuristicBuilder::AssignTorsions(const mol::ChainHandle& chain)
   }
 }
 
-void HeuristicBuilder::ConnectResidueToPrev(const mol::ResidueHandle& rh,
-                                            const mol::ResidueHandle& prev) {
+void HeuristicBuilder::ConnectResidueToPrev(mol::ResidueHandle rh,
+                                            mol::ResidueHandle prev) {
   ConnectPrevNext<false>(this, rh, prev);
 }
 
-void HeuristicBuilder::ConnectResidueToNext(const mol::ResidueHandle& rh,
-                                            const mol::ResidueHandle& next) {
+void HeuristicBuilder::ConnectResidueToNext(mol::ResidueHandle rh,
+                                            mol::ResidueHandle next) {
   ConnectPrevNext<true>(this, rh, next);
 }
 
@@ -434,15 +445,14 @@ std::pair<detail::ConnResEntry,bool> HeuristicBuilder::LookupResEntry(const mol:
 {
   static detail::ConnResEntry dummy;
 
-  LOG_DUMP("Looking for reskey '" << key << "' in connectivity map... ");
+
 
   detail::ConnResEntryMap::iterator pos = emap_.find(key);
   if(pos!=emap_.end()) {
-    LOGN_DUMP("found");
+    LOG_DEBUG("reskey '" << key << "' found in connectivity map");
     return std::make_pair(pos->second,true);
-  } else {
-    LOGN_DUMP("not found");
   }
+  LOG_DEBUG("reskey '" << key << "' not found connectivity map");
   return std::make_pair(dummy,false);
 }
 
diff --git a/modules/conop/src/heuristic_builder.hh b/modules/conop/src/heuristic_builder.hh
index d251e53bfd582afe276fea730e513ad5d77eb041..bcfccdbb1e05de6f8aac5b555929e53cd6d640ff 100644
--- a/modules/conop/src/heuristic_builder.hh
+++ b/modules/conop/src/heuristic_builder.hh
@@ -79,26 +79,28 @@ public:
   HeuristicBuilder();
   virtual ~HeuristicBuilder();
 
-  virtual void AssignTorsions(const mol::ChainHandle& ch);
+  virtual void AssignTorsions(mol::ChainHandle ch);
 
   //! \brief connect by using information in the heuristic connectivity table.
   //
   // This does not make any assumption on the correctness of internal or external
   // coordinates. Only the atom names and residue need to be known.
-  virtual void ConnectAtomsOfResidue(const mol::ResidueHandle& rh);
+  virtual void ConnectAtomsOfResidue(mol::ResidueHandle rh);
   
   virtual bool IsResidueComplete(const mol::ResidueHandle& rh);
 //  virtual char GetOneLetterCode(const mol::ResidueKey& residue) const;
 
   //!\brief connect to previous residue in chain.
-  virtual void ConnectResidueToPrev(const mol::ResidueHandle& rh, const mol::ResidueHandle& prev);
+  virtual void ConnectResidueToPrev(mol::ResidueHandle rh, 
+                                    mol::ResidueHandle prev);
   //!
-  virtual void AssignTorsionsToResidue(const mol::ResidueHandle& residue);
+  virtual void AssignTorsionsToResidue(mol::ResidueHandle residue);
 
   virtual void FillResidueProps(mol::ResidueHandle residue);
 
   //!\brief connect to next residue in chain.
-  virtual void ConnectResidueToNext(const mol::ResidueHandle& rh, const mol::ResidueHandle& next);
+  virtual void ConnectResidueToNext(mol::ResidueHandle rh, 
+                                    mol::ResidueHandle next);
 
   //!\brief get connectivity table for residues
   // Retrieve connectiviy information based on residue key. The returned
diff --git a/modules/conop/src/heuristic_connect.cc b/modules/conop/src/heuristic_connect.cc
index aaab318b2829f4a28751dfc4eaf7b1474a72f780..1e20c3e44f6a0fc7652cef7596adcc79bf2043f4 100644
--- a/modules/conop/src/heuristic_connect.cc
+++ b/modules/conop/src/heuristic_connect.cc
@@ -133,7 +133,7 @@ void fill_map(ConnResEntryMap& em)
   for(int ec=0;ec<def_entry_count;++ec) {
     heuristic_connect::CONN_DEF_ENTRY& def_entry = heuristic_connect::def_entry_table[ec];
     ConnResEntry entry(def_entry.abbrev);
-    LOG_DUMP("creating default entry for " << def_entry.abbrev << std::endl);
+    LOG_DEBUG("creating default entry for " << def_entry.abbrev << std::endl);
     // first the connectivity entries
     for(int cc=0;cc<def_entry.conn_count;++cc) {
       int conn_id[] = {def_entry.conn_list[cc][0],def_entry.conn_list[cc][1]};
@@ -160,9 +160,9 @@ void fill_map(ConnResEntryMap& em)
         else if(conn_nam[1]==String("-")) { entry.SetPrev(conn_nam[0]);}
         else if(conn_nam[0]==String("+")) { entry.SetNext(conn_nam[1]);}
         else if(conn_nam[1]==String("+")) { entry.SetNext(conn_nam[0]);}
-        LOG_DUMP(" " << conn_nam[0] << " " << conn_nam[1] << std::endl);
+        LOG_DEBUG(" " << conn_nam[0] << " " << conn_nam[1] << std::endl);
       } else {
-        LOG_DUMP(" " << conn_nam[0] << " " << conn_nam[1] << std::endl);
+        LOG_DEBUG(" " << conn_nam[0] << " " << conn_nam[1] << std::endl);
         entry.AddConn(conn_nam[0],conn_nam[1]);
       }
     }
@@ -203,14 +203,14 @@ std::pair<ConnResEntry,bool> LookupResEntry(const ResidueKey& key)
     initialized=true;
   }
 
-  LOG_DUMP("Looking for reskey '" << key << "' in connectivity map... ");
+  LOG_DEBUG("Looking for reskey '" << key << "' in connectivity map... ");
 
   ConnResEntryMap::iterator pos = emap.find(key);
   if(pos!=emap.end()) {
-    LOG_DUMP("found" << std::endl);
+    LOG_DEBUG("found" << std::endl);
     return std::make_pair(pos->second,true);
   } else {
-    LOG_DUMP("not found" << std::endl);
+    LOG_DEBUG("not found" << std::endl);
   }
   return std::make_pair(dummy,false);
 }
@@ -222,7 +222,7 @@ public:
 
   // visitor interface
   virtual bool VisitChain(const ChainHandle& chain) {
-    LOG_DUMP("connect: setting current chain to " << chain.GetName() << std::endl);
+    LOG_DEBUG("connect: setting current chain to " << chain.GetName() << std::endl);
     curr_chain_=chain;
     curr_residue_=ResidueHandle();
     prev_residue_=ResidueHandle();
@@ -232,13 +232,13 @@ public:
   }
 
   virtual bool VisitResidue(const ResidueHandle& res) {
-    LOG_DUMP("connect: setting current residue to " << res.GetKey() << " " << res.GetNumber() << std::endl);
+    LOG_DEBUG("connect: setting current residue to " << res.GetKey() << " " << res.GetNumber() << std::endl);
     // residue has changed
     curr_residue_=res;
     AtomHandleList atomlist = res.GetAtomList();
-    LOG_DUMP( "using atom list:" << std::endl);
+    LOG_DEBUG( "using atom list:" << std::endl);
     for(AtomHandleList::iterator it=atomlist.begin();it!=atomlist.end();++it) {
-      LOG_DUMP( " " << it->GetName() << " @" << it->GetPos() << std::endl);
+      LOG_DEBUG( " " << it->GetName() << " @" << it->GetPos() << std::endl);
     }
     
     std::pair<ConnResEntry,bool> ret = LookupResEntry(res.GetKey());
@@ -251,16 +251,16 @@ public:
         ++it2;
         for(;it2!=atomlist.end();++it2) {
           bool ex1,ex2;
-          LOG_DUMP( "checking for atom pair (" << it1->GetName() << "," << it2->GetName() << ") in connectivity table of " << res.GetKey() << "... ");
+          LOG_DEBUG( "checking for atom pair (" << it1->GetName() << "," << it2->GetName() << ") in connectivity table of " << res.GetKey() << "... ");
           int conn=centry.Check(it1->GetName(),it2->GetName(),ex1,ex2);
           if (conn==1) {
-            LOG_DUMP( "found" << std::endl);
+            LOG_DEBUG( "found" << std::endl);
             res.GetEntity().Connect(*it1,*it2);
           } else if(conn==2) {
-            LOG_DUMP( "found (reversed)" << std::endl);
+            LOG_DEBUG( "found (reversed)" << std::endl);
             res.GetEntity().Connect(*it2,*it1);
           } else {
-            LOG_DUMP( "not found" << std::endl);
+            LOG_DEBUG( "not found" << std::endl);
             // check ex1 and/or ex2
           }
         }
@@ -272,7 +272,7 @@ public:
           - previous residue number is consecutive to this one
         */
         if(centry.GetPrev()==it1->GetName()) { // 'PREV' entry
-          LOG_DUMP( "found 'prev' atom entry: " << it1->GetName() << std::endl);
+          LOG_DEBUG( "found 'prev' atom entry: " << it1->GetName() << std::endl);
           if(prev_residue_) { // previous residue exists
             if(!next_atom_name_.empty()) { // previous residue 'NEXT' atom set
               if(InSequence(prev_residue_,res)) {
@@ -280,7 +280,7 @@ public:
                 for(AtomHandleList::iterator pit=prev_atomlist.begin();
                     pit!=prev_atomlist.end();++pit) {
                   if(pit->GetName()==next_atom_name_) {
-                    LOG_DUMP( "connecting previous atom " << pit->GetName() << " to "  << it1->GetName() << std::endl);
+                    LOG_DEBUG( "connecting previous atom " << pit->GetName() << " to "  << it1->GetName() << std::endl);
                     res.GetEntity().Connect(*pit,*it1);
                   }
                 }
@@ -290,7 +290,7 @@ public:
         }
 
         if(centry.GetNext()==it1->GetName()) {
-          LOG_DUMP( "found 'next' atom entry: " << it1->GetName() << std::endl);
+          LOG_DEBUG( "found 'next' atom entry: " << it1->GetName() << std::endl);
           // remember this atom for the next residue
           next_atom_name_=it1->GetName();
         }
@@ -386,9 +386,9 @@ public:
           if(ah[0] && ah[1] && ah[2] && ah[3]) {
             TorsionHandle th = chain.GetEntity().AddTorsion(tel[ti].name,ah[0],ah[1],ah[2],ah[3]);
             if(th) {
-              LOG_DUMP("added torsion entry for " << tel[ti].a[0] << " " << tel[ti].a[1] << " " << tel[ti].a[2] << " " << tel[ti].a[3] << std::endl);
+              LOG_DEBUG("added torsion entry for " << tel[ti].a[0] << " " << tel[ti].a[1] << " " << tel[ti].a[2] << " " << tel[ti].a[3] << std::endl);
             } else {
-              LOG_DUMP("no torsion entry for " << tel[ti].a[0] << " " << tel[ti].a[1] << " " << tel[ti].a[2] << " " << tel[ti].a[3] << std::endl);
+              LOG_DEBUG("no torsion entry for " << tel[ti].a[0] << " " << tel[ti].a[1] << " " << tel[ti].a[2] << " " << tel[ti].a[3] << std::endl);
             }
           }
         } // ti
diff --git a/modules/conop/src/heuristic_connect.hh b/modules/conop/src/heuristic_connect.hh
index cea8c6962c16ffc65ed092d681d0aa3643be3641..c3f6336a0575f1c651b7c6863e2c003d25d0c79a 100644
--- a/modules/conop/src/heuristic_connect.hh
+++ b/modules/conop/src/heuristic_connect.hh
@@ -19,11 +19,7 @@
 #ifndef OST_CONOP_HEURISTIC_CONNECT_H
 #define OST_CONOP_HEURISTIC_CONNECT_H
 
-namespace ost {
-
-class EntityHandle;
-
-namespace conop {
+namespace ost { namespace conop {
 
 void HeuristicConnect(EntityHandle& eh);
 
diff --git a/modules/conop/src/rule_based_builder.cc b/modules/conop/src/rule_based_builder.cc
index f2a8fd18f28672d36bf6f1e9a816f6b1c231ac9c..e47c96e358850eb5f89111d575366577e2e9eab7 100644
--- a/modules/conop/src/rule_based_builder.cc
+++ b/modules/conop/src/rule_based_builder.cc
@@ -31,10 +31,11 @@
 namespace ost { namespace conop {
 
 
-void RuleBasedBuilder::CompleteAtoms(const mol::ResidueHandle& rh) {}
+void RuleBasedBuilder::CompleteAtoms(mol::ResidueHandle rh) {}
 
-void RuleBasedBuilder::CheckResidueCompleteness(const mol::ResidueHandle& rh) {
-  LookupCompound(rh);
+void RuleBasedBuilder::CheckResidueCompleteness(const mol::ResidueHandle& rh) 
+{
+  this->LookupCompound(rh);
   if (!last_compound_) {
     mol::AtomHandleList atoms=rh.GetAtomList();    
     for (mol::AtomHandleList::const_iterator i=atoms.begin(), 
@@ -43,7 +44,7 @@ void RuleBasedBuilder::CheckResidueCompleteness(const mol::ResidueHandle& rh) {
     }
     return;
   }
-  ReorderAtoms(rh , last_compound_);
+  this->ReorderAtoms(rh , last_compound_);
   AtomSpecList::const_iterator j=last_compound_->GetAtomSpecs().begin();
   mol::AtomHandleList atoms=rh.GetAtomList();
   mol::AtomHandleList::iterator i=atoms.begin();
@@ -53,19 +54,40 @@ void RuleBasedBuilder::CheckResidueCompleteness(const mol::ResidueHandle& rh) {
     if ((*j).ordinal!=static_cast<int>((*i).Impl()->GetState())) {
       this->OnMissingAtom(rh, (*j).name);
     } else {
-      this->FillAtomProps(*i, *j);
       ++i;
     }
   }
 }
 
+bool RuleBasedBuilder::HasUnknownAtoms(mol::ResidueHandle res)
+{
+  this->LookupCompound(res);
+  if (!last_compound_) {
+    return true;
+  }
+  this->ReorderAtoms(res, last_compound_);
+  AtomSpecList::const_iterator j=last_compound_->GetAtomSpecs().begin();
+  mol::AtomHandleList atoms=res.GetAtomList();
+  mol::AtomHandleList::iterator i=atoms.begin();
+  for (mol::AtomHandleList::iterator 
+       i=atoms.begin(), e=atoms.end(); i!=e; ++i) {
+    if ((*i).Impl()->GetState()==std::numeric_limits<unsigned int>::max()) {
+      if ((*i).GetElement()=="H" && this->GetStrictHydrogenMode()==false) {
+        continue;
+      }
+      return true;
+    }
+  }
+  return false;
+}
+
 void RuleBasedBuilder::FillAtomProps(mol::AtomHandle atom, const AtomSpec& spec) 
 {
+  Conopology& conop_inst=Conopology::Instance();
   mol::AtomProp props=atom.GetAtomProps();
-  if (props.element=="") {
+  if (!conop_inst.IsValidElement(props.element)) {
     props.element=spec.element;
   }
-  Conopology& conop_inst=Conopology::Instance();  
   if (props.radius==0.0) {
     props.radius=conop_inst.GetDefaultAtomRadius(spec.element);    
   }
@@ -75,8 +97,9 @@ void RuleBasedBuilder::FillAtomProps(mol::AtomHandle atom, const AtomSpec& spec)
   atom.SetAtomProps(props);  
 }
 
-void RuleBasedBuilder::FillResidueProps(mol::ResidueHandle residue) {
-  LookupCompound(residue);
+void RuleBasedBuilder::FillResidueProps(mol::ResidueHandle residue) 
+{
+  this->LookupCompound(residue);
   if (!last_compound_)
     return;
   residue.SetChemClass(last_compound_->GetChemClass());
@@ -91,16 +114,24 @@ struct OrdinalComp {
 };
 
 
-void RuleBasedBuilder::LookupCompound(const mol::ResidueHandle& rh) {
-   if ((last_compound_) && (rh.GetName()==last_compound_->GetID())) {
-     return;
-   } else {
-     last_compound_= compound_lib_->FindCompound(rh.GetName());
-   }
+void RuleBasedBuilder::LookupCompound(const mol::ResidueHandle& rh) 
+{
+  Compound::Dialect dialect=this->GetDialect()==PDB_DIALECT ? Compound::PDB : Compound::CHARMM;  
+  if ((last_compound_) && (rh.GetName()==last_compound_->GetID())) {
+   return;
+  }
+  last_compound_=compound_lib_->FindCompound(rh.GetName(), dialect);
+  if (!last_compound_ && this->GetDialect()!=PDB_DIALECT) {
+    last_compound_=compound_lib_->FindCompound(rh.GetName(), Compound::PDB);
+  }
 }
 
-void RuleBasedBuilder::ReorderAtoms(const mol::ResidueHandle& residue,
-                             CompoundPtr compound) {
+void RuleBasedBuilder::ReorderAtoms(mol::ResidueHandle residue,
+                                    CompoundPtr compound) 
+{
+  if (last_residue_==residue) {
+    return;
+  }
   mol::impl::ResidueImplPtr impl=residue.Impl();
   mol::impl::AtomImplList::iterator i=impl->GetAtomList().begin();
   for (; i!=impl->GetAtomList().end(); ++i) {
@@ -108,7 +139,7 @@ void RuleBasedBuilder::ReorderAtoms(const mol::ResidueHandle& residue,
     int index=compound->GetAtomSpecIndex(atom->GetName());
     if (index==-1) {
       if (!this->OnUnknownAtom(mol::AtomHandle(atom))) {
-        atom->SetState(std::numeric_limits<int>::max());
+        atom->SetState(std::numeric_limits<unsigned int>::max());
       }
       continue;
     }
@@ -116,6 +147,14 @@ void RuleBasedBuilder::ReorderAtoms(const mol::ResidueHandle& residue,
   }
   std::sort(impl->GetAtomList().begin(), impl->GetAtomList().end(),
             OrdinalComp());
+  last_residue_=residue;
+  unknown_atoms_=this->HasUnknownAtoms(residue);
+  if (unknown_atoms_) {
+    LOG_WARNING("residue " << residue << " doesn't look like a standard " 
+                << residue.GetKey());
+    residue.SetChemClass(mol::ChemClass(mol::ChemClass::Unknown));
+    residue.SetOneLetterCode('?');
+  }
 }
 
 
@@ -130,7 +169,9 @@ mol::ResidueKey RuleBasedBuilder::IdentifyResidue(const mol::ResidueHandle& rh)
   }
 }
 
-mol::AtomHandle RuleBasedBuilder::LocateAtom(const mol::AtomHandleList& ahl, int ordinal) {
+mol::AtomHandle RuleBasedBuilder::LocateAtom(const mol::AtomHandleList& ahl, 
+                                             int ordinal) 
+{
   if (ahl.empty())
     return mol::AtomHandle();
   const mol::AtomHandle* r_it=&ahl.back();
@@ -146,14 +187,26 @@ mol::AtomHandle RuleBasedBuilder::LocateAtom(const mol::AtomHandleList& ahl, int
   return  not_found ? mol::AtomHandle() : *r_it;
 }
 
-void RuleBasedBuilder::ConnectAtomsOfResidue(const mol::ResidueHandle& rh) {
+
+inline void dist_connect(RuleBasedBuilder* b, mol::AtomHandleList atoms)
+{
+  for (mol::AtomHandleList::const_iterator i=atoms.begin(), 
+       e=atoms.end(); i!=e; ++i) {
+    b->DistanceBasedConnect(*i);
+  }  
+}
+void RuleBasedBuilder::ConnectAtomsOfResidue(mol::ResidueHandle rh) 
+{
+
   LookupCompound(rh);
+    
   if (!last_compound_) {
-    mol::AtomHandleList atoms=rh.GetAtomList();
-    for (mol::AtomHandleList::const_iterator i=atoms.begin(), 
-         e=atoms.end(); i!=e; ++i) {
-      this->DistanceBasedConnect(*i);
-    }
+    dist_connect(this, rh.GetAtomList());
+    return;
+  }
+  this->ReorderAtoms(rh, last_compound_);
+  if (unknown_atoms_) {
+    dist_connect(this, rh.GetAtomList());
     return;
   }
   mol::XCSEditor e=rh.GetEntity().RequestXCSEditor(mol::BUFFERED_EDIT);
@@ -164,25 +217,30 @@ void RuleBasedBuilder::ConnectAtomsOfResidue(const mol::ResidueHandle& rh) {
       mol::AtomHandle a1=this->LocateAtom(atoms, bond.atom_one);
       mol::AtomHandle a2=this->LocateAtom(atoms, bond.atom_two);
       if (a1.IsValid() && a2.IsValid() && this->IsBondFeasible(a1, a2)) {
-          e.Connect(a1, a2, bond.order);
+        if (this->GetStrictHydrogenMode() && 
+            (a1.GetElement()=="H" || a2.GetElement()=="H")) {
+          continue;
+        }
+        e.Connect(a1, a2, bond.order);
       }
   }
-  for (mol::AtomHandleList::const_iterator i=atoms.begin(),
-       e=atoms.end(); i!=e; ++i) {
-    if (int((*i).Impl()->GetState())==std::numeric_limits<int>::max()) {
-      this->DistanceBasedConnect(*i);      
+  for (mol::AtomHandleList::iterator i=atoms.begin(), e=atoms.end(); i!=e; ++i) {
+    if ((*i).GetElement()=="H" && (*i).GetBondCount()==0) {
+      this->DistanceBasedConnect(*i);
     }
   }
 }
 
-void RuleBasedBuilder::ConnectResidueToNext(const mol::ResidueHandle& rh,
-                                            const mol::ResidueHandle& next) {
+void RuleBasedBuilder::ConnectResidueToNext(mol::ResidueHandle rh,
+                                            mol::ResidueHandle next) 
+{
   if (!next.IsValid()) {
     return;
   }
+  Compound::Dialect dialect=this->GetDialect()==PDB_DIALECT ? Compound::PDB : Compound::CHARMM;
   mol::XCSEditor e=rh.GetEntity().RequestXCSEditor(mol::BUFFERED_EDIT);
-  CompoundPtr mc=compound_lib_->FindCompound(rh.GetName());
-  CompoundPtr nc=compound_lib_->FindCompound(next.GetName());
+  CompoundPtr mc=compound_lib_->FindCompound(rh.GetName(), dialect);
+  CompoundPtr nc=compound_lib_->FindCompound(next.GetName(), dialect);
   if (!(mc && nc))
     return;
   // check if both of the residues are able to form a peptide bond.
@@ -200,11 +258,14 @@ void RuleBasedBuilder::ConnectResidueToNext(const mol::ResidueHandle& rh,
   // the peptide bond.
   if (c.IsValid() && n.IsValid() && this->DoesPeptideBondExist(c, n)) {
     e.Connect(c, n, 1);
+    rh.SetIsProtein(true);
+    next.SetIsProtein(true);
   }
 }
 
 
-void RuleBasedBuilder::AssignTorsions(const mol::ChainHandle& chain) {
+void RuleBasedBuilder::AssignTorsions(mol::ChainHandle chain) 
+{
   if (chain.GetResidueCount()==0)
     return;
   std::vector<mol::ResidueHandle> rlist = chain.GetResidueList();
@@ -215,11 +276,13 @@ void RuleBasedBuilder::AssignTorsions(const mol::ChainHandle& chain) {
   }
 }
 
-void RuleBasedBuilder::AssignTorsionsToResidue(const mol::ResidueHandle& residue) {
+void RuleBasedBuilder::AssignTorsionsToResidue(mol::ResidueHandle residue) 
+{
   /// The only components having named torsions are the standard set of amino
   /// acids, plus some of compounds derived from them such as selenium
   /// methionine. Things are simplified a lot by only storing the torsions
-  /// of the side chains in the database. PHI, PSI and OMEGA torsions are    checked without a lookup in the database.
+  /// of the side chains in the database. PHI, PSI and OMEGA torsions are    
+  /// checked without a lookup in the database.
   LookupCompound(residue);
   if (!last_compound_)
     return;  
@@ -253,10 +316,12 @@ void RuleBasedBuilder::FillAtomProps(mol::AtomHandle atom)
 {
   LookupCompound(atom.GetResidue());
   if (!last_compound_) {
+    this->OnUnknownAtom(atom);
     return;
   }
   int index=last_compound_->GetAtomSpecIndex(atom.GetName());
   if (index==-1) {
+    this->OnUnknownAtom(atom);
     return;
   }
   const AtomSpec& atom_spec=last_compound_->GetAtomSpecs()[index];
@@ -266,10 +331,10 @@ void RuleBasedBuilder::FillAtomProps(mol::AtomHandle atom)
 bool RuleBasedBuilder::OnUnknownAtom(mol::AtomHandle atom)
 {
   mol::AtomProp props=atom.GetAtomProps();
-  if (props.element=="") {
+  Conopology& conop_inst=Conopology::Instance();
+  if (!conop_inst.IsValidElement(props.element)) {
     props.element=Builder::GuessAtomElement(atom.GetName(), props.is_hetatm);
   }
-  Conopology& conop_inst=Conopology::Instance();  
   if (props.radius==0.0) {
     props.radius=conop_inst.GetDefaultAtomRadius(props.element);    
   }
diff --git a/modules/conop/src/rule_based_builder.hh b/modules/conop/src/rule_based_builder.hh
index bd1af72f50e8a9973a8e4117593c83b92876e4e5..ff35e0adb1cd47f79b36fcc3ec80fa941a2f39cf 100644
--- a/modules/conop/src/rule_based_builder.hh
+++ b/modules/conop/src/rule_based_builder.hh
@@ -43,10 +43,18 @@ public:
     : compound_lib_(compound_lib), last_compound_() {
   }
   
+  virtual void SetDialect(Dialect dialect) {
+    if (this->GetDialect()!=dialect) {
+      Builder::SetDialect(dialect);
+      last_compound_=CompoundPtr();
+      compound_lib_->ClearCache();
+    }
+  }
+  
   /// \brief fill atom properties such as element and radius
   virtual void FillAtomProps(mol::AtomHandle atom);
   
-  virtual void CompleteAtoms(const mol::ResidueHandle& rh);
+  virtual void CompleteAtoms(mol::ResidueHandle rh);
 
   /// \brief  Check residue completeness
   ///
@@ -68,7 +76,7 @@ public:
   virtual mol::ResidueKey IdentifyResidue(const mol::ResidueHandle& rh);
 
 
-  virtual void ConnectAtomsOfResidue(const mol::ResidueHandle& rh);
+  virtual void ConnectAtomsOfResidue(mol::ResidueHandle rh);
 
   /// \brief  Connects the two residues together.
   ///
@@ -79,11 +87,11 @@ public:
   ///         bond.
   /// \param next
   ///          is the C-terminal partner, donating the nitrogen to the bond.
-  virtual void ConnectResidueToNext(const mol::ResidueHandle& rh,
-                                    const mol::ResidueHandle& next);
+  virtual void ConnectResidueToNext(mol::ResidueHandle rh,
+                                    mol::ResidueHandle next);
   /// \brief requires chemical types
-  virtual void AssignTorsions(const mol::ChainHandle& ch);
-  virtual void AssignTorsionsToResidue(const mol::ResidueHandle& residue);
+  virtual void AssignTorsions(mol::ChainHandle ch);
+  virtual void AssignTorsionsToResidue(mol::ResidueHandle residue);
   /// \brief  Invoked whenever an unkknown atom has been encountered during a
   ///         residue completeness check.
   ///
@@ -108,21 +116,23 @@ public:
   /// \brief Set residue properties such as chemical class
   virtual void FillResidueProps(mol::ResidueHandle residue);
 
-
-                              
+  /// \brief whether the residue has unknown atoms
+  bool HasUnknownAtoms(mol::ResidueHandle res);                              
   /// \brief Check whether the residue has all required atoms. This does not
   ///        include hydrogens and leaving atoms such as the terminal OXT.
   virtual bool IsResidueComplete(const mol::ResidueHandle& residue);
 private:
   CompoundLibPtr      compound_lib_;
   CompoundPtr         last_compound_;
+  mol::ResidueHandle  last_residue_;
+  bool                unknown_atoms_;
   void LookupCompound(const mol::ResidueHandle& rh);
   /// Change internal order of atoms in residue to the order given by compound
-  void ReorderAtoms(const mol::ResidueHandle& residue, CompoundPtr compound);
+  void ReorderAtoms(mol::ResidueHandle residue, CompoundPtr compound);
 
   mol::AtomHandle LocateAtom(const mol::AtomHandleList& ahl, int ordinal);
 
-  void AssignBackBoneTorsionsToResidue(const mol::ResidueHandle& residue);
+  void AssignBackBoneTorsionsToResidue(mol::ResidueHandle residue);
 
 
 };
diff --git a/modules/conop/src/sanitizer.cc b/modules/conop/src/sanitizer.cc
deleted file mode 100644
index d7d8d42783840f49014d92e315dd9ed901360598..0000000000000000000000000000000000000000
--- a/modules/conop/src/sanitizer.cc
+++ /dev/null
@@ -1,108 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#include "sanitizer.hh"
-#include <ost/mol/impl/atom_impl.hh>
-#include <ost/log.hh>
-#include <limits>
-#include <ost/mol/impl/residue_impl.hh>
-namespace ost { namespace conop {
-
-
-Sanitizer::Sanitizer(const CompoundLibPtr& lib)
-  :compound_lib_(lib) {
-}
-bool Sanitizer::VisitAtom(const mol::AtomHandle& atom) {
-  return true;
-}
-
-bool Sanitizer::VisitResidue(const mol::ResidueHandle& residue) {
-  if (CompoundPtr comp=this->IdentifyResidue(residue)) {
-    this->ReorderAtoms(residue, comp);
-    this->VerifyCompleteness(residue, comp);
-    return true;
-  }
-  LOGN_ERROR("Unknown residue with name " << residue.GetName());
-  return false;
-}
-
-void Sanitizer::FillAtomProps(mol::AtomHandle atom, const AtomSpec& spec) {
-  mol::AtomProp props=atom.GetAtomProps();
-  if (props.element!=spec.element) {
-    props.element=spec.element;
-    LOGN_MESSAGE("Correcting element for " << atom.GetQualifiedName() <<
-                 " (now " << spec.element << ", was " << props.element << ")");
-    atom.SetAtomProps(props);
-  }
-}
-
-void Sanitizer::VerifyCompleteness(const mol::ResidueHandle& residue,
-                                   CompoundPtr compound) {
-  AtomSpecList::const_iterator j=compound->GetAtomSpecs().begin();
-  mol::AtomHandleList atoms=residue.GetAtomList();
-  mol::AtomHandleList::iterator i=atoms.begin();
-  for (; j!=compound->GetAtomSpecs().end() && i!=atoms.end(); ++j) {
-    if ((*j).is_leaving || (*j).element=="H")
-      continue;
-    if ((*j).ordinal!=static_cast<int>((*i).Impl()->GetState())) {
-      this->OnMissingAtom(residue, (*j).name);
-    } else {
-      this->FillAtomProps(*i, *j);
-      ++i;
-    }
-  }
-}
-
-struct OrdinalComp {
-  bool operator()(const mol::impl::AtomImplPtr& a,
-                  const mol::impl::AtomImplPtr& b) const {
-    return a->GetState()<b->GetState();
-  }
-};
-
-void Sanitizer::ReorderAtoms(const mol::ResidueHandle& residue,
-                             CompoundPtr compound) {
-  mol::impl::ResidueImplPtr impl=residue.Impl();
-  mol::impl::AtomImplList::iterator i=impl->GetAtomList().begin();
-  for (; i!=impl->GetAtomList().end(); ++i) {
-    mol::impl::AtomImplPtr atom=*i;
-    int index=compound->GetAtomSpecIndex(atom->GetName());
-    if (index==-1) {
-
-      this->OnUnknownAtom(mol::AtomHandle(atom));
-      atom->SetState(std::numeric_limits<int>::max());
-      continue;
-    }
-    atom->SetState((compound->GetAtomSpecs())[index].ordinal);
-  }
-  std::sort(impl->GetAtomList().begin(), impl->GetAtomList().end(),
-            OrdinalComp());
-}
-
-bool Sanitizer::VisitChain(const mol::ChainHandle& chain) {
-  return true;
-}
-
-CompoundPtr Sanitizer::IdentifyResidue(const mol::ResidueHandle& residue) {
-  CompoundPtr comp=compound_lib_->FindCompound(residue.GetName());
-  if (!comp) {
-    return this->OnUnknownResidue(residue);
-  }
-  return comp;
-}
-}}
diff --git a/modules/conop/src/sanitizer.hh b/modules/conop/src/sanitizer.hh
deleted file mode 100644
index 609414c7c420a59963bac2747d57cb7edfd58e95..0000000000000000000000000000000000000000
--- a/modules/conop/src/sanitizer.hh
+++ /dev/null
@@ -1,65 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef OST_CONOP_SANITIZER_HH
-#define OST_CONOP_SANITIZER_HH
-
-#include <ost/mol/mol.hh>
-#include <ost/conop/compound_lib.hh>
-
-namespace ost { namespace conop {
-
-/// \brief Structural cleanup
-/// 
-/// \todo Sanitizer acts both as the checker and the instance responsible for
-///       cleaning up structural problems. Is this desired?
-class DLLEXPORT_OST_CONOP Sanitizer : public mol::EntityVisitor {
-public:
-  Sanitizer(const CompoundLibPtr& compound_lib);
-  
-  virtual bool VisitAtom(const mol::AtomHandle& atom);
-  
-  virtual bool VisitResidue(const mol::ResidueHandle& residue);
-  
-  virtual bool VisitChain(const mol::ChainHandle& chain);
-  
-  virtual CompoundPtr OnUnknownResidue(const mol::ResidueHandle& residue) {
-    return CompoundPtr();
-  }
-  
-  virtual void OnUnknownAtom(const mol::AtomHandle& atom) { }
-  virtual void OnMissingAtom(const mol::ResidueHandle& residue,
-                             const String& atom_name) { }
-private:
-  void FillAtomProps(mol::AtomHandle atom, const AtomSpec& spec);
-  /// Change internal order of atoms in residue to the order given by compound
-  void ReorderAtoms(const mol::ResidueHandle& residue, CompoundPtr compound);
-  /// Verify all atoms are present. 
-  /// 
-  /// The check exludes hydrogen atoms as well as "leaving atoms", i.e.
-  /// carboxy-terminal atoms that leave when the peptide bond is formed.
-  
-  void VerifyCompleteness(const mol::ResidueHandle& residue, CompoundPtr compound);
-  CompoundPtr IdentifyResidue(const mol::ResidueHandle& residue);
-  
-
-  CompoundLibPtr     compound_lib_;
-};
-
-}}
-#endif
diff --git a/modules/doc/external.rst b/modules/doc/external.rst
new file mode 100644
index 0000000000000000000000000000000000000000..7ea3b22db79befda28b9a262e95a91cd64b26d6d
--- /dev/null
+++ b/modules/doc/external.rst
@@ -0,0 +1,111 @@
+Using External Programs within OpenStructure
+================================================================================
+
+Introduction
+--------------------------------------------------------------------------------
+
+It is often very useful to use external programs to do a specific task. In principle, this can be done by writing out files from OpenStructure and manually running an external program, however, for convenience, this can also be done directly from within OpenStructure using Python commands. 
+
+This tutorial will give you some hints how to do this for a new external program. The process basically consists of four steps:
+
+  * locate the executable of the external program
+  * prepare all necessary files
+  * execute the external program from python
+  * read in generated output
+
+
+Locating the Executable
+--------------------------------------------------------------------------------
+
+There is a helper function available to locate files, and especially executables: :func:`~ost.settings.Locate`. Using this, you can obtain the full path of an executable.
+
+As an example, we would like to obtain the full path of the msms executable (a program to calculate molecular surfaces):
+
+.. code-block:: python
+
+  from ost import settings
+  exe_path=settings.Locate('msms', search_paths=['/opt/app','/home/app'],
+              env_name='MSMS', search_system_paths=True)
+  print exe_path
+  
+The :func:`~ost.settings.Locate` command looks for the program with the name 
+`msms`. If env_name is set, it first looks if an environment variable with the 
+name `MSMS` is set. If not, all paths in search_paths are searched. If the 
+executable could still not be found and search_system_paths is set to True, the 
+binary search paths are searched. If the executable could not be found, a 
+:exc:`~ost.FileNotFound` exception is raised with a detailed description where 
+Locate was searching for the executable.
+    
+Prepare All Files
+--------------------------------------------------------------------------------
+
+The preparation of the necessary files is very dependent on the external program. Often it is useful to generate a temporary directory or file. For this, the python module tempfile is very handy.
+
+An example how to generate a temporary directory, open a file in this directory and write the position and radius of all atoms into this file is shown here:
+
+.. code-block:: python
+
+  import tempfile
+  import os
+  
+  # generate a temporary directory
+  tmp_dir_name=tempfile.mkdtemp()
+  print 'temporary directory:',tmp_dir_name
+  
+  # generate and open a file in the temp directory
+  tmp_file_name=os.path.join(tmp_dir_name,"entity")
+  tmp_file_handle=open(tmp_file_name, 'w')
+  print 'temporary file:',tmp_file_handle
+  
+  # write position and radius of all atoms to file
+  for a in entity.GetAtomList():
+    position=a.GetPos()
+    tmp_file_handle.write('%8.3f %8.3f %8.3f %4.2f\n' % (position[0],
+                          position[1], position[2], a.GetProp().radius))
+                          
+  # close the file
+  tmp_file_handle.close()
+
+Execute the External Program
+--------------------------------------------------------------------------------
+
+The external program can be executed from python using the python module subprocess.
+
+To run the external program msms from the above example, with the temporary file generated before, we can use the following:
+
+.. code-block:: python
+
+  import subprocess
+
+  # set the command to execute
+  command="%s -if %s -of %s" % (exe_path,
+            tmp_file_name, tmp_file_name)
+  print 'command:',command
+
+  # run the executable with the command
+  proc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
+  stdout_value, stderr_value = proc.communicate()
+
+  #check for successful completion of msms
+  if proc.returncode!=0:
+    print "WARNING: msms error\n", stdout_value
+    raise subprocess.CalledProcessError(proc.returncode, command)
+
+  # print everything written to the command line (stdout)
+  print stdout_value
+    
+Read Generated Output
+--------------------------------------------------------------------------------
+
+The last step includes reading of generated files (like in the case of msms) and/or processing of the generated command line output.
+
+Here we first print the command line output and then load the generated msms surface and print the number of vertex points:
+
+.. code-block:: python
+
+  # print everything written to the command line (stdout)
+  print stdout_value
+  
+  # read msms surface from file
+  surface=io.LoadSurface(tmp_file_name, "msms")
+  print 'number of vertices:',len(surface.GetVertexIDList())
diff --git a/modules/doc/install.rst b/modules/doc/install.rst
new file mode 100644
index 0000000000000000000000000000000000000000..abd0b2b88fc0b8a8847d45fecad463bda6219b5c
--- /dev/null
+++ b/modules/doc/install.rst
@@ -0,0 +1,180 @@
+Installing OpenStructure From Source
+================================================================================
+
+.. note::
+
+  This document describes how to install OpenStructure from source. If you are
+  mainly insterested in using OpenStructure and are not planning to modify the
+  code of OpenStructure itself, please use one of the binaries `available for
+  download <http://www.openstructure.org/download/>`_.
+
+Brief Overview
+--------------------------------------------------------------------------------
+
+Compiling OpenStructure consists of several steps that are described below in more detail. In essence, these steps are:
+
+ * Installing the Dependencies
+ * Checking out the source code from SVN
+ * Configuring the build with cmake
+ * Compiling an Linking
+ 
+
+.. installdeps_
+
+Installing the Dependencies
+--------------------------------------------------------------------------------
+
+OpenStructure uses a bunch of OpenSource libraries. If you haven't already installed them, please install them now! Where appropriate the minimally required version is given in parantheses.
+
+ * `CMake <http://cmake.org>`_ (2.6.4)
+ * `Eigen2 <http://eigen.tuxfamily.org>`_ (2.0.6)
+ * `Boost <http://boost.org>`_ (1.37)
+ * `libpng <http://www.libpng.org>`_ 
+ * `Python <http://python.org>`_ (2.4)
+ * `Qt <http://qt.nokia.com>`_ (4.5)
+
+When you enable support for image processing, you will need:
+
+ * `FFTW3 <http://fftw.org>`_. By default, OpenStructure is compiled with single precision and thus also requires FFTW to be compiled with single precision. Most platforms offer this as a second package. If you are compiling manually, use the `--enable-single` option.
+
+ * `libtiff <http://www.libtiff.org>`_
+
+
+
+If you would like to use the graphical user interface, also install:
+
+ * `SIP <http://www.riverbankcomputing.co.uk/software/sip/download>`_.
+ * `PyQt4 <http://www.riverbankcomputing.co.uk/software/pyqt/download>`_.
+
+In case you are compiling under Windows you have to install `Visualstudio
+2008 <http://www.microsoft.com/express/Downloads>`_. to compile the dependecies 
+and OpenStructure. We recommend to compile the dependecies manually. Enter the 
+directories where the dependencies are located in Tools->Options->Projects and 
+Solutions->VC++ directories. Choose 'bin' directories to enter program paths to 
+cmake, qmake and python, 'lib' directories to point to the location(s) of your 
+dependencies.
+
+Checking out the Source
+--------------------------------------------------------------------------------
+
+You can checkout the source from SVN. The repository is located at
+
+   https://dng.biozentrum.unibas.ch/svn/openstructure/trunk
+
+If you are using the commandline client, type in your shell 
+
+.. code-block:: bash
+
+   svn co https://dng.biozentrum.unibas.ch/svn/openstructure/trunk
+
+On Windows, we recommend to install a graphical frontend for svn, for example `tortoisesvn <http://tortoisesvn.tigris.org>`_. 
+
+
+Configuring
+--------------------------------------------------------------------------------
+
+
+OpenStructure uses `CMake <http://cmake.org>`_ for compiling and building the project. The next required step is to configure the build environment using cmake. You can do that by invoking `cmake` in the project directory.
+
+.. code-block:: bash
+
+  cmake . <options>
+
+There are two kinds of options: Options that let you control the building behaviour, enabling and disabling the compilation of certain modules and options that let you tell CMake where to find the dependencies. All of them are passed to CMake with via `-D<opt>=<value>`.
+
+On Windows, use Tools -> VisualStudio commandline prompt from within VisualStudio)
+
+Flag to choose build generator
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+CMake supports different build generators. On UNIX, that is MacOS X and Linux, the default build generator is Makefiles, but it is also possible to use other programs. For a list of supported build generators on your platform, start cmake without parameters. 
+
+On Windows you have to explicitly set the buil generator to "Visual Studio 9 2008":
+
+.. code-block:: bash
+
+  cmake -G"Visual Studio 9 2008"
+
+
+Flags to Control the Dependencies
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+By default, `CMake <http://cmake.org>`_ searches the standard directories for dependencies. However, on some systems, this might not be enough. Here is a short description of how CMake figures out what dependencies to take and how you can influence it.
+
+ * Boost is mainly controlled via the `BOOST_ROOT` option. If boost wasn't
+   found, it should be set to the prefix of the boost installation.
+
+ * `QT_QMAKE_EXECUTABLE` defines the exact Qt installation to take. It should 
+   be set to the full path to `qmake`.
+ 
+ * `PYTHON_ROOT` is the Python equivalent of BOOST_ROOT. It should be set to 
+   the prefix path containing the python binary, headers and libraries.
+
+ * `SYS_ROOT` controls the general prefix for searching libraries and headers.
+   By default, it is set to `/`.
+
+Build Options
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+ * `ENABLE_UI` controls whether to build the graphical user interface module. By
+   default it is set to true. 
+ * `ENABLE_IMG` controls whether to build the image processing module. This will
+   enable support for density maps, and general image processing in 1, 2 an 3
+   dimensions. By default it is set to true. 
+
+ * `ENABLE_GFX` controls whether to build the graphics module. By default, this
+   is set to true. If set to none, this implies `ENABLE_UI=NO`.
+   
+ * Shader support is controlled with `USE_SHADER`. By default, no shaders are
+   used.
+   
+ * If `OPTIMIZE` is set to 1, an optimized version of OpenStructure is built.
+
+Example Configurations
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+**Ubuntu 10.04 Lucid/Lynx**
+
+All the dependencies can be installed from the package manager and are thus located in standard locations. cmake will automatically find them without the need to pass any additional parameters. The only exception is -DOPTIMIZE, which will tell cmake to build an optimized (-O3 -DNDEBUG) version of OpenStructure.
+
+.. code-block:: bash
+
+  cmake . -DOPTIMIZE=1
+
+**MacOS X with MacPorts and optimization turned on**
+
+MacPorts installs all the software under /opt/local. Thus we have to tell cmake where to find Boost, Python and Qt.
+
+.. code-block:: bash
+  
+  cmake . -DBOOST_ROOT=/opt/local -DPYTHON_ROOT=/opt/local \
+        -DSYS_ROOT=/opt/local -DQT_QMAKE_EXECUTABLE=/opt/local/bin/qmake \
+        -DOPTIMIZE=1
+
+
+Building the Project
+--------------------------------------------------------------------------------
+
+Type `make`. If you are using a multi-core machine, you can use the `-j` flag to 
+run multiple jobs at once.
+
+On Windows run 'Build OpenStructure' from the build menu.
+
+
+
+What's next?
+--------------------------------------------------------------------------------
+
+On Linux and MacOS X, you can start dng from the command-line. The binaries are all located in stage/bin:
+
+.. code-block:: bash
+
+  stage/bin/dng
+  
+or, to start the command-line interpreter:
+
+.. code-block:: bash
+
+  stage/bin/ost
+  
+If you repeatedly use OpenStructure, it is recommended to add /path/to/dng/stage/bin to your path.
diff --git a/modules/doc/intro-01.rst b/modules/doc/intro-01.rst
new file mode 100644
index 0000000000000000000000000000000000000000..da448f8c3e05e5c03572377bf31e52af81df0c84
--- /dev/null
+++ b/modules/doc/intro-01.rst
@@ -0,0 +1,226 @@
+Introduction to the :mod:`~ost.mol` Module
+================================================================================
+
+For the course of this tutorial, we assume that you have :ref:`DNG up and running<start-dng>`.
+
+Loading and inspecting a protein structure
+--------------------------------------------------------------------------------
+
+The code to load and save structures is not directly part of the mol module, but rather lives in a module dedicated to input and output of any kind of data: The 
+:mod:`~ost.io` module. We will be using functions of this module to load 
+structures. 
+
+One of the most commonly used file formats for macromolecular structures are PDB 
+(Brookhaven Protein Databank) files. The official name for  molecules stored in 
+a PDB file is an *entity* and we decided to follow this convention in 
+OpenStructure. You will hear this word all the time, but you can replace the 
+word entity with molecule (or most of the time even protein) in your head.
+
+
+To load a PDB file, simply type
+
+.. code-block:: python
+
+   fragment=io.LoadPDB('/path/to/examples/entity/fragment.pdb')
+
+This will load the fragment from the specified file 'fragment.pdb' and store the 
+result in fragment.  The :func:`~ost.io.LoadPDB` has many option, which, for 
+simplicity will not be discussed here. If you want to know more about the 
+function, type:
+
+.. code-block:: python
+
+   help(io.LoadPDB)
+
+or read the :func:`online documentation <ost.io.LoadPDB>`.
+     
+The loaded structure is an instance of :class:`~ost.mol.EntityHandle` which offers a comprehensive interface to inspect an manipulate molecular structures. Now let's inspect what we just loaded:
+
+.. code-block:: python
+
+   print len(fragment.chains), fragment.chains
+   print len(fragment.residues), fragment.residues
+   print len(fragment.atoms), fragment.atoms
+
+As you can see, our fragment consists of one peptide chain of 12 amino acids and 
+has 81 atoms in total. Now let's examine our fragment in more detail. Enter the 
+command
+    
+.. code-block:: python
+
+  for residue in fragment.residues:
+    print residue, 'has', len(residue.atoms), 'atom(s).'
+    for atom in residue.atoms:
+      print ' ', atom.name, atom.pos
+
+
+This will group the atoms by residue. And, for completeness, we will first group them by chain, then by residues.
+
+.. code-block:: python
+
+  for chain in fragments.chains:
+    print 'chain', chain.name, 'has', len(chain.residues), 'residue(s)'
+    for residue in chain.residues:
+      print ' ', residue, 'has', len(residue.atoms), 'atom(s).'
+      for atom in residue.atoms:
+        print '    ', atom.name, atom.pos
+
+A protein fragment would not be complete without bonds: Let's see 
+what bonds we have in there:
+
+.. code-block:: python
+  
+  for bond in fragment.bonds:
+    print bond
+    
+From these short code examples we already see how the entity is structured: On 
+one hand we have a hierarchy of chains, residues and atoms. On the other hand, 
+we have bonds that form a network overlayed on the hierarchy. This is 
+illustrated in the picture on the left. An important feature of entities is that 
+we can always assume that the hierarchy is intact. You will never find an atom 
+without residues, no residue can exist without a parent chain and chains belong 
+always to an entity. 
+
+Let There Be Shiny Graphics
+--------------------------------------------------------------------------------
+
+For visually inspecting the fragment, we now create a graphical representation 
+of the entity. The graphical representation os completely separate from the :class:`~ost.mol.EntityHandle` class. This is on purpose. When writing processing scripts, usually no graphical representation is required and things would be slowed down without any reason. The following code will take our fragment and initialise a :class:`gfx.Entity<ost.gfx.Entity>`, add it to the scene, and center the camera on it.
+
+.. code-block:: python
+  
+  go=gfx.Entity("Fragment", fragment)
+  scene.Add(go)
+  scene.CenterOn(go)
+
+
+Now you will see the fragment in the 3D window.
+
+Use the mouse to rotate, zoom in an shift the camera. Double clicking on an atom 
+will center the camera on that atom. If you want to learn more about the 
+:mod:`~ost.gfx` module, you are encouraged to read :doc:`the gfx 
+intro<intro-03>` and the :mod:`gfx documentation<ost.gfx`.
+
+Introduction to Views
+--------------------------------------------------------------------------------
+
+Often during processing and visualisation of data, only parts of a protein 
+structure are of interest. This realisation has had a major impact on the design 
+of OpenStructure and is tied very deeply into the core of the framework. 
+Subparts of structure are modeled as so-called :class:`EntityViews 
+<ost.mol.EntityView>`. You can think of them as a selection of chains, residues, 
+atoms and bonds of an entity. A views has almost the same interface as the 
+underlying entity, making it very easy to mix entity views with handles in 
+Python due to the dynamic nature of the language. An algorithm that is written 
+for entities will almost always (with some care) also work for 
+:class:`EntityHandles <ost.mol.EntityHandle>`. This is referred to as 
+`duck-typing <http://en.wikipedia.org/wiki/Duck_typing>`_ (I don' t care if it 
+is a duck as long as it looks like a duck), a concept used all over the place in Python. 
+
+The view consists of one chain, one residue and two atoms. Again the same rule 
+applies: No atom can be part of the view without it's residue. In this example, 
+no bonds are included, since there is at most one atom per bond in the original structure.
+
+To familiarize yourself with the concept of views, we will use the fragment in 
+the 3D window.
+
+We will use several ways to select parts of our fragment:
+ * By using a dedicated query language
+ * By manually constructing a view
+
+The Query Language
+--------------------------------------------------------------------------------
+
+The first way to select parts of a structure is with a dedicated mini-language, 
+called :doc:`the query language <mol/base/query>`. In the Python Shell, type
+
+.. code-block:: python
+
+  go.selection=fragment.Select('')
+    
+The code performs a selection on the fragment and assigns the resulting view to 
+the selection of the graphical object. A green halo will be displayed around the 
+selected parts (image in the middle).
+
+.. image:: sel.png
+
+As you can see the previous statement created a “full view”, containing all the 
+chains, residues, atoms and bonds. To select lysine residues, type
+
+.. code-block:: python
+
+  go.selection=fragment.Select('rname=LYS')
+    
+
+As you can see (image on the right), the only lysine residue is now 
+highlighted in the 3D window, because it was the only one matching the predicate 
+"residue name must be equal to LYS". Several such predicates can be combined 
+with boolean operators such as *and* and *or*. To select residues with residue 
+number 1 to 3, the following statement will do the job:
+
+.. code-block:: python
+
+  go.selection=fragment.Select('rnum>=1 and rnum<=3')
+    
+but this is very cumbersome. That's why there is a shortcut to this statement. 
+You can specify a range of values.
+
+.. code-block:: python
+
+  go.selection=fragment.Select('rnum=1:3')
+
+For a complete description of what you can do with the query language, have a 
+look at the :doc:`../mol/base/query`.
+
+
+Constructing Views Manually
+--------------------------------------------------------------------------------
+
+Sometimes the query language Is Not Enough (TM). For these cases the 
+construction of manual entities becomes neccessary. This is pretty straight 
+forward:
+
+.. code-block:: python
+
+  view=fragment.CreateEmptyView()
+  ca=fragment.FindAtom('A', mol.ResNum(1), 'CA')
+  cb=fragment.FindAtom('A', mol.ResNum(1), 'CB')
+  view.AddAtom(ca)
+  view.AddAtom(cb)
+  go.SetSelection(view)
+
+The last step sets our constructed view as the current selection, displaying it 
+in the 3D window. As you can see, C-alpha and C-beta of the first residue are 
+not connected by bonds, even though both atoms are in the view. You have either 
+to add the bond manually with
+
+.. code-block:: python
+
+  ca_cb=ca.FindBondToAtom(cb)
+  view.AddBond(ca_cb)
+    
+Or, as a very convenient shortcut 
+:meth:`view.AddAllInclusiveBonds()<ost.mol.EntityView.AddAllInclusiveBonds>` to 
+add all bonds that have both bonding partners in the view.
+
+Don't forget to update the selection of the graphics object to see what view you 
+have created.
+
+Saving an Entity
+--------------------------------------------------------------------------------
+
+Saving an entity (or a view) is a breeze:
+
+.. code-block:: python
+
+   io.SavePDB(fragment, 'full.pdb')
+
+will save the full fragment. To save only the backbone atoms, we can first 
+select the backbone atoms and then save it:
+
+.. code-block:: python
+
+   io.SavePDB(fragment.Select('aname=CA,C,N,O'), 'backbone.pdb')
+
+That's it for the mol module. Continue with :doc:`part two<intro-02>` of the 
+tutorial.
diff --git a/modules/doc/intro-02.rst b/modules/doc/intro-02.rst
new file mode 100644
index 0000000000000000000000000000000000000000..95112b0bcc3accc7f5b883cd2e9730c9c1ee47e1
--- /dev/null
+++ b/modules/doc/intro-02.rst
@@ -0,0 +1,92 @@
+Introduction to the :mod:`~ost.img` Module
+================================================================================
+
+For the course of this tutorial, we assume that you have :ref:`DNG up and running<start-dng>`.
+
+
+Loading Images and Density Maps
+--------------------------------------------------------------------------------
+
+Openstructure features a :mod:`~ost.img` module that is dedicated to the 
+manipulation of images/density maps. The images or density maps can either be 
+one-, two- or three-dimensional. The most common formats used in X-ray and 
+electron  crystallography and atomic force microscope are supported in addition 
+to several general purpose image formats. See `supported file formats` for 
+details. The :mod:`~ost.img` module was originally developed as part of the 
+Image Processing Library & Toolbox IPLT. More documentation and examples can 
+also be found on the `IPLT website <http://www.iplt.org>`_.
+
+To load a density map, type
+
+.. code-block:: python
+
+   map=io.LoadImage('/path/to/examples/map/1ppt.map')
+
+This will load the fragment density map from the specified file 'fragment.map' 
+and store the result in map. 
+
+Now let's inspect what we just loaded:
+
+.. code-block:: python
+
+  print map.GetPixelSampling(), map.GetSize()
+    
+We can see that the sampling is set to 1.0 Angstroems in all three dimensions. The loaded map is an instance of :class:`~ost.img.ImageHandle`, a class to represent images in 1, 2 and 3 dimensions.
+
+Manipulating Images and Density Maps
+--------------------------------------------------------------------------------
+
+The algorithms used for manipulation of an image are found in the 
+:mod:`img.alg <ost.img.alg>` module. Therefore before using an algorithm we 
+first have to import the :mod:`img.alg <ost.img.alg>` module.
+
+.. code-block:: python
+
+  from ost.img import alg
+
+
+The :mod:`img.alg <ost.img.alg>` module provides a wide range of algorithm to 
+manipulate image data. Here for example we use a LowPassFilter to restrict the 
+resolution of the density map to frequencies lower than a treshold.
+
+.. code-block:: python
+
+   map_filtered=map.Apply(alg.LowPassFilter(3.0))
+
+The filtered map is stored in a new variable called `fragment_map_filtered`. A complete list of algorithms is available on the  :doc:`img/alg/alg` page.
+
+
+Displaying Images and Density Maps
+--------------------------------------------------------------------------------
+
+Now that we have a filtered map it's time to have a look at it. There are 
+fundamentally two ways to visualize 3-dimensional density maps. One is by 
+drawing isocontour surfaces. These are conceptually similar to contour lines 
+used in cartography: every point on an isosurface has the same density value. 
+Isosurfaces are easy to create in OpenStructure:
+
+.. code-block:: python
+
+   go=gfx.MapIso("filtered", map_filtered,0.5)
+   scene.Add(go)
+
+The other way to visualize a 3-dimensional map is by showing one 2-dimensional 
+density slice at a time, allowing the user to move through the slices. In 
+OpenStructure this is achieved using a DataViewer). 
+A DataViewer showing the filtered map is created using the following command:
+
+.. code-block:: python
+
+  gui.CreateDataViewer(map_filtered)
+
+This command displays a panel showing one slice of the density map lying on a 
+particular (x,y) plane in the coordinate reference system.
+The `z` and `x` keys can be used to move to slices lying at a lower or higher 
+coordinate along the `z` axis, allowing the examination of
+the full 3-dimensional volume.
+
+A more detailed explanation of the :mod:`~ost.img` module can be found in the 
+tutorial section for :mod:`~ost.img`.
+
+
+Continue with :doc:`part three <intro-03>` of the tutorial.
diff --git a/modules/doc/intro-03.rst b/modules/doc/intro-03.rst
new file mode 100644
index 0000000000000000000000000000000000000000..be0d793b049081f220e5dbff14d22e085fe53576
--- /dev/null
+++ b/modules/doc/intro-03.rst
@@ -0,0 +1,179 @@
+Introduction to the :mod:`~ost.gfx` Module
+================================================================================
+
+.. currentmodule:: ost.gfx
+
+For the course of this tutorial, we assume that you have :ref:`DNG up and 
+running<start-dng>`.
+
+As already mentioned in the :doc:`intro-01`, the basic representation of 
+molecular structures, sequences, images are completely independent from the 
+graphical rendering. Thus, to display it on the screen, we first have to create 
+a graphical representation of the object. This is illustrated for the entity 
+below, but follows a similar scheme for density maps, surfaces and other types 
+of data.
+
+.. code-block:: python
+  
+  pdb=io.LoadPDB('/path/to/molecule.pdb')
+  go=gfx.Entity('PROTEIN', pdb)
+  scene.Add(go)
+  scene.CenterOn(go)
+
+The last command is not mandatory, but very convenient to center the camera on the object. 
+
+
+The Scene
+--------------------------------------------------------------------------------
+
+
+The scene is the central registry for graphical objects and manages rendering 
+parameters. Among other parameters, it is used to setup the lighting, fog, 
+background color and the camera. The scene is a singleton, meaning that there is 
+only one scene available. The instance can be accessed via :func:`gfx.Scene`. 
+Because the scene is so important and commonly used, the scene is also available 
+as the `scene` variable in the interactive python shell as well as from scripts. 
+In fact, this is the preferred way to use functionality of the scene. As an easy example, let's change the background color:
+
+.. code-block:: python
+
+  scene.SetBackground(gfx.WHITE)
+
+Now, the color of the screen has changed to white. To set it back to black, simply assign :obj:`gfx.BLACK` to the background property.
+
+Objects are added to the scene by calling :meth:`Scene.Add`. Once added to the 
+scene, the objects will be rendered automatically. Since all the graphical 
+objects have a name that identifies them, they can be retrieved by name and 
+manipulated:
+
+.. code-block:: python
+
+  # retrieving the previously added protein
+  obj=scene['PROTEIN']
+  # set color of the protein to red
+  obj.SetColor(gfx.RED)
+
+
+The last command assigns a uniform red color to all atoms.
+
+
+The Graphical Entity
+--------------------------------------------------------------------------------
+
+Now let's look at the graphical entity in more detail. The graphical entity is 
+responsible for the rendering of :class:`~ost.mol.EntityHandle` and 
+:class:`~ost.mol.EntityView` instances.
+
+Render Modes
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Molecules are rendered in :ref:`different representations <render-mode>`. Some 
+representations show the structure at atomic detail (connectivity level display 
+styles), while others simplify the structure significantly (trace-based display 
+styles). 
+
+To change the display mode of an entity programmatically, use the :meth:`Entity.SetRenderMode` method:
+
+.. code-block:: python
+
+  # render the molecule with an interpolated line trace
+  obj.SetRenderMode(gfx.SLINE)
+  # switch back to simple line rendering
+  obj.SetRenderMode(gfx.SIMPLE)
+  # switch to helix-strand-coil cartoon
+  obj.SetRenderMode(gfx.HSC)
+
+It is also possible to change the render mode of only a part of the structure. 
+To display the ligand with balls and sticks and everything else in cartoon mode,
+we make use of the query language to select everything that is not part of the 
+protein. Remember from above, that we stored our molecule in the `pdb` variable.
+
+.. code-block:: python
+  
+  not_protein=pdb.Select('peptide=false')
+  obj.SetRenderMode(gfx.HSC)
+  obj.SetRenderMode(gfx.CUSTOM, not_protein)
+
+
+The Basics of Coloring
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The color of each atom can be set individually. The simplest coloring scheme is 
+to set all atoms to the same color:
+
+.. code-block:: python
+
+  obj.SetColor(gfx.YELLOW) 
+
+Assigning colors based on selections is also possible. To reproduce the 
+well-known `CPK coloring <http://en.wikipedia.org/wiki/CPK_coloring>`_, 4 
+consecutive coloring operations are sufficient:
+
+.. code-block:: python
+
+  obj.SetColor(gfx.WHITE, 'ele=C')
+  obj.SetColor(gfx.BLUE, 'ele=N')
+  obj.SetColor(gfx.RED, 'ele=O')
+  obj.SetColor(gfx.YELLOW, 'ele=S')
+
+
+But because this is such a common task, the entity provides a built-in method to color the atoms by element:
+
+.. code-block:: python
+
+  obj.ColorByElement()
+
+As already seen above, the coloring operations can be chained to achieve the desired effect. For example, sometimes one wants to apply conventional CPK coloring to the protein and then change the color of C-alpha atoms to pink:
+
+.. code-block:: python
+
+  obj.ColorByElement()
+  obj.SetColor(gfx.Color(1, 0, 1), 'aname=CA and ele=C')
+  
+
+
+Internally, the chain of calls to the coloring methods is stored as a list of 
+coloring operations that is reapplied sequentially. This makes sure that the 
+coloring remains when changing render modes or updating the geometry of the 
+molecule. This storage scheme has one drawback. Consider the following code:
+
+.. code-block:: python
+
+  for i in range(100): 
+    obj.SetColor(gfx.RED)
+
+While the code obviously achieves the desired effect, it is far for optimal 
+because all of the 100 color operations are applied every time the graphical 
+entity needs an update. When you see a slow down in rendering after playing 
+around with the coloring operations, consider calling 
+:meth:`Entity.ClearColorOps` and reapply only the set of coloring operations 
+that are required to achieve your rendering.
+
+Coloring the Entity By Property
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The most complex but also most powerful coloring method is 
+:meth:`Entity.ColorBy`, which allows to color atoms by a numeric property. This 
+property can either be built-in a property such as atomic b-factor, charge, 
+residue number or be :doc:`custom properties <../base/generic>` assigned by the 
+user or an algorithm and be defined at any level (chain, residue, atom). The 
+naming of the built-in properties is identical to the properties available in 
+:doc:`query language <../mol/base/query>`. For example, to achieve a heat-map 
+coloring for b-factors:
+
+.. code-block:: python  
+
+  # will color the atoms by the atomic b-factor, setting atoms with 
+  # a temperature factor of 0 to blue and atoms with a temperature factor of 
+  # 100 and higher to red. Values in between are linearly interpolated.
+  obj.ColorBy('abfac', gfx.BLUE, gfx.RED, 0, 100)
+
+Fine-tuning the Coloring
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The :obj:`HSC` render mode uses two colors to color the secondary structure 
+elements. The main color affects the top and bottom of extended  and the outside 
+of helical elements. The detail color is used for the inner side of helices and 
+the rim of extended elements. This color is changed with 
+:meth:`Entity.SetDetailColor`.
+ 
\ No newline at end of file
diff --git a/modules/doc/intro.rst b/modules/doc/intro.rst
new file mode 100644
index 0000000000000000000000000000000000000000..03bb173c67f54ca47ebb267505bc2ff2f5f11c6f
--- /dev/null
+++ b/modules/doc/intro.rst
@@ -0,0 +1,70 @@
+A gentle introduction to OpenStructure
+================================================================================
+
+In this tutorial you will be learning by example how to use the OpenStructure 
+framework. 
+
+We assume that you already have a version of OpenStructure installed. If not, 
+please refer to :doc:`install`.
+
+
+What will be covered in this tutorial?
+--------------------------------------------------------------------------------
+
+This tutorial is aimed at users that would like to get their hands dirty and 
+execute commands in Python and write scripts rather clicking their way through a 
+shiny user interface. The user interface of OpenStructure is in a very early 
+state anyway that you probably won't go far by clicking your way through...
+
+The tutorial is divided into several parts. The first part of the tutorial is a 
+walk-through of the basic functionality you will be using in your everyday work, followed by an introduction to the :mod:`~ost.mol`, :mod:`~ost.img` and :mod:`~ost.seq` modules.
+
+.. toctree::
+  :maxdepth: 1
+    
+  intro-01
+  intro-02
+  intro-03
+
+.. _start-dng:
+
+Getting ready to rumble
+--------------------------------------------------------------------------------
+
+The files we will be using in the tutorial are available in the examples folder 
+that comes with OpenStructure. Depending on your platform, the examples are 
+located at a different location:
+
+ * on *MacOS X* the files are located inside the application bundle. The file 
+   browser fill automatically point to the examples.
+ * on *Linux* and *Windows* PREFIX/share/openstructure/examples, where PREFIX is 
+   the path to the directory containing OpenStructure.
+
+Starting DNG
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The graphical user interface of OpenStructure is called DNG (Dino/DeepView Next 
+Generation). To start it, 
+
+ * on *MacOS X* double click DNG.app
+ * on *Windows* double click dng.bat inside the PREFIX/bin directory
+ * on *Linux* fire up a terminal change into the OpenStructure installation 
+   directory and type 'bin/dng'. If you have the binary directory in the PATH, 
+   typing dng is sufficient.
+
+Interactive Python Shell
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Now we will enter commands in the Python Shell (in the screenshot above, the 
+python shell is located at the bottom of the main window). If you want to get 
+more information on any object, function or class, the python help command may 
+be useful. For example:
+
+  .. code-block:: python
+
+    # get list of methods of EntityView
+    help(mol.EntityView)
+    # get help for method Select
+    help(mol.EntityView.Select)
+    
+Continue with :doc:`part one <intro-01>`
diff --git a/modules/doc/newmodule.rst b/modules/doc/newmodule.rst
new file mode 100644
index 0000000000000000000000000000000000000000..d821de02c707988b92138eae1426e70407e7bc53
--- /dev/null
+++ b/modules/doc/newmodule.rst
@@ -0,0 +1,301 @@
+Creating a New Module
+================================================================================
+
+OpenStructure can be extended by writing additional modules. A module will 
+usually consist of a set of C++ classes and methods, most of which will also be 
+exported to Python. It is also possible to write modules completely in Python.
+
+The build system of OpenStructure is quite simple. The main difference to other 
+projects is the use of a so-called stage  directory. The stage directory 
+replicates the normal layout of a standard Linux directory structure, with an 
+'include' directory for the headers, a 'lib' directory containing the shared 
+library files, a `bin` directory  for the executables and a 'share' directory 
+for the platform-independent data like icons, images and examples.
+
+OpenStructure uses `CMake <http://www.cmake.org>`_ to build the project. The 
+rules for the build-system are defined in `CMakeLists.txt` files. When running 
+`cmake`, the files are  compiled and copied into stage. The 
+real installation, if necessary, happens at a later stage. This is referred to 
+as staging of the files.
+
+If a new module is written following the guidelines in this page, it will be
+seamlessly included in the build system and will then be available form both
+the DNG python console and the OpenStructure command line as any other native 
+module.
+
+As a first step, a new directory structure must be created to accommodate the 
+new module.
+
+Directory Structure
+--------------------------------------------------------------------------------
+
+For the purpose of this example, let's assume we are creating a new module 
+called 'mod' (for 'modeling'). Let's create a directory named `mod` under the 
+'modules' directory in the OpenStructure development tree, and  populate it with 
+the three subdirectories `src`, `pymod`, and `tests`.  Then we add a 
+`CMakeLists.txt` file in the 'mod' directory, consisting of three lines:
+
+.. code-block:: bash
+
+  add_subdirectory(src)
+  add_subdirectory(pymod)
+  add_subdirectory(tests)
+  
+The Module Code
+--------------------------------------------------------------------------------
+
+In the `src` subdirectory we put the code that implements the functionality of 
+the new module, plus a `config.hh` header file.
+
+Here is a skeleton of one of the files in  the directory , `modeling_new_class.hh`:
+
+.. code-block:: cpp 
+
+  #ifndef OST_MOD_NEW_CLASS_H
+  #define OST_MOD_NEW_CLASS_H
+  
+  #include <ost/mod/module_config.hh>
+  
+  // All other necessary includes go here
+  
+  namespace ost { namespace mod {
+  
+  class DLLEXPORT_OST_MOD NewClass {
+   public:
+     void NewMethod();
+           
+    // All declarations of NewClass go here 
+  
+  };
+  
+  }} // namespaces
+  
+  #endif
+  
+And here is the skeleton of the corresponding `modeling_new_class.cc` file:
+
+.. code-block:: cpp
+
+  #include "modeling_new_class.hh"
+  
+  using namespace ost::mol;
+  using namespace ost::mod;
+  
+  // All other necessary includes and namespace directives
+  // go here
+  
+  void NewClass::NewMethod():
+  {
+    // Implementation     
+  }
+  
+  // Implementation code for NewClass goes here
+  
+Obviously, the `src` directory can contain many files, each implementing classes
+and functions that will end up in the module. In order to build and stage
+the module shared library, a `CMakeLists.txt` file needs to be written for the
+`src` directory:
+
+.. code-block:: bash
+
+  set(OST_MOD_SOURCES 
+  modeling_new_class.cc
+  // All other source files 
+  )
+  
+  set(OST_MOD_HEADERS
+  modeling_new_class.hh
+  // All other header files
+  )
+  
+   module(NAME mod SOURCES "${OST_MOD_SOURCES}"
+          HEADERS ${OST_MOD_HEADERS}
+          DEPENDS_ON mol mol_alg)
+  
+
+The line containing the `DEPENDS_ON` directive lists all the modules on which
+the new module depends (in this case :mod:`mol` and :mod:`ost.mol.alg`).  The 
+`module` macro will take care of staging the headers, in this case into 
+`ost/mod` and compiling, linking and staging of a library with the  name 
+`libost_mod.so` (`libost_gmod.dylib` on MacOS X).
+
+.. note:: 
+
+  Due to a limitation in the built-int install command of CMake, for modules
+  that have their headers in several directories, it is required to group the
+  headers by directory, leading to a call of module like:
+
+.. code-block:: bash
+
+  module(NAME mol SOURCES atom_handle.cc impl/atom_impl.cc
+         HEADERS atom_impl.hh IN_DIR impl
+         atom_handle.hh)   
+
+The `module_config.hh` header is required for each module to setup the 
+environment on Windows: Each public class, method and function needs to marked 
+with `DLLEXPORT` or `DLLIMPORT` to teach the linker where to look for the 
+symbol. The correct use of either `DLLIMPORT` and `DLLEXPORT` is depending on 
+the context: While compiling a header file that is part of the same shared
+library, `DLLEXPORT` must be used. When compiling a header that is part of
+an external shared library, `DLLIMPORT` must be used. A typical module_config
+header looks like this:
+
+.. code-block:: cpp   
+
+  #ifndef OST_MOD_MODULE_CONFIG_HH
+  #define OST_MOD_MODULE_CONFIG_HH
+  
+  #include <ost/base.hh>
+  
+  #if defined(OST_MODULE_OST_MOD)
+  #  define DLLEXPORT_OST_MOD DLLEXPORT
+  #else
+  #  define DLLEXPORT_OST_MOD DLLIMPORT
+  #endif
+  #endif
+      
+The Testing Framework
+--------------------------------------------------------------------------------
+
+The `tests` directory contains code for unit tests. The code is compiled and 
+executed when one invokes compilation using the 'make check' command.  Tests are 
+run by means of the `Boost Unitests Library 
+<http://www.boost.org/doc/libs/1_37_0/libs/test/doc/html/index.html>`_, which is 
+used throughout OpenStructure. Before coding the test routines, the required 
+skeleton needs to be put in place.
+
+The main code is put into 'tests.cc', which will become the test executable:
+    
+.. code-block:: cpp
+
+  #include <boost/test/unit_test.hpp>
+  using boost::unit_test_framework::test_suite;
+  
+  #include "test_modeling.hh"
+  
+  test_suite*
+  unit_unit_test_suite( int argc, char * argv[] ) {
+    std::auto_ptr<test_suite> test(BOOST_TEST_SUITE( "Module Mod Test" ));
+  
+    test->add(CreateModelingTest()); 
+  
+    return test.release(); 
+  }
+  
+        
+The most relevant line adds the test suite for the new module to the global test 
+list. The test suite is created by the factory function CreateModelingTest(), 
+which is declared in the `test_modeling.hh` header file. 
+
+.. code-block:: cpp
+
+  #ifndef OST_MOD_TEST_MODELING_H
+  #define OST_MOD_TEST_MODELING_H
+  
+  #include <boost/test/unit_test.hpp>
+  using boost::unit_test_framework::test_suite;
+  
+  test_suite* CreateModelingTest();
+  
+  #endif
+      
+The definition of the factory function is found in the actual test code,
+which we put in `test_modeling.cc`. Here is a skeleton version of that file:
+
+.. code-block:: cpp
+
+  #include "test_modeling.hh"
+  
+  // additional include statements will go here
+  
+  namespace test_modeling {
+  
+    void test() 
+    {
+      // test code will go here
+    }
+  
+  }
+  
+  test_suite* CreateModelingTest()
+  {
+    using namespace test_modeling;
+    test_suite* ts=BOOST_TEST_SUITE("Modeling Test");
+     ts->add(BOOST_TEST_CASE(&test));
+  
+     return ts;
+  }
+  
+In this file, all the normal Boost Test Library macros and functions can be used. (For example `BOOST_CHECK`, `BOOST_FAIL`, etc.)
+
+Here is finally the build script skeleton that needs to be put into 
+`mod/tests/`:
+
+.. code-block:: bash
+
+  set(OST_MOD_UNIT_TESTS
+  tests.cc
+  test_modeling.cc
+  )
+  
+  ost_unittest(mod "${OST_MOD_UNIT_TESTS}")
+  target_link_libraries(ost_mol ost_mol_alg ost_mod)
+  
+In the last line the call to the 'target\_link\_libraries' function contains the 
+names of the modules on which the 'mod' unit test code depends (in this case, 
+the :mod:`mol` and :mod:`ost.mol.alg` modules), in addition to the `mod` module 
+itself.
+
+The Python Wrapper
+--------------------------------------------------------------------------------
+
+Finally, the module API is exported to Python using the `Boost Python 
+Library <http://www.boost.org/doc/libs/1_37_0/libs/python/doc/index.html>`_.
+In `mod/pymod`, the wrapper code for the classes in the new module is put into a 
+file named `wrap\_mod.cc`:
+
+.. code-block:: cpp
+
+  #include <boost/python.hpp>
+  using namespace boost::python;
+  
+  #include <ost/mod/modeling_new_class.hh>
+  
+  using namespace ost::mol;
+  using namespace ost::mod;
+  
+  // All other necessary includes and namespace directives
+  // go here
+  
+  BOOST_PYTHON_MODULE(_mod)
+  {
+    class_<NewClass>("NewClass", init<>() )
+      .def("NewMethod", &NewClass::NewMethod)
+    ;
+  
+    // All other Boost Python code goes here    
+  }
+
+The `mod/pymod` directory must obviously contain a `CMakeLists.txt` file:
+
+.. code-block:: bash
+
+  set(OST_MOD_PYMOD_SOURCES
+  wrap_mod.cc
+  )
+  
+  pymod(NAME mod OUTPUT_DIR ost/mod 
+        CPP ${OST_MOD_PYMOD_SOURCES} PY __init__.py)
+  
+The directory should also contain an `__init.py__` file with the
+following content:
+
+.. code-block:: python
+  
+  from _mod import *
+    
+In case one wants to implement Python-only functionality for the new module, any
+number of function definitions can be added to the `__init.py__` file.
+
+That's it!. The next time the OpenStructure project is compiled, the new module 
+will be built and made available at both the C++ and the Python level.
diff --git a/website/raw/docs/tut/sel.png b/modules/doc/sel.png
similarity index 100%
rename from website/raw/docs/tut/sel.png
rename to modules/doc/sel.png
diff --git a/modules/geom/doc/composite.rst b/modules/geom/doc/composite.rst
new file mode 100644
index 0000000000000000000000000000000000000000..0271a206bc9d82d42a7661a58a3ab73deac27f2f
--- /dev/null
+++ b/modules/geom/doc/composite.rst
@@ -0,0 +1,529 @@
+Geometric Objects
+================================================================================
+
+.. currentmodule:: ost.geom
+
+Geometrical Objects in Two Dimensions
+--------------------------------------------------------------------------------
+
+.. class:: Line2()
+           Line2(from, to)
+  
+  Parametric line in two dimensions as defined by an origin and a normalized
+  direction vector. The first constructor creates a line with origin (0,0) and 
+  direction along the x axis. The second signature creates a line originating 
+  from `from` and pointing towards `to`.
+  
+  .. method:: At(t)
+    
+    Returns the point on the line at (signed) distance t from origin.
+    
+    :param t: free parameter
+    :type  t: float
+    :rtype:   :class:`Vec2`
+  
+
+  .. method:: GetOrigin()
+  
+    Returns the origin of the line: Also available as :attr:`origin`.
+    
+    :rtype: :class:`Vec2`
+    
+  .. method:: GetDirection()
+  
+    Returns the normalized direction vector. Also available as
+    :attr:`direction`.
+    
+    :rtype: :class:`Vec2`
+    
+  .. attribute:: direction
+  
+  .. attribute:: origin
+
+    
+.. class:: Rectangle2()
+           Rectangle2(top_left, bottom_right)
+  
+  Axis aligned rectangle. The first signature creates a rectangle with top-left 
+  corner (-1, -1) and bottom-right corner (1, 1), wheras the second method 
+  allows to set the top-left and bottom-right corners directly.
+  
+  :type top_left: :class:`Vec2`
+  :param top_left: The top-left corner
+  :param bottom_right: The bottom-right corner  
+  :type bottom_right: :class:`Vec2`  
+
+  .. method:: GetWidth()
+    
+    Returns the width of the rectangle. Also available as :attr:`width`.  
+  
+  .. method:: GetHeight()
+  
+    Returns the height of the rectangle. Also available as :attr:`height`.  
+    
+  .. attribute:: width
+  
+    :type: float
+    
+  .. attribute:: height
+
+    :type: float  
+    
+  .. method:: GetStart()
+  
+    Get top-left corner
+    
+    :rtype: :class:`Vec2`
+    
+  .. method:: GetEnd()
+
+    Get bottom-right corner
+
+    :rtype: :class:`Vec2`    
+  
+  .. method:: SetStart(top_left)
+  
+    Set top-left corner, leaving the bottom-right corner untouched.
+    
+  .. method:: SetEnd(bottom_right)
+  
+    Set the bottom-right corner, leaving the top-left corner untouched.
+
+.. class:: Circle2()
+           Circle2(circle)
+           Circle2(center, radius)
+
+  The first signature creates a circle centered at (0, 0) and radius 1.0. The 
+  second signature creates a circle with the same paramters as `circle`. The 
+  third signature creates a new circle with given center and radius.
+     
+  .. method:: SetCenter(center)
+  
+    Set center of circle
+    
+    :type center: :class:`Vec2`
+    :param center: The new center
+    
+  .. method:: SetRadius(radius)
+  
+    Set radius of circle
+  
+    :type radius: float
+    :param center: The new radius
+    
+  .. method:: GetCenter()
+  
+    Returns the center of the circle
+    
+  .. method:: GetRadius()
+  
+    Returns the radius of the circle
+    
+  .. method:: GetArea()
+  
+    Returns the area of the circle
+    
+  .. method:: GetCircumference()
+  
+    Returns the circumference of the circle
+
+
+.. class:: Ellipse2()
+           Ellipse2(center, a, b, gamma)
+
+  An ellipse is defined by a center, two principal axis and gamma that 
+  defines the angle between the first principal axis an the x-axis.
+  
+  .. method:: At(t)
+  
+    ?
+  
+  .. method:: AtAngle(angle)
+  
+    ?
+  
+  .. method:: GetBoundingBox()
+  
+    Returns the bounding rectangle (axis-aligned) of the ellipse
+    
+    :rtype: :class:`Rectangle2`
+    
+
+  .. method:: GetA()
+  
+    Returns the first principal-axis
+  
+  .. method:: GetB()
+  
+    Returns the second principal-axis
+    
+  .. method:: GetGamma()
+    
+    Returns the angle of the first principal axis to the x-axis
+    
+  .. method:: GetArea()
+  
+    Returns the area of the ellipse
+    
+  .. method:: GetOrigin()
+  
+    Returns the center of the ellipse
+    
+  .. method:: SetA(a)
+  
+    Set the length of the first principal axis
+    
+  .. method:: SetB(b)
+  
+    Set the length of the second principal axis
+    
+  .. method:: SetGamma(gamma)
+  
+    Set the angle of the first principal axis to the x-axis
+    
+  .. method:: SetOrigin(ori)
+  
+    Set the center of the ellipse
+    
+Geometrical Objects in Three Dimensions
+-------------------------------------------------------------------------------
+
+.. class:: Line3()
+           Line3(from, to)
+  
+  Parametric line in three dimensions as defined by an origin and a normalized
+  direction vector. The first constructor creates a line with origin (0,0) and 
+  direction along the x axis. The second signature creates a line originating 
+  from `from` and pointing towards `to`.
+  
+  .. method:: At(t)
+    
+    Returns the point on the line at (signed) distance t from origin.
+    
+    :param t: free parameter
+    :type  t: float
+    :rtype:   :class:`Vec3`
+  
+
+  .. method:: GetOrigin()
+  
+    Returns the origin of the line: Also available as :attr:`origin`.
+    
+    :rtype: :class:`Vec3`
+    
+  .. method:: GetDirection()
+  
+    Returns the normalized direction vector. Also available as
+    :attr:`direction`.
+    
+    :rtype: :class:`Vec3`
+    
+  .. attribute:: direction
+  
+    :type: :class:`Vec3`
+  
+  .. attribute:: origin
+    
+    :type: :class:`Vec3`
+
+.. class:: Plane()
+           Plane(p1, p2, p3)
+           Plane(x, y, z, p)
+           Plane(line, point)
+           Plane(point, normal)
+  
+  A plane in 3d-space. The plane can be constructed by either passing in 3 
+  points (p1, p2, p3), a normal and a point, the four parameters that define the 
+  implicit plane equation (`x`, `y`, `z`, `p`) or a line and a point.
+  
+  .. method:: GetNormal()
+  
+    Returns the normal of the plane. Also available as :attr:`normal`
+    
+    :rtype: :class:`Vec3`
+    
+  .. method:: GetP()
+  
+    Returns the plane offset, i.e. the projection of any point on the plane onto
+    the normal. Also available as :attr:`p`.
+    
+    :rtype: float
+    
+  .. method:: GetOrigin()
+  
+    Get the origin of the plane. Also available as :attr:`origin`.
+    
+    :rtype: :class:`Vec3`
+
+  .. attribute:: origin
+  
+    :type: :class:`Vec3`
+  .. attribute:: normal
+  
+    :type: :class:`Vec3`
+      
+  .. attribute:: p
+  
+    :type: float
+ 
+
+.. class:: Sphere()
+           Sphere(center, radius)
+           
+  Represents a sphere in 3d space. The first constructor creates a sphere with 
+  radius 1, centered at (0, 0, 0), the second allows you to set the radius and 
+  center directly.
+  
+  :param center: The center
+  :type  center: :class:`Vec3`
+  :param radius: The radius
+  :type  radius: float
+  
+  .. attribute:: radius
+    
+    The radius of the sphere. Read-write. Also available as :meth:`GetRadius`, 
+    :meth:`SetRadius`.
+    
+    :type: float
+    
+  .. attribute:: origin
+  
+    The center of the sphere. Read-write. Also available as :meth:`GetOrigin`,
+    :meth:`SetOrigin`.
+    
+    :type: :class:`Vec3`
+
+  .. method:: GetOrigin()  
+  
+    See :attr:`origin`
+    
+  .. method:: SetOrigin(origin)
+    
+    See :attr:`origin`
+    
+  .. method:: GetRadius()
+  
+    See :attr:`radius`
+     
+  .. method:: SetRadius(radius)
+    
+    See :attr:`radius`
+
+.. class:: AlignedCuboid(min, max)
+  
+  Axis aligned cuboid is a cuboid whose axes are aligned to the x-, y-, and z- 
+  axes of the coordinate system. For arbitrarily oriented bounding cuboid 
+  class, see :class:`Cuboid`.
+  
+  .. method:: GetMin()
+  
+    Get minimum coordinate, i.e. the lower bound of x-, y-, and z for 
+    any point in the cuboid
+    
+    :rtype: :class:`Vec3`
+    
+  .. method:: GetMax()
+  
+    Get maximum coordinate, i.e. the upper bound of x-, y-, and z for
+    any point in the cuboid.
+    
+    :rtype: :class:`Vec3`
+
+.. class:: CuboidAxis()
+           CuboidAxis(dir, half_extent)
+  
+  A cuboid axis is defined by a half-extent, and a direction vector. This class 
+  is used in together with the :class:`Cuboid` class.
+  
+  :param dir: Direction vector, will be normalized
+  :type  dir: :class:`Vec3`
+  :param half_extent: The half extent
+  :type half_extent: float
+  
+  .. attribute:: vector
+  
+    The normalized direction vector of the cuboid axis. Also available as 
+    :meth:`GetVector`
+    
+    :type: :class:`Vec3`
+  
+  .. attribute:: half_extent
+  
+    The half extent of the cuboid axis is the magnitude of the cuboid 
+    axis measured from the center to the corner. Also available as
+    :meth:`GetHalfExtent`
+    
+    :type: float
+  
+  .. attribute:: extent
+  
+    The extent of the cuboid axis. This value is always twice the 
+    :attr:`half_extent`. Read-only. Also available as 
+    :meth:`GetExtent`.
+    
+    :type: float
+    
+  .. method:: GetHalfExtent()
+  
+    See :attr:`half_extent`
+  .. method:: GetExtent()
+  
+    See :attr:`extent`
+    
+  .. method:: GetVector()
+  
+    See :attr:`vector`
+    
+.. class:: Cuboid(center, axis_a, axis_b, axis_c)
+  
+  An arbitrarily oriented cuboid defined by a center and 3 axis. The 3 cuboid 
+  axis are stored in the order they are passed to the constructor. This means, 
+  that there is no guarantee that the 3 axes form a right-handed coordinate 
+  system. If a right-handed coordinate system is a requirement, you have to 
+  ensure this on your own:
+  
+  .. code-block:: python
+  
+    center=...
+    axis_a=geom.CuboidAxis(...)
+    axis_b=geom.CuboidAxis(...)
+    axis_c=geom.CuboidAxis(geom.Cross(axis_a.vector, axis_b.vector), ...)
+    
+    cuboid=geom.Cuboid(center, axis_a, axis_b, axis_c)
+  
+  :param center: The center
+  :type  center: :class:`Vec3`
+  :param axis_a: The first axis
+  :type  axis_a: :class:`CuboidAxis`
+  :param axis_b: The second axis
+  :type  axis_b: :class:`CuboidAxis`
+  :param axis_c: The third axis
+  :type  axis_c: :class:`CuboidAxis`
+  
+  .. attribute:: center
+  
+    The center of the cuboid.
+    
+    :type: :class:`Vec3`
+    
+  .. attribute:: axis_a
+  
+    The first cuboid axis
+    
+    :type: :class:`CuboidAxis`
+    
+  .. attribute:: axis_b
+
+    The second cuboid axis
+
+    :type: :class:`CuboidAxis`
+    
+  .. attribute:: axis_c
+
+    The third cuboid axis
+
+    :type: :class:`CuboidAxis`    
+
+Operations on Geometrical Objects
+--------------------------------------------------------------------------------
+
+.. function:: Angle(lhs, rhs)
+
+  Calculate the angle (in radians) between `lhs` and `rhs`. 
+  
+  :param lhs: First object
+  :type  lhs: :class:`Line2`, :class:`Line3`, :class:`Plane`
+  
+  :param rhs: Second object
+  :type  rhs: :class:`Line2`, :class:`Line3`, :class:`Plane`
+  
+  :rtype: float
+
+.. function:: IntersectionPoint(lhs, rhs)
+
+  Calculates and returns the intersection point between `lhs` and `rhs`
+  
+  :param lhs: First object
+  :type  lhs: :class:`Line2`, :class:`Line3`, :class:`Plane`
+  
+  :param rhs: Second object
+  :type  rhs: :class:`Line2`, :class:`Line3`, :class:`Plane`
+  
+  :raises: :exc:`GeomException` when the two objects do not intersect
+  :rtype: :class:`Vec3` (:class:`Vec2` in case of :class:`Line2`)
+
+.. function:: IntersectionLine(plane2, plane2)
+
+  Returns the intersection line between `plane1` and `plane2`.
+  
+  :param plane1: The first plane
+  :type  plane1: :class:`Plane`
+  :param plane2: The second plane
+  :type  plane2: :class:`Plane`  
+  
+  :raises: :exc:GeomException if the two planes are parallel.
+  
+.. function:: Distance(lhs, rhs)
+
+  Returns the minimal distance between `lhs` and `rhs`. 
+  
+  :param lhs: First object
+  :type  lhs: :class:`Line2`, :class:`Line3`, :class:`Plane`
+  
+  :param rhs: Second object
+  :type  rhs: :class:`Line2`, :class:`Line3`, :class:`Plane`
+  
+  :rtype: float
+
+.. function:: IsOnLine(line, point, epsilon=geom.EPSILON)
+
+  Check whether `point` lies on `line` and returns true if point i no further 
+  away than `epsilon`.
+  
+  :rtype: bool
+
+.. function:: IsInPlane(plane, object, epsilon=geom.EPSILON)
+  
+  Check whether `object` lies in `plane` and returns true if the difference is 
+  no bigger than `epsilon`.
+  
+  :param plane: The plane
+  :type  plane: :class:`Plane`
+  :param object: The object
+  :type  object: :class:`Vec3` or :class:`Line3`
+  
+  :rtype: bool
+
+.. function:: AreParallel(lhs, rhs, epsilon=geom.EPSILON)
+
+  Check whether `lhs` and `rhs` are parallel and returns true, if the difference 
+  is below the given treshold `epsilon`.
+  
+  :param lhs: First object
+  :type  lhs: :class:`Line2`, :class:`Line3`, :class:`Plane`
+  
+  :param rhs: Second object
+  :type  rhs: :class:`Line2`, :class:`Line3`, :class:`Plane`
+  
+  :rtype: bool
+
+.. function:: AreIntersecting(line1, line2, epsilon=geom.EPSILON)
+
+  Check whether `line1` and `line2` are intersecting and returns true, if they 
+  intersect below the given threshold `epsilon`.
+  
+  :param lhs: First line
+  :type  lhs: :class:`Line2`, :class:`Line3`
+  
+  :param rhs: Second line
+  :type  rhs: :class:`Line2`, :class:`Line3`
+  
+  :rtype: bool
+  
+
+  
+.. function:: IsInSphere(sphere, point)
+
+  Check whether the `sphere` contains `point`.
+  
+  :rtype: bool
\ No newline at end of file
diff --git a/modules/geom/doc/geom.rst b/modules/geom/doc/geom.rst
index 27accb014bd6291c9c96b861ecc4e4fb232c48da..d0412a1340ae8ebf248e3193f381801f85d0b05b 100644
--- a/modules/geom/doc/geom.rst
+++ b/modules/geom/doc/geom.rst
@@ -1,15 +1,16 @@
-:mod:`geom` -- vectors, matrices and geometrical objects
+:mod:`~ost.geom` -- vectors, matrices and geometrical objects
 ================================================================================
 
-.. module:: geom
+.. module:: ost.geom
    :synopsis: Functions and classes for vectors, matrices and geometrical
               objects in 2, 3 and four dimensions
 
-The geom modules contains functions and classes for vectors, matrices and other geometrical objects in 2, 3 and four dimensions.
+The geom modules contains functions and classes for vectors, matrices and other 
+geometrical objects in 2, 3 and four dimensions.
 
 
 .. toctree::
 
   vec
-              
-              
\ No newline at end of file
+  mat
+  composite
\ No newline at end of file
diff --git a/modules/geom/doc/mat.rst b/modules/geom/doc/mat.rst
new file mode 100644
index 0000000000000000000000000000000000000000..c8736733a7a18533cf18e6fcf40ddecf6b3a52c7
--- /dev/null
+++ b/modules/geom/doc/mat.rst
@@ -0,0 +1,167 @@
+Matrices
+================================================================================
+
+.. currentmodule:: ost.geom
+
+The :mod:`~ost.geom` module defines matrices in two, three and four dimensions. 
+All matrices store the values in row-major order, meaning that, the matrix ((1, 
+2), (3,4)) stores the values as (1, 2, 3, 4). This is illustrated in 
+the following code examples:
+
+.. code-block:: python
+
+  m=geom.Mat2(1, 2, 3, 4)
+  print m # will print {{1,2},{3,4}}
+  print m[(0,0)], m[(0,1)], m[(1,0)], m[(1,1)] # will print 1, 2, 3, 4
+
+Matrices support arithmetic via overloaded operators. The following operations are 
+supported:
+
+  * adding and subtracting two matrices
+  * negation
+  * multiplication of matrices
+  * multiplying and dividing by scalar value
+
+The Matrix Classes
+--------------------------------------------------------------------------------
+
+.. class:: Mat2()
+           Mat2(d00, d01, d10, d11)
+
+  2x2 real-valued matrix. The first signature creates a new identity matrix. The 
+  second signature initializes the matrix in row-major order. 
+
+  .. staticmethod:: Identity()
+  
+    Returns the 2x2 identity matrix
+  
+  
+.. class:: Mat3()
+           Mat3(d00, d01, d02, d10, d11, d12, d20, d21, d22)
+
+  3x3 real-valued matrix. The first signature creates a new identity matrix. The 
+  second signature initializes the matrix in row-major order.
+  
+  .. staticmethod:: Identity()
+  
+    Returns the 3x3 identity matrix
+    
+.. class:: Mat4()
+           Mat4(d00, d01, d02, d03, d10, d11, d12, d13, d20, d21, d22, d23, d30, d31, d32, d33)
+
+  4x4 real-valued matrix. The first signature creates a new identity matrix. The 
+  second signature initializes the matrix in row-major order.
+  
+  .. method:: ExtractRotation()
+    
+    Returns the 3x3 submatrix
+    
+  .. method:: PasteRotation(mat)
+  
+    Set the 3x3 submatrix of the top-left corner to `mat`
+    
+  .. method:: ExtractTranslation()
+  
+    Extract translation component from matrix. Only meaningful when matrix 
+    is a combination of rotation and translation matrices, otherwise the result 
+    is undefined.
+    
+  .. PasteTranslation(trans)
+  
+    Set the translation component of the matrix to `trans`
+    
+    :param trans: The translation
+    :type  trans: :class:`Vec3`
+    
+  .. staticmethod:: Identity()
+  
+    Returns the 4x4 identity matrix
+
+Functions Operating on Matrices
+--------------------------------------------------------------------------------
+.. function:: Equal(lhs, rhs, epsilon=geom.EPSILON)
+
+  Compares the two matrices `lhs` and `rhs` and returns True, if all 
+  of the element-wise differences are smaller than epsilon. `lhs` 
+  and `rhs` must be matrices of the same dimension.
+  
+  :param lhs: First matrix
+  :type  lhs: :class:`Mat2`, :class:`Mat3` or :class:`Mat4`
+  :param rhs: Second matrix
+  :type  rhs: :class:`Mat2`, :class:`Mat3` or :class:`Mat4`
+
+.. function:: Transpose(mat)
+
+  Returns the transpose of `mat`
+  
+  :param mat: The matrix to be transposed
+  :type  lhs: :class:`Mat2`, :class:`Mat3` or :class:`Mat4`
+
+.. function:: Invert(mat)
+
+  Returns the inverse of `mat`
+  
+  :param mat: The matrix to be inverted
+  :type  mat: :class:`Mat2`, :class:`Mat3` or :class:`Mat4`
+  
+  What happens when determinant is 0?
+  
+.. function:: CompMultiply(lhs, rhs)
+
+  Returns the component-wise product of `lhs` and `rhs`. `lhs` and 
+  `rhs` must be vectors of the same dimension.
+  
+  :param lhs: The lefthand-side vector
+  :type  lhs: :class:`~Vec2`, :class:`~Vec3` or 
+              :class:`~Vec4`
+  :param rhs: The righthand-side vector
+  :type  rhs: :class:`~Vec2`, :class:`~Vec3` or 
+              :class:`~Vec4`
+              
+.. function:: CompDivide(lhs, rhs)
+
+  Returns the component-wise quotient of `lhs` divided by `rhs`. `lhs` 
+  and `rhs` must be vectors of the same dimension.
+
+  :param lhs: The lefthand-side vector
+  :type  lhs: :class:`~Vec2`, :class:`~Vec3` or 
+              :class:`~Vec4`
+  :param rhs: The righthand-side vector
+  :type  rhs: :class:`~Vec2`, :class:`~Vec3` or 
+              :class:`~Vec4`
+
+.. function:: Det(mat)
+
+  Returns the determinant of `mat`
+  :param mat: A matrix
+  :type  mat: :class:`~Mat2`, :class:`~Mat3` or :class:`~Mat4`
+
+.. function:: Minor(mat, i, j)
+  
+  Returns the determinant of the 2x2 matrix generated from `mat`  by 
+  removing the ith row and jth column.
+
+.. function:: EulerTransformation(phi, theta, xi)
+  
+  Returns a rotation matrix for the 3 euler angles `phi`, `theta`, and
+  `xi`. The 3 angles are given in radians.
+  
+  
+.. function:: AxisRotation(axis, angle)
+
+  Returns a rotation matrix that represents a rotation of `angle` 
+  around the `axis`. 
+  
+  :param axis: The rotation axis. Will be normalized
+  :type  axis: :class:`Vec3`
+  :param angle: Rotation angle (radians) in clockwise direction when 
+      looking down the axis.
+  
+.. function:: OrthogonalVector(vec)
+
+  Get arbitrary vector orthogonal to `vec`. The returned vector is of length 
+  1, except when `vec` is a zero vector. In that case, the returned vector is 
+  (0, 0, 0).
+  
+  :param vec: A vector of arbitrary length
+  :type vec: :class:`Vec3`
\ No newline at end of file
diff --git a/modules/geom/doc/vec.rst b/modules/geom/doc/vec.rst
index b3da8088bc8748bdede06b340ecb3e0222db4555..bc88b3f2b0e020bdfa0b96480c561414e8f2fa7f 100644
--- a/modules/geom/doc/vec.rst
+++ b/modules/geom/doc/vec.rst
@@ -1,9 +1,10 @@
 Vectors
 ================================================================================
-.. currentmodule:: geom
+.. currentmodule:: ost.geom
 
-
-The :class:`Vec2`, :class:`Vec3`, :class:`Vec4` classes implement vectors in 2, 3 and four dimensions. They support basic arithmetic via overloaded operators. Essentially, the following basic operations are available:
+The :class:`Vec2`, :class:`Vec3`, :class:`Vec4` classes implement vectors in 2, 
+3 and four dimensions. They support basic arithmetic via overloaded operators. 
+Essentially, the following basic operations are available:
 
  * adding and subtracting two vectors
  * negation
@@ -19,7 +20,8 @@ This is shown in the following example:
    print vec_a+vec_b
    print vec_a*3-vec_b
 
-The standard vector operations are implemented as :ref:`free standing functions <vector-functions>`:
+The standard vector operations are implemented as :ref:`free standing functions 
+<vector-functions>`:
 
 
 .. code-block:: python
diff --git a/modules/geom/pymod/export_composite2.cc b/modules/geom/pymod/export_composite2.cc
index f9e793ee10d7e05eddc608113e3d28c43146ec8e..96f42ab26ebfb5ed216aa285d2d3499ecb626bb7 100644
--- a/modules/geom/pymod/export_composite2.cc
+++ b/modules/geom/pymod/export_composite2.cc
@@ -42,6 +42,8 @@ void export_Composite2()
     .def("At",&Line2::At)
     .def("GetOrigin",&Line2::GetOrigin)
     .def("GetDirection",&Line2::GetDirection)
+    .add_property("direction", &Line2::GetDirection)
+    .add_property("origin", &Line2::GetOrigin)
   ;
 
   class_<Polygon2>("Polygon2",init<>())
diff --git a/modules/geom/pymod/export_composite3.cc b/modules/geom/pymod/export_composite3.cc
index 8468578df28234c4b1d2ad11eafa6b57a4cde915..df7cafa3c1bcd44d30d4200f18f0de90730c8b1c 100644
--- a/modules/geom/pymod/export_composite3.cc
+++ b/modules/geom/pymod/export_composite3.cc
@@ -18,10 +18,9 @@
 //------------------------------------------------------------------------------
 #include <boost/python.hpp>
 #include <boost/python/suite/indexing/vector_indexing_suite.hpp>
-using namespace boost::python;
-
 #include <ost/geom/geom.hh>
 
+using namespace boost::python;
 void export_Composite3()
 {
   using namespace geom;
@@ -32,6 +31,8 @@ void export_Composite3()
     .def("At",&Line3::At)
     .def("GetOrigin",&Line3::GetOrigin)
     .def("GetDirection",&Line3::GetDirection)
+    .add_property("origin", &Line3::GetOrigin)
+    .add_property("direction", &Line3::GetDirection)
   ;
 
 { // scope
@@ -49,6 +50,7 @@ scope PlaneScope =
     .def("GetNormal",&Plane::GetNormal)
     .add_property("normal", &Plane::GetNormal)
     .add_property("origin", &Plane::GetOrigin)
+    .add_property("p", &Plane::GetP)
     .def("GetP",&Plane::GetP)
   ;
 
@@ -105,6 +107,8 @@ scope PlaneScope =
     .def(init<const Vec3&,Real>())
     .def("GetOrigin",&Sphere::GetOrigin)
     .def("GetRadius",&Sphere::GetRadius)
+    .add_property("origin", &Sphere::GetOrigin, &Sphere::SetOrigin)
+    .add_property("radius", &Sphere::GetRadius, &Sphere::SetRadius)
   ;
   
   class_<CuboidAxis>("CuboidAxis", init<>())
@@ -113,29 +117,58 @@ scope PlaneScope =
     .def("GetVector", &CuboidAxis::GetVector,
          return_value_policy<copy_const_reference>())
     .def("GetExtent", &CuboidAxis::GetExtent)
+    
+    .add_property("vector", make_function(&CuboidAxis::GetVector,
+                  return_value_policy<copy_const_reference>()))
+    .add_property("half_extent", &CuboidAxis::GetHalfExtent)
+    .add_property("extent", &CuboidAxis::GetExtent)
   ;
   
   class_<Cuboid>("Cuboid", init<>())
     .def(init<const geom::Vec3&, const CuboidAxis&,const CuboidAxis&, 
               const CuboidAxis&>())
     .def("GetCenter",&Cuboid::GetCenter)
+    .add_property("center", &Cuboid::GetCenter)
     .def("GetVecA", &Cuboid::GetVecA,
          return_value_policy<copy_const_reference>())
+    .add_property("vec_a", make_function(&Cuboid::GetVecA,
+              return_value_policy<copy_const_reference>()))
     .def("GetVecB", &Cuboid::GetVecB,
          return_value_policy<copy_const_reference>())
+   .add_property("vec_b", make_function(&Cuboid::GetVecB,
+             return_value_policy<copy_const_reference>()))         
     .def("GetVecC", &Cuboid::GetVecC,
          return_value_policy<copy_const_reference>())
+    .add_property("vec_c", make_function(&Cuboid::GetVecC,
+                  return_value_policy<copy_const_reference>()))         
     .def("GetAxisA", &Cuboid::GetAxisA, 
          return_value_policy<copy_const_reference>())
+    .add_property("axis_a", make_function(&Cuboid::GetAxisA,
+                 return_value_policy<copy_const_reference>()))
     .def("GetAxisB", &Cuboid::GetAxisB, 
          return_value_policy<copy_const_reference>())
+    .add_property("axis_b", make_function(&Cuboid::GetAxisB,
+                  return_value_policy<copy_const_reference>()))
     .def("GetAxisC", &Cuboid::GetAxisC, 
-         return_value_policy<copy_const_reference>())                  
+         return_value_policy<copy_const_reference>())              
+    .add_property("axis_c", make_function(&Cuboid::GetAxisC,
+                  return_value_policy<copy_const_reference>()))             
     .def("GetHalfExtents", &Cuboid::GetHalfExtents)
+    .add_property("half_extents", &Cuboid::GetHalfExtents)
   ;
   class_<AlignedCuboid>("AlignedCuboid", init<geom::Vec3, geom::Vec3>())
-    .def("GetMin", &AlignedCuboid::GetMin, return_value_policy<copy_const_reference>())
-    .def("GetMax", &AlignedCuboid::GetMax, return_value_policy<copy_const_reference>())
+    .def("GetMin", &AlignedCuboid::GetMin, 
+         return_value_policy<copy_const_reference>())
+    .def("GetMax", &AlignedCuboid::GetMax, 
+         return_value_policy<copy_const_reference>())
+    .def("GetCenter", &AlignedCuboid::GetCenter)
+    .def("GetSize", &AlignedCuboid::GetSize)
+    .add_property("max", make_function(&AlignedCuboid::GetMax,
+         return_value_policy<copy_const_reference>()))
+    .add_property("min", make_function(&AlignedCuboid::GetMin,
+         return_value_policy<copy_const_reference>()))
+    .add_property("center", &AlignedCuboid::GetCenter)
+    .add_property("size", &AlignedCuboid::GetSize)
   ;
 }
 
diff --git a/modules/geom/pymod/export_vec2.cc b/modules/geom/pymod/export_vec2.cc
index d32c72ad96b063fc432c7bb976277df966fd67e6..43366e6db85008f940401a3d5e5e5252bbbcb339 100644
--- a/modules/geom/pymod/export_vec2.cc
+++ b/modules/geom/pymod/export_vec2.cc
@@ -17,10 +17,13 @@
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
 #include <boost/python.hpp>
-using namespace boost::python;
+#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
+
 
 #include <ost/geom/geom.hh>
 
+using namespace boost::python;
+
 const Real Vec2_getitem(const geom::Vec2& v, int i) {return v[i];}
 void Vec2_setitem(geom::Vec2& v,const  int i,const  Real val) {v[i]=val;}
 
@@ -54,6 +57,8 @@ void export_Vec2()
     .def("GetY", &Vec2::GetY)
     .add_property("x", &Vec2::GetX, &Vec2::SetX)
     .add_property("y", &Vec2::GetY, &Vec2::SetY)
-
   ;
+  class_<Vec2List>("Vec2List", init<>())
+    .def(vector_indexing_suite<Vec2List>())
+  ;  
 }
diff --git a/modules/geom/pymod/export_vec3.cc b/modules/geom/pymod/export_vec3.cc
index b9bf4edea774e85e83916826d2f6b77ace2b35d6..d37fc6a535502bd9e3191e768b4e249fde42c179 100644
--- a/modules/geom/pymod/export_vec3.cc
+++ b/modules/geom/pymod/export_vec3.cc
@@ -17,11 +17,11 @@
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
 #include <boost/python.hpp>
-using namespace boost::python;
+#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
 
 #include <ost/geom/geom.hh>
 
-
+using namespace boost::python;
 
 const Real Vec3_getitem(const geom::Vec3& v, int i) {return v[i];}
 void Vec3_setitem(geom::Vec3& v,const  int i,const  Real val) {v[i]=val;}
@@ -65,4 +65,8 @@ void export_Vec3()
   ;
   def("Normalize", &NormalizeV3);
   def("Cross", &Cross);
+  
+  class_<Vec3List>("Vec3List", init<>())
+    .def(vector_indexing_suite<Vec3List>())
+  ;
 }
diff --git a/modules/geom/src/CMakeLists.txt b/modules/geom/src/CMakeLists.txt
index 7e651b5e33a40e60065cd8cdb407072bb4045d7f..bfb20fce4f63305fab0fe2e15c2013c559f013da 100644
--- a/modules/geom/src/CMakeLists.txt
+++ b/modules/geom/src/CMakeLists.txt
@@ -32,9 +32,6 @@ set(OST_GEOM_SOURCES
 mat2.cc
 mat3.cc
 mat4.cc
-vec2.cc
-vec3.cc
-vec4.cc
 vecmat2_op.cc
 vecmat3_op.cc
 vecmat4_op.cc
diff --git a/modules/geom/src/composite2.cc b/modules/geom/src/composite2.cc
index b8300fcfb559afe9244583c7b679b1419ef85ead..f6d7f685743c3962d8b8e5acf1a1280b1688b210 100644
--- a/modules/geom/src/composite2.cc
+++ b/modules/geom/src/composite2.cc
@@ -88,16 +88,16 @@ Vec2 Ellipse2::calc_(Real t) const
 Rectangle2 Ellipse2::GetBoundingBox() const
 {
   if(gamma_==0.0 || gamma_==M_PI){
-    return Rectangle2(Vec2(origin_.GetX()-a_,origin_.GetY()-b_),Vec2(origin_.GetX()+a_/2,origin_.GetY()+b_));
+    return Rectangle2(Vec2(origin_.x-a_,origin_.y-b_),Vec2(origin_.x+a_/2,origin_.y+b_));
   }
   if(gamma_==M_PI*0.5 || gamma_==3*M_PI*0.5){
-    return Rectangle2(Vec2(origin_.GetX()-b_,origin_.GetY()-a_),Vec2(origin_.GetX()+b_/2,origin_.GetY()+a_));
+    return Rectangle2(Vec2(origin_.x-b_,origin_.y-a_),Vec2(origin_.x+b_/2,origin_.y+a_));
   }
   Real t=atan(-b_/a_*tan(gamma_));
   Vec2 vx=calc_(t);
   t=atan(b_/a_/tan(gamma_));
   Vec2 vy=calc_(t);
-  return Rectangle2(Vec2(origin_.GetX()-vx.GetX(),origin_.GetY()-vy.GetY()),Vec2(origin_.GetX()+vx.GetX(),origin_.GetY()+vy.GetY()));
+  return Rectangle2(Vec2(origin_.x-vx.x,origin_.y-vy.y),Vec2(origin_.x+vx.x,origin_.y+vy.y));
 }
 
 Rectangle2::Rectangle2():
@@ -112,11 +112,11 @@ bottomright_(bottomright)
 }
 Real Rectangle2::GetWidth() const
 {
-    return bottomright_.GetX()-topleft_.GetX();
+    return bottomright_.x-topleft_.x;
 }
 Real Rectangle2::GetHeight() const
 {
-    return bottomright_.GetY()-topleft_.GetY();
+    return bottomright_.y-topleft_.y;
 }
 Real Rectangle2::GetArea() const
 {
@@ -207,7 +207,7 @@ Real Polygon2::GetArea() const
     unsigned int ip1=(i+1)%nodecount;
     Vec2 n1=GetNode(i);
     Vec2 n2=GetNode(ip1);
-    area+=n1.GetX()*n2.GetY()-n2.GetX()*n1.GetY();
+    area+=n1.x*n2.y-n2.x*n1.y;
   }
   return area/2.0;
 }
@@ -220,8 +220,8 @@ Vec2 Polygon2::GetCentroid() const
     unsigned int ip1=(i+1)%nodecount;
     Vec2 n1=GetNode(i);
     Vec2 n2=GetNode(ip1);
-    cx+=(n1.GetX()+n2.GetX())*(n1.GetX()*n2.GetY()-n2.GetX()*n1.GetY());
-    cy+=(n1.GetY()+n2.GetY())*(n1.GetX()*n2.GetY()-n2.GetX()*n1.GetY());
+    cx+=(n1.x+n2.x)*(n1.x*n2.y-n2.x*n1.y);
+    cy+=(n1.y+n2.y)*(n1.x*n2.y-n2.x*n1.y);
   }
   Real area=GetArea();
   return Vec2(cx/(6.0*area),cy/(6.0*area));
@@ -255,17 +255,17 @@ Rectangle2 Polygon2::GetBoundingBox() const
   {
     return Rectangle2(Vec2(0.0,0.0),Vec2(0.0,0.0));
   }
-  Real x_min=operator[](0).GetX();
+  Real x_min=operator[](0).x;
   Real x_max=x_min;
-  Real y_min=operator[](0).GetY();
+  Real y_min=operator[](0).y;
   Real y_max=y_min;
   unsigned int nodecount=GetNodeCount();
   for(unsigned int i=0;i<nodecount;++i){
     Vec2 n=operator[](i);
-    x_min=std::min<Real>(n.GetX(),x_min);
-    x_max=std::max<Real>(n.GetX(),x_max);
-    y_min=std::min<Real>(n.GetY(),y_min);
-    y_max=std::max<Real>(n.GetY(),y_max);
+    x_min=std::min<Real>(n.x,x_min);
+    x_max=std::max<Real>(n.x,x_max);
+    y_min=std::min<Real>(n.y,y_min);
+    y_max=std::max<Real>(n.y,y_max);
   }
   return Rectangle2(Vec2(x_min,y_min),Vec2(x_max,y_max));
 }
diff --git a/modules/geom/src/composite2_op.cc b/modules/geom/src/composite2_op.cc
index cc660f821eb782bcb6e56a0c4f4dc01002747e6d..5044771a8f5ca2223520692f8a2206c470c05421 100644
--- a/modules/geom/src/composite2_op.cc
+++ b/modules/geom/src/composite2_op.cc
@@ -88,11 +88,11 @@ bool IsInPolygon(const Polygon2& p, const Vec2& v)
   }
   bool c = false;
   Vec2 old=p.GetNode(p.GetNodeCount()-1);
-  bool oldcomp= v.GetY()<old.GetY();
+  bool oldcomp= v.y<old.y;
   for (Polygon2::const_iterator it=p.begin();it!=p.end(); ++it) {
-    bool comp= v.GetY() < (*it).GetY();
+    bool comp= v.y < (*it).y;
     if( comp ^ oldcomp ) {
-      if( (v.GetX() < (old.GetX() - (*it).GetX()) * (v.GetY() - (*it).GetY()) / (old.GetY() - (*it).GetY()) + (*it).GetX()) ){
+      if( (v.x < (old.x - (*it).x) * (v.y - (*it).y) / (old.y - (*it).y) + (*it).x) ){
         c = !c;
       }
     }
@@ -123,7 +123,7 @@ DLLEXPORT bool IsInRectangle(const Rectangle2& r, const Vec2& v)
 {
   Vec2 start=r.GetStart();
   Vec2 end=r.GetEnd();
-  return v.GetX()>=start.GetX() && v.GetX()<=end.GetX() &&  v.GetY()>=start.GetY() && v.GetY()<=end.GetY();
+  return v.x>=start.x && v.x<=end.x &&  v.y>=start.y && v.y<=end.y;
 }
 DLLEXPORT bool IsInCircle(const Circle2& c, const Vec2& v)
 {
diff --git a/modules/geom/src/mat2.cc b/modules/geom/src/mat2.cc
index ac34069dfe055e2dcce97e0e4a5294209a93b5bd..06e196d8cb987f1e4162345a37e40cdcaa764a9a 100644
--- a/modules/geom/src/mat2.cc
+++ b/modules/geom/src/mat2.cc
@@ -65,20 +65,6 @@ bool Mat2::operator==(const Mat2& rhs) const
     data_[1][1] == rhs.data_[1][1];
 }
 
-
-Real& Mat2::operator()(std::size_t r, std::size_t c)
-{
-  if(r>1 || c>1) throw OutOfRangeException();
-  return data_[r][c];
-}
-
-const Real& Mat2::operator()(std::size_t r, std::size_t c) const
-{
-  if(r>1 || c>1) throw OutOfRangeException();
-  return data_[r][c];
-}
-
-
 Mat2& Mat2::operator+=(const Mat2& rhs)
 {
   data_[0][0]+=rhs(0,0);
diff --git a/modules/geom/src/mat2.hh b/modules/geom/src/mat2.hh
index 9231cb7100e3f35541b59608e11c894751448775..bc53416f2caac2772706d50cacb09a76a39effd3 100644
--- a/modules/geom/src/mat2.hh
+++ b/modules/geom/src/mat2.hh
@@ -21,6 +21,7 @@
 
 #include <cstddef> // for size_t
 #include <ostream>
+#include <cassert>
 
 #include <boost/operators.hpp>
 
@@ -63,9 +64,17 @@ public:
   bool operator==(const Mat2& rhs) const;
 
   //! element access
-  Real& operator()(std::size_t r, std::size_t c);
+  Real& operator()(std::size_t r, std::size_t c)
+  {
+    assert(r<=1 && c<=1);
+    return data_[r][c];
+  }
   //! const element access
-  const Real& operator()(std::size_t r, std::size_t c) const;
+  const Real& operator()(std::size_t r, std::size_t c) const
+  {
+    assert(r<=1 && c<=1);
+    return data_[r][c];
+  }
 
   //! addable op
   Mat2& operator+=(const Mat2& rhs);
diff --git a/modules/geom/src/mat3.cc b/modules/geom/src/mat3.cc
index f9492d3d4b4ec7d209de1cde92e31f2d727ceeb9..a202f20a3795fca2a9e36148e9d7f0dd34789900 100644
--- a/modules/geom/src/mat3.cc
+++ b/modules/geom/src/mat3.cc
@@ -24,132 +24,6 @@
 
 namespace geom {
 
-Mat3::Mat3()
-{
-  this->set(1.0,0.0,0.0, 0.0,1.0,0.0, 0.0,0.0,1.0);
-}
-
-Mat3::Mat3(Real i00, Real i01, Real i02,Real i10, Real i11, Real i12,Real i20, Real i21, Real i22)
-{
-  this->set(i00,i01,i02,i10,i11,i12,i20,i21,i22);
-}
-
-Mat3::Mat3(const Mat3& m)
-{
-  this->set(m(0,0),m(0,1),m(0,2),m(1,0),m(1,1),m(1,2),m(2,0),m(2,1),m(2,2));
-}
-
-Mat3::Mat3(const Mat2& m)
-{
-  this->set(m(0,0),m(0,1),0.0, m(1,0),m(1,1),0.0, 0.0,0.0,1.0);
-}
-
-Mat3::Mat3(const Real arr[9])
-{
-  this->set(arr[0],arr[1],arr[2],arr[3],arr[4],arr[5],arr[6],arr[7],arr[8]);
-}
-
-Mat3& Mat3::operator=(const Mat3& m)
-{
-  if(&m!=this) {
-    this->set(m(0,0),m(0,1),m(0,2),m(1,0),m(1,1),m(1,2),m(2,0),m(2,1),m(2,2));
-  }
-  return *this;
-}
-
-Mat3 Mat3::Identity() 
-{
-  static Mat3 i(1.0,0.0,0.0,
-                0.0,1.0,0.0,
-                0.0,0.0,1.0);
-  return i;
-}
-
-bool Mat3::operator==(const Mat3& rhs) const
-{
-  return data_[0][0] ==  rhs.data_[0][0] &&
-    data_[1][0] == rhs.data_[1][0] &&
-    data_[2][0] == rhs.data_[2][0] &&
-    data_[0][1] == rhs.data_[0][1] &&
-    data_[1][1] ==  rhs.data_[1][1] &&
-    data_[2][1] ==  rhs.data_[2][1] &&
-    data_[0][2] ==  rhs.data_[0][2] &&
-    data_[1][2] ==  rhs.data_[1][2] &&
-    data_[2][2] ==  rhs.data_[2][2];
-}
-
-Real& Mat3::operator()(std::size_t r, std::size_t c)
-{
-  if(r>2 || c>2) throw OutOfRangeException();
-  return data_[r][c];
-}
-
-const Real& Mat3::operator()(std::size_t r, std::size_t c) const
-{
-  if(r>2 || c>2) throw OutOfRangeException();
-  return data_[r][c];
-}
-
-
-Mat3& Mat3::operator+=(const Mat3& rhs)
-{
-  data_[0][0]+=rhs(0,0);
-  data_[0][1]+=rhs(0,1);
-  data_[0][2]+=rhs(0,2);
-  data_[1][0]+=rhs(1,0);
-  data_[1][1]+=rhs(1,1);
-  data_[1][2]+=rhs(1,2);
-  data_[2][0]+=rhs(2,0);
-  data_[2][1]+=rhs(2,1);
-  data_[2][2]+=rhs(2,2);
-  return *this;
-}
-Mat3& Mat3::operator-=(const Mat3& rhs)
-{
-  data_[0][0]-=rhs(0,0);
-  data_[0][1]-=rhs(0,1);
-  data_[0][2]-=rhs(0,2);
-  data_[1][0]-=rhs(1,0);
-  data_[1][1]-=rhs(1,1);
-  data_[1][2]-=rhs(1,2);
-  data_[2][0]-=rhs(2,0);
-  data_[2][1]-=rhs(2,1);
-  data_[2][2]-=rhs(2,2);
-  return *this;
-}
-Mat3& Mat3::operator*=(const Real d)
-{
-  data_[0][0]*=d;
-  data_[0][1]*=d;
-  data_[0][2]*=d;
-  data_[1][0]*=d;
-  data_[1][1]*=d;
-  data_[1][2]*=d;
-  data_[2][0]*=d;
-  data_[2][1]*=d;
-  data_[2][2]*=d;
-  return *this;
-}
-Mat3& Mat3::operator/=(const Real d)
-{
-  data_[0][0]/=d;
-  data_[0][1]/=d;
-  data_[0][2]/=d;
-  data_[1][0]/=d;
-  data_[1][1]/=d;
-  data_[1][2]/=d;
-  data_[2][0]/=d;
-  data_[2][1]/=d;
-  data_[2][2]/=d;
-  return *this;
-}
-
-Mat3& Mat3::operator*=(const Mat3& m)
-{
-  (*this)=operator*(*this,m);
-  return *this;
-}
-
 geom::Vec3 Mat3::GetCol(int index) const
 {
   return geom::Vec3(data_[0][index], data_[1][index], data_[2][index]);  
@@ -163,12 +37,6 @@ geom::Vec3 Mat3::GetRow(int index) const
 
 ////////////////////////////////////////////
 // private member functions
-void Mat3::set(Real i00, Real i01, Real i02,Real i10, Real i11, Real i12,Real i20, Real i21, Real i22)
-{
-  data_[0][0]=i00; data_[0][1]=i01; data_[0][2]=i02;
-  data_[1][0]=i10; data_[1][1]=i11; data_[1][2]=i12;
-  data_[2][0]=i20; data_[2][1]=i21; data_[2][2]=i22;
-}
 
 std::ostream& operator<<(std::ostream& os, const Mat3& m)
 {
diff --git a/modules/geom/src/mat3.hh b/modules/geom/src/mat3.hh
index f7d90c3f313dff15a1dffb2bd72b5c80fdc4e7ec..15815863328fe4ca1039ced2b5d48250eef952cd 100644
--- a/modules/geom/src/mat3.hh
+++ b/modules/geom/src/mat3.hh
@@ -21,10 +21,12 @@
 
 #include <cstddef> // for size_t
 #include <ostream>
+#include <cassert>
 
 #include <boost/operators.hpp>
 
 #include <ost/geom/module_config.hh>
+#include <ost/geom/mat2.hh>
 
 namespace geom {
 
@@ -36,12 +38,12 @@ class DLLEXPORT_OST_GEOM Mat3:
     private boost::additive1<Mat3>,
     private boost::multiplicative2<Mat3, Real>
 {
-public:
-  static Mat3 Identity();
-  
-  //! Default initialization, identity matrix
-  Mat3();
-
+public:  
+  //! Default initialization, identity matrix  
+  Mat3()
+  {
+    this->set(1.0,0.0,0.0, 0.0,1.0,0.0, 0.0,0.0,1.0);
+  }
   //! In with 9 values in row-major order
   /*!
     row-major order means that the matrix
@@ -52,37 +54,138 @@ public:
 
     is initialized with (a,b,c, d,e,f, g,h,i)
   */
-  Mat3(Real i00, Real i01, Real i02,Real i10, Real i11, Real i12,Real i20, Real i21, Real i22);
-
-  //! Copy ctor
-  Mat3(const Mat3& m);
-
-  // initialization with 2d matrix
-  explicit Mat3(const Mat2& m);
-
-  //! initialization from array
-  explicit Mat3(const Real[9]);
-
-  //! assignement op
-  Mat3& operator=(const Mat3& m);
-
-  //! comparable
-  bool operator==(const Mat3& rhs) const;
+  Mat3(Real i00, Real i01, Real i02,
+       Real i10, Real i11, Real i12,
+       Real i20, Real i21, Real i22)
+  {
+    this->set(i00,i01,i02,i10,i11,i12,i20,i21,i22);
+  }
+
+  Mat3(const Mat3& m)
+  {
+    this->set(m(0,0),m(0,1),m(0,2),m(1,0),m(1,1),m(1,2),m(2,0),m(2,1),m(2,2));
+  }
+
+  Mat3(const Mat2& m)
+  {
+    this->set(m(0, 0), m(0, 1), Real(0.0),
+              m(1, 0), m(1, 1), Real(0.0),
+              Real(0.0), Real(0.0), Real(1.0));
+  }
+  
+  explicit Mat3(const Real arr[9])
+  {
+    this->set(arr[0],arr[1],arr[2],arr[3],arr[4],arr[5],arr[6],arr[7],arr[8]);
+  }  
 
   //! element access
-  Real& operator()(std::size_t r, std::size_t c);
+  Real& operator()(std::size_t r, std::size_t c)
+  {
+    assert(r<=2 && c<=2);
+    return data_[r][c];
+  }
   //! const element access
-  const Real& operator()(std::size_t r, std::size_t c) const;
-
-  //! addable op
-  Mat3& operator+=(const Mat3& rhs);
-  //! subtractable op
-  Mat3& operator-=(const Mat3& rhs);
-
-  Mat3& operator*=(const Real d);
-  Mat3& operator/=(const Real d);
-
-  Mat3& operator*=(const Mat3& m);
+  const Real& operator()(std::size_t r, std::size_t c) const
+  {
+    assert(r<=2 && c<=2);
+    return data_[r][c];
+  }
+
+  Mat3& operator=(const Mat3& m)
+  {
+    if(&m!=this) {
+      this->set(m(0,0),m(0,1),m(0,2),m(1,0),m(1,1),m(1,2),m(2,0),m(2,1),m(2,2));
+    }
+    return *this;
+  }
+
+  static Mat3 Identity() 
+  {
+    static Mat3 i(1.0,0.0,0.0,
+                  0.0,1.0,0.0,
+                  0.0,0.0,1.0);
+    return i;
+  }
+
+  bool operator==(const Mat3& rhs) const
+  {
+    return data_[0][0] ==  rhs.data_[0][0] &&
+      data_[1][0] == rhs.data_[1][0] &&
+      data_[2][0] == rhs.data_[2][0] &&
+      data_[0][1] == rhs.data_[0][1] &&
+      data_[1][1] ==  rhs.data_[1][1] &&
+      data_[2][1] ==  rhs.data_[2][1] &&
+      data_[0][2] ==  rhs.data_[0][2] &&
+      data_[1][2] ==  rhs.data_[1][2] &&
+      data_[2][2] ==  rhs.data_[2][2];
+  }
+
+  Mat3& operator+=(const Mat3& rhs)
+  {
+    data_[0][0]+=rhs(0,0);
+    data_[0][1]+=rhs(0,1);
+    data_[0][2]+=rhs(0,2);
+    data_[1][0]+=rhs(1,0);
+    data_[1][1]+=rhs(1,1);
+    data_[1][2]+=rhs(1,2);
+    data_[2][0]+=rhs(2,0);
+    data_[2][1]+=rhs(2,1);
+    data_[2][2]+=rhs(2,2);
+    return *this;
+  }
+  Mat3& operator-=(const Mat3& rhs)
+  {
+    data_[0][0]-=rhs(0,0);
+    data_[0][1]-=rhs(0,1);
+    data_[0][2]-=rhs(0,2);
+    data_[1][0]-=rhs(1,0);
+    data_[1][1]-=rhs(1,1);
+    data_[1][2]-=rhs(1,2);
+    data_[2][0]-=rhs(2,0);
+    data_[2][1]-=rhs(2,1);
+    data_[2][2]-=rhs(2,2);
+    return *this;
+  }
+  Mat3& operator*=(const Real d)
+  {
+    data_[0][0]*=d;
+    data_[0][1]*=d;
+    data_[0][2]*=d;
+    data_[1][0]*=d;
+    data_[1][1]*=d;
+    data_[1][2]*=d;
+    data_[2][0]*=d;
+    data_[2][1]*=d;
+    data_[2][2]*=d;
+    return *this;
+  }
+  Mat3& operator/=(const Real d)
+  {
+    data_[0][0]/=d;
+    data_[0][1]/=d;
+    data_[0][2]/=d;
+    data_[1][0]/=d;
+    data_[1][1]/=d;
+    data_[1][2]/=d;
+    data_[2][0]/=d;
+    data_[2][1]/=d;
+    data_[2][2]/=d;
+    return *this;
+  }
+
+  Mat3& operator*=(const Mat3& m)
+  {
+    (*this)=Mat3((*this)(0,0)*m(0,0)+(*this)(0,1)*m(1,0)+(*this)(0,2)*m(2,0),
+                 (*this)(0,0)*m(0,1)+(*this)(0,1)*m(1,1)+(*this)(0,2)*m(2,1),
+                 (*this)(0,0)*m(0,2)+(*this)(0,1)*m(1,2)+(*this)(0,2)*m(2,2),
+                 (*this)(1,0)*m(0,0)+(*this)(1,1)*m(1,0)+(*this)(1,2)*m(2,0),
+                 (*this)(1,0)*m(0,1)+(*this)(1,1)*m(1,1)+(*this)(1,2)*m(2,1),
+                 (*this)(1,0)*m(0,2)+(*this)(1,1)*m(1,2)+(*this)(1,2)*m(2,2),                                   
+                 (*this)(2,0)*m(0,0)+(*this)(2,1)*m(1,0)+(*this)(2,2)*m(2,0),
+                 (*this)(2,0)*m(0,1)+(*this)(2,1)*m(1,1)+(*this)(2,2)*m(2,1),
+                 (*this)(2,0)*m(0,2)+(*this)(2,1)*m(1,2)+(*this)(2,2)*m(2,2));
+    return *this;
+  }
 
   Real* Data() {return &data_[0][0];}
   const Real* Data() const {return &data_[0][0];}
@@ -92,9 +195,16 @@ public:
 private:
   Real data_[3][3];
 
-  void set(Real i00, Real i01, Real i02,Real i10, Real i11, Real i12,Real i20, Real i21, Real i22);
+  void set(Real i00, Real i01, Real i02,
+           Real i10, Real i11, Real i12,
+           Real i20, Real i21, Real i22)
+  {
+    data_[0][0]=i00; data_[0][1]=i01; data_[0][2]=i02;
+    data_[1][0]=i10; data_[1][1]=i11; data_[1][2]=i12;
+    data_[2][0]=i20; data_[2][1]=i21; data_[2][2]=i22;
+  }
 };
-
+  
 DLLEXPORT_OST_GEOM std::ostream& operator<<(std::ostream& o, const Mat3& m);
 
 } // ns geom
diff --git a/modules/geom/src/quat.cc b/modules/geom/src/quat.cc
index abfa6c80f5055f877126aa2424b8d88cd86a6b39..ceb178713e8641862d763a06f09023faa039004b 100644
--- a/modules/geom/src/quat.cc
+++ b/modules/geom/src/quat.cc
@@ -316,11 +316,20 @@ Quat& Quat::operator*=(Real s)
 }
 
 Quat& Quat::operator*=(const Quat& q)
-{
-  w = this->w*q.w - this->x*q.x - this->y*q.y - this->z*q.z;
-  x = this->w*q.x + this->x*q.w + this->y*q.z - this->z*q.y;
-  y = this->w*q.y + this->y*q.w - this->x*q.z + this->z*q.x;
-  z = this->w*q.z + this->z*q.w + this->x*q.y - this->y*q.x;
+{  
+  Vec3 v00 (x,y,z);
+  Vec3 v10 (q.x,q.y,q.z);
+
+  Real w2=w*q.w-Dot(v00,v10);
+  Vec3 v2=Cross(v00,v10);
+  Vec3 v3=v10;  v3 *= w;
+  Vec3 v4=v00;  v4 *= q.w;
+  Vec3 v5=v2+v3+v4;
+  
+  w=w2;
+  x=v5[0];
+  y=v5[1];
+  z=v5[2];
   return *this;
 }
 
@@ -357,54 +366,6 @@ Quat Conjugate(const Quat& q)
   return Quat(q.w,-q.x,-q.y,-q.z);
 }
 
-namespace {
-
-
-/*
-  for a unit quaternion defined as (cos[theta],sin[theta] * [x,y,z])
-  the log is given by (0,theta * [x,y,z])
-*/
-Quat log(const Quat& q) 
-{
-  Quat nrvo;
-  Real sin_theta = std::sqrt(q.x*q.x+q.y*q.y+q.z*q.z);
-  if(std::fabs(sin_theta)<1e-30) {
-    /*
-      for a theta of zero, cos(theta)=1, the log if which is zero,
-      and hence an all zero quat is the result, but this may lead to
-      trouble...
-    */
-    nrvo = Quat(0.0,0.0,0.0,0.0);
-  } else {
-
-    Real theta = std::atan2(sin_theta,q.w);
-    Real f = theta/sin_theta;
-    // assume cos(theta) == w, since we are supposed to have a unit quaternion
-    nrvo = Quat(0.0,q.x*f,q.y*f,q.z*f);
-
-  }
-  return nrvo;
-}
-
-Quat exp(const Quat& q)
-{
-  Quat nrvo;
-  Real theta = std::sqrt(q.x*q.x+q.y*q.y+q.z*q.z);
-  if(std::fabs(theta)<1e-30) {
-    /*
-      see log special case above; this will now
-      return a 'proper' quaternion
-    */
-    nrvo = Quat(1.0,0.0,0.0,0.0);
-  } else {
-    Real f = sin(theta)/theta;
-    nrvo = Quat(cos(theta),f*q.x,f*q.y,f*q.z);
-  }
-  return nrvo;
-}
-
-}
-
 /*
   qt = q0 ( q0* q1) ^t
   qt  = q0 Exp[t Log[ Conj[q0] q1]]
@@ -453,21 +414,21 @@ Vec3 Quat::Rotate(const Vec3& vec) const {
 Quat Grassmann(const Quat& lhs, const Quat& rhs)
 {
   return Quat(lhs.GetAngle()*rhs.GetAngle()-
-              lhs.GetAxis().GetX()*rhs.GetAxis().GetX()-
-              lhs.GetAxis().GetY()*rhs.GetAxis().GetY()-
-              lhs.GetAxis().GetZ()*rhs.GetAxis().GetZ(),
-                    lhs.GetAngle()*rhs.GetAxis().GetX()+
-                    lhs.GetAxis().GetX()*rhs.GetAngle()+
-                    lhs.GetAxis().GetY()*rhs.GetAxis().GetZ()-
-                    lhs.GetAxis().GetZ()*rhs.GetAxis().GetY(),
-               lhs.GetAngle()*rhs.GetAxis().GetY()-
-               lhs.GetAxis().GetX()*rhs.GetAxis().GetZ()+
-               lhs.GetAxis().GetY()*rhs.GetAngle()+
-               lhs.GetAxis().GetZ()*rhs.GetAxis().GetX(),
-                    lhs.GetAngle()*rhs.GetAxis().GetZ()+
-                    lhs.GetAxis().GetX()*rhs.GetAxis().GetY()-
-                    lhs.GetAxis().GetY()*rhs.GetAxis().GetX()+
-                    lhs.GetAxis().GetZ()*rhs.GetAngle());
+              lhs.GetAxis().x*rhs.GetAxis().x-
+              lhs.GetAxis().y*rhs.GetAxis().y-
+              lhs.GetAxis().z*rhs.GetAxis().z,
+                    lhs.GetAngle()*rhs.GetAxis().x+
+                    lhs.GetAxis().x*rhs.GetAngle()+
+                    lhs.GetAxis().y*rhs.GetAxis().z-
+                    lhs.GetAxis().z*rhs.GetAxis().y,
+               lhs.GetAngle()*rhs.GetAxis().y-
+               lhs.GetAxis().x*rhs.GetAxis().z+
+               lhs.GetAxis().y*rhs.GetAngle()+
+               lhs.GetAxis().z*rhs.GetAxis().x,
+                    lhs.GetAngle()*rhs.GetAxis().z+
+                    lhs.GetAxis().x*rhs.GetAxis().y-
+                    lhs.GetAxis().y*rhs.GetAxis().x+
+                    lhs.GetAxis().z*rhs.GetAngle());
 }
 
 std::ostream& operator<<(std::ostream& str, const Quat& q)
diff --git a/modules/geom/src/vec2.cc b/modules/geom/src/vec2.cc
deleted file mode 100644
index 129a2745c25a2cfcec1dcd0a497a9016858b1dfb..0000000000000000000000000000000000000000
--- a/modules/geom/src/vec2.cc
+++ /dev/null
@@ -1,179 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#include "vec2.hh"
-#include "vec3.hh"
-#include "vec4.hh"
-
-#include "exc.hh"
-
-namespace geom {
-
-Vec2::Vec2()
-{
-  this->set(0.0,0.0);
-}
-
-Vec2::Vec2(Real x, Real y)
-{
-  this->set(x,y);
-}
-
-Vec2::Vec2(const Vec2& v)
-{
-  this->set(v.data_[0],v.data_[1]);
-}
-
-Vec2::Vec2(const Vec3& v)
-{
-  this->set(v[0],v[1]); // z is silenly swallowed
-}
-
-Vec2::Vec2(const Vec4& v) 
-{
-  if(v[3]==0.0) {
-    throw DivideByZeroException("zero w component in Vec4->Vec2 conversion");
-  }
-  this->set(v[0]/v[3],v[1]/v[3]); // z is silently swallowed
-}
-
-Vec2::Vec2(const Real d[2])
-{
-  this->set(d[0],d[1]);
-}
-
-/*Vec2::Vec2(const float d[2])
-{
-  this->set(d[0],d[1]);
-}
-*/
-Vec2& Vec2::operator=(const Vec2& v)
-{
-  if(&v!=this) {
-    this->set(v[0],v[1]);
-  }
-  return *this;
-}
-
-bool Vec2::operator==(const Vec2& v) const
-{
-  return data_[0]==v.data_[0] && 
-    data_[1]==v.data_[1];
-}
-
-
-Real& Vec2::operator[](std::size_t indx)
-{
-  if(indx>1) throw OutOfRangeException();
-  return data_[indx];
-}
-
-
-const Real& Vec2::operator[](std::size_t indx) const
-{
-  if(indx>1) throw OutOfRangeException();
-  return data_[indx];
-}
-
-
-Vec2 Vec2::operator-() const
-{
-  Vec2 nrvo(-data_[0],-data_[1]);
-  return nrvo;
-}
-
-Vec2& Vec2::operator+=(const Vec2& rhs)
-{
-  data_[0]+=rhs[0]; data_[1]+=rhs[1];
-  return *this;
-}
-
-Vec2& Vec2::operator-=(const Vec2& rhs)
-{
-  data_[0]-=rhs[0]; data_[1]-=rhs[1];
-  return *this;
-}
-
-Vec2& Vec2::operator*=(Real d)
-{
-  data_[0]*=d; data_[1]*=d;
-  return *this;
-}
-
-Vec2& Vec2::operator+=(Real d)
-{
-  data_[0]+=d; data_[1]+=d;
-  return *this;
-}
-
-Vec2& Vec2::operator-=(Real d)
-{
-  data_[0]-=d; data_[1]-=d;
-  return *this;
-}
-
-Vec2& Vec2::operator/=(Real d)
-{
-  data_[0]/=d; data_[1]/=d;
-  return *this;
-}
-
-////////////////////////////////////////////
-// private member functions
-
-void Vec2::set(Real x, Real y)
-{
-  data_[0]=x; data_[1]=y;
-}
-
-////////////////////////////////////////////
-// functions
-
-Vec2 operator/(Real d, const Vec2& v)
-{
-  Vec2 nrvo(d/v[0],d/v[1]);
-  return nrvo;
-}
-
-std::ostream& operator<<(std::ostream& os, const Vec2& v)
-{
-  os << "(" << v[0] << "," << v[1] << ")";
-  return os;
-}
-
-Real Vec2::GetX() const
-{
-  return data_[0];
-}
-
-Real Vec2::GetY() const
-{
-  return data_[1];
-}
-
-void Vec2::SetX(Real v)
-{
-  data_[0]=v;
-}
-void Vec2::SetY(Real v)
-{
-  data_[1]=v;
-}
-
-
-} // ns
diff --git a/modules/geom/src/vec2.hh b/modules/geom/src/vec2.hh
index de3012f8a39839d945136478bb486789399e8f58..8432856ead98214eccd77c9deeebeb9c064014f8 100644
--- a/modules/geom/src/vec2.hh
+++ b/modules/geom/src/vec2.hh
@@ -19,13 +19,15 @@
 #ifndef GEOM_VEC2_H
 #define GEOM_VEC2_H
 
+#include <stdexcept>
 #include <cstddef> // for size_t
 #include <ostream>
-
+#include <vector>
 #include <boost/operators.hpp>
 
-#include <ost/geom/module_config.hh>
+
 #include <ost/config.hh>
+#include <ost/geom/module_config.hh>
 
 namespace geom {
 
@@ -36,7 +38,7 @@ class Vec4;
 /*
   Two dimensional vector class, using Real precision.
 */
-class DLLEXPORT_OST_GEOM Vec2:
+class DLLEXPORT Vec2:
     private boost::equality_comparable<Vec2>,
     private boost::additive<Vec2>,
     private boost::additive<Vec2, Real>,
@@ -44,13 +46,13 @@ class DLLEXPORT_OST_GEOM Vec2:
 {
 public:
   //! Default initialization, all components are set to zero
-  Vec2();
+  Vec2(): x(0), y(0) { }
 
   //! Initialization with x, y and z component
-  Vec2(Real x, Real y);
+  Vec2(Real px, Real py): x(px), y(py) { }
 
   //! copy ctor
-  Vec2(const Vec2& v);
+  Vec2(const Vec2& v): x(v.x), y(v.y) { }
 
   //! explicit initialization with 3D vector
   explicit Vec2(const Vec3& v);
@@ -59,53 +61,127 @@ public:
   explicit Vec2(const Vec4& v);
 
   //! explicit initialization with an array of doubles
-  explicit Vec2(const Real[2]);
+  explicit Vec2(const float v[2]): x(v[0]), y(v[1]) { }
+
 
-#if OST_DOUBLE_PRECISION
   //! explicit initialization with an array of floats
-  explicit Vec2(const float[2]);
-#endif
-  //! assignement op
-  Vec2& operator=(const Vec2& v);
+  explicit Vec2(const double v[2]): x(v[0]), y(v[1]) { }
 
-  //! element access
-  Real& operator[](std::size_t indx);
-  //! const element access
-  const Real& operator[](std::size_t indx) const;
-  //! element access
-  Real GetX() const;
-  Real GetY() const;
-  void SetX(Real v);
-  void SetY(Real v);
+
+  Real GetX() const { return x; }
+  Real GetY() const { return y; }
+
+  void SetX(Real d) { x=d; }
+  void SetY(Real d) { y=d; }
 
   //! comparable
-  bool operator==(const Vec2& rhs) const;
+  bool operator==(const Vec2& rhs) const
+  {
+    return x==rhs.x && y==rhs.y;
+  }
 
+  //! element access
+  Real& operator[](std::size_t indx)
+  {
+    if (indx>1) {
+      throw std::out_of_range("Index must be in the range [0-1]");
+    }
+    return (&x)[indx];
+  }
+  
+  //! const element access
+  const Real& operator[](std::size_t indx) const
+  {
+    if (indx>1) {
+      throw std::out_of_range("Index must be in the range [0-1]");
+    }
+    return (&x)[indx];
+  }
+  
   //! addable op
-  Vec2& operator+=(const Vec2& rhs);
-  Vec2& operator+=(Real d);
+  Vec2& operator+=(const Vec2& rhs)
+  {
+    x+=rhs.x;
+    y+=rhs.y;
+    return *this;
+  }
+  
+  Vec2& operator+=(Real d)
+  {
+    x+=d;
+    y+=d;
+    return *this;
+  }
+  
   //! subtractable op
-  Vec2& operator-=(const Vec2& rhs);
-  Vec2& operator-=(Real d);
+  Vec2& operator-=(const Vec2& rhs)
+  {
+    x-=rhs.x;
+    y-=rhs.y;
+    return *this;
+  }
+  
+  Vec2& operator-=(Real d)
+  {
+    x-=d;
+    y-=d;
+    return *this;
+  }
   //! negateable
-  Vec2 operator-() const;
+  Vec2 operator-() const
+  {
+    return Vec2(-x, -y);
+  }
+
   //! multipliable
-  Vec2& operator*=(Real d);
+  Vec2& operator*=(Real d)
+  {
+    x*=d;
+    y*=d;
+    return *this;
+  }
+
   //! dividable
-  Vec2& operator/=(Real d);
+  Vec2& operator/=(Real d)
+  {
+    Real one_over_d=Real(1.0)/d;
+    x*=one_over_d;
+    y*=one_over_d;
+    return *this;
+  }
+
+  Real* Data() {return &x;}
+  const Real* Data() const { return &x; }
+
+  Real x;
+  Real y;
+};
 
-  Real* Data() {return data_;}
-  const Real* Data() const {return data_;}
+inline Vec2 operator/(Real d, const Vec2& v)
+{
+  return Vec2(d/v.x, d/v.y);
+}
 
-private:
-  Real data_[2];
+inline std::ostream& operator<<(std::ostream& os, const Vec2& v)
+{
+  os << "(" << v[0] << "," << v[1] << ")";
+  return os;  
+}
 
-  void set(Real x, Real y);
-};
+}
+
+#include <ost/geom/vec3.hh>
+#include <ost/geom/vec4.hh>
+
+namespace geom {
+
+inline Vec2::Vec2(const Vec3& v): x(v.x), y(v.y) { }
+
+
+inline Vec2::Vec2(const Vec4& v): x(v.x), y(v.y) { }
 
-DLLEXPORT_OST_GEOM Vec2 operator/(Real d, const Vec2& v);
 
-DLLEXPORT_OST_GEOM std::ostream& operator<<(std::ostream&, const Vec2&);
+typedef std::vector<Vec2> Vec2List;
 
 } // namespace geom
 
diff --git a/modules/geom/src/vec3.cc b/modules/geom/src/vec3.cc
deleted file mode 100644
index 1e48f270c9417419adeb1096ca02acbc049d0740..0000000000000000000000000000000000000000
--- a/modules/geom/src/vec3.cc
+++ /dev/null
@@ -1,196 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#include "vec2.hh"
-#include "vec3.hh"
-#include "vec4.hh"
-
-#include "exc.hh"
-#include <ost/config.hh>
-namespace geom {
-
-Vec3::Vec3()
-{
-  this->set(0.0,0.0,0.0);
-}
-
-Vec3::Vec3(Real x, Real y, Real z)
-{
-  this->set(x,y,z);
-}
-
-//#if OST_DOUBLE_PRECISION
-//Vec3::Vec3(float x, float y, float z)
-//{
-//  this->set(x,y,z);
-//}
-//#endif
-
-Vec3::Vec3(const Vec3& v)
-{
-  this->set(v.data_[0],v.data_[1],v.data_[2]);
-}
-
-Vec3::Vec3(const Vec2& v)
-{
-  this->set(v[0],v[1],0.0);
-}
-
-Vec3::Vec3(const Vec4& v)
-{
-  if(v[3]==0.0) {
-    throw DivideByZeroException("zero w component in Vec4->Vec3 conversion");
-  }
-  this->set(v[0]/v[3],v[1]/v[3],v[2]/v[3]);
-}
-
-
-Vec3::Vec3(const Real d[3])
-{
-  this->set(d[0],d[1],d[2]);
-}
-#if OST_DOUBLE_PRECISION
-Vec3::Vec3(const float d[3])
-{
-  this->set(d[0],d[1],d[2]);
-}
-#endif
-
-Vec3& Vec3::operator=(const Vec3& v)
-{
-  if(&v!=this) {
-    this->set(v[0],v[1],v[2]);
-  }
-  return *this;
-}
-
-bool Vec3::operator==(const Vec3& v) const
-{
-  return data_[0]==v.data_[0] &&
-    data_[1]==v.data_[1] &&
-    data_[2]==v.data_[2];
-}
-
-Real& Vec3::operator[](std::size_t indx)
-{
-  if(indx>2) throw OutOfRangeException();
-  return data_[indx];
-}
-
-
-const Real& Vec3::operator[](std::size_t indx) const
-{
-  if(indx>2) throw OutOfRangeException();
-  return data_[indx];
-}
-
-Real Vec3::GetX() const
-{
-  return data_[0];
-}
-
-Real Vec3::GetY() const
-{
-  return data_[1];
-}
-
-Real Vec3::GetZ() const
-{
-  return data_[2];
-}
-
-void Vec3::SetX(Real v)
-{
-  data_[0]=v;
-}
-void Vec3::SetY(Real v)
-{
-  data_[1]=v;
-}
-void Vec3::SetZ(Real v)
-{
-  data_[2]=v;
-}
-
-Vec3 Vec3::operator-() const
-{
-  Vec3 nrvo(-data_[0],-data_[1],-data_[2]);
-  return nrvo;
-}
-
-Vec3& Vec3::operator+=(const Vec3& rhs)
-{
-  data_[0]+=rhs[0]; data_[1]+=rhs[1]; data_[2]+=rhs[2];
-  return *this;
-}
-
-Vec3& Vec3::operator-=(const Vec3& rhs)
-{
-  data_[0]-=rhs[0]; data_[1]-=rhs[1]; data_[2]-=rhs[2];
-  return *this;
-}
-
-Vec3& Vec3::operator*=(Real d)
-{
-  data_[0]*=d; data_[1]*=d; data_[2]*=d;
-  return *this;
-}
-
-Vec3& Vec3::operator+=(Real d)
-{
-  data_[0]+=d; data_[1]+=d; data_[2]+=d;
-  return *this;
-}
-
-Vec3& Vec3::operator-=(Real d)
-{
-  data_[0]-=d; data_[1]-=d; data_[2]-=d;
-  return *this;
-}
-
-Vec3& Vec3::operator/=(Real d)
-{
-  data_[0]/=d; data_[1]/=d; data_[2]/=d;
-  return *this;
-}
-
-////////////////////////////////////////////
-// private member functions
-
-void Vec3::set(Real x, Real y, Real z)
-{
-  data_[0]=x; data_[1]=y; data_[2]=z;
-}
-
-////////////////////////////////////////////
-// functions
-
-Vec3 operator/(Real d, const Vec3& v)
-{
-  Vec3 nrvo(d/v[0],d/v[1],d/v[2]);
-  return nrvo;
-}
-
-std::ostream& operator<<(std::ostream& os, const Vec3& v)
-{
-  os << "(" << v[0] << "," << v[1] << "," << v[2] << ")";
-  return os;
-}
-
-} // ns geom
-
diff --git a/modules/geom/src/vec3.hh b/modules/geom/src/vec3.hh
index fecac337051c6b0f8fbe05eab6212ba6eef8fac8..7c0d92046f93f727631a55ca95a4d1e4cfb42f8b 100644
--- a/modules/geom/src/vec3.hh
+++ b/modules/geom/src/vec3.hh
@@ -19,13 +19,15 @@
 #ifndef GEOM_VEC3_H
 #define GEOM_VEC3_H
 
+#include <stdexcept>
 #include <cstddef> // for size_t
 #include <ostream>
-
+#include <vector>
 #include <boost/operators.hpp>
 
-#include <ost/geom/module_config.hh>
+
 #include <ost/config.hh>
+#include <ost/geom/module_config.hh>
 
 namespace geom {
 
@@ -43,13 +45,13 @@ class DLLEXPORT_OST_GEOM Vec3:
 {
 public:
   //! Default initialization, all components are set to zero
-  Vec3();
+  Vec3(): x(0), y(0), z(0) {}
 
   //! Initialization with x, y and z component
-  Vec3(Real x, Real y, Real z);
+  Vec3(Real px, Real py, Real pz): x(px), y(py), z(pz) {}
 
   //! copy ctor
-  Vec3(const Vec3& v);
+  Vec3(const Vec3& v): x(v.x), y(v.y), z(v.z) { }
 
   //! (implicit) initialization with 2D vector
   Vec3(const Vec2& v);
@@ -60,58 +62,144 @@ public:
     to a 3D vector, resulting in (x/w,y/w,z/w)
   */
   explicit Vec3(const Vec4& v);
-
+  
+  explicit Vec3(Real v): x(v), y(v), z(v) { }
+  
   //! explicit initialization with an array of doubles
-  explicit Vec3(const Real[3]);
+  explicit Vec3(const double v[3]): x(v[0]), y(v[1]), z(v[2]) { }
 
-#if OST_DOUBLE_PRECISION
   //! explicit initialization with an array of floats
-  explicit Vec3(const float[3]);
-#endif
+  explicit Vec3(const float v[3]): x(v[0]), y(v[1]), z(v[2]) { }
+
   //! assignement op
-  Vec3& operator=(const Vec3& v);
+  Vec3& operator=(const Vec3& v)
+  {
+    x=v.x;
+    y=v.y;
+    z=v.z;
+    return *this;
+  }
 
   //! comparable
-  bool operator==(const Vec3& rhs) const;
+  bool operator==(const Vec3& rhs) const
+  {
+    return x==rhs.x && y==rhs.y && z==rhs.z;
+  }
 
   //! element access
-  Real& operator[](std::size_t indx);
+  Real& operator[](std::size_t indx)
+  {
+    if (indx>2) {
+      throw std::out_of_range("Index must be in the range [0-2]");
+    }
+    return (&x)[indx];
+  }
+  
   //! const element access
-  const Real& operator[](std::size_t indx) const;
+  const Real& operator[](std::size_t indx) const
+  {
+    if (indx>2) {
+      throw std::out_of_range("Index must be in the range [0-2]");
+    }
+    return (&x)[indx];
+  }
   //! element access
-  Real GetX() const;
-  Real GetY() const;
-  Real GetZ() const;
-  void SetX(Real v);
-  void SetY(Real v);
-  void SetZ(Real v);
+  Real GetX() const { return x; }
+  Real GetY() const { return y; }
+  Real GetZ() const { return z; }
+  void SetX(Real v) { x=v; }
+  void SetY(Real v) { y=v; }
+  void SetZ(Real v) { z=v; }
 
   //! addable op
-  Vec3& operator+=(const Vec3& rhs);
-  Vec3& operator+=(Real d);
+  Vec3& operator+=(const Vec3& rhs)
+  {
+    x+=rhs.x;
+    y+=rhs.y;
+    z+=rhs.z;
+    return *this;
+  }
+  
+  Vec3& operator+=(Real d)
+  {
+    x+=d;
+    y+=d;
+    z+=d;
+    return *this;
+  }
+  
   //! subtractable op
-  Vec3& operator-=(const Vec3& rhs);
-  Vec3& operator-=(Real d);
+  Vec3& operator-=(const Vec3& rhs)
+  {
+    x-=rhs.x;
+    y-=rhs.y;
+    z-=rhs.z;
+    return *this;
+  }
+  
+  Vec3& operator-=(Real d)
+  {
+    x-=d;
+    y-=d;
+    z-=d;
+    return *this;
+  }
   //! negateable
-  Vec3 operator-() const;
+  Vec3 operator-() const
+  {
+    return Vec3(-x, -y, -z);
+  }
+  
   //! multipliable
-  Vec3& operator*=(Real d);
+  Vec3& operator*=(Real d)
+  {
+    x*=d;
+    y*=d;
+    z*=d;
+    return *this;
+  }
+  
   //! dividable
-  Vec3& operator/=(Real d);
+  Vec3& operator/=(Real d)
+  {
+    Real one_over_d=Real(1.0)/d;
+    x*=one_over_d;
+    y*=one_over_d;
+    z*=one_over_d;
+    return *this;
+  }
+
+  Real* Data() {return &x;}
+  const Real* Data() const {return &x;}
+
+  Real x;
+  Real y;
+  Real z;
+};
 
-  Real* Data() {return data_;}
-  const Real* Data() const {return data_;}
+inline Vec3 operator/(Real d, const Vec3& v)
+{
+  Vec3 nrvo(d/v[0],d/v[1],d/v[2]);
+  return nrvo;
+}
 
-private:
-  Real data_[3];
+inline std::ostream& operator<<(std::ostream& os, const Vec3& v)
+{
+  os << "[" << v.x << ", " << v.y << ", " << v.z << "]";
+  return os;
+}
+}
 
-  void set(Real x, Real y, Real z);
-};
+#include <ost/geom/vec2.hh>
+#include <ost/geom/vec4.hh>
 
-DLLEXPORT_OST_GEOM Vec3 operator/(Real, const Vec3& v);
+namespace geom {
 
-DLLEXPORT_OST_GEOM std::ostream& operator<<(std::ostream&, const Vec3&);
+typedef std::vector<Vec3> Vec3List;
 
+inline Vec3::Vec3(const Vec2& v): x(v.x), y(v.y), z(0.0) { }
+inline Vec3::Vec3(const Vec4& v): x(v.x/v.w), y(v.y/v.w), z(v.z/v.w) { }
+  
 } // namespace geom
 
 
diff --git a/modules/geom/src/vec4.cc b/modules/geom/src/vec4.cc
deleted file mode 100644
index 8f53869a97983bea6f0ae6adc116327cfe9323bd..0000000000000000000000000000000000000000
--- a/modules/geom/src/vec4.cc
+++ /dev/null
@@ -1,157 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#include "vec2.hh"
-#include "vec3.hh"
-#include "vec4.hh"
-
-#include "exc.hh"
-
-namespace geom {
-
-Vec4::Vec4()
-{
-  this->set(0.0,0.0,0.0,1.0);
-}
-
-Vec4::Vec4(Real x, Real y, Real z, Real w)
-{
-  this->set(x,y,z,w);
-}
-
-Vec4::Vec4(const Vec4& v)
-{
-  this->set(v.data_[0],v.data_[1],v.data_[2],v.data_[3]);
-}
-
-Vec4::Vec4(const Vec2& v)
-{
-  this->set(v[0],v[1],0.0,1.0);
-}
-
-Vec4::Vec4(const Vec3& v)
-{
-  this->set(v[0],v[1],v[2],1.0);
-}
-
-Vec4::Vec4(const Real d[4])
-{
-  this->set(d[0],d[1],d[2],d[3]);
-}
-
-#if OST_DOUBLE_PRECISION
-Vec4::Vec4(const float d[4])
-{
-  this->set(d[0],d[1],d[2],d[3]);
-}
-#endif
-
-Vec4& Vec4::operator=(const Vec4& v)
-{
-  if(&v!=this) {
-    this->set(v[0],v[1],v[2],v[3]);
-  }
-  return *this;
-}
-
-bool Vec4::operator==(const Vec4& v) const
-{
-  return data_[0]==v.data_[0] && 
-    data_[1]==v.data_[1] &&
-    data_[2]==v.data_[2] &&
-    data_[3]==v.data_[3];
-}
-
-Real& Vec4::operator[](std::size_t indx)
-{
-  if(indx>3) throw OutOfRangeException();
-  return data_[indx];
-}
-
-const Real& Vec4::operator[](std::size_t indx) const
-{
-  if(indx>3) throw OutOfRangeException();
-  return data_[indx];
-}
-
-Vec4 Vec4::operator-() const
-{
-  Vec4 nrvo(-data_[0],-data_[1],-data_[2],-data_[3]);
-  return nrvo;
-}
-
-Vec4& Vec4::operator+=(const Vec4& rhs)
-{
-  data_[0]+=rhs[0]; data_[1]+=rhs[1]; data_[2]+=rhs[2]; data_[3]+=rhs[3];
-  return *this;
-}
-
-Vec4& Vec4::operator-=(const Vec4& rhs)
-{
-  data_[0]-=rhs[0]; data_[1]-=rhs[1]; data_[2]-=rhs[2]; data_[3]-=rhs[3];
-  return *this;
-}
-
-Vec4& Vec4::operator*=(Real d)
-{
-  data_[0]*=d; data_[1]*=d; data_[2]*=d; data_[3]*=d;
-  return *this;
-}
-
-Vec4& Vec4::operator+=(Real d)
-{
-  data_[0]+=d; data_[1]+=d; data_[2]+=d; data_[3]+=d;
-  return *this;
-}
-
-Vec4& Vec4::operator-=(Real d)
-{
-  data_[0]-=d; data_[1]-=d; data_[2]-=d; data_[3]-=d;
-  return *this;
-}
-
-Vec4& Vec4::operator/=(Real d)
-{
-  data_[0]/=d; data_[1]/=d; data_[2]/=d; data_[3]/=d;
-  return *this;
-}
-
-////////////////////////////////////////////
-// private member functions
-
-void Vec4::set(Real x, Real y, Real z, Real w)
-{
-  data_[0]=x; data_[1]=y; data_[2]=z; data_[3]=w;
-}
-
-////////////////////////////////////////////
-// functions
-
-Vec4 operator/(Real d, const Vec4& v)
-{
-  Vec4 nrvo(d/v[0],d/v[1],d/v[2],d/v[3]);
-  return nrvo;
-}
-
-std::ostream& operator<<(std::ostream& os, const Vec4& v)
-{
-  os << "(" << v[0] << "," << v[1] << "," << v[2] << "," << v[3] << ")";
-  return os;
-}
-
-}
diff --git a/modules/geom/src/vec4.hh b/modules/geom/src/vec4.hh
index b114713ddd232a269b892da4edd62044ba202c3a..5442fc2037b6238a8e84858eb814159b9d7f52d3 100644
--- a/modules/geom/src/vec4.hh
+++ b/modules/geom/src/vec4.hh
@@ -19,6 +19,7 @@
 #ifndef GEOM_VEC4_H
 #define GEOM_VEC4_H
 
+#include <stdexcept>
 #include <cstddef> // for size_t
 #include <ostream>
 
@@ -32,12 +33,11 @@ namespace geom {
 // fw decl
 class Vec2;
 class Vec3;
-class Mat4;
 
 /*
   Four dimensional, homogeneous vector class, using Real precision.
 */
-class DLLEXPORT_OST_GEOM Vec4:
+class DLLEXPORT Vec4:
     private boost::equality_comparable<Vec4>,
     private boost::additive<Vec4>,
     private boost::additive<Vec4, Real>,
@@ -45,13 +45,13 @@ class DLLEXPORT_OST_GEOM Vec4:
 {
 public:
   //! Default initialization, all components are set to zero
-  Vec4();
+  Vec4(): x(0), y(0), z(0), w(0) { }
 
   //! Initialization with x, y and z component
-  Vec4(Real x, Real y, Real z, Real w);
+  Vec4(Real px, Real py, Real pz, Real pw): x(px), y(py), z(pz), w(pw) { }
 
   //! copy ctor
-  Vec4(const Vec4& v);
+  Vec4(const Vec4& v): x(v[0]), y(v[1]), z(v[2]), w(v[3]) { }
 
   //! (implicit) initialization with 2D vector
   Vec4(const Vec2& v);
@@ -59,50 +59,151 @@ public:
   //! (implicit) initialization with 3D vector
   Vec4(const Vec3& v);
 
-  //! explicit initialization with an array of doubles
-  explicit Vec4(const Real[4]);
-
-#if OST_DOUBLE_PRECISION
   //! explicit initialization with an array of floats
-  explicit Vec4(const float[4]);
-#endif
-
+  explicit Vec4(const float v[4]): x(v[0]), y(v[1]), z(v[2]), w(v[3]) { }
+  
+  //! explicit initialization with an array of doubles  
+  explicit Vec4(const double v[4]): x(v[0]), y(v[1]), z(v[2]), w(v[3]) { }
   //! assignement op
-  Vec4& operator=(const Vec4& v);
+  Vec4& operator=(const Vec4& v)
+  {
+    x=v.x;
+    y=v.y;
+    z=v.z;
+    w=v.w;
+    return *this;
+  }
 
   //! comparable
-  bool operator==(const Vec4& rhs) const;
+  bool operator==(const Vec4& rhs) const
+  {
+    return x==rhs.x && y==rhs.y && z==rhs.z && w==rhs.w;
+  }
 
   //! element access
-  Real& operator[](std::size_t indx);
+  Real& operator[](std::size_t indx)
+  {
+    if (indx>3) {
+      throw std::out_of_range("Index must be in the range [0-3]");
+    }
+    return (&x)[indx];
+  }
+  
   //! const element access
-  const Real& operator[](std::size_t indx) const;
+  const Real& operator[](std::size_t indx) const
+  {
+    if (indx>3) {
+      throw std::out_of_range("Index must be in the range [0-3]");
+    }
+    return (&x)[indx];
+  }
+  //! element access
+  Real GetX() const { return x; }
+  Real GetY() const { return y; }
+  Real GetZ() const { return z; }
+  Real GetW() const { return w; }
+  
+  void SetX(Real v) { x=v; }
+  void SetY(Real v) { y=v; }
+  void SetZ(Real v) { z=v; }
+  void SetW(Real v) { w=v; }  
 
   //! addable op
-  Vec4& operator+=(const Vec4& rhs);
-  Vec4& operator+=(Real d);
+  Vec4& operator+=(const Vec4& rhs)
+  {
+    x+=rhs.x;
+    y+=rhs.y;
+    z+=rhs.z;
+    w+=rhs.w;
+    return *this;
+  }
+  
+  Vec4& operator+=(Real d)
+  {
+    x+=d;
+    y+=d;
+    z+=d;
+    w+=d;
+    return *this;
+  }
+  
   //! subtractable op
-  Vec4& operator-=(const Vec4& rhs);
-  Vec4& operator-=(Real d);
+  Vec4& operator-=(const Vec4& rhs)
+  {
+    x-=rhs.x;
+    y-=rhs.y;
+    z-=rhs.z;
+    w-=rhs.w;
+    return *this;
+  }
+  
+  Vec4& operator-=(Real d)
+  {
+    x-=d;
+    y-=d;
+    z-=d;
+    w-=d;
+    return *this;
+  }
   //! negateable
-  Vec4 operator-() const;
+  Vec4 operator-() const
+  {
+    return Vec4(-x, -y, -z, -w);
+  }
+  
   //! multipliable
-  Vec4& operator*=(Real d);
+  Vec4& operator*=(Real d)
+  {
+    x*=d;
+    y*=d;
+    z*=d;
+    w*=d;
+    return *this;
+  }
+  
   //! dividable
-  Vec4& operator/=(Real d);
+  Vec4& operator/=(Real d)
+  {
+    Real one_over_d=Real(1.0)/d;
+    x*=one_over_d;
+    y*=one_over_d;
+    z*=one_over_d;
+    w*=one_over_d;
+    return *this;
+  }
+
+  Real* Data() {return &x;}
+  const Real* Data() const {return &x;}
+
+  Real x;
+  Real y;
+  Real z;
+  Real w;
+};
 
-  Real* Data() {return data_;}
-  const Real* Data() const {return data_;}
+inline Vec4 operator/(Real d, const Vec4& v)
+{
+  Vec4 nrvo(d/v[0],d/v[1],d/v[2],d/v[3]);
+  return nrvo;
+}
 
-private:
-  Real data_[4];
+inline std::ostream& operator<<(std::ostream& os, const Vec4& v)
+{
+  os << "(" << v[0] << "," << v[1] << "," << v[2] << "," << v[3] << ")";
+  return os;
+}
+}
 
-  void set(Real x, Real y, Real z, Real w);
-};
+#include <ost/geom/vec2.hh>
+#include <ost/geom/vec3.hh>
 
-DLLEXPORT_OST_GEOM Vec4 operator/(Real, const Vec4& v);
+namespace geom {
+  
+//! (implicit) initialization with 2D vector
+inline Vec4::Vec4(const Vec2& v): x(v.x), y(v.y), z(0), w(1) { }
 
-DLLEXPORT_OST_GEOM std::ostream& operator<<(std::ostream&, const Vec4&);
+//! (implicit) initialization with 3D vector
+inline Vec4::Vec4(const Vec3& v): x(v.x), y(v.y), z(v.z), w(1.0) { }
 
 } // namespace geom
 
diff --git a/modules/geom/src/vecmat2_op.cc b/modules/geom/src/vecmat2_op.cc
index 6bda1a12a5cdbadc6735c8d2f5e665a91bcc1133..c23866293e72f928ed79d7938ad45c22f0b46d19 100644
--- a/modules/geom/src/vecmat2_op.cc
+++ b/modules/geom/src/vecmat2_op.cc
@@ -26,70 +26,6 @@
 #include "mat2.hh"
 
 namespace geom {
-
-Real Length(const Vec2& v)
-{
-  return std::sqrt(Length2(v));
-}
-
-Real Length2(const Vec2& v)
-{
-  return v[0]*v[0]+v[1]*v[1];
-}
-
-bool Equal(const Vec2& v1, const Vec2& v2, Real ephilon)
-{
-  return std::fabs(v1[0]-v2[0])<ephilon &&
-    std::fabs(v1[1]-v2[1])<ephilon;
-}
-bool Equal(const Mat2& m1, const Mat2& m2, Real ephilon)
-{
-  return std::fabs(m1(0,0)-m2(0,0))<ephilon &&
-    std::fabs(m1(0,1)-m2(0,1))<ephilon &&
-    std::fabs(m1(1,0)-m2(1,0))<ephilon &&
-    std::fabs(m1(1,1)-m2(1,1))<ephilon;
-}
-
-Real Dot(const Vec2& v1, const Vec2& v2)
-{
-  return v1[0]*v2[0]+v1[1]*v2[1];
-}
-
-Vec2 Normalize(const Vec2& v)
-{
-  Real l=Length(v);
-  if(l==0.0) {
-    return v;
-  }
-  return v/l;
-}
-
-
-Vec2 CompMultiply(const Vec2& v1, const Vec2& v2)
-{
-  Vec2 nrvo(v1[0]*v2[0],v1[1]*v2[1]);
-  return nrvo;
-}
-
-Vec2 CompDivide(const Vec2& v1, const Vec2& v2)
-{
-  Vec2 nrvo(v1[0]/v2[0],v1[1]/v2[1]);
-  return nrvo;
-}
-
-Vec2 operator*(const Vec2& v,const Mat2& m)
-{
-  Vec2 nrvo(v[0]*m(0,0)+v[1]*m(1,0),
-      v[0]*m(0,1)+v[1]*m(1,1));
-  return nrvo;
-}
-
-Vec2 operator*(const Mat2& m, const Vec2& v)
-{
-  Vec2 nrvo(v[0]*m(0,0)+v[1]*m(0,1),
-      v[0]*m(1,0)+v[1]*m(1,1));
-  return nrvo;
-}
 // determinant
 Real Det(const Mat2& m)
 {
@@ -116,14 +52,6 @@ Real Angle(const Vec2& v1, const Vec2& v2)
 {
   return std::acos(Dot(v1,v2)/Length(v1)/Length(v2));
 }
-Mat2 operator*(const Mat2& m1, const Mat2& m2)
-{
-  Mat2 nrvo(m1(0,0)*m2(0,0)+m1(0,1)*m2(1,0),
-      m1(0,0)*m2(0,1)+m1(0,1)*m2(1,1),
-      m1(1,0)*m2(0,0)+m1(1,1)*m2(1,0),
-      m1(1,0)*m2(0,1)+m1(1,1)*m2(1,1));
-  return nrvo;
-}
 
 Real SignedAngle(const Vec2& v1, const Vec2& v2)
 {
@@ -131,21 +59,7 @@ Real SignedAngle(const Vec2& v1, const Vec2& v2)
   vc=Cross(Vec3(v1),Vec3(v2));
   if(Length(v1)==0.0 || Length(v2)==0.0 || Length(vc)==0.0)
     return 0.0;
-  return acos(Dot(v1,v2)/Length(v1)/Length(v2))*vc.GetZ()/std::fabs(vc.GetZ());
-}
-
-Vec2 Min(const Vec2& v1, const Vec2& v2)
-{
-  Vec2 nrvo(std::min(v1[0],v2[0]),
-            std::min(v1[1],v2[1]));
-  return nrvo;
-}
-
-Vec2 Max(const Vec2& v1, const Vec2& v2)
-{
-  Vec2 nrvo(std::max(v1[0],v2[0]),
-            std::max(v1[1],v2[1]));
-  return nrvo;
+  return acos(Dot(v1,v2)/Length(v1)/Length(v2))*vc.z/std::fabs(vc.z);
 }
 
 Vec2 Rotate(const Vec2& v,Real ang)
diff --git a/modules/geom/src/vecmat2_op.hh b/modules/geom/src/vecmat2_op.hh
index cf20513678438ae61f390aea724cd8bcc933c6f2..31ae6430aca27c9ade3a3df4ec3a4786fb0c8cdb 100644
--- a/modules/geom/src/vecmat2_op.hh
+++ b/modules/geom/src/vecmat2_op.hh
@@ -23,33 +23,71 @@
 
 #include <ost/geom/module_config.hh>
 
+#include <ost/geom/vec2.hh>
+#include <ost/geom/mat2.hh>
+
 namespace geom {
 
 class Vec2;
 class Mat2;
 
-//! returns length of vector
-Real DLLEXPORT_OST_GEOM Length(const Vec2& v);
-
 //! returns squared length of vector
-Real DLLEXPORT_OST_GEOM Length2(const Vec2& v);
+inline Real Length2(const Vec2& v)
+{
+  return v[0]*v[0]+v[1]*v[1];
+}
+
+//! returns length of vector
+inline Real Length(const Vec2& v)
+{
+  return std::sqrt(Length2(v));
+}
 
 //! return true if components differ not more than ephilon
-bool DLLEXPORT_OST_GEOM Equal(const Vec2& v1, const Vec2& v2, Real ephilon=EPSILON);
+inline bool Equal(const Vec2& v1, const Vec2& v2, Real ephilon=EPSILON)
+{
+  return std::fabs(v1[0]-v2[0])<ephilon &&
+    std::fabs(v1[1]-v2[1])<ephilon;
+}
+
 //! return true if components differ not more than ephilon
-bool DLLEXPORT_OST_GEOM Equal(const Mat2& m1, const Mat2& m2, Real ephilon=EPSILON);
+inline bool Equal(const Mat2& m1, const Mat2& m2, Real ephilon=EPSILON)
+{
+  return std::fabs(m1(0,0)-m2(0,0))<ephilon &&
+    std::fabs(m1(0,1)-m2(0,1))<ephilon &&
+    std::fabs(m1(1,0)-m2(1,0))<ephilon &&
+    std::fabs(m1(1,1)-m2(1,1))<ephilon;
+}
 
 //! vector dot product
-Real DLLEXPORT_OST_GEOM Dot(const Vec2& v1, const Vec2& v2);
+inline Real Dot(const Vec2& v1, const Vec2& v2)
+{
+    return v1[0]*v2[0]+v1[1]*v2[1];
+}
 
 //! Normalize vector
-Vec2 DLLEXPORT_OST_GEOM Normalize(const Vec2& v);
+inline Vec2 Normalize(const Vec2& v)
+{
+  Real l=Length(v);
+  if(l==0.0) {
+    return v;
+  }
+  return v/l;
+}
 
 //! multiply each component of v1 with that of v2
-Vec2 DLLEXPORT_OST_GEOM CompMultiply(const Vec2& v1, const Vec2& v2);
+inline Vec2 CompMultiply(const Vec2& v1, const Vec2& v2)
+{
+  Vec2 nrvo(v1[0]*v2[0],v1[1]*v2[1]);
+  return nrvo;
+}
 
 //! divide each component of v1 by that of v2
-Vec2 DLLEXPORT_OST_GEOM CompDivide(const Vec2& v1, const Vec2& v2);
+inline Vec2 CompDivide(const Vec2& v1, const Vec2& v2)
+{
+  Vec2 nrvo(v1[0]/v2[0],v1[1]/v2[1]);
+  return nrvo;
+}
 
 //! vector matrix multiplication
 /*!
@@ -58,7 +96,12 @@ Vec2 DLLEXPORT_OST_GEOM CompDivide(const Vec2& v1, const Vec2& v2);
           |a b|
   (x,y) * |c d| = (ax+cy, bx+dy)
 */
-Vec2 DLLEXPORT_OST_GEOM operator*(const Vec2& v,const Mat2& m);
+inline Vec2 operator*(const Vec2& v,const Mat2& m)
+{
+  Vec2 nrvo(v[0]*m(0,0)+v[1]*m(1,0),
+      v[0]*m(0,1)+v[1]*m(1,1));
+  return nrvo;
+}
 
 //! vector matrix multiplication
 /*!
@@ -67,7 +110,12 @@ Vec2 DLLEXPORT_OST_GEOM operator*(const Vec2& v,const Mat2& m);
    |a b|   (x)   (ax+by)
    |c d| * (y)  =(cx+dy)
 */
-Vec2 DLLEXPORT_OST_GEOM operator*(const Mat2& m, const Vec2& v);
+inline Vec2 operator*(const Mat2& m, const Vec2& v)
+{
+  Vec2 nrvo(v[0]*m(0,0)+v[1]*m(0,1),
+      v[0]*m(1,0)+v[1]*m(1,1));
+  return nrvo;
+}
 
 //! determinant
 Real DLLEXPORT_OST_GEOM Det(const Mat2& m);
@@ -83,13 +131,28 @@ Real DLLEXPORT_OST_GEOM Angle(const Vec2& v1, const Vec2& v2);
 Real  DLLEXPORT_OST_GEOM SignedAngle(const Vec2& v1, const Vec2& v2);
 
 //! matrix matrix multiplication
-Mat2 DLLEXPORT_OST_GEOM operator*(const Mat2& m1, const Mat2& m2);
-
-//! returns std::min of each component
-Vec2 DLLEXPORT_OST_GEOM Min(const Vec2& v1, const Vec2& v2);
-
-//! returns std::max of each component
-Vec2 DLLEXPORT_OST_GEOM Max(const Vec2& v1, const Vec2& v2);
+inline Mat2 operator*(const Mat2& m1, const Mat2& m2)
+{
+  Mat2 nrvo(m1(0,0)*m2(0,0)+m1(0,1)*m2(1,0),
+      m1(0,0)*m2(0,1)+m1(0,1)*m2(1,1),
+      m1(1,0)*m2(0,0)+m1(1,1)*m2(1,0),
+      m1(1,0)*m2(0,1)+m1(1,1)*m2(1,1));
+  return nrvo;
+}
+
+inline Vec2 Min(const Vec2& v1, const Vec2& v2)
+{
+  Vec2 nrvo(std::min(v1[0],v2[0]),
+            std::min(v1[1],v2[1]));
+  return nrvo;
+}
+
+inline Vec2 Max(const Vec2& v1, const Vec2& v2)
+{
+  Vec2 nrvo(std::max(v1[0],v2[0]),
+            std::max(v1[1],v2[1]));
+  return nrvo;
+}
 
 //! Rotation
 DLLEXPORT Vec2 Rotate(const Vec2& v,Real ang);
diff --git a/modules/geom/src/vecmat3_op.cc b/modules/geom/src/vecmat3_op.cc
index 5487c5d57bf406eff9e29232fd8583815b5e14b6..4c6a2732a70ecb9f02b0325300bd534aaa64e7fb 100644
--- a/modules/geom/src/vecmat3_op.cc
+++ b/modules/geom/src/vecmat3_op.cc
@@ -29,102 +29,6 @@
 
 namespace geom {
 
-Real Length(const Vec3& v)
-{
-  return std::sqrt(Length2(v));
-}
-
-Real Length2(const Vec3& v)
-{
-  return v[0]*v[0]+v[1]*v[1]+v[2]*v[2];
-}
-
-bool Equal(const Vec3& v1, const Vec3& v2, Real ephilon)
-{
-  return std::fabs(v1[0]-v2[0])<ephilon &&
-    std::fabs(v1[1]-v2[1])<ephilon &&
-    std::fabs(v1[2]-v2[2])<ephilon;
-}
-
-bool Equal(const Mat3& m1, const Mat3& m2, Real ephilon)
-{
-  return std::fabs(m1(0,0)-m2(0,0))<ephilon &&
-    std::fabs(m1(0,1)-m2(0,1))<ephilon &&
-    std::fabs(m1(0,2)-m2(0,2))<ephilon &&
-    std::fabs(m1(1,0)-m2(1,0))<ephilon &&
-    std::fabs(m1(1,1)-m2(1,1))<ephilon &&
-    std::fabs(m1(1,2)-m2(1,2))<ephilon &&
-    std::fabs(m1(2,0)-m2(2,0))<ephilon &&
-    std::fabs(m1(2,1)-m2(2,1))<ephilon &&
-    std::fabs(m1(2,2)-m2(2,2))<ephilon;
-}
-
-Real Dot(const Vec3& v1, const Vec3& v2)
-{
-  return v1[0]*v2[0]+v1[1]*v2[1]+v1[2]*v2[2];
-}
-
-Vec3 Cross(const Vec3& v1, const Vec3& v2)
-{
-  Vec3 nrvo(v1[1]*v2[2]-v2[1]*v1[2],
-      v1[2]*v2[0]-v2[2]*v1[0],
-      v1[0]*v2[1]-v2[0]*v1[1]);
-  return nrvo;
-}
-
-Vec3 Normalize(const Vec3& v)
-{
-  Real l=Length(v);
-  if(l==0.0) {
-    return v;
-  }
-  return v/l;
-}
-
-Vec3 CompMultiply(const Vec3& v1, const Vec3& v2)
-{
-  Vec3 nrvo(v1[0]*v2[0],v1[1]*v2[1],v1[2]*v2[2]);
-  return nrvo;
-}
-
-Vec3 CompDivide(const Vec3& v1, const Vec3& v2)
-{
-  Vec3 nrvo(v1[0]/v2[0],v1[1]/v2[1],v1[2]/v2[2]);
-  return nrvo;
-}
-
-Vec3 operator*(const Vec3& v,const Mat3& m)
-{
-  Vec3 nrvo(v[0]*m(0,0)+v[1]*m(1,0)+v[2]*m(2,0),
-      v[0]*m(0,1)+v[1]*m(1,1)+v[2]*m(2,1),
-      v[0]*m(0,2)+v[1]*m(1,2)+v[2]*m(2,2));
-  return nrvo;
-}
-
-Vec3 operator*(const Mat3& m, const Vec3& v)
-{
-  Vec3 nrvo(v[0]*m(0,0)+v[1]*m(0,1)+v[2]*m(0,2),
-      v[0]*m(1,0)+v[1]*m(1,1)+v[2]*m(1,2),
-      v[0]*m(2,0)+v[1]*m(2,1)+v[2]*m(2,2));
-  return nrvo;
-}
-
-Mat3 operator*(const Mat3& m1, const Mat3& m2)
-{
-  Mat3 nrvo(m1(0,0)*m2(0,0)+m1(0,1)*m2(1,0)+m1(0,2)*m2(2,0),
-      m1(0,0)*m2(0,1)+m1(0,1)*m2(1,1)+m1(0,2)*m2(2,1),
-      m1(0,0)*m2(0,2)+m1(0,1)*m2(1,2)+m1(0,2)*m2(2,2),
-
-      m1(1,0)*m2(0,0)+m1(1,1)*m2(1,0)+m1(1,2)*m2(2,0),
-      m1(1,0)*m2(0,1)+m1(1,1)*m2(1,1)+m1(1,2)*m2(2,1),
-      m1(1,0)*m2(0,2)+m1(1,1)*m2(1,2)+m1(1,2)*m2(2,2),
-
-      m1(2,0)*m2(0,0)+m1(2,1)*m2(1,0)+m1(2,2)*m2(2,0),
-      m1(2,0)*m2(0,1)+m1(2,1)*m2(1,1)+m1(2,2)*m2(2,1),
-      m1(2,0)*m2(0,2)+m1(2,1)*m2(1,2)+m1(2,2)*m2(2,2));
-  return nrvo;
-}
-
 Real Comp(const Mat3& m,unsigned int i_in, unsigned int j_in)
 {
   return Minor(m,i_in,j_in)* static_cast<Real>( ((i_in+j_in)&0x1) ? -1 : 1);
@@ -191,7 +95,10 @@ Real Det(const Mat3& m)
 
 Real Angle(const Vec3& v1, const Vec3& v2)
 {
-  return std::acos(Dot(Normalize(v1), Normalize(v2)));
+  Real dot_product = Dot(Normalize(v1), Normalize(v2));
+  dot_product=std::max(static_cast<Real>(-1.0),dot_product);
+  dot_product=std::min(static_cast<Real>(1.0),dot_product);
+  return std::acos(dot_product);
 }
 
 Mat3 EulerTransformation(Real theta, Real phi, Real xi)
@@ -264,25 +171,4 @@ Mat3 AxisRotation(const Vec3& axis, Real angle)
           xz-ca*xz-sa*y, yz-ca*yz+sa*x,zz+ca-ca*zz);
 }
 
-Vec3 Min(const Vec3& v1, const Vec3& v2)
-{
-  Vec3 nrvo(std::min(v1[0],v2[0]),
-            std::min(v1[1],v2[1]),
-            std::min(v1[2],v2[2]));
-  return nrvo;
-}
-
-Vec3 Max(const Vec3& v1, const Vec3& v2)
-{
-  Vec3 nrvo(std::max(v1[0],v2[0]),
-            std::max(v1[1],v2[1]),
-            std::max(v1[2],v2[2]));
-  return nrvo;
-}
-
-Real  Distance(const Vec3& p1, const Vec3& p2)
-{
-  return Length(p1-p2);
-}
-
 } // ns
diff --git a/modules/geom/src/vecmat3_op.hh b/modules/geom/src/vecmat3_op.hh
index 43961e798eebaea9a6943e0d59ed4ceb5531b9f6..e4ca5a65b5eb0b2a9d11717fb68fa7a2c2c14a9d 100644
--- a/modules/geom/src/vecmat3_op.hh
+++ b/modules/geom/src/vecmat3_op.hh
@@ -23,46 +23,121 @@
 #include "constants.hh"
 
 #include <ost/geom/module_config.hh>
+#include <ost/geom/vec3.hh>
+#include <ost/geom/mat3.hh>
 
 namespace geom {
 
-class Vec3;
-class Mat3;
-
-//! returns length of vector
-Real DLLEXPORT_OST_GEOM Length(const Vec3& v);
 
 //! returns squared length of vector
-Real DLLEXPORT_OST_GEOM Length2(const Vec3& v);
+inline Real Length2(const Vec3& v)
+{
+  return v[0]*v[0]+v[1]*v[1]+v[2]*v[2];
+}
 
-//! return true if components differ not more than ephilon
-bool DLLEXPORT_OST_GEOM Equal(const Vec3& v1, const Vec3& v2, Real ephilon=EPSILON);
+//! returns length of vector
+inline Real Length(const Vec3& v)
+{
+  return std::sqrt(Length2(v));
+}
+
+//! return true if components differ not more than epsilon
+inline bool Equal(const Vec3& v1, const Vec3& v2, 
+                  Real ephilon=EPSILON)
+{
+  return std::fabs(v1[0]-v2[0])<ephilon &&
+    std::fabs(v1[1]-v2[1])<ephilon &&
+    std::fabs(v1[2]-v2[2])<ephilon;
+}
 
 //! return true if components differ not more than ephilon
-bool DLLEXPORT_OST_GEOM Equal(const Mat3& m1, const Mat3& m2, Real ephilon=EPSILON);
+inline bool Equal(const Mat3& m1, const Mat3& m2, 
+                  Real ephilon=EPSILON)
+{
+  return std::fabs(m1(0,0)-m2(0,0))<ephilon &&
+    std::fabs(m1(0,1)-m2(0,1))<ephilon &&
+    std::fabs(m1(0,2)-m2(0,2))<ephilon &&
+    std::fabs(m1(1,0)-m2(1,0))<ephilon &&
+    std::fabs(m1(1,1)-m2(1,1))<ephilon &&
+    std::fabs(m1(1,2)-m2(1,2))<ephilon &&
+    std::fabs(m1(2,0)-m2(2,0))<ephilon &&
+    std::fabs(m1(2,1)-m2(2,1))<ephilon &&
+    std::fabs(m1(2,2)-m2(2,2))<ephilon;
+}
 
 //! vector dot product
-Real DLLEXPORT_OST_GEOM Dot(const Vec3& v1, const Vec3& v2);
+inline Real Dot(const Vec3& v1, const Vec3& v2)
+{
+  return v1[0]*v2[0]+v1[1]*v2[1]+v1[2]*v2[2];
+}
 
 //! Normalize
-Vec3 DLLEXPORT_OST_GEOM Normalize(const Vec3& v);
+inline Vec3 Normalize(const Vec3& v)
+{
+  Real l=Length(v);
+  if(l==0.0) {
+    return v;
+  }
+  return v/l;
+}
 
 //! vector cross product
-Vec3 DLLEXPORT_OST_GEOM Cross(const Vec3& v1, const Vec3& v2);
+inline Vec3 Cross(const Vec3& v1, const Vec3& v2)
+{
+  Vec3 nrvo(v1[1]*v2[2]-v2[1]*v1[2],
+      v1[2]*v2[0]-v2[2]*v1[0],
+      v1[0]*v2[1]-v2[0]*v1[1]);
+  return nrvo;
+}
 
 //! multiply each component of v1 with that of v2
-Vec3 DLLEXPORT_OST_GEOM CompMultiply(const Vec3& v1, const Vec3& v2);
+inline Vec3 CompMultiply(const Vec3& v1, const Vec3& v2)
+{
+  Vec3 nrvo(v1[0]*v2[0],v1[1]*v2[1],v1[2]*v2[2]);
+  return nrvo;
+}
 
 //! divide each component of v1 by that of v2
-Vec3 DLLEXPORT_OST_GEOM CompDivide(const Vec3& v1, const Vec3& v2);
+inline Vec3 CompDivide(const Vec3& v1, const Vec3& v2)
+{
+  Vec3 nrvo(v1[0]/v2[0],v1[1]/v2[1],v1[2]/v2[2]);
+  return nrvo;
+}
 
 //! vector matrix multiplication
-Vec3 DLLEXPORT_OST_GEOM operator*(const Vec3& v,const Mat3& m);
+inline Vec3 operator*(const Vec3& v,const Mat3& m)
+{
+  Vec3 nrvo(v[0]*m(0,0)+v[1]*m(1,0)+v[2]*m(2,0),
+      v[0]*m(0,1)+v[1]*m(1,1)+v[2]*m(2,1),
+      v[0]*m(0,2)+v[1]*m(1,2)+v[2]*m(2,2));
+  return nrvo;
+}
+
 //! vector matrix multiplication
-Vec3 DLLEXPORT_OST_GEOM operator*(const Mat3& m, const Vec3& v);
+inline Vec3 operator*(const Mat3& m, const Vec3& v)
+{
+  Vec3 nrvo(v[0]*m(0,0)+v[1]*m(0,1)+v[2]*m(0,2),
+      v[0]*m(1,0)+v[1]*m(1,1)+v[2]*m(1,2),
+      v[0]*m(2,0)+v[1]*m(2,1)+v[2]*m(2,2));
+  return nrvo;
+}
 
 //! matrix matrix multiplication
-Mat3 DLLEXPORT_OST_GEOM operator*(const Mat3& m1, const Mat3& m2);
+inline Mat3 operator*(const Mat3& m1, const Mat3& m2)
+{
+  Mat3 nrvo(m1(0,0)*m2(0,0)+m1(0,1)*m2(1,0)+m1(0,2)*m2(2,0),
+      m1(0,0)*m2(0,1)+m1(0,1)*m2(1,1)+m1(0,2)*m2(2,1),
+      m1(0,0)*m2(0,2)+m1(0,1)*m2(1,2)+m1(0,2)*m2(2,2),
+
+      m1(1,0)*m2(0,0)+m1(1,1)*m2(1,0)+m1(1,2)*m2(2,0),
+      m1(1,0)*m2(0,1)+m1(1,1)*m2(1,1)+m1(1,2)*m2(2,1),
+      m1(1,0)*m2(0,2)+m1(1,1)*m2(1,2)+m1(1,2)*m2(2,2),
+
+      m1(2,0)*m2(0,0)+m1(2,1)*m2(1,0)+m1(2,2)*m2(2,0),
+      m1(2,0)*m2(0,1)+m1(2,1)*m2(1,1)+m1(2,2)*m2(2,1),
+      m1(2,0)*m2(0,2)+m1(2,1)*m2(1,2)+m1(2,2)*m2(2,2));
+  return nrvo;
+}
 
 Mat3 DLLEXPORT_OST_GEOM Invert(const Mat3& m);
 Mat3 DLLEXPORT_OST_GEOM Transpose(const Mat3& m);
@@ -89,13 +164,28 @@ Mat3 DLLEXPORT_OST_GEOM AxisRotation(const Vec3& axis, Real angle);
 Vec3 DLLEXPORT_OST_GEOM OrthogonalVector(const Vec3& axis);
 
 //! returns std::min of each component
-Vec3 DLLEXPORT_OST_GEOM Min(const Vec3& v1, const Vec3& v2);
+inline Vec3 Min(const Vec3& v1, const Vec3& v2)
+{
+  Vec3 nrvo(std::min(v1[0],v2[0]),
+            std::min(v1[1],v2[1]),
+            std::min(v1[2],v2[2]));
+  return nrvo;
+}
 
 //! returns std::max of each component
-Vec3 DLLEXPORT_OST_GEOM Max(const Vec3& v1, const Vec3& v2);
+inline Vec3 Max(const Vec3& v1, const Vec3& v2)
+{
+  Vec3 nrvo(std::max(v1[0],v2[0]),
+            std::max(v1[1],v2[1]),
+            std::max(v1[2],v2[2]));
+  return nrvo;
+}
 
 //! returns the distance between two points
-Real DLLEXPORT_OST_GEOM Distance(const Vec3& p1, const Vec3& p2);
+inline Real Distance(const Vec3& p1, const Vec3& p2)
+{
+    return Length(p1-p2);
+}
 
 } // ns
 
diff --git a/modules/geom/src/vecmat4_op.cc b/modules/geom/src/vecmat4_op.cc
index a677c788229be3dd48834acd0ebd2e42dcc401bd..4567575413b9950f4e67d185018a6561b0fbaf56 100644
--- a/modules/geom/src/vecmat4_op.cc
+++ b/modules/geom/src/vecmat4_op.cc
@@ -23,93 +23,9 @@
 #include "vecmat3_op.hh"
 
 #include "exc.hh"
-#include "vec4.hh"
-#include "mat4.hh"
-#include "mat3.hh"
 
-namespace geom {
-
-Real Length(const Vec4& v)
-{
-  return std::sqrt(Length2(v));
-}
-
-Real Length2(const Vec4& v)
-{
-  return v[0]*v[0]+v[1]*v[1]+v[2]*v[2]+v[3]*v[3];
-}
-
-bool Equal(const Vec4& v1, const Vec4& v2, Real epsilon)
-{
-  return std::fabs(v1[0]-v2[0])<epsilon &&
-    std::fabs(v1[1]-v2[1])<epsilon &&
-    std::fabs(v1[2]-v2[2])<epsilon &&
-    std::fabs(v1[3]-v2[3])<epsilon;
-}
-
-bool Equal(const Mat4& m1, const Mat4& m2, Real epsilon)
-{
-  return std::fabs(m1(0,0)-m2(0,0))<epsilon &&
-    std::fabs(m1(0,1)-m2(0,1))<epsilon &&
-    std::fabs(m1(0,2)-m2(0,2))<epsilon &&
-    std::fabs(m1(0,3)-m2(0,3))<epsilon &&
-    std::fabs(m1(1,0)-m2(1,0))<epsilon &&
-    std::fabs(m1(1,1)-m2(1,1))<epsilon &&
-    std::fabs(m1(1,2)-m2(1,2))<epsilon &&
-    std::fabs(m1(1,3)-m2(1,3))<epsilon &&
-    std::fabs(m1(2,0)-m2(2,0))<epsilon &&
-    std::fabs(m1(2,1)-m2(2,1))<epsilon &&
-    std::fabs(m1(2,2)-m2(2,2))<epsilon &&
-    std::fabs(m1(2,3)-m2(2,3))<epsilon &&
-    std::fabs(m1(3,0)-m2(3,0))<epsilon &&
-    std::fabs(m1(3,1)-m2(3,1))<epsilon &&
-    std::fabs(m1(3,2)-m2(3,2))<epsilon &&
-    std::fabs(m1(3,3)-m2(3,3))<epsilon;
-}
-
-Real Dot(const Vec4& v1, const Vec4& v2)
-{
-  return v1[0]*v2[0]+v1[1]*v2[1]+v1[2]*v2[2]+v1[3]*v2[3];
-}
-
-Vec4 Normalize(const Vec4& v)
-{
-  Real l=Length(v);
-  if(l==0.0) {
-    return v;
-  }
-  return v/l;
-}
-
-Vec4 CompMultiply(const Vec4& v1, const Vec4& v2)
-{
-  Vec4 nrvo(v1[0]*v2[0],v1[1]*v2[1],v1[2]*v2[2],v1[3]*v2[3]);
-  return nrvo;
-}
-
-Vec4 CompDivide(const Vec4& v1, const Vec4& v2)
-{
-  Vec4 nrvo(v1[0]/v2[0],v1[1]/v2[1],v1[2]/v2[2],v1[3]/v2[3]);
-  return nrvo;
-}
 
-Vec4 operator*(const Vec4& v,const Mat4& m)
-{
-  Vec4 nrvo(v[0]*m(0,0)+v[1]*m(1,0)+v[2]*m(2,0)+v[3]*m(3,0),
-      v[0]*m(0,1)+v[1]*m(1,1)+v[2]*m(2,1)+v[3]*m(3,1),
-      v[0]*m(0,2)+v[1]*m(1,2)+v[2]*m(2,2)+v[3]*m(3,2),
-      v[0]*m(0,3)+v[1]*m(1,3)+v[2]*m(2,3)+v[3]*m(3,3));
-  return nrvo;
-}
-
-Vec4 operator*(const Mat4& m, const Vec4& v)
-{
-  Vec4 nrvo(v[0]*m(0,0)+v[1]*m(0,1)+v[2]*m(0,2)+v[3]*m(0,3),
-      v[0]*m(1,0)+v[1]*m(1,1)+v[2]*m(1,2)+v[3]*m(1,3),
-      v[0]*m(2,0)+v[1]*m(2,1)+v[2]*m(2,2)+v[3]*m(2,3),
-      v[0]*m(3,0)+v[1]*m(3,1)+v[2]*m(3,2)+v[3]*m(3,3));
-  return nrvo;
-}
+namespace geom {
 
 Real Comp(const Mat4& m, unsigned int i_in, unsigned int j_in)
 {
@@ -158,7 +74,6 @@ Mat4 Transpose(const Mat4& m)
   return r;
 }
 
-#if 1
 Mat4 Invert(const Mat4& in)
 {
   Mat4 m(in);
@@ -221,22 +136,6 @@ Mat4 Invert(const Mat4& in)
   return m;
 }
 
-#else
-
-Mat4 Invert(const Mat4& m)
-{
-  Mat4 r;
-  Real d=Det(m);
-  for (int i=0;i<4;i++){
-    for (int j=0;j<4;j++){
-      r(j,i)=Comp(m,i,j)/d;
-    }
-  }
-  return r;
-}
-
-#endif
-
 Mat4 operator*(const Mat4& m1, const Mat4& m2)
 {
   Mat4 nrvo(m1(0,0)*m2(0,0)+m1(0,1)*m2(1,0)+m1(0,2)*m2(2,0)+m1(0,3)*m2(3,0),
@@ -267,22 +166,4 @@ Real Angle(const Vec4& v1, const Vec4& v2)
   return std::acos(t);
 }
 
-Vec4 Min(const Vec4& v1, const Vec4& v2)
-{
-  Vec4 nrvo(std::min(v1[0],v2[0]),
-            std::min(v1[1],v2[1]),
-            std::min(v1[2],v2[2]),
-            std::min(v1[3],v2[3]));
-  return nrvo;
-}
-
-Vec4 Max(const Vec4& v1, const Vec4& v2)
-{
-  Vec4 nrvo(std::max(v1[0],v2[0]),
-            std::max(v1[1],v2[1]),
-            std::max(v1[2],v2[2]),
-            std::max(v1[3],v2[3]));
-  return nrvo;
-}
-
 } // ns
diff --git a/modules/geom/src/vecmat4_op.hh b/modules/geom/src/vecmat4_op.hh
index 501a09ebbe0f2684e383c2c5d8c675504b085629..7f7d6a2a95909da8dae244be343366106b7e5d8d 100644
--- a/modules/geom/src/vecmat4_op.hh
+++ b/modules/geom/src/vecmat4_op.hh
@@ -22,39 +22,104 @@
 #include "constants.hh"
 
 #include <ost/geom/module_config.hh>
+#include <ost/geom/vec4.hh>
+#include <ost/geom/vec3.hh>
+#include <ost/geom/mat4.hh>
+#include <ost/geom/mat3.hh>
 
 namespace geom {
 
-class Vec4;
-class Mat4;
-
-//! returns length of vector
-Real DLLEXPORT_OST_GEOM Length(const Vec4& v);
 
 //! returns squared length of vector
-Real DLLEXPORT_OST_GEOM Length2(const Vec4& v);
+inline Real Length2(const Vec4& v)
+{
+    return v[0]*v[0]+v[1]*v[1]+v[2]*v[2]+v[3]*v[3];
+}
+
+//! returns length of vector
+inline Real Length(const Vec4& v)
+{
+  return std::sqrt(Length2(v));
+}
 
 //! return true if components differ not more than ephilon
-bool DLLEXPORT_OST_GEOM Equal(const Vec4& v1, const Vec4& v2, Real ephilon=EPSILON);
+inline bool Equal(const Vec4& v1, const Vec4& v2, Real epsilon=EPSILON)
+{
+  return std::fabs(v1[0]-v2[0])<epsilon &&
+    std::fabs(v1[1]-v2[1])<epsilon &&
+    std::fabs(v1[2]-v2[2])<epsilon &&
+    std::fabs(v1[3]-v2[3])<epsilon;
+}
 
 //! return true if components differ not more than ephilon
-bool DLLEXPORT_OST_GEOM Equal(const Mat4& m1, const Mat4& v2, Real ephilon=EPSILON);
+inline bool Equal(const Mat4& m1, const Mat4& m2, Real epsilon=EPSILON)
+{
+  return std::fabs(m1(0,0)-m2(0,0))<epsilon &&
+    std::fabs(m1(0,1)-m2(0,1))<epsilon &&
+    std::fabs(m1(0,2)-m2(0,2))<epsilon &&
+    std::fabs(m1(0,3)-m2(0,3))<epsilon &&
+    std::fabs(m1(1,0)-m2(1,0))<epsilon &&
+    std::fabs(m1(1,1)-m2(1,1))<epsilon &&
+    std::fabs(m1(1,2)-m2(1,2))<epsilon &&
+    std::fabs(m1(1,3)-m2(1,3))<epsilon &&
+    std::fabs(m1(2,0)-m2(2,0))<epsilon &&
+    std::fabs(m1(2,1)-m2(2,1))<epsilon &&
+    std::fabs(m1(2,2)-m2(2,2))<epsilon &&
+    std::fabs(m1(2,3)-m2(2,3))<epsilon &&
+    std::fabs(m1(3,0)-m2(3,0))<epsilon &&
+    std::fabs(m1(3,1)-m2(3,1))<epsilon &&
+    std::fabs(m1(3,2)-m2(3,2))<epsilon &&
+    std::fabs(m1(3,3)-m2(3,3))<epsilon;
+}
 
 //! vector dot product
-Real DLLEXPORT_OST_GEOM Dot(const Vec4& v1, const Vec4& v2);
-
-Vec4 DLLEXPORT_OST_GEOM Normalize(const Vec4& v);
+inline Real Dot(const Vec4& v1, const Vec4& v2)
+{
+    return v1[0]*v2[0]+v1[1]*v2[1]+v1[2]*v2[2]+v1[3]*v2[3];
+}
+
+inline Vec4 Normalize(const Vec4& v)
+{
+  Real l=Length(v);
+  if(l==0.0) {
+    return v;
+  }
+  return v/l;
+}
 
 //! multiply each component of v1 with that of v2
-Vec4 DLLEXPORT_OST_GEOM CompMultiply(const Vec4& v1, const Vec4& v2);
+inline Vec4 CompMultiply(const Vec4& v1, const Vec4& v2)
+{
+  Vec4 nrvo(v1[0]*v2[0],v1[1]*v2[1],v1[2]*v2[2],v1[3]*v2[3]);
+  return nrvo;
+}
 
 //! divide each component of v1 by that of v2
-Vec4 DLLEXPORT_OST_GEOM CompDivide(const Vec4& v1, const Vec4& v2);
+inline Vec4 CompDivide(const Vec4& v1, const Vec4& v2)
+{
+  Vec4 nrvo(v1[0]/v2[0],v1[1]/v2[1],v1[2]/v2[2],v1[3]/v2[3]);
+  return nrvo;
+}
 
 //! vector matrix multiplication
-Vec4 DLLEXPORT_OST_GEOM operator*(const Vec4& v,const Mat4& m);
+inline Vec4 operator*(const Vec4& v,const Mat4& m)
+{
+  Vec4 nrvo(v[0]*m(0,0)+v[1]*m(1,0)+v[2]*m(2,0)+v[3]*m(3,0),
+      v[0]*m(0,1)+v[1]*m(1,1)+v[2]*m(2,1)+v[3]*m(3,1),
+      v[0]*m(0,2)+v[1]*m(1,2)+v[2]*m(2,2)+v[3]*m(3,2),
+      v[0]*m(0,3)+v[1]*m(1,3)+v[2]*m(2,3)+v[3]*m(3,3));
+  return nrvo;
+}
+
 //! vector matrix multiplication
-Vec4 DLLEXPORT_OST_GEOM operator*(const Mat4& m, const Vec4& v);
+inline Vec4 operator*(const Mat4& m, const Vec4& v)
+{
+  Vec4 nrvo(v[0]*m(0,0)+v[1]*m(0,1)+v[2]*m(0,2)+v[3]*m(0,3),
+      v[0]*m(1,0)+v[1]*m(1,1)+v[2]*m(1,2)+v[3]*m(1,3),
+      v[0]*m(2,0)+v[1]*m(2,1)+v[2]*m(2,2)+v[3]*m(2,3),
+      v[0]*m(3,0)+v[1]*m(3,1)+v[2]*m(3,2)+v[3]*m(3,3));
+  return nrvo;
+}
 
 // algebraic complement
 Real DLLEXPORT_OST_GEOM Comp(const Mat4& m, unsigned int i, unsigned int j);
@@ -69,10 +134,24 @@ Mat4 DLLEXPORT_OST_GEOM operator*(const Mat4& m1, const Mat4& m2);
 Real DLLEXPORT_OST_GEOM Angle(const Vec4& v1, const Vec4& v2);
 
 //! returns std::min of each component
-Vec4 DLLEXPORT_OST_GEOM Min(const Vec4& v1, const Vec4& v2);
+inline Vec4 Min(const Vec4& v1, const Vec4& v2)
+{
+  Vec4 nrvo(std::min(v1[0],v2[0]),
+            std::min(v1[1],v2[1]),
+            std::min(v1[2],v2[2]),
+            std::min(v1[3],v2[3]));
+  return nrvo;
+}
 
 //! returns std::max of each component
-Vec4 DLLEXPORT_OST_GEOM Max(const Vec4& v1, const Vec4& v2);
+inline Vec4  Max(const Vec4& v1, const Vec4& v2)
+{
+  Vec4 nrvo(std::max(v1[0],v2[0]),
+            std::max(v1[1],v2[1]),
+            std::max(v1[2],v2[2]),
+            std::max(v1[3],v2[3]));
+  return nrvo;
+}
 
 } // ns
 
diff --git a/modules/gfx/doc/cpk.png b/modules/gfx/doc/cpk.png
new file mode 100644
index 0000000000000000000000000000000000000000..38808e16817504447d7b260ff14f208cb8de30fe
Binary files /dev/null and b/modules/gfx/doc/cpk.png differ
diff --git a/modules/gfx/doc/custom.png b/modules/gfx/doc/custom.png
new file mode 100644
index 0000000000000000000000000000000000000000..812c317d520a0e9fb66342050b77b74748c42cd3
Binary files /dev/null and b/modules/gfx/doc/custom.png differ
diff --git a/modules/gfx/doc/entity.rst b/modules/gfx/doc/entity.rst
new file mode 100644
index 0000000000000000000000000000000000000000..42fa5e38b16fe4c2ba300ed85c0aafcb08787810
--- /dev/null
+++ b/modules/gfx/doc/entity.rst
@@ -0,0 +1,214 @@
+The Graphical Entity
+================================================================================
+
+.. currentmodule:: ost.gfx
+  
+.. note::
+
+  This document describes the API of the :class:`Entity` and related classes. 
+  For an overview of the graphical entity, see :doc:`../intro-03`.
+
+.. _render-mode:
+
+Render Modes
+--------------------------------------------------------------------------------
+
+The entity supports different render modes. They are depicted in the following 
+images together with the options they support. To change the render mode of the 
+full entity or part of the entity, use the :meth:`Entity.SetRenderMode` method.
+
+Render Modes at the Connectivity Level
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. data:: SIMPLE
+
+  .. image:: simple.png 
+  
+  Renders bonds as lines and single atoms as crosses.
+
+.. data:: CPK
+  
+  .. image:: cpk.png
+
+  
+  Renders atoms as spheres with radii proportional to their van-der-Waals 
+  radius.
+
+.. data:: CUSTOM
+  
+  .. image:: custom.png
+
+Render Modes at the Trace Level
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. data:: TUBE
+
+  .. image:: tube.png
+  
+  Renders a smooth backbone trace with circular profiles.
+
+.. data:: SLINE
+
+  .. image:: sline.png
+  
+  Renders a smooth backbone trace with lines.
+  
+.. data:: TRACE
+
+  .. image:: trace.png
+  
+  Renders the Calpha atoms connected by tubes.
+  
+.. data:: LINE_TRACE
+
+  .. image:: line_trace.png
+
+  Renders the Calpha connected bys lines.
+  
+.. data:: HSC
+
+  .. image:: hsc.png
+
+  Renders a Helix/Strand/Coil Cartoon.
+
+
+.. _render-options:
+
+Render Options
+--------------------------------------------------------------------------------
+
+
+**line_width**
+
+  The line width. Defaults to 1.0
+  
+  :type: float
+
+**aa_lines**
+
+  Controls whether antialiased lines are enabled. Only available when
+  compiled with shaders. Defaults to false.
+  
+  :type: bool
+  
+**draw_bond_order**
+
+  Controls whether double/triple bonds are drawn as multiple lines. This 
+  requires that the bond order information has been assigned. As of now, 
+  only the  :class:`~ost.conop.RuleBasedBuilder` assigns this information.
+  
+  Defaults to off.
+  
+  :type: bool
+  
+
+
+
+**bond_order_distance**
+
+  The distance between the lines depicting higher order bonds.
+
+
+Loading and Displaying an Entity  
+--------------------------------------------------------------------------------
+
+This code examples shows how to load a structure and display it on the screen. It also shows how to programmatically combine different render modes in one graphical entity.
+
+.. literalinclude:: /../../examples/demos/load_and_display.py
+
+
+Entity API Reference
+--------------------------------------------------------------------------------
+
+.. class:: Entity(name, entity)
+           Entity(name, render_mode, entity)
+
+  Graphical representation of entitites. 
+  
+  
+  .. attribute:: name
+  
+    The name of the entity. Read-only. Also available as :meth:`GetName`
+    
+    :type: str
+    
+  .. attribute:: selection
+  
+    The selection of the entity is rendered with a green halo. 
+    
+    :type: :class:`~ost.mol.EntityView`
+  
+  .. attribute:: center
+  
+    The geometric center of the graphical entity. Read-only.
+    
+    :type: :class:`~ost.geom.Vec3`
+  
+  :param name: Name of the entity
+  :type  name: str
+  :param render_mode: One of the :ref:`render-mode`.
+     Defaults to :obj:`SIMPLE`.
+  :param entity: The entity. Only atoms and bonds that part part of the entity
+     view (or handle) are rendered.
+  :type  entity: :class:`~ost.mol.EntityView`, or :class:`~ost.mol.EntityHandle`
+  
+  .. method:: SetRenderMode(render_mode)
+              SetRenderMode(render_mode, view, keep=False)
+    
+    Changes the render mode of the graphical entity. The first signature changes 
+    the render mode of all atoms and bonds, whereas the second only changes the 
+    display of atoms/bonds that are part of the view. If `keep` is set to false,
+    the atoms and bonds that are part of the view will only be displayed in the 
+    new render mode, if keep is set to true, the atoms and bonds will be 
+    rendered with the new render mode in addition to whatever render mode they 
+    were rendered previously.
+    
+    :param render_mode: One of the :ref:`render-mode`.
+       Defaults to :obj:`SIMPLE`.
+    :param view: A valid entity view
+    :type  view: :class:`~ost.mol.EntityView`
+
+  .. method:: SetColor(color, selection='')
+  
+    Sets the atoms matching the selection predicates to `color`.
+    
+    :param color: The new color
+    :type  color: :class:`Color`
+    :param selection: A valid :doc:`query <../mol/base/query>`
+    :type  selection: str
+    
+  .. method:: ColorByElement()
+  
+    Apply `CPK coloring <http://en.wikipedia.org/wiki/CPK_coloring>`_ coloring
+    to atoms. This will color the carbon atoms in white, nitrogen in blue, 
+    oxygen in red, phosphorous in pink and sulfur in yellow.
+    
+  
+  .. method:: ColorBy(prop, color1, color2, min, max, hint='U')
+              ColorBy(prop, color1, color2, hint='U')
+              ColorBy(prop, gradient, min, max, hint='U')              
+              ColorBy(prop, gradient, hint='U')
+    
+    Colors the entity by mapping a numeric property to a color. This property 
+    can be a built-in a property such as atomic b-factor, charge, residue number 
+    or be a :doc:`custom property <../base/generic>` assigned by the user or an 
+    algorithm and be defined at any level (chain, residue, atom). The naming of 
+    the built-in properties is identical to the properties available in 
+    :doc:`query language <../mol/base/query>`.
+    
+    In case a generic property is undefined for a certain element, the property 
+    the value of min is used for that element.
+    
+    :param prop: The name of the numeric property
+    :type  prop: str
+    :param color1: Color corresponding to min value
+    :type color1: :class:`Color`
+    :param color2: Color corresponding to max value
+    :type color2: :class:`Color`    
+    :param gradient: The gradient to be used
+    :type gradient: :class:`Gradient`
+    :type min: Value mapped to `color1`, or the color at 0.0 in the gradient
+    :type max: Value mapped to `color2` or the color at 1.0 in the gradient
+    :param hint: When `prop` refers to a generic property, hint must be set to
+       the hierarchy level at which the property is defined. 
+    :type hint: str
diff --git a/modules/gfx/doc/gfx.rst b/modules/gfx/doc/gfx.rst
new file mode 100644
index 0000000000000000000000000000000000000000..de9cf3ddbcf1170f9cfac59f7377ec284fdf3b5a
--- /dev/null
+++ b/modules/gfx/doc/gfx.rst
@@ -0,0 +1,13 @@
+:mod:`~ost.gfx` - Realtime 3D Rendering
+================================================================================
+
+For a introduction to the :mod:`~ost.gfx` module, please have a look at the :doc:`../intro-03`.
+
+.. module:: ost.gfx
+  :synopsis: Realtime 3D Rendering
+  
+.. toctree::
+  :maxdepth: 2
+  
+  scene
+  entity
\ No newline at end of file
diff --git a/modules/gfx/doc/hsc.png b/modules/gfx/doc/hsc.png
new file mode 100644
index 0000000000000000000000000000000000000000..62ec72c8a392ad715481a64e70f4397e0be24e46
Binary files /dev/null and b/modules/gfx/doc/hsc.png differ
diff --git a/modules/gfx/doc/line_trace.png b/modules/gfx/doc/line_trace.png
new file mode 100644
index 0000000000000000000000000000000000000000..73e48987c6593ba9b43b9faaa99c09322728924a
Binary files /dev/null and b/modules/gfx/doc/line_trace.png differ
diff --git a/modules/gfx/doc/scene.rst b/modules/gfx/doc/scene.rst
new file mode 100644
index 0000000000000000000000000000000000000000..d1eb368c3a75b5b6fdd45ad80d28e5636582b7bf
--- /dev/null
+++ b/modules/gfx/doc/scene.rst
@@ -0,0 +1,350 @@
+The Scene
+================================================================================
+
+.. currentmodule:: ost.gfx
+
+The scene is the central registry for graphical objects and manages rendering 
+parameters. Among other parameters, it is used to setup the lighting, fog, 
+background color and the position and viewing direction of the user. The scene
+is a singleton, meaning that there is only one scene available. The instance can
+be accessed via :func:`gfx.Scene`. Because the scene is so important and
+commonly used, the scene is also available as the `scene` variable in the 
+interactive python shell as well as from scripts.
+
+Manipulating the Camera
+--------------------------------------------------------------------------------
+
+The users position and orientation in the scene is specified by the camera. The camera is represented by a center, a rotation and an offset from the center. These 3 attributes can be set independently. Manipulation of the camera is done by assigning a new :class:`~ost.mol.Transform` to the :attr:`Scene.transform` attribute. 
+
+.. _camera-orbit:
+
+Orbiting around a Point
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The following code example will let the camera orbit around the center of the camera.
+
+.. code-block:: python
+
+  # tweakable parameters:
+  #  - axis of rotation
+  #  - angular step size. Making it bigger speeds up the rotation
+  #  - number of frames
+  axis=geom.Vec3(0, 1, 0)
+  step_size=0.01
+  num_frames=100
+  
+  angle=0.0
+  for i in range(num_frames):
+    angle+=step_size
+    if angle>math.pi*2:
+      angle-=math.pi*2
+    camera=scene.transform
+    rot=geom.AxisRotation(axis, angle)
+    camera.SetRot(rot)
+    camera.SetTrans(geom.Vec3(25.0, 0.0, -50))
+    scene.transform=camera
+    scene.Export('frame-%03d.png' % i, 500, 500)
+
+It is interesting to note that the offset from center (`trans`) is given in rotated coordinates. Transforming along z shifts the camera along the viewing direction. Setting x and y to non-zero causes the center of the camera not to be projected onto the center of the screen any longer. For example, setting the value `trans` to `geom.Vec3(50, 0, 0)` gives a viewing direction perpendicular to the vector from the camera position to the center.
+
+.. class:: Scene
+
+  .. attribute:: background
+
+    The background color of the scene. By default the background color is
+    transparent black.
+  
+    :type: :class:`Color`
+  
+  .. attribute:: center
+  
+    The center of the scene. Read-write. Changing the center affects the 
+    orientation of the camera, but not its position. To change the camera
+    position, use :attr:`transform`. Also available as 
+    :meth:`GetCenter`/:meth:`SetCenter`.
+    
+    See also :meth:`CenterOn`.
+    
+    :type: :class:`~ost.geom.Vec3`
+  
+  .. attribute:: transform
+  
+    The camera transformation. Read-write. For an example usage see
+    :ref:`camera-orbit`. Also available as
+    :meth:`GetTransform`/:meth:`SetTransform`.
+        
+    :type: :class:`~ost.mol.Transform`
+    
+    
+  .. attribute:: fov
+  
+    The field of view angle (in degrees) in vertical direction. Read-write.
+    Also available as :meth:`GetFOV`/:meth:`SetFOV`.
+    
+    :type: float. 
+
+  .. method:: Add(obj[, replace_existing])
+
+    Add an object to the root node of the scene. This means that
+    
+     * The object will be rendered on the screen.    
+     * The object's bounding box affects the slabbing operations.     
+
+    :param obj: The object to be added.
+    :type  obj: :class:`GfxNode`
+    :param replace_existing: If true, existing objects of the same name are
+       silently replaced. If false (the default), trying to add an object with
+       an existing name will raise a RuntimeError.
+       
+    :type replace_existing: bool
+
+
+  .. method:: AttachObserver(obs)
+
+    Attach a :class:`scene observer <SceneObserver>`. The new scene observer 
+    will get notified when the scene's state changes or objects get updated. 
+    
+    :param obs:
+    :type  obs: :class:`SceneObserver`
+
+
+  .. method:: AutoAutoslab(flag)
+
+    Enable/disable autoslabbing. If autoslabbing is enabled, the near and far 
+    clipping planes will automatically be adjusted to contain all the objects in 
+    the scene. This calculation is done before every redraw. Note that, 
+    autoslabbing is not rotation invariant. See :meth:`AutoslabMax` for a
+    rotation-invariant version.
+    
+    :param flag:
+    :type  flag: bool
+
+
+  .. method:: Autoslab(fast[, force])
+
+    .. note::
+      
+      This method looks stale. Remove it?
+
+    :param fast:
+    :type  fast: bool
+    :param force:
+    :type  force: bool
+
+  .. method:: AutoslabMax()
+
+    Adjust the near and far clipping planes in such a way that they contain the 
+    bounding sphere of all the objects in the scene. In constrast to AutoSlab() 
+    the near/far clipping planes calculated with :meth:`AutoslabMax` are 
+    invariant to rotation.
+
+  .. method:: CenterOn(obj)
+    
+    Center the camera on the center of the obj. This does not update offset and 
+    rotation of the camera. However, since the offset and rotation are applied 
+    after the centering, the position and viewing direction are affected by the 
+    change of center.
+    
+    :param obj: Object, or name of the object
+    :type  obj: str, or :class:`GfxNode`
+
+
+  .. method:: Export(filename, width, height[, transparent])
+              Export(filename[, transparent])
+              
+    Renders (exports) the scene into a PNG image.
+    
+    :param filename: The output filename
+    :type  filename: str
+    :param width: The width of the image. Defaults to the width of the 
+      OpenGL window
+    :type  width: int
+    :param height: The height of the image. Defaults to the height of the OpenGL
+        window.
+    :type  height: int
+    :param transparent: If true, and the background color of the scene is 
+      transparent, will produce a transparent image. If false, the alpha 
+      component will be set to opaque.
+    :type  transparent: bool
+
+  .. method:: ExportPov(filename[, working_dir])
+    
+    Export the scene to POV-Ray format. The export will generate two files, one 
+    containing a general description of the scene, including camera position and 
+    materials and a second containing the geometric description of the objects.
+    The first file will be named `filename.pov`, the second `filename.inc`.
+    
+    The files will be placed in working directory
+    
+    .. note::
+    
+      This method is highly experimental and does not work for more complex
+      objects. Stay tuned for updates.
+      
+
+    :param filename: The base filename without file extension. `.pov` and `.inc`
+       will automatically be appended to te filename.
+    :type  filename: str
+    :param working_dir: The working directory. Defaults to the current
+       directory.
+    :type  working_dir: str
+
+
+  .. method:: GetFOV()
+
+    Get the field of view angle in the y direction (in degrees).
+    
+    :rtype: float
+
+  .. method:: GetRTC()
+    
+    .. note::
+    
+      Looks stale. Remove it?
+      
+    :rtype: :class:`~ost.geom.Mat4`
+
+  .. method:: GetTransform()
+
+    See :attr:`transform`
+
+  .. method:: Remove(obj)
+
+    Remove the given object from the scene.
+    
+    :param obj:
+    :type  obj: :class:`GfxNode`
+  
+  .. method:: RemoveAll()
+  
+    Remove all objects from the scene
+    
+    
+  .. method:: RenderGL()
+
+    Renders the scene.
+
+  .. method:: RequestRedraw()
+
+    Request a redraw of the scene. 
+
+
+  .. method:: Resize(width, height)
+    
+    Resize the OpenGL context.
+    
+    :param width: The new width
+    :type  width: int
+    :param height: The new height
+    :type  height: int
+
+  .. method:: SetBackground(color)
+
+    See :attr:`background`
+    
+    :param color:
+    :type  color: :class:`Color`
+
+  .. method:: SetBlur(arg2)
+
+    :param arg2:
+    :type  arg2: int
+
+  .. method:: SetFOV(angle)
+
+    See :attr:`fov`.
+    
+    :param angle:
+    :type  angle: float
+
+  .. method:: SetFog(arg2)
+
+    :param arg2:
+    :type  arg2: bool
+
+  .. method:: SetFogColor(arg2)
+
+    :param arg2:
+    :type  arg2: :class:`Color`
+
+  .. method:: SetFogOffsets(arg2, arg3)
+
+    :param arg2:
+    :type  arg2: float
+    :param arg3:
+    :type  arg3: float
+
+  .. method:: SetLightDir(arg2)
+
+    :param arg2:
+    :type  arg2: :class:`~ost.geom.Vec3`
+
+  .. method:: SetLightProp(arg2, arg3, arg4)
+
+    :param arg2:
+    :type  arg2: :class:`Color`
+    :param arg3:
+    :type  arg3: :class:`Color`
+    :param arg4:
+    :type  arg4: :class:`Color`
+
+  .. method:: SetNearFar(near, far)
+
+    Manually sets the near and far clipping planes to the given values. Before 
+    using this method, make sure :meth:`AutoAutoslab` is disabled.
+    
+    :param near:
+    :type  near: float
+    :param far:
+    :type  far: float
+
+  .. method:: UnProject(point[, ignore_vp])
+
+    Apply the inverse of the current camera and perspective transformation. This 
+    essentially gives the screen (or normalized view coordinates) of a point in
+    global coordinates. The inverse operations is available as  :meth:`Project`.
+    
+    :param point: The point in global coordinates.
+    :type  point: :class:`~ost.geom.Vec3`
+    :param ignore_vp: If set to false (the default), also performs the viewport 
+      transformation. Points inside the viewing frustum will have x and y 
+      coordinates in the range [0, width)x[0, height]. If true, the returned 
+      coordinates will be between [-1,1]x[-1,1].
+    :type  ignore_vp: bool
+    :rtype: :class:`~ost.geom.Vec3`
+
+  .. method:: SetRTC(arg2)
+
+    :param arg2:
+    :type  arg2: :class:`~ost.geom.Mat4`
+
+  .. method:: SetShadow(arg2)
+
+    :param arg2:
+    :type  arg2: bool
+
+  .. method:: SetShadowQuality(arg2)
+
+    :param arg2:
+    :type  arg2: int
+
+  .. method:: SetStereoEye(arg2)
+
+    :param arg2:
+    :type  arg2: int
+
+  .. method:: SetStereoInverted(arg2)
+
+    :param arg2:
+    :type  arg2: bool
+
+  .. method:: SetTransform(new_transform)
+
+    See :attr:`transform`
+
+  .. method:: Stereo(mode)
+
+    :param mode:
+    :type  mode: int
+
+  
\ No newline at end of file
diff --git a/modules/gfx/doc/simple.png b/modules/gfx/doc/simple.png
new file mode 100644
index 0000000000000000000000000000000000000000..e6a4d8cd8369fc8cc7c9151b1e0424138d9ba859
Binary files /dev/null and b/modules/gfx/doc/simple.png differ
diff --git a/modules/gfx/doc/sline.png b/modules/gfx/doc/sline.png
new file mode 100644
index 0000000000000000000000000000000000000000..79ee2f533764fda141b1783c3391b750de0a8f6d
Binary files /dev/null and b/modules/gfx/doc/sline.png differ
diff --git a/modules/gfx/doc/trace.png b/modules/gfx/doc/trace.png
new file mode 100644
index 0000000000000000000000000000000000000000..8f7f5e6754c9d0d19ec3f357886bf2e65d84f6cb
Binary files /dev/null and b/modules/gfx/doc/trace.png differ
diff --git a/modules/gfx/doc/tube.png b/modules/gfx/doc/tube.png
new file mode 100644
index 0000000000000000000000000000000000000000..5256aa3dd62bdfa24068114a442d84fd1b97fa13
Binary files /dev/null and b/modules/gfx/doc/tube.png differ
diff --git a/modules/gfx/pymod/CMakeLists.txt b/modules/gfx/pymod/CMakeLists.txt
index 9cf5614851a11d7eb449e88f2a5b075352d9a6c5..52eac70f7c440e256ffbb9a604eb7a23195c26c0 100644
--- a/modules/gfx/pymod/CMakeLists.txt
+++ b/modules/gfx/pymod/CMakeLists.txt
@@ -17,4 +17,12 @@ if (ENABLE_IMG)
   set(OST_GFX_PYMOD_SOURCES ${OST_GFX_PYMOD_SOURCES} export_map.cc)
 endif()
 
-pymod(NAME gfx CPP ${OST_GFX_PYMOD_SOURCES} PY __init__.py)
\ No newline at end of file
+pymod(NAME gfx CPP ${OST_GFX_PYMOD_SOURCES} PY __init__.py)
+
+set(GRADIENT_FILE
+  gradients.xml
+)
+copy_if_different("./" "${STAGE_DIR}/share/openstructure/scene" 
+                  "${GRADIENT_FILE}" "PRESET GRADIENTS" _gfx)
+                  
+install(FILES ${GRADIENT_FILE} DESTINATION "share/openstructure/scene")
\ No newline at end of file
diff --git a/modules/gfx/pymod/export_color_ops.cc b/modules/gfx/pymod/export_color_ops.cc
index d24a15179a9bbecbc7d10ee32c4454f288fd868d..e0863e3621f78952e288ac47ee085b60e4067290 100644
--- a/modules/gfx/pymod/export_color_ops.cc
+++ b/modules/gfx/pymod/export_color_ops.cc
@@ -41,10 +41,14 @@ using namespace ost::gfx;
 void export_ColorOps()
 {
   class_<ColorOp>("ColorOp", init<const String& >())
+    .def(init<const ColorOp&>())
     .def(init<const mol::QueryViewWrapper&, int>())
     .def("CanApplyTo",&ColorOp::CanApplyTo)
+    .def("GetName",&ColorOp::GetName,return_value_policy<copy_const_reference>())
     .def("SetSelection",&ColorOp::SetSelection)
     .def("GetSelection",&ColorOp::GetSelection)
+    .def("SetSelectionFlags",&ColorOp::SetSelectionFlags)
+    .def("GetSelectionFlags",&ColorOp::GetSelectionFlags)
     .def("SetMask",&ColorOp::SetMask)
     .def("GetMask",&ColorOp::GetMask)
     .def("ToInfo",&ColorOp::ToInfo)
@@ -53,6 +57,7 @@ void export_ColorOps()
   ;
 
   class_<BasicGradientColorOp, bases<ColorOp> >("BasicGradientColorOp", init<const String& , const gfx::Gradient& , mol::Prop::Level>())
+    .def(init<const BasicGradientColorOp&>())
     .def("SetGradient",&BasicGradientColorOp::SetGradient)
     .def("GetGradient",&BasicGradientColorOp::GetGradient)
     .def("SetLevel",&BasicGradientColorOp::SetLevel)
@@ -62,6 +67,7 @@ void export_ColorOps()
   ;
 
   class_<ByElementColorOp, bases<ColorOp> >("ByElementColorOp", init<>())
+    .def(init<const ByElementColorOp&>())
     .def(init<const String&>())
     .def(init<const mol::QueryViewWrapper&>())
     .def(init<const String&, int>())
@@ -71,15 +77,19 @@ void export_ColorOps()
   ;
 
   class_<ByChainColorOp, bases<ColorOp> >("ByChainColorOp", init<>())
+    .def(init<const ByChainColorOp&>())
     .def(init<const String&>())
     .def(init<const mol::QueryViewWrapper&>())
     .def(init<const String&, int>())
     .def(init<const mol::QueryViewWrapper&, int>())
+    .def("GetChainCount",&ByChainColorOp::GetChainCount)
+    .def("SetChainCount",&ByChainColorOp::SetChainCount)
     .def("FromInfo",&ByChainColorOp::FromInfo)
     .staticmethod("FromInfo")
   ;
 
   class_<UniformColorOp, bases<ColorOp> >("UniformColorOp", init<>())
+    .def(init<const UniformColorOp&>())
     .def(init<const String&, const gfx::Color&>())
     .def(init<const String&, int, const gfx::Color&>())
     .def(init<const mol::QueryViewWrapper&, const gfx::Color&>())
@@ -91,6 +101,7 @@ void export_ColorOps()
   ;
 
   class_<GradientColorOp, bases<ColorOp> >("GradientColorOp", init<>())
+    .def(init<const GradientColorOp&>())
     .def(init<const String&, const String&, const gfx::Gradient&, float, float>())
     .def(init<const String&, int, const String&, const gfx::Gradient&, float, float>())
     .def(init<const mol::QueryViewWrapper&, const String&, const gfx::Gradient&, float, float>())
@@ -109,6 +120,7 @@ void export_ColorOps()
   ;
 
   class_<GradientLevelColorOp, bases<GradientColorOp> >("GradientLevelColorOp", init<>())
+    .def(init<const GradientLevelColorOp&>())
     .def(init<const String&, const String&, const gfx::Gradient&, float, float, mol::Prop::Level>())
     .def(init<const String&, int, const String&, const gfx::Gradient&, float, float, mol::Prop::Level>())
     .def(init<const String&, const String&, const gfx::Gradient&, mol::Prop::Level>())
@@ -125,6 +137,7 @@ void export_ColorOps()
 
 
   class_<EntityViewColorOp, bases<GradientColorOp> >("EntityViewColorOp", init<>())
+    .def(init<const EntityViewColorOp&>())
     .def(init<const String&, const gfx::Gradient&, float, float, const mol::EntityView&>())
     .def(init<int, const String&, const gfx::Gradient&, float, float, const mol::EntityView&>())
     .def("SetEntityView",&EntityViewColorOp::SetEntityView)
@@ -135,6 +148,7 @@ void export_ColorOps()
 
 #if OST_IMG_ENABLED
   class_<MapHandleColorOp, bases<GradientColorOp> >("MapHandleColorOp", init<>())
+    .def(init<const MapHandleColorOp&>())
     .def(init<const String&, const String&, const gfx::Gradient&, float, float, const img::MapHandle&>())
     .def(init<const String&, int, const String&, const gfx::Gradient&, float, float, const img::MapHandle&>())
     .def(init<const mol::QueryViewWrapper&, const String&, const gfx::Gradient&, float, float, const img::MapHandle&>())
diff --git a/modules/gfx/pymod/export_entity.cc b/modules/gfx/pymod/export_entity.cc
index 4edf1a012ee42117f0b9167a1cea35498e56bd23..8c4781d0a4019f9c0befe857bb64746a5272ab9e 100644
--- a/modules/gfx/pymod/export_entity.cc
+++ b/modules/gfx/pymod/export_entity.cc
@@ -198,11 +198,6 @@ RenderOptionsPtr ent_trace_opts(Entity* ent)
   return ent->GetOptions(RenderMode::TRACE);
 }
 
-RenderOptionsPtr ent_line_trace_opts(Entity* ent)
-{
-  return ent->GetOptions(RenderMode::LINE_TRACE);
-}
-
 RenderOptionsPtr ent_simple_opts(Entity* ent)
 {
   return ent->GetOptions(RenderMode::SIMPLE);
@@ -238,6 +233,11 @@ void set_query2(Entity* e, const std::string& q)
   e->SetQuery(mol::Query(q));
 }
 
+RenderOptionsPtr ent_ltrace_opts(Entity* ent)
+{
+  return ent->GetOptions(RenderMode::LINE_TRACE);
+}
+
 }
 
 void export_Entity()
@@ -301,7 +301,7 @@ void export_Entity()
     .add_property("cartoon_options", &ent_hsc_opts)    
     .add_property("cpk_options", &ent_cpk_opts)
     .add_property("trace_options", &ent_trace_opts)
-    .add_property("line_trace_options", &ent_line_trace_opts)
+    .add_property("line_trace_options", &ent_ltrace_opts)
     .def("ApplyOptions", &Entity::ApplyOptions)
     .def("SetOptions", &Entity::SetOptions)
     .def("Apply",&ent_apply_11)
diff --git a/modules/gfx/pymod/export_gfx_node.cc b/modules/gfx/pymod/export_gfx_node.cc
index f11814317d3b6666d1345f068da68b7068e323a1..b7791e8e67e51232d3988876d2b44d6a697fb179 100644
--- a/modules/gfx/pymod/export_gfx_node.cc
+++ b/modules/gfx/pymod/export_gfx_node.cc
@@ -39,6 +39,7 @@ void export_GfxNode()
     .def("Add",node_add1)
     .def("Remove",node_rem1)
     .def("Add",node_add2)
+    .add_property("name", &GfxNode::GetName)    
     .def("Remove",node_rem2)
     .def("Remove",node_rem3)
     ;
diff --git a/modules/gfx/pymod/export_map.cc b/modules/gfx/pymod/export_map.cc
index f4957efb4f2847c0d84f2facf2eca9f7c82343ea..7ba389b904f3ede92584241eb1890bce10833387 100644
--- a/modules/gfx/pymod/export_map.cc
+++ b/modules/gfx/pymod/export_map.cc
@@ -17,6 +17,7 @@
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
 #include <boost/python.hpp>
+#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
 using namespace boost::python;
 
 #include <ost/gfx/map_iso.hh>
@@ -60,7 +61,13 @@ void export_Map()
          boost::noncopyable>("MapIso", init<const String&, const ::img::MapHandle&, float, optional<uint> >())
     .def("SetLevel",&MapIso::SetLevel)
     .def("GetLevel",&MapIso::GetLevel)
+    .def("GetMinLevel",&MapIso::GetMinLevel)
+    .def("GetMaxLevel",&MapIso::GetMaxLevel)
     .def("GetMean", &MapIso::GetMean)
+    .def("GetHistogram",&MapIso::GetHistogram)
+    .def("SetHistogramBinCount",&MapIso::SetHistogramBinCount)
+    .def("GetHistogramBinCount",&MapIso::GetHistogramBinCount)
+
     .def("GetMap", &MapIso::GetMap,return_value_policy<reference_existing_object>())
     .def("GetOriginalMap", &MapIso::GetOriginalMap,return_value_policy<reference_existing_object>())
     .def("GetDownsampledMap", &MapIso::GetDownsampledMap,return_value_policy<reference_existing_object>())
diff --git a/modules/gfx/pymod/export_render_options.cc b/modules/gfx/pymod/export_render_options.cc
index ab4e9425c79f99408533352056227f6c11288dfe..6cdc169a6633169bde303afc5b1b53c623023011 100644
--- a/modules/gfx/pymod/export_render_options.cc
+++ b/modules/gfx/pymod/export_render_options.cc
@@ -36,6 +36,9 @@ void export_RenderOptions()
 {
   class_<RenderOptions, boost::shared_ptr<RenderOptions>, boost::noncopyable>("RenderOptions", no_init)
     .def("GetRenderMode",&RenderOptions::GetRenderMode)
+    .def("NotifyStateChange",&RenderOptions::NotifyStateChange)
+    .def("AddObserver",&RenderOptions::AddObserver)
+    .def("RemoveObserver",&RenderOptions::RemoveObserver)
   ;
 
   class_<LineRenderOptions, boost::shared_ptr<LineRenderOptions>, bases<RenderOptions>, boost::noncopyable>("LineRenderOptions", no_init)
@@ -43,31 +46,50 @@ void export_RenderOptions()
     .def("GetLineWidth",&LineRenderOptions::GetLineWidth)
     .def("SetAALines",&LineRenderOptions::SetAALines)
     .def("GetAALines",&LineRenderOptions::GetAALines)
+    .add_property("aa_lines", &LineRenderOptions::GetAALines, 
+                  &LineRenderOptions::SetAALines)
+    .add_property("line_width", &LineRenderOptions::GetLineWidth, 
+                  &LineRenderOptions::SetLineWidth)    
   ;
 
   class_<SimpleRenderOptions, boost::shared_ptr<SimpleRenderOptions>, bases<LineRenderOptions>, boost::noncopyable>("SimpleRenderOptions")
+    .def(init<const SimpleRenderOptions&>())
     .def("SetBondOrderFlag", &SimpleRenderOptions::SetBondOrderFlag)
     .def("SetBondOrderDistance", &SimpleRenderOptions::SetBondOrderDistance)
     .def("GetBondOrderFlag", &SimpleRenderOptions::GetBondOrderFlag)
     .def("GetBondOrderDistance", &SimpleRenderOptions::GetBondOrderDistance)
+    .add_property("draw_bond_order", &SimpleRenderOptions::GetBondOrderFlag, 
+                  &SimpleRenderOptions::SetBondOrderFlag)
+    .add_property("bond_order_distance", &SimpleRenderOptions::GetBondOrderDistance, 
+                  &SimpleRenderOptions::SetBondOrderDistance)    
   ;
 
   class_<LineTraceRenderOptions, boost::shared_ptr<LineTraceRenderOptions>, bases<LineRenderOptions>, boost::noncopyable>("LineTraceRenderOptions")
+    .def(init<const LineTraceRenderOptions&>())
   ;
 
   class_<SlineRenderOptions, boost::shared_ptr<SlineRenderOptions>, bases<LineRenderOptions>, boost::noncopyable>("SlineRenderOptions")
+    .def(init<const SlineRenderOptions&>())
     .def("SetSplineDetail", &SlineRenderOptions::SetSplineDetail)
     .def("GetSplineDetail", &SlineRenderOptions::GetSplineDetail)
   ;
 
   class_<CPKRenderOptions, boost::shared_ptr<CPKRenderOptions>, bases<RenderOptions>, boost::noncopyable>("CPKRenderOptions")
+    .def(init<const CPKRenderOptions&>())
     .def("SetSphereDetail", &CPKRenderOptions::SetSphereDetail)
     .def("GetSphereDetail", &CPKRenderOptions::GetSphereDetail)
     .def("SetSphereMode", &CPKRenderOptions::SetSphereMode)
     .def("GetSphereMode", &CPKRenderOptions::GetSphereMode)
+    .def("SetCPKMode", &CPKRenderOptions::SetCPKMode)
+    .def("GetCPKMode", &CPKRenderOptions::GetCPKMode)
+    .add_property("cpk_mode", &CPKRenderOptions::GetCPKMode, 
+                  &CPKRenderOptions::SetCPKMode)
+    .add_property("sphere_detail", &CPKRenderOptions::GetSphereDetail, 
+                  &CPKRenderOptions::SetSphereDetail)
   ;
 
   class_<CustomRenderOptions, boost::shared_ptr<CustomRenderOptions>, bases<RenderOptions>, boost::noncopyable>("CustomRenderOptions")
+    .def(init<const CustomRenderOptions&>())
     .def("SetSphereDetail", &CustomRenderOptions::SetSphereDetail)
     .def("GetSphereDetail", &CustomRenderOptions::GetSphereDetail)
     .def("SetArcDetail", &CustomRenderOptions::SetArcDetail)
@@ -76,9 +98,15 @@ void export_RenderOptions()
     .def("GetSphereRad", &CustomRenderOptions::GetSphereRad)
     .def("SetBondRad", &CustomRenderOptions::SetBondRad)
     .def("GetBondRad", &CustomRenderOptions::GetBondRad)
+    .add_property("sphere_detail", &CustomRenderOptions::GetSphereDetail, &CustomRenderOptions::SetSphereDetail)
+    .add_property("bond_rad", &CustomRenderOptions::GetBondRad, &CustomRenderOptions::SetBondRad)
+    .add_property("sphere_rad", &CustomRenderOptions::GetSphereRad, &CustomRenderOptions::SetSphereRad)    
+    .add_property("arc_detail", &CustomRenderOptions::GetArcDetail, 
+                  &CustomRenderOptions::SetArcDetail)
   ;
 
   class_<CartoonRenderOptions, boost::shared_ptr<CartoonRenderOptions>, bases<RenderOptions>, boost::noncopyable>("CartoonRenderOptions")
+    .def(init<const CartoonRenderOptions&>())
     .def(init<optional<bool> >())
     .def("SetSplineDetail", &CartoonRenderOptions::SetSplineDetail)
     .def("GetSplineDetail", &CartoonRenderOptions::GetSplineDetail)
@@ -119,14 +147,20 @@ void export_RenderOptions()
   ;
   
   class_<TraceRenderOptions, boost::shared_ptr<TraceRenderOptions>, bases<RenderOptions>, boost::noncopyable>("TraceRenderOptions")
+    .def(init<const TraceRenderOptions&>())
     .def("SetArcDetail", &TraceRenderOptions::SetArcDetail)
     .def("GetArcDetail", &TraceRenderOptions::GetArcDetail)
     .def("SetNormalSmoothFactor", &TraceRenderOptions::SetNormalSmoothFactor)
     .def("GetNormalSmoothFactor", &TraceRenderOptions::GetNormalSmoothFactor)
     .def("SetTubeRadius", &TraceRenderOptions::SetTubeRadius)
     .def("GetTubeRadius", &TraceRenderOptions::GetTubeRadius)
-    .def("SetRadius", &TraceRenderOptions::SetTubeRadius)
-    .def("GetRadius", &TraceRenderOptions::GetTubeRadius)
+    .add_property("tube_radius", &TraceRenderOptions::GetTubeRadius, 
+                  &TraceRenderOptions::SetTubeRadius)
+    .add_property("arc_detail", &TraceRenderOptions::GetArcDetail, 
+                  &TraceRenderOptions::SetArcDetail)
+    .add_property("normal_smooth_factor", 
+                  &TraceRenderOptions::GetNormalSmoothFactor, 
+                  &TraceRenderOptions::SetNormalSmoothFactor)    
   ;
 }
 
diff --git a/modules/gfx/pymod/export_scene.cc b/modules/gfx/pymod/export_scene.cc
index 1eb5a8fe2c97d56690552cc35be5d7b7c9dd99f3..08b98b41959af2c44ce69d73bb27e6fe8ec3be87 100644
--- a/modules/gfx/pymod/export_scene.cc
+++ b/modules/gfx/pymod/export_scene.cc
@@ -87,7 +87,13 @@ void export_Scene()
     .def("InitGL", &Scene::InitGL)
     .def("RenderGL", &Scene::RenderGL)
     .def("Resize", &Scene::Resize)
+    .def("HasNode", &Scene::HasNode)
     .def("SetBackground", &Scene::SetBackground)
+    .add_property("transform", &Scene::GetTransform, &Scene::SetTransform)
+    .add_property("fov", &Scene::GetFOV, &Scene::SetFOV)
+    .add_property("center", &Scene::GetCenter, &Scene::SetCenter)
+    .add_property("near", &Scene::GetNear, &Scene::SetNear)
+    .add_property("far", &Scene::GetFar, &Scene::SetFar)
     .def("SetNearFar",&Scene::SetNearFar)
     .def("SetFog",&Scene::SetFog)
     .def("SetFogColor",&Scene::SetFogColor)
@@ -117,6 +123,7 @@ void export_Scene()
     .def("GetSelectionMode",&Scene::GetSelectionMode)
     .def("SetBlur",&Scene::SetBlur)
     .def("BlurSnapshot",&Scene::BlurSnapshot)
+    .def("RemoveAll", &Scene::RemoveAll)
     .def("SetShadow",&Scene::SetShadow)
     .def("SetShadowQuality",&Scene::SetShadowQuality)
     .def("SetShadowWeight",&Scene::SetShadowWeight)
diff --git a/modules/gfx/pymod/gradients.xml b/modules/gfx/pymod/gradients.xml
new file mode 100644
index 0000000000000000000000000000000000000000..dc3e03fd2ed56d5d5c7dee6729625d733cfbde52
--- /dev/null
+++ b/modules/gfx/pymod/gradients.xml
@@ -0,0 +1,66 @@
+<!DOCTYPE EMDataInfo>
+<EMDataInfo>
+ <Gradients>
+  <Gradient Name="GREENS" >2
+0.0609137	0.333333	1	0	1
+0.954315	0	0.501961	0	1
+</Gradient>
+  <Gradient Name="BLUES" >2
+0.0615451	0.567727	0.988205	1	1
+0.978541	0.0335241	0.286625	0.501961	1
+</Gradient>
+  <Gradient Name="REDS" >2
+0.0512002	1	0.532174	0	1
+0.978541	1	0	0	1
+</Gradient>
+  <Gradient Name="HEAT_MAP" >3
+0.0615451	0.0313726	0.286275	0.501961	1
+0.502146	1	1	1	1
+0.978541	0.890105	0.075639	0.0546578	1
+</Gradient>
+  <Gradient Name="AUTUMN" >3
+0.0615451	1	0.972015	0.0132753	1
+0.502146	1	0.699229	0.0974136	1
+0.978541	0.890105	0.075639	0.0546578	1
+</Gradient>
+  <Gradient Name="UGLY" >6
+0.0615451	0.223087	0.501961	0.330602	1
+0.244635	0.318853	0.472465	1	1
+0.420601	0.896193	0.480751	1	1
+0.596566	1	0.670039	0.550607	1
+0.776824	0.890105	0.075639	0.0546578	1
+0.961373	1	0.943923	0.407279	1
+</Gradient>
+  <Gradient Name="RAINBOW" >12
+0.0555187	0.890105	0.075639	0.0546578	1
+0.139951	1	0.505974	0	1
+0.225206	0.989929	1	0	1
+0.313909	0.676997	1	0	1
+0.397518	0.177951	1	0	1
+0.478502	0	1	0.520333	1
+0.555216	0	1	1	1
+0.637844	0	0.625711	1	1
+0.718006	0	0.135302	1	1
+0.80655	0.570611	0	1	1
+0.889655	1	0	0.741695	1
+0.975862	1	0	0.285039	1
+</Gradient>
+  <Gradient Name="FIRE" >4
+0.0609137	0.472526	0.472526	0.472526	1
+0.348276	1	0.97792	0.00274662	1
+0.631034	1	0.63331	0	1
+0.954315	1	0	0	1
+</Gradient>
+  <Gradient Name="RED_TO_BLUE">9
+0.0545827 0.886275  0.0745098 0.0509804 1
+0.171838  1 0.505882  0 1
+0.284924  0.988235  1 0 1
+0.403739  0.67451 1 0 1
+0.521744  0.176471  1 0 1
+0.641707  0 1 0.517647  1
+0.748835  0 1 1 1
+0.857779  0 0.623529  1 1
+0.97541 0 0.133333  1 1
+</Gradient>
+ </Gradients>
+</EMDataInfo>
diff --git a/modules/gfx/pymod/wrap_gfx.cc b/modules/gfx/pymod/wrap_gfx.cc
index cd308a6a7b7d3e26f51a6636308a0271d3d9be14..7c3655aa3db2136236f7bd9e4096db485391fc0f 100644
--- a/modules/gfx/pymod/wrap_gfx.cc
+++ b/modules/gfx/pymod/wrap_gfx.cc
@@ -157,12 +157,14 @@ BOOST_PYTHON_MODULE(_gfx)
     ;
   
   class_<Gradient>("Gradient", init<>())
+    .def(init<const String&>())
     .def("SetColorAt", &Gradient::SetColorAt)
     .def("GetColorAt", &Gradient::GetColorAt)
     .def("GetStops", &Gradient::GetStops)
     .def("GradientToInfo", &Gradient::GradientToInfo)
     .def("GradientFromInfo", &Gradient::GradientFromInfo).staticmethod("GradientFromInfo")
   ;
+  implicitly_convertible<String, Gradient>();
 
   class_<StopList>("StopList", init<>())
     .def(vector_indexing_suite<StopList>())
diff --git a/modules/gfx/src/CMakeLists.txt b/modules/gfx/src/CMakeLists.txt
index ee2a67f4ee4b5f1c60de7c17630e040d3f531b94..b34e424a10d41b4f97cb7cbdaf32a056d139cf62 100644
--- a/modules/gfx/src/CMakeLists.txt
+++ b/modules/gfx/src/CMakeLists.txt
@@ -32,6 +32,7 @@ glext_include.hh
 render_mode.hh
 material.hh
 gradient.hh
+gradient_manager.hh
 module_config.hh
 primitives.hh
 povray_fw.hh
@@ -102,6 +103,7 @@ scene.cc
 selection.cc
 surface.cc
 gradient.cc
+gradient_manager.cc
 vertex_array.cc
 vertex_array_helper.cc
 material.cc
diff --git a/modules/gfx/src/bitmap_io.cc b/modules/gfx/src/bitmap_io.cc
index 3f16451371417244d16e7fb8027e3c7544d1edb2..fedb463afa9debfe85773aa5b4b2e55e9cbda45b 100644
--- a/modules/gfx/src/bitmap_io.cc
+++ b/modules/gfx/src/bitmap_io.cc
@@ -35,7 +35,7 @@ void export_png(const String& filename, unsigned int width, unsigned int height,
   FILE *fp;
   
   if((fp=fopen(filename.c_str(),"wb"))==NULL) {
-    LOGN_ERROR("error opening" << filename << " for exporting");
+    LOG_ERROR("error opening" << filename << " for exporting");
     return;
   }
 
@@ -44,7 +44,7 @@ void export_png(const String& filename, unsigned int width, unsigned int height,
                                                 NULL, NULL, NULL);
   if (png_ptr == NULL) {
     fclose(fp);
-    LOGN_ERROR("error creating png write struct");
+    LOG_ERROR("error creating png write struct");
     return;
   }
   
@@ -53,14 +53,14 @@ void export_png(const String& filename, unsigned int width, unsigned int height,
   if (info_ptr == NULL) {
     fclose(fp);
     png_destroy_read_struct(&png_ptr, (png_infopp)NULL, (png_infopp)NULL);
-    LOGN_ERROR("error creating png info struct");
+    LOG_ERROR("error creating png info struct");
     return;
   }
   
   if (setjmp(png_jmpbuf(png_ptr))) {
     png_destroy_read_struct(&png_ptr, &info_ptr, (png_infopp)NULL);
     fclose(fp);
-    LOGN_ERROR("error in png setjmp");
+    LOG_ERROR("error in png setjmp");
     return;
   }
   
@@ -113,7 +113,7 @@ Bitmap import_png(const String& filename)
   png_uint_32 width,height,bpp;
   
   if((fp=fopen(filename.c_str(),"rb"))==NULL) {
-    LOGN_ERROR("error opening " << filename);
+    LOG_ERROR("error opening " << filename);
     return bm;
   }
   
@@ -121,7 +121,7 @@ Bitmap import_png(const String& filename)
 				   NULL,NULL,NULL);
   if (png_ptr == NULL) {
     fclose(fp);
-    LOGN_ERROR("unexpected error #1 in png lib");
+    LOG_ERROR("unexpected error #1 in png lib");
     return bm;
   }
   
@@ -129,14 +129,14 @@ Bitmap import_png(const String& filename)
   if (info_ptr == NULL) {
     fclose(fp);
     png_destroy_read_struct(&png_ptr, (png_infopp)NULL, (png_infopp)NULL);
-    LOGN_ERROR("unexpected error #2 in png lib");
+    LOG_ERROR("unexpected error #2 in png lib");
     return bm;
   }
   
   if (setjmp(png_jmpbuf(png_ptr))) {
     png_destroy_read_struct(&png_ptr, &info_ptr, (png_infopp)NULL);
     fclose(fp);
-    LOGN_ERROR("unexpected error #3 in png lib");
+    LOG_ERROR("unexpected error #3 in png lib");
     return bm;
   }
   
@@ -148,7 +148,7 @@ Bitmap import_png(const String& filename)
   channels=png_get_channels(png_ptr,info_ptr);
 
   if(channels<1 || channels>4) {
-    LOGN_ERROR("error importing bitmap: " << filename << " has " << channels << " channels, expected 1-4");
+    LOG_ERROR("error importing bitmap: " << filename << " has " << channels << " channels, excpected 1-4");
     return bm;
   }
   
@@ -168,7 +168,7 @@ Bitmap import_png(const String& filename)
     }
   }
 
-  LOGN_DEBUG("loaded " << width << "x" << height << ":" << channels << " bitmap");
+  LOG_DEBUG("loaded " << width << "x" << height << ":" << channels << " bitmap");
 
   bm.channels=channels;
   bm.width=width;
diff --git a/modules/gfx/src/color_ops/basic_gradient_color_op.cc b/modules/gfx/src/color_ops/basic_gradient_color_op.cc
index 8648a8304e2974f2c75ef956e7093fc0a58ce115..39733eb6b8c06332cc4b7ff86b13d9956ae57ef6 100644
--- a/modules/gfx/src/color_ops/basic_gradient_color_op.cc
+++ b/modules/gfx/src/color_ops/basic_gradient_color_op.cc
@@ -26,12 +26,17 @@
 namespace ost { namespace gfx {
 
 BasicGradientColorOp::BasicGradientColorOp() : ColorOp(), gradient_(){
-
+  this->Init();
 }
 
 BasicGradientColorOp::BasicGradientColorOp(const String& selection, const gfx::Gradient& gradient, mol::Prop::Level level) :
   ColorOp(selection), gradient_(gradient), level_(level){
+  this->Init();
+}
 
+void BasicGradientColorOp::Init()
+{
+  this->SetName("Basic gradient");
 }
 
 bool BasicGradientColorOp::CanApplyTo(const GfxObjP& obj) const{
diff --git a/modules/gfx/src/color_ops/basic_gradient_color_op.hh b/modules/gfx/src/color_ops/basic_gradient_color_op.hh
index b00a092e210675cb73d05159e0255c84f09c1317..d8a4d3c4436b79b61e6afc8c54f8b41546df333c 100644
--- a/modules/gfx/src/color_ops/basic_gradient_color_op.hh
+++ b/modules/gfx/src/color_ops/basic_gradient_color_op.hh
@@ -52,6 +52,7 @@ public:
   static gfx::BasicGradientColorOp FromInfo(info::InfoGroup& group);
 
 private:
+  void Init();
   gfx::Gradient gradient_;
   mol::Prop::Level level_;
 };
diff --git a/modules/gfx/src/color_ops/by_chain_color_op.cc b/modules/gfx/src/color_ops/by_chain_color_op.cc
index 908fb591ff42e49f66d885dabee617ef33bb193e..e760d0e38aa7c2f677d81bd644b1a31eebea8763 100644
--- a/modules/gfx/src/color_ops/by_chain_color_op.cc
+++ b/modules/gfx/src/color_ops/by_chain_color_op.cc
@@ -26,19 +26,24 @@
 
 namespace ost { namespace gfx {
 
-ByChainColorOp::ByChainColorOp() : ColorOp(){this->init();}
+ByChainColorOp::ByChainColorOp() : ColorOp(),chain_count_(0),color_grad_("RAINBOW")
+{
+  this->Init();
+}
 
-ByChainColorOp::ByChainColorOp(const String& selection, int mask) : ColorOp(selection,mask){this->init();}
+ByChainColorOp::ByChainColorOp(const String& selection, int mask) : ColorOp(selection,mask),chain_count_(0),color_grad_("RAINBOW")
+{
+  this->Init();
+}
 
-ByChainColorOp::ByChainColorOp(const mol::QueryViewWrapper& query_view, int mask) : ColorOp(query_view,mask){this->init();}
+ByChainColorOp::ByChainColorOp(const mol::QueryViewWrapper& query_view, int mask) : ColorOp(query_view,mask),chain_count_(0),color_grad_("RAINBOW")
+{
+  this->Init();
+}
 
-void ByChainColorOp::init(){
-  color_grad_.SetColorAt(0,Color(1,1,0));
-  color_grad_.SetColorAt(0.16666,Color(1,0,0));
-  color_grad_.SetColorAt(0.33333,Color(0,1,1));
-  color_grad_.SetColorAt(0.5,Color(0,1,0));
-  color_grad_.SetColorAt(0.66666,Color(1,0,1));
-  color_grad_.SetColorAt(0.83333,Color(0,0,1));
+void ByChainColorOp::Init()
+{
+  this->SetName("By chain");
 }
 
 bool ByChainColorOp::CanApplyTo(const GfxObjP& obj) const{
@@ -62,27 +67,32 @@ gfx::Color ByChainColorOp::GetColor(String ident) const{
   return colors_[ident];
 }
 
+int ByChainColorOp::GetChainCount() const
+{
+  return chain_count_;
+}
+
+void ByChainColorOp::SetChainCount(int chain_count)
+{
+  chain_count_ = chain_count;
+}
+
 gfx::ByChainColorOp ByChainColorOp::FromInfo(info::InfoGroup& group){
   gfx::ColorOp op = ColorOp::FromInfo(group);
-  String selection = op.GetSelection();
+  mol::QueryViewWrapper wrapper(op.GetSelection(),op.GetSelectionFlags());
   int mask = op.GetMask();
-  return gfx::ByChainColorOp(selection, mask);
+  return gfx::ByChainColorOp(wrapper, mask);
 }
 
 gfx::Color ByChainColorOp::GenerateColor(String& ident) const{
   unsigned int size=colors_.size()-1;
-  int cnt = size % 6;
-  int factor = abs(size/6.0)+1;
-  float start = 1.0/(6.0*factor);
-  if(factor > 1 && !((factor+1) & 1)){
-    float old_start = 1.0 / (6.0 *abs(size/6.0));
-    start += old_start;
+  if(size<=0){
+    colors_[ident] = color_grad_.GetColorAt(0.0);
   }
-  float value = start + (cnt / 6.0);
-  if(value >= 1){
-    value -=1;
+  else{
+    colors_[ident] = color_grad_.GetColorAt(float(size) / chain_count_);
   }
-  return color_grad_.GetColorAt(value);
+  return colors_[ident];
 }
 
 }}
diff --git a/modules/gfx/src/color_ops/by_chain_color_op.hh b/modules/gfx/src/color_ops/by_chain_color_op.hh
index fffc8966864ea7d9770d79ffe59053f5cb2b4964..75193354b4337ad2b0ba97b031d2bfdcaed4d0ad 100644
--- a/modules/gfx/src/color_ops/by_chain_color_op.hh
+++ b/modules/gfx/src/color_ops/by_chain_color_op.hh
@@ -43,13 +43,17 @@ public:
 
   virtual gfx::Color GetColor(String ident) const;
 
+  virtual int GetChainCount() const;
+  virtual void SetChainCount(int chain_count);
+
   //virtual void ToInfo(info::InfoGroup& group) const;
   static gfx::ByChainColorOp FromInfo(info::InfoGroup& group);
 
 private:
-  void init();
+  void Init();
   gfx::Color GenerateColor(String& ident) const;
 
+  mutable int chain_count_;
   mutable std::map<String,gfx::Color> colors_;
 
   gfx::Gradient color_grad_;
diff --git a/modules/gfx/src/color_ops/by_element_color_op.cc b/modules/gfx/src/color_ops/by_element_color_op.cc
index e2bac71b0bd02e88c333b8b55a3f4ca858358eb5..c09e542d4995e0e434cb25a6c31bb3e2db38b614 100644
--- a/modules/gfx/src/color_ops/by_element_color_op.cc
+++ b/modules/gfx/src/color_ops/by_element_color_op.cc
@@ -25,11 +25,25 @@
 
 namespace ost { namespace gfx {
 
-ByElementColorOp::ByElementColorOp() : ColorOp(){}
+ByElementColorOp::ByElementColorOp() : ColorOp()
+{
+  this->Init();
+}
 
-ByElementColorOp::ByElementColorOp(const String& selection, int mask) : ColorOp(selection,mask){}
+ByElementColorOp::ByElementColorOp(const String& selection, int mask) : ColorOp(selection,mask)
+{
+  this->Init();
+}
 
-ByElementColorOp::ByElementColorOp(const mol::QueryViewWrapper& query_view, int mask) : ColorOp(query_view,mask){}
+ByElementColorOp::ByElementColorOp(const mol::QueryViewWrapper& query_view, int mask) : ColorOp(query_view,mask)
+{
+  this->Init();
+}
+
+void ByElementColorOp::Init()
+{
+  this->SetName("By element");
+}
 
 bool ByElementColorOp::CanApplyTo(const GfxObjP& obj) const{
   if(dynamic_cast<Entity*>(obj.get()))
@@ -46,9 +60,9 @@ void ByElementColorOp::ApplyTo(GfxObjP& objP) const{
 
 gfx::ByElementColorOp ByElementColorOp::FromInfo(info::InfoGroup& group){
   gfx::ColorOp op = ColorOp::FromInfo(group);
-  String selection = op.GetSelection();
+  mol::QueryViewWrapper wrapper(op.GetSelection(),op.GetSelectionFlags());
   int mask = op.GetMask();
-  return gfx::ByElementColorOp(selection, mask);
+  return gfx::ByElementColorOp(wrapper, mask);
 }
 
 }}
diff --git a/modules/gfx/src/color_ops/by_element_color_op.hh b/modules/gfx/src/color_ops/by_element_color_op.hh
index 2de442121cc12f0433a702a02a3e09bac79e5b10..defceee742d9990dae8e387719a0a13fb5421348 100644
--- a/modules/gfx/src/color_ops/by_element_color_op.hh
+++ b/modules/gfx/src/color_ops/by_element_color_op.hh
@@ -44,6 +44,8 @@ public:
   virtual void ApplyTo(GfxObjP& obj) const;
 
   static ost::gfx::ByElementColorOp FromInfo(info::InfoGroup& group);
+private:
+  void Init();
 };
 
 }}
diff --git a/modules/gfx/src/color_ops/color_op.cc b/modules/gfx/src/color_ops/color_op.cc
index bca45b744617f8140fb4cf4c5038c35e2a89c621..5003f90988a10dcfdb3f7fc4ff06cb8e4186e181 100644
--- a/modules/gfx/src/color_ops/color_op.cc
+++ b/modules/gfx/src/color_ops/color_op.cc
@@ -21,16 +21,16 @@
 
 namespace ost { namespace gfx {
 
-ColorOp::ColorOp(): query_view_(), mask_(DETAIL_COLOR|MAIN_COLOR)
+ColorOp::ColorOp():  name_("Abstract coloring"), query_view_(), mask_(DETAIL_COLOR|MAIN_COLOR)
 { }
 
 
 ColorOp::ColorOp(const String& selection, int mask):
-    query_view_(mol::Query(selection),mol::EntityView() ), mask_(mask)
+    name_("Abstract coloring"), query_view_(mol::Query(selection),mol::EntityView() ), mask_(mask)
 { }
 
 ColorOp::ColorOp(const mol::QueryViewWrapper& query_view, int mask):
-    query_view_(query_view), mask_(mask)
+    name_("Abstract coloring"), query_view_(query_view), mask_(mask)
 { }
 
 bool ColorOp::CanApplyTo(const GfxObjP& obj) const
@@ -43,6 +43,16 @@ void ColorOp::ApplyTo(GfxObjP& obj) const
   //Do Nothing
 }
 
+const String& ColorOp::GetName() const
+{
+  return name_;
+}
+
+void ColorOp::SetName(const String& name)
+{
+  name_=name;
+}
+
 void ColorOp::SetSelection(const String& selection)
 {
   query_view_.SetQuery(selection);
@@ -53,6 +63,16 @@ String ColorOp::GetSelection() const
   return query_view_.GetQuery().GetQueryString();
 }
 
+void ColorOp::SetSelectionFlags(mol::QueryFlags flags)
+{
+  query_view_.SetFlags(flags);
+}
+
+mol::QueryFlags ColorOp::GetSelectionFlags() const
+{
+  return query_view_.GetFlags();
+}
+
 bool ColorOp::IsSelectionOnly() const
 {
   return !query_view_.IsDataValid();
@@ -71,7 +91,7 @@ void ColorOp::SetView(const mol::EntityView& view)
 void ColorOp::ToInfo(info::InfoGroup& group) const
 {
   std::ostringstream ss;
-  ss << (int)mask_ << "\t" << query_view_.GetQuery().GetQueryString();
+  ss << (int)mask_ << "\t" << query_view_.GetFlags() << "\t" << query_view_.GetQuery().GetQueryString();
   group.SetTextData(ss.str());
 }
 
@@ -80,7 +100,8 @@ gfx::ColorOp ColorOp::FromInfo(ost::info::InfoGroup& group)
   ColorOp op;
   std::istringstream ss(group.GetTextData());
   int mask;
-  ss >> mask;
+  mol::QueryFlags flags;
+  ss >> mask >> flags;
   op.SetMask(mask);
   String selection;
   String part;
@@ -91,6 +112,7 @@ gfx::ColorOp ColorOp::FromInfo(ost::info::InfoGroup& group)
     part.clear();
   }
   op.SetSelection(selection);
+  op.SetSelectionFlags(flags);
   return op;
 }
 
diff --git a/modules/gfx/src/color_ops/color_op.hh b/modules/gfx/src/color_ops/color_op.hh
index c2c7c9360e610912922abdc84b96eddaf3079fdb..7d891039dd2574e54d07b59a8dd67d02a41440a2 100644
--- a/modules/gfx/src/color_ops/color_op.hh
+++ b/modules/gfx/src/color_ops/color_op.hh
@@ -51,6 +51,8 @@ public:
   virtual bool CanApplyTo(const GfxObjP& obj) const;
   virtual void ApplyTo(GfxObjP& obj) const;
 
+  virtual const String& GetName() const;
+
   ColorMask GetMask() const;
   
   void SetMask(ColorMask mask);
@@ -58,15 +60,22 @@ public:
   virtual void SetSelection(const String& selection);
   virtual String GetSelection() const;
 
+  virtual void SetSelectionFlags(mol::QueryFlags flags);
+  virtual mol::QueryFlags GetSelectionFlags() const;
+
   virtual bool IsSelectionOnly() const;
   virtual void SetView(const mol::EntityView& view);
   virtual mol::EntityView GetView() const;
 
   virtual void ToInfo(info::InfoGroup& group) const;
   static gfx::ColorOp FromInfo(info::InfoGroup& group);
+
+protected:
+  virtual void SetName(const String& name);
+
 private:
+  String name_;
   mol::QueryViewWrapper query_view_;
-  mol::EntityView view_;
   ColorMask mask_;
 };
 
diff --git a/modules/gfx/src/color_ops/entity_view_color_op.cc b/modules/gfx/src/color_ops/entity_view_color_op.cc
index 6cdbd75a127617e4a95979c9f60b5dc42f7aac49..e52a25b71018fba8ea6425d4a31948f55aec247c 100644
--- a/modules/gfx/src/color_ops/entity_view_color_op.cc
+++ b/modules/gfx/src/color_ops/entity_view_color_op.cc
@@ -27,16 +27,21 @@
 namespace ost { namespace gfx {
 
 EntityViewColorOp::EntityViewColorOp() : GradientColorOp(), ev_(){
-
+  this->Init();
 }
 EntityViewColorOp::EntityViewColorOp(int mask, const String& property, const gfx::Gradient& gradient, float minv, float maxv, const mol::EntityView& ev) :
   GradientColorOp("", mask, property, gradient, minv, maxv), ev_(ev){
-
+  this->Init();
 }
 
 EntityViewColorOp::EntityViewColorOp(const String& property, const gfx::Gradient& gradient, float minv, float maxv, const mol::EntityView& ev) :
   GradientColorOp("", property, gradient, minv, maxv), ev_(ev){
+  this->Init();
+}
 
+void EntityViewColorOp::Init()
+{
+  this->SetName("EntityView gradient");
 }
 
 bool EntityViewColorOp::CanApplyTo(const GfxObjP& obj) const{
@@ -84,7 +89,6 @@ gfx::EntityViewColorOp EntityViewColorOp::FromInfo(info::InfoGroup& group){
   info::InfoGroup super_group = group.GetGroup("GradientColorOp");
   gfx::GradientColorOp gop = GradientColorOp::FromInfo(super_group);
   std::istringstream ss(group.GetTextData());
-  String selection = gop.GetSelection();
   gfx::Gradient gradient = gop.GetGradient();
   int mask = gop.GetMask();
   String property = gop.GetProperty();
diff --git a/modules/gfx/src/color_ops/entity_view_color_op.hh b/modules/gfx/src/color_ops/entity_view_color_op.hh
index 9f5098faa64169d065284a7fa0cc29afcbb8c743..a0afba972956fc7d0014481f39cc47198f9296ef 100644
--- a/modules/gfx/src/color_ops/entity_view_color_op.hh
+++ b/modules/gfx/src/color_ops/entity_view_color_op.hh
@@ -52,6 +52,7 @@ public:
   static gfx::EntityViewColorOp FromInfo(info::InfoGroup& group);
 
 private:
+  void Init();
   mol::EntityView ev_;
 };
 
diff --git a/modules/gfx/src/color_ops/gradient_color_op.cc b/modules/gfx/src/color_ops/gradient_color_op.cc
index 82c06e144871ce127a2080c385d676ba6b2659ad..8b2bc6595c734a564d8aa728c3c0ffdf7d6b28ed 100644
--- a/modules/gfx/src/color_ops/gradient_color_op.cc
+++ b/modules/gfx/src/color_ops/gradient_color_op.cc
@@ -25,7 +25,7 @@
 namespace ost { namespace gfx {
 
 GradientColorOp::GradientColorOp() : ColorOp(), property_(), gradient_(){
-
+  this->Init();
 }
 
 GradientColorOp::GradientColorOp(const String& selection, const String& property,
@@ -33,48 +33,69 @@ GradientColorOp::GradientColorOp(const String& selection, const String& property
                                  float minv, float maxv):
   ColorOp(selection), property_(property), gradient_(gradient), calculate_(false),
   minv_(minv), maxv_(maxv)
-{ }
+{
+  this->Init();
+}
 
 GradientColorOp::GradientColorOp(const String& selection, int mask, const String& property,
                                  const gfx::Gradient& gradient,
                                  float minv, float maxv):
   ColorOp(selection,mask), property_(property), gradient_(gradient), calculate_(false),
   minv_(minv), maxv_(maxv)
-{ }
+{
+  this->Init();
+}
 
 GradientColorOp::GradientColorOp(const String& selection, const String& property,
                                  const gfx::Gradient& gradient):
   ColorOp(selection), property_(property), gradient_(gradient), calculate_(true)
-{ }
+{
+  this->Init();
+}
 
 GradientColorOp::GradientColorOp(const String& selection, int mask, const String& property,
                                  const gfx::Gradient& gradient):
   ColorOp(selection,mask), property_(property), gradient_(gradient), calculate_(true)
-{ }
+{
+  this->Init();
+}
 
 GradientColorOp::GradientColorOp(const mol::QueryViewWrapper& query_view, const String& property,
                                  const gfx::Gradient& gradient,
                                  float minv, float maxv):
   ColorOp(query_view), property_(property), gradient_(gradient), calculate_(false),
   minv_(minv), maxv_(maxv)
-{ }
+{
+  this->Init();
+}
 
 GradientColorOp::GradientColorOp(const mol::QueryViewWrapper& query_view, int mask, const String& property,
                                  const gfx::Gradient& gradient,
                                  float minv, float maxv):
   ColorOp(query_view,mask), property_(property), gradient_(gradient), calculate_(false),
   minv_(minv), maxv_(maxv)
-{ }
+{
+  this->Init();
+}
 
 GradientColorOp::GradientColorOp(const mol::QueryViewWrapper& query_view, const String& property,
                                  const gfx::Gradient& gradient):
   ColorOp(query_view), property_(property), gradient_(gradient), calculate_(true)
-{ }
+{
+  this->Init();
+}
 
 GradientColorOp::GradientColorOp(const mol::QueryViewWrapper& query_view, int mask, const String& property,
                                  const gfx::Gradient& gradient):
   ColorOp(query_view,mask), property_(property), gradient_(gradient), calculate_(true)
-{ }
+{
+  this->Init();
+}
+
+void GradientColorOp::Init()
+{
+  this->SetName("Gradient");
+}
 
 void GradientColorOp::SetProperty(const String& property)
 {
@@ -150,12 +171,12 @@ gfx::GradientColorOp GradientColorOp::FromInfo(info::InfoGroup& group)
     if(ss.good())property.append(" ");
     part.clear();
   }
-  String selection = op.GetSelection();
+  mol::QueryViewWrapper wrapper(op.GetSelection(),op.GetSelectionFlags());
   if(calculate) {
-    return gfx::GradientColorOp(selection,mask,property,gradient);
+    return gfx::GradientColorOp(wrapper,mask,property,gradient);
   }
   else {
-    return gfx::GradientColorOp(selection,mask,property,gradient, minv, maxv);
+    return gfx::GradientColorOp(wrapper,mask,property,gradient, minv, maxv);
   }
 }
 
diff --git a/modules/gfx/src/color_ops/gradient_color_op.hh b/modules/gfx/src/color_ops/gradient_color_op.hh
index 98a6df76caae580e89936d89e05495198ab3cc52..6823981da5ddc563bf8ec19d5891512a27a0227a 100644
--- a/modules/gfx/src/color_ops/gradient_color_op.hh
+++ b/modules/gfx/src/color_ops/gradient_color_op.hh
@@ -65,6 +65,7 @@ public:
   static gfx::GradientColorOp FromInfo(info::InfoGroup& group);
 
 private:
+  void Init();
   String property_;
   gfx::Gradient gradient_;
   bool calculate_;
diff --git a/modules/gfx/src/color_ops/gradient_level_color_op.cc b/modules/gfx/src/color_ops/gradient_level_color_op.cc
index e1e0f2940e94227de57752d7667c7d02ab2acf84..564fd763b8e2ed090ed66c88c751c9a775faf4a5 100644
--- a/modules/gfx/src/color_ops/gradient_level_color_op.cc
+++ b/modules/gfx/src/color_ops/gradient_level_color_op.cc
@@ -25,8 +25,9 @@
 
 namespace ost { namespace gfx {
 
-GradientLevelColorOp::GradientLevelColorOp() : GradientColorOp(), level_(){
-
+GradientLevelColorOp::GradientLevelColorOp() : GradientColorOp(), level_()
+{
+  this->Init();
 }
 
 GradientLevelColorOp::GradientLevelColorOp(const String& selection, 
@@ -34,8 +35,9 @@ GradientLevelColorOp::GradientLevelColorOp(const String& selection,
                                             const gfx::Gradient& gradient, 
                                             float minv, 
                                             float maxv, mol::Prop::Level level):
-  GradientColorOp(selection, property, gradient, minv, maxv), level_(level){
-
+  GradientColorOp(selection, property, gradient, minv, maxv), level_(level)
+{
+  this->Init();
 }
 
 GradientLevelColorOp::GradientLevelColorOp(const String& selection, int mask,
@@ -43,24 +45,27 @@ GradientLevelColorOp::GradientLevelColorOp(const String& selection, int mask,
                                             const gfx::Gradient& gradient,
                                             float minv,
                                             float maxv, mol::Prop::Level level):
-  GradientColorOp(selection, mask, property, gradient, minv, maxv), level_(level){
-
+  GradientColorOp(selection, mask, property, gradient, minv, maxv), level_(level)
+{
+  this->Init();
 }
 
 GradientLevelColorOp::GradientLevelColorOp(const String& selection,
                                             const String& property,
                                             const gfx::Gradient& gradient,
                                             mol::Prop::Level level):
-  GradientColorOp(selection, property, gradient), level_(level){
-
+  GradientColorOp(selection, property, gradient), level_(level)
+{
+  this->Init();
 }
 
 GradientLevelColorOp::GradientLevelColorOp(const String& selection, int mask,
                                             const String& property,
                                             const gfx::Gradient& gradient,
                                             mol::Prop::Level level):
-  GradientColorOp(selection, mask, property, gradient), level_(level){
-
+  GradientColorOp(selection, mask, property, gradient), level_(level)
+{
+  this->Init();
 }
 
 GradientLevelColorOp::GradientLevelColorOp(const mol::QueryViewWrapper& query_view,
@@ -68,8 +73,9 @@ GradientLevelColorOp::GradientLevelColorOp(const mol::QueryViewWrapper& query_vi
                                             const gfx::Gradient& gradient,
                                             float minv,
                                             float maxv, mol::Prop::Level level):
-  GradientColorOp(query_view, property, gradient, minv, maxv), level_(level){
-
+  GradientColorOp(query_view, property, gradient, minv, maxv), level_(level)
+{
+  this->Init();
 }
 
 GradientLevelColorOp::GradientLevelColorOp(const mol::QueryViewWrapper& query_view, int mask,
@@ -77,24 +83,32 @@ GradientLevelColorOp::GradientLevelColorOp(const mol::QueryViewWrapper& query_vi
                                             const gfx::Gradient& gradient,
                                             float minv,
                                             float maxv, mol::Prop::Level level):
-  GradientColorOp(query_view, mask, property, gradient, minv, maxv), level_(level){
-
+  GradientColorOp(query_view, mask, property, gradient, minv, maxv), level_(level)
+{
+  this->Init();
 }
 
 GradientLevelColorOp::GradientLevelColorOp(const mol::QueryViewWrapper& query_view,
                                             const String& property,
                                             const gfx::Gradient& gradient,
                                             mol::Prop::Level level):
-  GradientColorOp(query_view, property, gradient), level_(level){
-
+  GradientColorOp(query_view, property, gradient), level_(level)
+{
+  this->Init();
 }
 
 GradientLevelColorOp::GradientLevelColorOp(const mol::QueryViewWrapper& query_view, int mask,
                                             const String& property,
                                             const gfx::Gradient& gradient,
                                             mol::Prop::Level level):
-  GradientColorOp(query_view, mask, property, gradient), level_(level){
+  GradientColorOp(query_view, mask, property, gradient), level_(level)
+{
+  this->Init();
+}
 
+void GradientLevelColorOp::Init()
+{
+  this->SetName("Gradient level");
 }
 
 bool GradientLevelColorOp::CanApplyTo(const GfxObjP& obj) const{
@@ -143,17 +157,17 @@ gfx::GradientLevelColorOp GradientLevelColorOp::FromInfo(info::InfoGroup& group)
   int l;
   ss >> l;
   mol::Prop::Level level = mol::Prop::Level(l);
-  String selection = gop.GetSelection();
+  mol::QueryViewWrapper wrapper(gop.GetSelection(),gop.GetSelectionFlags());
   String property = gop.GetProperty();
   int mask = gop.GetMask();
   gfx::Gradient gradient = gop.GetGradient();
   float minv = gop.GetMinV();
   float maxv = gop.GetMaxV();
   if(gop.GetCalculateMinMax()){
-    return gfx::GradientLevelColorOp(selection, mask, property, gradient, level);
+    return gfx::GradientLevelColorOp(wrapper, mask, property, gradient, level);
   }
   else{
-    return gfx::GradientLevelColorOp(selection, mask, property, gradient, minv, maxv, level);
+    return gfx::GradientLevelColorOp(wrapper, mask, property, gradient, minv, maxv, level);
   }
 }
 
diff --git a/modules/gfx/src/color_ops/gradient_level_color_op.hh b/modules/gfx/src/color_ops/gradient_level_color_op.hh
index d0c1cac667f41b28f9b7b8b5e4cf11c656f6d686..5dd6a854b6d9b9c96d7327a65600f10b3f3e12eb 100644
--- a/modules/gfx/src/color_ops/gradient_level_color_op.hh
+++ b/modules/gfx/src/color_ops/gradient_level_color_op.hh
@@ -76,6 +76,7 @@ public:
   static gfx::GradientLevelColorOp FromInfo(info::InfoGroup& group);
 
 private:
+  void Init();
   mol::Prop::Level level_;
 };
 
diff --git a/modules/gfx/src/color_ops/map_handle_color_op.cc b/modules/gfx/src/color_ops/map_handle_color_op.cc
index c8cf2ebb7a9895187140f314f50c038a13b5eb6d..0bb2fc598d2607408f043ee9cf7f61ee26225dd8 100644
--- a/modules/gfx/src/color_ops/map_handle_color_op.cc
+++ b/modules/gfx/src/color_ops/map_handle_color_op.cc
@@ -26,20 +26,33 @@
 namespace ost { namespace gfx {
 
 MapHandleColorOp::MapHandleColorOp() : GradientColorOp(), mh_(){
-
+  this->Init();
 }
 
 MapHandleColorOp::MapHandleColorOp(const String& selection, const String& property, const gfx::Gradient& gradient, float minv, float maxv, const img::MapHandle& mh) :
-  GradientColorOp(selection, property, gradient, minv, maxv), mh_(mh){ }
+  GradientColorOp(selection, property, gradient, minv, maxv), mh_(mh){
+  this->Init();
+}
 
 MapHandleColorOp::MapHandleColorOp(const String& selection, int mask, const String& property, const gfx::Gradient& gradient, float minv, float maxv, const img::MapHandle& mh) :
-  GradientColorOp(selection, mask, property, gradient, minv, maxv), mh_(mh){ }
+  GradientColorOp(selection, mask, property, gradient, minv, maxv), mh_(mh){
+  this->Init();
+}
 
 MapHandleColorOp::MapHandleColorOp(const mol::QueryViewWrapper& query_view, const String& property, const gfx::Gradient& gradient, float minv, float maxv, const img::MapHandle& mh) :
-  GradientColorOp(query_view, property, gradient, minv, maxv), mh_(mh){ }
+  GradientColorOp(query_view, property, gradient, minv, maxv), mh_(mh){
+  this->Init();
+}
 
 MapHandleColorOp::MapHandleColorOp(const mol::QueryViewWrapper& query_view, int mask, const String& property, const gfx::Gradient& gradient, float minv, float maxv, const img::MapHandle& mh) :
-  GradientColorOp(query_view, mask, property, gradient, minv, maxv), mh_(mh){ }
+  GradientColorOp(query_view, mask, property, gradient, minv, maxv), mh_(mh){
+  this->Init();
+}
+
+void MapHandleColorOp::Init()
+{
+  this->SetName("MapHandle gradient");
+}
 
 bool MapHandleColorOp::CanApplyTo(const GfxObjP& obj) const{
   if(dynamic_cast<Entity*>(obj.get())){
@@ -82,14 +95,14 @@ gfx::MapHandleColorOp MapHandleColorOp::FromInfo(info::InfoGroup& group){
   info::InfoGroup super_group = group.GetGroup("GradientColorOp");
   gfx::GradientColorOp gop = GradientColorOp::FromInfo(super_group);
   std::istringstream ss(group.GetTextData());
-  String selection = gop.GetSelection();
+  mol::QueryViewWrapper wrapper(gop.GetSelection(),gop.GetSelectionFlags());
   gfx::Gradient gradient = gop.GetGradient();
   int mask = gop.GetMask();
   String property = gop.GetProperty();
   float minv = gop.GetMinV();
   float maxv = gop.GetMaxV();
   //TODO load map handle
-  return gfx::MapHandleColorOp(selection, mask, property, gradient, minv, maxv, img::MapHandle());
+  return gfx::MapHandleColorOp(wrapper, mask, property, gradient, minv, maxv, img::MapHandle());
 }
 
 }}
diff --git a/modules/gfx/src/color_ops/map_handle_color_op.hh b/modules/gfx/src/color_ops/map_handle_color_op.hh
index 3dd6b302c36f16e6883f0f805ea01d3ff6ed89ac..2340e334318e3c0dca265d46702f75e3d521614d 100644
--- a/modules/gfx/src/color_ops/map_handle_color_op.hh
+++ b/modules/gfx/src/color_ops/map_handle_color_op.hh
@@ -52,6 +52,7 @@ public:
   static gfx::MapHandleColorOp FromInfo(info::InfoGroup& group);
 
 private:
+  void Init();
   img::MapHandle mh_;
 };
 
diff --git a/modules/gfx/src/color_ops/uniform_color_op.cc b/modules/gfx/src/color_ops/uniform_color_op.cc
index 8247fb0d2e3bd6a41a246139f7c26472aad26be0..91f0fb2fb118789a725cd1b9a85cbc9cd4081d95 100644
--- a/modules/gfx/src/color_ops/uniform_color_op.cc
+++ b/modules/gfx/src/color_ops/uniform_color_op.cc
@@ -27,29 +27,36 @@
 namespace ost { namespace gfx {
 
 UniformColorOp::UniformColorOp() : ColorOp(), color_(){
-
+  this->Init();
 }
 
 UniformColorOp::UniformColorOp(const String& selection, 
                                const gfx::Color& color): 
   ColorOp(selection), color_(color){
-
+  this->Init();
 }
 
 UniformColorOp::UniformColorOp(const String& selection, int mask,
                                const gfx::Color& color):
   ColorOp(selection,mask), color_(color){
+  this->Init();
 }
 
 UniformColorOp::UniformColorOp(const mol::QueryViewWrapper& query_view,
                                const gfx::Color& color):
   ColorOp(query_view), color_(color){
-
+  this->Init();
 }
 
 UniformColorOp::UniformColorOp(const mol::QueryViewWrapper& query_view,
                                int mask, const gfx::Color& color):
   ColorOp(query_view,mask), color_(color){
+  this->Init();
+}
+
+void UniformColorOp::Init()
+{
+  this->SetName("Uniform color");
 }
 
 bool UniformColorOp::CanApplyTo(const GfxObjP& obj) const
@@ -97,9 +104,9 @@ gfx::UniformColorOp UniformColorOp::FromInfo(info::InfoGroup& group)
   float r, g, b, a;
   ss >> r >> g >> b >> a;
   Color c = Color(r,g,b,a);
-  String selection = op.GetSelection();
+  mol::QueryViewWrapper wrapper(op.GetSelection(),op.GetSelectionFlags());
   int mask = op.GetMask();
-  return gfx::UniformColorOp(selection,mask,c);
+  return gfx::UniformColorOp(wrapper,mask,c);
 }
 
 }}
diff --git a/modules/gfx/src/color_ops/uniform_color_op.hh b/modules/gfx/src/color_ops/uniform_color_op.hh
index 03e7ccd7f5f4f878b5cef81e7b8beb48bb5adb04..4ebef48bf70f2b656165e29ac3e41a20718efaa7 100644
--- a/modules/gfx/src/color_ops/uniform_color_op.hh
+++ b/modules/gfx/src/color_ops/uniform_color_op.hh
@@ -50,6 +50,7 @@ public:
   virtual void ToInfo(info::InfoGroup& group) const;
   static gfx::UniformColorOp FromInfo(info::InfoGroup& group);
 private:
+  void Init();
   gfx::Color color_;
 };
 
diff --git a/modules/gfx/src/entity.cc b/modules/gfx/src/entity.cc
index 7b816f33c3752fa6a95e6b4287d2d0cbf30030de..475b3b218c9ece756246399c44e9934fbb33a25e 100644
--- a/modules/gfx/src/entity.cc
+++ b/modules/gfx/src/entity.cc
@@ -439,7 +439,8 @@ bool Entity::OnSelect(const geom::Line3& line, geom::Vec3& result,
 
       std::ostringstream os;
       os << GetName() << ": " << sel.GetQualifiedName() << " " 
-         << sel.GetPos();
+         << sel.GetPos() << " (ele=" << sel.GetElement() << ", bfactor=" 
+         << sel.GetBFactor() << ")";
       Scene::Instance().StatusMessage(os.str());
 
       if(!pick_flag) {
@@ -449,13 +450,13 @@ bool Entity::OnSelect(const geom::Line3& line, geom::Vec3& result,
       if(smode==1) {
         AtomView av = sel_.FindAtom(sel.GetHandle());
         if(av.IsValid()) {
-          LOGN_DEBUG("de-selected atom: " << sel);
+          LOG_DEBUG("de-selected atom: " << sel);
           sel_.RemoveAtom(av);
           if(av.GetResidue().GetAtomCount()==0){
             av.GetResidue().GetChain().RemoveResidue(av.GetResidue());
           }
         } else {
-          LOGN_DEBUG("selected atom: " << sel);
+          LOG_DEBUG("selected atom: " << sel);
           sel_.AddAtom(sel.GetHandle());
         }
         result = sel.GetPos();
@@ -463,10 +464,10 @@ bool Entity::OnSelect(const geom::Line3& line, geom::Vec3& result,
         AtomView av=sel_.FindAtom(sel);
         ResidueView rv=sel_.FindResidue(sel.GetResidue());
         if(av.IsValid() && rv.IsValid()) {
-          LOGN_DEBUG("de-selected residue: " << sel.GetResidue());
+          LOG_DEBUG("de-selected residue: " << sel.GetResidue());
           sel_.RemoveResidue(rv);
         } else {
-          LOGN_DEBUG("selected residue: " << sel.GetResidue());
+          LOG_DEBUG("selected residue: " << sel.GetResidue());
           sel_.AddResidue(sel.GetResidue(),ViewAddFlag::INCLUDE_ALL);
         }
         AtomHandle ca=sel.GetHandle().GetResidue().GetCentralAtom();
@@ -478,10 +479,10 @@ bool Entity::OnSelect(const geom::Line3& line, geom::Vec3& result,
         ChainHandle chain=sel.GetHandle().GetResidue().GetChain();
         ChainView cv = sel_.FindChain(chain);
         if(cv.IsValid()) {
-          LOGN_DEBUG("de-selected chain: " << chain);
+          LOG_DEBUG("de-selected chain: " << chain);
           sel_.RemoveChain(cv);
         } else {
-          LOGN_DEBUG("selected chain: " << chain);
+          LOG_DEBUG("selected chain: " << chain);
           sel_.AddChain(chain, ViewAddFlag::INCLUDE_ALL);
         }
         result = geom::Vec3(); // todo calculate center of mass
@@ -497,7 +498,7 @@ bool Entity::OnSelect(const geom::Line3& line, geom::Vec3& result,
     }
   }
   if(sel) {
-    LOGN_MESSAGE("picked " << sel.GetResidue().GetChain().GetName() << " " 
+    LOG_INFO("picked " << sel.GetResidue().GetChain().GetName() << " " 
                  << sel.GetResidue().GetNumber() << " " << sel.GetName());
     return true;
   }
@@ -870,7 +871,7 @@ void Entity::RadiusBy(const String& prop,
         it->rad=clamp(normalize(epm.Get(it->atom), minv, maxv),0.0,1.0)*(rmax-rmin)+rmin;
         max_rad_=std::max(max_rad_,it->rad);
       } catch (std::exception&) {
-        LOGN_DEBUG("property " << prop << " not found");
+        LOG_DEBUG("property " << prop << " not found");
       }
     }
   }
@@ -963,11 +964,13 @@ void Entity::Apply(const gfx::ByElementColorOp& op, bool store)
 
 void Entity::Apply(const gfx::ByChainColorOp& op, bool store)
 {
+  const_cast<gfx::ByChainColorOp&>(op).SetChainCount(this->GetView().GetChainCount());
   if(store){
     ByChainColorOp* op_ptr = new ByChainColorOp(op);
     this->AppendColorOp(op_ptr);
   }
   apply_color_op_to_renderer_list(renderer_.begin(), renderer_.end(), op);
+  const_cast<gfx::ByChainColorOp&>(op).SetChainCount(0);
   FlagRebuild();
 }
 
diff --git a/modules/gfx/src/gfx_node.cc b/modules/gfx/src/gfx_node.cc
index 395658e960b3e6226edbdbfe2e346192d0b4ad4f..d4ba1d11740e626e916a35c2e849fedb304749f0 100644
--- a/modules/gfx/src/gfx_node.cc
+++ b/modules/gfx/src/gfx_node.cc
@@ -16,6 +16,7 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
+#include <boost/bind.hpp>
 #include <ost/dyn_cast.hh>
 #include "gfx_node.hh"
 #include "gfx_object.hh"
@@ -113,6 +114,17 @@ void GfxNode::Remove(GfxObjP obj)
     node_vector_.erase(it);
   }
 }
+using boost::bind;
+void GfxNode::RemoveAll()
+{
+  GfxNodeVector v=node_vector_;
+  node_vector_.clear();
+  for (GfxNodeVector::iterator i=v.begin(), e=v.end(); i!=e; ++i) {
+    if (GfxObjP o=dyn_cast<GfxObj>(*i)) {
+      Scene::Instance().NotifyObservers(bind(&SceneObserver::NodeRemoved, _1, o));
+    }
+  }
+}
 
 void GfxNode::Add(GfxNodeP node)
 {
diff --git a/modules/gfx/src/gfx_node.hh b/modules/gfx/src/gfx_node.hh
index eb4fcc2bb85b8243e87ced85c056c260c0fdb900..4f3ceaf1f9614d3b6532659878d32770ecb47679 100644
--- a/modules/gfx/src/gfx_node.hh
+++ b/modules/gfx/src/gfx_node.hh
@@ -68,6 +68,8 @@ class DLLEXPORT_OST_GFX GfxNode: public boost::enable_shared_from_this<GfxNode>
   // return name
   String GetName() const;
 
+  // remove all child nodes
+  void RemoveAll();
   // change name
   void Rename(const String& name);
 
diff --git a/modules/gfx/src/gfx_object.cc b/modules/gfx/src/gfx_object.cc
index 8e992a0f7d763da5197e4c1f0395aaa24991836a..0451739c2843b91b0f1af335bc587b48cd264c2c 100644
--- a/modules/gfx/src/gfx_object.cc
+++ b/modules/gfx/src/gfx_object.cc
@@ -490,7 +490,7 @@ void GfxObj::OnRenderModeChange()
 
 void GfxObj::PreRenderGL(bool f)
 {
-  LOGN_DUMP("object " << GetName() << ": PreRenderGL()");
+  LOG_DEBUG("object " << GetName() << ": PreRenderGL()");
   CustomPreRenderGL(f);
 }
 
diff --git a/modules/gfx/src/gfx_test_object.cc b/modules/gfx/src/gfx_test_object.cc
index 83ae9b329d38db8f17d534c4b871e65e008f0e64..71bae115a073d9557ca8a51251c7b6b3a87d66f8 100644
--- a/modules/gfx/src/gfx_test_object.cc
+++ b/modules/gfx/src/gfx_test_object.cc
@@ -60,11 +60,12 @@ GfxTestObj::GfxTestObj():
   String ost_root=GetSharedDataPath();
   bf::path ost_root_dir(ost_root);
   bf::path tex_file(ost_root_dir / "textures/test_texture.png");
+
   Texture tex(BitmapImport(tex_file.string(),".png"));
   if(!tex.IsValid()) {
     LOGN_ERROR("error loading " << tex_file.string());
   } else {
-    LOGN_VERBOSE("importing tex with id " << tex_id);
+    LOG_DEBUG("importing tex with id " << tex_id);
     glBindTexture(GL_TEXTURE_2D, tex_id);
     glPixelStorei(GL_UNPACK_ALIGNMENT,1);
     glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_S, GL_REPEAT);
diff --git a/modules/gfx/src/gradient.cc b/modules/gfx/src/gradient.cc
index 7b9566a1bb64d3c18bd13ed8e650e2f645c6cd11..e0b50a92f09e6a92ddf8892c58fbd3de1244e067 100644
--- a/modules/gfx/src/gradient.cc
+++ b/modules/gfx/src/gradient.cc
@@ -23,6 +23,8 @@
 #include <ost/info/info.hh>
 #include <ost/info/info_fw.hh>
 
+#include <ost/gfx/gradient_manager.hh>
+
 namespace ost { namespace gfx {
 
 
@@ -30,6 +32,16 @@ Gradient::Gradient()
 {
 }
 
+Gradient::Gradient(const String& name)
+{
+  Gradient gradient = GradientManager::Instance().GetGradient(name);
+  StopList stops = gradient.GetStops();
+  for(unsigned int i = 0; i < stops.size(); i++){
+    Stop stop = stops[i];
+    this->SetColorAt(stop.t, stop.color);
+  }
+}
+
 void Gradient::SetColorAt(float t, const Color& c)
 {
   std::vector<Stop>::iterator i;
@@ -44,7 +56,7 @@ void Gradient::SetColorAt(float t, const Color& c)
 Color Gradient::GetColorAt(float t) const
 {
   if (stops_.empty())
-    return Color(0.0, 0.0, 0.0, 1.0);
+    throw Error("Can not calculate color with 0 Stops set!");
   
   uint c=0;
   while (t>=stops_[c].t && c<stops_.size()) {
diff --git a/modules/gfx/src/gradient.hh b/modules/gfx/src/gradient.hh
index a27136528fa36cb52bf7a175191151d2fc08fee9..5b28b849b05e81af567bce2232b768f8b619ec62 100644
--- a/modules/gfx/src/gradient.hh
+++ b/modules/gfx/src/gradient.hh
@@ -71,6 +71,9 @@ class DLLEXPORT_OST_GFX Gradient {
 
 public:
   Gradient();
+
+  Gradient(const String& name);
+
   /// \brief get color
   Color GetColorAt(float t) const;
   /// \brief set color
diff --git a/modules/gfx/src/gradient_manager.cc b/modules/gfx/src/gradient_manager.cc
new file mode 100644
index 0000000000000000000000000000000000000000..9b6fb63f75e07f7d77e07fbde670251e3e717caa
--- /dev/null
+++ b/modules/gfx/src/gradient_manager.cc
@@ -0,0 +1,91 @@
+// Copyright (C) 2008-2010 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+//------------------------------------------------------------------------------
+/*
+  Author: Stefan Scheuber
+*/
+#include "boost/filesystem/operations.hpp"
+
+#include <ost/platform.hh>
+
+#include <ost/info/info.hh>
+
+#include "gradient_manager.hh"
+
+namespace ost { namespace gfx {
+
+String STORED_GRADIENT_PATH = "/scene/gradients.xml";
+
+GradientManager& GradientManager::Instance()
+{
+  static GradientManager inst;
+  return inst;
+}
+
+GradientManager::GradientManager()
+{
+  String path = GetSharedDataPath()+STORED_GRADIENT_PATH;
+  if(boost::filesystem::exists(path)){
+    info::InfoHandle info_handler = info::LoadInfo(path);
+    if(info_handler.HasGroup("Gradients")){
+      info::InfoGroup gradients = info_handler.GetGroup("Gradients");
+      info::InfoGroupList list = gradients.GetGroups("Gradient");
+      for(unsigned int i = 0; i< list.size();i++){
+        info::InfoGroup info_gradient = list[i];
+        String name = info_gradient.GetAttribute("Name");
+        Gradient gradient = Gradient::GradientFromInfo(info_gradient);
+        this->SetGradient(name,gradient);
+      }
+    }
+  }
+}
+
+GradientManager::~GradientManager()
+{
+
+}
+
+const std::vector<String> GradientManager::GetGradientNames() const
+{
+  std::vector<String> keys;
+  for(std::map<String , Gradient>::const_iterator it = gradients_.begin(); it != gradients_.end(); ++it) {
+    keys.push_back(it->first);
+  }
+  return keys;
+}
+
+const Gradient& GradientManager::GetGradient(String name) const
+{
+  std::map<String,Gradient>::const_iterator it=gradients_.find(name);
+  if(gradients_.end() != it){
+    return gradients_[name];
+  }
+  return empty_gradient_;
+}
+
+void GradientManager::SetGradient(String name, Gradient gradient)
+{
+  gradients_[name] = gradient;
+}
+
+void GradientManager::RemoveGradient(String name)
+{
+  std::map<String,Gradient>::const_iterator it=gradients_.find(name);
+  if(gradients_.end() != it){
+    gradients_.erase(name);
+  }
+}
+
+}} //ns
diff --git a/modules/gui/src/query_dialog.hh b/modules/gfx/src/gradient_manager.hh
similarity index 60%
rename from modules/gui/src/query_dialog.hh
rename to modules/gfx/src/gradient_manager.hh
index dc2deb91337e4760770b5e4f17928f37227d2f56..7551570bae93049c36a6d5bf4505ed2eafa07b86 100644
--- a/modules/gui/src/query_dialog.hh
+++ b/modules/gfx/src/gradient_manager.hh
@@ -16,44 +16,41 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#ifndef OST_GUI_QUERY_DIALOG_HH
-#define OST_GUI_QUERY_DIALOG_HH
+#ifndef OST_GFX_GRADIENT_MANAGER_HH
+#define OST_GFX_GRADIENT_MANAGER_HH
 
-/*
-  Author: Marco Biasini
- */
+#include <vector>
+#include <map>
+
+#include <ost/gfx/module_config.hh>
+#include <ost/gfx/gradient.hh>
 
-#include <ost/gui/module_config.hh>
+/*
+  Author: Stefan Scheuber
+*/
 
-#include <QLabel>
-#include <QDialog>
-#include <QTextEdit>
+namespace ost { namespace gfx {
 
-namespace ost { namespace gui {
+class
+//DLLEXPORT_OST_GFX
+GradientManager {
 
-/// \brief dialog to enter query statement
-class DLLEXPORT_OST_GUI QueryDialog : public QDialog {
-  Q_OBJECT  
 public:
-  QueryDialog(QWidget* parent=NULL);
-  QString GetQueryString() const;
+  static GradientManager& Instance();
+  const std::vector<String> GetGradientNames() const;
+  const Gradient& GetGradient(String name) const;
 
-public slots:
-  void OnTextChanged();
+  void SetGradient(String name, Gradient gradient);
+  void RemoveGradient(String name);
 
-protected:
-  virtual void keyPressEvent(QKeyEvent* event);
+  virtual ~GradientManager();
 
 private:
-  
-  void Colorize();
-  QTextEdit*       edit_;
-  QLabel*          status_;
-  QTextCharFormat  default_;
-  QTextCharFormat  error_;
-  bool             flag_set_;
+  GradientManager();
+  mutable std::map<String, Gradient> gradients_;
+  Gradient empty_gradient_;
 };
- 
-}}
 
-#endif
+}} //ns
+
+#endif /* OST_GFX_GRADIENT_MANAGER_HH */
diff --git a/modules/gfx/src/impl/cgl_offscreen_buffer.cc b/modules/gfx/src/impl/cgl_offscreen_buffer.cc
index 2fc1cd9d1f22d686fe385c97bbeb3c9a86838afd..ea5e3599b0c120240e369ecf5d20f7bfd976d56e 100644
--- a/modules/gfx/src/impl/cgl_offscreen_buffer.cc
+++ b/modules/gfx/src/impl/cgl_offscreen_buffer.cc
@@ -42,7 +42,7 @@ OffscreenBuffer::OffscreenBuffer(unsigned int width, unsigned int height,
   GLint npix=0;
   CGLError err=CGLChoosePixelFormat(attributes, &pix_format_, &npix);
   if(err) {
-    LOGN_ERROR("error creating offscreen rendering context. "
+    LOG_ERROR("error creating offscreen rendering context. "
                "CGLChoosePixFormat failed:" << CGLErrorString(err));
     return;
   }
@@ -54,14 +54,14 @@ OffscreenBuffer::OffscreenBuffer(unsigned int width, unsigned int height,
     err=CGLCreateContext(pix_format_, NULL, &context_);
   }
   if(err) {
-    LOGN_ERROR("error creating offscreen rendering context. "
+    LOG_ERROR("error creating offscreen rendering context. "
                "CGLCreateContext failed" << CGLErrorString(err));
     return;
   }
   err=CGLCreatePBuffer(width, height, GL_TEXTURE_RECTANGLE_EXT, GL_RGBA, 0, 
                        &pbuffer_);
   if (err) {
-    LOGN_ERROR("error creating offscreen rendering context. "
+    LOG_ERROR("error creating offscreen rendering context. "
                "CGLCreatePBuffer failed: " << CGLErrorString(err));
     return;
   }
@@ -69,7 +69,7 @@ OffscreenBuffer::OffscreenBuffer(unsigned int width, unsigned int height,
   assert(CGLGetVirtualScreen(context_, &screen)==0);  
   err=CGLSetPBuffer(context_, pbuffer_, 0, 0, screen);
   if (err) {
-    LOGN_ERROR("error creating offscreen rendering context. "
+    LOG_ERROR("error creating offscreen rendering context. "
                "CGLSetPBuffer failed: " << CGLErrorString(err));
     return;
   }
@@ -83,7 +83,7 @@ bool OffscreenBuffer::Resize(unsigned int width, unsigned int height)
   CGLError err=CGLCreatePBuffer(width, height, GL_TEXTURE_RECTANGLE_EXT,
                                 GL_RGBA, 0,  &new_pbuffer);
   if (err) {
-    LOGN_ERROR("error resizing offscreen rendering context: "
+    LOG_ERROR("error resizing offscreen rendering context: "
                "CGLCreatePBuffer failed: " << CGLErrorString(err));
     return false;
   }
@@ -95,7 +95,7 @@ bool OffscreenBuffer::Resize(unsigned int width, unsigned int height)
 
   err=CGLSetPBuffer(context_, new_pbuffer, 0, 0, screen);
   if (err) {
-    LOGN_ERROR("error resizing offscreen rendering context. "
+    LOG_ERROR("error resizing offscreen rendering context. "
                "CGLSetPBuffer failed: " << CGLErrorString(err));
     return false;
   }
@@ -112,7 +112,7 @@ bool OffscreenBuffer::MakeActive()
   if(active_) return true;
 
   if (CGLError err=CGLSetCurrentContext(context_)) {
-    LOGN_ERROR("error switching to offscreen rendering context. "
+    LOG_ERROR("error switching to offscreen rendering context. "
 	       "CGLSetCurrentContext failed: " << CGLErrorString(err));
     return false;
   }
diff --git a/modules/gfx/src/impl/connect_renderer_base.cc b/modules/gfx/src/impl/connect_renderer_base.cc
index bc1dab565c98ebee107ca2787c7b841247d763e8..e54763a161b656d1fab6252bd7e9494c6dcb135b 100644
--- a/modules/gfx/src/impl/connect_renderer_base.cc
+++ b/modules/gfx/src/impl/connect_renderer_base.cc
@@ -137,21 +137,16 @@ inline void apply_color_op(ConnectRendererBase* rend, GfxView* v, T1 get_col, co
     return;
   }
   rend->UpdateViews();
+  mol::EntityView view;
   if(op.IsSelectionOnly()){
-    mol::Query q(op.GetSelection());
-    for (AtomEntryMap::iterator it=v->atom_map.begin();
-         it!=v->atom_map.end();++it) {
-      if (q.IsAtomSelected(it->second.atom)) {
-        it->second.color=get_col.ColorOfAtom(it->second.atom);
-      }
-    }
+    view = rend->GetEffectiveView().Select(op.GetSelection(),op.GetSelectionFlags());
   }
   else{
-    mol::EntityView view = op.GetView();
-    for(AtomEntryMap::iterator it=v->atom_map.begin();it!=v->atom_map.end();++it){
-      if(view.FindAtom(it->second.atom)){
-        it->second.color=get_col.ColorOfAtom(it->second.atom);
-      }
+    view = op.GetView();
+  }
+  for(AtomEntryMap::iterator it=v->atom_map.begin();it!=v->atom_map.end();++it){
+    if(view.FindAtom(it->second.atom)){
+      it->second.color=get_col.ColorOfAtom(it->second.atom);
     }
   }
 };
diff --git a/modules/gfx/src/impl/entity_renderer.hh b/modules/gfx/src/impl/entity_renderer.hh
index c43bd5d3399ae6cf51bf3debe0aad3c623513c64..4b467c011087587a76a2b56343faacd240a527b4 100644
--- a/modules/gfx/src/impl/entity_renderer.hh
+++ b/modules/gfx/src/impl/entity_renderer.hh
@@ -207,17 +207,17 @@ struct UniformGetCol {
 };
 
 struct GradientLevelGetCol {
-  GradientLevelGetCol(const GradientLevelColorOp& op):property_(op.GetProperty()),
+  GradientLevelGetCol(const GradientLevelColorOp& op): property_(op.GetProperty()),
       epm_(property_, op.GetLevel()),
       gradient_(op.GetGradient()),
       minv_(op.GetMinV()),
       maxv_(op.GetMaxV()){}
   Color ColorOfAtom(mol::AtomHandle& atom) const{
     try{
-      float n=Normalize(epm_.Get(atom), minv_, maxv_);
+      float n=Normalize(epm_.Get(atom, minv_), minv_, maxv_);
       return gradient_.GetColorAt(n);
     }catch(std::exception&){
-      LOGN_DEBUG("property " << property_ << " not found");
+      LOG_DEBUG("property " << property_ << " not found");
       return Color();
     }
   }
diff --git a/modules/gfx/src/impl/glx_offscreen_buffer.cc b/modules/gfx/src/impl/glx_offscreen_buffer.cc
index 78fc8cc7a603a1afb4bda93a161d2cd3d6b0df86..12489282e2e069777b70946c399c18f2df8fb864 100644
--- a/modules/gfx/src/impl/glx_offscreen_buffer.cc
+++ b/modules/gfx/src/impl/glx_offscreen_buffer.cc
@@ -30,16 +30,16 @@ namespace ost { namespace gfx {
 OffscreenBuffer::OffscreenBuffer(unsigned int width, unsigned int height, const OffscreenBufferFormat& f, bool shared):
   width_(width), height_(height), valid_(false), active_(false)
 {
-  LOGN_DEBUG("offscreen buffer: checking for DISPLAY");
+  LOG_DEBUG("offscreen buffer: checking for DISPLAY");
   if(getenv("DISPLAY")==NULL) {
-    LOGN_ERROR("error creating offscreen rendering context: missing DISPLAY environment variable");
+    LOG_ERROR("error creating offscreen rendering context: missing DISPLAY environment variable");
     return;
   }
 
-  LOGN_DEBUG("offscreen buffer: XOpenDisplay");
+  LOG_DEBUG("offscreen buffer: XOpenDisplay");
   dpy_ = XOpenDisplay(getenv("DISPLAY"));
   if(dpy_==NULL) {
-    LOGN_ERROR("error creating offscreen rendering context: XOpenDisplay failed");
+    LOG_ERROR("error creating offscreen rendering context: XOpenDisplay failed");
     return;
   }
 
@@ -63,10 +63,10 @@ OffscreenBuffer::OffscreenBuffer(unsigned int width, unsigned int height, const
   attrib_list.push_back(0);
 
   int nelem=0;
-  LOGN_DEBUG("offscreen buffer: glXChooseFBConfig");
+  LOG_DEBUG("offscreen buffer: glXChooseFBConfig");
   fbconfig_ =glXChooseFBConfig(dpy_,0,&attrib_list[0],&nelem);
   if(fbconfig_==0 || nelem==0) {
-    LOGN_ERROR("error creating offscreen rendering context: glXChooseFBConfig failed");
+    LOG_ERROR("error creating offscreen rendering context: glXChooseFBConfig failed");
     return;
   }
 
@@ -77,26 +77,26 @@ OffscreenBuffer::OffscreenBuffer(unsigned int width, unsigned int height, const
   attrib_list.push_back(height_);
   attrib_list.push_back(0);
   
-  LOGN_DEBUG("offscreen buffer: glXCreatePBuffer");
+  LOG_DEBUG("offscreen buffer: glXCreatePBuffer");
   pbuffer_ = glXCreatePbuffer(dpy_, fbconfig_[0], &attrib_list[0]);
   if(!pbuffer_) {
-    LOGN_ERROR("error creating offscreen rendering context: glXCreatePBuffer failed");
+    LOG_ERROR("error creating offscreen rendering context: glXCreatePBuffer failed");
     return;
   }
 
   if(shared) {
-    LOGN_DEBUG("offscreen buffer: glxCreateNewContext(shared=true)");
+    LOG_DEBUG("offscreen buffer: glxCreateNewContext(shared=true)");
     context_ = glXCreateNewContext(dpy_, fbconfig_[0], GLX_RGBA_TYPE, 
 				   glXGetCurrentContext(), True);
   } else {
-    LOGN_DEBUG("offscreen buffer: glxCreateNewContext(shared=false)");
+    LOG_DEBUG("offscreen buffer: glxCreateNewContext(shared=false)");
     context_ = glXCreateNewContext(dpy_, fbconfig_[0], GLX_RGBA_TYPE, 
 				   NULL, True);
     
   }
 
   if(!context_) {
-    LOGN_ERROR("error creating offscreen rendering context: glXCreateNewContext failed");
+    LOG_ERROR("error creating offscreen rendering context: glXCreateNewContext failed");
     glXDestroyPbuffer(dpy_, pbuffer_);
     return;
   }
@@ -126,7 +126,7 @@ bool OffscreenBuffer::Resize(unsigned int width, unsigned int height)
   GLXPbuffer new_pbuffer = glXCreatePbuffer(dpy_, fbconfig_[0], &attrib_list[0]);
 
   if(!new_pbuffer) {
-    LOGN_ERROR("offscreen rendering resize failed to allocate new pbuffer");
+    LOG_ERROR("offscreen rendering resize failed to allocate new pbuffer");
     return false;
   }
   
@@ -134,7 +134,7 @@ bool OffscreenBuffer::Resize(unsigned int width, unsigned int height)
                                                glXGetCurrentContext(), True);
   
   if(!new_context) {
-    LOGN_ERROR("offscreen rendering resize failed to get new context");
+    LOG_ERROR("offscreen rendering resize failed to get new context");
     return false;
   }
 
@@ -155,7 +155,7 @@ bool OffscreenBuffer::MakeActive()
   if(active_) return true;
 
   if(!glXMakeContextCurrent(dpy_, pbuffer_, pbuffer_, context_)) {
-    LOGN_ERROR("error switching to offscreen rendering context: glXMakeContextCurrent failed");
+    LOG_ERROR("error switching to offscreen rendering context: glXMakeContextCurrent failed");
     return false;
   }
   return true;
diff --git a/modules/gfx/src/impl/map_iso_gen.cc b/modules/gfx/src/impl/map_iso_gen.cc
index 06e5fd1e633a59b3b3e7b65ca20c97fb59fce03b..d02ec1c4e88f49efc6491cda6817aad5502adf49 100644
--- a/modules/gfx/src/impl/map_iso_gen.cc
+++ b/modules/gfx/src/impl/map_iso_gen.cc
@@ -189,10 +189,9 @@ void IsosurfaceGenerator::Generate(const img::MapHandle& mh, IndexedVertexArray&
         if(static_cast<float>(rsis->Value(img::Point(us,vs+1,ws+1)))<level) pattern|=1<<5;
         if(static_cast<float>(rsis->Value(img::Point(us+1,vs+1,ws+1)))<level) pattern|=1<<6;
         if(static_cast<float>(rsis->Value(img::Point(us+1,vs,ws+1)))<level) pattern|=1<<7;
-        String msg;
-        std::stringstream msgs(msg);
-        msgs << u << " " << v << " " << w << ": " << pattern << " " << mh.GetReal(img::Point(u,v,w)) << std::endl;
-        LOG_VERBOSE(msgs);
+        
+        LOG_TRACE(u << " " << v << " " << w << ": " << pattern << " " 
+                  << mh.GetReal(img::Point(u,v,w)));
         
         /*
           set up already known vertex-ids from book keeping
diff --git a/modules/gfx/src/impl/simple_renderer.cc b/modules/gfx/src/impl/simple_renderer.cc
index 0d04e47c444ba3c6872a4611f6654f9163fb3185..a6684e5f9fcb7894453fcde0e265c647cbe101d5 100644
--- a/modules/gfx/src/impl/simple_renderer.cc
+++ b/modules/gfx/src/impl/simple_renderer.cc
@@ -80,7 +80,7 @@ geom::Vec3 SimpleRenderer::GetDoubleBondPlane(mol::BondHandle b)
   GetBondPartnerNormal(vec, n, bond_vec, partner2, a1, a2);
   if(n==0) {
     //set vec into x direction if no partners are present
-    vec.SetX(1);
+    vec.x=1;
   }
   vec=geom::Normalize(geom::Cross(vec,bond_vec));
   return vec;
@@ -140,7 +140,7 @@ void SimpleRenderer::PrepareRendering(GfxView& view, IndexedVertexArray& va)
         if(it->bond.GetBondOrder()==2) {
           vec=GetDoubleBondPlane(it->bond);
         } else {
-          vec.SetX(1);
+          vec.x=1;
         }
         Real dbd=options_->GetBondOrderDistance();
         VertexID id00 = va.Add(p0+dbd*vec,geom::Vec3(),it->atom1->color);
diff --git a/modules/gfx/src/impl/trace_renderer_base.cc b/modules/gfx/src/impl/trace_renderer_base.cc
index 8ccf5e26ee514d6a4dae4d54062b94d765e52598..74317a47386708779b383e034ce1cce523eee845 100644
--- a/modules/gfx/src/impl/trace_renderer_base.cc
+++ b/modules/gfx/src/impl/trace_renderer_base.cc
@@ -42,6 +42,7 @@ inline void apply_color_op(TraceRendererBase* rend, BackboneTrace& trace_subset,
 {
   rend->UpdateViews();
   ColorMask mask = op.GetMask();
+  mol::EntityView view;
   if(op.IsSelectionOnly()){
     mol::Query q(op.GetSelection());
     for (int node_list=0; node_list<trace_subset.GetListCount(); ++node_list) {
diff --git a/modules/gfx/src/input.hh b/modules/gfx/src/input.hh
index 0ff9915e163f20cc4820122fe18a0e7c5d88cc05..43c311e34e9506ec0d843593b28dcdc14dbfee23 100644
--- a/modules/gfx/src/input.hh
+++ b/modules/gfx/src/input.hh
@@ -59,7 +59,7 @@ enum TransformTarget {
   TRANSFORM_RIGID,
   TRANSFORM_TORSION,
   TRANSFORM_ANGLE,
-  TRANSFORM_ROTAMER,
+  TRANSFORM_ROTAMER
 };
 
 class DLLEXPORT_OST_GFX InputEvent {
diff --git a/modules/gfx/src/map_iso.cc b/modules/gfx/src/map_iso.cc
index 2c8c96d1e42edc92d328bd1f8ec99d6f54bff9fb..d8d0999e20f07dd82c45fa8b8f66446a0cbea097 100644
--- a/modules/gfx/src/map_iso.cc
+++ b/modules/gfx/src/map_iso.cc
@@ -24,8 +24,8 @@
 #include <ost/profile.hh>
 #include <ost/profile.hh>
 #include <ost/base.hh>
-#include <ost/img/alg/stat.hh>
 #include <ost/img/alg/discrete_shrink.hh>
+#include <ost/img/alg/histogram.hh>
 
 #include "gl_helper.hh"
 #include "glext_include.hh"
@@ -65,6 +65,9 @@ MapIso::MapIso(const String& name, const img::MapHandle& mh, float level):
   downsampled_mh_(),
   mh_(MapIso::DownsampleMap(mh)),
   octree_(mh_),
+  stat_calculated_(false),
+  histogram_calculated_(false),
+  histogram_bin_count_(100),
   level_(level),
   normals_calculated_(false),
   alg_(0),
@@ -95,6 +98,9 @@ MapIso::MapIso(const String& name, const img::MapHandle& mh,
   downsampled_mh_(),
   mh_(MapIso::DownsampleMap(mh)),
   octree_(mh_),
+  stat_calculated_(false),
+  histogram_calculated_(false),
+  histogram_bin_count_(100),
   level_(level),
   normals_calculated_(false),
   alg_(a),
@@ -129,8 +135,8 @@ geom::Vec3 MapIso::GetCenter() const
   geom::Vec3 nrvo = mh_.IndexToCoord(mh_.GetExtent().GetCenter());
   return nrvo;
 }
-  
-void MapIso::OnRenderModeChange()
+
+void MapIso::UpdateRenderParams()
 {
   if(GetRenderMode()==RenderMode::FILL ||
      GetRenderMode()==RenderMode::OUTLINE) {
@@ -153,7 +159,13 @@ void MapIso::OnRenderModeChange()
     va_.SetLineWidth(this->GetLineWidth());
     va_.SetMode(0x2); // only lines
     va_.SetTwoSided(true);
-  }
+  }  
+}
+
+void MapIso::OnRenderModeChange()
+{
+  this->UpdateRenderParams();
+  this->FlagRebuild();
   GfxObj::OnRenderModeChange();
 }
 
@@ -161,9 +173,8 @@ void MapIso::CustomPreRenderGL(bool flag)
 {
   if(flag) {
     Rebuild();
-  } else {
-    //RefreshVA(va_);
   }
+  RefreshVA(va_);
 }
 
 namespace {
@@ -284,7 +295,7 @@ void MapIso::Rebuild()
   va_.CalcNormals(1.0);
   va_.DrawNormals(true);
 #endif  
-  OnRenderModeChange();  
+  this->UpdateRenderParams();  
 }
 
 void MapIso::SetLevel(float l)
@@ -294,6 +305,32 @@ void MapIso::SetLevel(float l)
   Scene::Instance().RequestRedraw();
 }
 
+void MapIso::CalculateStat() const
+{
+  mh_.ApplyIP(stat_);
+  stat_calculated_=true;
+}
+
+void MapIso::CalculateHistogram() const
+{
+  histogram_ = img::alg::HistogramBase(histogram_bin_count_, 
+                                       this->GetMinLevel(), this->GetMaxLevel());
+  mh_.ApplyIP(histogram_);
+  histogram_calculated_=true;
+}
+
+float MapIso::GetMinLevel() const
+{
+  if(!stat_calculated_)CalculateStat();
+  return stat_.GetMinimum();
+}
+
+float MapIso::GetMaxLevel() const
+{
+  if(!stat_calculated_)CalculateStat();
+  return stat_.GetMaximum();
+}
+
 float MapIso::GetLevel() const
 {
   return level_;
@@ -301,9 +338,27 @@ float MapIso::GetLevel() const
 
 float MapIso::GetStdDev() const
 {
-  img::alg::Stat stat;
-  mh_.Apply(stat);
-  return stat.GetStandardDeviation();
+  if(!stat_calculated_)CalculateStat();
+  return stat_.GetStandardDeviation();
+}
+
+void MapIso::SetHistogramBinCount(int count)
+{
+  if (count > 0){
+    histogram_bin_count_ = count;
+    histogram_calculated_ = false;
+  }
+}
+
+int MapIso::GetHistogramBinCount() const
+{
+  return histogram_bin_count_;
+}
+
+std::vector<int> MapIso::GetHistogram() const
+{
+  if(!histogram_calculated_)CalculateHistogram();
+  return histogram_.GetBins();
 }
 
 img::ImageHandle& MapIso::GetMap()
@@ -323,9 +378,8 @@ img::ImageHandle& MapIso::GetDownsampledMap()
 
 float MapIso::GetMean() const
 {
-  img::alg::Stat stat;
-  mh_.Apply(stat);
-  return static_cast<float>(stat.GetMean());
+  if(!stat_calculated_)CalculateStat();
+  return static_cast<float>(stat_.GetMean());
 }
 
 void MapIso::SetNSF(float nsf)
@@ -340,6 +394,8 @@ void MapIso::ShowDownsampledMap()
 {
   if (downsampled_mh_.IsValid()) mh_ = downsampled_mh_;
   MakeOctreeDirty();
+  stat_calculated_ = false;
+  histogram_calculated_ = false;
   Rebuild();
   Scene::Instance().RequestRedraw();
 }
@@ -349,6 +405,8 @@ void MapIso::ShowOriginalMap()
 {
   if (original_mh_.IsValid()) mh_ = original_mh_;
   MakeOctreeDirty();
+  stat_calculated_ = false;
+  histogram_calculated_ = false;
   Rebuild();
   Scene::Instance().RequestRedraw();
 }
@@ -384,7 +442,7 @@ img::ImageHandle MapIso::DownsampleMap(const img::ImageHandle& mh)
   uint downsampling_fact = compute_downsampling_fact(mh);
   img:: ImageHandle ret_mh = mh;
   if (downsampling_fact != 1) {
-    LOG_MESSAGE("Downsampling map for more comfortable visualization")
+    LOG_INFO("Downsampling map for more comfortable visualization")
     img::alg::DiscreteShrink shrink_alg(img::Size(downsampling_fact,downsampling_fact,downsampling_fact));
     ret_mh = mh.Apply(shrink_alg);
   }
diff --git a/modules/gfx/src/map_iso.hh b/modules/gfx/src/map_iso.hh
index 5e45bd82f3881227634b63463c6a8c16253cdfc3..70319e7c7d310790d647d548902f1473da85f521 100644
--- a/modules/gfx/src/map_iso.hh
+++ b/modules/gfx/src/map_iso.hh
@@ -26,6 +26,9 @@
 #include <boost/shared_ptr.hpp>
 
 #include <ost/img/map.hh>
+#include <ost/img/alg/stat.hh>
+#include <ost/img/alg/histogram.hh>
+
 #include <ost/gfx/impl/map_octree.hh>
 #include "gfx_object.hh"
 #include "map_iso_prop.hh"
@@ -72,6 +75,9 @@ public:
   /// Will force rebuild of the vertex buffers/indices
   void SetLevel(float l);
   
+  float GetMinLevel() const;
+  float GetMaxLevel() const;
+
   /// \brief get current isocontouring level
   float GetLevel() const;
 
@@ -81,6 +87,16 @@ public:
   /// \brief get std dev of map.
   float GetStdDev() const;
   
+
+  /// \brief get histogram
+  std::vector<int> GetHistogram() const;
+
+  /// \brief set Histogram bin count
+  void SetHistogramBinCount(int count);
+
+  /// \brief get Histogram bin count
+  int GetHistogramBinCount() const;
+
   /// \brief get the map handle of the currently displayed map
   // The following is a hack. For the DataViewer I need to pass a reference to an ImagHandle
   // that never goes out of scope, so I get a reference from here
@@ -130,25 +146,33 @@ public:
   bool IfOctreeDirty() const;
 
 protected:
+  void UpdateRenderParams();
+  void CalculateStat() const;
+  void CalculateHistogram() const;
   virtual void CustomPreRenderGL(bool flag);
   static img::ImageHandle DownsampleMap(const img::ImageHandle& mh);
 
 private:
-  img::MapHandle   original_mh_;
-  img::MapHandle   downsampled_mh_;
-  img::MapHandle   mh_;
-  impl::MapOctree  octree_;
-  float            level_;
-  bool             normals_calculated_;
-  uint             alg_;
-  float            smoothf_;
-  float            min_;
-  float            max_;
-  float            std_dev_;
-  float            min_max_;
-  bool             debug_octree_;
-  Color            color_; 
-  bool             dirty_octree_;
+  img::MapHandle           original_mh_;
+  img::MapHandle           downsampled_mh_;
+  img::MapHandle           mh_;
+  impl::MapOctree          octree_;
+  mutable img::alg::Stat   stat_;
+  mutable bool             stat_calculated_;
+  mutable img::alg::Histogram   histogram_;
+  mutable bool             histogram_calculated_;
+  int                      histogram_bin_count_;
+  float                    level_;
+  bool                     normals_calculated_;
+  uint                     alg_;
+  float                    smoothf_;
+  float                    min_;
+  float                    max_;
+  float                    std_dev_;
+  float                    min_max_;
+  bool                     debug_octree_;
+  Color                    color_;
+  bool                     dirty_octree_;
 };
 
 }}
diff --git a/modules/gfx/src/offscreen_buffer.cc b/modules/gfx/src/offscreen_buffer.cc
index 278c77bb1fe85f7595716ecacd0d926064e8cdb0..b7b18792800465cefe69f3e96e5a1daac38a14fc 100644
--- a/modules/gfx/src/offscreen_buffer.cc
+++ b/modules/gfx/src/offscreen_buffer.cc
@@ -38,7 +38,7 @@ OffscreenBuffer& OffscreenBuffer::Instance()
 
 bool OffscreenBuffer::Begin() 
 {
-  LOGN_DEBUG("switching to offscreen rendering");
+  LOG_DEBUG("switching to offscreen rendering");
 
   if(active_) return true;
   
@@ -52,7 +52,7 @@ bool OffscreenBuffer::Begin()
     old_dr2_ = glXGetCurrentReadDrawable();
     
     if(!glXMakeContextCurrent(dpy_, pbuffer_, pbuffer_, context_)) {
-      LOGN_ERROR("error switching to offscreen rendering context: glXMakeContextCurrent failed");
+      LOG_ERROR("error switching to offscreen rendering context: glXMakeContextCurrent failed");
       return false;
     }
   }
@@ -62,7 +62,7 @@ bool OffscreenBuffer::Begin()
 
   if(context_ != old_context_) {
     if (CGLError err=CGLSetCurrentContext(context_)) {
-      LOGN_ERROR("error switching to offscreen rendering context. "
+      LOG_ERROR("error switching to offscreen rendering context. "
                  "CGLSetCurrentContext failed: " << CGLErrorString(err));
       return false;
     }
@@ -73,7 +73,7 @@ bool OffscreenBuffer::Begin()
   if(context_ != old_context_) {
     dev_context_=wglGetCurrentDC();
     if (BOOL err=wglMakeCurrent(dev_context_, context_)) {
-      LOGN_ERROR("error switching to offscreen rendering context. "
+      LOG_ERROR("error switching to offscreen rendering context. "
                  "wglMakeCurrent failed: ");
       return false;
     }
@@ -86,7 +86,7 @@ bool OffscreenBuffer::Begin()
 
 bool OffscreenBuffer::End() 
 {
-  LOGN_DEBUG("switching back to normal rendering");
+  LOG_DEBUG("switching back to normal rendering");
 
   if(!active_) return true;
 
@@ -132,7 +132,7 @@ bool OffscreenBuffer::Resize(unsigned int width, unsigned int height)
   GLXPbuffer new_pbuffer = glXCreatePbuffer(dpy_, fbconfig_[0], &attrib_list[0]);
 
   if(!new_pbuffer) {
-    LOGN_ERROR("offscreen rendering resize failed");
+    LOG_ERROR("offscreen rendering resize failed");
     return false;
   }
   
@@ -140,7 +140,7 @@ bool OffscreenBuffer::Resize(unsigned int width, unsigned int height)
                                                glXGetCurrentContext(), True);
   
   if(!new_context) {
-    LOGN_ERROR("offscreen rendering resize failed to get new context");
+    LOG_ERROR("offscreen rendering resize failed to get new context");
     return false;
   }
 
@@ -155,7 +155,7 @@ bool OffscreenBuffer::Resize(unsigned int width, unsigned int height)
   CGLError err=CGLCreatePBuffer(width, height, GL_TEXTURE_RECTANGLE_EXT,
                                 GL_RGBA, 0,  &new_pbuffer);
   if (err) {
-    LOGN_ERROR("error resizing offscreen rendering context: "
+    LOG_ERROR("error resizing offscreen rendering context: "
                "CGLCreatePBuffer failed: " << CGLErrorString(err));
     return false;
   }
@@ -163,7 +163,7 @@ bool OffscreenBuffer::Resize(unsigned int width, unsigned int height)
   assert(CGLGetVirtualScreen(context_, &screen)==0);  
   err=CGLSetPBuffer(context_, new_pbuffer, 0, 0, screen);
   if (err) {
-    LOGN_ERROR("error resizing offscreen rendering context. "
+    LOG_ERROR("error resizing offscreen rendering context. "
                "CGLSetPBuffer failed: " << CGLErrorString(err));
     return false;
   }
@@ -178,27 +178,27 @@ bool OffscreenBuffer::Resize(unsigned int width, unsigned int height)
   new_pbuffer = wglCreatePbufferARB(dev_context_, format, width, height, attribList);
   if (new_pbuffer == NULL) 
   {
-    LOGN_ERROR("Error resizing offscreen rendering context (wglCreatePbufferARB failed)\n");
+    LOG_ERROR("Error resizing offscreen rendering context (wglCreatePbufferARB failed)\n");
     return false;
   }
 
   dev_context_ = wglGetPbufferDCARB(new_pbuffer);
   if (dev_context_ == NULL) 
   {
-    LOGN_ERROR("Unable to retrieve handle to resized pbuffer device context\n");
+    LOG_ERROR("Unable to retrieve handle to resized pbuffer device context\n");
     return false;
   }
 
   context_ = wglCreateContext(dev_context_);
   if (context_ == NULL) 
   {
-    LOGN_ERROR("Unable to create a rendering context for the resized pbuffer\n");
+    LOG_ERROR("Unable to create a rendering context for the resized pbuffer\n");
     return false;
   }
   //
   //if (!wglShareLists(old_context_, context_)) 
   //{
-  //  LOGN_ERROR("Unable to share data between resized rendering contexts\n");
+  //  LOG_ERROR("Unable to share data between resized rendering contexts\n");
   //  return;
   //}
   */
@@ -228,12 +228,12 @@ OffscreenBuffer::OffscreenBuffer(int width, int height, int r_bits,
 #if defined(__linux__)
 
   if(getenv("DISPLAY")==NULL) {
-    LOGN_ERROR("error creating offscreen rendering context: missing DISPLAY environment variable");
+    LOG_ERROR("error creating offscreen rendering context: missing DISPLAY environment variable");
     return;
   }
   dpy_ = XOpenDisplay(getenv("DISPLAY"));
   if(dpy_==NULL) {
-    LOGN_ERROR("error creating offscreen rendering context: XOpenDisplay failed");
+    LOG_ERROR("error creating offscreen rendering context: XOpenDisplay failed");
     return;
   }
 
@@ -259,7 +259,7 @@ OffscreenBuffer::OffscreenBuffer(int width, int height, int r_bits,
   int nelem=0;
   fbconfig_ =glXChooseFBConfig(dpy_,0,&attrib_list[0],&nelem);
   if(fbconfig_==0 || nelem==0) {
-    LOGN_ERROR("error creating offscreen rendering context: glXChooseFBConfig failed");
+    LOG_ERROR("error creating offscreen rendering context: glXChooseFBConfig failed");
     return;
   }
 
@@ -272,14 +272,14 @@ OffscreenBuffer::OffscreenBuffer(int width, int height, int r_bits,
   
   pbuffer_ = glXCreatePbuffer(dpy_, fbconfig_[0], &attrib_list[0]);
   if(!pbuffer_) {
-    LOGN_ERROR("error creating offscreen rendering context: glXCreatePBuffer failed");
+    LOG_ERROR("error creating offscreen rendering context: glXCreatePBuffer failed");
     return;
   }
 
   context_ = glXCreateNewContext(dpy_, fbconfig_[0], GLX_RGBA_TYPE, 
                                  glXGetCurrentContext(), True);
   if(!context_) {
-    LOGN_ERROR("error creating offscreen rendering context: glXCreateNewContext failed");
+    LOG_ERROR("error creating offscreen rendering context: glXCreateNewContext failed");
     return;
   }
 
@@ -294,7 +294,7 @@ OffscreenBuffer::OffscreenBuffer(int width, int height, int r_bits,
   GLint npix=0;
   CGLError err=CGLChoosePixelFormat(attributes, &pix_format_, &npix);
   if(err) {
-    LOGN_ERROR("error creating offscreen rendering context. "
+    LOG_ERROR("error creating offscreen rendering context. "
                "CGLChoosePixFormat failed:" << CGLErrorString(err));
     return;
   }
@@ -302,14 +302,14 @@ OffscreenBuffer::OffscreenBuffer(int width, int height, int r_bits,
   // lists.
   err=CGLCreateContext(pix_format_, CGLGetCurrentContext(), &context_);
   if(err) {
-    LOGN_ERROR("error creating offscreen rendering context. "
+    LOG_ERROR("error creating offscreen rendering context. "
                "CGLCreateContext failed" << CGLErrorString(err));
     return;
   }
   err=CGLCreatePBuffer(width, height, GL_TEXTURE_RECTANGLE_EXT, GL_RGBA, 0, 
                        &pbuffer_);
   if (err) {
-    LOGN_ERROR("error creating offscreen rendering context. "
+    LOG_ERROR("error creating offscreen rendering context. "
                "CGLCreatePBuffer failed: " << CGLErrorString(err));
     return;
   }
@@ -317,7 +317,7 @@ OffscreenBuffer::OffscreenBuffer(int width, int height, int r_bits,
   assert(CGLGetVirtualScreen(context_, &screen)==0);  
   err=CGLSetPBuffer(context_, pbuffer_, 0, 0, screen);
   if (err) {
-    LOGN_ERROR("error creating offscreen rendering context. "
+    LOG_ERROR("error creating offscreen rendering context. "
                "CGLSetPBuffer failed: " << CGLErrorString(err));
     return;
   }
@@ -346,7 +346,7 @@ OffscreenBuffer::OffscreenBuffer(int width, int height, int r_bits,
   wglChoosePixelFormatARB(dev_context_, attribList, NULL, 1, &format, &nformats);
   if (nformats == 0)
   {
-    LOGN_ERROR("Unable to find any RGBA32 floating point pixel formats\n");
+    LOG_ERROR("Unable to find any RGBA32 floating point pixel formats\n");
     return;
   }
 
@@ -366,27 +366,27 @@ OffscreenBuffer::OffscreenBuffer(int width, int height, int r_bits,
   pbuffer_ = wglCreatePbufferARB(dev_context_, format, width, height, attribs);
   if (pbuffer_ == NULL) 
   {
-    LOGN_ERROR("Unable to create floating point pbuffer (wglCreatePbufferARB failed)\n");
+    LOG_ERROR("Unable to create floating point pbuffer (wglCreatePbufferARB failed)\n");
     return;
   }
 
   old_dev_context_ = wglGetPbufferDCARB(pbuffer_);
   if (dev_context_ == NULL) 
   {
-    LOGN_ERROR("Unable to retrieve handle to pbuffer device context\n");
+    LOG_ERROR("Unable to retrieve handle to pbuffer device context\n");
     return;
   }
 
   context_ = wglCreateContext(dev_context_);
   if (context_ == NULL) 
   {
-    LOGN_ERROR("Unable to create a rendering context for the pbuffer\n");
+    LOG_ERROR("Unable to create a rendering context for the pbuffer\n");
     return;
   }
   
   if (!wglShareLists(old_context_, context_)) 
   {
-    LOGN_ERROR("Unable to share data between rendering contexts\n");
+    LOG_ERROR("Unable to share data between rendering contexts\n");
     return;
   }
 */
diff --git a/modules/gfx/src/render_options/custom_render_options.cc b/modules/gfx/src/render_options/custom_render_options.cc
index 8d121ca9d5948c6317587247a818094fd349c6da..eb4f62a43957d83045f1155939fb4e0758a2504c 100644
--- a/modules/gfx/src/render_options/custom_render_options.cc
+++ b/modules/gfx/src/render_options/custom_render_options.cc
@@ -46,6 +46,8 @@ void CustomRenderOptions::ApplyRenderOptions(RenderOptionsPtr render_options){
 
   sphere_detail_=options->GetSphereDetail();
   arc_detail_=options->GetArcDetail();
+  sphere_rad_=options->GetSphereRad();
+  bond_rad_=options->GetBondRad();
   this->NotifyStateChange();
 }
 
diff --git a/modules/gfx/src/scene.cc b/modules/gfx/src/scene.cc
index b2fbd79d54eb53c6dfefdf80fc8f0942fcac5938..8fc5eacfbf0fb4c909ee377200029da796ed2b76 100644
--- a/modules/gfx/src/scene.cc
+++ b/modules/gfx/src/scene.cc
@@ -643,21 +643,16 @@ void Scene::RenderGL()
 
 void Scene::Register(GLWinBase* win)
 {
-  LOG_DEBUG("scene: registered win @" << win << std::endl);
+  LOG_DEBUG("scene: registered win @" << win);
   win_=win;
 }
 
 void Scene::Unregister(GLWinBase* win)
 {
-  LOG_DEBUG("scene: unregistered win @" << win << std::endl);
+  LOG_DEBUG("scene: unregistered win @" << win);
   win_=0;
 }
 
-template <typename ACTION>
-void Scene::NotifyObservers(const ACTION& action) {
-  std::for_each(observers_.begin(), observers_.end(), action);
-}
-
 namespace {
   struct FindNode: public GfxNodeVisitor {
     FindNode(const String& n): nam(n), node() {}
@@ -776,7 +771,7 @@ bool Scene::IsNameAvailable(String name)
   FindNode fn(name);
   Apply(fn);
   if(fn.node) {
-    LOGN_MESSAGE(name << " already exists as a scene node");
+    LOG_INFO(name << " already exists as a scene node");
     return false;
   }
   return true;
@@ -826,6 +821,12 @@ void Scene::Remove(const GfxNodeP& go)
   this->NotifyObservers(bind(&SceneObserver::NodeRemoved, _1,go));
 }
 
+void Scene::RemoveAll()
+{
+  root_node_->RemoveAll();
+  this->RequestRedraw();
+}
+
 void Scene::Remove(const String& name)
 {
   FindNode fn(name);
@@ -858,19 +859,27 @@ GfxObjP Scene::operator[](const String& name)
   FindNode fn(name);
   Apply(fn);
   if(!fn.node) {
-    LOGN_ERROR("error: " << name << " not found");
+    LOG_ERROR("error: " << name << " not found");
     return GfxObjP();
   }
   GfxObjP nrvo = dyn_cast<GfxObj>(fn.node);
   if(!nrvo) {
-    LOGN_ERROR("error: " << name << " points to invalid entry");
+    LOG_ERROR("error: " << name << " points to invalid entry");
   }
   return nrvo;
 }
 
+bool Scene::HasNode(const String& name) const
+{
+  FindNode fn(name);
+  this->Apply(fn);
+  return fn.node;
+}
+
 void Scene::Apply(const InputEvent& e, bool request_redraw)
 {
-  LOG_TRACE("Scene: received input: c=" << e.GetCommand() << " i=" << e.GetIndex() << " t=" << e.GetTarget() << std::endl);
+  LOG_TRACE("Scene: received input: c=" << e.GetCommand() 
+             << " i=" << e.GetIndex() << " t=" << e.GetTarget());
   /*
     TODO
     distribute event to transform that
@@ -973,7 +982,7 @@ void Scene::Pick(int mx, int my, int mask)
   Vec3 v1=UnProject(Vec3(mx,my,0.0));
   Vec3 v2=UnProject(Vec3(mx,my,1.0));
 
-  LOG_DUMP("Scene pick: " << v1 << " " << v2 << " " << mask << std::endl);
+  LOG_DEBUG("Scene pick: " << v1 << " " << v2 << " " << mask);
 
   Scene::Instance().StatusMessage("");
 
@@ -1421,12 +1430,12 @@ void Scene::Export(const String& fname, unsigned int width,
 {
   int d_index=fname.rfind('.');
   if (d_index==-1) {
-    LOGN_ERROR("no file extension specified");
+    LOG_ERROR("no file extension specified");
     return;
   }
   String ext = fname.substr(d_index);
   if(!(ext==".png")) {
-    LOGN_ERROR("unknown file format (" << ext << ")");
+    LOG_ERROR("unknown file format (" << ext << ")");
     return;
   }
 
@@ -1476,12 +1485,12 @@ void Scene::Export(const String& fname, bool transparent)
   }
   int d_index=fname.rfind('.');
   if (d_index==-1) {
-    LOGN_ERROR("no file extension specified");
+    LOG_ERROR("no file extension specified");
     return;
   }
   String ext = fname.substr(d_index);
   if(ext!=".png") {
-    LOGN_ERROR("unknown file format (" << ext << ")");
+    LOG_ERROR("unknown file format (" << ext << ")");
     return;
   }
   GLint vp[4];
@@ -1527,7 +1536,7 @@ void Scene::ExportPov(const std::string& fname, const std::string& wdir)
 
 void Scene::ResetProjection()
 {
-  LOGN_TRACE("scene: projection matrix " << fov_ << " " << znear_ << " " << zfar_);
+  LOG_TRACE("scene: projection matrix " << fov_ << " " << znear_ << " " << zfar_);
   stereo_projection(stereo_eye_);
 }
 
@@ -1709,7 +1718,7 @@ void Scene::prep_glyphs()
   Bitmap bm = BitmapImport(tex_file.string(),".png");
   if(!bm.data) return;
 
-  LOGN_DEBUG("importing glyph tex with id " << glyph_tex_id_);
+  LOG_DEBUG("importing glyph tex with id " << glyph_tex_id_);
   glBindTexture(GL_TEXTURE_2D, glyph_tex_id_);
   glPixelStorei(GL_UNPACK_ALIGNMENT,1);
   glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_S, GL_CLAMP);
@@ -1723,7 +1732,7 @@ void Scene::prep_glyphs()
   } else if(bm.channels==4) {
     glTexImage2D(GL_TEXTURE_2D,0,GL_INTENSITY,bm.width,bm.height,0,GL_RGBA,GL_UNSIGNED_BYTE,bm.data.get());
   } else {
-    LOGN_ERROR("unsupported glyph texture channel count of " << bm.channels);
+    LOG_ERROR("unsupported glyph texture channel count of " << bm.channels);
     return;
   }
   float ir = 1.0/8.0;
@@ -1737,7 +1746,7 @@ void Scene::prep_glyphs()
   }
   for(int cc=128;cc<256;++cc) glyph_map_[cc]=Vec2(0.0,0.0);
 
-  LOGN_DEBUG("done loading glyphs");
+  LOG_VERBOSE("done loading glyphs");
 }
 
 void Scene::prep_blur()
diff --git a/modules/gfx/src/scene.hh b/modules/gfx/src/scene.hh
index 8f1b3b9c2f90557ed1e5e871e6c937b32ca519ea..ec4c0e13745832a3117d050899bb518da29c6739 100644
--- a/modules/gfx/src/scene.hh
+++ b/modules/gfx/src/scene.hh
@@ -315,6 +315,10 @@ class DLLEXPORT_OST_GFX Scene {
   void Remove(const GfxNodeP& go);
   /// remove graphical object from the scene
   void Remove(const String& name);
+  
+  /// \brief remove all objects from the scene
+  void RemoveAll();
+  
   /// \brief rename an existing graphical object
   /// defunct for now
   bool Rename(const String& old_name, const String& new_name);
@@ -322,6 +326,9 @@ class DLLEXPORT_OST_GFX Scene {
   /// \brief retrieve gfx object by name
   GfxObjP operator[](const String& name);
 
+  /// \brief whether the scene contains a node of the given name
+  bool HasNode(const String& name) const;
+  
   /// \brief actual event handling for scene (internal use)
   void Apply(const InputEvent& ie, bool request_redraw=true);
 
@@ -394,8 +401,11 @@ protected:
   void RenderModeChanged(const String& name);
 
 private:  
+
   template <typename ACTION>
-  void NotifyObservers(const ACTION& action);  
+  void NotifyObservers(const ACTION& action) {
+    std::for_each(observers_.begin(), observers_.end(), action);
+  }
   Scene();
   Scene(const Scene&) {}
   Scene& operator=(const Scene&) {return *this;}
diff --git a/modules/gfx/src/shader.cc b/modules/gfx/src/shader.cc
index e95bdf25bc34cf1f53a475b956bd4444e66b8cc2..73a7eb38530636440e3d4a5415f36c2b05f486be 100644
--- a/modules/gfx/src/shader.cc
+++ b/modules/gfx/src/shader.cc
@@ -61,7 +61,7 @@ void Shader::PreGLInit()
 #if !defined(__APPLE__)
   GLenum err = glewInit();
   if (GLEW_OK != err) {
-    LOGN_ERROR("glew failure: " << glewGetErrorString(err));
+    LOG_ERROR("glew failure: " << glewGetErrorString(err));
     assert(false);
   }
 #endif
@@ -79,13 +79,13 @@ bool Shader::Compile(std::string shader_name, std::string shader_code,
   GLint sh_compiled;
   glGetShaderiv(shader_id, GL_COMPILE_STATUS, &sh_compiled);
   if(sh_compiled==GL_TRUE) {
-    LOGN_DEBUG("shader [" << shader_name << "] successfully compiled (" << shader_id << ")");
+    LOG_VERBOSE("shader [" << shader_name << "] successfully compiled (" << shader_id << ")");
   } else {
     GLint sh_log_length;
     glGetShaderiv(shader_id, GL_INFO_LOG_LENGTH, &sh_log_length);
     std::vector<GLchar> sh_log(sh_log_length+1);
     glGetShaderInfoLog(shader_id, sh_log_length, NULL, &sh_log[0]);
-    LOGN_VERBOSE("shader [" << shader_name << "] compilation failed:" << std::endl << String(&sh_log[0]));
+    LOG_ERROR("shader [" << shader_name << "] compilation failed:" << std::endl << String(&sh_log[0]));
     return false;
   }
   return true;
@@ -96,10 +96,10 @@ bool Shader::Link(const std::vector<GLuint>& code_list, std::string pr_name, GLu
   shader_pr = glCreateProgram();
   for(std::vector<GLuint>::const_iterator it=code_list.begin();it!=code_list.end();++it) {
     if(*it == 0) {
-      LOGN_DEBUG("skipping shader [" << pr_name << "] due to missing compiled code");
+      LOG_WARNING("skipping shader [" << pr_name << "] due to missing compiled code");
       return false;
     }
-    LOGN_DEBUG("attaching compiled shader id " << *it << " to " << shader_pr);
+    LOG_VERBOSE("attaching compiled shader id " << *it << " to " << shader_pr);
     glAttachShader(shader_pr,*it);
   }
     
@@ -107,13 +107,13 @@ bool Shader::Link(const std::vector<GLuint>& code_list, std::string pr_name, GLu
   GLint pr_linked;
   glGetProgramiv(shader_pr,GL_LINK_STATUS,&pr_linked);
   if(pr_linked==GL_TRUE) {
-    LOGN_DEBUG("shader [" << pr_name << "] sucessfully linked");
+    LOG_VERBOSE("shader [" << pr_name << "] sucessfully linked");
   } else {
     GLint pr_log_length;
     glGetProgramiv(shader_pr, GL_INFO_LOG_LENGTH, &pr_log_length);
     std::vector<GLchar> pr_log(pr_log_length+1);
     glGetProgramInfoLog(shader_pr, pr_log_length, NULL, &pr_log[0]);
-    LOGN_VERBOSE("shader [" << pr_name << "] linking failed:" << std::endl << String(&pr_log[0]));
+    LOG_ERROR("shader [" << pr_name << "] linking failed:" << std::endl << String(&pr_log[0]));
     return false;
   }
   return true;
@@ -197,7 +197,7 @@ void Shader::Setup()
     bf::path shader_file(shader_dir / shader_name);
 
     if(!bf::exists(shader_file)){
-      LOGN_ERROR("not found: [" << shader_file.string() << "], cannot create shaders");
+      LOG_ERROR("not found: [" << shader_file.string() << "], cannot create shaders");
       continue;
     }
 
@@ -347,7 +347,7 @@ void Shader::Activate(const String& name)
   if(!name.empty()) {
     std::map<String, GLuint>::iterator it = shader_program_map_.find(name);
     if(it!=shader_program_map_.end()) {
-      LOGN_DUMP("switching to shader [" << name << "]");
+      LOG_VERBOSE("switching to shader [" << name << "]");
       glUseProgram(it->second);
       current_program_=it->second;
       current_name_=name;
@@ -356,11 +356,11 @@ void Shader::Activate(const String& name)
       return;
 
     } else {
-      LOGN_MESSAGE("shader program [" << name << "] not present");
+      LOG_WARNING("shader program [" << name << "] not present");
       return;
     }
   }
-  LOGN_DUMP("switching to fixed pipeline");
+  LOG_VERBOSE("switching to fixed pipeline");
   glUseProgram(0);
   current_program_=0;
   current_name_="";
@@ -410,14 +410,14 @@ void Shader::UpdateState()
     // update all settings
     GLint result;
     glGetIntegerv(GL_LIGHTING,&result);
-    LOGN_TRACE("setting lighting flag to " << result);
+    LOG_TRACE("setting lighting flag to " << result);
     glUniform1i(glGetUniformLocation(current_program_,"lighting_flag"),result);
     GLboolean bresult;
     glGetBooleanv(GL_LIGHT_MODEL_TWO_SIDE,&bresult);
-    LOGN_TRACE("setting two_sided flag to " << bresult);
+    LOG_TRACE("setting two_sided flag to " << bresult);
     glUniform1i(glGetUniformLocation(current_program_,"two_sided_flag"),bresult);
     glGetIntegerv(GL_FOG,&result);
-    LOGN_TRACE("setting fog flag to " << result);
+    LOG_TRACE("setting fog flag to " << result);
     glUniform1i(glGetUniformLocation(current_program_,"fog_flag"),result);
     glDisable(GL_COLOR_MATERIAL);
 
diff --git a/modules/gfx/src/vertex_array.cc b/modules/gfx/src/vertex_array.cc
index b47a682a9a8be373d41d61d3a9acf61af5fc12b1..ccd54b63e391c64047d94f270d741f9bd13a94db 100644
--- a/modules/gfx/src/vertex_array.cc
+++ b/modules/gfx/src/vertex_array.cc
@@ -38,7 +38,7 @@
 
 #define VERTEX_ARRAY_CHECK_GL_ERROR(m) \
   if((glerr=glGetError())!=0) {  \
-    LOGN_VERBOSE("Error during va buffer prep: " << m << " : " << gluErrorString(glerr)); \
+    LOG_ERROR("Error during va buffer prep: " << m << " : " << gluErrorString(glerr)); \
     return false; \
   }
 
@@ -159,7 +159,7 @@ unsigned int IndexedVertexArray::GetVertexCount() const
 void IndexedVertexArray::DumpVertices() const
 {
   for(uint i=0;i<entry_list_.size();++i) {
-    LOGN_MESSAGE("id=" << i << " v=" << entry_list_[i].v << " n=" << entry_list_[i].n << " c=" << entry_list_[i].c);
+    LOG_INFO("id=" << i << " v=" << entry_list_[i].v << " n=" << entry_list_[i].n << " c=" << entry_list_[i].c);
   }
 }
 
@@ -390,7 +390,7 @@ void IndexedVertexArray::RenderGL()
   static bool use_buff=false;
   
   if(!initialized_) {
-    LOGN_DUMP("initializing vertex array lists");
+    LOG_DEBUG("initializing vertex array lists");
 #if OST_SHADER_SUPPORT_ENABLED
     if(!Scene::Instance().InOffscreenMode()) {
       glGenBuffers(7,buffer_id_);
@@ -404,7 +404,7 @@ void IndexedVertexArray::RenderGL()
     dirty_=false;
 #if OST_SHADER_SUPPORT_ENABLED
 
-    LOGN_DUMP("checking buffer object availability");
+    LOG_DEBUG("checking buffer object availability");
     if(mode_&0x2 && aalines_flag_) {
       use_buff=false;
     } else {
@@ -415,7 +415,7 @@ void IndexedVertexArray::RenderGL()
       glBindBuffer(GL_ARRAY_BUFFER,0);
       glBindBuffer(GL_ELEMENT_ARRAY_BUFFER,0);
     } else {
-      LOGN_DUMP("using buffer objects for vertex array");
+      LOG_DEBUG("using buffer objects for vertex array");
     }
 #endif
   }
@@ -424,7 +424,7 @@ void IndexedVertexArray::RenderGL()
   glPushClientAttrib(GL_CLIENT_VERTEX_ARRAY_BIT);
 
   if(outline_mode_>0) {
-    LOGN_TRACE("outline rendering");
+    LOG_TRACE("outline rendering");
     if(outline_mat_update_) {
       glNewList(outline_mat_dlist_,GL_COMPILE);
       outline_mat_.RenderGL();
@@ -730,7 +730,7 @@ void IndexedVertexArray::CalcNormals(float smoothf)
 
 void IndexedVertexArray::CalcFullNormals() 
 {
-  LOGN_DUMP("calculating normals for vertex array");
+  LOG_DEBUG("calculating normals for vertex array");
   
   // book keeping setup
   static NormalizerTriEntry nte={0,0,0,0,Vec3(),1.0};
@@ -788,7 +788,7 @@ void IndexedVertexArray::CalcFullNormals()
           norm+=nte.norm*nte.weight;
           //norm+=nte.norm*nve.weight;
         } else {
-          LOGN_DUMP("faulty vertex lookup in VA Normalize");
+          LOG_DEBUG("faulty vertex lookup in VA Normalize");
         }
       }
       norm=Normalize(norm);
@@ -1110,9 +1110,9 @@ bool IndexedVertexArray::prep_buff()
     glBindBuffer(GL_ELEMENT_ARRAY_BUFFER, buffer_id_[VA_LINEINDEX_BUFFER]);
     VERTEX_ARRAY_CHECK_GL_ERROR("bind lindex buf");
     glBufferData(GL_ELEMENT_ARRAY_BUFFER, 
-		 sizeof(unsigned int) * line_index_list_.size(),
-		 &line_index_list_[0],
-		 GL_STATIC_DRAW);
+                 sizeof(unsigned int) * line_index_list_.size(),
+                 &line_index_list_[0],
+                 GL_STATIC_DRAW);
     VERTEX_ARRAY_CHECK_GL_ERROR("set lindex buf");
   }
 
@@ -1120,9 +1120,9 @@ bool IndexedVertexArray::prep_buff()
     glBindBuffer(GL_ELEMENT_ARRAY_BUFFER, buffer_id_[VA_TRIINDEX_BUFFER]);
     VERTEX_ARRAY_CHECK_GL_ERROR("bind tindex buf");
     glBufferData(GL_ELEMENT_ARRAY_BUFFER, 
-		 sizeof(unsigned int) * tri_index_list_.size(),
-		 &tri_index_list_[0],
-		 GL_STATIC_DRAW);
+                 sizeof(unsigned int) * tri_index_list_.size(),
+                 &tri_index_list_[0],
+                 GL_STATIC_DRAW);
     VERTEX_ARRAY_CHECK_GL_ERROR("set tindex buf");
   }
 
@@ -1130,9 +1130,9 @@ bool IndexedVertexArray::prep_buff()
     glBindBuffer(GL_ELEMENT_ARRAY_BUFFER, buffer_id_[VA_QUADINDEX_BUFFER]);
     VERTEX_ARRAY_CHECK_GL_ERROR("bind qindex buf");
     glBufferData(GL_ELEMENT_ARRAY_BUFFER, 
-		 sizeof(unsigned int) * quad_index_list_.size(),
-		 &quad_index_list_[0],
-		 GL_STATIC_DRAW);
+                 sizeof(unsigned int) * quad_index_list_.size(),
+                 &quad_index_list_[0],
+                 GL_STATIC_DRAW);
     VERTEX_ARRAY_CHECK_GL_ERROR("set qindex buf");
   }
 
@@ -1184,19 +1184,19 @@ void IndexedVertexArray::draw_ltq(bool use_buff)
 #endif
   } else {
     
-    LOGN_TRACE("setting up vertex array");
+    LOG_TRACE("setting up vertex array");
     glInterleavedArrays(GetFormat(),sizeof(Entry),&entry_list_[0]);
     
     if(!tri_index_list_.empty() && (mode_ & 0x4)) {
-      LOGN_TRACE("rendering vertex arras tris");
+      LOG_TRACE("rendering vertex arras tris");
       glDrawElements(GL_TRIANGLES,tri_index_list_.size(),GL_UNSIGNED_INT,&tri_index_list_[0]);
     }
     if(!quad_index_list_.empty() && (mode_ & 0x4)) {
-      LOGN_TRACE("rendering vertex arras quads");
+      LOG_TRACE("rendering vertex arras quads");
       glDrawElements(GL_QUADS,quad_index_list_.size(),GL_UNSIGNED_INT,&quad_index_list_[0]);
     }
     if(!line_index_list_.empty() && (mode_ & 0x2)) {
-      LOGN_TRACE("rendering vertex arras lines");
+      LOG_TRACE("rendering vertex arras lines");
       glDrawElements(GL_LINES,line_index_list_.size(),GL_UNSIGNED_INT,&line_index_list_[0]);
     }
   }
@@ -1216,7 +1216,7 @@ void IndexedVertexArray::draw_p(bool use_buff)
     glDrawArrays(GL_POINTS,0,entry_list_.size());
 #endif
   } else {
-    LOGN_TRACE("calling vertex array");
+    LOG_TRACE("calling vertex array");
     glInterleavedArrays(GetFormat(),sizeof(Entry),&entry_list_[0]);
     glDrawArrays(GL_POINTS,0,entry_list_.size());
   }
diff --git a/modules/gfx/tests/CMakeLists.txt b/modules/gfx/tests/CMakeLists.txt
index fe6a3d670aac004534f5c650421273d47930cc3b..eff4ec11fa761b2dab392c8bd06c8e4952c8f249 100644
--- a/modules/gfx/tests/CMakeLists.txt
+++ b/modules/gfx/tests/CMakeLists.txt
@@ -1,5 +1,4 @@
 set(OST_GFX_UNIT_TESTS
-  test_ent_pov_export.cc
   tests.cc
 )
 if (ENABLE_IMG)
diff --git a/modules/gui/doc/gui.rst b/modules/gui/doc/gui.rst
new file mode 100644
index 0000000000000000000000000000000000000000..675bf6b139294abb9507955d9e4b1978ffb075b7
--- /dev/null
+++ b/modules/gui/doc/gui.rst
@@ -0,0 +1,22 @@
+:mod:`~ost.gui` -- Graphical User Interface
+================================================================================
+
+.. module:: ost.gui
+
+The GUI of OpenStructure is designed to be intuitive, flexible and extensible. 
+
+.. image:: images/100622_gui.png
+    :width: 600
+
+All parts of the GUI are exported to Python and can be expanded with 
+C++ Qt widgets as well as with PyQt widgets. Learn more about :doc:`python_cpp`.
+
+.. toctree::
+
+  layout
+  python_cpp
+  scene_win
+  tools
+  python_shell
+  sequence_viewer
+
diff --git a/website/raw/docs/tut/100208_OpenStructure_UI_Colored.png b/modules/gui/doc/images/100208_OpenStructure_UI_Colored.png
similarity index 100%
rename from website/raw/docs/tut/100208_OpenStructure_UI_Colored.png
rename to modules/gui/doc/images/100208_OpenStructure_UI_Colored.png
diff --git a/website/raw/docs/tut/100208_Scene_Win.png b/modules/gui/doc/images/100208_Scene_Win.png
similarity index 100%
rename from website/raw/docs/tut/100208_Scene_Win.png
rename to modules/gui/doc/images/100208_Scene_Win.png
diff --git a/website/raw/docs/tut/100208_Tools.png b/modules/gui/doc/images/100208_Tools.png
similarity index 100%
rename from website/raw/docs/tut/100208_Tools.png
rename to modules/gui/doc/images/100208_Tools.png
diff --git a/website/raw/docs/tut/100210_auto_completion.png b/modules/gui/doc/images/100210_auto_completion.png
similarity index 100%
rename from website/raw/docs/tut/100210_auto_completion.png
rename to modules/gui/doc/images/100210_auto_completion.png
diff --git a/website/raw/docs/tut/100210_multi_line.png b/modules/gui/doc/images/100210_multi_line.png
similarity index 100%
rename from website/raw/docs/tut/100210_multi_line.png
rename to modules/gui/doc/images/100210_multi_line.png
diff --git a/website/raw/docs/tut/100210_path_completion.png b/modules/gui/doc/images/100210_path_completion.png
similarity index 100%
rename from website/raw/docs/tut/100210_path_completion.png
rename to modules/gui/doc/images/100210_path_completion.png
diff --git a/website/raw/docs/tut/100210_single_line.png b/modules/gui/doc/images/100210_single_line.png
similarity index 100%
rename from website/raw/docs/tut/100210_single_line.png
rename to modules/gui/doc/images/100210_single_line.png
diff --git a/modules/gui/doc/images/100614_Inspector_gadget.png b/modules/gui/doc/images/100614_Inspector_gadget.png
new file mode 100644
index 0000000000000000000000000000000000000000..a51df19f08231202b5697e2956c7e27c9db35fd2
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diff --git a/modules/gui/doc/images/100614_context_menu_view.png b/modules/gui/doc/images/100614_context_menu_view.png
new file mode 100644
index 0000000000000000000000000000000000000000..39a95e7c646360b13dfc3d8b133b5e60fc8695e1
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diff --git a/modules/gui/doc/images/100614_entity_context_menu.png b/modules/gui/doc/images/100614_entity_context_menu.png
new file mode 100644
index 0000000000000000000000000000000000000000..edd1884276d890f2733130c7b34098ba37cb2e48
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diff --git a/modules/gui/doc/images/100615_conservation_1.png b/modules/gui/doc/images/100615_conservation_1.png
new file mode 100644
index 0000000000000000000000000000000000000000..3425bc9ec9c839ae00c48008ee64f93aad32acbf
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diff --git a/modules/gui/doc/images/100615_conservation_2.png b/modules/gui/doc/images/100615_conservation_2.png
new file mode 100644
index 0000000000000000000000000000000000000000..62fa128fbe19f06eb79585c163f649948d6f7982
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diff --git a/modules/gui/doc/images/100615_property_type.png b/modules/gui/doc/images/100615_property_type.png
new file mode 100644
index 0000000000000000000000000000000000000000..e29b26d9be74dbca371044c0ccf1857fdf3a5e6c
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diff --git a/modules/gui/doc/images/100615_secondary_structure.png b/modules/gui/doc/images/100615_secondary_structure.png
new file mode 100644
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diff --git a/modules/gui/doc/images/100615_select_display_style.png b/modules/gui/doc/images/100615_select_display_style.png
new file mode 100644
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diff --git a/modules/gui/doc/images/100616_copy_paste.png b/modules/gui/doc/images/100616_copy_paste.png
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diff --git a/modules/gui/doc/layout.rst b/modules/gui/doc/layout.rst
new file mode 100644
index 0000000000000000000000000000000000000000..a36e78e59baf429c75f3a1cb2d6b42619fd3875e
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+++ b/modules/gui/doc/layout.rst
@@ -0,0 +1,328 @@
+Layout
+================================================================================
+.. currentmodule:: ost.gui
+
+Most of the widgets are organized in a big main window which is divided into
+four parts: the :class:`MainArea` and three panels (which are organized by the 
+:class:`PanelManager`) containing one or more smaller widgets:
+
+.. image:: images/100208_OpenStructure_UI_Colored.png
+
+The panels primarily contain widgets interacting with the 3D window.
+
+Drag and Drop support
+--------------------------------------------------------------------------------
+The user interface of OpenStructure supports drag and drop events. Every file
+format that is supported by Openstructure can be opened by dragging and dropping
+it on the main window. When a python script (ending with .py) is being dropped
+on the UI, the script will be executed. For any other file type (for example PDB
+files, images and density maps), OpenStructure will try to load the file and
+display it in the 3D window, in the data viewer for images or in the sequence
+viewer.
+
+Perspective
+--------------------------------------------------------------------------------
+
+.. class:: Perspective
+
+  The perspective manages the layout of the widgets inside the main window.
+  It contains important classes which itself manages again a sub part of the whole layout.
+  You can get the active perspective object from the gosty app:
+
+  .. code-block:: python
+  
+    app=gui.GostyApp.Instance()
+    perspective=app.perspective
+
+  .. method:: GetMainArea()
+  
+    Returns the main area which is used in this perspective.
+    
+    :rtype: :class:`MainArea`
+
+  .. method:: GetMenu(name)
+    
+    Get QMenu that corresponds to the given name.
+    If it does not exist, it will be created and returned.
+    
+    :param name: The name of the menu
+    :type  arg2: :class:`str`
+    :rtype: :class:`QtCore.QMenu`
+
+  .. method:: GetMenuBar()
+  
+    Returns the Menubar of the Application. Can be used to add some menupoints.
+    
+    :rtype: :class:`QtCore.QMenuBar`
+
+  .. method:: GetPanels()
+
+    The PanelManager class organizes all the widgets in the side panels.
+    Returns the PanelManager instance which is used in this perspective.
+
+    :rtype: :class:`PanelManager`
+
+  .. method:: HideAllBars()
+
+     Hides all side bars. Can be used if the MainArea should be expanded to full size.
+  
+  .. method:: StatusMessage(message)
+  
+    Set a status message. This method can also be called from Qt as slot.
+    
+    :param message: The message that will be displayed in the status bar.
+    :type  message: :class:`str`
+
+
+
+
+Main Area
+--------------------------------------------------------------------------------
+Adding an own Widget
+^^^^^^^^^^^^^^^^^^^^
+The :class:`MainArea` is a mdi (multi document interface). Therefore it's
+possible to display multiple widgets in it. The following example demonstrates 
+how to add a  widget to the MDI area:
+
+  .. code-block:: python
+  
+    app=gui.GostyApp.Instance()
+    main_area=app.perspective.main_area
+    label=QtGui.QLabel("Hello World")
+    main_area.AddWidget("The beginning..", label)
+    
+.. class:: MainArea
+
+   It is implemented as a MDI (multi document interface). This allows you to add custom widgets to it.
+
+  .. method:: AddPersistentWidget(title, name, widget [, window_state])
+
+    add a widget whose geometry is preserved across application relaunches.
+    For widgets that are volatile, use :meth:`AddWidget`
+    If tabbed mode is enabled, the widget geometry is ignored.
+
+    :param title: string that is displayed in the gui
+    :type  title: :class:`str`
+    :param name: is the unique name (within the scope of the main area) for the widget that is used to restore and save the widget geometry.
+    :type  name: :class:`str`
+    :param widget: is the widget to be added to the main area
+    :type  widget: :class:`QtCore.QWidget`
+    :param window_state: custom window_state for the widget. See Qt Documentation to learn more about WindowStates.
+    :type  name: :class:`QWindowState`
+
+  .. method:: AddPersistentWidget(title, name, widget, width, height, x, y)
+
+     add a widget whose geometry is preserved across application relaunches
+     For widgets that are volatile, use #AddWidget()
+     If tabbed mode is enabled, the widget geometry is ignored.
+
+    :param title: string that is displayed in the gui
+    :type  title: :class:`str`
+    :param name: is the unique name (within the scope of the main area) for the widget that is used to restore and save the widget geometry.
+    :type  name: :class:`str`
+    :param widget: is the widget to be added to the main area
+    :type  widget: :class:`QtCore.QWidget`
+    :param width: width of the widget inside the mdi
+    :type  width: :class:`int`
+    :param height: height of the widget inside the mdi
+    :type  height: :class:`int`
+    :param x: x position of the widget inside the mdi
+    :type  x: :class:`int`
+    :param y: y position of the widget inside the mdi
+    :type  y: :class:`int`
+
+  .. method:: AddWidget(title, widget)
+  
+    add volatile widget
+  
+    :param title: string that is displayed in the gui
+    :type  title: :class:`str`
+    :param widget: is the widget to be added to the main area
+    :type  widget: :class:`QtCore.QWidget`
+
+  .. method:: ShowSubWindow(widget)
+  
+    display the given widget inside the main area
+    This method can be used to make a widget visible that has been added to the mdi area.
+    This method should only be called if you are sure, that the widget has been added to the main area.
+    Otherwise, there might be an unexpected behavior!
+  
+    :param widget: widget which you want to make visible
+    :type  widget: :class:`QtCore.QWidget`
+
+  
+  .. method:: HideSubWindow(widget)
+  
+    brief hides the given widget inside the main area
+    This method can be used to hide a widget that has been added to this mdi area.
+    This method should only be called if you are sure, that the widget has been added to the main area.
+    Otherwise, there might be an unexpected behavior!
+  
+    :param widget: widget which you want to hide
+    :type  widget: :class:`QtCore.QWidget`
+  
+  .. method:: EnableTabbedMode(tabbed_mode)
+    
+    brief switch between free window and tabbed window mode
+     
+    :param tabbed_mode: whether you want to enable or disable the tabbed mode. Default is True
+    :type  tabbed_mode: :class:`bool`
+  
+Panels
+--------------------------------------------------------------------------------
+
+View Modes
+^^^^^^^^^^
+
+Each side panel can have different view modes. View modes can display the widgets 
+which are held by the Side Panel in a different style. Every panel has the 
+`splitter` and the `tabbed` view mode. The view mode can be changed in the Window 
+menu of the Menubar:
+
+.. image:: images/100622_view_modes.png
+
+Drag and Drop
+^^^^^^^^^^^^^
+
+The widgets which are held by a Side Panel can be moved to an other position in 
+the panel or even to another side panel. The widget can be moved by simply 
+clicking on the border of the widget and drag and drop it to the desired position.
+The drag and drop feature is currently supported by the splitter as well as the tabbed view mode.
+
+Adding a custom Widget
+^^^^^^^^^^^^^^^^^^^^^^
+
+The Left-, Bottom- and Right-Panel are organized by the :class:`PanelManager`. It is only 
+possible to display a widget which is in the widget pool of the PanelManager class. 
+Once a widget is in the pool all the methods of the PanelManager class can be used to 
+display / hide the widget in any position of the panels. OpenStructure remembers 
+the size and location of a Widget. So, OpenStructure should look the same after 
+restarting it.
+
+The following example shows, how to add a PyQt Widget to the widget pool and finally 
+display it in the right side bar:
+
+  .. code-block:: python
+  
+    qwidget = QtGui.QLabel("Test")
+    widget=gui.WrappedWidget(qwidget)
+    panels=gui.GostyApp.Instance().perspective.GetPanels()
+    panels.AddWidgetToPool("Test Label",widget)
+    panels.AddWidget(gui.PanelPosition.RIGHT_PANEL, widget)
+    qwidget.show()
+
+.. class:: PanelManager
+
+  Class which organizes all widgets which are in the side panels
+  This class handles all side bar widgets. It can be used to display, hide or move a widget to a :class:`PanelBar`. There are three Bars (left, bottom, right) which are organized by this class.
+  Whenever a widget is being removed or added it checks first if the widget type is known and if there are available instances.
+  
+  .. method:: AddWidget(pos, widget[, hidden])
+
+    Display a Widget in a PanelBar. 
+    With Method you can add a widget to the given PanelBar. The widget which finally will be added to the gui will be created from the WidgetRegistry.
+    If the WidgetPool does not know the class name of the given widget or if there are no instances left, nothing will happen.
+
+    :param pos: Indicates which PanelBar is affected
+    :type  pos: :data:`PanelPosition`
+    :param widget: the widget will not directly added to the PanelBar. The class_name will be used to identify the widget in the WidgetRegistry which will return a fresh instance of this class.
+    :type  arg3: :class:`int`
+    :param hidden: marks if the class should be displayed in the gui. Default the widget will be shown. By default False is set
+    :type  hidden: bool
+
+  .. method:: AddWidgetByName(pos, class_name, hidden)
+
+    Display a Widget in a PanelBar
+    Same as :meth:`AddWidget`
+
+    :param pos: Indicates which PanelBar is affected
+    :type  pos: :class:`PanelPosition`
+    :param class_name: the class_name of the widget you would like to add.
+    :type  class_name: :class:`str`
+    :param hidden: marks if the class should be displayed in the gui. Default the widget will be shown.
+    :type  hidden: bool
+
+  .. method:: AddWidgetToPool(class_name, limit)
+
+     Add a widget to the widget pool.
+     The widget must already be in the WidgetRegistry.
+     If you are not sure if the Widget is in the WidgetRegistry, use the other `AddWidgetToPool` Method instead.
+
+    :param class_name: class name of class which should be added to the widget pool.
+    :type  class_name: :class:`str`
+    :param limit: amount of parallel instances allowed (-1 if infinite)
+    :type  limit: :class:`int`
+
+  .. method:: AddWidgetToPool(name, widget)
+
+     Add a widget to the widget pool. Same as :meth:`AddWidgetToPool`
+     
+    :param name: Name which is displayed in the gui.
+    :type  name: :class:`str`
+    :param widget: Widget which will be added to the WidgetPool of this class and the WidgetRegistry. 
+    :type  widget: :class:`WrappedWidget`
+
+  .. method:: GetMenu()
+    
+     The GetMenu method returns a QMenu reference, which contains various actions. The action states will be updated automatically.
+     Returns a reference to a QMenu which can be used for example in a QMenuBar
+     
+    :rtype: :class:`QObject`
+
+  .. method:: GetQObject()
+
+    Get the SIP-QObject (QObject), learn more about :doc:`python_cpp`.
+    
+    :rtype: PyQt4.QObject
+
+  .. method:: RemoveWidget(widget)
+
+    Remove a Widget out of a PanelBar
+    The widget will be removed if it is in a PanelBar
+  
+    :param arg2: widget which should be removed
+    :type  arg2: :class:`WrappedWidget`
+
+.. data:: PanelPosition
+ 
+  This enum indicates the Position of the Panel
+
+  * BOTTOM_PANEL
+     The bottom panel  
+  * LEFT_PANEL
+     The left panel
+  * RIGHT_PANEL
+      The right panel
+
+Menubar
+--------------------------------------------------------------------------------
+Adding an new Menupoint
+^^^^^^^^^^^^^^^^^^^^^^^
+It is really straightforward to add a custom menupoint. Since the menubar is 
+exported to Python it is even easier to create such e menupoint. The following example 
+describes how this is done within python and PyQt:
+
+.. code-block:: python
+
+  menu_bar=gui.GostyApp.Instance().perspective.GetMenuBar()
+  test_action = QtGui.QAction('Test Menu Point', menu_bar) 
+  test = menu_bar.addMenu('&Test')
+  test.addAction(test_action)
+
+The MenuBar class is a normal Qt QMenubar (see the Qt Documentation for more information 
+about QMenubar). By getting the Menubar from the perspective, it is automatically 
+converted to a SIP Object which can be used within python.
+
+The Inspector Gadget
+--------------------------------------------------------------------------------
+
+.. currentmodule:: ost.gui
+
+With our Inspector Gadget it is straightforward to modify rendering and coloring
+options of scene objects without using the keyboard:
+ 
+.. image:: images/100614_Inspector_gadget.png
+   
+The render and coloring options affect only the currently selected objects of
+the scene win. The Shortcut `Ctrl+I` toggles the visibility of the inspector.
+ 
\ No newline at end of file
diff --git a/modules/gui/doc/python_cpp.rst b/modules/gui/doc/python_cpp.rst
new file mode 100644
index 0000000000000000000000000000000000000000..9ec7c5f72717881278db000f22bb67e0c5464730
--- /dev/null
+++ b/modules/gui/doc/python_cpp.rst
@@ -0,0 +1,25 @@
+Mixing PyQt and C++ Widgets
+================================================================================
+.. currentmodule:: ost.gui
+
+PyQt4 is a set of python bindings for Qt4. The exposure from C++ to Python is 
+done with SIP, which has a different mechanism than boost::python.
+ 
+To access a exported boost::python Qt-Object from python we provide a method 
+which wraps the Object into a Python SIP Object.
+
+.. code-block:: python
+   
+  seq_viewer = gui.SequenceViewer() # Create SequenceViewer Object
+  qobj = seq_viewer.qobject #Get Python SIP Object
+  print qobj.size()   # Call function on QWidget
+
+The other way around, each boost::python Qt Object accepts python objects as 
+input for Qt Objects. It handles the cast to a C++ Qt Object internally.
+
+.. code-block:: python
+  
+  persp=gui.GostyApp.Instance().perspective
+  test=persp.GetMenu("Test") #Get boost::python qobject
+  test_action = QtGui.QAction('&Test me', test) #Create Python SIP Object 
+  test.addAction(test_action) #Add Action to boost::python object
diff --git a/modules/gui/doc/python_shell.rst b/modules/gui/doc/python_shell.rst
new file mode 100644
index 0000000000000000000000000000000000000000..780bd42bfba20e774da06af7e8356ffb0fc46edd
--- /dev/null
+++ b/modules/gui/doc/python_shell.rst
@@ -0,0 +1,40 @@
+The Python Shell
+================================================================================
+.. currentmodule:: ost.gui
+
+.. class:: PythonShell
+
+OpenStructure has a powerful Python Shell which has some handy features. It is 
+completely integrated into OpenStructure and allows you enter Python code. 
+
+Multi line detection
+--------------------------------------------------------------------------------
+The Python Shell detects automatically if a code block is complete or not. 
+For example a simple print statement in the command line is a complete code 
+block. Therefore the code will be executed after pressing enter:
+ 
+.. image:: images/100210_single_line.png
+
+When a multiline codeblock (like a for loop or an if instruction) is being 
+entered in the command line, the code is not executed until the code block is 
+complete:
+
+.. image:: images/100210_multi_line.png
+ 
+When a code block is not complete, pressing enter appends an empty line at the 
+end of the code block. To execute such a code block, you simply have to press 
+enter twice. 
+
+Auto completion
+--------------------------------------------------------------------------------
+After pressing tab in the Python Shell, it returns you possible extensions 
+to your entered text. This feature can be used for completing variable names 
+or functions:
+  
+.. image:: images/100210_auto_completion.png
+ 
+It is also possible to complete a file system path string. By pressing tab while
+editing a string, the shell displays all file or folders of the given 
+directory: 
+ 
+.. image:: images/100210_path_completion.png
diff --git a/modules/gui/doc/scene_win.rst b/modules/gui/doc/scene_win.rst
new file mode 100644
index 0000000000000000000000000000000000000000..fcb6b9a27cfdea498b0cfa8a16004c573d98ab7f
--- /dev/null
+++ b/modules/gui/doc/scene_win.rst
@@ -0,0 +1,124 @@
+Scene Window
+================================================================================
+.. currentmodule:: ost.gui
+
+The scene win holds a list of all graphical objects currently registered to
+the :class:`gfx.Scene`.
+
+.. image:: images/100208_Scene_Win.png
+
+Every node of the graphical scene tree is shown as a subnode of the scene. It 
+is possible to select one or more objects in the scenewin (`ctrl + <left mouse>`
+). The available actions of the context menu are applied to all currently 
+selected objects.
+
+.. class:: SceneWin
+
+  .. method:: GetContextMenu()
+  
+    Returns the :class:`ContextMenu`-instance.
+     
+    :rtype: ContextMenu
+
+  .. method:: GetQObject()
+
+    Get the SIP-QObject (QWidget), learn more about :doc:`python_cpp`.
+    
+    :rtype: PyQt4.QWidget
+
+  .. method:: Hide()
+  
+    Hide the Widget
+
+  .. method:: Show()
+
+    Shows the Widget
+    
+Context Menu
+--------------------------------------------------------------------------------
+
+The Context Menu of the Scene Window is context sensitive. So, dependent on what
+is selected in the :class:`SceneWin` the context menu changes.
+
+Context menu of an entity
+  .. image:: images/100614_entity_context_menu.png
+ 
+Context menu of an entity view
+  .. image:: images/100614_context_menu_view.png
+  
+It is possible to extend the Context Menu from python, by creating a QAction and 
+add it to the ContextMenu-Class. If you want to display the action only for 
+certain objects / states, you can pass flags which marks when the action should 
+be shown.
+
+  .. code-block:: python
+  
+    cm=gui.GostyApp.Instance().scene_win.GetContextMenu()
+    action = QtGui.QAction("Test single entity", cm.qobject)
+    cm.AddAction(action, gui.ContextActionType.ENTITY | gui.ContextActionType.SINGLE)
+
+.. class:: ContextMenu
+  
+  The ContextMenu is shown whenever the user presses `<right click>` on the :class:`SceneWin` 
+  
+  .. method:: AddAction(action, flags)
+  
+     Adds the given action to the context menu of the scene window. 
+
+     :param action: The Action which should be displayed in the context menu
+    
+     :type  action: :class:`QtCore.QAction`
+     
+     :param flags: Flags that indicates, when the context_menu should be active. The action 
+                   will be shown, when all flags are true.
+    
+     :type  flags: :data:`ContextActionTypes`
+
+
+  .. method:: GetQObject()
+
+    Get the SIP-QObject (QObject), learn more about :doc:`python_cpp`.
+    
+    :rtype: PyQt4.QObject
+
+    
+.. data:: ContextActionType
+ 
+  It is possible to specify flags for new :class:`ContextMenu` actions of the :class:`SceneWin`
+  These flags are used, to specify when the action should be shown on the scene window. The 
+  actions can be combined by `oring` them (|). When flags are combined with an `or`, the 
+  resulting object is a :data:`ContextActionTypes`-object.
+  The following flags are defined by default: 
+
+  * NOT_SCENE
+     All selected objects are not the root node  
+  * GFX_OBJECT
+     All selected objects are :class:`gfx.GfxObj`
+  * ENTITY
+      All selected objects are :class:`gfx.Entity`
+  * MAP
+      All selected objects are :class:`gfx.MapIso`
+  * ENTITY_VIEW
+      All selected objects are parts of the same Entity (either Queries or Views)
+  * CUSTOM_VIEW
+      All selected objects are named views (created by the user)  
+  * NOT_HIDDEN
+      All selected objects are visible (can not be combined with the ENTITY_VIEW flag)
+  * NOT_VISIBLE
+      All selected objects are hidden (can not be combined with the ENTITY_VIEW flag)
+  * SINGLE
+      There is only one selected object in the :class:`SceneWin`
+  * MULTI
+      There are multiple objects selected object in the :class:`SceneWin`
+   
+.. data:: ContextActionTypes
+
+  When multiple :data:`ContextActionType` objects are being combined with an or (|) you will get an 
+  :data:`ContextActionTypes`-Object.
+  
+  .. code-block:: python
+    
+    ctx_act_types = gui.ContextActionType.ENTITY | gui.ContextActionType.SINGLE
+
+  
+  
\ No newline at end of file
diff --git a/modules/gui/doc/sequence_viewer.rst b/modules/gui/doc/sequence_viewer.rst
new file mode 100644
index 0000000000000000000000000000000000000000..8b654a1c7cdd1fe3eb03445f83f63467a8c3b3a4
--- /dev/null
+++ b/modules/gui/doc/sequence_viewer.rst
@@ -0,0 +1,192 @@
+The Sequence Viewer
+================================================================================
+.. currentmodule:: ost.gui
+
+The sequence viewer of OpenStructure can be used to display sequences or
+alignments.
+
+The following example adds an alignment to a sequence viewer and shows it in a 
+new sequence viewer instance:
+
+.. code-block:: python
+  
+  aln=io.LoadAlignment('sh2.aln')
+  v=gui.SequenceViewer()
+  v.AddAlignment(aln)
+  v.Show()
+
+Core Features
+--------------------------------------------------------------------------------
+
+Display styles
+^^^^^^^^^^^^^^
+It is possible to display the data in different ways. To change the display 
+style, click the tool icon of the menubar and select the 
+display style from the list.
+
+  .. image:: images/100615_select_display_style.png
+
+For the moment there are four different display styles:
+
+
+
+  **1. Highlight propteries**
+    
+    .. image:: images/100615_property_type.png
+       :width: 500pt
+    
+    Color groups of amino acids
+  
+    =====  ======  ======  =====  ===  ====  ====
+    grey   orange  yellow  green  red  blue  cyan
+    =====  ======  ======  =====  ===  ====  ====
+    G      F       C       S      K    D     P
+    A      Y       M       T      R    E      
+    V      W                      H    N      
+    L                                  Q      
+    I                                         
+    =====  ======  ======  =====  ===  ====  ====
+
+  
+  **2. Secondary structure**
+  
+    .. image:: images/100615_secondary_structure.png
+       :width: 500pt
+      
+    Display secondary structure information
+    
+    This mode is only available, when a :class:`mol.EntityView` is connected to 
+    the sequence.
+   
+  **3. Highlight conservation 1**
+  
+    .. image:: images/100615_conservation_1.png
+       :width: 500pt
+  
+    Display conservation
+     
+    This display style uses the :meth:`seq.alg.Conservation`-Algorithm which calculates
+    the Conservation for each column. This Mode is only available for alignments.
+  
+  **4. Highlight conservation 2**
+  
+    .. image:: images/100615_conservation_2.png
+       :width: 500pt
+      
+    Display conservation
+    
+    This implementation of conservation colors the columns grey, if all amino acids are 
+    from the same type. If all amino acids are from the same group, it colors the column with 
+    a light grey. Otherwise the column is colored white. This Mode is also only available for
+    alignments.
+
+
+Zoom
+^^^^
+
+With the sequence viewer of Openstructure it is possible to zoom in and out `<ctrl + mousewheel>`.
+
+ .. image:: images/100616_zoom_in.png
+ 
+ Zoom in, if you lost your glasses at home 
+ 
+ .. image:: images/100616_zoom_out.png
+ 
+ Zoom out, if you need a better overview of the sequence 
+ 
+Copy and Paste
+^^^^^^^^^^^^^^
+
+It is possible to copy sequence text from the sequence viewer by pressing `<ctrl + c>`. If you paste 
+the text (for example into a text editor), all the gaps will be filled with `-`.
+
+ .. image:: images/100616_copy_paste.png
+
+Search
+^^^^^^
+
+With `<ctrl + f>` you can show or hide the search bar which help you finding parts of a sequence.
+
+ .. image:: images/100617_search_bar.png
+
+.. class:: SequenceViewer
+  
+The SequenceViewer class represents a graphical sequence viewer. To see the sequences of a :class:`gfx.Entity`, you
+can use the :meth:`AddEntity` method. If you want to load an alignment, the :meth:`AddAlignment` method can be used.
+
+  .. method:: AddEntity(entity)
+        
+    Add :class:`gfx.Entity` to SequenceViewer.  
+    
+    :param entity: an entity instance 
+    :type  entity: :class:`gfx.Entity`
+
+  .. method:: RemoveEntity(entity)
+  
+    Remove entity from sequence viewer.
+    
+    :param entity: an entity instance
+    :type  entity: :class:`gfx.Entity`
+
+  .. method:: AddAlignment(alignment)
+        
+    Add :class:`seq.AlignmentHandle` to SequenceViewer.  
+    
+    :param alignment: an alignment instance
+    :type  alignment: :class:`seq.AlignmentHandle`
+
+  .. method:: RemoveAlignment(alignment)
+  
+    Remove alignment from sequence viewer.
+    
+    :param alignment: an alignment instance
+    :type  alignment: :class:`seq.AlignmentHandle`
+    :rtype: None
+
+  .. method:: ChangeDisplayMode(style [, obj : None])
+    
+    Change the display style of all alignments and sequences to the given style. If the obj parameter is given, it 
+    changes only the display style of the given object. 
+
+    If the style is not known, nothing happens
+    
+    See also :meth:`GetDisplayModes`, :meth:`GetCurrentDisplayMode`
+    
+    :param style: The display style
+    :type  style: :class:`string`
+    :param obj: The object you would like to change
+    :type obj: :class:`gfx.Entity`, :class:`seq.AlignmentHandle`
+    
+
+  .. method:: GetCurrentDisplayMode([obj : None])
+    
+    Returns the current display style. If there are objects with different display styles, " " will be returned 
+    otherwise the string of the display style.
+
+    :rtype: str
+    :param obj: The object you would like to get the display style
+    :type obj: :class:`gfx.Entity`, :class:`seq.AlignmentHandle`
+
+  .. method:: GetDisplayModes([obj : None])
+
+    Returns a list with all available display styles. If you pass an object, you will get only the display styles for 
+    the given object.
+
+    :rtype: StringList
+    :param obj: The object you would like to get all display styles
+    :type obj: :class:`gfx.Entity`, :class:`seq.AlignmentHandle`
+
+  .. method:: GetQObject()
+    
+    Get the SIP-QObject (QWidget), learn more about :doc:`python_cpp`.
+    
+    :rtype: PyQt4.QWidget
+
+  .. method:: Hide()
+  
+    Hide the Widget
+
+  .. method:: Show()
+
+    Shows the Widget
+
diff --git a/modules/gui/doc/tools.rst b/modules/gui/doc/tools.rst
new file mode 100644
index 0000000000000000000000000000000000000000..9c0da468bdeea30d310410c5607e223db3aa6877
--- /dev/null
+++ b/modules/gui/doc/tools.rst
@@ -0,0 +1,77 @@
+Tools
+--------------------------------------------------------------------------------
+.. currentmodule:: ost.gui
+
+OpenStructure has several :class:`Tool` which are all listed in the toolbar
+close to the 3D window. A tool is activated upon selecting it in the toolbar.
+Input events are sent to the tool as long as the `Ctrl` key (`Cmd` on Mac) is
+pressed. For example the rigid body manipulator will rotate and shift the
+currently selected nodes in the scene win. Upon releasing `Ctrl`, the events are
+sent to the camera, making it possible to rapidly switch between adjusting the
+viewing angle of the camera and manipulating the position and orientation of
+scene objects.
+ 
+.. image:: images/100208_Tools.png  
+ 
+The example `Write a Tool in Python` demonstrates how to add a simple tool
+(written in python) to OpenStructure.
+
+.. class:: Tool
+
+  Parameters of the tool that are configurable should be implemented using the
+  ToolOptions facility. This automatically takes care of remembering the
+  used options over different sessions (in the future) and creates a widget 
+  to modify these options.
+
+  input_events Input Events
+
+  Tools receive input events when the Control key (Command on MacOS X) is
+  pressed. This includes both keyboard events and mouse events such as mouse
+  move events, clicks and Real clicks.
+
+  Tools only receive mouse move events when one of the mouse buttons is 
+  pressed. 
+
+  .. method:: CanOperateOn(nodes)
+
+    determines if the tool can manipulate a certain :class:`gfx.GfxNode`. 
+    This method is used to enabled/disable certain actions (in the toolbar, for example).
+
+    Return True if the Tool can operate on all GfxNodes which are in the given list. Otherwise False 
+
+    :param nodes: List with :class:`gfx.GfxNode`
+    :type  nodes: :class:`NodePtrList`
+    :rtype: bool
+
+  .. method:: Click(event)
+
+    left mouse click
+
+    :param event: object with the event information
+    :type  arg2: :class:`MouseEvent`
+
+  .. method:: DoubleClick(event)
+    
+    double click
+    
+    :param event: object with the event information
+    :type  event: :class:`MouseEvent`
+
+  .. method:: GetIconPath()
+    
+    Returns the path to an shiny icon. 
+    If no path is given, no icon will be displayed
+    
+    :rtype: :class:`str`
+
+  .. method:: GetName()
+    
+    Returns the name of the Tool which will be displayed in the gui.
+    
+    :rtype: :class:`str`
+
+  .. method:: GetToolOptions()
+
+       
+    :rtype: :class:`ToolOptions`
+
diff --git a/modules/gui/pymod/CMakeLists.txt b/modules/gui/pymod/CMakeLists.txt
index 200515b96aa0b9986eb890f68f03f957b6a1196e..d4661d360c1ba770af5f67e884a4e9c1072f091a 100644
--- a/modules/gui/pymod/CMakeLists.txt
+++ b/modules/gui/pymod/CMakeLists.txt
@@ -1,22 +1,22 @@
 set(OST_GUI_PYMOD_SOURCES
   wrap_gui.cc
   export_alignment_view.cc
+  export_message_widget.cc  
   export_gl_win.cc
-  export_plot.cc
   export_tool.cc
   export_py_shell.cc
   export_gosty.cc
   export_remote_site_loader.cc
   export_scene_win.cc
   export_sequence_viewer.cc
-  export_sequence_viewerV2.cc
   export_perspective.cc
   export_sip_handler.cc
   export_scene_selection.cc
   export_main_area.cc
-  export_panel_bar.cc
+  export_panels.cc
   export_menu_bar.cc
   export_file_loader.cc
+  export_file_viewer.cc
   export_widget.cc
 )
 set(OST_GUI_SCENE_PYMOD_MODULES
@@ -35,6 +35,7 @@ immutable_gradient_info_handler.py
 immutable_preset_info_handler.py
 init_inspector.py
 inspector_widget.py
+map_level_widget.py
 preset.py
 preset_editor_list_model.py
 preset_editor_widget.py
@@ -45,6 +46,7 @@ render_mode_widget.py
 render_op.py
 render_options_widget.py
 scene_observer_impl.py
+scene_selection_helper.py
 simple_widget.py
 sline_widget.py
 toolbar_options_widget.py
@@ -58,11 +60,14 @@ loader_list_model.py
 loader_manager_widget.py
 immutable_loader_info_handler.py
 line_trace_widget.py
+wireframe_widget.py
+query_editor.py
 )
 if (ENABLE_IMG)
   list(APPEND OST_GUI_PYMOD_SOURCES
   export_data_viewer.cc
   export_overlay.cc
+  export_overlay_manager.cc
   )
 endif()
 
@@ -77,14 +82,20 @@ set(OST_GUI_PYMOD_MODULES
   init_context_menu.py
   init_menubar.py
   init_spacenav.py
+  init_splash.py
+)
+
+set(OST_GUI_PYMOD_DNG_MODULES
+  __init__.py
+  termuse.py
 )
 
 pymod(NAME gui CPP ${OST_GUI_PYMOD_SOURCES} 
       PY ${OST_GUI_SCENE_PYMOD_MODULES} IN_DIR scene
+         ${OST_GUI_PYMOD_DNG_MODULES} IN_DIR dng
          ${OST_GUI_PYMOD_MODULES})
 
 set(PRESET_FILES
-  scene/gradients.xml
   scene/presets.xml
   scene/loaders.xml
 )
diff --git a/modules/gui/pymod/__init__.py b/modules/gui/pymod/__init__.py
index 517c21dae855d66bdf7d2ee987ef4877b11177f8..500c31ece281ed8968dc3b5dc34ffcf6f77e580c 100644
--- a/modules/gui/pymod/__init__.py
+++ b/modules/gui/pymod/__init__.py
@@ -17,8 +17,46 @@
 # 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #------------------------------------------------------------------------------
 from _gui import *
+import sip
+
 
 ## \brief Opens a DataViewer 
 # \sa \ref fft_li.py "View Fourier Transform Example" \sa \ref modulate_image.py "Modulate Image Example"
-def CreateDataViewer(ih):
-      return GostyApp.Instance().CreateDataViewer(ih)
\ No newline at end of file
+def _close_event_override_(event):
+  print "close event"
+def _set_data_override_(data):
+  print "set data"
+
+def CreateDataViewer(ih,flag=False):
+      viewer=GostyApp.Instance().CreateDataViewer(ih)
+      if flag:
+        viewer.image_=ih
+        sip_viewer=viewer.qobject
+        sip_viewer.closeEvent=_close_event_override_
+        sip_viewer.setData=_set_data_override_
+      return viewer
+
+def ClearMessageWidget():
+      gosty=GostyApp.Instance()
+      gosty.message_widget.Clear()
+
+
+from PyQt4.QtGui import *
+from ost import gfx
+
+def PickColor(default=gfx.WHITE):
+  """
+  Pops up a color chooser that lets' the user pick a color and returns the 
+  selected color. If the user cancels the color chooser, None is returned.
+  
+  :rtype: :class:`~ost.gfx.Color`
+  """
+  dialog=QColorDialog()
+  qt_color=QColor(int(min(255,default.Red()*256)),
+                  int(min(255,default.Green()*256)),
+                  int(min(255,default.Blue()*256)))
+  qt_color=dialog.getColor(qt_color)
+  if not qt_color.isValid():
+    return None
+  return gfx.Color(qt_color.red()/256.0, qt_color.green()/256.0,
+                   qt_color.blue()/256.0)
\ No newline at end of file
diff --git a/modules/gui/pymod/dng/__init__.py b/modules/gui/pymod/dng/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/modules/gui/pymod/dng/termuse.py b/modules/gui/pymod/dng/termuse.py
new file mode 100644
index 0000000000000000000000000000000000000000..8f90c4c47f785f571771bc9a5e09c913f87b71e0
--- /dev/null
+++ b/modules/gui/pymod/dng/termuse.py
@@ -0,0 +1,71 @@
+from PyQt4.QtGui import *
+from PyQt4.QtCore import *
+from ost.gui import AdminRights
+import ost
+import os
+#from ost.gui import AdminRights
+
+usage='''The DNG application bundle contains two shell commands ('ost' and 'dng') that lets you use the OpenStructure command-line interpreter and dng from the terminal. If you want to use these commands, it is recommended that a symbolic link is created. 
+'''
+class TerminalUsageDialog(QDialog):
+  def __init__(self, parent=None):
+    QDialog.__init__(self, parent)
+    self.setWindowTitle('Enhanced Terminal Usage')
+    self.setFixedSize(QSize(480, 300))
+    l=QVBoxLayout(self)
+    title=QLabel('Enhanced Terminal Usage')
+    font=title.font()
+    font.setPointSize(20)
+    title.setFont(font)
+    l.addWidget(title)
+    text=QLabel(usage)
+    l.addWidget(text)
+    l2=QHBoxLayout()
+    l2.addWidget(QLabel('If you proceed, the link will be created in: '))
+    self.path_combo=QComboBox()
+    self.path_combo.setFixedWidth(150)
+    for path in os.getenv('PATH').split(':'):
+      exp_path=os.path.expanduser(path)
+      if os.path.exists(exp_path) and exp_path.find('DNG.app')==-1:
+        self.path_combo.addItem(path)
+    l2.addWidget(self.path_combo)
+    l.addLayout(l2)
+    l3=QHBoxLayout()
+    ab=QPushButton('Create Link')
+    ab.setDefault(True)
+    cb=QPushButton('Don\'t Create')
+    l3.addStretch(1)
+    l3.addWidget(cb, 0)
+    l3.addWidget(ab, 0)
+    l.addLayout(l3)
+    text.setWordWrap(True)
+    QObject.connect(cb, SIGNAL('clicked()'), self.reject)
+    QObject.connect(ab, SIGNAL('clicked()'), self.accept)    
+  def GetSelectedPath(self):
+    return str(self.path_combo.currentText())
+
+def _CreateLinks(bin_dir, sel_dir):
+  for bin in ('ost', 'dng',):
+    if os.path.exists(os.path.join(sel_dir, bin)):
+      os.unlink(os.path.join(sel_dir, bin))
+    os.system('ln -s "%s" "%s"' % (os.path.join(bin_dir, bin), 
+                                   os.path.join(sel_dir, bin)))
+def InstallTerminalPrograms():
+  """
+  Installs symlinks to the 'ost' and 'dng' command line programs into a 
+  user-specified directory in the path.
+  """  
+  term_use=TerminalUsageDialog()
+  if term_use.exec_():
+    prefix=ost.GetPrefixPath()
+    bin_dir=os.path.join(prefix, 'bin')
+    sel_path=term_use.GetSelectedPath()    
+    if not os.access(sel_path, os.W_OK):
+      admin_rights=AdminRights()
+      if admin_rights.Acquire():
+        for bin in ('ost', 'dng'):
+          admin_rights.CreateLink(os.path.join(bin_dir, bin), 
+                                  os.path.join(sel_path, bin))
+      admin_rights.Release()
+    else:
+      _CreateLinks(bin_dir, sel_path)
diff --git a/modules/gui/pymod/export_file_loader.cc b/modules/gui/pymod/export_file_loader.cc
index 5e006fb2cea35df25a72e46dfe6c2c3850a55216..9853d5bc77184d76f2365469bb3993c8d668f924 100644
--- a/modules/gui/pymod/export_file_loader.cc
+++ b/modules/gui/pymod/export_file_loader.cc
@@ -68,6 +68,8 @@ void export_FileLoader()
     .def("GetSiteLoaderIdents", &LoaderManager::GetSiteLoaderIdents)
     .def("AddRemoteSiteLoader", &add_remote_site_loader)
     .def("RemoveRemoteSiteLoader", &LoaderManager::RemoveRemoteSiteLoader)
+    .def("SetDefaultRemoteSiteIdent", &LoaderManager::SetDefaultRemoteSiteIdent)
+    .def("GetDefaultRemoteSiteIdent", &LoaderManager::GetDefaultRemoteSiteIdent)
   ;
 
   class_<FileLoader, boost::noncopyable>("FileLoader", no_init)
diff --git a/modules/gui/pymod/export_sequence_viewerV2.cc b/modules/gui/pymod/export_file_viewer.cc
similarity index 76%
rename from modules/gui/pymod/export_sequence_viewerV2.cc
rename to modules/gui/pymod/export_file_viewer.cc
index cd010952fb9b6a32a06b85aafbeac16e08ced672..57dd381126f2d8be778b4d342b2036b7930d8de9 100644
--- a/modules/gui/pymod/export_sequence_viewerV2.cc
+++ b/modules/gui/pymod/export_file_viewer.cc
@@ -18,7 +18,7 @@
 //------------------------------------------------------------------------------
 #include <boost/python.hpp>
 
-#include <ost/gui/sequence/sequence_viewer.hh>
+#include <ost/gui/file_viewer.hh>
 
 #include "sip_handler.hh"
 
@@ -27,13 +27,14 @@ using namespace ost;
 using namespace ost::gui;
 
 
-void export_SequenceViewerV2()
+void export_FileViewer()
 {
-  class_<SequenceViewerV2, boost::noncopyable >("SequenceViewerV2",init<>())
-    .def("Show", &SequenceViewerV2::show)
-    .def("Hide", &SequenceViewerV2::hide)
-    .def("GetQObject",&get_py_qobject<SequenceViewerV2>)
-    .add_property("qobject", &get_py_qobject<SequenceViewerV2>)
+  class_<FileViewer, boost::noncopyable >("FileViewer",init<>())
+    .def(init<const QString&, optional<QWidget*> >())
+    .def("Show", &FileViewer::show)
+    .def("Hide", &FileViewer::hide)
+    .def("GetQObject",&get_py_qobject<FileViewer>)
+    .add_property("qobject", &get_py_qobject<FileViewer>)
   ;
 }
 
diff --git a/modules/gui/pymod/export_gosty.cc b/modules/gui/pymod/export_gosty.cc
index ba5d47ea36010ffb498672079e3411d604489e56..152e221104cc55fef419a7d0b881045ef1e4291b 100644
--- a/modules/gui/pymod/export_gosty.cc
+++ b/modules/gui/pymod/export_gosty.cc
@@ -27,7 +27,6 @@ using namespace boost::python;
 #include <ost/gui/perspective.hh>
 #include <ost/gui/python_shell/python_shell.hh>
 #include <ost/gui/scene_win/scene_win.hh>
-#include <ost/gui/sequence_viewer/sequence_viewer.hh>
 #include <ost/gui/tools/tool_options_win.hh>
 
 #include "transfer_ownership.hh"
@@ -96,14 +95,14 @@ void export_Gosty()
         return_value_policy<reference_existing_object>())
     .add_property("seq_viewer", make_function(&GostyApp::GetSequenceViewer,
         return_value_policy<reference_existing_object>()))
-    .def("GetSequenceViewerV2", &GostyApp::GetSequenceViewerV2,
-        return_value_policy<reference_existing_object>())
-    .add_property("seq_viewer_v2", make_function(&GostyApp::GetSequenceViewerV2,
-        return_value_policy<reference_existing_object>()))
     .def("GetToolOptionsWin", &GostyApp::GetToolOptionsWin,
         return_value_policy<reference_existing_object>())
     .add_property("tool_options_win", make_function(&GostyApp::GetToolOptionsWin,
         return_value_policy<reference_existing_object>()))
+    .def("GetMessageWidget", &GostyApp::GetMessageWidget,
+        return_value_policy<reference_existing_object>())
+    .add_property("message_widget", make_function(&GostyApp::GetMessageWidget,
+        return_value_policy<reference_existing_object>()))
      #if OST_IMG_ENABLED
     .def("CreateDataViewer", &app_create_data_viewer1,return_value_policy<reference_existing_object>())
     .def("CreateDataViewer", &app_create_data_viewer2,return_value_policy<reference_existing_object>())
diff --git a/modules/gui/pymod/export_main_area.cc b/modules/gui/pymod/export_main_area.cc
index 5a9dfed583e4a7ef237528b4f593d6b9508a0bf3..4e6b793b5f5655b997da9174807ee87b89cd6048 100644
--- a/modules/gui/pymod/export_main_area.cc
+++ b/modules/gui/pymod/export_main_area.cc
@@ -142,6 +142,20 @@ void main_area_hide_sub_window(MainArea* m, const SipHandlerBase& sh)
 
 }
 
+void main_area_show_sub_window_b(MainArea* m, object py_object)
+{
+  if(QWidget* widget = get_cpp_qobject<QWidget>(py_object)){
+    m->ShowSubWindow(widget);
+  }
+}
+
+void main_area_hide_sub_window_b(MainArea* m, object py_object)
+{
+  if(QWidget* widget = get_cpp_qobject<QWidget>(py_object)){
+    m->HideSubWindow(widget);
+  }
+}
+
 void export_MainArea()
 {  
   class_<MainArea, boost::noncopyable>("MainArea", no_init)
@@ -161,8 +175,10 @@ void export_MainArea()
     .def("width", &MainArea::width)
     .def("height", &MainArea::height)
     .def("ShowSubWindow", &MainArea::ShowSubWindow)
-    .def("ShowSubWindow", &main_area_show_sub_window)        
+    .def("ShowSubWindow", &main_area_show_sub_window)
+    .def("ShowSubWindow", &main_area_show_sub_window_b)
     .def("HideSubWindow", &MainArea::HideSubWindow)
+    .def("HideSubWindow", &main_area_hide_sub_window_b)
     .def("HideSubWindow", &main_area_hide_sub_window)            
     .def("EnableTabbedMode", &MainArea::EnableTabbedMode, arg("flag")=true)
     .def("GetQObject",&get_py_qobject<MainArea>)
diff --git a/modules/gui/pymod/export_message_widget.cc b/modules/gui/pymod/export_message_widget.cc
new file mode 100644
index 0000000000000000000000000000000000000000..0a9c2d7dcedcf10d616793f5924ac8a3082824cc
--- /dev/null
+++ b/modules/gui/pymod/export_message_widget.cc
@@ -0,0 +1,75 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+//------------------------------------------------------------------------------
+
+#include <boost/python.hpp>
+#include <vector>
+#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
+
+#include <ost/gui/messages/message_widget.hh>
+
+#include "sip_handler.hh"
+
+using namespace boost::python;
+using namespace ost;
+using namespace ost::gui;
+
+namespace {
+
+void log_message_a(MessageWidget* message_widget, const QString& message, QMessageBox::Icon icon = QMessageBox::Information)
+{
+  message_widget->LogMessage(message,icon);
+}
+
+void log_message_b(MessageWidget * message_widget, object py_object)
+{
+  if(py_object.ptr() != Py_None){
+    if(PyObject_IsInstance(py_object.ptr(), (PyObject*)&PyString_Type)){
+    String message = extract < std::string > (py_object);
+    message_widget->LogMessage(QString(message.c_str()));
+    }
+    else if(QStandardItem* item = get_cpp_qobject<QStandardItem>(py_object)){
+      message_widget->LogMessage(item);
+    }
+  }
+}
+
+}
+
+void export_MessageWidget()
+{
+  enum_<QMessageBox::Icon>("MessageIcon")
+      .value("QUESTION", QMessageBox::Question)
+      .value("INFORMATION", QMessageBox::Information)
+      .value("WARNING", QMessageBox::Warning)
+      .value("CRITICAL", QMessageBox::Critical)
+      .export_values()
+      ;
+
+  class_<MessageWidget, boost::noncopyable>("MessageWidget", no_init)
+     .def("Show", &MessageWidget::show)
+     .def("Hide", &MessageWidget::hide)
+     .def("Clear", &MessageWidget::Clear)
+     .def("RemoveSelected", &MessageWidget::RemoveSelected)
+     .def("LogMessage", &log_message_a)
+     .def("LogMessage", &log_message_b)
+     .def("GetQObject",&get_py_qobject<MessageWidget>)
+     .add_property("qobject", &get_py_qobject<MessageWidget>)
+   ;
+}
+
diff --git a/modules/gui/pymod/export_overlay.cc b/modules/gui/pymod/export_overlay.cc
index d5293ddd01be9df97d9afc52ec3fb0aa4a9c0f45..03131dfcc2880f95584e91ecb9dc72972e931cac 100644
--- a/modules/gui/pymod/export_overlay.cc
+++ b/modules/gui/pymod/export_overlay.cc
@@ -47,7 +47,7 @@ void plo_add2(PointlistOverlay& plo, const PointList& p)
   plo.Add(p);
 }
 
-/*void plo_add3(PointlistOverlay& plo, const Point& p, double scale)
+void plo_add3(PointlistOverlay& plo, const Point& p, double scale)
 {
   plo.Add(p,scale);
 }
@@ -56,7 +56,7 @@ void plo_add4(PointlistOverlay& plo, const PointList& p, double scale)
 {
   plo.Add(p,scale);
 }
-*/
+
 QColor qcolor_from_pyobj(boost::python::object& obj)
 {
 return QColor(boost::python::extract<int>(obj.attr("red")()),
@@ -64,7 +64,7 @@ return QColor(boost::python::extract<int>(obj.attr("red")()),
               boost::python::extract<int>(obj.attr("blue")()));
 }
 
-/*void set_active_color(PointlistOverlayBase& plo,boost::python::object& obj)
+void set_active_color(PointlistOverlayBase& plo,boost::python::object& obj)
 {
   QColor color=qcolor_from_pyobj(obj);
   plo.SetActiveColor(color);
@@ -73,7 +73,7 @@ void set_passive_color(PointlistOverlayBase& plo,boost::python::object& obj)
 {
   QColor color=qcolor_from_pyobj(obj);
   plo.SetPassiveColor(color);
-}*/
+}
 
 }//ns
 
@@ -94,16 +94,16 @@ void export_overlay()
     .def("GetSymbolShape",&PointlistOverlayBase::GetSymbolShape)
     .def("SetCrosshair",&PointlistOverlayBase::SetCrosshair)
     .def("GetCrosshair",&PointlistOverlayBase::GetCrosshair)
-   // .def("SetActiveColor",set_active_color)
-  //  .def("SetPassiveColor",set_passive_color)
+    .def("SetActiveColor",set_active_color)
+    .def("SetPassiveColor",set_passive_color)
     ;
 
   class_<PointlistOverlay,bases<PointlistOverlayBase>,boost::noncopyable>("PointlistOverlay",init<optional<const String&> >())
     .def(init<const PointList&,optional<const String&> >())
     .def("Add",plo_add1)
     .def("Add",plo_add2)
- //   .def("Add",plo_add3)
- //   .def("Add",plo_add4)
+    .def("Add",plo_add3)
+    .def("Add",plo_add4)
     .def("Remove",&PointlistOverlay::Remove)
     .def("Clear",&PointlistOverlay::Clear)
     ;
@@ -118,8 +118,8 @@ void export_overlay()
     .def("ClearMask",&MaskOverlay::ClearMask)
     .def("GetShift",&MaskOverlay::GetShift)
     .def("ClearShift",&MaskOverlay::ClearShift)
-   // .def("SetShift",&MaskOverlay::SetShift)
-   // .def("ApplyShiftToMask",&MaskOverlay::ApplyShiftToMask)
+    .def("SetShift",&MaskOverlay::SetShift)
+    .def("ApplyShiftToMask",&MaskOverlay::ApplyShiftToMask)
     ;
 
 /*  class_<Gauss2DOverlay,bases<Overlay>,boost::noncopyable>("Gauss2DOverlay",init<const alg::ParamsGauss2D&>())
diff --git a/modules/gui/pymod/export_overlay_manager.cc b/modules/gui/pymod/export_overlay_manager.cc
new file mode 100644
index 0000000000000000000000000000000000000000..bd866122419e2243531bab72cf6546edfb718f3b
--- /dev/null
+++ b/modules/gui/pymod/export_overlay_manager.cc
@@ -0,0 +1,56 @@
+/////////////////////////////////////////////////////////
+// IPLT - Image Processing Library & Toolkit
+// Copyright (c) 2003-2007 University of Basel
+//
+// The usage terms and conditions of this software 
+// are governed by the GNU General Public License, 
+// as described in the accompanying text file LICENSE.
+// Please review this information carefully and contact
+// info@iplt.org should questions arise.
+/////////////////////////////////////////////////////////
+
+/*
+  Author: Ansgar Philippsen
+*/
+
+#include <boost/python.hpp>
+
+#include <ost/gui/data_viewer/overlay_manager.hh>
+#include <ost/gui/data_viewer/overlay_base.hh>
+
+
+using namespace boost::python;
+using namespace ost;
+using namespace ost::img;
+using namespace ost::img::gui;
+
+void export_overlay_manager()
+{
+  void (OverlayManager::*ActivateOverlay1)(const String& name) = &OverlayManager::ActivateOverlay;
+  void (OverlayManager::*ActivateOverlay2)(int id) = &OverlayManager::ActivateOverlay;
+  void (OverlayManager::*SetOverlayVisibility1)(const String& name, bool visible) = &OverlayManager::SetOverlayVisibility;
+  void (OverlayManager::*SetOverlayVisibility2)(int id, bool visible ) = &OverlayManager::SetOverlayVisibility;
+  OverlayPtr (OverlayManager::*RetrieveOverlay1)(const String& name) = &OverlayManager::RetrieveOverlay;
+  OverlayPtr (OverlayManager::*RetrieveOverlay2)(int id) = &OverlayManager::RetrieveOverlay;
+  bool (OverlayManager::*IsVisible1)(const String& name) = &OverlayManager::IsVisible;
+  bool (OverlayManager::*IsVisible2)(int id) = &OverlayManager::IsVisible;
+  bool (OverlayManager::*IsActive1)(const String& name) = &OverlayManager::IsActive;
+  bool (OverlayManager::*IsActive2)(int id) = &OverlayManager::IsActive;
+
+  class_<OverlayManager, OverlayManagerPtr, boost::noncopyable>("OverlayManager", no_init)
+    .def("AddOverlay",&OverlayManager::AddOverlay)
+    .def("GetActiveOverlay",&OverlayManager::GetActiveOverlay)
+    .def("ActivateOverlay",ActivateOverlay1)
+    .def("ActivateOverlay",ActivateOverlay2)
+    .def("SetOverlayVisibility",SetOverlayVisibility1)
+    .def("SetOverlayVisibility",SetOverlayVisibility2)
+    .def("RetrieveOverlay",RetrieveOverlay1)
+    .def("RetrieveOverlay",RetrieveOverlay2)
+    .def("IsVisible",IsVisible1)
+    .def("IsVisible",IsVisible2)
+    .def("IsActive",IsActive1)
+    .def("IsActive",IsActive2)
+    .def("GetOverlayName",&OverlayManager::GetOverlayName)
+    .def("GetOverlayId",&OverlayManager::GetOverlayId)
+    ;
+}
diff --git a/modules/gui/pymod/export_panel_bar.cc b/modules/gui/pymod/export_panels.cc
similarity index 74%
rename from modules/gui/pymod/export_panel_bar.cc
rename to modules/gui/pymod/export_panels.cc
index cfac8c128a7b8ea7c5d0a66abb62edaf1df4f144..580f82c5f3a9aff4602a3908dd78dc095a00fd4e 100644
--- a/modules/gui/pymod/export_panel_bar.cc
+++ b/modules/gui/pymod/export_panels.cc
@@ -18,8 +18,8 @@
 //------------------------------------------------------------------------------
 #include <boost/python.hpp>
 
-#include <ost/gui/panel_bar/panels.hh>
-#include <ost/gui/panel_bar/panel_bar.hh>
+#include <ost/gui/panels/panel_manager.hh>
+#include <ost/gui/panels/panel_bar.hh>
 #include "ost/gui/widget.hh"
 
 #include "sip_handler.hh"
@@ -31,69 +31,69 @@ using namespace ost;
 using namespace ost::gui;
 
 namespace{
-void panels_add_widget_a(Panels * panels, PanelPosition pos, const SipHandlerBase& sh, bool hidden=false)
+void panels_add_widget_a(PanelManager * panels, PanelPosition pos, const SipHandlerBase& sh, bool hidden=false)
 {
   if(Widget* widget = reinterpret_cast<Widget*>(sh.GetSipHandle())){
     panels->AddWidget(pos,widget,hidden);
   }
 }
 
-void panels_add_widget_b(Panels * panels, PanelPosition pos, Widget* widget, bool hidden=false)
+void panels_add_widget_b(PanelManager * panels, PanelPosition pos, Widget* widget, bool hidden=false)
 {
   panels->AddWidget(pos,widget,hidden);
 }
 
-void panels_add_widget_c(Panels * panels, PanelPosition pos, object py_object, bool hidden=false)
+void panels_add_widget_c(PanelManager * panels, PanelPosition pos, object py_object, bool hidden=false)
 {
   if(Widget* widget = get_cpp_qobject<Widget>(py_object)){
     panels->AddWidget(pos,widget,hidden);
   }
 }
 
-void panels_remove_widget_a(Panels * panels, Widget* w)
+void panels_remove_widget_a(PanelManager * panels, Widget* w)
 {
   panels->RemoveWidget(w);
 }
 
-void panels_remove_widget_b(Panels * panels, const SipHandlerBase& sh)
+void panels_remove_widget_b(PanelManager * panels, const SipHandlerBase& sh)
 {
   if(Widget* widget = reinterpret_cast<Widget*>(sh.GetSipHandle())){
     panels->RemoveWidget(widget);
   }
 }
 
-void panels_remove_widget_c(Panels * panels, object py_object)
+void panels_remove_widget_c(PanelManager * panels, object py_object)
 {
   if(Widget* widget = get_cpp_qobject<Widget>(py_object)){
     panels->RemoveWidget(widget);
   }
 }
 
-void panels_add_widget_to_pool_a(Panels * panels, const QString& full_name, Widget* widget)
+void panels_add_widget_to_pool_a(PanelManager * panels, const QString& full_name, Widget* widget)
 {
   panels->AddWidgetToPool(full_name,widget);
 }
 
-void panels_add_widget_to_pool_b(Panels * panels, const QString& full_name, const SipHandlerBase& sh)
+void panels_add_widget_to_pool_b(PanelManager * panels, const QString& full_name, const SipHandlerBase& sh)
 {
   if(Widget* widget = reinterpret_cast<Widget*>(sh.GetSipHandle())){
     panels->AddWidgetToPool(full_name,widget);
   }
 }
 
-void panels_add_widget_to_pool_c(Panels * panels, const QString& full_name, object py_object)
+void panels_add_widget_to_pool_c(PanelManager * panels, const QString& full_name, object py_object)
 {
   if(Widget* widget = get_cpp_qobject<Widget>(py_object)){
     panels->AddWidgetToPool(full_name,widget);
   }
 }
 
-void panels_add_widget_to_pool_d(Panels * panels, const QString& name, int limit=-1)
+void panels_add_widget_to_pool_d(PanelManager * panels, const QString& name, int limit=-1)
 {
   panels->AddWidgetToPool(name,limit);
 }
 
-object panels_get_menu(Panels* panels)
+object panels_get_menu(PanelManager* panels)
 {
   return get_py_qobject<QMenu>(panels->GetMenu());
 }
@@ -119,7 +119,7 @@ void panel_bar_add_widget_c(PanelBar * pb, object py_object, bool hidden=false)
 
 }
 
-void export_PanelBar()
+void export_Panels()
 {
   enum_<PanelPosition>("PanelPosition")
       .value("LEFT_PANEL", LEFT_PANEL)
@@ -129,11 +129,11 @@ void export_PanelBar()
       .export_values()
       ;
 
-  class_<Panels, boost::noncopyable>("Panels", no_init)
+  class_<PanelManager, boost::noncopyable>("PanelManager", no_init)
     .def("AddWidget", &panels_add_widget_a, arg("hidden")=false)
     .def("AddWidget", &panels_add_widget_b, arg("hidden")=false)
     .def("AddWidget", &panels_add_widget_c, arg("hidden")=false)
-    .def("AddWidgetByName", &Panels::AddWidgetByName)
+    .def("AddWidgetByName", &PanelManager::AddWidgetByName)
     .def("RemoveWidget", &panels_remove_widget_a)
     .def("RemoveWidget", &panels_remove_widget_b)
     .def("RemoveWidget", &panels_remove_widget_c)
@@ -142,11 +142,11 @@ void export_PanelBar()
     .def("AddWidgetToPool", &panels_add_widget_to_pool_b)
     .def("AddWidgetToPool", &panels_add_widget_to_pool_c)
     .def("AddWidgetToPool", &panels_add_widget_to_pool_d)
-    .def("Save", &Panels::Save)
-    .def("Restore", &Panels::Restore)
+    .def("Save", &PanelManager::Save)
+    .def("Restore", &PanelManager::Restore)
     .add_property("menu", &panels_get_menu)
-    .def("GetQObject",&get_py_qobject<Panels>)
-    .add_property("qobject", &get_py_qobject<Panels>)
+    .def("GetQObject",&get_py_qobject<PanelManager>)
+    .add_property("qobject", &get_py_qobject<PanelManager>)
   ;
 
   class_<PanelBar, boost::noncopyable>("PanelBar", no_init)
diff --git a/modules/gui/pymod/export_remote_site_loader.cc b/modules/gui/pymod/export_remote_site_loader.cc
index 91b80ca7727c7abc619749f1bf311977906bbfd0..d864b87e4b4e06bae2d47ff081ff9ceb41c0966d 100644
--- a/modules/gui/pymod/export_remote_site_loader.cc
+++ b/modules/gui/pymod/export_remote_site_loader.cc
@@ -16,20 +16,20 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#include <string>
 
 #include <boost/python.hpp>
-#include <boost/python/register_ptr_to_python.hpp>
-#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
+#include <string>
 
-using namespace boost::python;
 
 #include <ost/gui/remote_site_loader.hh>
+#include <boost/python/register_ptr_to_python.hpp>
+#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
 
 #include "sip_handler.hh"
 
 using namespace ost;
 using namespace ost::gui;
+using namespace boost::python;
 
 struct WrappedRemoteSiteLoader : public RemoteSiteLoader
 {
diff --git a/modules/gui/pymod/export_scene_win.cc b/modules/gui/pymod/export_scene_win.cc
index 1d659c420b6de545bd22ece7daea12333dbe546c..6db3578c74e4e5535787d65ee0f04c839aa21833 100644
--- a/modules/gui/pymod/export_scene_win.cc
+++ b/modules/gui/pymod/export_scene_win.cc
@@ -16,7 +16,6 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#include <QAction>
 
 #include <boost/python.hpp>
 
@@ -25,6 +24,7 @@
 
 #include "sip_handler.hh"
 
+#include <QAction>
 
 using namespace boost::python;
 using namespace ost;
@@ -53,6 +53,7 @@ void export_SceneWin()
       .value("NOT_VISIBLE", NOT_VISIBLE)
       .value("NOT_HIDDEN", NOT_HIDDEN)
       .value("NOT_SCENE", NOT_SCENE)
+      .value("VIEWS_SAME_OBJECT", VIEWS_SAME_OBJECT)
       .value("SINGLE", SINGLE)
       .value("MULTI", MULTI)
 #if OST_IMG_ENABLED
diff --git a/modules/gui/pymod/export_sequence_viewer.cc b/modules/gui/pymod/export_sequence_viewer.cc
index e6127166c5cb2c23903b9d407ad7437959c0addb..268b4dd2b28d3779d9b5d2260c978f21cdb0c293 100644
--- a/modules/gui/pymod/export_sequence_viewer.cc
+++ b/modules/gui/pymod/export_sequence_viewer.cc
@@ -16,7 +16,10 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
+
 #include <boost/python.hpp>
+#include <vector>
+#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
 
 #include <ost/gui/sequence_viewer/sequence_viewer.hh>
 
@@ -26,12 +29,90 @@ using namespace boost::python;
 using namespace ost;
 using namespace ost::gui;
 
+namespace {
+
+void change_display_mode_a(SequenceViewer* seq_viewer, const QString& mode)
+{
+  seq_viewer->ChangeDisplayMode(mode);
+}
+
+void change_display_mode_b(SequenceViewer* seq_viewer, const gfx::EntityP& entity, const QString& mode)
+{
+  seq_viewer->ChangeDisplayMode(entity, mode);
+}
+
+void change_display_mode_c(SequenceViewer* seq_viewer, const seq::AlignmentHandle& alignment, const QString& mode)
+{
+  seq_viewer->ChangeDisplayMode(alignment, mode);
+}
+
+String get_current_display_mode_a(SequenceViewer* seq_viewer)
+{
+  return seq_viewer->GetCurrentDisplayMode().toStdString();
+}
+
+String get_current_display_mode_b(SequenceViewer* seq_viewer, const gfx::EntityP& entity)
+{
+  return seq_viewer->GetCurrentDisplayMode(entity).toStdString();
+}
+
+String get_current_display_mode_c(SequenceViewer* seq_viewer, const seq::AlignmentHandle& alignment)
+{
+  return seq_viewer->GetCurrentDisplayMode(alignment).toStdString();
+}
+
+std::vector<String> get_display_modes_a(SequenceViewer* seq_viewer)
+{
+  std::vector<String> modes;
+  const QStringList& list = seq_viewer->GetDisplayModes();
+  for (int i=0; i<list.size(); i++){
+    modes.push_back(list.at(i).toStdString());
+  }
+  return modes;
+}
+
+std::vector<String> get_display_modes_b(SequenceViewer* seq_viewer, const gfx::EntityP& entity)
+{
+  std::vector<String> modes;
+  const QStringList& list = seq_viewer->GetDisplayModes(entity);
+  for (int i=0; i<list.size(); i++){
+    modes.push_back(list.at(i).toStdString());
+  }
+  return modes;
+}
+
+std::vector<String> get_display_modes_c(SequenceViewer* seq_viewer, const seq::AlignmentHandle& alignment)
+{
+  std::vector<String> modes;
+  const QStringList& list = seq_viewer->GetDisplayModes(alignment);
+  for (int i=0; i<list.size(); i++){
+    modes.push_back(list.at(i).toStdString());
+  }
+  return modes;
+}
+
+}
+
 
 void export_SequenceViewer()
 {
-  class_<SequenceViewer, boost::noncopyable >("SequenceViewer", no_init)
+  class_<SequenceViewer, boost::noncopyable >("SequenceViewer",init<>())
+    .def(init<bool, optional<QWidget*> >())
     .def("Show", &SequenceViewer::show)
     .def("Hide", &SequenceViewer::hide)
+    .def("AddEntity", &SequenceViewer::AddEntity)
+    .def("RemoveEntity", &SequenceViewer::RemoveEntity)
+    .def("AddAlignment", &SequenceViewer::AddAlignment)
+    .def("RemoveAlignment", &SequenceViewer::RemoveAlignment)
+    .def("GetDisplayModes", &get_display_modes_a)
+    .def("GetDisplayModes", &get_display_modes_b)
+    .def("GetDisplayModes", &get_display_modes_c)
+    .def("GetCurrentDisplayMode", &get_current_display_mode_a)
+    .def("GetCurrentDisplayMode", &get_current_display_mode_b)
+    .def("GetCurrentDisplayMode", &get_current_display_mode_c)
+    .def("ChangeDisplayMode",&change_display_mode_a)
+    .def("ChangeDisplayMode",&change_display_mode_b)
+    .def("ChangeDisplayMode",&change_display_mode_c)
     .def("GetQObject",&get_py_qobject<SequenceViewer>)
     .add_property("qobject", &get_py_qobject<SequenceViewer>)
   ;
diff --git a/modules/gui/pymod/export_tool.cc b/modules/gui/pymod/export_tool.cc
index 946340659ba6bbf7aa8f26c161dd163adffc8124..1d050038fb3854d45b797b56994c6bbe872d55df 100644
--- a/modules/gui/pymod/export_tool.cc
+++ b/modules/gui/pymod/export_tool.cc
@@ -17,9 +17,8 @@
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
 
-#include <vector>
-
 #include <boost/python.hpp>
+#include <vector>
 #include <boost/python/register_ptr_to_python.hpp>
 #include <boost/python/suite/indexing/vector_indexing_suite.hpp>
 
diff --git a/modules/gui/pymod/export_widget.cc b/modules/gui/pymod/export_widget.cc
index 0834cec320d4fbe31425328066c3ad6b66d35529..f548e52ff1f6518c1d887440d08e27af11e2eb4c 100644
--- a/modules/gui/pymod/export_widget.cc
+++ b/modules/gui/pymod/export_widget.cc
@@ -16,21 +16,17 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#include <string>
 
 #include <boost/python.hpp>
+#include <string>
 #include <boost/python/register_ptr_to_python.hpp>
-#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
-using namespace boost::python;
+
 
 #include <ost/gui/widget.hh>
-#include <ost/gui/widget_registry.hh>
-#include <ost/gui/gosty_app.hh>
-#include <ost/gui/perspective.hh>
-#include <ost/gui/panel_bar/panels.hh>
 
 #include "sip_handler.hh"
 
+using namespace boost::python;
 using namespace ost;
 using namespace ost::gui;
 
@@ -39,22 +35,22 @@ struct WrappedWidget : public Widget
 {
   WrappedWidget(PyObject *p, object py_object):
        Widget(NULL,NULL){
-    if(QWidget* widget = get_cpp_qobject<QWidget>(py_object)){
+    if (QWidget* widget=get_cpp_qobject<QWidget>(py_object)) {
       this->SetInternalWidget(widget);
     }
   }
-
   virtual bool Restore(const QString& prefix){return true;}
 
   virtual bool Save(const QString& prefix){return true;}
 
   virtual ~WrappedWidget(){ }
-
+private:
+  QString   unique_id_;
 };
 
 void export_Widget()
 {
-  class_<Widget, WrappedWidget, boost::noncopyable>("WrappedWidget",init<object>())
+  class_<Widget, WrappedWidget, boost::noncopyable>("Widget", init<object>())
     .def("Save", &WrappedWidget::Save)
     .def("Restore", &WrappedWidget::Restore)
     .def("SetDestroyOnClose", &WrappedWidget::SetDestroyOnClose)
diff --git a/modules/gui/pymod/init_context_menu.py b/modules/gui/pymod/init_context_menu.py
index e2d68d1ce3fa7cf7584dafdf688647c31ef2538d..bddcda7fd2533e347ae910e7c5f361f680043cc4 100644
--- a/modules/gui/pymod/init_context_menu.py
+++ b/modules/gui/pymod/init_context_menu.py
@@ -1,8 +1,17 @@
+import platform
+
 from PyQt4 import QtCore, QtGui
 
-from ost import geom, gfx, gui
+import sip
+
+from ost import geom, gfx, gui, seq
 from ost import settings
+from ost import LogError, mol
 from ost.bindings import tmtools
+from ost.bindings import msms
+from ost.seq import alg
+import ost
+from ost.gui.scene.query_editor import QueryEditorWidget,QueryDialog
 
 class SelectRefDialog(QtGui.QDialog):
   def __init__(self, ent_list, parent=None):
@@ -21,6 +30,14 @@ class SelectRefDialog(QtGui.QDialog):
     self.list.setSelectionMode(QtGui.QAbstractItemView.SingleSelection)
     vb.addWidget(self.label)
     vb.addWidget(self.list)
+    self.show_scores = QtGui.QCheckBox(self)
+    self.show_scores.setText("Show Scores")
+    self.show_scores.setChecked(True)
+    vb.addWidget(self.show_scores)
+    self.show_alignment = QtGui.QCheckBox(self)
+    self.show_alignment.setText("Display Alignment")
+    self.show_alignment.setChecked(False)
+    vb.addWidget(self.show_alignment)
     hb = QtGui.QHBoxLayout()
     hb.setDirection(QtGui.QBoxLayout.LeftToRight)
     cancel_btn = QtGui.QPushButton("Cancel", self)
@@ -56,7 +73,13 @@ class SelectRefDialog(QtGui.QDialog):
         self.ent_list_.remove(ent)
         self.ent_list_.insert(0,ent)
     self.accept()
-      
+     
+  def GetShowScores(self):
+    return self.show_scores.isChecked()
+  
+  def GetDisplayAlignment(self):
+    return self.show_alignment.isChecked()
+  
   def GetEntities(self):
     return self.ent_list_
 
@@ -102,15 +125,136 @@ class ShowResultDialog(QtGui.QDialog):
           
     self.list.resizeColumnsToContents()
 
+class CalculateSurfaceSettingsDialog(QtGui.QDialog):
+  def __init__(self, executable, parent=None):
+    QtGui.QDialog.__init__(self, parent)
+    vb = QtGui.QGridLayout()
+    self.setLayout(vb)
+    self.setWindowTitle("MSMS Surface Settings")
+    msmsexe_label=QtGui.QLabel("executable")
+    self.msmsexe_field=QtGui.QLineEdit()
+    self.msmsexe_field.setText(executable)
+    msmsexe_browsebutton=QtGui.QPushButton("Browse")
+    vb.addWidget(msmsexe_label, 0, 0)
+    vb.addWidget(self.msmsexe_field, 0, 1)
+    vb.addWidget(msmsexe_browsebutton, 0, 2)
+    surfname_label=QtGui.QLabel("surface name")
+    self.surfname_field=QtGui.QLineEdit()
+    self.surfname_field.setText("surface")
+    vb.addWidget(surfname_label, 1, 0)
+    vb.addWidget(self.surfname_field, 1, 1, 1, 2)
+    density_label=QtGui.QLabel("density")
+    self.density_spinbox=QtGui.QSpinBox()
+    self.density_spinbox.setRange(1, 10)
+    self.density_spinbox.setValue(4)
+    vb.addWidget(density_label, 2, 0)
+    vb.addWidget(self.density_spinbox, 2, 1, 1, 2)
+    probe_label=QtGui.QLabel("probe radius")
+    self.probe_spinbox=QtGui.QDoubleSpinBox()
+    self.probe_spinbox.setDecimals(1)
+    self.probe_spinbox.setSingleStep(0.1)
+    self.probe_spinbox.setRange(0.3, 5.0)
+    self.probe_spinbox.setValue(1.4)
+    vb.addWidget(probe_label, 3, 0)
+    vb.addWidget(self.probe_spinbox, 3, 1, 1, 2)
+    selection_label=QtGui.QLabel("selection")
+    self.selection_field=QtGui.QLineEdit()
+    self.selection_field.setText("")
+    vb.addWidget(selection_label, 4, 0)
+    vb.addWidget(self.selection_field, 4, 1, 1, 2)
+    self.noh_box=QtGui.QCheckBox("no hydrogens")
+    vb.addWidget(self.noh_box, 5, 0)
+    self.nohet_box=QtGui.QCheckBox("no hetatoms")
+    vb.addWidget(self.nohet_box, 5, 1)
+    self.nowat_box=QtGui.QCheckBox("no waters")
+    vb.addWidget(self.nowat_box, 5, 2)
+    
+    cancel_btn = QtGui.QPushButton("Cancel", self)
+    ok_btn = QtGui.QPushButton("OK", self)
+    vb.addWidget(cancel_btn, 6, 1)
+    vb.addWidget(ok_btn, 6, 2)
+    
+    QtCore.QObject.connect(msmsexe_browsebutton, QtCore.SIGNAL("clicked()"), self.GetPath)
+    QtCore.QObject.connect(ok_btn, QtCore.SIGNAL("clicked()"), self.accept)
+    QtCore.QObject.connect(cancel_btn, QtCore.SIGNAL("clicked()"), self.reject)
+    
+  def GetPath(self):
+    path=QtGui.QFileDialog().getOpenFileName(self, "Choose MSMS Executable")
+    if path!='':
+      self.msmsexe_field.setText(path)
+
+class SurfaceContextMenu(QtCore.QObject):
+  def __init__(self, context_menu):
+    try:
+      settings_name="msms"
+      self.executable=settings.Locate(settings_name)
+    except settings.FileNotFound:
+      self.executable=""
+    QtCore.QObject.__init__(self, context_menu.qobject)
+    self.action = QtGui.QAction("Calculate Surface", self)
+    QtCore.QObject.connect(self.action, QtCore.SIGNAL("triggered()"),
+                           self.CalculateSurface)
+    context_menu.AddAction(self.action, gui.ContextActionType.ENTITY)
+    
+  def CalculateSurface(self):
+    scene_selection = gui.SceneSelection.Instance()
+    ent_list = list()
+    for i in range(0,scene_selection.GetActiveNodeCount()):
+      ent_list.append(scene_selection.GetActiveNode(i))
+    cssd = CalculateSurfaceSettingsDialog(self.executable)
+    if(cssd.exec_()):
+      self.__CalculateSurface(ent_list,
+                              str(cssd.surfname_field.text()),
+                              str(cssd.msmsexe_field.text()),
+                              cssd.density_spinbox.value(),
+                              cssd.probe_spinbox.value(),
+                              str(cssd.selection_field.text()),
+                              cssd.noh_box.isChecked(),
+                              cssd.nohet_box.isChecked(),
+                              cssd.nowat_box.isChecked())
+      
+  def __CalculateSurface(self,ent_list,name,msms_exe,density,
+                         radius,selection,noh,nohet,nowat):
+    for entity in ent_list:
+      if isinstance(entity, gfx.Entity):
+        try:
+          s=msms.CalculateSurface(entity.view.handle,
+                                  msms_exe=msms_exe,
+                                  density=density,
+                                  radius=radius,
+                                  selection=selection,
+                                  no_hydrogens=noh,
+                                  no_hetatoms=nohet,
+                                  no_waters=nowat)[0]
+          gfx.Scene().Add(gfx.Surface("%s_%s"%(entity.GetName(),name),s))
+        except (RuntimeError, msms.MsmsProcessError):
+          LogError("WARNING: Surface could not be calculated")
+          return
+        except UserWarning:
+          LogError("WARNING: Entry with the same name already present in scene")
+          return
+  
 class AlignmentContextMenu(QtCore.QObject):
+
   def __init__(self, context_menu):
     try:
-      settings.Locate('tmalign')
+      try: # workaround for interrupted system call bug on OSX
+        if platform.system() == "Windows":
+          settings_name="tmalign.exe"
+        else:
+          settings_name="tmalign"
+      except IOError:
+        # if platform.system() fails with an IOError we are most likely on a buggy mac an therefore
+        # use "tmalign"
+        settings_name="tmalign"
+
+      settings.Locate(settings_name)
       QtCore.QObject.__init__(self, context_menu.qobject)
 
       self.action = QtGui.QAction("Align", self)
       QtCore.QObject.connect(self.action,QtCore.SIGNAL("triggered()"), self.Align)
       context_menu.AddAction(self.action, gui.ContextActionType.ENTITY | gui.ContextActionType.MULTI)
+      self.seq_viewer = None
     except settings.FileNotFound:
       return
     
@@ -119,14 +263,11 @@ class AlignmentContextMenu(QtCore.QObject):
     ent_list = list()
     for i in range(0,scene_selection.GetActiveNodeCount()):
       ent_list.append(scene_selection.GetActiveNode(i))
-    if len(ent_list) == 2:
-      self.__Align(ent_list)
-    elif len(ent_list) > 2:
-      sd = SelectRefDialog(ent_list)
-      if(sd.exec_()):
-        self.__Align(sd.GetEntities())
+    sd = SelectRefDialog(ent_list)
+    if(sd.exec_()):
+      self.__Align(sd.GetEntities(),sd.GetShowScores(), sd.GetDisplayAlignment())
         
-  def __Align(self, ent_list):
+  def __Align(self, ent_list,show_scores=True, display_alignment=False):
     node = ent_list[0]
     res_list = list()
     if isinstance(node, gfx.Entity):
@@ -136,7 +277,10 @@ class AlignmentContextMenu(QtCore.QObject):
         if isinstance(node, gfx.Entity):
           res_list.append(tmtools.TMAlign(node.view.handle, ref))
           node.UpdatePositions()
-    self.__ShowScore(ent_list, res_list)
+    if show_scores:
+      self.__ShowScore(ent_list, res_list)
+    if display_alignment:
+      self.__DisplayAlignment(ent_list, res_list)
     
   def __ShowScore(self, ent_list, res_list):
     if(len(res_list)==1):
@@ -146,7 +290,92 @@ class AlignmentContextMenu(QtCore.QObject):
     elif(len(res_list)>1):
       ShowResultDialog(ent_list, res_list).exec_()
       
-    
+  def __DisplayAlignment(self, ent_list, res_list):
+    if(len(res_list)>0):
+      ref_seq = seq.CreateSequence("%s (ref)"%ent_list[0].GetName(),res_list[0].ref_sequence.GetGaplessString())
+      aln_list = seq.AlignmentList()
+      if(ref_seq.IsValid()):
+        for i in range(0, len(res_list)):
+          res_list[i].alignment.SetSequenceName(1,ent_list[i+1].GetName())
+          aln_list.append(res_list[i].alignment)
+        alignment = alg.MergePairwiseAlignments(aln_list, ref_seq)
+        gosty = gui.GostyApp.Instance()
+        main_area = gosty.perspective.GetMainArea()
+        if self.seq_viewer:
+          self.seq_viewer.qobject.close()
+        self.seq_viewer = gui.SequenceViewer(True)
+        self.seq_viewer.AddAlignment(alignment)
+        self.seq_viewer.ChangeDisplayMode("Highlight conservation 1")
+        self.seq_viewer.Show()
+
+class SelectMenuPoints(QtCore.QObject):
+  def __init__(self, context_menu):
+    QtCore.QObject.__init__(self, context_menu.qobject)
+    action=QtGui.QAction("Select...", self)
+    QtCore.QObject.connect(action, QtCore.SIGNAL('triggered()'),
+                           self._Select)
+    context_menu.AddAction(action, gui.ENTITY)
+    action=QtGui.QAction("Copy Selection...", self)
+    QtCore.QObject.connect(action, QtCore.SIGNAL('triggered()'),
+                           self._CopyViews)
+    context_menu.AddAction(action, gui.ENTITY)
+    action=QtGui.QAction('Select...', self)
+    QtCore.QObject.connect(action, QtCore.SIGNAL('triggered()'),
+                           self._SelectViewsSameEntity)
+    context_menu.AddAction(action, gui.ENTITY_VIEW|gui.VIEWS_SAME_OBJECT)    
+  def _Select(self):
+    scene_selection=gui.SceneSelection.Instance()
+    ent=scene_selection.GetActiveNode(0)
+    dialog=QueryDialog('Select...')
+    if dialog.exec_():
+      q=mol.Query(dialog.query)
+      if q.IsValid():
+        ent.selection=ent.view.Select(dialog.query, dialog.query_flags)
+      else:
+        ost.LogError("invalid query: %s" % q.error)
+
+  def _UniqueName(self, ent):
+    """
+    Returns a name based on ent that is unique within the scene
+    """
+    ent_name=ent.GetName()
+    num=2
+    while True:
+      candidate_name='%s-%d' % (ent_name, num)
+      if not gfx.Scene().HasNode(candidate_name):
+        return candidate_name
+      num+=1
+
+  def _SelectViewsSameEntity(self):
+
+    union=gui.SceneSelection.Instance().GetViewUnion()
+    dialog=QueryDialog('Select...')
+    if dialog.exec_():
+      q=mol.Query(dialog.query)    
+      if q.IsValid():
+        ve=gui.SceneSelection.Instance().GetViewEntity()
+        ve.selection=union.Select(q, dialog.query_flags)
+      else:    
+        ost.LogError("invalid query: %s" % q.error)    
+  
+  def _CopyViews(self):
+    views_to_add=[]
+    scene_selection=gui.SceneSelection.Instance()
+    ent=scene_selection.GetActiveNode(0)
+    dialog=QueryDialog('Select...')
+    if dialog.exec_():
+      q=mol.Query(dialog.query)
+      if q.IsValid():
+        for i in range(scene_selection.GetActiveNodeCount()):
+          ent=scene_selection.GetActiveNode(i)
+          selected=ent.view.Select(q, dialog.query_flags)
+          gfx_ent=gfx.Entity(self._UniqueName(ent),selected)
+          gfx.Scene().Add(gfx_ent)
+      else:    
+        ost.LogError("invalid query: %s" % q.error)
+   
 def _InitContextMenu(app):
   cm=app.scene_win.GetContextMenu()
-  AlignmentContextMenu(cm)
\ No newline at end of file
+  AlignmentContextMenu(cm)
+  SurfaceContextMenu(cm)
+  SelectMenuPoints(cm)
diff --git a/modules/gui/pymod/init_menubar.py b/modules/gui/pymod/init_menubar.py
index 360b02b1b692ead1983d5962ae4aac83328b6dcc..ac5c23e23dd0aebcc57f297ea3bd42fa6d11386a 100644
--- a/modules/gui/pymod/init_menubar.py
+++ b/modules/gui/pymod/init_menubar.py
@@ -26,9 +26,9 @@ import ost
 from PyQt4 import QtCore, QtGui
 from ost.gui import FileLoader
 from ost.gui.scene.file_loader import GenericLoader
-
 from ost.gui.scene.loader_manager_widget import LoaderManagerWidget
-
+from ost.gui.init_splash import _InitSplash
+from ost.gui.dng import termuse
 class InitMenuBar(QtCore.QObject):
   def __init__(self, menu_bar=None):
     QtCore.QObject.__init__(self, menu_bar)
@@ -50,8 +50,30 @@ class InitMenuBar(QtCore.QObject):
     webpage.setShortcut('Ctrl+D')
     self.connect(webpage, QtCore.SIGNAL('triggered()'), self.OpenDocs)
     help.addAction(webpage)
+    if sys.platform=='darwin':
+      install_ctl=QtGui.QAction('Install Command Line Tool', self)    
+      self.connect(install_ctl, QtCore.SIGNAL('triggered()'), 
+                   termuse.InstallTerminalPrograms)
+      help.addAction(install_ctl)
+    about = QtGui.QAction('&About', self)
+    about.setStatusTip('About')
+    about.setShortcut('Ctrl+A')
+    self.connect(about, QtCore.SIGNAL('triggered()'), self.About)
+    help.addAction(about)
+    
         
     window.addMenu(persp.panels.menu)
+    gl_win = QtGui.QAction('&GL Window', self)
+    gl_win.setStatusTip('Display gl windows')
+    gl_win.setShortcut('Ctrl+G')
+    self.connect(gl_win, QtCore.SIGNAL('triggered()'), self.ShowGLWin)
+    window.addAction(gl_win)
+    
+    reset = QtGui.QAction('Reset View', self)
+    reset.setStatusTip('Reset the Panels and Widgets')
+    self.connect(reset, QtCore.SIGNAL('triggered()'), self.ResetView)
+    window.addAction(reset)
+    
     #Options
     #Add file loader to menu
     loader_manager = QtGui.QAction('File &Loader', self)
@@ -75,8 +97,35 @@ class InitMenuBar(QtCore.QObject):
     self.loader_manager.exec_()
   
   def OpenDocs(self):
-    QtGui.QDesktopServices.openUrl(QtCore.QUrl("http://www.openstructure.org/docs/index.html"))
+    QtGui.QDesktopServices.openUrl(QtCore.QUrl("http://www.openstructure.org/docs/"))
     
+  def About(self):
+    _InitSplash()
+  
+  def ShowGLWin(self):
+    gosty=gui.GostyApp.Instance()
+    gl_win=gosty.GetGLWin()
+    if gl_win and gl_win.qobject.isHidden():
+      gl_win.Show()
+  
+  def ResetView(self):
+    msg_box = QtGui.QMessageBox()
+    msg_box.setWindowTitle("Reset the Panels and Widget");
+    msg_box.setIcon(QtGui.QMessageBox.Question)
+    msg_box.setText("Do you really want to reset the Panels and Widgets?");
+    msg_box.setStandardButtons(QtGui.QMessageBox.Yes | QtGui.QMessageBox.Cancel);
+    msg_box.setDefaultButton(QtGui.QMessageBox.Cancel);
+    ret = msg_box.exec_();
+    if(ret == QtGui.QMessageBox.Yes):
+      settings = QtCore.QSettings()
+      settings.setValue("restore_settings",QtCore.QVariant(False))
+      info_box = QtGui.QMessageBox()
+      info_box.setStandardButtons(QtGui.QMessageBox.Ok)
+      info_box.setIcon(QtGui.QMessageBox.Information)
+      info_box.setWindowTitle("Restart OpenStructure")
+      info_box.setText("You must restart OpenStructure for the changes to take effect!");
+      info_box.exec_();
+            
 def _InitMenuBar(app):
   InitMenuBar(app.perspective.menubar)
   
diff --git a/modules/gui/pymod/init_splash.py b/modules/gui/pymod/init_splash.py
new file mode 100644
index 0000000000000000000000000000000000000000..33263606301d852f81414bfffcf62d2f8acfa215
--- /dev/null
+++ b/modules/gui/pymod/init_splash.py
@@ -0,0 +1,27 @@
+from PyQt4 import QtCore, QtGui
+
+import os
+import ost
+from ost import gui
+
+LOGO_PATH = os.path.join(ost.GetSharedDataPath(), "gui", "images", "logo-small.png")
+
+class SplashDialog(QtGui.QDialog):
+  def __init__(self, parent=None):
+    QtGui.QDialog.__init__(self, parent)
+    layout = QtGui.QHBoxLayout(self)
+    self.setLayout(layout)
+    imageLabel = QtGui.QLabel();
+    self.pix_map = QtGui.QPixmap(LOGO_PATH);
+    imageLabel.setPixmap(self.pix_map);
+    layout.addWidget(imageLabel)
+    self.label = QtGui.QTextEdit()
+    self.label.setReadOnly(True)
+    self.label.setHtml("Welcome to <b>Openstructure</b>!<br /><br />You are running version 1.0.0a<br /><br />If you are new to OpenStructure, we invite you to run the demos from the examples directory. Scripts can be displayed by right clicking on the file and selecting 'Show source'.<br /><br />Feel free visit our website at:<br /> http://www.openstructure.org")
+    layout.addWidget(self.label)
+    
+def _InitSplash():
+  splash = SplashDialog(gui.GostyApp.Instance().perspective.main_area.qobject)
+  splash.exec_()
+
+  #QtCore.QTimer.singleShot(30000, splash.close);
diff --git a/modules/gui/pymod/scene/color_options_widget.py b/modules/gui/pymod/scene/color_options_widget.py
index 2683a745dfdf180e4e1ebe1ccbac474342b24d06..4171e8c408eae6645f90fc0b75870ccee17c6659 100644
--- a/modules/gui/pymod/scene/color_options_widget.py
+++ b/modules/gui/pymod/scene/color_options_widget.py
@@ -22,7 +22,15 @@ import sys
 from ost import mol
 from ost import gui
 from ost import gfx
+try: 
+  from ost import img
+  _img_present=True
+except ImportError:
+  _img_present=False
+  pass
+
 from PyQt4 import QtCore, QtGui
+from scene_selection_helper import SelHelper
 from gradient_editor_widget import GradientEditor
 from uniform_color_widget import UniformColorWidget
 from combo_options_widget import ComboOptionsWidget
@@ -35,15 +43,22 @@ class ColorOptionsWidget(ComboOptionsWidget):
     self.text_ = "Color Options"
     
     #Add options to menu
-    self.AddWidget("Color by Element", ByElementWidget("Color by Element"))
-    self.AddWidget("Color by Chain", ByChainWidget("Color by Chain"))
-    self.AddWidget("Color by Property", GradientEditor(self))
-    self.AddWidget("Uniform",UniformColorWidget(self))
+    self.entity_widgets_ = list()
+    self.entity_widgets_.append(["Color by Element", ByElementWidget("Color by Element")])
+    self.entity_widgets_.append(["Color by Chain", ByChainWidget("Color by Chain")])
+    self.entity_widgets_.append(["Color by Entity", ByEntityWidget("Color by Entity")])
+    self.entity_widgets_.append(["Color by Property", GradientEditor()])
+    self.entity_widgets_.append(["Uniform",UniformColorWidget()])
   
+    self.img_widgets_ = list()
+    self.img_widgets_.append(["Uniform",UniformColorWidget()])
+
     self.setMinimumSize(250,200)
     
   def DoSomething(self, item):
     scene_selection = gui.SceneSelection.Instance()
+    if hasattr(item,"PrepareColoring"):
+      item.PrepareColoring()
     for i in range(0,scene_selection.GetActiveNodeCount()):
       node = scene_selection.GetActiveNode(i)
       item.ChangeColor(node)
@@ -57,26 +72,38 @@ class ColorOptionsWidget(ComboOptionsWidget):
     
     
   def Update(self):
+    
     ComboOptionsWidget.setEnabled(self,True)
-    scene_selection = gui.SceneSelection.Instance()
     
-    if scene_selection.GetActiveNodeCount() == 0 and scene_selection.GetActiveViewCount() == 0:
+    if SelHelper().CheckAllFlags(SelHelper.NO_SELECTION):
       ComboOptionsWidget.setEnabled(self,False)
       return
-        
-    for i in range(0,scene_selection.GetActiveNodeCount()):
-      node = scene_selection.GetActiveNode(i)
-      if not (isinstance(node, gfx.Entity) or isinstance(node, gfx.Surface)):
-        ComboOptionsWidget.setEnabled(self,False)
-        return
-
+    
+    for w in self.entity_widgets_:
+      self.RemoveWidget(w[0])
+    for w in self.img_widgets_:
+      self.RemoveWidget(w[0])
+    
+    
+    if SelHelper().CheckFlags(SelHelper.HAS_IMG | SelHelper.IS_ONE_TYPE):
+      for w in self.img_widgets_:
+        self.AddWidget(w[0], w[1])
+    elif SelHelper().CheckMinOneFlag(SelHelper.HAS_ENTITY| SelHelper.HAS_VIEW| SelHelper.HAS_SURFACE) and SelHelper().CheckNotFlags(SelHelper.HAS_IMG):
+      for w in self.entity_widgets_:
+        self.AddWidget(w[0], w[1])
+    else:
+      ComboOptionsWidget.setEnabled(self,False)
+      return
+    
+    self.GetCurrentWidget().Update()
+    
   def GetText(self):
     return self.text_
   
 
 class ByElementWidget(QtGui.QWidget):
   def __init__(self, text, parent=None):
-    QtGui.QLabel.__init__(self, parent)
+    QtGui.QWidget.__init__(self, parent)
     
     #Title
     self.text_ = text
@@ -112,7 +139,7 @@ class ByElementWidget(QtGui.QWidget):
   
 class ByChainWidget(QtGui.QWidget):
   def __init__(self, text, parent=None):
-    QtGui.QLabel.__init__(self, parent)
+    QtGui.QWidget.__init__(self, parent)
     
     #Title
     self.text_ = text
@@ -144,3 +171,49 @@ class ByChainWidget(QtGui.QWidget):
       
   def GetText(self):
     return self.text_
+
+class ByEntityWidget(QtGui.QWidget):
+  def __init__(self, text, parent=None):
+    QtGui.QWidget.__init__(self, parent)
+    
+    #Title
+    self.text_ = text
+    
+    #UI
+    text_label = QtGui.QLabel(text)
+    font = text_label.font()
+    font.setBold(True)
+    
+    grid = QtGui.QGridLayout()
+    grid.addWidget(text_label,0,0,1,1)
+    grid.addWidget(QtGui.QLabel("No Settings available"), 1, 0, 1, 3)
+    grid.setRowStretch(2,1)
+    self.setLayout(grid)
+    self.setMinimumSize(250,60)
+    
+    self.gradient_ = gfx.Gradient("RAINBOW")
+    
+  def Update(self):
+   pass #Do Nothing
+    
+  def PrepareColoring(self):
+    scene_selection = gui.SceneSelection.Instance()
+    entity_count = scene_selection.GetActiveNodeCount()
+    for i in range(0,scene_selection.GetActiveNodeCount()):
+      if i<=0:
+        color=self.gradient_.GetColorAt(0.0)
+      else:
+        color=self.gradient_.GetColorAt(float(i) / entity_count)
+      node = scene_selection.GetActiveNode(i)
+      node.SetColor(color)
+  
+  def ChangeColor(self, node):
+    pass
+     
+  def ChangeViewColor(self, entity, view):
+    if isinstance(entity, gfx.Entity) and isinstance(view, mol.EntityView):
+      bco=gfx.ByChainColorOp(mol.QueryViewWrapper(view))
+      entity.Apply(bco)
+      
+  def GetText(self):
+    return self.text_
diff --git a/modules/gui/pymod/scene/color_select_widget.py b/modules/gui/pymod/scene/color_select_widget.py
index a02986b7b92d1a6ab4684ff5689a2a8f447169b5..2fdf19bb17fc9a336365e01d754f9ff119e1bc5b 100644
--- a/modules/gui/pymod/scene/color_select_widget.py
+++ b/modules/gui/pymod/scene/color_select_widget.py
@@ -51,7 +51,7 @@ class ColorSelectWidget(QtGui.QWidget):
   def ChangeColor(self):
     color = QtGui.QColorDialog.getColor(self.color_, self)
     
-    if(color != self.color_):
+    if(color != self.color_ and color.isValid()):
       self.color_ = color
       self.emit(QtCore.SIGNAL("colorChanged"))
       self.update()
@@ -59,11 +59,19 @@ class ColorSelectWidget(QtGui.QWidget):
   def GetColor(self):
     return self.color_
   
+  def GetGfxColor(self):
+    color = self.GetColor()
+    return gfx.Color(color.redF(), color.greenF(), color.blueF())
+  
   def SetColor(self, color):
     if(self.color_ != color):
       self.color_ = color
       self.emit(QtCore.SIGNAL("colorChanged"))
       self.update()
+  
+  def SetGfxColor(self, color):
+    qcolor= QtGui.QColor(color.Red()*255,color.Green()*255,color.Blue()*255,color.Alpha()*255)
+    self.SetColor(qcolor)
             
   def paintEvent(self, event):
     if self.isEnabled():
diff --git a/modules/gui/pymod/scene/combo_options_widget.py b/modules/gui/pymod/scene/combo_options_widget.py
index dea16f03730573a16f4ea2e542e12b44395a12b5..b84630cc1bfd94f42b15d5f09904e73fada359d1 100644
--- a/modules/gui/pymod/scene/combo_options_widget.py
+++ b/modules/gui/pymod/scene/combo_options_widget.py
@@ -81,7 +81,7 @@ class ComboOptionsWidget(QtGui.QWidget):
   def RemoveWidget(self,ident):
     index = self.__GetIndex(ident)
     if(index >= 0):
-      self.stacked_widget_.removeWidget(self.combo_box_.itemData().toPyObject()[1])
+      self.stacked_widget_.removeWidget(self.combo_box_.itemData(index).toPyObject()[1])
       self.combo_box_.removeItem(index)
   
   def DoSomething(self, item):
@@ -103,7 +103,9 @@ class ComboOptionsWidget(QtGui.QWidget):
       self.__UpdateView(None)
   
   def GetCurrentWidget(self):
-    return self.__GetCurrentPair()[1]
+    if(self.combo_box_.currentIndex() >= 0):
+      return self.__GetCurrentPair()[1]
+    return None
   
   def DoResize(self):
     item = self.GetCurrentWidget()
@@ -127,7 +129,7 @@ class ComboOptionsWidget(QtGui.QWidget):
   def __GetIndex(self, ident):
     for i in range(self.combo_box_.count()):
       pair = self.combo_box_.itemData(i).toPyObject()
-      if ident == pair[0] and i != self.combo_box_.currentIndex():
+      if ident == pair[0]:
         return i
     return -1
   
diff --git a/modules/gui/pymod/scene/cpk_widget.py b/modules/gui/pymod/scene/cpk_widget.py
index d57b21591bb56b1ee3f9d71d160502fb66bffd4c..9a15dce91543a23bde329fff8b95411949c6bada 100644
--- a/modules/gui/pymod/scene/cpk_widget.py
+++ b/modules/gui/pymod/scene/cpk_widget.py
@@ -65,9 +65,11 @@ class CPKWidget(RenderModeWidget):
     
   def UpdateSphereDetail(self, value):
     self.GetOptions().SetSphereDetail(value)
+    self.ApplyOptions()
 
   def UpdateSphereMode(self, value):
     self.GetOptions().SetSphereMode(value)
+    self.ApplyOptions()
     
   def UpdateGui(self,options):
     self.sphere_spinbox_.setValue(options.GetSphereDetail())
diff --git a/modules/gui/pymod/scene/custom_widget.py b/modules/gui/pymod/scene/custom_widget.py
index 9f8c3ffc0b9c08bd72829d0856b841451fc3724d..a778ed436cd9576816e66ebc57a51abce007d35a 100644
--- a/modules/gui/pymod/scene/custom_widget.py
+++ b/modules/gui/pymod/scene/custom_widget.py
@@ -128,7 +128,7 @@ class CustomWidget(RenderModeWidget):
   def UpdateSphereDetail(self, value):
     self.GetOptions().SetSphereDetail(value)
     self.ApplyOptions()
-    
+
   def UpdateArcDetail(self, value):
     self.GetOptions().SetArcDetail(value)
     self.ApplyOptions()
@@ -137,18 +137,22 @@ class CustomWidget(RenderModeWidget):
     self.GetOptions().SetBondRad(value)
     if(self.GetOptions().GetSphereRad()<self.GetOptions().GetBondRad()):
       self.GetOptions().SetSphereRad(value)
+    self.ApplyOptions()
     
   def UpdateSliderBondRadius(self, value):
     self.GetOptions().SetBondRad(value/100.0)
-
+    self.ApplyOptions()
+    
   def UpdateSphereRadius(self, value):
     self.GetOptions().SetSphereRad(value)
     if(self.GetOptions().GetSphereRad()<self.GetOptions().GetBondRad()):
       self.GetOptions().SetBondRad(value)
+    self.ApplyOptions()
     
   def UpdateSliderSphereRadius(self, value):
     self.GetOptions().SetSphereRad(value/100.0)
-
+    self.ApplyOptions()
+    
   def UpdateSphereRadiusGui(self,value):
     if(abs(value*100.0 - self.radius_sphere_slider_.value())>=self.radius_sphere_spinbox_.singleStep()):
       self.radius_sphere_slider_.setValue(value*100.0)
diff --git a/modules/gui/pymod/scene/file_loader.py b/modules/gui/pymod/scene/file_loader.py
index 522dd6934deeb8bfa45b17ebd1aea6646ecf3d44..98319a43688019997f62f5fe0716b34513393a33 100644
--- a/modules/gui/pymod/scene/file_loader.py
+++ b/modules/gui/pymod/scene/file_loader.py
@@ -52,6 +52,9 @@ class BaseRemoteLoader(gui.RemoteSiteLoader):
   def IsImg(self):
     return False
     
+  def IsDefault(self):
+    return False
+
   def GetRemoteSiteName(self):
     pass  
   
@@ -83,13 +86,14 @@ class GenericLoader(BaseRemoteLoader):
   FILE_TYPE_ATTRIBUTE_NAME = "FileType"
   TMP_URL_ATTRIBUTE_NAME= "TmpUrl"
   IMG_ATTRIBUTE_NAME= "Img"
-  
-  def __init__(self, name, url, up_case, file_type, tmp_url=None, img=False):
+  DEFAULT_ATTRIBUTE_NAME= "Default"
+  def __init__(self, name, url, up_case, file_type, tmp_url=None, img=False, default=False):
     BaseRemoteLoader.__init__(self)
     self.name_ = QtCore.QString(name)
     self.url_ = QtCore.QString(url)
     self.up_case_ = up_case
     self.img_ = img
+    self.default_ = default
     if file_type is not None:
       self.file_type_ = QtCore.QString(file_type)
     else:
@@ -103,6 +107,9 @@ class GenericLoader(BaseRemoteLoader):
   def IsImg(self):
     return self.img_    
 
+  def IsDefault(self):
+    return self.default_
+  
   def GetRemoteSiteName(self):
     return self.name_
   
@@ -133,14 +140,14 @@ class GenericLoader(BaseRemoteLoader):
         file_type = remote_url.right(remote_url.size()-index-1)
     if file_type is None:
       file_type = self.file_type_
-    
-    return url+formatted_id +"_"+self.name_+"."+file_type
+    if len(self.name_)>0:
+      return url+formatted_id +"_"+self.name_+"."+file_type
+    else:
+      return url+formatted_id+"."+file_type
   
   def HandleError(self, message):
-    messageBox =QtGui.QMessageBox(QtGui.QMessageBox.Warning,
-            "Error while Loading PDB from "+self.name_, "Could not download file ("+message+")!")
-    messageBox.exec_()
-    
+    ost.LogError(str("Could not download file\n"+message+""))
+   
   def ToInfo(self,group):
     group.SetAttribute(GenericLoader.EXT_NAME_ATTRIBUTE_NAME, str(self.name_))
     group.SetAttribute(GenericLoader.URL_ATTRIBUTE_NAME, str(self.url_))
@@ -152,6 +159,8 @@ class GenericLoader(BaseRemoteLoader):
       group.SetAttribute(GenericLoader.TMP_URL_ATTRIBUTE_NAME, str(self.tmp_url_))
     if self.img_ is not None:
       group.SetAttribute(GenericLoader.IMG_ATTRIBUTE_NAME, str(int(self.img_)))
+    if self.default_ is not None:
+      group.SetAttribute(GenericLoader.DEFAULT_ATTRIBUTE_NAME, str(int(self.default_)))
       
   @staticmethod
   def FromInfo(group):
@@ -161,6 +170,7 @@ class GenericLoader(BaseRemoteLoader):
     file_type = None
     tmp_url = None
     img = False
+    default = False
     
     if group.HasAttribute(GenericLoader.EXT_NAME_ATTRIBUTE_NAME):
       name = QtCore.QString(group.GetAttribute(GenericLoader.EXT_NAME_ATTRIBUTE_NAME))
@@ -179,5 +189,8 @@ class GenericLoader(BaseRemoteLoader):
     
     if group.HasAttribute(GenericLoader.IMG_ATTRIBUTE_NAME):
       img = bool(int(group.GetAttribute(GenericLoader.IMG_ATTRIBUTE_NAME)))
+      
+    if group.HasAttribute(GenericLoader.DEFAULT_ATTRIBUTE_NAME):
+      default = bool(int(group.GetAttribute(GenericLoader.DEFAULT_ATTRIBUTE_NAME)))
 
-    return GenericLoader(name, url, up_case, file_type, tmp_url, img)
+    return GenericLoader(name, url, up_case, file_type, tmp_url, img, default)
diff --git a/modules/gui/pymod/scene/gradient_preset_widget.py b/modules/gui/pymod/scene/gradient_preset_widget.py
index 69aa610df15e9c6caef687e9f6fb035a5a7c4da0..99beffeb97d045656bf47112e79747bf26ecc76e 100644
--- a/modules/gui/pymod/scene/gradient_preset_widget.py
+++ b/modules/gui/pymod/scene/gradient_preset_widget.py
@@ -107,10 +107,12 @@ class GradientPresetWidget(QtGui.QWidget):
         self.immucontextMenu_.popup(QtGui.QCursor.pos())
   
   def Add(self):
+    if(self.list_view_.currentIndex().isValid()):
+      self.list_view_.closePersistentEditor(self.list_view_.currentIndex())
     row = self.list_model_.GetLastRow()
     if self.list_model_.AddItem(datetime.now().isoformat(' '), self.gradient_edit_.GetGradient(), row, True, True):
       index = self.list_model_.index(row)
-      self.self.list_view__.setCurrentIndex(index)
+      self.list_view_.setCurrentIndex(index)
       self.Rename()
     else:
       QtGui.QMessageBox.information(self, "Gradient not added", "The gradient could not be added!")
diff --git a/modules/gui/pymod/scene/gradients.xml b/modules/gui/pymod/scene/gradients.xml
deleted file mode 100644
index acbe86c2d3d0d26bd0efb351f3ddf16784c343fb..0000000000000000000000000000000000000000
--- a/modules/gui/pymod/scene/gradients.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<!DOCTYPE EMDataInfo>
-<EMDataInfo>
- <Gradients>
-  <Gradient Name="Green Godzilla" >2
-0.0609137	0.333333	1	0	1
-0.954315	0	0.501961	0	1
-</Gradient>
- </Gradients>
-</EMDataInfo>
diff --git a/modules/gui/pymod/scene/hsc_widget.py b/modules/gui/pymod/scene/hsc_widget.py
index b5f716a0af5449f5cd49ebb8bbb3137556701fbe..8a0464841f48d262cb074fed1594ff47be9a6d5b 100644
--- a/modules/gui/pymod/scene/hsc_widget.py
+++ b/modules/gui/pymod/scene/hsc_widget.py
@@ -325,70 +325,92 @@ class HSCWidget(RenderModeWidget):
     
   def UpdatePolyMode(self, value):
     self.GetOptions().SetPolyMode(value)
+    self.ApplyOptions()
     
   def UpdateSplineDetail(self, value):
     self.GetOptions().SetSplineDetail(value)
+    self.ApplyOptions()
     
   def UpdateArcDetail(self, value):
     self.GetOptions().SetArcDetail(value)
+    self.ApplyOptions()
     
   def UpdateTubeRadius(self, value):
     self.GetOptions().SetTubeRadius(value)
+    self.ApplyOptions()
     
   def UpdateSliderTubeRadius(self, value):
     self.GetOptions().SetTubeRadius(value/10.0)
-
+    self.ApplyOptions()
+    
   def UpdateTubeRatio(self, value):
     self.GetOptions().SetTubeRatio(value)
-
+    self.ApplyOptions()
+    
   def UpdateSliderTubeRatio(self, value):
     self.GetOptions().SetTubeRatio(value/10.0)
-
+    self.ApplyOptions()
+    
   def UpdateTubeProfileType(self, value):
     self.GetOptions().SetTubeProfileType(value)
+    self.ApplyOptions()
     
   def UpdateHelixWidth(self, value):
     self.GetOptions().SetHelixWidth(value) 
+    self.ApplyOptions()
     
   def UpdateSliderHelixWidth(self, value):
     self.GetOptions().SetHelixWidth(value/10.0)
+    self.ApplyOptions()
     
   def UpdateHelixThickness(self, value):
     self.GetOptions().SetHelixThickness(value)
-
+    self.ApplyOptions()
+    
   def UpdateSliderHelixThickness(self, value):
     self.GetOptions().SetHelixThickness(value/10.0)
+    self.ApplyOptions()
     
   def UpdateHelixEcc(self, value):
     self.GetOptions().SetHelixEcc(value)
+    self.ApplyOptions()
     
   def UpdateHelixProfileType(self, value):
     self.GetOptions().SetHelixProfileType(value)
-
+    self.ApplyOptions()
+    
   def UpdateSliderHelixEcc(self, value):
     self.GetOptions().SetHelixEcc(value/10.0)
+    self.ApplyOptions()
     
   def UpdateStrandWidth(self, value):
     self.GetOptions().SetStrandWidth(value)
-
+    self.ApplyOptions()
+    
   def UpdateSliderStrandWidth(self, value):
     self.GetOptions().SetStrandWidth(value/10.0)
+    self.ApplyOptions()
     
   def UpdateStrandThickness(self, value):
     self.GetOptions().SetStrandThickness(value)
+    self.ApplyOptions()
     
   def UpdateSliderStrandThickness(self, value):
     self.GetOptions().SetStrandThickness(value/10.0)
+    self.ApplyOptions()
     
   def UpdateStrandEcc(self, value):
     self.GetOptions().SetStrandEcc(value)
+    self.ApplyOptions()
     
   def UpdateSliderStrandEcc(self, value):
     self.GetOptions().SetStrandEcc(value/10.0)
-
+    self.ApplyOptions()
+    
   def UpdateStrandProfileType(self, value):
     self.GetOptions().SetStrandProfileType(value)
-
+    self.ApplyOptions()
+    
   def UpdateTubeRadiusGui(self,value):
     if(abs(value*10.0 - self.width_tube_slider_.value())>=self.width_tube_spinbox_.singleStep()):
       self.width_tube_slider_.setValue(value*10.0)
diff --git a/modules/gui/pymod/scene/immutable_gradient_info_handler.py b/modules/gui/pymod/scene/immutable_gradient_info_handler.py
index 6eb2b75450e210c3f92384ce0cee24ba55171c53..e1fbb49c3fc4afd18e8a6426f3ad88fedf0b13a7 100644
--- a/modules/gui/pymod/scene/immutable_gradient_info_handler.py
+++ b/modules/gui/pymod/scene/immutable_gradient_info_handler.py
@@ -24,7 +24,7 @@ from ost import info
 from PyQt4 import QtCore, QtGui
 
 #Gradient Editor
-class ImmutableGradientInfoHandler():
+class ImmutableGradientInfoHandler:
   def __init__(self, fileName):
     
     self.FILE_NAME = fileName    
@@ -36,10 +36,7 @@ class ImmutableGradientInfoHandler():
         
     self.root_ = self.handle_.Root()
     
-    try:
-      self.gradients_ = self.root_.GetGroup(self.GRADIENTS_GROUP_NAME)
-    except UserWarning:
-      self.gradients_ = self.root_.CreateGroup(self.GRADIENTS_GROUP_NAME)
+    self.gradients_ = self.root_.RetrieveGroup(self.GRADIENTS_GROUP_NAME)
 
     
   def GetGfxGradient(self, name):
@@ -82,4 +79,4 @@ class ImmutableGradientInfoHandler():
       rel=s[0]
       color=s[1]
       gfx_gradient.SetColorAt(s[0], gfx.Color(s[1].redF(), s[1].greenF(), s[1].blueF()));
-    return gfx_gradient;
\ No newline at end of file
+    return gfx_gradient;
diff --git a/modules/gui/pymod/scene/immutable_info_handler.py b/modules/gui/pymod/scene/immutable_info_handler.py
index c75c14f5ceca7b64b5683ef555b91a729a28891d..cbebc45867c044facf16bc478eab82d3a3c83f04 100644
--- a/modules/gui/pymod/scene/immutable_info_handler.py
+++ b/modules/gui/pymod/scene/immutable_info_handler.py
@@ -24,7 +24,7 @@ from ost import info
 from PyQt4 import QtCore, QtGui
 
 #Gradient Editor
-class ImmutableInfoHandler():
+class ImmutableInfoHandler:
   def __init__(self, fileName):
     
     self.FILE_NAME = fileName    
@@ -36,10 +36,7 @@ class ImmutableInfoHandler():
         
     self.root_ = self.handle_.Root()
     
-    try:
-      self.gradients_ = self.root_.GetGroup(self.GRADIENTS_GROUP_NAME)
-    except UserWarning:
-      self.gradients_ = self.root_.CreateGroup(self.GRADIENTS_GROUP_NAME)
+    self.gradients_ = self.root_.RetrieveGroup(self.GRADIENTS_GROUP_NAME)
 
     
   def GetGfxGradient(self, name):
diff --git a/modules/gui/pymod/scene/immutable_loader_info_handler.py b/modules/gui/pymod/scene/immutable_loader_info_handler.py
index 80e906ea851722100e87b45e7800c48bde3aed01..fc21986074fa1f516918215cf4628707d6d39c7a 100644
--- a/modules/gui/pymod/scene/immutable_loader_info_handler.py
+++ b/modules/gui/pymod/scene/immutable_loader_info_handler.py
@@ -25,7 +25,7 @@ from PyQt4 import QtCore, QtGui
 
 from file_loader import GenericLoader
 
-class ImmutableLoaderInfoHandler():
+class ImmutableLoaderInfoHandler:
   LOADERS_GROUP_NAME = "GenericLoaders"
   LOADER_GROUP_NAME = "GenericLoader"
   NAME_ATTRIBUTE_NAME = "Name"
@@ -36,10 +36,7 @@ class ImmutableLoaderInfoHandler():
     
     self.root_ = self.handle_.Root()
     
-    try:
-      self.loaders_ = self.root_.GetGroup(ImmutableLoaderInfoHandler.LOADERS_GROUP_NAME)
-    except UserWarning:
-      self.loaders_ = self.root_.CreateGroup(ImmutableLoaderInfoHandler.LOADERS_GROUP_NAME)
+    self.loaders_ = self.root_.RetrieveGroup(ImmutableLoaderInfoHandler.LOADERS_GROUP_NAME)
 
     
   def GetLoader(self, name):
diff --git a/modules/gui/pymod/scene/immutable_preset_info_handler.py b/modules/gui/pymod/scene/immutable_preset_info_handler.py
index 8fc24539c200748637ad8abcc4c666b77807b2f2..131b0e1bcbb1ab108918e0e0d4315e89dd675210 100644
--- a/modules/gui/pymod/scene/immutable_preset_info_handler.py
+++ b/modules/gui/pymod/scene/immutable_preset_info_handler.py
@@ -25,7 +25,7 @@ from PyQt4 import QtCore, QtGui
 from ost.gui.scene.preset import Preset
 
 #Gradient Editor
-class ImmutablePresetInfoHandler():
+class ImmutablePresetInfoHandler:
   PRESETS_GROUP_NAME = "Presets"
   PRESET_GROUP_NAME = "Preset"
   NAME_ATTRIBUTE_NAME = "Name"
@@ -36,10 +36,7 @@ class ImmutablePresetInfoHandler():
     
     self.root_ = self.handle_.Root()
     
-    try:
-      self.presets_ = self.root_.GetGroup(ImmutablePresetInfoHandler.PRESETS_GROUP_NAME)
-    except UserWarning:
-      self.presets_ = self.root_.CreateGroup(ImmutablePresetInfoHandler.PRESETS_GROUP_NAME)
+    self.presets_ = self.root_.RetrieveGroup(ImmutablePresetInfoHandler.PRESETS_GROUP_NAME)
 
     
   def GetPreset(self, name):
diff --git a/modules/gui/pymod/scene/init_inspector.py b/modules/gui/pymod/scene/init_inspector.py
index 3009a57ca9031e450b99c1095b92f1b60cc59866..462ef4b3b04121a7d42e11f17c86d0f45262ff11 100644
--- a/modules/gui/pymod/scene/init_inspector.py
+++ b/modules/gui/pymod/scene/init_inspector.py
@@ -37,10 +37,15 @@ class InitInspectorMenu(QtCore.QObject):
     self.show_.setCheckable(True)
     self.show_.setChecked(not self.inspector_.isHidden())
     self.connect(self.show_, QtCore.SIGNAL('triggered()'), self.Toggle)
-    
+    self.connect(inspectordialog, QtCore.SIGNAL('visible'), self.UpdateCheckbox)
   def Toggle(self):
-    self.inspector_.setVisible(self.show_.isChecked())
-    
+    self.inspector_.setVisible(not self.inspector_.isVisible())
+  
+  def UpdateCheckbox(self, visibility):
+    self.disconnect(self.show_, QtCore.SIGNAL('triggered()'), self.Toggle)
+    self.show_.setChecked(visibility)
+    self.connect(self.show_, QtCore.SIGNAL('triggered()'), self.Toggle)
+  
 def _InitInspector(app):
   mywidget = InspectorDialog(app.gl_win.qobject)
   mywidget.setWindowFlags(QtCore.Qt.Dialog | QtCore.Qt.Tool)
diff --git a/modules/gui/pymod/scene/inspector_widget.py b/modules/gui/pymod/scene/inspector_widget.py
index 4e7e7f76155f5c51219aaae95daa91967b3e6f03..d5f29f05a7dd4ddb15e81341a96fc7235e604dc3 100644
--- a/modules/gui/pymod/scene/inspector_widget.py
+++ b/modules/gui/pymod/scene/inspector_widget.py
@@ -28,7 +28,8 @@ from toolbar_options_widget import ToolBarOptionsWidget
 from render_options_widget import RenderOptionsWidget
 from color_options_widget import ColorOptionsWidget
 from ost.gui.scene.scene_observer_impl import SceneObserverImpl
-from preset_widget import PresetWidget
+from map_level_widget import AdditionalSettingsWidget
+from scene_selection_helper import SelHelper
 
 class InspectorWidget(ToolBarOptionsWidget):
   ICONS_PATH = os.path.join(ost.GetSharedDataPath(), "scene", "icons/")
@@ -38,7 +39,7 @@ class InspectorWidget(ToolBarOptionsWidget):
     options = [
                 [InspectorWidget.ICONS_PATH+"render_icon.png",RenderOptionsWidget(self),None], 
                 [InspectorWidget.ICONS_PATH+"color_icon.png",ColorOptionsWidget(self),None],
-                [InspectorWidget.ICONS_PATH+"preset_icon.png", PresetWidget(self),None],
+                [InspectorWidget.ICONS_PATH+"preset_icon.png", AdditionalSettingsWidget(self),"Additional Node Settings"],
                 [InspectorWidget.ICONS_PATH+"tool_icon.png",app.tool_options_win.qobject,"Tool Options"]
               ]
     for o in options:
@@ -46,8 +47,7 @@ class InspectorWidget(ToolBarOptionsWidget):
     
     self.obs = SceneObserverImpl()
     self.obs.AttachObserver(self)
-    ost.scene.AttachObserver(self.obs)    
-    self.scene_selection_ = gui.SceneSelection.Instance()
+    ost.scene.AttachObserver(self.obs)
     QtCore.QObject.connect(app.scene_win.qobject,QtCore.SIGNAL("ActiveNodesChanged()"),
                            self.ActiveNodesChanged)     
     
@@ -58,15 +58,19 @@ class InspectorWidget(ToolBarOptionsWidget):
         
   #Observer Methods    
   def NodeRemoved(self, node):
+    SelHelper().Update()
     ToolBarOptionsWidget.Update(self)  
   
   def RenderModeChanged(self, node):
+    SelHelper().Update()
     ToolBarOptionsWidget.Update(self)
    
   def NodeChanged(self, node):
+    SelHelper().Update()
     ToolBarOptionsWidget.Update(self)
 
   def ActiveNodesChanged(self):
+    SelHelper().Update()
     ToolBarOptionsWidget.Update(self)
 
 class InspectorDialog(QtGui.QDialog):
@@ -91,3 +95,11 @@ class InspectorDialog(QtGui.QDialog):
     
   def ToggleHide(self,checked):
     self.setHidden(not self.isHidden())
+
+  def hideEvent(self, event):
+    self.emit(QtCore.SIGNAL("visible"),False)
+    QtGui.QDialog.hideEvent(self,event)
+    
+  def showEvent(self, event):
+    self.emit(QtCore.SIGNAL("visible"),True)
+    QtGui.QDialog.showEvent(self,event)
\ No newline at end of file
diff --git a/modules/gui/pymod/scene/line_trace_widget.py b/modules/gui/pymod/scene/line_trace_widget.py
index 1b06bb96d3e2447f9000a04852b85a32eb61ddbd..fc851034662d0684984c50b901dd8768c4e511d0 100644
--- a/modules/gui/pymod/scene/line_trace_widget.py
+++ b/modules/gui/pymod/scene/line_trace_widget.py
@@ -72,9 +72,11 @@ class LineTraceWidget(RenderModeWidget):
     
   def UpdateAA(self, value):
     self.GetOptions().SetAALines(value)
+    self.ApplyOptions()
     
   def UpdateLineWidth(self, value):
     self.GetOptions().SetLineWidth(value)
+    self.ApplyOptions()
     
   def UpdateGui(self,options):
     self.aa_rendering_cb_.setChecked(options.GetAALines())    
diff --git a/modules/gui/pymod/scene/loader_list_model.py b/modules/gui/pymod/scene/loader_list_model.py
index 26557a49c9135512eca070ae4fd0b7a7b81b44c5..c033df0388f7f6f36e1290c371318d4b4c91a6a4 100644
--- a/modules/gui/pymod/scene/loader_list_model.py
+++ b/modules/gui/pymod/scene/loader_list_model.py
@@ -36,6 +36,8 @@ class LoaderListModel(QtCore.QAbstractListModel):
         self.AddLoaderToInfo(name, loader)
       self.emit(QtCore.SIGNAL("dataChanged"),model_index, end_index)
       gui.FileLoader.GetLoaderManager().AddRemoteSiteLoader(name, loader)
+      if(loader.IsDefault()):
+        gui.FileLoader.GetLoaderManager().SetDefaultRemoteSiteIdent(name)
       return True
     return False
   
diff --git a/modules/gui/pymod/scene/loaders.xml b/modules/gui/pymod/scene/loaders.xml
index dd1ad36c32fe3ce0fca9b6754b99375d27f16cff..90021f812619a5d9cfd78745ff439b0fc9db0819 100644
--- a/modules/gui/pymod/scene/loaders.xml
+++ b/modules/gui/pymod/scene/loaders.xml
@@ -2,7 +2,7 @@
 <EMDataInfo>
  <GenericLoaders>
   <GenericLoader ExtName="pdbredo" Name="pdbredo" Url="http://www.cmbi.ru.nl/pdb_redo/ak/${ID}/${ID}_besttls.pdb" />
-  <GenericLoader ExtName="pdborg" Name="pdb.org" Url="http://www.pdb.org/pdb/files/${ID}.pdb" />
+  <GenericLoader ExtName="" Name="pdb.org" Url="http://www.pdb.org/pdb/files/${ID}.pdb" Default="1" />
   <GenericLoader ExtName="emdb" Name="emdb" Url="ftp://emdb.rutgers.edu/structures/EMD-${ID}/map/emd_${ID}.map.gz" FileType="map.gz" Img="1"/>  
  </GenericLoaders>
 </EMDataInfo>
diff --git a/modules/gui/pymod/scene/map_level_widget.py b/modules/gui/pymod/scene/map_level_widget.py
new file mode 100644
index 0000000000000000000000000000000000000000..8ef01e08c0713691fc4637148525891a90f20821
--- /dev/null
+++ b/modules/gui/pymod/scene/map_level_widget.py
@@ -0,0 +1,255 @@
+#------------------------------------------------------------------------------
+# This file is part of the OpenStructure project <www.openstructure.org>
+#
+# Copyright (C) 2008-2010 by the OpenStructure authors
+#
+# This library is free software; you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation; either version 3.0 of the License, or (at your option)
+# any later version.
+# This library is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this library; if not, write to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+#------------------------------------------------------------------------------
+# -*- coding: utf-8 -*-
+import math
+from ost import gui
+from ost import gfx
+try: 
+  from ost import img
+  _img_present=True
+except ImportError:
+  _img_present=False
+  pass
+from PyQt4 import QtCore, QtGui
+
+from preset_widget import PresetWidget
+
+class AdditionalSettingsWidget(QtGui.QStackedWidget):
+  def __init__(self, parent=None):
+    QtGui.QStackedWidget.__init__(self, parent)
+    self.map_widget_ = MapLevelWidget(self)
+    self.preset_widget_ = PresetWidget(self)
+    self.addWidget(self.preset_widget_);
+    self.addWidget(self.map_widget_);
+    self.setContentsMargins(0,0,0,0)
+    self.setMinimumSize(self.preset_widget_.minimumSize())
+    
+  def Update(self):
+    self.setEnabled(True)
+    scene_selection = gui.SceneSelection.Instance()
+    all_img = True
+    all_entity = True
+    for i in range(0,scene_selection.GetActiveNodeCount()):
+      node = scene_selection.GetActiveNode(i)
+      if not (isinstance(node, gfx.Entity) or isinstance(node, gfx.Surface)):
+        all_entity = False
+      if (not _img_present) or (not isinstance(node, gfx.MapIso)):
+        all_img = False
+    if all_img:
+      self.map_widget_.Update()
+      self.setMinimumSize(self.map_widget_.minimumSize())
+      self.resize(self.map_widget_.minimumSize())
+      self.setMinimumSize(self.map_widget_.minimumSize())
+      self.setCurrentWidget(self.map_widget_)
+    elif all_entity:
+      self.preset_widget_.Update()
+      self.setMinimumSize(self.preset_widget_.minimumSize())
+      self.resize(self.preset_widget_.minimumSize())
+      self.setMinimumSize(self.preset_widget_.minimumSize())
+      self.setCurrentWidget(self.preset_widget_)
+    else:
+      self.setEnabled(False)
+    
+#Map Level Widget
+class MapLevelWidget(QtGui.QWidget):
+  def __init__(self, parent=None):
+    QtGui.QWidget.__init__(self, parent)
+    
+    #Create Ui elements
+    self.map_level_label_ = QtGui.QLabel("Map Contour Level")
+    self.font = self.map_level_label_.font()
+    self.font.setBold(True)
+    
+    self.level_preview_ = LevelPreview()
+    
+    self.level_spinbox_ = QtGui.QDoubleSpinBox()
+    self.level_spinbox_.setDecimals(3)
+    self.level_spinbox_.setSingleStep(0.05)
+    
+    grid = QtGui.QGridLayout()
+    grid.setContentsMargins(0,5,0,0)
+    grid.addWidget(self.level_preview_, 0, 0, 1, 4)
+    grid.addWidget(self.map_level_label_, 1, 0, 1, 3)
+    grid.addWidget(self.level_spinbox_,1,3,1,1)
+    grid.setRowStretch(3, 1)
+    self.setLayout(grid)
+    
+    QtCore.QObject.connect(self.level_preview_, QtCore.SIGNAL("levelUpdated"), self.UpdateLevel)
+    QtCore.QObject.connect(self.level_preview_, QtCore.SIGNAL("levelModified"), self.ModifySpinBox)
+    QtCore.QObject.connect(self.level_spinbox_, QtCore.SIGNAL("valueChanged(double)"), self.UpdateLevel)
+
+    self.setMinimumSize(250,200)
+        
+  def Update(self):
+    scene_selection = gui.SceneSelection.Instance()
+    if(scene_selection.GetActiveNodeCount()==1):
+      node = scene_selection.GetActiveNode(0)
+      if _img_present and isinstance(node, gfx.MapIso):
+        try:
+          self.level_preview_.SetBins(node.GetHistogram())
+          self.level_preview_.SetMinimum(node.GetMinLevel())
+          self.level_spinbox_.setMinimum(node.GetMinLevel())
+          self.level_preview_.SetMaximum(node.GetMaxLevel())
+          self.level_spinbox_.setMaximum(node.GetMaxLevel())
+          self.level_preview_.SetLevel(node.GetLevel())
+          self.level_spinbox_.show()
+          self.font.setBold(True)
+          self.map_level_label_.setText("Map Contour Level")
+          self.setEnabled(True)
+        except UserWarning:
+          self.font.setBold(False)
+          self.map_level_label_.setText("Map uniformly filled with level %s"%node.GetLevel())
+          self.level_spinbox_.hide()
+          self.setEnabled(False)
+      else:
+        self.setEnabled(False)
+    else:
+      self.setEnabled(False)
+        
+  def UpdateLevel(self, level):
+    scene_selection = gui.SceneSelection.Instance()
+    if(scene_selection.GetActiveNodeCount()==1):
+      node = scene_selection.GetActiveNode(0)
+      node.SetLevel(level)
+      
+  def ModifySpinBox(self, level):
+    QtCore.QObject.disconnect(self.level_spinbox_, QtCore.SIGNAL("valueChanged(double)"), self.UpdateLevel)
+    self.level_spinbox_.setValue(level)
+    QtCore.QObject.connect(self.level_spinbox_, QtCore.SIGNAL("valueChanged(double)"), self.UpdateLevel)
+        
+#Level Preview
+class LevelPreview(QtGui.QWidget):
+  def __init__(self, parent=None):
+    QtGui.QWidget.__init__(self, parent)
+    
+    #Defaults
+    self.border_offset_ = 3
+    self.preview_height_ = 150
+    QtGui.QWidget.__init__(self, parent)
+    
+    #Ui
+    self.setMinimumSize(0, self.preview_height_ + 4)
+
+    self.bins_ = None
+    self.level_ = 0
+    self.minimum_ = 0
+    self.maximum_ = 0
+    
+    self.paint_mouse_=False
+    
+  def SetBins(self, bins):
+    self.bins_ = bins
+    self.update()
+
+  def SetMaximum(self, max):
+    self.maximum_ = max
+
+  def SetMinimum(self, min):
+    self.minimum_ = min
+    
+  def SetLevel(self, level):
+    self.level_ = level
+
+  def GetLevel(self):
+    return self.level_
+    
+  def paintEvent(self, event):   
+    if self.isEnabled() and self.bins_ is not None:
+      painter = QtGui.QPainter()
+      if painter.begin(self):
+        self.PaintBackground(painter)
+        self.PaintBins(painter)
+        self.PaintLevel(painter)
+        if(self.paint_mouse_):
+          self.PaintMouse(painter)
+      painter.end()
+
+  def PaintBackground(self,painter):
+    size = self.size()
+    painter.setBrush(QtCore.Qt.white)
+    painter.setPen(QtCore.Qt.white)
+    painter.drawRect(self.border_offset_,
+                   self.border_offset_,
+                   size.width() - 2 * self.border_offset_,
+                   self.preview_height_)
+
+  def PaintBins(self,painter):
+    size = self.size()
+    bin_cnt = len(self.bins_)
+    bin_width = (size.width()-2* self.border_offset_) / float(bin_cnt)
+    max=0
+    for b in self.bins_:
+      if(b>max):
+        max = b
+    max = math.log(max)
+    if(max > 0):
+      painter.setBrush(QtCore.Qt.black)
+      painter.setPen(QtCore.Qt.black)
+      for i in range(0,bin_cnt):
+        bin_height = self.bins_[i]
+        if(bin_height>0):
+          bin_height = math.floor((math.log(bin_height)/max)*(self.preview_height_-2*(self.border_offset_)))
+          painter.drawRect(self.border_offset_ + (i*bin_width),
+                         self.preview_height_ - bin_height,
+                         bin_width,
+                         bin_height)
+
+  def PaintLevel(self,painter):
+    size = self.size()
+    width = size.width()-(2* self.border_offset_)
+    tot_len = self.maximum_-self.minimum_
+    if(tot_len>0):
+      cur_len = self.level_-self.minimum_
+      painter.setBrush(QtCore.Qt.red)
+      painter.setPen(QtCore.Qt.red)
+      painter.drawRect((width / tot_len) * cur_len,
+                     self.border_offset_,
+                     1,
+                     self.preview_height_)
+
+  def PaintMouse(self,painter):
+    size = self.size()
+    width = size.width()-(2* self.border_offset_)
+    painter.setBrush(QtCore.Qt.gray)
+    painter.setPen(QtCore.Qt.gray)
+    pos=self.mapFromGlobal(QtGui.QCursor.pos())
+    painter.drawRect(pos.x(),
+                   self.border_offset_,
+                   1,
+                   self.preview_height_)
+
+  def mouseReleaseEvent(self, event):
+    self.paint_mouse_=False
+    size = self.size()
+    width = size.width()-(2* self.border_offset_)
+    tot_len = self.maximum_-self.minimum_
+    self.level_ = self.minimum_ + float(event.x())/width * tot_len
+    self.update()
+    self.emit(QtCore.SIGNAL("levelUpdated"),(self.level_))
+  
+  def mousePressEvent(self,event):
+    self.paint_mouse_=True
+    
+  def mouseMoveEvent(self, event):
+    size = self.size()
+    width = size.width()-(2* self.border_offset_)
+    tot_len = self.maximum_-self.minimum_
+    level = self.minimum_ + float(event.x())/width * tot_len
+    self.emit(QtCore.SIGNAL("levelModified"),(level))
+    self.update()
\ No newline at end of file
diff --git a/modules/gui/pymod/scene/preset.py b/modules/gui/pymod/scene/preset.py
index f46c3cd07dbd007b14bd0cff495568fa919bb26c..2b4f41ba0454d85e49a71a52c653b6b485bda2e3 100644
--- a/modules/gui/pymod/scene/preset.py
+++ b/modules/gui/pymod/scene/preset.py
@@ -25,7 +25,7 @@ from PyQt4 import QtGui
 from ost.gfx import ColorOp
 
 #Rendering Preset
-class Preset():
+class Preset:
   NAME_ATTRIBUTE_NAME = "Name"
   OP_GROUP_NAME = "Op"
   CLASS_NAME_ATTRIBUTE_NAME = "ClassName"
diff --git a/modules/gui/pymod/scene/preset_editor_list_model.py b/modules/gui/pymod/scene/preset_editor_list_model.py
index d796e5352c009075e8c236673ebcad6c0dbcdea0..a30fc13c31f098081f587978d9c0039110fcec42 100644
--- a/modules/gui/pymod/scene/preset_editor_list_model.py
+++ b/modules/gui/pymod/scene/preset_editor_list_model.py
@@ -42,11 +42,12 @@ class PresetEditorListModel(QtCore.QAbstractListModel):
     if index.isValid() and index.row()< self.rowCount():
       data = self.preset_.GetOp(index.row())
       if role == QtCore.Qt.DisplayRole:
+        name=data.GetName()
         selection=str(data.GetSelection())
         if(len(selection)>0):
-          return QtCore.QVariant(selection)
+          return QtCore.QVariant(str("%s (%s)"%(name,selection.replace(os.linesep, " "))))
         else:
-          return QtCore.QVariant("all")
+          return QtCore.QVariant(str("%s (all)"%name))
     return QtCore.QVariant()
 
   def setData(self, index, value, role):
diff --git a/modules/gui/pymod/scene/preset_editor_widget.py b/modules/gui/pymod/scene/preset_editor_widget.py
index 513040bfc2bb08bdcb2998736209ae3231754ba9..457cda457fa8a09f1ffd54cf13bc03dc79ceeb20 100644
--- a/modules/gui/pymod/scene/preset_editor_widget.py
+++ b/modules/gui/pymod/scene/preset_editor_widget.py
@@ -20,6 +20,7 @@
 
 from ost import gui
 from ost import gfx
+from ost import mol
 from datetime import datetime
 from datetime import datetime
 from PyQt4 import QtCore, QtGui
@@ -29,6 +30,7 @@ from gradient_editor_widget import GradientPreview
 from gradient_editor_widget import GradientEdit
 from preset_editor_list_model import PresetEditorListModel
 from immutable_gradient_info_handler import ImmutableGradientInfoHandler
+from query_editor import QueryEditorWidget
 from ost.mol import Prop
 from ost.gfx import ByElementColorOp
 from ost.gfx import ByChainColorOp
@@ -181,8 +183,7 @@ class PresetEditor(QtGui.QDialog):
 class UniformColorOpWidget(QtGui.QDialog):
   def __init__(self, parent=None):
     QtGui.QDialog.__init__(self, parent)
-    selection_label = QtGui.QLabel("Selection")
-    self.selection_edit_ = QtGui.QLineEdit()
+    self.query_editor_ = QueryEditorWidget(self)
 
     detail_label = QtGui.QLabel("Parts")
     self.detail_selection_cb_ = QtGui.QComboBox()
@@ -203,8 +204,7 @@ class UniformColorOpWidget(QtGui.QDialog):
         
     grid = QtGui.QGridLayout()
     grid.setContentsMargins(0,5,0,0)
-    grid.addWidget(selection_label, 0, 0, 1, 1)
-    grid.addWidget(self.selection_edit_, 0, 1, 1, 1)
+    grid.addWidget(self.query_editor_, 0, 0, 1, 2)
     grid.addWidget(detail_label, 1, 0, 1, 1)
     grid.addWidget(self.detail_selection_cb_, 1, 1, 1, 1)
     grid.addWidget(color_label, 2, 0, 1, 1)
@@ -217,18 +217,19 @@ class UniformColorOpWidget(QtGui.QDialog):
     QtCore.QObject.connect(self.cancel_button_, QtCore.SIGNAL("clicked()"), self.Cancel)
     
   def GetOp(self):
-    ufco = UniformColorOp("",gfx.Color(1,1,1,1))
+    qv=mol.QueryViewWrapper(self.query_editor_.GetQuery(),self.query_editor_.GetQueryFlags())
+    ufco = UniformColorOp(qv,gfx.Color(1,1,1,1))
     
     detail = self.detail_selection_cb_.itemData(self.detail_selection_cb_.currentIndex()).toPyObject()
     ufco.SetMask(detail)
     qcolor = self.color_select_widget_.GetColor()
     color=gfx.Color(qcolor.red()/255.0,qcolor.green()/255.0,qcolor.blue()/255.0,qcolor.alpha()/255.0)
     ufco.SetColor(color)
-    ufco.SetSelection(str(self.selection_edit_.text()))
     return ufco
 
   def SetOp(self, ufco):
-    self.selection_edit_.setText(ufco.GetSelection())
+    self.query_editor_.SetQuery(ufco.GetSelection())
+    self.query_editor_.SetQueryFlags(ufco.GetSelectionFlags())
     found=False
     for i in range(0,self.detail_selection_cb_.count()):
       mask = self.detail_selection_cb_.itemData(i).toPyObject()
@@ -253,8 +254,7 @@ class GradientLevelColorOpWidget(QtGui.QDialog):
   def __init__(self, parent=None):
     QtGui.QDialog.__init__(self, parent)
     
-    selection_label = QtGui.QLabel("Selection")
-    self.selection_edit_ = QtGui.QLineEdit()
+    self.query_editor_ = QueryEditorWidget(self)
     
     detail_label = QtGui.QLabel("Parts")
     self.detail_selection_cb_ = QtGui.QComboBox()
@@ -313,8 +313,7 @@ class GradientLevelColorOpWidget(QtGui.QDialog):
         
     grid = QtGui.QGridLayout()
     grid.setContentsMargins(0,5,0,0)
-    grid.addWidget(selection_label, 0, 0, 1, 1)
-    grid.addWidget(self.selection_edit_, 0, 1, 1, 1)
+    grid.addWidget(self.query_editor_, 0, 0, 1, 2)
     grid.addWidget(detail_label, 1, 0, 1, 1)
     grid.addWidget(self.detail_selection_cb_, 1, 1, 1, 1)
     grid.addWidget(property_label, 2, 0, 1, 1)
@@ -347,7 +346,7 @@ class GradientLevelColorOpWidget(QtGui.QDialog):
     gradient = self.gradient_edit_.GetGfxGradient()
     
     detail = self.detail_selection_cb_.itemData(self.detail_selection_cb_.currentIndex()).toPyObject()
-    selection = str(self.selection_edit_.text())
+    qv=mol.QueryViewWrapper(self.query_editor_.GetQuery(),self.query_editor_.GetQueryFlags())
     prop = str()
     level = Prop.Level()
     if(self.property_edit_.isEnabled()):
@@ -357,15 +356,16 @@ class GradientLevelColorOpWidget(QtGui.QDialog):
       prop = str(self.prop_combo_box_.itemData(self.prop_combo_box_.currentIndex()).toPyObject())
     
     if(self.auto_calc_.isChecked()):
-      return GradientLevelColorOp(selection, detail, prop, gradient, level)
+      return GradientLevelColorOp(qv, detail, prop, gradient, level)
     else:
       minv = self.minv_.value()
       maxv = self.maxv_.value()
-      return GradientLevelColorOp(selection, detail, prop, gradient, minv, maxv, level)
+      return GradientLevelColorOp(qv, detail, prop, gradient, minv, maxv, level)
       
     
   def SetOp(self, glco):
-    self.selection_edit_.setText(glco.GetSelection())
+    self.query_editor_.SetQuery(glco.GetSelection())
+    self.query_editor_.SetQueryFlags(glco.GetSelectionFlags())
     found=False
     for i in range(0,self.detail_selection_cb_.count()):
       mask = self.detail_selection_cb_.itemData(i).toPyObject()
@@ -422,8 +422,7 @@ class GradientLevelColorOpWidget(QtGui.QDialog):
 class ByElementColorOpWidget(QtGui.QDialog):
   def __init__(self, parent=None):
     QtGui.QDialog.__init__(self, parent)
-    selection_label = QtGui.QLabel("Selection")
-    self.selection_edit_ = QtGui.QLineEdit()
+    self.query_editor_ = QueryEditorWidget(self)
 
     detail_label = QtGui.QLabel("Parts")
     self.detail_selection_cb_ = QtGui.QComboBox()
@@ -440,8 +439,7 @@ class ByElementColorOpWidget(QtGui.QDialog):
     
     grid = QtGui.QGridLayout()
     grid.setContentsMargins(0,5,0,0)
-    grid.addWidget(selection_label, 0, 0, 1, 1)
-    grid.addWidget(self.selection_edit_, 0, 1, 1, 1)
+    grid.addWidget(self.query_editor_, 0, 0, 1, 2)
     grid.addWidget(detail_label, 1, 0, 1, 1)
     grid.addWidget(self.detail_selection_cb_, 1, 1, 1, 1)
     grid.addLayout(self.hbox_,2,0,1,2)
@@ -453,12 +451,13 @@ class ByElementColorOpWidget(QtGui.QDialog):
     
   def GetOp(self):
     detail = self.detail_selection_cb_.itemData(self.detail_selection_cb_.currentIndex()).toPyObject()
-    selection = str(self.selection_edit_.text())
-    beco = ByElementColorOp(selection, detail)
+    qv=mol.QueryViewWrapper(self.query_editor_.GetQuery(),self.query_editor_.GetQueryFlags())
+    beco = ByElementColorOp(qv, detail)
     return beco
 
   def SetOp(self, beco):
-    self.selection_edit_.setText(beco.GetSelection())
+    self.query_editor_.SetQuery(beco.GetSelection())
+    self.query_editor_.SetQueryFlags(beco.GetSelectionFlags())
     found=False
     for i in range(0,self.detail_selection_cb_.count()):
       mask = self.detail_selection_cb_.itemData(i).toPyObject()
@@ -479,8 +478,7 @@ class ByElementColorOpWidget(QtGui.QDialog):
 class ByChainColorOpWidget(QtGui.QDialog):
   def __init__(self, parent=None):
     QtGui.QDialog.__init__(self, parent)
-    selection_label = QtGui.QLabel("Selection")
-    self.selection_edit_ = QtGui.QLineEdit()
+    self.query_editor_ = QueryEditorWidget(self)
 
     detail_label = QtGui.QLabel("Parts")
     self.detail_selection_cb_ = QtGui.QComboBox()
@@ -497,8 +495,7 @@ class ByChainColorOpWidget(QtGui.QDialog):
     
     grid = QtGui.QGridLayout()
     grid.setContentsMargins(0,5,0,0)
-    grid.addWidget(selection_label, 0, 0, 1, 1)
-    grid.addWidget(self.selection_edit_, 0, 1, 1, 1)
+    grid.addWidget(self.query_editor_, 0, 0, 1, 2)
     grid.addWidget(detail_label, 1, 0, 1, 1)
     grid.addWidget(self.detail_selection_cb_, 1, 1, 1, 1)
     grid.addLayout(self.hbox_,2,0,1,2)
@@ -510,12 +507,13 @@ class ByChainColorOpWidget(QtGui.QDialog):
     
   def GetOp(self):
     detail = self.detail_selection_cb_.itemData(self.detail_selection_cb_.currentIndex()).toPyObject()
-    selection = str(self.selection_edit_.text())
-    bcco = ByChainColorOp(selection, detail)
+    qv=mol.QueryViewWrapper(self.query_editor_.GetQuery(),self.query_editor_.GetQueryFlags())
+    bcco = ByChainColorOp(qv, detail)
     return bcco
 
   def SetOp(self, bcco):
-    self.selection_edit_.setText(bcco.GetSelection())
+    self.query_editor_.SetQuery(bcco.GetSelection())
+    self.query_editor_.SetQueryFlags(bcco.GetSelectionFlags())
     found=False
     for i in range(0,self.detail_selection_cb_.count()):
       mask = self.detail_selection_cb_.itemData(i).toPyObject()
@@ -536,8 +534,7 @@ class ByChainColorOpWidget(QtGui.QDialog):
 class RenderOpWidget(QtGui.QDialog):
   def __init__(self, parent=None):
     QtGui.QDialog.__init__(self, parent)
-    selection_label = QtGui.QLabel("Selection")
-    self.selection_edit_ = QtGui.QLineEdit()
+    self.query_editor_ = QueryEditorWidget(self)
   
     self.keep_ = QtGui.QCheckBox("Keep")
     self.keep_.setChecked(False)
@@ -571,8 +568,7 @@ class RenderOpWidget(QtGui.QDialog):
     
     grid = QtGui.QGridLayout()
     grid.setContentsMargins(0,5,0,0)
-    grid.addWidget(selection_label, 0, 0, 1, 1)
-    grid.addWidget(self.selection_edit_, 0, 1, 1, 1)
+    grid.addWidget(self.query_editor_, 0, 0, 1, 2)
     grid.addWidget(self.keep_, 1, 1, 1, 1)
     grid.addWidget(render_label,2,0,1,1)
     grid.addWidget(self.render_modes_,2,1,1,1)
@@ -584,13 +580,15 @@ class RenderOpWidget(QtGui.QDialog):
     QtCore.QObject.connect(self.cancel_button_, QtCore.SIGNAL("clicked()"), self.Cancel)
     
   def GetOp(self):
-    selection = str(self.selection_edit_.text())
+    selection = self.query_editor_.GetQueryText()
+    flags = self.query_editor_.GetQueryFlags()
     render_mode = self.render_modes_list_[self.render_modes_.currentIndex()]
-    ro = RenderOp(render_mode, selection, self.keep_.isChecked())
+    ro = RenderOp(render_mode, selection, flags, self.keep_.isChecked())
     return ro
 
   def SetOp(self, ro):
-    self.selection_edit_.setText(ro.GetSelection())
+    self.query_editor_.SetQuery(ro.GetSelection())
+    self.query_editor_.SetQueryFlags(ro.GetSelectionFlags())
     found=False
     for i in range(0,self.render_modes_.count()):
       render_mode = self.render_modes_list_[i]
@@ -611,8 +609,7 @@ class RenderOpWidget(QtGui.QDialog):
 class VisibilityOpWidget(QtGui.QDialog):
   def __init__(self, parent=None):
     QtGui.QDialog.__init__(self, parent)
-    selection_label = QtGui.QLabel("Selection")
-    self.selection_edit_ = QtGui.QLineEdit()
+    self.query_editor_ = QueryEditorWidget(self)
   
     self.visible_ = QtGui.QCheckBox("Visible")
     self.visible_.setChecked(True)
@@ -626,8 +623,7 @@ class VisibilityOpWidget(QtGui.QDialog):
     
     grid = QtGui.QGridLayout()
     grid.setContentsMargins(0,5,0,0)
-    grid.addWidget(selection_label, 0, 0, 1, 1)
-    grid.addWidget(self.selection_edit_, 0, 1, 1, 1)
+    grid.addWidget(self.query_editor_, 0, 0, 1, 2)
     grid.addWidget(self.visible_, 1, 1, 1, 1)
     grid.addLayout(self.hbox_,2,0,1,2)
     grid.setRowStretch(1, 1)
@@ -637,16 +633,18 @@ class VisibilityOpWidget(QtGui.QDialog):
     QtCore.QObject.connect(self.cancel_button_, QtCore.SIGNAL("clicked()"), self.Cancel)
     
   def GetOp(self):
-    selection = str(self.selection_edit_.text())
-    vo = VisibilityOp(selection, self.visible_.isChecked())
+    selection = self.query_editor_.GetQueryText()
+    flags = self.query_editor_.GetQueryFlags()
+    vo = VisibilityOp(selection, flags, self.visible_.isChecked())
     return vo
 
-  def SetOp(self, ro):
-    self.selection_edit_.setText(ro.GetSelection())
-    self.visible_.setChecked(ro.IsVisible())
+  def SetOp(self, vo):
+    self.query_editor_.SetQuery(vo.GetSelection())
+    self.query_editor_.SetQueryFlags(vo.GetSelectionFlags())
+    self.visible_.setChecked(vo.IsVisible())
   
   def Ok(self):
     self.accept()
     
   def Cancel(self):
-    self.reject()
\ No newline at end of file
+    self.reject()
diff --git a/modules/gui/pymod/scene/preset_widget.py b/modules/gui/pymod/scene/preset_widget.py
index d581a38ea137c80a16baaf07584f8ed81f25986d..dc97b10f78d5d0be6700b9b435e3702cdf7f9833 100644
--- a/modules/gui/pymod/scene/preset_widget.py
+++ b/modules/gui/pymod/scene/preset_widget.py
@@ -23,6 +23,7 @@ import ost
 import os
 from datetime import datetime
 from PyQt4 import QtCore, QtGui
+from scene_selection_helper import SelHelper
 from preset_list_model import PresetListModel
 from preset_editor_widget import PresetEditor
 from preset import Preset
@@ -67,7 +68,7 @@ class PresetWidget(QtGui.QWidget):
   
     QtCore.QObject.connect(self.list_view_, QtCore.SIGNAL("doubleClicked(const QModelIndex)"), self.Load)
     
-    self.setMinimumSize(250,150)
+    self.setMinimumSize(250,200)
     
   def CreateImmutableContextMenu(self):  
     self.immucontext_menu_ = QtGui.QMenu("Context menu", self)
@@ -145,16 +146,13 @@ class PresetWidget(QtGui.QWidget):
   
   def Update(self):
     self.setEnabled(True)
-    scene_selection = gui.SceneSelection.Instance()
-    if scene_selection.GetActiveNodeCount() == 0:
+    if SelHelper().CheckAllFlags(SelHelper.NO_SELECTION):
       self.setEnabled(False)
       return
     
-    for i in range(0,scene_selection.GetActiveNodeCount()):
-      entity = scene_selection.GetActiveNode(i)
-      if not isinstance(scene_selection.GetActiveNode(i), gfx.Entity):
-        self.setEnabled(False)
-        return
+    if SelHelper().CheckNotFlags(SelHelper.HAS_ENTITY | SelHelper.IS_ONE_TYPE):
+      self.setEnabled(False)
+      return
 
   def Rename(self):
     if(self.list_view_.currentIndex().isValid()):
diff --git a/modules/gui/pymod/scene/presets.xml b/modules/gui/pymod/scene/presets.xml
index f73dbd879951224b5d7e1d75b5f03878a68618b4..4659e4e26f3ee17c6555e0edc5e4938f9943161c 100644
--- a/modules/gui/pymod/scene/presets.xml
+++ b/modules/gui/pymod/scene/presets.xml
@@ -2,28 +2,54 @@
 <EMDataInfo>
  <Presets>
   <Preset Name="Secondary Structure" >
-   <Op ClassName="VisibilityOp" Index="0"  Visible="1" />
+   <Op ClassName="VisibilityOp" Index="0"  Visible="1" Flags="0"/>
    <Op ClassName="UniformColorOp" Index="1">
-    <ColorOp>2 rtype=helix</ColorOp>0	1	0	1</Op>
+    <ColorOp>2 0 rtype=helix</ColorOp>0	1	0	1</Op>
    <Op ClassName="UniformColorOp" Index="2">
-    <ColorOp>2 rtype=ext</ColorOp>1	0	0	1</Op>
+    <ColorOp>2 0 rtype=ext</ColorOp>1	0	0	1</Op>
    <Op ClassName="UniformColorOp" Index="3">
-    <ColorOp>2 rtype!=ext,helix</ColorOp>0.5  0.5	0.5	1</Op>
+    <ColorOp>2 0 rtype!=ext,helix</ColorOp>0.5  0.5	0.5	1</Op>
    <Op ClassName="UniformColorOp" Index="4">
-    <ColorOp>1 rtype=helix</ColorOp>0.7 1.0 0.8 1</Op>
+    <ColorOp>1 0 rtype=helix</ColorOp>0.7 1.0 0.8 1</Op>
    <Op ClassName="UniformColorOp" Index="5">
-    <ColorOp>1 rtype!=ext,helix</ColorOp>1.0 0.8 0.2 1</Op>
+    <ColorOp>1 0 rtype!=ext,helix</ColorOp>1.0 0.8 0.2 1</Op>
   </Preset>
   <Preset Name="Highlight Ligand (Carbon)" >
-   <Op Keep="0" RenderMode="HSC" ClassName="RenderOp" Index="0" ></Op>
-   <Op Keep="0" RenderMode="CUSTOM" ClassName="RenderOp" Index="1" >ishetatm=1 and not rname==HOH</Op>
-   <Op ClassName="ByElementColorOp" Index="2" >3 </Op>
+   <Op Keep="0" RenderMode="HSC" ClassName="RenderOp" Index="0" Flags="0"></Op>
+   <Op Keep="0" RenderMode="CUSTOM" ClassName="RenderOp" Index="1" Flags="0">ishetatm=1 and not rname==HOH</Op>
+   <Op ClassName="ByElementColorOp" Index="2" >3 0</Op>
    <Op ClassName="UniformColorOp" Index="3">
-    <ColorOp>2 ishetatm=1 and ele=C</ColorOp>0     1       0       1</Op>
+    <ColorOp>2 0 ishetatm=1 and ele=C</ColorOp>0     1       0       1</Op>
   </Preset>
   <Preset Name="Hydrophobic" >
    <Op ClassName="UniformColorOp" Index="0" >
-    <ColorOp>3  rname=GLY,ALA,VAL,LEU,ILE,PHE,TYR,TRP,LYS,HIS,CYS,THR</ColorOp>0  0.666667  1 1</Op>
+    <ColorOp>3  0 rname=GLY,ALA,VAL,LEU,ILE,PHE,TYR,TRP,LYS,HIS,CYS,THR</ColorOp>0  0.666667  1 1</Op>
+  </Preset>
+  <Preset Name="Chains">
+   <Op Keep="0" Flags="0" RenderMode="HSC" ClassName="RenderOp" Index="0"/>
+   <Op ClassName="ByChainColorOp" Index="1">2 0 </Op>
+   <Op ClassName="UniformColorOp" Index="2">
+    <ColorOp>1  0 </ColorOp>1 1 1 1</Op>
+   <Op Keep="1" Flags="0" RenderMode="CUSTOM" ClassName="RenderOp" Index="3">ishetatm=1 and rname!=HOH</Op>
+   <Op ClassName="ByElementColorOp" Index="4">3 0 ishetatm=1 and rname!=HOH</Op>
+   <Op ClassName="UniformColorOp" Index="5">
+    <ColorOp>3  0 ishetatm=1 and ele=C</ColorOp>0 1 0 1</Op>
+  </Preset>
+  <Preset Name="Property">
+   <Op ClassName="UniformColorOp" Index="0">
+    <ColorOp>3  0 rname=GLY,ALA,VAL,LEU,ILE</ColorOp>0.658824 0.658824  0.658824  1</Op>
+   <Op ClassName="UniformColorOp" Index="1">
+    <ColorOp>3  0 rname=PHE,TYR,TRP</ColorOp>1  0.666667  0 1</Op>
+   <Op ClassName="UniformColorOp" Index="2">
+    <ColorOp>3  0 rname=CYS,MET</ColorOp>1  1 0 1</Op>
+   <Op ClassName="UniformColorOp" Index="3">
+    <ColorOp>3  0 rname=SER,THR</ColorOp>0  0.666667  0 1</Op>
+   <Op ClassName="UniformColorOp" Index="4">
+    <ColorOp>3  0 rname=LYS,ARG,HIS</ColorOp>1  0 0 1</Op>
+   <Op ClassName="UniformColorOp" Index="5">
+    <ColorOp>3  0 rname=ASP,GLU,ASN,GLN</ColorOp>0.0980392  0.443137  1 1</Op>
+   <Op ClassName="UniformColorOp" Index="6">
+    <ColorOp>3  0 rname=PRO</ColorOp>0  1 1 1</Op>
   </Preset>
  </Presets>
 </EMDataInfo>
diff --git a/modules/gui/pymod/scene/query_editor.py b/modules/gui/pymod/scene/query_editor.py
new file mode 100644
index 0000000000000000000000000000000000000000..fcdfc43395dd383503f796c734641e987622c8cc
--- /dev/null
+++ b/modules/gui/pymod/scene/query_editor.py
@@ -0,0 +1,142 @@
+from ost import mol
+from PyQt4 import QtCore, QtGui
+
+class QueryEditorWidget(QtGui.QWidget):
+  def __init__(self, parent=None): 
+    QtGui.QWidget.__init__(self, parent)
+    self.default_font_=QtGui.QTextCharFormat()
+    self.default_font_.setForeground(QtGui.QBrush(QtGui.QColor(0,0,0)))
+    self.error_font_=QtGui.QTextCharFormat()
+    self.error_font_.setForeground(QtGui.QBrush(QtGui.QColor(255,0,0))) 
+    self.selection_edit_=QtGui.QTextEdit(self)
+    self.selection_edit_.setFixedHeight(40)
+    self.selection_edit_.updateGeometry()
+    self.status_=QtGui.QLabel(" ",self);
+    self.status_.setWordWrap(True)
+    self.status_.setMargin(0)
+    self.status_.setAlignment(QtCore.Qt.AlignRight)
+    self.status_.setSizePolicy(QtGui.QSizePolicy(QtGui.QSizePolicy.Minimum,
+                                                 QtGui.QSizePolicy.Expanding))
+    vl=QtGui.QVBoxLayout()
+    vl.addWidget(self.selection_edit_)
+    self.no_bonds_=QtGui.QRadioButton('none')
+    self.ex_bonds_=QtGui.QRadioButton('exclusive')
+    self.in_bonds_=QtGui.QRadioButton('inclusive')
+    self.in_bonds_.setChecked(True)
+    self.match_res_=QtGui.QCheckBox('match residues')
+    
+    vl.setMargin(0)
+    vl.setSpacing(0)
+    self.setLayout(vl)
+    vl.addWidget(self.status_)
+    hl=QtGui.QHBoxLayout()
+    l=QtGui.QLabel("bonds:")
+
+    hl.addWidget(l)
+    hl.addSpacing(5)
+    hl.addWidget(self.no_bonds_)
+    hl.addWidget(self.ex_bonds_)
+    hl.addWidget(self.in_bonds_)
+    hl.addStretch(1)
+    vl.addLayout(hl)
+    vl.addWidget(self.match_res_)
+
+    self.changing_text_=False;
+    self.connect(self.selection_edit_,QtCore.SIGNAL("textChanged()"),
+                 self._StartTimer)
+    self.timer_=QtCore.QTimer()
+    QtCore.QObject.connect(self.timer_, QtCore.SIGNAL('timeout()'),
+                           self._UpdateMessage)
+    
+  def GetQueryFlags(self):
+    flags=0
+    if self.no_bonds_.isChecked():
+      flags|=mol.NO_BONDS
+    if self.ex_bonds_.isChecked():
+      flags|=mol.EXCLUSIVE_BONDS
+    if self.match_res_.isChecked():
+      flags|=mol.MATCH_RESIDUES
+    return flags
+  
+  def GetQuery(self):
+    return mol.Query(str(self.selection_edit_.toPlainText()))
+
+  def GetQueryText(self):
+    return str(self.selection_edit_.toPlainText())
+  
+  def SetQueryFlags(self,flags):
+    self.no_bonds_.setChecked(flags & mol.NO_BONDS)
+    self.ex_bonds_.setChecked(flags & mol.EXCLUSIVE_BONDS)
+    self.in_bonds_.setChecked(not (flags & mol.NO_BONDS|mol.EXCLUSIVE_BONDS))
+    self.match_res_.setChecked(flags & mol.MATCH_RESIDUES)
+  
+  def SetQuery(self,query):
+    self.selection_edit_.setText(query)
+    
+  def _StartTimer(self):
+    self.timer_.stop()
+    self.timer_.start(500)
+
+  def _UpdateMessage(self):
+    if self.changing_text_:
+      return
+    self.changing_text_ = True
+    query=self.GetQuery()
+    
+    cursor=self.selection_edit_.textCursor()
+    cursor.select(QtGui.QTextCursor.Document)
+    cursor.setCharFormat(self.default_font_)  
+    
+    if query.IsValid():
+      self.status_.setText("")
+    else:      
+      d=query.GetErrorDescription()
+      self.status_.setText("<font color='red'>%s</font>"%d.msg.strip())
+      #self.status_.setFixedSize(self.width(),self.status_.height())
+      cursor.movePosition(QtGui.QTextCursor.Start)
+      if d.range.Loc<len(query.string):
+        
+        cursor.movePosition(QtGui.QTextCursor.NextCharacter, 
+                            QtGui.QTextCursor.MoveAnchor, d.range.Loc)
+        cursor.movePosition(QtGui.QTextCursor.NextCharacter, 
+                            QtGui.QTextCursor.KeepAnchor, d.range.Length)
+        cursor.setCharFormat(self.error_font_)
+    self.changing_text_=False
+    
+class QueryDialog(QtGui.QDialog):
+  def __init__(self, title, parent=None):
+    QtGui.QDialog.__init__(self, parent)
+    l=QtGui.QVBoxLayout(self)
+    self.setWindowTitle(title)
+    self.editor=QueryEditorWidget(self)
+    l.addWidget(self.editor)
+    l.addSpacing(10)
+    l3=QtGui.QHBoxLayout()
+    ab=QtGui.QPushButton('OK')
+    ab.setDefault(True)
+    cb=QtGui.QPushButton('Cancel')
+    l3.addStretch(1)
+    l3.addWidget(cb, 0)
+    l3.addWidget(ab, 0)
+    l.addLayout(l3)
+    QtCore.QObject.connect(cb, QtCore.SIGNAL('clicked()'), self.reject)
+    QtCore.QObject.connect(ab, QtCore.SIGNAL('clicked()'), self.accept)
+    self.connect(self.editor.selection_edit_,QtCore.SIGNAL("textChanged()"),self._CheckNewline)
+
+  @property 
+  def query_flags(self):
+    return self.editor.GetQueryFlags()
+  @property
+  def query(self):
+    return self.editor.GetQueryText()
+  
+  def event(self, e):
+    if e.type() == QtCore.QEvent.KeyPress and (e.key () == QtCore.Qt.Key_Return or e.key () == QtCore.Qt.Key_Enter):
+      self.accept()
+      return True
+    else:
+      return QtGui.QDialog.event(self, e)
+  
+  def _CheckNewline(self):
+    if self.editor.GetQueryText().endswith("\n"):
+      self.accept()
\ No newline at end of file
diff --git a/modules/gui/pymod/scene/render_mode_widget.py b/modules/gui/pymod/scene/render_mode_widget.py
index 68150543a8e39cea5203021e4977590c3c8a99fe..17f099223a7bc1f0cc762fc3028998491c53481f 100644
--- a/modules/gui/pymod/scene/render_mode_widget.py
+++ b/modules/gui/pymod/scene/render_mode_widget.py
@@ -44,7 +44,7 @@ class RenderModeWidget(QtGui.QWidget):
     
     scene_selection = gui.SceneSelection.Instance()
     if scene_selection.GetActiveNodeCount() == 0 and scene_selection.GetActiveViewCount() == 0:
-      ComboOptionsWidget.setEnabled(self,False)
+      self.setEnabled(False)
       return
     
     if scene_selection.GetActiveNodeCount() > 0 :
@@ -53,24 +53,24 @@ class RenderModeWidget(QtGui.QWidget):
         if isinstance(entity, gfx.Entity):
           self.entities_.add(entity)
         else:
-          ComboOptionsWidget.setEnabled(self,False)
+          self.setEnabled(False)
           return
 
     if scene_selection.GetActiveViewCount() > 0 :
       entity = scene_selection.GetViewEntity()
       self.entities_.add(entity)
     
-    for entity in self.entities_:
+    if len(self.entities_)>0:
+      entity = self.entities_.pop()
       self.options_=entity.GetOptions(self.GetRenderMode())
-      self.entities_.remove(entity)
-      break
-    self.UpdateGui(self.options_)
-    
-    QtGui.QWidget.setEnabled(self,True)
+      self.UpdateGui(self.options_)
+      QtGui.QWidget.setEnabled(self,True)
+    else:
+      QtGui.QWidget.setEnabled(self,False)
     
   def ApplyOptions(self):
     for entity in self.entities_:
-      entity.SetOptions(self.GetRenderMode(),self.options_)
+      entity.ApplyOptions(self.GetRenderMode(), self.GetOptions())
 
   def GetOptions(self):
     return self.options_
\ No newline at end of file
diff --git a/modules/gui/pymod/scene/render_op.py b/modules/gui/pymod/scene/render_op.py
index 722bf7bc853cdcc9ddc7c009da2b420ad2d80fea..f161eff2f18937416735f04d0ea622a4ad5765c8 100644
--- a/modules/gui/pymod/scene/render_op.py
+++ b/modules/gui/pymod/scene/render_op.py
@@ -22,15 +22,20 @@ from ost import info
 from ost import gfx
 from PyQt4 import QtGui
 
-class RenderOp():
+class RenderOp:
   RENDERMODE_ATTRIBUTE_NAME = "RenderMode"
   KEEP_ATTRIBUTE_NAME = "Keep"
+  FLAGS_ATTRIBUTE_NAME = "Flags"
     
-  def __init__(self, render_mode, selection, keep=False):
+  def __init__(self, render_mode, selection, flags, keep=False):
     self.render_mode_ = render_mode
     self.selection_ = selection
     self.keep_ = keep
-    
+    self.flags_ = flags
+
+  def GetName(self):
+    return "Render mode: %s"%str(self.GetRenderMode())
+
   def SetRenderMode(self, render_mode):
     self.render_mode_ = render_mode
     
@@ -43,6 +48,12 @@ class RenderOp():
   def GetSelection(self):
     return self.selection_
 
+  def SetSelectionFlags(self, flags):
+    self.flags_ = flags
+    
+  def GetSelectionFlags(self):
+    return self.flags_
+
   def SetKeep(self, keep):
     self.keep_ = keep
 
@@ -51,11 +62,12 @@ class RenderOp():
 
   def ApplyOn(self, entity):
     if (entity is not None) and isinstance(entity, gfx.Entity):
-      entity.SetRenderMode(self.GetRenderMode(),entity.view.Select(self.GetSelection()),self.IsKept())
+      entity.SetRenderMode(self.GetRenderMode(),entity.view.Select(self.GetSelection(),self.GetSelectionFlags()),self.IsKept())
   
   def ToInfo(self,group):
     group.SetAttribute(RenderOp.RENDERMODE_ATTRIBUTE_NAME, str(self.GetRenderMode().name))
     group.SetAttribute(RenderOp.KEEP_ATTRIBUTE_NAME, str(int(self.IsKept())))
+    group.SetAttribute(RenderOp.FLAGS_ATTRIBUTE_NAME, str(self.GetSelectionFlags()))
     group.SetTextData(str(self.GetSelection()))
     
   @staticmethod
@@ -65,6 +77,9 @@ class RenderOp():
     and  group.HasAttribute(RenderOp.KEEP_ATTRIBUTE_NAME)):
       render_mode = getattr(gfx.RenderMode, group.GetAttribute(RenderOp.RENDERMODE_ATTRIBUTE_NAME))
       keep = bool(int(group.GetAttribute(RenderOp.KEEP_ATTRIBUTE_NAME)))
+      flags=0
+      if group.HasAttribute(RenderOp.FLAGS_ATTRIBUTE_NAME):
+        flags = int(group.GetAttribute(RenderOp.FLAGS_ATTRIBUTE_NAME))
       selection = group.GetTextData()
-      render_op = RenderOp(render_mode,selection,keep)
+      render_op = RenderOp(render_mode,selection,flags,keep)
     return render_op
diff --git a/modules/gui/pymod/scene/render_options_widget.py b/modules/gui/pymod/scene/render_options_widget.py
index 4b61a12166713e17f21888350171b1577806a778..cc22f3cc1f28f035b1fc4710872cca5f663cc9cc 100644
--- a/modules/gui/pymod/scene/render_options_widget.py
+++ b/modules/gui/pymod/scene/render_options_widget.py
@@ -21,7 +21,15 @@
 import sys
 from ost import gui
 from ost import gfx
+try: 
+  from ost import img
+  from wireframe_widget import WireframeWidget
+  _img_present=True
+except ImportError:
+  _img_present=False
+  pass
 from PyQt4 import QtCore, QtGui
+from scene_selection_helper import SelHelper
 from combo_options_widget import ComboOptionsWidget
 from custom_widget import CustomWidget
 from cpk_widget import CPKWidget
@@ -50,34 +58,41 @@ class RenderOptionsWidget(ComboOptionsWidget):
     self.grid_layout_.addWidget(self.stacked_widget_, 1, 0, 1, 2)
     
     #Add options to menu    
-    ComboOptionsWidget.AddWidget(self, "", EmptyMode())
-    ComboOptionsWidget.AddWidget(self, gfx.RenderMode.SIMPLE, SimpleWidget(self))
-    ComboOptionsWidget.AddWidget(self, gfx.RenderMode.CUSTOM, CustomWidget(self))
-    ComboOptionsWidget.AddWidget(self, gfx.RenderMode.CPK, CPKWidget(self))
-    ComboOptionsWidget.AddWidget(self, gfx.RenderMode.LINE_TRACE, LineTraceWidget(self))    
-    ComboOptionsWidget.AddWidget(self, gfx.RenderMode.TRACE, TraceWidget(self))
-    ComboOptionsWidget.AddWidget(self, gfx.RenderMode.SLINE, SlineWidget(self))
-    ComboOptionsWidget.AddWidget(self, gfx.RenderMode.TUBE, TubeWidget(self))
-    ComboOptionsWidget.AddWidget(self, gfx.RenderMode.HSC, HSCWidget(self))
+    self.entity_widgets_ = list()
+    self.entity_widgets_.append(["", EmptyMode()])
+    self.entity_widgets_.append([gfx.RenderMode.SIMPLE, SimpleWidget()])
+    self.entity_widgets_.append([gfx.RenderMode.CUSTOM, CustomWidget()])
+    self.entity_widgets_.append([gfx.RenderMode.CPK, CPKWidget()])
+    self.entity_widgets_.append([gfx.RenderMode.LINE_TRACE, LineTraceWidget()])
+    self.entity_widgets_.append([gfx.RenderMode.TRACE, TraceWidget()])
+    self.entity_widgets_.append([gfx.RenderMode.SLINE, SlineWidget()])
+    self.entity_widgets_.append([gfx.RenderMode.TUBE, TubeWidget()])
+    self.entity_widgets_.append([gfx.RenderMode.HSC, HSCWidget()])
 
+    self.img_widgets_ = list()
+    if _img_present:
+      self.img_widgets_.append(["", EmptyMode()])
+      self.img_widgets_.append([gfx.RenderMode.SIMPLE, WireframeWidget()])
+      self.img_widgets_.append([gfx.RenderMode.FILL, EmptyMode("Fill",gfx.RenderMode.FILL)])
+
+    self._in_view_method = False
     self.setMinimumSize(250,200)
     
   def DoSomething(self, item):
     scene_selection = gui.SceneSelection.Instance()
     for i in range(0,scene_selection.GetActiveNodeCount()):
       node = scene_selection.GetActiveNode(i)
-      if isinstance(node, gfx.Entity):
+      if isinstance(node, gfx.Entity) or (_img_present and isinstance(node, gfx.MapIso)):
         render_mode = item.GetRenderMode()
         if render_mode is not None:
           node.SetRenderMode(render_mode)     
     
     if(scene_selection.GetActiveViewCount() > 0):
       entity = scene_selection.GetViewEntity()
-      for i in range(0,scene_selection.GetActiveViewCount()):
-        view = scene_selection.GetActiveView(i)
-        render_mode = item.GetRenderMode()
-        if render_mode is not None:
-          entity.SetRenderMode(item.GetRenderMode(),view,self.keep_action_.isChecked())
+      view = scene_selection.GetViewUnion()        
+      render_mode = item.GetRenderMode()
+      if render_mode is not None:
+        entity.SetRenderMode(item.GetRenderMode(),view,self.keep_action_.isChecked())
         
     item.Update()
     self.DoResize()
@@ -85,49 +100,85 @@ class RenderOptionsWidget(ComboOptionsWidget):
   def Update(self):
     if hasattr(self, "keep_button_"):
       self.keep_button_.setEnabled(True)
-    scene_selection = gui.SceneSelection.Instance()
-    if scene_selection.GetActiveNodeCount() == 0 and scene_selection.GetActiveViewCount() == 0:
+    
+    ComboOptionsWidget.setEnabled(self,True)
+    
+    cur_widget = self.GetCurrentWidget()
+    new_render_mode = None
+    if cur_widget is not None:
+      new_render_mode = cur_widget.GetRenderMode()
+    
+    if SelHelper().CheckAllFlags(SelHelper.NO_SELECTION):
       ComboOptionsWidget.setEnabled(self,False)
       return
     
+    if not self._in_view_method:
+      for w in self.entity_widgets_:
+        self.RemoveWidget(w[0])
+      for w in self.img_widgets_:
+        self.RemoveWidget(w[0])
+
+    scene_selection = gui.SceneSelection.Instance()        
     if scene_selection.GetActiveNodeCount() > 0 :
       if hasattr(self, "keep_button_"):
         self.keep_button_.setEnabled(False)
       render_mode_valid = True
       render_mode = None
       for i in range(0,scene_selection.GetActiveNodeCount()):
-        entity = scene_selection.GetActiveNode(i)
-        if isinstance(scene_selection.GetActiveNode(i), gfx.Entity):
+        node = scene_selection.GetActiveNode(i)
+        if isinstance(scene_selection.GetActiveNode(i), gfx.GfxObj):
           if render_mode is None:
-            render_mode = entity.GetRenderMode()
-          elif render_mode != entity.GetRenderMode():
+            render_mode = node.GetRenderMode()
+          elif render_mode != node.GetRenderMode():
             render_mode_valid = False
-            break
-        else:
-          ComboOptionsWidget.setEnabled(self,False)
-          return
+ 
+    if SelHelper().CheckFlags(SelHelper.HAS_IMG | SelHelper.IS_ONE_TYPE):
+      for w in self.img_widgets_:
+        self.AddWidget(w[0], w[1])
+    elif SelHelper().CheckMinOneFlag(SelHelper.HAS_ENTITY| SelHelper.HAS_VIEW) and SelHelper().CheckNotFlags(SelHelper.HAS_IMG):
+      if not self._in_view_method:
+        for w in self.entity_widgets_:
+          self.AddWidget(w[0], w[1])
+    else:
+      ComboOptionsWidget.setEnabled(self,False)
+      return
+    
+    if SelHelper().CheckMinOneFlag(SelHelper.HAS_ENTITY| SelHelper.HAS_IMG) and SelHelper().CheckNotFlags(SelHelper.HAS_VIEW):
       if(render_mode_valid):
         ComboOptionsWidget.ChangeSelectedItem(self,render_mode)
       else:
         ComboOptionsWidget.ChangeSelectedItem(self,"")
-    
+    else:
+      if not self._in_view_method:
+        self._in_view_method = True
+      ComboOptionsWidget.ChangeSelectedItem(self,new_render_mode)
     self.GetCurrentWidget().Update()
-    
-    ComboOptionsWidget.setEnabled(self,True)
-  
+      
   def GetText(self):
     return self.text_
         
 class EmptyMode(QtGui.QWidget):
-  def __init__(self, parent=None):
+  def __init__(self, text="", render_mode=None, parent=None):
     QtGui.QLabel.__init__(self, parent)
     self.setMinimumSize(250,30)
-  
+    self.text = text
+    self.render_mode = render_mode
+    if(render_mode):
+      text_label = QtGui.QLabel(text)
+      font = text_label.font()
+      font.setBold(True)
+      grid = QtGui.QGridLayout()
+      grid.addWidget(text_label,0,0,1,1)
+      grid.addWidget(QtGui.QLabel("No Settings available"), 1, 0, 1, 3)
+      grid.setRowStretch(2,1)
+      self.setLayout(grid)
+      self.setMinimumSize(250,60)
+      
   def Update(self):
    True #Do Nothing
 
   def GetText(self):
-    return ""
+    return self.text
 
   def GetRenderMode(self):
-    return None
+    return self.render_mode
diff --git a/modules/gui/pymod/scene/scene_selection_helper.py b/modules/gui/pymod/scene/scene_selection_helper.py
new file mode 100644
index 0000000000000000000000000000000000000000..96d9cc9ff3e5802dcffadca7f215c86434c111b0
--- /dev/null
+++ b/modules/gui/pymod/scene/scene_selection_helper.py
@@ -0,0 +1,106 @@
+#------------------------------------------------------------------------------
+# This file is part of the OpenStructure project <www.openstructure.org>
+#
+# Copyright (C) 2008-2010 by the OpenStructure authors
+#
+# This library is free software; you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation; either version 3.0 of the License, or (at your option)
+# any later version.
+# This library is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this library; if not, write to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+#------------------------------------------------------------------------------
+
+import sys
+from ost import gui
+import sip
+from ost import gfx
+import ost
+import os
+try: 
+  from ost import img
+  _img_present=True
+except ImportError:
+  _img_present=False
+  pass
+
+class SelHelper:
+  __shared_state = {}
+  
+  NO_SELECTION = 0
+  HAS_ENTITY = 1
+  HAS_VIEW = 2
+  HAS_IMG = 4
+  HAS_SURFACE = 8
+  IS_ONE_TYPE = 16
+  IS_MULTI_TYPE = 32
+  SINGLE_SELECTION = 64
+  MULTI_SELECTION = 128
+    
+  def __init__(self):
+    self.__dict__ = self.__shared_state
+    if not '_ready' in dir(self):
+      self.scene_sel_ = gui.SceneSelection.Instance()
+      self.current_flags_ = 0
+      self._ready = True
+
+  def Update(self):
+    self.current_flags_ = 0
+    if self.scene_sel_.GetActiveNodeCount() == 0 and self.scene_sel_.GetActiveViewCount() == 0:
+      return
+    
+    for i in range(0,self.scene_sel_.GetActiveNodeCount()):
+      node = self.scene_sel_.GetActiveNode(i)
+      if isinstance(node, gfx.Entity):
+        self.current_flags_ = self.current_flags_ | SelHelper.HAS_ENTITY 
+      if isinstance(node, gfx.Surface):
+        self.current_flags_ = self.current_flags_ | SelHelper.HAS_SURFACE
+      if (_img_present) and isinstance(node, gfx.MapIso):
+        self.current_flags_ = self.current_flags_ | SelHelper.HAS_IMG
+    
+    if self.scene_sel_.GetActiveViewCount() > 0:
+      self.current_flags_ = self.current_flags_ | SelHelper.HAS_VIEW
+    
+    cnt = 0
+    if self.current_flags_ & SelHelper.HAS_ENTITY:
+      cnt += 1
+    if self.current_flags_ & SelHelper.HAS_SURFACE:
+      cnt += 1
+    if self.current_flags_ & SelHelper.HAS_IMG:
+      cnt += 1
+    if self.current_flags_ & SelHelper.HAS_VIEW:
+      cnt += 1
+    
+    if cnt == 1:
+      self.current_flags_ = self.current_flags_ | SelHelper.IS_ONE_TYPE
+    elif cnt > 1:
+      self.current_flags_ = self.current_flags_ | SelHelper.IS_MULTI_TYPE
+    
+    if self.scene_sel_.GetActiveNodeCount()==1:
+      self.current_flags_ = self.current_flags_ | SelHelper.SINGLE_SELECTION
+    elif self.scene_sel_.GetActiveNodeCount()>1:
+      self.current_flags_ = self.current_flags_ | SelHelper.MULTI_SELECTION
+    
+  def CheckAllFlags(self, flags):
+    if(flags == self.current_flags_ & flags) and (flags == self.current_flags_ | flags):
+      return True
+    return False
+  
+  def CheckNotFlags(self, flags):
+    return not self.CheckFlags(flags)
+    
+  def CheckFlags(self, flags):
+    if(flags == self.current_flags_ & flags):
+      return True
+    return False
+  
+  def CheckMinOneFlag(self, flags):
+    if((self.current_flags_ - (self.current_flags_ & flags)) < self.current_flags_):
+      return True
+    return False
diff --git a/modules/gui/pymod/scene/simple_widget.py b/modules/gui/pymod/scene/simple_widget.py
index 958d8bdc746817ace26df5f2507e2a009f0cdf19..f757f8877cb015bce07082a816914c0bf56fcb41 100644
--- a/modules/gui/pymod/scene/simple_widget.py
+++ b/modules/gui/pymod/scene/simple_widget.py
@@ -92,7 +92,7 @@ class SimpleWidget(RenderModeWidget):
   def UpdateLineWidth(self, value):
     self.GetOptions().SetLineWidth(value)
     self.ApplyOptions()
-
+    
   def UpdateBO(self, value):
     self.GetOptions().SetBondOrderFlag(value)
     self.ApplyOptions()
diff --git a/modules/gui/pymod/scene/sline_widget.py b/modules/gui/pymod/scene/sline_widget.py
index e4bffa439c94536081b653b36d09ede09e7eb554..6b45cb76cf09b1a6f76d12803800e0fb1c907b22 100644
--- a/modules/gui/pymod/scene/sline_widget.py
+++ b/modules/gui/pymod/scene/sline_widget.py
@@ -79,12 +79,15 @@ class SlineWidget(RenderModeWidget):
   
   def UpdateDetail(self, value):
     self.GetOptions().SetSplineDetail(value)
-  
+    self.ApplyOptions()
+    
   def UpdateAA(self, value):
     self.GetOptions().SetAALines(value)
+    self.ApplyOptions()
     
   def UpdateLineWidth(self, value):
     self.GetOptions().SetLineWidth(value)
+    self.ApplyOptions()
     
   def UpdateGui(self,options):
     self.detail_spinbox_.setValue(options.GetSplineDetail())
diff --git a/modules/gui/pymod/scene/toolbar_options_widget.py b/modules/gui/pymod/scene/toolbar_options_widget.py
index 006c09b160ba710c83d15679706c1ff20aa4cbf2..d331b62b4cd15d5b5ddfc22f83c2b5fbb13951e1 100644
--- a/modules/gui/pymod/scene/toolbar_options_widget.py
+++ b/modules/gui/pymod/scene/toolbar_options_widget.py
@@ -126,13 +126,13 @@ class ToolBarOptionsWidget(QtGui.QWidget):
        self.current_action_ = action
     widget = action.data().toPyObject()[1]
     self.stackedWidget.setCurrentWidget(widget)
-    self.DoSomething(widget)
     if hasattr(widget, "Update"): 
       widget.Update()
     if(self.current_action_ == action):
       self.current_action_.setChecked(True)
     else:
       self.current_action_=action
+    self.DoSomething(widget)
   #Private Methods
   def __GetCurrentWidget(self):
       return self.stackedWidget.currentWidget();
diff --git a/modules/gui/pymod/scene/trace_widget.py b/modules/gui/pymod/scene/trace_widget.py
index 8fd8a0c16ac09899b8f49ac4fa38e76ba393eeec..a676490714a412de934ae2abf47dda5a3e1105f7 100644
--- a/modules/gui/pymod/scene/trace_widget.py
+++ b/modules/gui/pymod/scene/trace_widget.py
@@ -92,9 +92,11 @@ class TraceWidget(RenderModeWidget):
     
   def UpdatePolyMode(self, value):
     self.GetOptions().SetPolyMode(value)
+    self.ApplyOptions()
         
   def UpdateArcDetail(self, value):
     self.GetOptions().SetArcDetail(value)
+    self.ApplyOptions()
     
   def UpdateTubeRadius(self, value):
     self.GetOptions().SetTubeRadius(value)
@@ -102,7 +104,6 @@ class TraceWidget(RenderModeWidget):
   def UpdateSliderTubeRadius(self, value):
     self.GetOptions().SetTubeRadius(value/10.0)
 
-
   def UpdateTubeRadiusGui(self,value):
     if(abs(value*10.0 - self.width_tube_slider_.value())>=self.width_tube_spinbox_.singleStep()):
       self.width_tube_slider_.setValue(value*10.0)
diff --git a/modules/gui/pymod/scene/tube_widget.py b/modules/gui/pymod/scene/tube_widget.py
index 033d09ea76a74ce255740cb5a95d7c96a219b5fe..e2148ac67126abf5aac0ca312c6a60e9f3e3ccc1 100644
--- a/modules/gui/pymod/scene/tube_widget.py
+++ b/modules/gui/pymod/scene/tube_widget.py
@@ -134,15 +134,19 @@ class TubeWidget(RenderModeWidget):
    
   def UpdatePolyMode(self, value):
     self.GetOptions().SetPolyMode(value)
+    self.ApplyOptions()
     
   def UpdateSplineDetail(self, value):
     self.GetOptions().SetSplineDetail(value)
-    
+    self.ApplyOptions()
+        
   def UpdateArcDetail(self, value):
     self.GetOptions().SetArcDetail(value)
-
+    self.ApplyOptions()
+    
   def UpdateRadius(self, value):
     self.GetOptions().SetTubeRadius(value)
+    self.ApplyOptions()
     
   def UpdateSliderRadius(self, value):
     self.GetOptions().SetTubeRadius(value/10.0)
diff --git a/modules/gui/pymod/scene/uniform_color_widget.py b/modules/gui/pymod/scene/uniform_color_widget.py
index ff2cdc2ddfcd52a0a0ea828f812c2d161e176f32..b5c074c9c89d70aaa5ed9b5eaa582a171b3da672 100644
--- a/modules/gui/pymod/scene/uniform_color_widget.py
+++ b/modules/gui/pymod/scene/uniform_color_widget.py
@@ -21,6 +21,12 @@
 from ost import gui
 from ost import gfx
 from ost import mol
+try: 
+  from ost import img
+  _img_present=True
+except ImportError:
+  _img_present=False
+  pass
 from PyQt4 import QtCore, QtGui
 from color_select_widget import ColorSelectWidget
 
@@ -52,37 +58,45 @@ class UniformColorWidget(QtGui.QWidget):
     top_layout.addLayout(grid)
     self.setLayout(top_layout)
     
-    QtCore.QObject.connect(self.color_select_widget_, QtCore.SIGNAL("colorChanged"), self.Update)
+    QtCore.QObject.connect(self.color_select_widget_, QtCore.SIGNAL("colorChanged"), self.ChangeColors)
     
     self.setMinimumSize(250,150)
 
   def Update(self):
+    scene_selection = gui.SceneSelection.Instance()
+    for i in range(0,scene_selection.GetActiveNodeCount()):
+      node = scene_selection.GetActiveNode(i)
+      if _img_present and isinstance(node, gfx.MapIso):
+        if self.color_select_widget_.GetGfxColor() != node.GetColor():
+          self.color_select_widget_.SetGfxColor(node.GetColor())
+      else:
+        self.ChangeColors()
+        
+  def ChangeColors(self):
     scene_selection = gui.SceneSelection.Instance()
     for i in range(0,scene_selection.GetActiveNodeCount()):
       node = scene_selection.GetActiveNode(i)
       self.ChangeColor(node)
-      
+    
     if(scene_selection.GetActiveViewCount() > 0):
       entity = scene_selection.GetViewEntity()
       view = scene_selection.GetViewUnion()
       self.ChangeViewColor(entity,view)
-        
+  
   def ChangeColor(self, node):
+    gfx_color = self.color_select_widget_.GetGfxColor()
     if isinstance(node, gfx.Entity) or isinstance(node, gfx.Surface):
-      gfx_color = self.GetGfxColor()
-      node.CleanColorOps()
-      node.SetColor(gfx_color,"")
+        node.CleanColorOps()
+        node.SetColor(gfx_color,"")
+    elif _img_present and isinstance(node, gfx.MapIso):
+        node.SetColor(gfx_color)
   
   def ChangeViewColor(self, entity, view):
     if isinstance(entity, gfx.Entity) and isinstance(view, mol.EntityView):
-      gfx_color = self.GetGfxColor()
+      gfx_color = self.color_select_widget_.GetGfxColor()
       ufco=gfx.UniformColorOp(mol.QueryViewWrapper(view),gfx_color)
       entity.Apply(ufco)
-  
-  def GetGfxColor(self):
-    color = self.color_select_widget_.GetColor()
-    return gfx.Color(color.redF(), color.greenF(), color.blueF())
-  
+    
   def resizeEvent(self, event):
     self.color_select_widget_.SetSize(self.width()/2,self.height()/2)
     
diff --git a/modules/gui/pymod/scene/visibility_op.py b/modules/gui/pymod/scene/visibility_op.py
index cb6ec07d68c2ff6a00ad47c29841ca2b66941e80..6a377b5fc47ec48199f8050808fd4693142e9536 100644
--- a/modules/gui/pymod/scene/visibility_op.py
+++ b/modules/gui/pymod/scene/visibility_op.py
@@ -22,13 +22,18 @@ from ost import info
 from ost import gfx
 from PyQt4 import QtGui
 
-class VisibilityOp():
+class VisibilityOp:
   VISIBLE_ATTRIBUTE_NAME = "Visible"
+  FLAGS_ATTRIBUTE_NAME = "Flags"
     
-  def __init__(self, selection, visible=False):    
+  def __init__(self, selection, flags, visible=False):    
     self.selection_ = selection
     self.visible_ = visible
+    self.flags_ = flags
     
+  def GetName(self):
+    return "Visible: %s"%str(self.IsVisible())
+  
   def SetSelection(self, selection):
     self.selection_ = selection
     
@@ -38,15 +43,22 @@ class VisibilityOp():
   def SetVisible(self, visible):
     self.visible_ = visible
 
+  def SetSelectionFlags(self, flags):
+    self.flags_ = flags
+    
+  def GetSelectionFlags(self):
+    return self.flags_
+
   def IsVisible(self):
     return self.visible_
 
   def ApplyOn(self, entity):
     if (entity is not None) and isinstance(entity, gfx.Entity):
-      entity.SetVisible(entity.view.Select(self.GetSelection()),self.IsVisible())
+      entity.SetVisible(entity.view.Select(self.GetSelection(),self.GetSelectionFlags()),self.IsVisible())
   
   def ToInfo(self,group):
       group.SetAttribute(VisibilityOp.VISIBLE_ATTRIBUTE_NAME, str(int(self.IsVisible())))
+      group.SetAttribute(VisibilityOp.FLAGS_ATTRIBUTE_NAME, str(self.GetSelectionFlags()))
       group.SetTextData(str(self.GetSelection()))
     
   @staticmethod
@@ -54,6 +66,9 @@ class VisibilityOp():
     visible_op = None
     if group.HasAttribute(VisibilityOp.VISIBLE_ATTRIBUTE_NAME):
       visible = bool(int(group.GetAttribute(VisibilityOp.VISIBLE_ATTRIBUTE_NAME)))
+      flags = 0
+      if group.HasAttribute(VisibilityOp.FLAGS_ATTRIBUTE_NAME):
+        flags = int(group.GetAttribute(VisibilityOp.FLAGS_ATTRIBUTE_NAME))
       selection = group.GetTextData()
-      visible_op = VisibilityOp(selection,visible)
+      visible_op = VisibilityOp(selection,flags,visible)
     return visible_op
diff --git a/modules/gui/pymod/scene/wireframe_widget.py b/modules/gui/pymod/scene/wireframe_widget.py
new file mode 100644
index 0000000000000000000000000000000000000000..997003743cc7a6eb564ea542e3c18bf48762713f
--- /dev/null
+++ b/modules/gui/pymod/scene/wireframe_widget.py
@@ -0,0 +1,103 @@
+#------------------------------------------------------------------------------
+# This file is part of the OpenStructure project <www.openstructure.org>
+#
+# Copyright (C) 2008-2010 by the OpenStructure authors
+#
+# This library is free software; you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation; either version 3.0 of the License, or (at your option)
+# any later version.
+# This library is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this library; if not, write to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+#------------------------------------------------------------------------------
+# -*- coding: utf-8 -*-
+
+from ost import gui
+from ost import gfx
+from PyQt4 import QtCore, QtGui
+try: 
+  from ost import img
+  _img_present=True
+except ImportError:
+  _img_present=False
+  pass
+from scene_selection_helper import SelHelper
+
+#Wireframe Options
+class WireframeWidget(QtGui.QWidget):
+  def __init__(self, parent=None):
+    QtGui.QWidget.__init__(self, parent)
+    
+    #Title
+    self.text_ = "Wireframe"
+        
+    #Defaults
+    min_line_width = 0.01
+    max_line_width = 20
+    
+    #Set Render Mode
+    self.mode_ = gfx.RenderMode.SIMPLE
+        
+    #Create Ui elements
+    self.aa_rendering_cb_ = QtGui.QCheckBox()
+  
+    self.radius_spinbox_ = QtGui.QDoubleSpinBox()
+    self.radius_spinbox_.setRange(min_line_width, max_line_width)
+    self.radius_spinbox_.setDecimals(2)
+    self.radius_spinbox_.setSingleStep(0.1)
+
+    simple_label = QtGui.QLabel("Wireframe Settings")
+    font = simple_label.font()
+    font.setBold(True)
+    
+    radius_label = QtGui.QLabel("Line Width")
+    aa_label = QtGui.QLabel("AA-Lines")
+
+    grid = QtGui.QGridLayout()
+    grid.addWidget(simple_label,0,0,1,3)
+    grid.addWidget(aa_label, 1, 0, 1, 3)
+    grid.addWidget(self.aa_rendering_cb_, 1, 2, 1, 1)
+    grid.addWidget(radius_label,2,0,1,3)
+    grid.addWidget(self.radius_spinbox_,2,2,1,1)
+    grid.setRowStretch(5,1)
+    self.setLayout(grid)
+    
+    QtCore.QObject.connect(self.radius_spinbox_, QtCore.SIGNAL("valueChanged(double)"), self.UpdateLineWidth)
+    QtCore.QObject.connect(self.aa_rendering_cb_, QtCore.SIGNAL("stateChanged(int)"), self.UpdateAA)  
+    
+    self.setMinimumSize(250,100)
+    
+  def UpdateAA(self, value):
+    scene_selection = gui.SceneSelection.Instance()
+    for i in range(0,scene_selection.GetActiveNodeCount()):
+      node = scene_selection.GetActiveNode(i)
+      node.SetAALines(value)
+          
+  def UpdateLineWidth(self, value):
+    scene_selection = gui.SceneSelection.Instance()
+    for i in range(0,scene_selection.GetActiveNodeCount()):
+      node = scene_selection.GetActiveNode(i)
+      node.SetLineWidth(value)
+
+  def UpdateGui(self):
+    scene_selection = gui.SceneSelection.Instance()
+    node = scene_selection.GetActiveNode(0)
+    self.radius_spinbox_.setValue(node.GetLineWidth())
+
+  def Update(self):
+    self.setEnabled(True)
+    self.UpdateGui()
+    if SelHelper().CheckNotFlags(SelHelper.HAS_IMG | SelHelper.IS_ONE_TYPE):
+      self.setEnabled(False)          
+
+  def GetText(self):
+    return self.text_
+
+  def GetRenderMode(self):
+    return self.mode_
\ No newline at end of file
diff --git a/modules/gui/pymod/wrap_gui.cc b/modules/gui/pymod/wrap_gui.cc
index 149c7885f69b5b5fb4df54bb63f18104696aae57..09f24fe82ea3fde760f14da2138af50963d97bac 100644
--- a/modules/gui/pymod/wrap_gui.cc
+++ b/modules/gui/pymod/wrap_gui.cc
@@ -21,20 +21,18 @@
 #include <boost/python.hpp>
 #include <QString>
 #include <ost/config.hh>
-
-
+#include <ost/gui/admin.hh>
 using namespace boost::python;
 
 void export_AlignmentView();
 void export_Tool();
-void export_Plot();
 void export_GLWin();
+void export_MessageWidget();
 void export_Gosty();
 void export_PyShell();
 void export_SceneWin();
 void export_SequenceViewer();
-void export_SequenceViewerV2();
-void export_PanelBar();
+void export_Panels();
 void export_Perspective();
 void export_SipHandler();
 void export_SceneSelection();
@@ -42,6 +40,7 @@ void export_MainArea();
 void export_MenuBar();
 void export_RemoteSiteLoader();
 void export_FileLoader();
+void export_FileViewer();
 void export_Widget();
 
 #if OST_SPNAV_ENABLED
@@ -51,6 +50,7 @@ void export_Input();
 #ifdef OST_IMG_ENABLED
 void export_data_viewer();
 void export_overlay();
+void export_overlay_manager();
 #endif
 
 #include <boost/python/to_python_converter.hpp>
@@ -97,6 +97,7 @@ namespace {
 
 
 }
+using namespace ost::gui;
 
 BOOST_PYTHON_MODULE(_gui)
 {
@@ -107,19 +108,19 @@ BOOST_PYTHON_MODULE(_gui)
   export_Gosty();
   export_AlignmentView();
   export_Tool();
-  export_Plot();
+  export_MessageWidget();
   export_GLWin();
   export_MainArea();
   export_PyShell();
-  export_PanelBar();
+  export_Panels();
   export_MenuBar();
   export_Perspective();  
   export_SceneWin();
   export_SceneSelection();
   export_SequenceViewer();
-  export_SequenceViewerV2();
   export_RemoteSiteLoader();
   export_FileLoader();
+  export_FileViewer();
   export_Widget();
 
   #if OST_SPNAV_ENABLED
@@ -129,5 +130,12 @@ BOOST_PYTHON_MODULE(_gui)
   #if OST_IMG_ENABLED
   export_data_viewer();
   export_overlay();
+  export_overlay_manager();
   #endif
+  
+  class_<AdminRights>("AdminRights", init<>())
+    .def("Acquire", &AdminRights::Acquire)
+    .def("Release", &AdminRights::Release)
+    .def("CreateLink", &AdminRights::CreateLink)
+  ;
 }
diff --git a/modules/gui/share/CMakeLists.txt b/modules/gui/share/CMakeLists.txt
index d755bcd3a784ad2af217bc54b2456627126a16c5..c87f561e8eb50e4a7743063d3b70d090280f24e1 100644
--- a/modules/gui/share/CMakeLists.txt
+++ b/modules/gui/share/CMakeLists.txt
@@ -2,15 +2,31 @@
 set(GUI_ICONS
   icons/add_icon.png
   icons/close_icon.png
+  icons/critical_icon.png
+  icons/delete_icon.png
   icons/distance_icon.png
+  icons/find_icon.png
+  icons/information_icon.png
   icons/map_icon.png
+  icons/menubar_icon.png
   icons/rigid_body_manipulator_icon.png
   icons/selection_icon.png
   icons/show_sidebar_icon.png
   icons/site_icon.png
   icons/split_icon.png
+  icons/warning_icon.png
 )
+
+set(GUI_IMAGES
+  images/logo-small.png
+)
+
 add_custom_target(scene_icons ALL)
 copy_if_different("./" "${STAGE_DIR}/share/openstructure/gui/icons" 
                   "${GUI_ICONS}" "ICONS_FOR_GUI" scene_icons)
 install(FILES ${GUI_ICONS} DESTINATION "share/openstructure/gui/icons")
+
+add_custom_target(gui_images ALL)
+copy_if_different("./" "${STAGE_DIR}/share/openstructure/gui/images" 
+                  "${GUI_IMAGES}" "IMAGES_FOR_GUI" gui_images)
+install(FILES ${GUI_IMAGES} DESTINATION "share/openstructure/gui/images")
\ No newline at end of file
diff --git a/modules/gui/share/icons/add_icon.png b/modules/gui/share/icons/add_icon.png
index 92611c58f1413e215b2e8f5f58f986e5d8d4ea53..5f059bcdae8a4b6fe17ca2773f39c161c4abdcbd 100644
Binary files a/modules/gui/share/icons/add_icon.png and b/modules/gui/share/icons/add_icon.png differ
diff --git a/modules/gui/share/icons/close_icon.png b/modules/gui/share/icons/close_icon.png
index 3df20f23d0c40a3a66f484f6b3397f495103c4a8..376f51609396dca265f9c591af173f8dfe8153a6 100644
Binary files a/modules/gui/share/icons/close_icon.png and b/modules/gui/share/icons/close_icon.png differ
diff --git a/modules/gui/share/icons/critical_icon.png b/modules/gui/share/icons/critical_icon.png
new file mode 100644
index 0000000000000000000000000000000000000000..0e362b6fb3eef525896e6d173c2ceb42c9109f4a
Binary files /dev/null and b/modules/gui/share/icons/critical_icon.png differ
diff --git a/modules/gui/share/icons/delete_icon.png b/modules/gui/share/icons/delete_icon.png
new file mode 100644
index 0000000000000000000000000000000000000000..998b49070fc98a0a67dc79392eebb879a9af7937
Binary files /dev/null and b/modules/gui/share/icons/delete_icon.png differ
diff --git a/modules/gui/share/icons/find_icon.png b/modules/gui/share/icons/find_icon.png
new file mode 100644
index 0000000000000000000000000000000000000000..39f6331715ea8fce80451c6314e9eac45193dabe
Binary files /dev/null and b/modules/gui/share/icons/find_icon.png differ
diff --git a/modules/gui/share/icons/information_icon.png b/modules/gui/share/icons/information_icon.png
new file mode 100644
index 0000000000000000000000000000000000000000..7d224adeb079092587a099fe310379a918df6147
Binary files /dev/null and b/modules/gui/share/icons/information_icon.png differ
diff --git a/modules/gui/share/icons/menubar_icon.png b/modules/gui/share/icons/menubar_icon.png
new file mode 100644
index 0000000000000000000000000000000000000000..7a87198cfdf7ba396a2858dde79474df773118c1
Binary files /dev/null and b/modules/gui/share/icons/menubar_icon.png differ
diff --git a/modules/gui/share/icons/split_icon.png b/modules/gui/share/icons/split_icon.png
index c81d1224feb09e0e34c6280af9abec992d25aad2..783e6afe9ba0f398104140472f3e198ae1257681 100644
Binary files a/modules/gui/share/icons/split_icon.png and b/modules/gui/share/icons/split_icon.png differ
diff --git a/modules/gui/share/icons/warning_icon.png b/modules/gui/share/icons/warning_icon.png
new file mode 100644
index 0000000000000000000000000000000000000000..b1a2dc196e0adc0d420ad5304e47d8926bc6637c
Binary files /dev/null and b/modules/gui/share/icons/warning_icon.png differ
diff --git a/modules/gui/share/images/logo-small.png b/modules/gui/share/images/logo-small.png
new file mode 100644
index 0000000000000000000000000000000000000000..37bfaf42f21d3e6a5b68c05fb4dfe7186b603d4f
Binary files /dev/null and b/modules/gui/share/images/logo-small.png differ
diff --git a/modules/gui/src/CMakeLists.txt b/modules/gui/src/CMakeLists.txt
index b4ca43ed392d7f8088acc611f71ce05dec3b5ed0..1a5104a0ae28d8670eb8887fa8c3c85f4567c1ae 100644
--- a/modules/gui/src/CMakeLists.txt
+++ b/modules/gui/src/CMakeLists.txt
@@ -1,8 +1,8 @@
 set(OST_GUI_PANEL_BAR_HEADERS
 button_bar.hh
 drop_box.hh
-panels.hh
 panel_bar.hh
+panel_manager.hh
 bottom_bar.hh
 button_box.hh
 event_button.hh
@@ -12,17 +12,12 @@ side_bar.hh
 splitter_panel_bar.hh
 tabbed_panel_bar.hh
 )
-set(OST_GUI_SEQUENCE_VIEWER_HEADERS
-sequence_item.hh
-sequence_viewer_base.hh
-sequence_viewer.hh
-sequence_scene.hh
-sequence_search_bar.hh
-)
 
-set(OST_GUI_SEQUENCE_VIEW_HEADERS
+set(OST_GUI_SEQUENCE_VIEWER_HEADERS
+align_properties_painter.hh
 base_row.hh
 background_painter.hh
+conservation_painter.hh
 painter.hh
 secstr_row.hh
 seq_secstr_painter.hh
@@ -36,6 +31,7 @@ sequence_table_view.hh
 sequence_viewer.hh
 tick_painter.hh
 title_row.hh
+alignment_view_object.hh
 base_view_object.hh
 sequence_view_object.hh
 )
@@ -70,9 +66,13 @@ python_tokenizer.hh
 python_syntax_highlighter.hh
 text_logger.hh
 python_interpreter.hh
-python_interpreter_proxy.hh
+python_interpreter_worker.hh
 python_shell_text_document_layout.hh
 shell_history.hh
+state_machine.hh
+state.hh
+transition.hh
+transition_guard.hh
 )
 
 set(OST_GUI_SCENE_WIN_HEADERS
@@ -91,6 +91,11 @@ scene_win.hh
 scene_win_model.hh
 )
 
+set(OST_GUI_MESSAGES_HEADERS
+message_widget.hh
+message_box_widget.hh
+log_reader.hh
+)
 
 if (ENABLE_SPNAV)
 set(OST_GUI_INPUT_HEADERS
@@ -125,10 +130,6 @@ plot_legend_panel.hh
 plot_ticker.hh
 plot_ticker_fw.hh
 plot_types.hh
-plot_viewer.hh
-plot_viewer_panel.hh
-plot_viewer_proxy.hh
-plot_viewer_proxy_fw.hh
 )
 
 if (ENABLE_IMG)
@@ -161,25 +162,23 @@ if (ENABLE_IMG)
 endif()
 
 set(OST_GUI_HEADERS
-change_process_name.hh
 file_browser.hh
 file_type_dialog.hh
+file_viewer.hh
 remote_loader.hh
 gl_canvas.hh
 gl_win.hh
 scene_menu.hh
 gosty_app.hh
+admin.hh
 main.hh
 main_area.hh
-mdi_sub_window.hh
 module_config.hh
 perspective.hh
-query_dialog.hh
 remote_site_loader.hh
 scene_selection.hh
 main_window.hh
 dock_widget.hh
-main_window.hh
 dock_widget.hh
 thin_splitter.hh
 widget.hh
@@ -197,59 +196,59 @@ perspective.cc
 widget_registry.cc
 file_browser.cc
 file_type_dialog.cc
+file_viewer.cc
 remote_loader.cc
 main.cc
-mdi_sub_window.cc
 gl_canvas.cc
 dock_widget.cc
 main_window.cc
 gl_win.cc
 scene_menu.cc
 widget.cc
+admin.cc
 widget_pool.cc
 remote_site_loader.cc
-sequence_viewer/sequence_item.cc
-sequence_viewer/sequence_viewer_base.cc
-sequence_viewer/sequence_viewer.cc
-sequence_viewer/sequence_scene.cc
+messages/message_widget.cc
+messages/message_box_widget.cc
+messages/log_reader.cc
+sequence_viewer/align_properties_painter.cc
+sequence_viewer/base_row.cc
+sequence_viewer/background_painter.cc
+sequence_viewer/conservation_painter.cc
+sequence_viewer/secstr_row.cc
+sequence_viewer/seq_secstr_painter.cc
+sequence_viewer/seq_selection_painter.cc
+sequence_viewer/seq_text_painter.cc
+sequence_viewer/sequence_delegate.cc
+sequence_viewer/sequence_model.cc
+sequence_viewer/sequence_row.cc
 sequence_viewer/sequence_search_bar.cc
-sequence/base_row.cc
-sequence/background_painter.cc
-sequence/secstr_row.cc
-sequence/seq_secstr_painter.cc
-sequence/seq_selection_painter.cc
-sequence/seq_text_painter.cc
-sequence/sequence_delegate.cc
-sequence/sequence_model.cc
-sequence/sequence_row.cc
-sequence/sequence_search_bar.cc
-sequence/sequence_table_view.cc
-sequence/sequence_viewer.cc
-sequence/tick_painter.cc
-sequence/title_row.cc
-sequence/base_view_object.cc
-sequence/sequence_view_object.cc
+sequence_viewer/sequence_table_view.cc
+sequence_viewer/sequence_viewer.cc
+sequence_viewer/tick_painter.cc
+sequence_viewer/title_row.cc
+sequence_viewer/alignment_view_object.cc
+sequence_viewer/base_view_object.cc
+sequence_viewer/sequence_view_object.cc
 gosty_app.cc
-change_process_name.cc
 main_area.cc
-query_dialog.cc
 widget_state_saver.cc
 scene_selection.cc
 widget_geom_handler.cc
 file_loader.cc
 loader_manager.cc
-panel_bar/button_bar.cc
-panel_bar/drop_box.cc
-panel_bar/panel_bar.cc
-panel_bar/bottom_bar.cc
-panel_bar/button_box.cc
-panel_bar/event_button.cc
-panel_bar/panels.cc
-panel_bar/panel_widget_container.cc
-panel_bar/panel_bar_widget_holder.cc
-panel_bar/side_bar.cc
-panel_bar/splitter_panel_bar.cc
-panel_bar/tabbed_panel_bar.cc
+panels/button_bar.cc
+panels/drop_box.cc
+panels/panel_bar.cc
+panels/bottom_bar.cc
+panels/button_box.cc
+panels/event_button.cc
+panels/panel_manager.cc
+panels/panel_widget_container.cc
+panels/panel_bar_widget_holder.cc
+panels/side_bar.cc
+panels/splitter_panel_bar.cc
+panels/tabbed_panel_bar.cc
 tools/tool_option_group.cc
 tools/tool_options.cc
 tools/tool_option.cc
@@ -262,30 +261,6 @@ tools/tool_options_widget.cc
 tools/tool_bar.cc
 tools/selection_tool.cc
 tools/measure_tool.cc
-plot_viewer/plot_axis_base.cc
-plot_viewer/plot_axis_vertical.cc
-plot_viewer/plot_axis_horizontal.cc
-plot_viewer/plot_data_graphics_item.cc
-plot_viewer/plot_data_graphics_item_base.cc
-plot_viewer/plot_graphics_ellipse_item.cc
-plot_viewer/plot_graphics_rectangle_item.cc
-plot_viewer/plot_graphics_diagonal_cross_item.cc
-plot_viewer/plot_graphics_cross_item.cc
-plot_viewer/plot_data.cc
-plot_viewer/plot_data_base.cc
-plot_viewer/plot_data_info.cc
-plot_viewer/plot_function.cc
-plot_viewer/plot_function_graphics_item.cc
-plot_viewer/plot_function_info.cc
-plot_viewer/plot_info_base.cc
-plot_viewer/plot_group.cc
-plot_viewer/plot_group_info.cc
-plot_viewer/plot_group_graphics_item.cc
-plot_viewer/plot_ticker.cc
-plot_viewer/plot_viewer.cc
-plot_viewer/plot_viewer_proxy.cc
-plot_viewer/plot_viewer_panel.cc
-plot_viewer/plot_legend_panel.cc
 python_shell/gutter.cc
 python_shell/main_thread_runner.cc
 python_shell/output_redirector.cc
@@ -295,7 +270,7 @@ python_shell/path_completer.cc
 python_shell/python_context_parser.cc
 python_shell/python_completer.cc
 python_shell/python_interpreter.cc
-python_shell/python_interpreter_proxy.cc
+python_shell/python_interpreter_worker.cc
 python_shell/python_namespace_tree_model.cc
 python_shell/python_namespace_tree_item.cc
 python_shell/python_shell.cc
@@ -306,6 +281,10 @@ python_shell/python_syntax_highlighter.cc
 python_shell/shell_history.cc
 python_shell/string_literal_positions.cc
 python_shell/text_logger.cc
+python_shell/state_machine.cc
+python_shell/state.cc
+python_shell/transition.cc
+python_shell/transition_guard.cc
 scene_win/context_menu.cc
 scene_win/current_selection_node.cc
 scene_win/custom_part_node.cc
@@ -324,6 +303,7 @@ scene_win/scene_win_model.cc
 set(HEADERS_TO_BE_MOCCED
 file_browser.hh
 file_type_dialog.hh
+file_viewer.hh
 remote_loader.hh
 gl_canvas.hh
 gl_win.hh
@@ -331,65 +311,64 @@ scene_menu.hh
 gosty_app.hh
 main.hh
 main_area.hh
-mdi_sub_window.hh
 perspective.hh
-query_dialog.hh
 dock_widget.hh
 main_window.hh
 scene_selection.hh
 widget.hh
 widget_geom_handler.hh
 widget_pool.hh
-sequence_viewer/sequence_item.hh
-sequence_viewer/sequence_viewer_base.hh
-sequence_viewer/sequence_viewer.hh
-sequence_viewer/sequence_scene.hh
+messages/message_widget.hh
+messages/message_box_widget.hh
+messages/log_reader.hh
+sequence_viewer/align_properties_painter.hh
+sequence_viewer/background_painter.hh
+sequence_viewer/base_row.hh
+sequence_viewer/conservation_painter.hh
+sequence_viewer/painter.hh
+sequence_viewer/secstr_row.hh
+sequence_viewer/seq_secstr_painter.hh
+sequence_viewer/seq_selection_painter.hh
+sequence_viewer/seq_text_painter.hh
+sequence_viewer/sequence_delegate.hh
+sequence_viewer/sequence_model.hh
+sequence_viewer/sequence_row.hh
 sequence_viewer/sequence_search_bar.hh
-sequence/background_painter.hh
-sequence/base_row.hh
-sequence/painter.hh
-sequence/secstr_row.hh
-sequence/seq_secstr_painter.hh
-sequence/seq_selection_painter.hh
-sequence/seq_text_painter.hh
-sequence/sequence_delegate.hh
-sequence/sequence_model.hh
-sequence/sequence_row.hh
-sequence/sequence_search_bar.hh
-sequence/sequence_table_view.hh
-sequence/sequence_viewer.hh
-sequence/tick_painter.hh
-sequence/title_row.hh
-sequence/base_view_object.hh
-sequence/sequence_view_object.hh
-plot_viewer/plot_axis_base.hh
-plot_viewer/plot_data_graphics_item_base.hh
-plot_viewer/plot_function_info.hh
-plot_viewer/plot_info_base.hh
-plot_viewer/plot_viewer_panel.hh
-plot_viewer/plot_legend_panel.hh
+sequence_viewer/sequence_table_view.hh
+sequence_viewer/sequence_viewer.hh
+sequence_viewer/tick_painter.hh
+sequence_viewer/title_row.hh
+sequence_viewer/alignment_view_object.hh
+sequence_viewer/base_view_object.hh
+sequence_viewer/sequence_view_object.hh
 python_shell/main_thread_runner.hh
 python_shell/completer_base.hh
 python_shell/gutter.hh
+python_shell/output_redirector.hh
 python_shell/path_completer.hh
 python_shell/python_completer.hh
 python_shell/python_interpreter.hh
+python_shell/python_interpreter_worker.hh
 python_shell/python_namespace_tree_model.hh
 python_shell/python_shell.hh
 python_shell/python_shell_widget.hh
 python_shell/text_logger.hh
-panel_bar/button_bar.hh
-panel_bar/drop_box.hh
-panel_bar/panel_bar.hh
-panel_bar/panels.hh
-panel_bar/bottom_bar.hh
-panel_bar/button_box.hh
-panel_bar/event_button.hh
-panel_bar/panel_widget_container.hh
-panel_bar/panel_bar_widget_holder.hh
-panel_bar/side_bar.hh
-panel_bar/splitter_panel_bar.hh
-panel_bar/tabbed_panel_bar.hh
+python_shell/state_machine.hh
+python_shell/state.hh
+python_shell/transition.hh
+python_shell/transition_guard.hh
+panels/button_bar.hh
+panels/drop_box.hh
+panels/panel_bar.hh
+panels/panel_manager.hh
+panels/bottom_bar.hh
+panels/button_box.hh
+panels/event_button.hh
+panels/panel_widget_container.hh
+panels/panel_bar_widget_holder.hh
+panels/side_bar.hh
+panels/splitter_panel_bar.hh
+panels/tabbed_panel_bar.hh
 scene_win/context_menu.hh
 scene_win/current_selection_node.hh
 scene_win/custom_part_node.hh
@@ -455,24 +434,31 @@ if (ENABLE_SPNAV)
       input/spnav_input.hh
   )
 endif()
-
+if (APPLE)
+  set(ADDITIONAL_LIBRARIES "-framework Security")
+endif()
 set(QT_USE_QTOPENGL 1)
 set(QT_USE_QTNETWORK 1)
 include(${QT_USE_FILE})
 qt4_wrap_cpp(OST_GUI_MOCS "${HEADERS_TO_BE_MOCCED}")
 module(NAME gui SOURCES ${OST_GUI_MOCS} ${OST_GUI_SOURCES}
        HEADERS ${OST_GUI_TOOLS_HEADERS} IN_DIR tools
-               ${OST_GUI_PLOT_VIEWER_HEADERS} IN_DIR plot_viewer
                ${OST_GUI_SEQUENCE_VIEWER_HEADERS} IN_DIR sequence_viewer
-               ${OST_GUI_SEQUENCE_VIEW_HEADERS} IN_DIR sequence
                ${OST_GUI_PYTHON_SHELL_HEADERS} IN_DIR python_shell
-               ${OST_GUI_PANEL_BAR_HEADERS} IN_DIR panel_bar
+               ${OST_GUI_PANEL_BAR_HEADERS} IN_DIR panels
                ${OST_GUI_SCENE_WIN_HEADERS} IN_DIR scene_win
+               ${OST_GUI_MESSAGES_HEADERS} IN_DIR messages
                ${OST_GUI_INPUT_HEADERS}
                ${OST_GUI_DATA_VIEWER_HEADERS}
                ${OST_GUI_HEADERS}
-       DEPENDS_ON gfx io mol_alg
-       LINK ${QT_LIBRARIES} ${PYTHON_LIBRARIES} ${BOOST_PYTHON_LIBRARIES} ${SPNAV_LIBRARIES})
+       DEPENDS_ON gfx io mol_alg seq_alg
+       LINK ${QT_LIBRARIES} ${PYTHON_LIBRARIES} ${BOOST_PYTHON_LIBRARIES}
+            ${SPNAV_LIBRARIES})
+            
+if (ADDITIONAL_LIBRARIES)
+  target_link_libraries(ost_gui "${ADDITIONAL_LIBRARIES}")
+endif()
+
 include_directories(${PYTHON_INCLUDE_PATH})
 qt4_add_resources(OST_QT_RESOURCE dngr.qrc)
 qt4_wrap_cpp(OST_GOSTY_MOC "gosty.hh")
@@ -485,7 +471,3 @@ endif()
 
 executable(NAME gosty SOURCES gosty.cc ${OST_GOSTY_MOC} ${OST_QT_RESOURCE} 
            DEPENDS_ON gui ${LINK})
-#if (APPLE)
-#  set_source_files_properties(change_process_name.cc
-#                              PROPERTIES COMPILE_FLAGS "-ObjC++")
-#endif()
diff --git a/modules/gui/src/admin.cc b/modules/gui/src/admin.cc
new file mode 100644
index 0000000000000000000000000000000000000000..4163750a4af3c623babe9d45cfdae76d60a702dd
--- /dev/null
+++ b/modules/gui/src/admin.cc
@@ -0,0 +1,96 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+//------------------------------------------------------------------------------
+
+#include "admin.hh"
+
+namespace ost { namespace gui {
+
+#if defined(__APPLE__)
+
+AdminRights::AdminRights(): auth_(NULL)
+{
+  
+}
+AdminRights::~AdminRights()
+{
+  this->Release();
+}
+
+bool AdminRights::Acquire()
+{
+  // Connect to Authorization Services.
+  if (AuthorizationCreate(NULL, NULL, 0, &auth_)!=noErr) {
+    return false;
+  }
+    
+  static const AuthorizationFlags  kFlags =
+                kAuthorizationFlagInteractionAllowed
+              | kAuthorizationFlagExtendRights;
+  AuthorizationItem   kActionRight = { "", 0, 0, 0 };
+  AuthorizationRights kRights      = { 1, &kActionRight };
+
+  // Request the application-specific right.
+  return noErr==AuthorizationCopyRights(auth_, &kRights, NULL, kFlags, NULL);
+}
+
+void AdminRights::Release()
+{
+  if (auth_) {
+    AuthorizationFree(auth_, kAuthorizationFlagDestroyRights);
+    auth_=NULL;
+  }
+}
+
+void AdminRights::CreateLink(const String& from, const String& to)
+{
+  static const char* minus_sf="-sf";
+  // const_casts are gross, but at least that way we keep gcc happy
+  char* const args[]={
+    const_cast<char*>(minus_sf),
+    const_cast<char*>(from.c_str()),
+    const_cast<char*>(to.c_str()),
+    NULL
+  };
+  AuthorizationExecuteWithPrivileges(auth_, "/bin/ln", 
+                                     kAuthorizationFlagDefaults,
+                                     args, NULL);
+}
+
+#else
+
+AdminRights::AdminRights()
+{ }
+
+void AdminRights::CreateLink(const String& from, const String& to)
+{
+  
+}
+AdminRights::~AdminRights()
+{ }
+
+bool AdminRights::Acquire()
+{ return false; }
+
+void AdminRights::Release()
+{ }
+#endif
+
+
+}}
+
diff --git a/modules/gui/src/change_process_name.hh b/modules/gui/src/admin.hh
similarity index 75%
rename from modules/gui/src/change_process_name.hh
rename to modules/gui/src/admin.hh
index 69bf57b129e3792715194e6aae827050b37919c5..99e43e86067b459646e2d2a5c0f9230589ad3ac6 100644
--- a/modules/gui/src/change_process_name.hh
+++ b/modules/gui/src/admin.hh
@@ -16,20 +16,34 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#ifndef OST_GUI_CHANGE_PROCESS_NAME_HH
-#define OST_GUI_CHANGE_PROCESS_NAME_HH
+
+#ifndef OST_GUI_ADMIN_HH
+#define OST_GUI_ADMIN_HH
 
 #include <ost/gui/module_config.hh>
 
-/*
-  Author: Marco Biasini
- */
+#if defined(__APPLE__)
+#include <Security/Security.h>
+#endif
 
 namespace ost { namespace gui {
 
-/// \brief change process name that shows up in ps and top
-void DLLEXPORT_OST_GUI ChangeProcessName(const char* proc_name);
+
+class DLLEXPORT_OST_GUI AdminRights {
+public:
+  AdminRights();
+  ~AdminRights();
   
+  bool Acquire();
+  
+  void CreateLink(const String& from, const String& to);
+  void Release();
+private:  
+#if defined(__APPLE__)
+  AuthorizationRef  auth_;
+#endif
+};
+
 }}
 
 #endif
diff --git a/modules/gui/src/data_viewer/argand.cc b/modules/gui/src/data_viewer/argand.cc
index 7c536a36001b22584a63936f6c790a30d62e36e3..e9d65dee8ab5f0dcdf0a14ae59499688211d5a40 100644
--- a/modules/gui/src/data_viewer/argand.cc
+++ b/modules/gui/src/data_viewer/argand.cc
@@ -22,13 +22,13 @@
   Authors: Ansgar Philippsen, Andreas Schenk
 */
 
-#include <QPainter>
-#include <QResizeEvent>
 
 #include <ost/base.hh>
 
 #include "argand.hh"
 
+#include <QPainter>
+#include <QResizeEvent>
 namespace ost { namespace img { namespace gui {
 
 Argand::Argand(const Data& data, QWidget* p):
diff --git a/modules/gui/src/data_viewer/argand.hh b/modules/gui/src/data_viewer/argand.hh
index cc337c661eb88f1283b63c75ba2ee5bb6becdaf0..346cee3b0ac4101d2a7c59bcd0f4921a836f4733 100644
--- a/modules/gui/src/data_viewer/argand.hh
+++ b/modules/gui/src/data_viewer/argand.hh
@@ -25,8 +25,6 @@
 #ifndef OST_GUI_ARGAND_H
 #define OST_GUI_ARGAND_H
 
-#include <QWidget>
-#include <QPixmap>
 
 #include <ost/base.hh>
 #include <ost/img/data.hh>
@@ -35,6 +33,8 @@
 
 #include <ost/gui/module_config.hh>
 
+#include <QWidget>
+#include <QPixmap>
 namespace ost { namespace img { namespace gui {
 
 class DLLEXPORT_OST_GUI Argand: public QWidget, public DataObserver 
diff --git a/modules/gui/src/data_viewer/data_viewer.cc b/modules/gui/src/data_viewer/data_viewer.cc
index a02a2f86203924d45505ed8a1b7b4ff1b852b706..11edbf9daa95c400b85c99fd2b48a439e2954112 100644
--- a/modules/gui/src/data_viewer/data_viewer.cc
+++ b/modules/gui/src/data_viewer/data_viewer.cc
@@ -28,14 +28,6 @@
 //#include <cstring>
 //#include <sstream>
 
-#include <QLabel>
-#include <QStatusBar>
-#include <QMouseEvent>
-#include <QVariant>
-#include <QMenu>
-#include <QMenuBar>
-#include <QApplication>
-#include <QDesktopWidget>
 
 //#include <ost/img/io/io_manager.hh>
 #include <ost/message.hh>
@@ -48,6 +40,14 @@
 #include "overlay_base.hh"
 #include "overlay_manager.hh"
 
+#include <QLabel>
+#include <QStatusBar>
+#include <QMouseEvent>
+#include <QVariant>
+#include <QMenu>
+#include <QMenuBar>
+#include <QApplication>
+#include <QDesktopWidget>
 namespace ost { namespace img { namespace gui {
 
 namespace {
@@ -72,7 +72,7 @@ DataViewer::DataViewer(QWidget* p, const Data& data, const QString& name):
   lastmouse_()
 {
   connect(ov_manager_gui_,SIGNAL(SettingsChanged()),this,SLOT(UpdateView()));
-  setWindowTitle("GIPLT Viewer");
+  setWindowTitle("OpenStructure Data Viewer");
   build(data);
 }
 
diff --git a/modules/gui/src/data_viewer/data_viewer_panel_base.cc b/modules/gui/src/data_viewer/data_viewer_panel_base.cc
index 0fb9c0c5b3c85c4c4ca8086becbc4fc1e88a4e47..7a098921db753ca1e7fbe596281536ee71947f42 100644
--- a/modules/gui/src/data_viewer/data_viewer_panel_base.cc
+++ b/modules/gui/src/data_viewer/data_viewer_panel_base.cc
@@ -30,6 +30,9 @@
 //#include "bitmaps/rotate.xpm"
 //#include "bitmaps/arrowmove.xpm"
 
+#include "img2qt.hh"
+#include "data_viewer_panel_base.hh"
+
 #include <QResizeEvent>
 #include <QPainter>
 #include <QColor>
@@ -37,8 +40,6 @@
 #include <QPixmapCache>
 #include <ost/message.hh>
 
-#include "img2qt.hh"
-#include "data_viewer_panel_base.hh"
 
 #define USE_PIXMAP_CACHE
 
@@ -431,7 +432,7 @@ void DataViewerPanelBase::paintEvent(QPaintEvent* event)
   painter.drawPixmap(QPoint(0,0),*pixmap_);
 #endif
 
-  if(zoom_level_ >= 6 && display_pixel_values_) {
+  if(zoom_level_ >= 7 && display_pixel_values_) {
     draw_pixel_values(painter);
   }
 
@@ -554,9 +555,9 @@ void DataViewerPanelBase::mouseMoveEvent(QMouseEvent* event)
     Point max_pos=WinToPoint(vsize.width(),vsize.height());
     Point min_pos=WinToPoint(0,0);
     selection_=Extent(Point(std::max(min_pos[0],std::min(drag_start[0],mouse_pos[0])),
-                            std::max(min_pos[1],std::min(drag_start[1],mouse_pos[1]))),
+                            std::max(min_pos[1],std::min(drag_start[1],mouse_pos[1])), slab_),
                       Point(std::max(drag_start[0],std::min(max_pos[0],mouse_pos[0])),
-                            std::max(drag_start[1],std::min(max_pos[1],mouse_pos[1]))));
+                            std::max(drag_start[1],std::min(max_pos[1],mouse_pos[1])), slab_));
     if(selection_mode_>0){
       Size s=selection_.GetSize();
       int minsize=std::min<int>(s[0],s[1]);
@@ -1009,20 +1010,37 @@ void DataViewerPanelBase::draw_pixel_values(QPainter& painter)
 
   QFont fnt("Courier",(zoom_level_-6)*2+7);
   painter.setFont(fnt);
-  
-  for(int i = 0; i <= (b[0] - a[0]); ++i) {
-    for(int j = 0; j <= (b[1] - a[1]); ++j) {
-      Real pixel_value = GetObservedData().GetReal(Point(a[0]+i, 
-                                                               a[1]+j,slab_));
-      QString value_string = QString("%1").arg(pixel_value,0,'g',5);
-      Real rv = GetNormalizer()->Convert(pixel_value);
-      QPoint p = FracPointToWinCenter(geom::Vec2(static_cast<Real>(a[0]+i),
-                                                 static_cast<Real>(a[1]+j)));
-      unsigned char rgb = (rv>130.0) ? 0 : 255;
-      painter.setPen(QColor(rgb,rgb,rgb));
-      int string_h=painter.fontMetrics().height();
-      int string_w=painter.fontMetrics().width(value_string);
-      painter.drawText(p.x() - string_w/2, p.y() + string_h/2, value_string);
+  if(GetObservedData().GetType()==REAL){
+    for(int i = 0; i <= (b[0] - a[0]); ++i) {
+      for(int j = 0; j <= (b[1] - a[1]); ++j) {
+        Real pixel_value = GetObservedData().GetReal(Point(a[0]+i,
+                                                                 a[1]+j,slab_));
+        QString value_string = QString("%1").arg(pixel_value,0,'g',5);
+        Real rv = GetNormalizer()->Convert(pixel_value);
+        QPoint p = FracPointToWinCenter(geom::Vec2(static_cast<Real>(a[0]+i),
+                                                   static_cast<Real>(a[1]+j)));
+        unsigned char rgb = (rv>130.0) ? 0 : 255;
+        painter.setPen(QColor(rgb,rgb,rgb));
+        int string_h=painter.fontMetrics().height();
+        int string_w=painter.fontMetrics().width(value_string);
+        painter.drawText(p.x() - string_w/2, p.y() + string_h/2, value_string);
+      }
+    }
+  }else{
+    for(int i = 0; i <= (b[0] - a[0]); ++i) {
+      for(int j = 0; j <= (b[1] - a[1]); ++j) {
+        Complex pixel_value = GetObservedData().GetComplex(Point(a[0]+i,
+                                                                 a[1]+j,slab_));
+        QString value_string = QString("%1+i%2").arg(pixel_value.real(),0,'g',5).arg(pixel_value.imag(),0,'g',5);
+        Real rv = GetNormalizer()->Convert(abs(pixel_value));
+        QPoint p = FracPointToWinCenter(geom::Vec2(static_cast<Real>(a[0]+i),
+                                                   static_cast<Real>(a[1]+j)));
+        unsigned char rgb = (rv>130.0) ? 0 : 255;
+        painter.setPen(QColor(rgb,rgb,rgb));
+        int string_h=painter.fontMetrics().height();
+        int string_w=painter.fontMetrics().width(value_string);
+        painter.drawText(p.x() - string_w/2, p.y() + string_h/2, value_string);
+      }
     }
   }
 }
diff --git a/modules/gui/src/data_viewer/data_viewer_panel_base.hh b/modules/gui/src/data_viewer/data_viewer_panel_base.hh
index d3a6b01d0c282ff611f59d97cf0661217391d8b1..16339e55f66ae13a120d2b31891d95426fcb1ba1 100644
--- a/modules/gui/src/data_viewer/data_viewer_panel_base.hh
+++ b/modules/gui/src/data_viewer/data_viewer_panel_base.hh
@@ -28,12 +28,6 @@
 #include <map>    
 #include <boost/shared_ptr.hpp>
 
-#include <QWidget>
-#include <QCursor>
-#include <QMenu>
-#include <QPen>
-#include <QBrush>
-#include <QRubberBand>
 
 
 #include <ost/base.hh>
@@ -46,6 +40,12 @@
 
 #include <ost/img/normalizer_impl.hh>
 
+#include <QWidget>
+#include <QCursor>
+#include <QMenu>
+#include <QPen>
+#include <QBrush>
+#include <QRubberBand>
 
 namespace ost { namespace img { namespace gui {
 
diff --git a/modules/gui/src/data_viewer/drawing_functions.hh b/modules/gui/src/data_viewer/drawing_functions.hh
index c27e66345bf8287afee3c2ed3330ddbbd85026cf..b3374a12df5cf73aaf5822d8e069de46d5758b7d 100644
--- a/modules/gui/src/data_viewer/drawing_functions.hh
+++ b/modules/gui/src/data_viewer/drawing_functions.hh
@@ -25,11 +25,11 @@
 #ifndef IMG_GUI_DRAWING_FUNCTIONS_HH_
 #define IMG_GUI_DRAWING_FUNCTIONS_HH_
 
+#include <ost/geom/geom.hh>
 #include <QPainter>
 #include <QPoint>
 #include <QSize>
 
-#include <ost/geom/geom.hh>
 
 namespace ost { namespace img { namespace gui {
 
diff --git a/modules/gui/src/data_viewer/fft_panel.cc b/modules/gui/src/data_viewer/fft_panel.cc
index d764d5f9c110ec6820982725b285e3ad07c14ec4..6b14752a05242e5efe461f7cd01e4d784721d9fd 100644
--- a/modules/gui/src/data_viewer/fft_panel.cc
+++ b/modules/gui/src/data_viewer/fft_panel.cc
@@ -22,11 +22,11 @@
   Author: Andreas Schenk
 */
 
-#include <QInputDialog>
 #include <ost/img/alg/fft.hh>   
 #include "fft_panel.hh"
 
 
+#include <QInputDialog>
 
 
 namespace ost { namespace img { namespace gui {
diff --git a/modules/gui/src/data_viewer/img2qt.cc b/modules/gui/src/data_viewer/img2qt.cc
index d89a24c4699893718b6d0c418b2e1c7c5205fa18..9d0defcc4018f37f6b44a913805572bdede1581a 100644
--- a/modules/gui/src/data_viewer/img2qt.cc
+++ b/modules/gui/src/data_viewer/img2qt.cc
@@ -17,7 +17,6 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#include <QImage>
 
 #include <ost/img/data.hh>
 #include <ost/img/algorithm.hh>
@@ -25,6 +24,7 @@
 #include <ost/stdint.hh>
 #include "img2qt.hh"
 
+#include <QImage>
 using namespace ost::img;
 
 
diff --git a/modules/gui/src/data_viewer/info_panel.cc b/modules/gui/src/data_viewer/info_panel.cc
index 7bdf2a514df7ca43215126c027d81b4eb3f18182..4ebd0b53e7788015b53e0ab20858ecc3045af735 100644
--- a/modules/gui/src/data_viewer/info_panel.cc
+++ b/modules/gui/src/data_viewer/info_panel.cc
@@ -24,14 +24,14 @@
 */
 #include <boost/format.hpp>
 
-#include <QHBoxLayout>
-#include <QVBoxLayout>
-#include <QGroupBox>
 
 #include <ost/img/image.hh>
 
 #include "info_panel.hh"
 
+#include <QHBoxLayout>
+#include <QVBoxLayout>
+#include <QGroupBox>
 namespace ost { namespace img { namespace gui {
 
 InfoPanelLabel::InfoPanelLabel(const QString& t, QWidget* parent):
diff --git a/modules/gui/src/data_viewer/info_panel.hh b/modules/gui/src/data_viewer/info_panel.hh
index 388248dabacfb1f2d2467bec2f6819add3e429cf..d229555065146f9fcf9963d9917eb3dd1fdd2e55 100644
--- a/modules/gui/src/data_viewer/info_panel.hh
+++ b/modules/gui/src/data_viewer/info_panel.hh
@@ -25,9 +25,6 @@
 #ifndef IMG_GUI_DATAVIEWER_INFO_PANEL_H_
 #define IMG_GUI_DATAVIEWER_INFO_PANEL_H_
 
-#include <QWidget>
-#include <QLabel>
-#include <QMenu>
 
 #include <ost/img/data_types.hh>
 #include <ost/img/extent.hh>
@@ -35,6 +32,9 @@
 
 #include <ost/gui/module_config.hh>
 
+#include <QWidget>
+#include <QLabel>
+#include <QMenu>
 namespace ost { namespace img { namespace gui {
 
 class DLLEXPORT_OST_GUI InfoPanelLabel: public QLabel
diff --git a/modules/gui/src/data_viewer/mask_overlay.cc b/modules/gui/src/data_viewer/mask_overlay.cc
index a10082a3408b0988c2c38bda0230b6440d7916ff..b53678ad18fdf8f7dcb3adaa9fb45d88d09e0fce 100644
--- a/modules/gui/src/data_viewer/mask_overlay.cc
+++ b/modules/gui/src/data_viewer/mask_overlay.cc
@@ -73,7 +73,7 @@ void MaskOverlay::OnDraw(QPainter& pnt, DataViewerPanel* dvp, bool is_active)
     geom::Polygon2 pol=polygons_[i];
     QPolygon qpol;
     for(int j=0;j<static_cast<int>(pol.GetNodeCount());++j){
-      qpol << dvp->FracPointToWinCenter(pol.GetNode(j));
+      qpol << dvp->FracPointToWinCenter(pol.GetNode(j)+shift_);
       pnt.drawEllipse(qpol.back(),3,3);
     }
     pnt.drawPolygon(qpol);
@@ -89,7 +89,7 @@ void MaskOverlay::OnDraw(QPainter& pnt, DataViewerPanel* dvp, bool is_active)
     }
     QPolygon qpol;
     for(int j=0;j<static_cast<int>(new_poly_.GetNodeCount());++j){
-      qpol << dvp->FracPointToWinCenter(new_poly_.GetNode(j));
+      qpol << dvp->FracPointToWinCenter(new_poly_.GetNode(j)+shift_);
       pnt.drawEllipse(qpol.back(),3,3);
     }
     pnt.drawPolygon(qpol);
@@ -103,11 +103,7 @@ bool MaskOverlay::OnMouseEvent(QMouseEvent* e,  DataViewerPanel* dvp,
 
   geom::Vec2 mousepos=dvp->WinToFracPoint(e->pos());
   geom::Vec2 diffpos=mousepos-old_mouse_pos_;
-  if(e->buttons() & Qt::RightButton){
-    for(std::vector<geom::Polygon2>::iterator it=polygons_.begin();it!=polygons_.end();++it){
-      (*it)=(*it)+diffpos;
-    }
-    new_poly_=new_poly_+diffpos;
+  if(e->buttons() & Qt::RightButton && e->button()==Qt::NoButton){
     shift_+=diffpos;
   }
   old_mouse_pos_=mousepos;
@@ -214,5 +210,19 @@ void MaskOverlay::ClearMask()
   add_mode_=false;
 }
 
+void MaskOverlay::SetShift(geom::Vec2 shift)
+{
+  shift_=shift;
+}
+
+void MaskOverlay::ApplyShiftToMask()
+{
+  for(std::vector<geom::Polygon2>::iterator it=polygons_.begin();it!=polygons_.end();++it){
+    (*it)=(*it)+shift_;
+  }
+  new_poly_=new_poly_+shift_;
+  shift_=geom::Vec2(0.0,0.0);
+}
+
 
 }}}  //ns
diff --git a/modules/gui/src/data_viewer/mask_overlay.hh b/modules/gui/src/data_viewer/mask_overlay.hh
index e274f315756060af5001d610e550b42f410a1e83..36feb893d9d0d71893568fab4273c96314636ca0 100644
--- a/modules/gui/src/data_viewer/mask_overlay.hh
+++ b/modules/gui/src/data_viewer/mask_overlay.hh
@@ -56,6 +56,8 @@ public:
   void ClearMask();
   void ClearShift(){shift_=geom::Vec2();}
   geom::Vec2 GetShift(){return shift_;}
+  void SetShift(geom::Vec2 shift);
+  void ApplyShiftToMask();
 
 protected:
   std::vector<geom::Polygon2> polygons_;
diff --git a/modules/gui/src/data_viewer/overlay_base.hh b/modules/gui/src/data_viewer/overlay_base.hh
index edef14985af6d488413334b98837c37ab90de75b..05c3d6d08f263f1986c49176e2f434bb26c5259b 100644
--- a/modules/gui/src/data_viewer/overlay_base.hh
+++ b/modules/gui/src/data_viewer/overlay_base.hh
@@ -25,18 +25,18 @@
 #ifndef IMG_GUI_OVERLAY_BASE_H
 #define IMG_GUI_OVERLAY_BASE_H
 
-#include <QObject>
-#include <QEvent>
-#include <QPainter>
-#include <QMenu>
-#include <QMouseEvent>
-#include <QKeyEvent>
 
 #include <ost/base.hh>
 
 #include <ost/gui/module_config.hh>
 #include "overlay_base_fw.hh"
 
+#include <QObject>
+#include <QEvent>
+#include <QPainter>
+#include <QMenu>
+#include <QMouseEvent>
+#include <QKeyEvent>
 namespace ost { namespace img { namespace gui {
 
 // fw decl
diff --git a/modules/gui/src/data_viewer/overlay_manager.hh b/modules/gui/src/data_viewer/overlay_manager.hh
index 033d78663ce99f5fa37a26f87cc022716f8a03cf..cef91ac91201ae46c87ded349b8ed95069debdef 100644
--- a/modules/gui/src/data_viewer/overlay_manager.hh
+++ b/modules/gui/src/data_viewer/overlay_manager.hh
@@ -28,9 +28,6 @@
 #include <vector>
 #include <list>
 
-#include <QWidget>
-#include <QPainter>
-#include <QEvent>
 
 
 #include <ost/base.hh>
@@ -41,6 +38,9 @@
 #include "overlay_manager_fw.hh"
 #include "overlay_manager_observer.hh"
 
+#include <QWidget>
+#include <QPainter>
+#include <QEvent>
 namespace ost { namespace img { namespace gui {
 
 class DataViewerPanel;
diff --git a/modules/gui/src/data_viewer/overlay_manager_gui.cc b/modules/gui/src/data_viewer/overlay_manager_gui.cc
index c947d50cd1454a49bede8558efd6c9e020407c18..1944c42f6b7552be0bc5f215ff2f08d0f2007425 100644
--- a/modules/gui/src/data_viewer/overlay_manager_gui.cc
+++ b/modules/gui/src/data_viewer/overlay_manager_gui.cc
@@ -22,7 +22,6 @@
   Authors: Ansgar Philippsen, Andreas Schenk
 */
 
-#include <QScrollArea>
 
 #include <ost/message.hh>
 
@@ -30,6 +29,7 @@
 #include "overlay_manager.hh"
 #include "overlay.hh"
 
+#include <QScrollArea>
 namespace ost { namespace img { namespace gui {
 
 ////////////////////////////
diff --git a/modules/gui/src/data_viewer/overlay_manager_gui.hh b/modules/gui/src/data_viewer/overlay_manager_gui.hh
index b12adca5a74c99a32ccbdd79ccadff8dfbdb1595..a601832e061a30e0d8f03c166a36b2cd88c30c06 100644
--- a/modules/gui/src/data_viewer/overlay_manager_gui.hh
+++ b/modules/gui/src/data_viewer/overlay_manager_gui.hh
@@ -26,6 +26,11 @@
 #ifndef IMG_OV_GUI_OVDIALOG_H
 #define IMG_OV_GUI_OVDIALOG_H
 
+
+#include <vector>
+#include <map>
+#include "overlay_manager_observer.hh"
+
 #include <QWidget>
 #include <QRadioButton>
 #include <QCheckBox>
@@ -34,11 +39,6 @@
 #include <QLabel>
 #include <QPushButton>
 #include <QButtonGroup>
-
-#include <vector>
-#include <map>
-#include "overlay_manager_observer.hh"
-
 namespace ost { namespace img { namespace gui {
 
 class OverlayCustomActCheckBox: public QRadioButton
diff --git a/modules/gui/src/data_viewer/pointlist_overlay.cc b/modules/gui/src/data_viewer/pointlist_overlay.cc
index c031b8eef986581d3ea6043a7f2a7ad4817d3eac..899372608a3bf9607a26a1b64639496ac8e60a7a 100644
--- a/modules/gui/src/data_viewer/pointlist_overlay.cc
+++ b/modules/gui/src/data_viewer/pointlist_overlay.cc
@@ -31,15 +31,17 @@
 namespace ost { namespace img { namespace gui {
 
 PointlistOverlay::PointlistOverlay(const String& name):
-  PointlistOverlayBase(name)
+  PointlistOverlayBase(name),
+  pointlist_()
 {
-  build();
+  build_();
 }
 
 PointlistOverlay::PointlistOverlay(const PointList& pl, const String& name):
-  PointlistOverlayBase(name)
+  PointlistOverlayBase(name),
+  pointlist_()
 {
-  build();
+  build_();
   Add(pl);
 }
 
@@ -52,22 +54,22 @@ void PointlistOverlay::OnMenuEvent(QAction* e)
   }
 }
 
-void PointlistOverlay::Add(const Point& pnt)
+void PointlistOverlay::Add(const Point& pnt, double scale)
 {
-  pointlist_.push_back(pnt);
+  pointlist_.push_back(std::pair<Point,double>(pnt,scale));
 }
 
-void PointlistOverlay::Add(const PointList& pl)
+void PointlistOverlay::Add(const PointList& pl, double scale)
 {
   for(PointList::const_iterator it=pl.begin();it!=pl.end();++it) {
-    Add(*it);
+    Add(*it,scale);
   }
 }
 
 void PointlistOverlay::Remove(const Point& pnt)
 {
-  for(PointList::iterator it=pointlist_.begin();it!=pointlist_.end();++it){
-    if (*it==pnt) {
+  for(std::vector<std::pair<Point,double> >::iterator it=pointlist_.begin();it!=pointlist_.end();++it){
+    if (it->first==pnt) {
       pointlist_.erase(it);
     }
   }
@@ -80,13 +82,14 @@ void PointlistOverlay::Clear()
 
 void PointlistOverlay::OnDraw(QPainter& pnt, DataViewerPanel* dvp, bool is_active)
 {
-  std::vector<QPoint> qpointlist;
-  for(PointList::iterator it=pointlist_.begin();it!=pointlist_.end();++it){
-    qpointlist.push_back(dvp->FracPointToWinCenter((*it).ToVec2()));
+  std::vector<std::pair<QPoint,double> > qpointlist;
+  for(std::vector<std::pair<Point,double> >::iterator it=pointlist_.begin();it!=pointlist_.end();++it){
+    qpointlist.push_back(std::pair<QPoint,double> (dvp->FracPointToWinCenter((it->first).ToVec2()),it->second));
   }
   
-  DrawPointList(pnt,dvp, is_active? active_color_ : passive_color_,
-                qpointlist);
+  DrawVariableSizePointList(pnt,dvp,
+		is_active? active_color_ : passive_color_,
+		qpointlist);
 }
 
 bool PointlistOverlay::OnMouseEvent(QMouseEvent* e, 
@@ -96,19 +99,20 @@ bool PointlistOverlay::OnMouseEvent(QMouseEvent* e,
   if(e->buttons()==Qt::LeftButton && e->modifiers()&Qt::ShiftModifier) {
     // toggle point at mouse position
     Point mpoint = dvp->WinToPoint(e->x(),e->y());
-    PointList::iterator pos=find(pointlist_.begin(),
-                                       pointlist_.end(),mpoint);
-    if(pos!=pointlist_.end()) {
-      pointlist_.erase(pos);
-    } else {
-      pointlist_.push_back(mpoint);
+    for(std::vector<std::pair<Point,double> >::iterator it=pointlist_.begin();it!=pointlist_.end();++it){
+      if (it->first==mpoint) {
+        pointlist_.erase(it);
+        return true;
+      }
     }
+    pointlist_.push_back(std::pair<Point,double>(mpoint,1.0));
     return true;
   }
   return false;
 }
 
-void PointlistOverlay::build()
+
+void PointlistOverlay::build_()
 {
   menu_->addSeparator();
   a_clr_ = menu_->addAction("Clear");
diff --git a/modules/gui/src/data_viewer/pointlist_overlay.hh b/modules/gui/src/data_viewer/pointlist_overlay.hh
index 1095f2191f448dc4d9ac5fa318d59719a817b292..bbec437c4e5665c054390e8feb648dd2e6fc70df 100644
--- a/modules/gui/src/data_viewer/pointlist_overlay.hh
+++ b/modules/gui/src/data_viewer/pointlist_overlay.hh
@@ -45,8 +45,8 @@ public:
   virtual bool OnMouseEvent(QMouseEvent* e,  DataViewerPanel* dvp, 
                             const QPoint& lastmouse);
   
-  void Add(const Point& pnt);
-  void Add(const PointList& pl);
+  void Add(const Point& pnt, double scale=1.0);
+  void Add(const PointList& pl, double scale=1.0);
   
   //! remove all points on the given point
   void Remove(const Point& pnt);
@@ -55,11 +55,11 @@ public:
   void Clear();
   
 private:
-  PointList pointlist_;
+  std::vector<std::pair<Point,double> > pointlist_;
 
   QAction* a_clr_;
 
-  void build();
+  void build_();
 };
 
 }}}  //ns
diff --git a/modules/gui/src/data_viewer/pointlist_overlay_base.cc b/modules/gui/src/data_viewer/pointlist_overlay_base.cc
index fe76e291ef0614e15764766646ec78a67ff353f7..13392d28df7ab4d967f244e9b00a82f05146a925 100644
--- a/modules/gui/src/data_viewer/pointlist_overlay_base.cc
+++ b/modules/gui/src/data_viewer/pointlist_overlay_base.cc
@@ -21,6 +21,9 @@
 /*
   Authors: Ansgar Philippsen, Andreas Schenk
 */
+#include "data_viewer_panel.hh"
+#include "pointlist_overlay_base.hh"
+#include "strategies.hh"
 
 #include <QActionGroup>
 #include <QGridLayout>
@@ -33,9 +36,6 @@
 #include <QIcon>
 #include <QColorDialog>
 
-#include "data_viewer_panel.hh"
-#include "pointlist_overlay_base.hh"
-#include "strategies.hh"
 
 namespace ost { namespace img { namespace gui {
 
@@ -197,30 +197,39 @@ void PointlistOverlayBase::DrawPointList(QPainter& pnt, DataViewerPanel* dvp,
   }
   strategy_->SetSymbolSize(static_cast<int>((GetSymbolSize()-0.5) * dvp->GetZoomScale()));
 }
+void PointlistOverlayBase::DrawVariableSizePointList(QPainter& pnt, DataViewerPanel* dvp, 
+                                                     const QColor& color,
+                                                     const std::vector<std::pair<QPoint,double> >& pointlist)
+{
+  strategy_->SetPenColor(color);
+  strategy_->SetSymbolStrength(symbolstrength_);
+  for(unsigned int i = 0; i < pointlist.size(); i++) {
+    strategy_->SetSymbolSize(static_cast<int>((GetSymbolSize()-0.5) * dvp->GetZoomScale()*pointlist[i].second));
+    strategy_->Draw(pnt,pointlist[i].first);
+  }
+  strategy_->SetSymbolSize(static_cast<int>((GetSymbolSize()-0.5) * dvp->GetZoomScale()));
+}
 
 bool PointlistOverlayBase::GetCrosshair() const
 {
-  //return menu_->IsChecked(ID_Crosshair);
-  return false;
+  return a_cr_->isChecked();
 }
 
 void PointlistOverlayBase::SetCrosshair(bool flag)
 {
-  /*
-  if(menu_->IsChecked(ID_Crosshair))	{
-    if(menu_->IsChecked(ID_Square)){
+  if(a_cr_->isChecked())	{
+    if(a_sq_->isChecked()){
       ReplaceStrategy<CrosshairSquareDrawingStrategy>();
     }else{
       ReplaceStrategy<CrosshairCircleDrawingStrategy>();
     }
   } else {
-    if(menu_->IsChecked(ID_Square)){
+    if(a_sq_->isChecked()){
       ReplaceStrategy<SquareDrawingStrategy>();
     }else{
       ReplaceStrategy<CircleDrawingStrategy>();
     }
   }
-  */
 }
 
 unsigned int PointlistOverlayBase::GetSymbolSize() const 
@@ -235,30 +244,28 @@ void PointlistOverlayBase::SetSymbolSize(unsigned int symbolsize)
 
 unsigned int PointlistOverlayBase::GetSymbolShape() const
 {
-  //return menu_->IsChecked(ID_Circle) ? 0 : 1;
-  return 0;
+  return a_sq_->isChecked() ? 1 : 0;
 }
 
 void PointlistOverlayBase::SetSymbolShape(unsigned int symbolshape)
 {
-  /*
   switch(symbolshape){
   case 1:
-    if(menu_->IsChecked(ID_Crosshair)){
+    if(a_cr_->isChecked()){
       ReplaceStrategy<CrosshairSquareDrawingStrategy>();
     }else{
       ReplaceStrategy<SquareDrawingStrategy>();
     }
     break;
   case 0:
-    if(menu_->IsChecked(ID_Crosshair)){
+    if(a_cr_->isChecked()){
         ReplaceStrategy<CrosshairCircleDrawingStrategy>();
     }else{
       ReplaceStrategy<CircleDrawingStrategy>();
     }
     break;
   }
-  */
+  
 }
 
 template <class StrategyClass>
@@ -276,4 +283,14 @@ void PointlistOverlayBase::SetProps(PointlistOverlayBaseSettings* props)
   symbolstrength_=props->symbol_strength;
 }
 
+void PointlistOverlayBase::SetActiveColor(const QColor& col)
+{
+  active_color_=col;
+}
+
+void PointlistOverlayBase::SetPassiveColor(const QColor& col)
+{
+  passive_color_=col;
+}
+
 }}}  //ns
diff --git a/modules/gui/src/data_viewer/pointlist_overlay_base.hh b/modules/gui/src/data_viewer/pointlist_overlay_base.hh
index 606c859a1dcc32b2ff17eb1d2836cd17ab621e53..3c0f709d837e068c08e9223a2b4b0a54215beb5c 100644
--- a/modules/gui/src/data_viewer/pointlist_overlay_base.hh
+++ b/modules/gui/src/data_viewer/pointlist_overlay_base.hh
@@ -26,13 +26,6 @@
 #ifndef IMG_POINTLIST_OVERLAY_BASE_HH
 #define IMG_POINTLIST_OVERLAY_BASE_HH
 
-#include <QColor>
-#include <QAction>
-#include <QDialog>
-#include <QLineEdit>
-#include <QColorDialog>
-#include <QPushButton>
-#include <QVBoxLayout>
 
 
 #include <ost/img/point.hh>
@@ -43,6 +36,13 @@
 
 #include "strategies_fw.hh"
 
+#include <QColor>
+#include <QAction>
+#include <QDialog>
+#include <QLineEdit>
+#include <QColorDialog>
+#include <QPushButton>
+#include <QVBoxLayout>
 
 
 namespace ost { namespace img { namespace gui {
@@ -85,6 +85,7 @@ public:
 
   // own virtual interface
   virtual void DrawPointList(QPainter& pnt, DataViewerPanel* dvp, const QColor& col ,const std::vector<QPoint>& pointlist);
+  virtual void DrawVariableSizePointList(QPainter& pnt, DataViewerPanel* dvp, const QColor& col ,const std::vector<std::pair<QPoint,double> >& pointlist);
 
   //
   unsigned int GetSymbolSize() const;
@@ -93,6 +94,8 @@ public:
   void SetSymbolShape(unsigned int symbolshape);
   bool GetCrosshair() const;
   void SetCrosshair(bool flag);
+  void SetActiveColor(const QColor& col);
+  void SetPassiveColor(const QColor& col);
 private:
 
   template <class StrategyClass> 
diff --git a/modules/gui/src/data_viewer/strategies.hh b/modules/gui/src/data_viewer/strategies.hh
index a6abb3d3866c843b53e0dfe5f658e8fe633d0f63..0989492c877aebc916016c919b43db3b540de640 100644
--- a/modules/gui/src/data_viewer/strategies.hh
+++ b/modules/gui/src/data_viewer/strategies.hh
@@ -25,16 +25,16 @@
 #ifndef IMG_GUI_STRATEGIES_HH_
 #define IMG_GUI_STRATEGIES_HH_
 
-#include <QPainter>
-#include <QPoint>
-#include <QColor>
-#include <QPen>
-#include <QBrush>
 
 #include <ost/geom/geom.hh>
 
 #include "strategies_fw.hh"
 
+#include <QPainter>
+#include <QPoint>
+#include <QColor>
+#include <QPen>
+#include <QBrush>
 namespace ost { namespace img { namespace gui {
 
 
diff --git a/modules/gui/src/dock_widget.hh b/modules/gui/src/dock_widget.hh
index eefecd21db62df3116ca96d76141fad5a78ce051..6668b50aae12ddfc2b686e0bd6322c4c0fb3e218 100644
--- a/modules/gui/src/dock_widget.hh
+++ b/modules/gui/src/dock_widget.hh
@@ -25,10 +25,10 @@
 #ifndef OST_GUI_DOCK_WIDGET_HH
 #define OST_GUI_DOCK_WIDGET_HH
 
-#include <QDockWidget>
 
 #include <ost/gui/module_config.hh>
 
+#include <QDockWidget>
 namespace ost { namespace gui {
 
 class DLLEXPORT_OST_GUI DockWidget: public QDockWidget
diff --git a/modules/gui/src/entity_explorer/entity_explorer_model.hh b/modules/gui/src/entity_explorer/entity_explorer_model.hh
index 51545794268157494efa0fa8154bb7881c32ef38..8071a7c8748887b2562aa333a80ab341cf806d60 100644
--- a/modules/gui/src/entity_explorer/entity_explorer_model.hh
+++ b/modules/gui/src/entity_explorer/entity_explorer_model.hh
@@ -24,11 +24,11 @@
 
 #include <ost/gfx/scene_observer.hh>
 #include <ost/gfx/gfx_object.hh>
+#include <ost/gui/module_config.hh>
 
 // Qt includes must come last
 #include <QAbstractItemModel>
 
-#include <ost/gui/module_config.hh>
 
 namespace ost { namespace gui {
 
diff --git a/modules/gui/src/file_browser.cc b/modules/gui/src/file_browser.cc
index c854be414df655e39e187ae2fa8efd21988dc963..ca7092684382517d25fdc7128b215e05f147ee4f 100644
--- a/modules/gui/src/file_browser.cc
+++ b/modules/gui/src/file_browser.cc
@@ -16,13 +16,8 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#include <QVBoxLayout>
-#include <QDir>
-#include <QHeaderView>
-#include <QFileInfo>
-#include <QMessageBox>
-#include <QApplication>
 
+#include <ost/gui/gosty_app.hh>
 #include <ost/platform.hh>
 #include <ost/config.hh>
 #include <ost/mol/mol.hh>
@@ -34,10 +29,10 @@
 #include <ost/gfx/entity.hh>
 #include <ost/gfx/scene.hh>
 
-#include <ost/gui/gosty_app.hh>
 #include <ost/gui/perspective.hh>
-#include <ost/gui/panel_bar/panels.hh>
+#include <ost/gui/panels/panel_manager.hh>
 #include <ost/gui/file_loader.hh>
+#include <ost/gui/file_viewer.hh>
 
 #include <ost/gui/python_shell/python_interpreter.hh>
 
@@ -50,48 +45,74 @@
 #include "widget_registry.hh"
 #include "file_browser.hh"
 
+#include <QCoreApplication>
+#include <QCursor>
+#include <QVBoxLayout>
+#include <QDesktopServices>
+#include <QDir>
+#include <QFileInfo>
+#include <QUrl>
+
 namespace ost { namespace gui {
 
 FileBrowser::FileBrowser(QWidget* parent):
- Widget(NULL, parent)
+ Widget(NULL, parent),
+ menu_(new QComboBox(this)),
+ model_(new QDirModel),
+ view_(new QListView(this)),
+ action_list_()
 {
   QString path=QDir::currentPath();
+  QDir dir(QCoreApplication::applicationDirPath());
 # if defined(_MSC_VER)
-    QDir dir(QCoreApplication::applicationDirPath());
     dir.cdUp();
     dir.cdUp();
     path=dir.path();
-    QString example_path=path+"/share/openstructure/examples/entity";
+    QString example_path=path+"/share/openstructure/examples/";
     if (QDir(example_path).exists()) {
       path=example_path;
     } 
 # elif defined(__APPLE__)
   if (path.contains("DNG.app") || path=="/") {
-    QString example_path="/Applications/OpenStructure/Examples/entity";    
+    QString example_path="/Applications/OpenStructure/Examples/";
     if (QDir(example_path).exists()) {
       path=example_path;
-    }    
+    }    else{
+      dir.cdUp();
+      example_path=dir.path()+"/examples";
+      if (QDir(example_path).exists()) {
+        path=example_path;
+      }
+    }
+  }
+# else
+  QString example_path=path+"/share/openstructure/examples/";
+  if (QDir(example_path).exists()) {
+    path=example_path;
   }
 #endif
   this->Init(path);
 }
 
 FileBrowser::FileBrowser(const QString& path, QWidget* parent):
- Widget(NULL, parent)
+ Widget(NULL, parent),
+ menu_(new QComboBox(this)),
+ model_(new QDirModel),
+ view_(new QListView(this)),
+ action_list_()
 {
   this->Init(path);
 }
 
 void FileBrowser::Init(const QString& path)
 {
-  model_=new QDirModel;
   model_->setSorting(QDir::Name|QDir::DirsFirst|QDir::IgnoreCase);
 
-  view_=new QListView(this);
   view_->setModel(model_);
   view_->setRootIndex(model_->index(path));
   view_->setAttribute(Qt::WA_MacShowFocusRect, false);
-  menu_= new QComboBox(this);
+  view_->setContextMenuPolicy(Qt::CustomContextMenu);
+  connect(view_,SIGNAL(customContextMenuRequested(const QPoint&)),this,SLOT(ShowContextMenu(const QPoint&)));
   UpdateMenu(path);
 
   QVBoxLayout* l=new QVBoxLayout(this);
@@ -137,13 +158,7 @@ bool FileBrowser::Restore(const QString& prefix)
 
 void FileBrowser::DoubleClicked(const QModelIndex& index)
 {
-  if(model_->isDir(index)){
-    view_->setRootIndex(index);
-    UpdateMenu(model_->filePath(index));
-  }
-  else{
-    LoadObject(index);
-  }
+  LoadObject(index);
 }
 
 void FileBrowser::ChangeToParentDirectory(int index){
@@ -176,7 +191,7 @@ void FileBrowser::UpdateMenu(const QString& path){
 }
 
 void FileBrowser::Split(){
-  Panels* panels = GostyApp::Instance()->GetPerspective()->GetPanels();
+  PanelManager* panels = GostyApp::Instance()->GetPerspective()->GetPanels();
   QString current_path = model_->filePath(view_->rootIndex());
   Widget* new_file_browser = new FileBrowser(current_path);
   panels->MoveNextTo(qobject_cast<Widget*>(this), new_file_browser);
@@ -193,10 +208,15 @@ void FileBrowser::AddItem(const QDir& directory, const QString& mypath){
 }
 
 void FileBrowser::LoadObject(const QModelIndex& index){
-  gfx::GfxObjP obj;
   if (index.isValid()) {
-    QString file_name=model_->filePath(index);
-    FileLoader::LoadObject(file_name);
+    if(model_->isDir(index)){
+      view_->setRootIndex(index);
+      UpdateMenu(model_->filePath(index));
+    }
+    else{
+      QString file_name=model_->filePath(index);
+      FileLoader::LoadObject(file_name);
+    }
   }
 }
 
@@ -206,6 +226,55 @@ void FileBrowser::keyPressEvent(QKeyEvent* event){
   }
 }
 
+void FileBrowser::ShowContextMenu(const QPoint& pos){
+
+  QModelIndex index = view_->selectionModel()->currentIndex();
+  QMenu* menu = new QMenu(this);
+  if(model_->isDir(index)){
+    QAction* open_action = new QAction(menu);
+    open_action->setText("Open");
+    connect(open_action,SIGNAL(triggered(bool)),this,SLOT(LoadCurrentObject()));
+    menu->addAction(open_action);
+  }
+  if(!model_->isDir(index)){
+    QAction* load_action = new QAction(menu);
+    load_action->setText("Load");
+    connect(load_action,SIGNAL(triggered(bool)),this,SLOT(LoadCurrentObject()));
+    menu->addAction(load_action);
+    QAction* system_open_action = new QAction(menu);
+    if(model_->filePath(index).endsWith(".py")){
+      system_open_action->setText("Show source");
+      connect(system_open_action,SIGNAL(triggered(bool)),this,SLOT(LoadWithSourceViewer()));
+    }
+    else{
+      system_open_action->setText("Open with system default");
+      connect(system_open_action,SIGNAL(triggered(bool)),this,SLOT(LoadWithSystemEditor()));
+    }
+    menu->addAction(system_open_action);
+  }
+  if(menu->actions().size()>0){
+    menu->exec(QCursor::pos());
+  }
+}
+
+void FileBrowser::LoadCurrentObject(){
+  QModelIndex index = view_->selectionModel()->currentIndex();
+  this->LoadObject(index);
+}
+
+void FileBrowser::LoadWithSystemEditor(){
+  QModelIndex index = view_->selectionModel()->currentIndex();
+  QString file_name=model_->filePath(index);
+  QDesktopServices::openUrl(QUrl::fromLocalFile(file_name));
+}
+
+void FileBrowser::LoadWithSourceViewer(){
+  QModelIndex index = view_->selectionModel()->currentIndex();
+  QString file_name=model_->filePath(index);
+  FileViewer* file_viewer = new FileViewer(file_name);
+  file_viewer->show();
+}
+
 OST_REGISTER_WIDGET_WITH_DEFAULT_FACTORY(ost::gui, FileBrowser, "File Browser");  
 
 
diff --git a/modules/gui/src/file_browser.hh b/modules/gui/src/file_browser.hh
index 78ad1acf73a5453febeb092cc01c2a747ed1474c..902291746cb23d08703ec670b33eedd8a10f78aa 100644
--- a/modules/gui/src/file_browser.hh
+++ b/modules/gui/src/file_browser.hh
@@ -19,14 +19,14 @@
 #ifndef OST_GUI_FILE_BROWSER_HH
 #define OST_GUI_FILE_BROWSER_HH
 
-#include <QDirModel>
-#include <QListView>
-#include <QComboBox>
 
 #include <ost/gfx/gfx_object.hh>
 #include <ost/gui/module_config.hh>
 #include <ost/gui/widget.hh>
 
+#include <QDirModel>
+#include <QListView>
+#include <QComboBox>
 namespace ost { namespace gui {
 
 
@@ -51,6 +51,11 @@ private slots:
   void DoubleClicked(const QModelIndex& index);
   void ChangeToParentDirectory(int index);
   void Split();
+  void ShowContextMenu(const QPoint& pos);
+  void LoadCurrentObject();
+  void LoadWithSystemEditor();
+  void LoadWithSourceViewer();
+
 private:
   void LoadObject(const QModelIndex& index);
   void UpdateMenu(const QString& path);
diff --git a/modules/gui/src/file_loader.cc b/modules/gui/src/file_loader.cc
index 258d0ac024421a439cbec541aadd42ac54cd0faf..a874742bce365399da8a5c89328fd2d19436a1e3 100644
--- a/modules/gui/src/file_loader.cc
+++ b/modules/gui/src/file_loader.cc
@@ -16,16 +16,9 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
+#include <ost/gui/gosty_app.hh>
 #include "file_loader.hh"
 
-#include <QDir>
-#include <QAction>
-#include <QMenu>
-#include <QFileInfo>
-#include <QMessageBox>
-#include <QMenuBar>
-
-
 #include <ost/config.hh>
 #include <ost/mol/mol.hh>
 #include <ost/mol/surface.hh>
@@ -38,15 +31,18 @@
 
 #include <ost/conop/conop.hh>
 
+#include <ost/seq/sequence_list.hh>
+#include <ost/seq/alignment_handle.hh>
+#include <ost/seq/invalid_sequence.hh>
 #include <ost/gfx/entity.hh>
 #include <ost/gfx/surface.hh>
 #include <ost/gfx/scene.hh>
 
-#include <ost/gui/gosty_app.hh>
 #include <ost/gui/perspective.hh>
 #include <ost/gui/python_shell/python_interpreter.hh>
 #include <ost/gui/main_area.hh>
 #include <ost/gui/file_type_dialog.hh>
+#include <ost/gui/sequence_viewer/sequence_viewer.hh>
 
 #if OST_IMG_ENABLED
   #include <ost/io/img/load_map.hh>
@@ -54,6 +50,12 @@
   #include <ost/img/extent.hh>
 #endif
 
+#include <QDir>
+#include <QAction>
+#include <QMenu>
+#include <QFileInfo>
+#include <QMessageBox>
+#include <QMenuBar>
 namespace ost { namespace gui {
 
 LoaderManagerPtr FileLoader::loader_manager_ = LoaderManagerPtr();
@@ -88,11 +90,22 @@ void FileLoader::LoadObject(const QString& filename, const QString& selection)
         }
       }
   #endif
+      if (!obj)  {
+        try{
+          obj=FileLoader::TryLoadAlignment(filename);
+        } catch (io::IOFileAlreadyLoadedException&) {
+          return;
+        }
+      }
       if (!obj) {
         obj=FileLoader::TryLoadSurface(filename);
       }
       if (!obj) {
-        obj=FileLoader::NoHandlerFound(filename);
+        try{
+          obj=FileLoader::NoHandlerFound(filename);
+        } catch (io::IOFileAlreadyLoadedException&) {
+          return;
+        }
       }
       if (!obj){
         return;
@@ -112,7 +125,7 @@ void FileLoader::AddToScene(const QString& filename, gfx::GfxObjP obj)
       gfx::Scene::Instance().SetCenter(obj->GetCenter());
     }
   }
-  catch (Message m) {
+  catch (Error m) {
     FileLoader::HandleError(m, GFX_ADD, filename, obj);
   }
 }
@@ -120,18 +133,26 @@ void FileLoader::AddToScene(const QString& filename, gfx::GfxObjP obj)
 gfx::GfxObjP FileLoader::NoHandlerFound(const QString& filename)
 {
   FileTypeDialog dialog(filename);
-  if(dialog.exec()){
-    if(dialog.GetEntityHandler()){
-      return TryLoadEntity(filename, dialog.GetEntityHandler());
-    }
-    if(dialog.GetSurfaceHandler()){
-      return TryLoadSurface(filename,dialog.GetSurfaceHandler());
-    }
-#if OST_IMG_ENABLED
-    if(dialog.GetMapHandler()){
-      return TryLoadMap(filename,dialog.GetMapHandler());
+  try{
+    if(dialog.exec()){
+      if(dialog.GetEntityHandler()){
+        return TryLoadEntity(filename, dialog.GetEntityHandler());
+      }
+      if(dialog.GetSequenceHandler()){
+        return TryLoadAlignment(filename, dialog.GetSequenceHandler());
+      }
+      if(dialog.GetSurfaceHandler()){
+        return TryLoadSurface(filename,dialog.GetSurfaceHandler());
+      }
+  #if OST_IMG_ENABLED
+      if(dialog.GetMapHandler()){
+        return TryLoadMap(filename,dialog.GetMapHandler());
+      }
+  #endif
     }
-#endif
+  }
+  catch (io::IOException& e) {
+    FileLoader::HandleError(e,IO_LOADING,filename);
   }
   return gfx::GfxObjP();
 }
@@ -166,11 +187,11 @@ std::vector<String> FileLoader::GetSiteLoaderIdents()
   return loader_manager_->GetSiteLoaderIdents();
 }
 
-void FileLoader::HandleError(Message m, ErrorType type, const QString& filename, gfx::GfxObjP obj)
+void FileLoader::HandleError(const Error& e, ErrorType type, const QString& filename, gfx::GfxObjP obj)
 {
   if(type==GFX_ADD || type==GFX_MULTIPLE_ADD){
     QMessageBox message_box(QMessageBox::Warning,
-        "Error while adding Node to Scene", m._mesg.c_str());
+        "Error while adding Node to Scene", e.what());
     if(type==GFX_ADD){
       message_box.setStandardButtons( QMessageBox::Yes | QMessageBox::Cancel);
       message_box.setButtonText(QMessageBox::Yes, "Reload");
@@ -189,7 +210,7 @@ void FileLoader::HandleError(Message m, ErrorType type, const QString& filename,
   }
   else if(type==IO_LOADING){
     QMessageBox message_box(QMessageBox::Warning,
-                "Error while loading file", m._mesg.c_str());
+                "Error while loading file", e.what());
     message_box.setStandardButtons( QMessageBox::Yes | QMessageBox::Cancel);
     message_box.setButtonText(QMessageBox::Yes, "Chose format");
     int value = message_box.exec();
@@ -199,6 +220,12 @@ void FileLoader::HandleError(Message m, ErrorType type, const QString& filename,
       break;
     }
   }
+  else if(type==INFO){
+    QMessageBox message_box(QMessageBox::Information,
+        "Information", e.what());
+    message_box.setStandardButtons( QMessageBox::Ok);
+    message_box.exec();
+  }
 }
 
 gfx::GfxObjP FileLoader::TryLoadEntity(const QString& filename, io::EntityIOHandlerP handler, const QString& selection)
@@ -296,16 +323,55 @@ gfx::GfxObjP FileLoader::TryLoadSurface(const QString& filename, io::SurfaceIOHa
   return gfx::GfxObjP();
 }
 
+gfx::GfxObjP FileLoader::TryLoadAlignment(const QString& filename, 
+                                          io::SequenceIOHandlerPtr handler)
+{
+  if(!handler){
+    try{
+      handler = io::IOManager::Instance().FindAlignmentImportHandler(filename.toStdString(),"auto");
+    }
+    catch(io::IOUnknownFormatException e){
+      handler = io::SequenceIOHandlerPtr();
+    }
+  }
+  if(handler){
+    seq::SequenceList seq_list = seq::CreateSequenceList();
+    try {
+      handler->Import(seq_list,filename.toStdString());      
+    } catch(io::IOException& e) {
+      LOG_ERROR(e.what());
+      return gfx::GfxObjP();
+    }
+    catch(seq::InvalidSequence& e) {
+      LOG_ERROR(e.what());
+      return gfx::GfxObjP();
+    }
+    seq::AlignmentHandle alignment = seq::AlignmentFromSequenceList(seq_list);
+    gui::MainArea* main_area = gui::GostyApp::Instance()->GetPerspective()->GetMainArea();
+    SequenceViewer* viewer = new SequenceViewer(true,main_area);
+    viewer->AddAlignment(alignment);
+    main_area->AddWidget(filename,viewer);
+    throw io::IOFileAlreadyLoadedException("Loaded in DataViewer");
+  }
+  return gfx::GfxObjP();
+}
+
 void FileLoader::RunScript(const QString& filename)
 {
   PythonInterpreter& pi = PythonInterpreter::Instance();
   //HackerMode On
   //The following code lines are just temporary
   //TODO create class or function which can load any kind of files and execute scripts
+  pi.RunCommand("_sys_argv_backup=sys.argv");
+  pi.RunCommand("sys.argv=list()");
+  pi.RunCommand("sys.argv.append('"+QFileInfo(filename).fileName()+"')");
   pi.RunCommand("_dir=os.getcwd()");
   pi.RunCommand("os.chdir('"+QFileInfo(filename).absolutePath()+"')");
   pi.RunCommand("execfile('"+QFileInfo(filename).fileName()+"')");
   pi.RunCommand("os.chdir(_dir)");
+  pi.RunCommand("del(_dir)");
+  pi.RunCommand("sys.argv=_sys_argv_backup");
+  pi.RunCommand("del(_sys_argv_backup)");
   //HackerMode Off
 }
 
@@ -316,33 +382,38 @@ void FileLoader::LoadPDB(const QString& filename, const QString& selection)
   conop::BuilderP builder=conop::Conopology::Instance().GetBuilder("DEFAULT");
   while (reader.HasNext()){
     mol::EntityHandle ent=mol::CreateEntity();
-    reader.Import(ent);
+    try {
+      reader.Import(ent);      
+    } catch (io::IOException &e) {
+      LOG_ERROR(e.what());
+      continue;
+    }
     conop::Conopology::Instance().ConnectAll(builder,ent,0);
     entities.append(ent);
   }
-
   QFileInfo file_info(filename);
-  if(entities.size()==1){
+  if(entities.empty()){
+    FileLoader::HandleError(Error(QString("No entities found in file: "+ filename).toStdString()),INFO,filename);
+  }else if (entities.size()==1){
     gfx::EntityP gfx_ent(new gfx::Entity(file_info.baseName().toStdString(),entities.first(),mol::Query(selection.toStdString())));
     try{
       gfx::Scene::Instance().Add(gfx_ent);
     }
-    catch (Message m) {
-      HandleError(m, GFX_ADD, filename, gfx_ent);
+    catch (Error e) {
+      HandleError(e, GFX_ADD, filename, gfx_ent);
     }
     if (gfx::Scene::Instance().GetRootNode()->GetChildCount()==1) {
       gfx::Scene::Instance().SetCenter(gfx_ent->GetCenter());
     }
-  }
-  else{
-    try{
+  } else {
+    try {
       for(int i = 0 ; i<entities.size(); i++){
         gfx::EntityP gfx_ent(new gfx::Entity(QString(file_info.baseName()+" ("+QString::number(i)+")").toStdString(),entities[i],mol::Query(selection.toStdString())));
         gfx::Scene::Instance().Add(gfx_ent);
       }
     }
-    catch (Message m) {
-      FileLoader::HandleError(m,GFX_MULTIPLE_ADD,filename);
+    catch (Error e) {
+      FileLoader::HandleError(e,GFX_MULTIPLE_ADD,filename);
     }
   }
 }
diff --git a/modules/gui/src/file_loader.hh b/modules/gui/src/file_loader.hh
index 7dc110ab1a33ff8c49f65341471570fb5965be8b..c9f7fbc533b8493068d5168250443526fe03f565 100644
--- a/modules/gui/src/file_loader.hh
+++ b/modules/gui/src/file_loader.hh
@@ -20,9 +20,6 @@
 #define OST_GUI_FILE_LOADER_HH
 #include <vector>
 
-#include <QString>
-#include <QList>
-#include <QMap>
 
 #include <ost/gfx/gfx_object.hh>
 
@@ -32,11 +29,15 @@
 
 #include <ost/io/io_exception.hh>
 #include <ost/io/entity_io_handler.hh>
+#include <ost/io/sequence_io_handler.hh>
 #include <ost/io/surface_io_handler.hh>
 #if OST_IMG_ENABLED
 #include <ost/io/map_io_handler.hh>
 #endif
 
+#include <QString>
+#include <QList>
+#include <QMap>
 namespace ost { namespace gui {
 
 class DLLEXPORT_OST_GUI FileLoader {
@@ -45,19 +46,21 @@ private:
   enum ErrorType { DEFAULT = 0,
     IO_LOADING,
     GFX_ADD,
-    GFX_MULTIPLE_ADD
+    GFX_MULTIPLE_ADD,
+    INFO
   };
 
   FileLoader();
   static gfx::GfxObjP TryLoadEntity(const QString& filename, io::EntityIOHandlerP handler=io::EntityIOHandlerP(), const QString& selection=QString());
   static gfx::GfxObjP TryLoadSurface(const QString& filename, io::SurfaceIOHandlerPtr handler=io::SurfaceIOHandlerPtr());
+  static gfx::GfxObjP TryLoadAlignment(const QString& filename, io::SequenceIOHandlerPtr handler=io::SequenceIOHandlerPtr());
 #if OST_IMG_ENABLED
   static gfx::GfxObjP TryLoadMap(const QString& filename, io::MapIOHandlerPtr handler=io::MapIOHandlerPtr());
 #endif
   static void RunScript(const QString& filename);
   static void LoadPDB(const QString& filename, const QString& selection=QString());
   static void AddToScene(const QString& filename, gfx::GfxObjP obj);
-  static void HandleError(Message m, ErrorType type, const QString& filename, gfx::GfxObjP obj=gfx::GfxObjP());
+  static void HandleError(const Error& e, ErrorType type, const QString& filename, gfx::GfxObjP obj=gfx::GfxObjP());
   static gfx::GfxObjP NoHandlerFound(const QString& filename);
   virtual ~FileLoader();
 
diff --git a/modules/gui/src/file_type_dialog.cc b/modules/gui/src/file_type_dialog.cc
index cba2cba951411a1347fc962bda008fae828dbccf..caf11bc83b38de6232557828feb57da9cd1e93cb 100644
--- a/modules/gui/src/file_type_dialog.cc
+++ b/modules/gui/src/file_type_dialog.cc
@@ -18,29 +18,34 @@
 //------------------------------------------------------------------------------
 #include "file_type_dialog.hh"
 
+
+#include <ost/io/io_manager.hh>
+#include <ost/io/io_exception.hh>
+
 #include <QPushButton>
 #include <QVBoxLayout>
 #include <QHBoxLayout>
 #include <QTableWidgetItem>
 #include <QHeaderView>
-
-#include <ost/io/io_manager.hh>
-#include <ost/io/io_exception.hh>
-
 namespace ost { namespace gui {
 
 FileTypeDialog::FileTypeDialog(const QString& file_name, QWidget* parent):
-  QDialog(parent),entity_handler_(), surf_handler_()
+  QDialog(parent),entity_handler_(),seq_handler_(), surf_handler_()
 #if OST_IMG_ENABLED
       ,map_handler_()
 #endif
 {
   this->setWindowTitle("File format not recognized");
+  this->setFixedSize(QSize(400, 300));
   QVBoxLayout* vb=new QVBoxLayout(this);
-  label_ = new QLabel("The file format could not be recognized, please select the type of the file from the list:");
+  label_ = new QLabel("The file format could not be recognized, "
+                      "please select the type of the file from the list:");
+  label_->setWordWrap(true);
   list_ = new QTableWidget(this);
+  list_->setShowGrid(false);
   list_->horizontalHeader()->setStretchLastSection(true);
   list_->setColumnCount(2);
+  list_->setAttribute(Qt::WA_MacSmallSize);
   list_->verticalHeader()->setVisible(false);
   list_->horizontalHeader()->setVisible(false);
   list_->setSelectionBehavior(QAbstractItemView::SelectRows);
@@ -66,6 +71,13 @@ FileTypeDialog::FileTypeDialog(const QString& file_name, QWidget* parent):
     this->AddRow(list_->rowCount(),entity_handler[i]->GetFormatName().c_str(),entity_handler[i]->GetFormatDescription().c_str(),handler);
   }
 
+  io::AlignmentIOFList alignment_handler = io::IOManager::Instance().GetAvailableAlignmentHandler();
+  for(unsigned int i = 0 ; i < alignment_handler.size() ; i++){
+    QVariant handler = QVariant();
+    handler.setValue(alignment_handler[i]);
+    this->AddRow(list_->rowCount(),alignment_handler[i]->GetFormatName().c_str(),alignment_handler[i]->GetFormatDescription().c_str(),handler);
+  }
+
 #if OST_IMG_ENABLED
   io::MapIOFList map_handler = io::IOManager::Instance().GetAvailableMapHandler();
   for(unsigned int i = 0 ; i < map_handler.size() ; i++){
@@ -106,6 +118,11 @@ void FileTypeDialog::accept(){
         entity_handler_ = ent_handler_fac->Create();
         break;
       }
+      io::SequenceIOHandlerFactoryBasePtr seq_handler_fac = variant.value<io::SequenceIOHandlerFactoryBasePtr>();
+      if(seq_handler_fac){
+        seq_handler_ = seq_handler_fac->Create();
+        break;
+      }
       io::SurfaceIOHandlerFactoryBasePtr surf_handler_fac = variant.value<io::SurfaceIOHandlerFactoryBasePtr>();
       if(surf_handler_fac){
         surf_handler_ = surf_handler_fac->Create();
@@ -127,6 +144,9 @@ io::EntityIOHandlerP FileTypeDialog::GetEntityHandler(){
  return entity_handler_;
 }
 
+io::SequenceIOHandlerPtr FileTypeDialog::GetSequenceHandler(){
+ return seq_handler_;
+}
 
 io::SurfaceIOHandlerPtr FileTypeDialog::GetSurfaceHandler(){
   return surf_handler_;
diff --git a/modules/gui/src/file_type_dialog.hh b/modules/gui/src/file_type_dialog.hh
index 3efee2c535739d0c2e068600a25cd5a9da49e388..2ce157556ddd2a9623b80417e9d2e48f1fc48d58 100644
--- a/modules/gui/src/file_type_dialog.hh
+++ b/modules/gui/src/file_type_dialog.hh
@@ -26,16 +26,18 @@
 #include <ost/gui/module_config.hh>
 
 
-#include <QDialog>
-#include <QTableWidget>
-#include <QLabel>
 
 #include <ost/io/entity_io_handler.hh>
+#include <ost/io/sequence_io_handler.hh>
 #include <ost/io/surface_io_handler.hh>
 #if OST_IMG_ENABLED
 #include <ost/io/map_io_handler.hh>
 #endif
 
+#include <QDialog>
+#include <QTableWidget>
+#include <QLabel>
+
 namespace ost { namespace gui {
 
 /// \brief dialog to select a file type
@@ -44,6 +46,7 @@ class DLLEXPORT_OST_GUI FileTypeDialog : public QDialog {
 public:
   FileTypeDialog(const QString& file_name, QWidget* parent=NULL);
   io::EntityIOHandlerP GetEntityHandler();
+  io::SequenceIOHandlerPtr GetSequenceHandler();
   io::SurfaceIOHandlerPtr GetSurfaceHandler();
 #if OST_IMG_ENABLED
   io::MapIOHandlerPtr GetMapHandler();
@@ -59,6 +62,7 @@ private:
   QTableWidget* list_;
   QLabel* label_;
   io::EntityIOHandlerP entity_handler_;
+  io::SequenceIOHandlerPtr seq_handler_;
   io::SurfaceIOHandlerPtr surf_handler_;
 #if OST_IMG_ENABLED
   io::MapIOHandlerPtr map_handler_;
@@ -69,6 +73,7 @@ private:
 }}
 
 Q_DECLARE_METATYPE(ost::io::EntityIOHandlerFactoryBaseP);
+Q_DECLARE_METATYPE(ost::io::SequenceIOHandlerFactoryBasePtr);
 Q_DECLARE_METATYPE(ost::io::SurfaceIOHandlerFactoryBasePtr);
 #if OST_IMG_ENABLED
 Q_DECLARE_METATYPE(ost::io::MapIOHandlerFactoryBasePtr);
diff --git a/modules/gui/src/change_process_name.cc b/modules/gui/src/file_viewer.cc
similarity index 50%
rename from modules/gui/src/change_process_name.cc
rename to modules/gui/src/file_viewer.cc
index 91a7c247a7b5f688d1a0e66e7e7711baa348635c..4d284702ecac7fda249237f7dfb3a5c00cdd6ebe 100644
--- a/modules/gui/src/change_process_name.cc
+++ b/modules/gui/src/file_viewer.cc
@@ -16,28 +16,41 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#include "change_process_name.hh"
 
-#if defined(__APPLE__) && 0
-#include <Foundation/Foundation.h>
-#endif
+#include <ost/gui/python_shell/python_syntax_highlighter.hh>
 
-/*
-  Author: Marco Biasini
- */
-namespace ost { namespace gui {
-  
+#include "file_viewer.hh"
 
+#include <QtGui>
+namespace ost { namespace gui {
 
-void ChangeProcessName(const char* proc_name)
+FileViewer::FileViewer(const QString& path, QWidget* parent):
+ QWidget(parent)
 {
-  // commented out due to failure with scons. will be reenabled, when SCons is
-  // gone  
-#if defined(__APPLE__) && 0
-  NSString* pname=[[NSString alloc] initWithCString:proc_name 
-                                           encoding:NSASCIIStringEncoding];
-  [[NSProcessInfo processInfo] setProcessName:pname];
-#endif
+  QLayout* layout = new QVBoxLayout(this);
+  layout->setContentsMargins(0,0,0,0);
+  text_viewer_ = new QTextEdit(this);
+  text_viewer_->setReadOnly(true);
+
+  QFile file(path);
+  QTextDocument* doc = text_viewer_->document();
+  highlighter_ = new PythonSyntaxHighlighter(doc);
+  if (file.open(QFile::ReadOnly | QFile::Text))
+     text_viewer_->setText(file.readAll());
+  if(doc->blockCount()>1 && path.endsWith(".py")){
+    for(int i= 0; i< doc->lineCount();i++){
+      QTextBlock block = doc->findBlockByLineNumber(i);
+      block.setUserState(BLOCKTYPE_CODE);
+    }
+    QTextBlock start = doc->findBlockByLineNumber(0);
+    QTextBlock end = doc->findBlockByLineNumber(doc->lineCount()-1);
+    doc->markContentsDirty(start.position(),end.position()+end.length()-1);
+  }
+  layout->addWidget(text_viewer_);
+  this->setWindowTitle(path);
+  this->resize(800, 800);
+
 }
 
 }}
+
diff --git a/modules/gui/src/plot_viewer/plot_data_base.hh b/modules/gui/src/file_viewer.hh
similarity index 72%
rename from modules/gui/src/plot_viewer/plot_data_base.hh
rename to modules/gui/src/file_viewer.hh
index 587daf00411a8a946584203664d343080ff3b2c5..48f927a5cd3fb516b3e1fc95cd786a3a53dc87c9 100644
--- a/modules/gui/src/plot_viewer/plot_data_base.hh
+++ b/modules/gui/src/file_viewer.hh
@@ -16,28 +16,27 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#ifndef PLOT_DATA_BASE_HH_
-#define PLOT_DATA_BASE_HH_
+#ifndef OST_GUI_FILE_VIEWER_HH
+#define OST_GUI_FILE_VIEWER_HH
 
-/*
-  Author: Andreas Schenk
-*/
 
-#include <boost/shared_ptr.hpp>
 #include <ost/gui/module_config.hh>
 
-namespace ost{namespace gui{
+#include <QMainWindow>
+#include <QSyntaxHighlighter>
+#include <QTextEdit>
+namespace ost { namespace gui {
 
-class DLLEXPORT_OST_GUI PlotDataBase
-{
+/// \brief a simplistic file viewer
+class DLLEXPORT_OST_GUI FileViewer : public QWidget {
+  Q_OBJECT
 public:
-  PlotDataBase();
-  virtual ~PlotDataBase();
-protected:
+  FileViewer(const QString& path=QString(), QWidget* parent=NULL);
+  
+  QTextEdit* text_viewer_;
+  QSyntaxHighlighter* highlighter_;
 };
 
-typedef boost::shared_ptr<PlotDataBase> PlotDataBasePtr;
+}}
 
-}}//ns
-
-#endif /*PLOT_DATA_BASE_HH_*/
+#endif
diff --git a/modules/gui/src/gl_canvas.cc b/modules/gui/src/gl_canvas.cc
index d1bd25128092851ca528daaeb34bde8395ab1cda..eec0192e9506629550b08340c6d44f8de183eaf6 100644
--- a/modules/gui/src/gl_canvas.cc
+++ b/modules/gui/src/gl_canvas.cc
@@ -20,26 +20,26 @@
 #include <sys/time.h>
 #endif
 
+#include <ost/gui/python_shell/python_interpreter.hh>
 #include "gl_canvas.hh"
 #include "gl_win.hh"
 
 #include <ost/log.hh>
 #include <ost/dyn_cast.hh>
 #include <ost/mol/view_op.hh>
-#include <ost/gfx/scene.hh>
-#include <ost/gfx/entity.hh>
 
 #include <ost/seq/alignment_handle.hh>
 
-#include <ost/gui/python_shell/python_interpreter.hh>
 
-#include "tools/tool_manager.hh"
 
+#include <ost/gfx/scene.hh>
+#include <ost/gfx/entity.hh>
 #include <QTimer>
 #include <QStatusBar>
 #include <QApplication>
 #include <QClipboard>
 #include <QMenu>
+#include "tools/tool_manager.hh"
 
 namespace ost { namespace gui {
 
@@ -96,15 +96,15 @@ void GLCanvas::initializeGL()
     init=true;
   }
 
-  LOG_DEBUG("GLCanvas::initializeGL()"<<std::endl);
+  LOG_DEBUG("GLCanvas::initializeGL()");
   Scene::Instance().InitGL();
-  LOG_DEBUG("GLCanvas::registering with scene"<<std::endl);
+  LOG_DEBUG("GLCanvas::registering with scene");
   Scene::Instance().Register(this);
 }
 
 void GLCanvas::resizeGL(int w, int h)
 {
-  LOG_DUMP("GLCanvas::resizeGL("<<w<<","<<h<<")"<<std::endl);
+  LOG_DEBUG("GLCanvas::resizeGL("<<w<<","<<h<<")");
   Scene::Instance().Resize(w,h);
 }
 
@@ -437,7 +437,7 @@ void GLCanvas::timerEvent(QTimerEvent * event)
     if(count==20) {
       count=0;
       gettimeofday(&time1,NULL);
-      LOGN_ERROR(20.0/delta_time(time0,time1) << " fps");
+      LOG_ERROR(20.0/delta_time(time0,time1) << " fps");
       gettimeofday(&time0,NULL);
     }
   }
diff --git a/modules/gui/src/gl_canvas.hh b/modules/gui/src/gl_canvas.hh
index e20c3c5ce97bdca8040bbcc9d9fe9496040e0bf3..884588463fe49b9f5bd8346c29a8bcd871409178 100644
--- a/modules/gui/src/gl_canvas.hh
+++ b/modules/gui/src/gl_canvas.hh
@@ -19,21 +19,21 @@
 #ifndef OST_GUI_GL_CANVAS_HH
 #define OST_GUI_GL_CANVAS_HH
 
-#include <ost/gfx/glwin_base.hh>
-#include <ost/gfx/input.hh>
 
 // must come before QGLWidget
 #include <ost/mol/mol.hh>
-#include <ost/gfx/gfx_object_fw.hh>
 
-#include <ost/gui/tools/tool.hh>
-#include <ost/gui/scene_menu.hh>
 
 // Qt includes must come last
 #include <QGLWidget>
 #include <QTime>
 #include <QBasicTimer>
 #include <QMouseEvent>
+#include <ost/gui/tools/tool.hh>
+#include <ost/gui/scene_menu.hh>
+#include <ost/gfx/glwin_base.hh>
+#include <ost/gfx/input.hh>
+#include <ost/gfx/gfx_object_fw.hh>
 
 class QMenu;
 
diff --git a/modules/gui/src/gl_win.cc b/modules/gui/src/gl_win.cc
index d0ea7f00db3261b3311feda4c08a23ab0c08ad7c..56434e4bcf407f0ab6f4241c349b3da90932302f 100644
--- a/modules/gui/src/gl_win.cc
+++ b/modules/gui/src/gl_win.cc
@@ -16,6 +16,7 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
+#include <ost/gui/gosty_app.hh>
 #include <ost/log.hh>
 #include <ost/config.hh>
 #include <ost/gfx/scene.hh>
@@ -25,7 +26,6 @@
 #include <ost/gui/tools/selection_tool.hh>
 #include <ost/gui/tools/manipulator.hh>
 #include <ost/gui/tools/measure_tool.hh>
-#include <ost/gui/gosty_app.hh>
 #include <ost/gui/perspective.hh>
 
 #if OST_IMG_ENABLED
@@ -90,6 +90,7 @@ gl_canvas_(NULL)
   this->SetInternalWidget(main);
   gfx::Scene::Instance().AttachObserver(this);
   QGLFormat format = gl_canvas_->format();
+
   LOGN_DEBUG("GLCanvas: rbits=" << format.redBufferSize() 
                << " gbits=" << format.greenBufferSize() 
                << " bbits=" << format.blueBufferSize() 
diff --git a/modules/gui/src/gl_win.hh b/modules/gui/src/gl_win.hh
index 08cecfcad2c3c3162d80c4cec561fa485ab6d580..a693ef1d924033737ff52bb119419df22299c1d1 100644
--- a/modules/gui/src/gl_win.hh
+++ b/modules/gui/src/gl_win.hh
@@ -19,11 +19,6 @@
 #ifndef OST_GUI_GL_WIN_HH
 #define OST_GUI_GL_WIN_HH
 
-#include <QMainWindow>
-#include <QAction>
-
-#include <QActionGroup>
-#include <QStatusBar>
 
 #include <ost/gfx/scene_observer.hh>
 
@@ -34,6 +29,12 @@
 #include <ost/gui/tools/tool.hh>
 #include <ost/gui/tools/tool_bar.hh>
 
+#include <QMainWindow>
+#include <QAction>
+
+#include <QActionGroup>
+#include <QStatusBar>
+
 /*
   Authors: Ansgar Philippsen, Marco Biasini
  */
diff --git a/modules/gui/src/gosty.cc b/modules/gui/src/gosty.cc
index 6f5ceaa55b0b25dedf58315ad3a5f1c25dd9755d..2f50d596be7b73ae354f8bbf693f68c24599eacd 100644
--- a/modules/gui/src/gosty.cc
+++ b/modules/gui/src/gosty.cc
@@ -23,21 +23,22 @@
 #include <sstream>
 #include <ctime>
 
-#include <QDir>
-#include <QTimer>
 #include <ost/gui/module_config.hh>
 #include <ost/log.hh>
 #include <ost/platform.hh>
+#include <ost/gui/python_shell/text_logger.hh>
 #include <ost/gui/python_shell/python_shell.hh>
 #include <ost/gui/python_shell/python_interpreter.hh>
 #include "gl_win.hh"
 #include "widget_state_saver.hh"
 #include "gosty.hh"
-#include "change_process_name.hh"
+
 // must come last
 #include <QApplication>
 #include <QResource>
 #include <QFileInfo>
+#include <QDir>
+#include <QTimer>
 
 using namespace ost;
 using namespace ost::gui;
@@ -52,7 +53,7 @@ DelayedScriptExecutor::DelayedScriptExecutor()
 void DelayedScriptExecutor::Exec()
 {
   PythonInterpreter& interp=PythonInterpreter::Instance();  
-  interp.ExecRelease();
+  interp.Start();
 }
 
 }}}
@@ -109,7 +110,7 @@ int setup_resources(QApplication& app)
 {
   QResource qr(":/images");
    if(!qr.isValid()) {
-     LOGN_ERROR("no valid /image Qt resource found");
+     LOG_ERROR("no valid /image Qt resource found");
      return -1;
    }
    int sizes[]={512,256,128,32,16, 0};
@@ -124,12 +125,23 @@ int setup_resources(QApplication& app)
    return 0;
 }
 
+
+void read_logger_settings(const QString& group_name, TextLogger* logger)
+{
+  QSettings settings;
+  settings.beginGroup("logging");
+  settings.beginGroup(group_name);   
+  logger->SetCodeLogging(settings.value("log_code",QVariant(false)).toBool());
+  logger->SetOutputLogging(settings.value("log_output",QVariant(true)).toBool());
+  logger->SetErrorLogging(settings.value("log_error",QVariant(true)).toBool());
+  settings.endGroup();
+  settings.endGroup();
+}
+
 int init_python_interpreter()
 {
   // the order of these two calls is important!
-  PythonInterpreter::Instance(true);
-  // following command would instanciate a multithreaded python interpreter.
-  // Untested, use at your own risk!! PythonInterpreter::Instance(true,true);
+  PythonInterpreter::Instance();
   reclaim_signals();
   //
   PythonInterpreter& py=PythonInterpreter::Instance();
@@ -138,8 +150,23 @@ int init_python_interpreter()
   if(root == "") {
     return -1;
   }
+  // setup python shell logging
+  TextLogger* console_logger=new TextLogger(stdout);
+  read_logger_settings("console", console_logger);
+  if (console_logger->GetErrorLogging()) {
+    QObject::connect(&PythonInterpreter::Instance(),  
+                     SIGNAL(ErrorOutput(unsigned int, const QString &)),
+                     console_logger,
+                     SLOT(AppendOutput(unsigned int, const QString &)));
+  }
+  if (console_logger->GetOutputLogging()) {
+    QObject::connect(&PythonInterpreter::Instance(), 
+                     SIGNAL(Output(unsigned int, const QString &)),
+                     console_logger,
+                     SLOT(AppendOutput(unsigned int, const QString &)));
+  }  
   setup_python_search_path(root, py);
-  py.RunCommand("from ost import *");  
+  py.RunCommand("from ost import *");
   return 0;
 }
 
@@ -162,6 +189,7 @@ int main(int argc, char** argv)
   QCoreApplication::setOrganizationName("OpenStructure");
   QCoreApplication::setOrganizationDomain("openstructure.org");
   QCoreApplication::setApplicationName(argv[0]);
+	app.setLibraryPaths(QStringList());
   if (int rv=setup_resources(app)<0) {
     return rv;
   }
@@ -169,11 +197,10 @@ int main(int argc, char** argv)
     return r;
   }
   PythonInterpreter& py_int=PythonInterpreter::Instance();
-  py_int.ExecWait();  
-  py_int.RunInitRC();
+  // todo remove RunInitRC and replace with general call to run script (with dngrc as argument)
+  //py_int.RunInitRC();
+  prepare_scripts(argc,argv,py_int);
   //  delay all execution of python scripts after app.exec() has been called.
   ost::gui::detail::DelayedScriptExecutor delayed_executor;
-
-  prepare_scripts(argc,argv,py_int);
   return app.exec();
 }
diff --git a/modules/gui/src/gosty.hh b/modules/gui/src/gosty.hh
index 6f2b6bd56ee082c353852eb6fe7a191f6d9c488c..fe1d881f9a1cba9c0cd07e87f7b4b144d6c1801b 100644
--- a/modules/gui/src/gosty.hh
+++ b/modules/gui/src/gosty.hh
@@ -19,10 +19,10 @@
 #ifndef OST_GUI_GOSTY_HH
 #define OST_GUI_GOSTY_HH
 
-#include <QObject>
 
 #include <ost/gui/module_config.hh>
 
+#include <QObject>
 namespace ost { namespace gui { namespace detail {
 
 /// \brief helper class for delayed script execution
diff --git a/modules/gui/src/gosty_app.cc b/modules/gui/src/gosty_app.cc
index 08df5bcba68d4d142f6476c335c793b56535ab15..663c4f4e30b3d6e873e3db92dceca950ea64c4af 100644
--- a/modules/gui/src/gosty_app.cc
+++ b/modules/gui/src/gosty_app.cc
@@ -16,24 +16,22 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
+#include "gosty_app.hh"
 #include <iostream>
 
-#include <QApplication>
-#include <QMainWindow>
 
-#include <QMenuBar>
-#include <QDesktopWidget>
-
-#include <ost/gui/mdi_sub_window.hh>
 #include <ost/gui/python_shell/python_shell.hh>
 #include <ost/gui/gl_win.hh>
 #include <ost/gui/tools/tool_options_win.hh>
-#include <ost/gui/python_shell/text_logger.hh>
 #include <ost/gui/perspective.hh>
 #include <ost/gui/main_area.hh>
 
-#include "gosty_app.hh"
 
+#include <QApplication>
+#include <QMainWindow>
+
+#include <QMenuBar>
+#include <QDesktopWidget>
 /*
   Author: Marco Biasini, Andreas Schenk, Stefan Scheuber
  */
@@ -45,11 +43,9 @@ GostyApp* GostyApp::app_=NULL;
 
 
 GostyApp::GostyApp():
-  py_shell_(NULL), w_py_shell_(NULL), gl_win_(NULL), w_gl_win_(NULL),
-  scene_win_(NULL), w_scene_win_(NULL), seq_viewer_(NULL), seq_viewer_v2_(NULL), tool_options_win_(NULL),
-  w_tool_options_(NULL), main_(new GostyMainWindow), 
-  perspective_(NULL), external_widgets_(QMap<QString,WidgetGeomHandler *>()),
-  try_stereo_(false)
+  py_shell_(NULL), gl_win_(NULL), scene_win_(NULL), message_widget_(NULL), seq_viewer_(NULL),
+  tool_options_win_(NULL), main_(new GostyMainWindow),
+  perspective_(NULL), external_widgets_(QMap<QString,WidgetGeomHandler *>())
 {
   assert(GostyApp::app_==NULL);
   GostyApp::app_=this;
@@ -99,54 +95,24 @@ SceneWin* GostyApp::GetSceneWin()
 SequenceViewer* GostyApp::GetSequenceViewer()
 {
   if (seq_viewer_==NULL) {
-  seq_viewer_=new SequenceViewer;
-  seq_viewer_->SetDestroyOnClose(false);
+    seq_viewer_=new SequenceViewer(false);
+    seq_viewer_->SetDestroyOnClose(false);
   }
   return seq_viewer_;
 }
 
-SequenceViewerV2* GostyApp::GetSequenceViewerV2()
-{
-  if (seq_viewer_v2_==NULL) {
-    seq_viewer_v2_=new SequenceViewerV2;
-    seq_viewer_v2_->SetDestroyOnClose(false);
-  }
-  return seq_viewer_v2_;
-}
-
 #if OST_IMG_ENABLED
 ost::img::gui::DataViewer* GostyApp::CreateDataViewer(const ost::img::Data& d, const QString& name)
 {
   return new ost::img::gui::DataViewer(main_,d,name);
 }
 #endif
-
-void GostyApp::ReadLoggerSettings(const QString& group_name, TextLogger* logger)
-{
-  QSettings settings;
-  settings.beginGroup("logging");
-  settings.beginGroup(group_name);
-  logger->SetCodeLogging(settings.value("log_code",QVariant(false)).toBool());
-  logger->SetOutputLogging(settings.value("log_output",QVariant(true)).toBool());
-  logger->SetErrorLogging(settings.value("log_error",QVariant(true)).toBool());
-  settings.endGroup();
-  settings.endGroup();
-}
   
-void GostyApp::SetupPyShellLogging()
-{
-  TextLogger* console_logger=new TextLogger(stdout);
-  this->ReadLoggerSettings("console", console_logger);
-  py_shell_->AddLogger(console_logger);  
-  // TODO: Setup file logging
-}
-
 PythonShell* GostyApp::GetPyShell()
 {
   if (py_shell_==NULL) {
     py_shell_=new PythonShell;
-    this->SetupPyShellLogging();             
-    py_shell_->SetDestroyOnClose(false);                 
+    py_shell_->SetDestroyOnClose(false);
   }
   return py_shell_;
 }
@@ -173,6 +139,14 @@ Perspective* GostyApp::GetPerspective()
   return perspective_;
 }
 
+MessageWidget* GostyApp::GetMessageWidget()
+{
+  if (message_widget_==NULL) {
+    message_widget_=new MessageWidget;
+  }
+  return message_widget_;
+}
+
 void GostyApp::AddWidgetToApp(const QString& ident, QWidget* widget)
 {
   external_widgets_[ident] = new WidgetGeomHandler(ident,widget);
diff --git a/modules/gui/src/gosty_app.hh b/modules/gui/src/gosty_app.hh
index 2ed5e693fa53845436ad445064b6c5bacf1eb2eb..45e4080b1bd5acb21c0b86694e6fb10329592c05 100644
--- a/modules/gui/src/gosty_app.hh
+++ b/modules/gui/src/gosty_app.hh
@@ -23,21 +23,24 @@
   Author: Marco Biasini, Andreas Schenk
  */
 
-#include <QObject>
-#include <QString>
-#include <QMap>
 
 #include <ost/config.hh>
 #include <ost/gui/module_config.hh>
-#include <ost/gui/scene_win/scene_win.hh>
-#include <ost/gui/sequence_viewer/sequence_viewer.hh>
-#include <ost/gui/sequence/sequence_viewer.hh>
 #include <ost/gui/main.hh>
 #include <ost/gui/widget_geom_handler.hh>
+#include <ost/gui/scene_win/scene_win.hh>
+#include <ost/gui/sequence_viewer/sequence_viewer.hh>
+#include <ost/gui/messages/message_widget.hh>
+
 #if OST_IMG_ENABLED
   #include <ost/gui/data_viewer/data_viewer.hh>
 #endif
 
+#include <QObject>
+#include <QString>
+#include <QMap>
+
+
 class QMainWindow;
 class QMdiArea;
 class QWidget;
@@ -89,7 +92,6 @@ public:
   /// The sequence viewer is initialized when this method is first called. All
   /// subsequent calls will return the same SequenceViewer instance.
   SequenceViewer* GetSequenceViewer();
-  SequenceViewerV2* GetSequenceViewerV2();
   
   /// \brief get tool options window
   /// 
@@ -97,6 +99,12 @@ public:
   /// All subsequent calls will return the same SceneWin instance.  
   ToolOptionsWin* GetToolOptionsWin();
   
+  /// \brief get message widget
+  ///
+  /// The MessageWidget is initialized when this method is first called.
+  /// All subsequent calls will return the same MessageWidget instance.
+  MessageWidget* GetMessageWidget();
+
 #if OST_IMG_ENABLED
   /// \brief create new DataViewer
   /// 
@@ -143,23 +151,18 @@ public slots:
   /// \brief This slot must be called when the application is going to be terminated.
   void OnQuit();
 private:  
-  void SetupPyShellLogging();
-  void ReadLoggerSettings(const QString& group_name, TextLogger* logger);
   GostyApp();  
   PythonShell*      py_shell_;
-  QWidget*          w_py_shell_;
                     
   GLWin*            gl_win_;
-  QWidget*          w_gl_win_;
                     
   SceneWin*         scene_win_;
-  QWidget*          w_scene_win_;
 
-  SequenceViewer*   seq_viewer_;
-  SequenceViewerV2* seq_viewer_v2_;
+  MessageWidget*       message_widget_;
+
+  SequenceViewer* seq_viewer_;
 
   ToolOptionsWin*   tool_options_win_;
-  QWidget*          w_tool_options_;  
   GostyMainWindow*  main_;
 
   Perspective*      perspective_;
diff --git a/modules/gui/src/input/spnav_input.hh b/modules/gui/src/input/spnav_input.hh
index 776fd5de425179ab59bb39c9fa144ae12bee4b81..557934967aba609e1f8f86f76315e770486d9b2c 100644
--- a/modules/gui/src/input/spnav_input.hh
+++ b/modules/gui/src/input/spnav_input.hh
@@ -23,12 +23,12 @@
 #ifndef OST_GUI_SPNAV_INPUT_HH
 #define OST_GUI_SPNAV_INPUT_HH
 
-#include <QThread>
-#include <QMetaType>
 
 #include <ost/geom/geom.hh>
 #include <ost/gui/module_config.hh>
 
+#include <QThread>
+#include <QMetaType>
 Q_DECLARE_METATYPE(geom::Mat4);
 
 namespace ost { namespace gui {
diff --git a/modules/gui/src/loader_manager.cc b/modules/gui/src/loader_manager.cc
index f9e83c7599a53b825a7b13eedfeecaa57fcbeb5a..30a80a7a8940fac7789f1da29f1ab520ac93e58d 100644
--- a/modules/gui/src/loader_manager.cc
+++ b/modules/gui/src/loader_manager.cc
@@ -16,7 +16,10 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
+#include <ost/gui/gosty_app.hh>
 #include "loader_manager.hh"
+
+#include <ost/gui/perspective.hh>
 #include <QDir>
 #include <QAction>
 #include <QMenu>
@@ -24,9 +27,6 @@
 #include <QMessageBox>
 #include <QMenuBar>
 
-#include <ost/gui/gosty_app.hh>
-#include <ost/gui/perspective.hh>
-
 
 namespace ost { namespace gui {
 
@@ -99,6 +99,19 @@ QMenu* LoaderManager::GetSiteMenu(){
   return site_menu_;
 }
 
+RemoteSiteLoader* LoaderManager::GetDefaultRemoteSiteLoader()
+{
+ return GetRemoteSiteLoader(GetDefaultRemoteSiteIdent());
+}
+
+QString LoaderManager::GetDefaultRemoteSiteIdent(){
+  return default_site_;
+}
+
+void LoaderManager::SetDefaultRemoteSiteIdent(const QString& ident){
+  default_site_ = ident;
+}
+
 LoaderManager::~LoaderManager(){}
 
 } }
diff --git a/modules/gui/src/loader_manager.hh b/modules/gui/src/loader_manager.hh
index a952b586b31ea951073820e849eb06f405850a63..12c5c59f29e3846312fca598749850d663946cf0 100644
--- a/modules/gui/src/loader_manager.hh
+++ b/modules/gui/src/loader_manager.hh
@@ -34,7 +34,7 @@ class DLLEXPORT_OST_GUI LoaderManager {
   QMap<QString,RemoteSiteLoader*> site_loaders_;
   QActionGroup* site_actions_;
   QMenu* site_menu_;
-
+  QString default_site_;
 
 public:
   LoaderManager();
@@ -44,6 +44,9 @@ public:
   void RemoveRemoteSiteLoader(const QString& ident);
   RemoteSiteLoader* GetRemoteSiteLoader(const QString& ident);
   RemoteSiteLoader* GetCurrentSiteLoader();
+  RemoteSiteLoader* GetDefaultRemoteSiteLoader();
+  QString GetDefaultRemoteSiteIdent();
+  void SetDefaultRemoteSiteIdent(const QString& ident);
   QMenu* GetSiteMenu();
 };
 
diff --git a/modules/gui/src/main.cc b/modules/gui/src/main.cc
index 9836c6e9057805a340c8559ee51183e08232581d..ba2dc6f3cd19a3892e044629149a301d03ab63fe 100644
--- a/modules/gui/src/main.cc
+++ b/modules/gui/src/main.cc
@@ -16,10 +16,21 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
+#include <ost/gui/gosty_app.hh>
 #include "main.hh"
 
 #include <sstream>
 
+
+#include <ost/log.hh>
+#include <ost/gui/python_shell/python_shell.hh>
+#include <ost/gui/file_loader.hh>
+
+#include "gl_win.hh"
+//#include "entity_explorer/entity_explorer.hh"
+#include "tools/tool_options_win.hh"
+
+
 #include <QApplication>
 #include <QDesktopWidget>
 #include <QAction>
@@ -34,21 +45,6 @@
 #include <QDragEnterEvent>
 #include <QList>
 #include <QUrl>
-
-#include <ost/log.hh>
-#include <ost/gui/python_shell/python_shell.hh>
-#include <ost/gui/gosty_app.hh>
-#include <ost/gui/file_loader.hh>
-
-#include "gl_win.hh"
-//#include "entity_explorer/entity_explorer.hh"
-#include "mdi_sub_window.hh"
-#include "sequence_viewer/sequence_viewer.hh"
-#include "tools/tool_options_win.hh"
-#include "plot_viewer/plot_viewer_proxy.hh"
-#include "plot_viewer/plot_viewer.hh"
-
-
 //#include "xpm/ost_small.xpm"
 
 namespace ost { namespace gui {
diff --git a/modules/gui/src/main.hh b/modules/gui/src/main.hh
index 8d718cfe43047f4c37fb1d55772fb505b5dc6a00..67f204518eaa7fe2066b821f4569d11e97b7e59b 100644
--- a/modules/gui/src/main.hh
+++ b/modules/gui/src/main.hh
@@ -27,7 +27,6 @@
 
 #include "widget_state_saver.hh"
 
-#include "plot_viewer/plot_viewer_proxy_fw.hh"
 
 // Qt headers must come last
 #include <QMainWindow>
diff --git a/modules/gui/src/main_area.cc b/modules/gui/src/main_area.cc
index 38717e46d800cc4b045ad11cae480be64a921f47..82ced876c696b2695f91ea01c5c0f54c0ff0cd3a 100644
--- a/modules/gui/src/main_area.cc
+++ b/modules/gui/src/main_area.cc
@@ -17,12 +17,12 @@
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
 #include <cassert>
-#include <QMdiSubWindow>
-#include <QSettings>
 
 #include <ost/gui/widget_geom_handler.hh>
 #include "main_area.hh"
 
+#include <QMdiSubWindow>
+#include <QSettings>
 /*
   Author: Marco Biasini
  */
diff --git a/modules/gui/src/main_area.hh b/modules/gui/src/main_area.hh
index 9616340b065209748c984fd7543d98661e2e5966..535b7465d7336c492d5865ef2bac2d9bdeca9550 100644
--- a/modules/gui/src/main_area.hh
+++ b/modules/gui/src/main_area.hh
@@ -19,10 +19,10 @@
 #ifndef OST_GUI_MAIN_AREA_HH
 #define OST_GUI_MAIN_AREA_HH
 
-#include <QMdiArea>
 
 #include <ost/gui/module_config.hh>
 
+#include <QMdiArea>
 /*
   Author: Marco Biasini
  */
diff --git a/modules/gui/src/main_window.hh b/modules/gui/src/main_window.hh
index 3d34956b261168491e2c703ea46dfd610d9e173a..4f0796e29877454cc727573c805f6f9193b125e3 100644
--- a/modules/gui/src/main_window.hh
+++ b/modules/gui/src/main_window.hh
@@ -27,13 +27,13 @@
 
 #include <map>
 
-#include <QMainWindow>
-#include <QMenu>
 
 #include <ost/base.hh>
 #include <ost/gui/module_config.hh>
 
 
+#include <QMainWindow>
+#include <QMenu>
 
 namespace ost { namespace gui {
 
diff --git a/modules/gui/src/mdi_sub_window.cc b/modules/gui/src/mdi_sub_window.cc
deleted file mode 100644
index d5934ae37f761d3f5fc809206c459b3411ce78a1..0000000000000000000000000000000000000000
--- a/modules/gui/src/mdi_sub_window.cc
+++ /dev/null
@@ -1,79 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#include "mdi_sub_window.hh"
-/* 
-  Author: Andreas Schenk
- */
-namespace ost{namespace gui{
-
-OstMdiSubWindow::OstMdiSubWindow(const QString& name,QPoint pos, QSize size, 
-                                  bool visible, QWidget* parent,
-                                 Qt::WindowFlags flags):
-  OstMdiSubWindowBase(name,pos,size, visible, parent,flags)
-{
-}
-OstMdiSubWindow::OstMdiSubWindow(const QString& name, QWidget* parent,
-                                 Qt::WindowFlags flags):
-  OstMdiSubWindowBase(name,parent,flags)
-{
-}
-
-OstMdiSubWindow::~OstMdiSubWindow()
-{
-}
-
-void OstMdiSubWindow::closeEvent( QCloseEvent * event )
-{
-  hide();
-}
-void OstMdiSubWindow::setVisible(bool visible)
-{
-  OstMdiSubWindowBase::setVisible(visible);
-  emit OnSetVisible(visible);
-}
-
-
-
-OstTopWindow::OstTopWindow(const QString& name,QPoint pos, QSize size, bool vis,
-                           QWidget* parent ,Qt::WindowFlags flags):
-  OstTopWindowBase(name,pos,size,vis,parent,flags)
-{
-}
-OstTopWindow::OstTopWindow(const QString& name, QWidget* parent,
-                           Qt::WindowFlags flags):
-  OstTopWindowBase(name,parent,flags)
-{
-}
-
-OstTopWindow::~OstTopWindow()
-{
-}
-
-void OstTopWindow::closeEvent( QCloseEvent * event )
-{
-  hide();
-}
-
-void OstTopWindow::setVisible(bool visible)
-{
-  OstTopWindowBase::setVisible(visible);
-  emit OnSetVisible(visible);
-}
-
-}}//ns
diff --git a/modules/gui/src/mdi_sub_window.hh b/modules/gui/src/mdi_sub_window.hh
deleted file mode 100644
index 82c2ed4c08475b2faec52fdfaae7bfec15468ca7..0000000000000000000000000000000000000000
--- a/modules/gui/src/mdi_sub_window.hh
+++ /dev/null
@@ -1,71 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef OST_MDI_SUB_WINDOW_HH_
-#define OST_MDI_SUB_WINDOW_HH_
-
-/*
-  Author: Andreas Schenk
- */
-
-#include <QMdiSubWindow>
-#include <QMainWindow>
-
-#include "widget_state_saver.hh"
-
-namespace ost{namespace gui{
-
-typedef WidgetStateSaver<QMdiSubWindow,Qt::WindowFlags> OstMdiSubWindowBase;
-
-class OstMdiSubWindow: public OstMdiSubWindowBase
-{
-  Q_OBJECT;
-public:
-  OstMdiSubWindow(const QString& name,QPoint pos, QSize size, bool visible,
-                  QWidget* parent, Qt::WindowFlags flags);
-  OstMdiSubWindow(const QString& name, QWidget* parent, Qt::WindowFlags flags);
-  virtual ~OstMdiSubWindow();
-public slots:
-  virtual void setVisible(bool visible=true);
-signals:
-  void OnSetVisible(bool visible);
-protected:
-  virtual void closeEvent( QCloseEvent * event );
-};
-
-typedef WidgetStateSaver<QMainWindow,Qt::WindowFlags> OstTopWindowBase;
-
-class OstTopWindow: public OstTopWindowBase
-{
-  Q_OBJECT;
-public:
-  OstTopWindow(const QString& name,QPoint pos, QSize size, bool visible,
-               QWidget* parent, Qt::WindowFlags flags);
-  OstTopWindow(const QString& name, QWidget* parent ,Qt::WindowFlags flags);
-  virtual ~OstTopWindow();
-public slots:
-  virtual void setVisible(bool visible=true);
-signals:
-  void OnSetVisible(bool visible);
-protected:
-  virtual void closeEvent( QCloseEvent * event );
-};
-
-}}//ns
-
-#endif /*OST_MDI_SUB_WINDOW_HH_*/
diff --git a/modules/gui/src/messages/log_reader.cc b/modules/gui/src/messages/log_reader.cc
new file mode 100644
index 0000000000000000000000000000000000000000..f4089ee557d359d2d66f4f85ec86c1b8745842ca
--- /dev/null
+++ b/modules/gui/src/messages/log_reader.cc
@@ -0,0 +1,79 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+//------------------------------------------------------------------------------
+/*
+ Author: Stefan Scheuber
+ */
+#include <ost/log.hh>
+
+#include "message_widget.hh"
+#include "log_reader.hh"
+
+namespace ost { namespace gui {
+
+LogReader::LogReader(QObject* parent) :
+  QObject(parent) {
+  ost::Logger& logger = ost::Logger::Instance();
+  LogSinkPtr lsp = LogSinkPtr(this);
+  logger.PushSink(lsp);
+}
+
+void LogReader::LogMessage(const String& message, int severity){
+  if(this->parent()){
+    if(MessageWidget* message_widget = qobject_cast<MessageWidget*>(this->parent())){
+      QString q_message(message.c_str());
+      if(q_message.endsWith("\n")){
+        q_message.remove(q_message.size()-1,q_message.size()-1);
+        if(!log_cache_.contains(severity)){
+          message_widget->LogMessage(q_message,GetIconForSeverity(severity));
+        }
+        else{
+          message_widget->LogMessage(log_cache_[severity]+q_message,GetIconForSeverity(severity));
+          log_cache_.remove(severity);
+        }
+      }
+      else{
+        if(!log_cache_.contains(severity)){
+          log_cache_[severity] = message.c_str();
+        }
+        else{
+          log_cache_[severity].append(message.c_str());
+        }
+      }
+    }
+  }
+}
+
+QMessageBox::Icon LogReader::GetIconForSeverity(int severity){
+  switch (severity) {
+    case 1:
+      return QMessageBox::Warning;
+    case 0:
+      return QMessageBox::Critical;
+    default :
+      return QMessageBox::Information;
+  }
+}
+
+LogReader::~LogReader() {
+  ost::Logger& logger = ost::Logger::Instance();
+  logger.PopSink();
+}
+
+}
+} // ns
diff --git a/modules/gui/src/plot_viewer/plot_function.hh b/modules/gui/src/messages/log_reader.hh
similarity index 67%
rename from modules/gui/src/plot_viewer/plot_function.hh
rename to modules/gui/src/messages/log_reader.hh
index c61e7e13504f95b270345e5683a1058262c5c701..e64565117f5c3758da5531935cef1e42057dc391 100644
--- a/modules/gui/src/plot_viewer/plot_function.hh
+++ b/modules/gui/src/messages/log_reader.hh
@@ -16,31 +16,37 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#ifndef PLOT_FUNCTION_HH_
-#define PLOT_FUNCTION_HH_
+#ifndef OST_GUI_MESSAGES_LOG_READER_HH
+#define OST_GUI_MESSAGES_LOG_READER_HH
 
-/*
-  Author: Andreas Schenk
-*/
 
-#include <boost/shared_ptr.hpp>
+#include <ost/log_sink.hh>
+
 #include <ost/gui/module_config.hh>
-#include "plot_data_base.hh"
 
-namespace ost{namespace gui{
+#include <QObject>
+#include <QMap>
+#include <QMessageBox>
+/*
+  Author: Stefan Scheuber
+*/
 
-class DLLEXPORT_OST_GUI PlotFunction: public PlotDataBase
+namespace ost { namespace gui {
+
+class DLLEXPORT_OST_GUI LogReader: public QObject, public LogSink
 {
+  Q_OBJECT;
 public:
-  PlotFunction();
-  virtual ~PlotFunction();
-  virtual Real Func(Real val) const=0;
-};
+  LogReader(QObject* parent=NULL);
+  ~LogReader();
 
-typedef boost::shared_ptr<PlotFunction> PlotFunctionPtr;
-
-}}//ns
+  void LogMessage(const String& message, int severity);
 
+private:
+  QMap<int, QString> log_cache_;
+  QMessageBox::Icon GetIconForSeverity(int severity);
+};
 
+}} // ns
 
-#endif /*PLOT_FUNCTION_HH_*/
+#endif
diff --git a/modules/gui/src/messages/message_box_widget.cc b/modules/gui/src/messages/message_box_widget.cc
new file mode 100644
index 0000000000000000000000000000000000000000..1be4b817c57fb7353ae094475993eb534721819e
--- /dev/null
+++ b/modules/gui/src/messages/message_box_widget.cc
@@ -0,0 +1,109 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+//------------------------------------------------------------------------------
+/*
+ Author: Stefan Scheuber
+ */
+
+#include <ost/gui/gosty_app.hh>
+#include <ost/platform.hh>
+
+#include <ost/gui/perspective.hh>
+#include <ost/gui/widget_registry.hh>
+
+#include <ost/gui/panels/panel_manager.hh>
+
+#include "log_reader.hh"
+#include "message_box_widget.hh"
+
+#include <QDir>
+#include <QLabel>
+#include <QMenu>
+#include <QVBoxLayout>
+namespace ost {namespace gui {
+
+MessageLevel::MessageLevel(QPixmap icon, QWidget* parent): QWidget(parent), message_count_(0), count_label_(new QLabel(QString::number(message_count_)+"  ",this)){
+  QHBoxLayout* layout = new QHBoxLayout(this);
+  layout->setMargin(0);
+  layout->setSpacing(0);
+  QLabel* icon_label = new QLabel(this);
+  icon_label->setFixedSize(20,20);
+  icon_label->setPixmap(icon.scaled(15,15, Qt::IgnoreAspectRatio, 
+                                    Qt::SmoothTransformation));
+  layout->addWidget(icon_label);
+  layout->addWidget(count_label_);
+}
+
+void MessageLevel::SetMessageCount(int message_count){
+  message_count_ = message_count;
+  count_label_->setText(QString::number(message_count_)+"  ");
+}
+
+int MessageLevel::GetMessageCount(){
+  return message_count_;
+}
+
+
+
+MessageBoxWidget::MessageBoxWidget(QWidget* parent) :
+  QWidget(parent) {
+  QHBoxLayout* layout = new QHBoxLayout(this);
+  layout->setMargin(0);
+  layout->setSpacing(0);
+  MessageWidget* message_widget = GostyApp::Instance()->GetMessageWidget();
+  this->connect(message_widget,SIGNAL(MessageCountChanged(QMessageBox::Icon)),this,SLOT(Update(QMessageBox::Icon)));
+  this->connect(message_widget,SIGNAL(AllCleared()),this,SLOT(UpdateAll()));
+}
+
+void MessageBoxWidget::Update(QMessageBox::Icon icon) {
+  MessageWidget* message_widget = GostyApp::Instance()->GetMessageWidget();
+  int count = message_widget->GetMessagesCount(icon);
+  if(!level_map_.contains(icon)){
+    level_map_[icon] = new MessageLevel(message_widget->GetIcon(icon,this),this);
+    this->layout()->addWidget(level_map_[icon]);
+  }
+  level_map_[icon]->SetMessageCount(count);
+  if(count > 0){
+    level_map_[icon]->show();
+  }
+  else{
+    level_map_[icon]->hide();
+  }
+}
+
+void MessageBoxWidget::UpdateAll() {
+  QMapIterator<QMessageBox::Icon,MessageLevel*> i(level_map_);
+  while (i.hasNext()) {
+      i.next();
+      this->Update(i.key());
+  }
+}
+
+void MessageBoxWidget::mouseDoubleClickEvent(QMouseEvent* event){
+  MessageWidget* message_widget = GostyApp::Instance()->GetMessageWidget();
+  PanelManager* manager = GostyApp::Instance()->GetPerspective()->GetPanels();
+  if(message_widget->isHidden()){
+    manager->MoveWidget(message_widget,RIGHT_PANEL,0);
+  }
+}
+
+MessageBoxWidget::~MessageBoxWidget() {
+}
+
+}
+} // ns
diff --git a/modules/gui/src/sequence/sequence_search_bar.hh b/modules/gui/src/messages/message_box_widget.hh
similarity index 57%
rename from modules/gui/src/sequence/sequence_search_bar.hh
rename to modules/gui/src/messages/message_box_widget.hh
index 865a42be22c30a828ba24285319f8f6d5bb592cc..5088397d05349f6b131622e5e6106bb8b3aa8c75 100644
--- a/modules/gui/src/sequence/sequence_search_bar.hh
+++ b/modules/gui/src/messages/message_box_widget.hh
@@ -16,44 +16,54 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#ifndef OST_SEQUENCE_VIEWER_SEQUENCE_SEARCH_BAR_HH
-#define OST_SEQUENCE_VIEWER_SEQUENCE_SEARCH_BAR_HH
+#ifndef OST_GUI_MESSAGES_BOX_MESSAGE_WIDGET_HH
+#define OST_GUI_MESSAGES_BOX_MESSAGE_WIDGET_HH
+
 
-/*
-  Author: Marco Biasini
- */
 #include <ost/gui/module_config.hh>
-#include <ost/seq/alignment_handle.hh>
+
 #include <QWidget>
-#include <QComboBox>
-#include <QCheckBox>
-#include <QSet>
+#include <QMap>
+#include <QMessageBox>
+/*
+  Author: Stefan Scheuber
+*/
 
 namespace ost { namespace gui {
 
-/// \brief search bar to search in multiple sequence alignment
-class DLLEXPORT_OST_GUI SeqSearchBar : public QWidget {
-  Q_OBJECT
+class DLLEXPORT_OST_GUI MessageLevel: public QWidget
+{
+  Q_OBJECT;
 public:
-  SeqSearchBar(QWidget* parent=NULL);
-  
-  void UpdateItems(const QStringList& sequences);
-signals:
-  void Changed(const QString&, bool, const QString&);
+  MessageLevel(QPixmap icon, QWidget* parent);
+
+  void SetMessageCount(int message_count);
+  int GetMessageCount();
+private:
+  int message_count_;
+  QLabel* count_label_;
+};
+
+// a summarized version for the the Log Messages
+class DLLEXPORT_OST_GUI MessageBoxWidget: public QWidget
+{
+  Q_OBJECT;
+public:
+  MessageBoxWidget(QWidget* parent=NULL);
+  ~MessageBoxWidget();
+
 public slots:
-   void OnSubjectChanged(const QString&);
-   void OnSearchInChanged(int);
-   void OnSearchAllChanged(int);
+  void Update(QMessageBox::Icon icon);
+  void UpdateAll();
+
 protected:
-  virtual void paintEvent(QPaintEvent* paint_event);
-  virtual void keyPressEvent(QKeyEvent* key_event);
+  void mouseDoubleClickEvent(QMouseEvent* event);
+
 private:
-  seq::AlignmentHandle ali_;
-  QLineEdit*           subject_;
-  QCheckBox*           search_all_;
-  QComboBox*           search_in_;
-}; 
-  
-}}
+  QMap<QMessageBox::Icon,MessageLevel*> level_map_;
+
+};
+
+}} // ns
 
 #endif
diff --git a/modules/gui/src/messages/message_widget.cc b/modules/gui/src/messages/message_widget.cc
new file mode 100644
index 0000000000000000000000000000000000000000..8a87b06c789e9c6f1e9ccf229ab594465e523045
--- /dev/null
+++ b/modules/gui/src/messages/message_widget.cc
@@ -0,0 +1,229 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+//------------------------------------------------------------------------------
+/*
+ Author: Stefan Scheuber
+ */
+
+#include <ost/gui/gosty_app.hh>
+#include <ost/platform.hh>
+
+#include <ost/gui/widget_registry.hh>
+
+#include "log_reader.hh"
+#include "message_widget.hh"
+
+#include <QApplication>
+#include <QDir>
+#include <QMenu>
+#include <QVBoxLayout>
+
+namespace ost {namespace gui {
+
+class MessageWidgetFactory: public WidgetFactory {
+public:
+  MessageWidgetFactory() :
+    WidgetFactory("ost::gui::MessageWidget", "Messages") {
+  }
+
+  virtual Widget* Create(QWidget* parent) {
+    return GostyApp::Instance()->GetMessageWidget();
+  }
+};
+
+OST_REGISTER_WIDGET(MessageWidget, MessageWidgetFactory);
+
+MessageWidget::MessageWidget(QWidget* parent) :
+  Widget(NULL, parent), model_(new QStandardItemModel(this)), view_(
+      new QListView(this)) {
+  QVBoxLayout* layout = new QVBoxLayout(this);
+  layout->setMargin(0);
+  layout->setSpacing(0);
+  view_->setAttribute(Qt::WA_MacShowFocusRect, false);
+  view_->setAttribute(Qt::WA_MacSmallSize, true);
+  view_->setModel(model_);
+  view_->setSelectionBehavior(QAbstractItemView::SelectRows);
+  view_->setDragEnabled(true);
+  view_->setContextMenuPolicy(Qt::CustomContextMenu);
+  view_->setFrameShape(QFrame::NoFrame);
+  layout->addWidget(view_);
+
+  connect(view_, SIGNAL(customContextMenuRequested(const QPoint&)), this,
+      SLOT(ContextMenuRequested(const QPoint&)));
+
+  QDir icon_path(GetSharedDataPath().c_str());
+  icon_path.cd("gui");
+  icon_path.cd("icons");
+
+  QAction* clear_action = new QAction(this);
+  clear_action->setToolTip("Clear info panel");
+  clear_action->setIcon(QIcon(icon_path.absolutePath() + QDir::separator()
+      + QString("delete_icon.png")));
+  connect(clear_action, SIGNAL(triggered(bool)), this, SLOT(Clear()));
+  this->actions_.append(clear_action);
+
+  new LogReader(this);
+}
+
+void MessageWidget::Update() {
+  view_->viewport()->update();
+}
+
+void MessageWidget::LogMessage(const QString& message, QMessageBox::Icon icon) {
+  QPixmap pix_icon = this->GetIcon(icon, this);
+  QStandardItem* item = new QStandardItem();
+  item->setData(QVariant(icon));
+  item->setText(message);
+  item->setIcon(QIcon(pix_icon));
+  item->setEditable(false);
+  this->model_->appendRow(item);
+  this->Increase(icon);
+}
+
+void MessageWidget::LogMessage(QStandardItem* item) {
+  item->setData(QVariant(QMessageBox::NoIcon));
+  this->model_->appendRow(item);
+  this->Increase(QMessageBox::NoIcon);
+}
+
+void MessageWidget::LogMessage(const QString& message, QIcon icon) {
+  QStandardItem* item = new QStandardItem();
+  item->setText(message);
+  item->setData(QVariant(QMessageBox::NoIcon));
+  item->setIcon(icon);
+  item->setEditable(false);
+  this->model_->appendRow(item);
+  this->Increase(QMessageBox::NoIcon);
+}
+
+void MessageWidget::Increase(QMessageBox::Icon icon){
+  if(count_map_.contains(icon)){
+    count_map_[icon] = count_map_[icon] + 1;
+  }
+  else{
+    count_map_[icon] = 1;
+  }
+  emit MessageCountChanged(icon);
+}
+
+void MessageWidget::Decrease(QMessageBox::Icon icon){
+  if(count_map_.contains(icon)){
+    if(count_map_[icon]>0){
+      count_map_[icon] = count_map_[icon] - 1;
+    }
+    else{
+      count_map_[icon] = 0;
+    }
+  }
+  emit MessageCountChanged(icon);
+}
+
+QPixmap MessageWidget::GetIcon(QMessageBox::Icon icon, QWidget* widget) {
+  QDir icon_path(GetSharedDataPath().c_str());
+  icon_path.cd("gui");
+  icon_path.cd("icons");
+
+  QStyle *style = widget ? widget->style() : QApplication::style();
+  int icon_size = style->pixelMetric(QStyle::PM_MessageBoxIconSize, 0, widget);
+  QIcon tmp_icon;
+#if  defined(__APPLE__)
+  switch (icon) {
+    case QMessageBox::Information:
+      tmp_icon = QIcon(icon_path.absolutePath()+QDir::separator()+QString("information_icon.png"));
+      break;
+    case QMessageBox::Warning:
+      tmp_icon = QIcon(icon_path.absolutePath()+QDir::separator()+QString("warning_icon.png"));
+      break;
+    case QMessageBox::Critical:
+      tmp_icon = QIcon(icon_path.absolutePath()+QDir::separator()+QString("critical_icon.png"));
+      break;
+    default:
+      break;
+  }
+#else
+  switch (icon) {
+  case QMessageBox::Information:
+    tmp_icon = style->standardIcon(QStyle::SP_MessageBoxInformation, 0, widget);
+    break;
+  case QMessageBox::Warning:
+    tmp_icon = style->standardIcon(QStyle::SP_MessageBoxWarning, 0, widget);
+    break;
+  case QMessageBox::Critical:
+    tmp_icon = style->standardIcon(QStyle::SP_MessageBoxCritical, 0, widget);
+    break;
+  case QMessageBox::Question:
+    tmp_icon = style->standardIcon(QStyle::SP_MessageBoxQuestion, 0, widget);
+  default:
+    break;
+  }
+#endif
+  if (!tmp_icon.isNull())
+    return tmp_icon.pixmap(icon_size, icon_size);
+  return QPixmap();
+}
+
+void MessageWidget::Clear() {
+  this->model_->clear();
+  this->count_map_.clear();
+  emit AllCleared();
+}
+
+void MessageWidget::RemoveSelected() {
+  QItemSelectionModel* selection_model = this->view_->selectionModel();
+  const QItemSelection& item_selection = selection_model->selection();
+  const QModelIndexList& model_indexes = item_selection.indexes();
+  for (int i = 0; i < model_indexes.size(); i++) {
+    int row = model_indexes[i].row();
+    QMessageBox::Icon icon = QMessageBox::Icon(this->model_->item(row)->data().toInt());
+    this->model_->removeRow(row);
+    this->Decrease(icon);
+  }
+}
+
+ActionList MessageWidget::GetActions() {
+  return this->actions_;
+}
+
+void MessageWidget::ContextMenuRequested(const QPoint& pos) {
+  QAction* remove_selected_action = new QAction("Remove", this);
+  remove_selected_action->setToolTip("Remove this item");
+  connect(remove_selected_action, SIGNAL(triggered(bool)), this,
+      SLOT(RemoveSelected()));
+
+  QMenu* menu = new QMenu();
+  menu->addAction(remove_selected_action);
+  if (menu->actions().size() > 0) {
+    menu->popup(view_->viewport()->mapToGlobal(pos));
+  }
+}
+
+int MessageWidget::GetMessagesCount(QMessageBox::Icon icon) {
+  if(count_map_.contains(icon)){
+    return count_map_[icon];
+  }
+  return 0;
+}
+
+int MessageWidget::GetTotalMessagesCount() {
+  return model_->rowCount();
+}
+
+MessageWidget::~MessageWidget() {}
+
+}
+} // ns
diff --git a/modules/gui/src/messages/message_widget.hh b/modules/gui/src/messages/message_widget.hh
new file mode 100644
index 0000000000000000000000000000000000000000..f126e0929944089b8dc5832d809fd45f88ea446f
--- /dev/null
+++ b/modules/gui/src/messages/message_widget.hh
@@ -0,0 +1,83 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+//------------------------------------------------------------------------------
+#ifndef OST_GUI_MESSAGES_MESSAGE_WIDGET_HH
+#define OST_GUI_MESSAGES_MESSAGE_WIDGET_HH
+
+
+#include <ost/gui/widget.hh>
+#include <ost/gui/module_config.hh>
+
+#include <QListView>
+#include <QMessageBox>
+#include <QStandardItemModel>
+
+/*
+  Author: Stefan Scheuber
+*/
+
+namespace ost { namespace gui {
+
+// the display window for Log Messages
+class DLLEXPORT_OST_GUI MessageWidget: public Widget
+{
+  Q_OBJECT;
+public:
+  MessageWidget(QWidget* parent=NULL);
+  ~MessageWidget();
+
+public:
+  virtual void LogMessage(const QString& message, QMessageBox::Icon icon=QMessageBox::Information);
+  virtual void LogMessage(QStandardItem* item);
+  virtual void LogMessage(const QString& message, QIcon icon);
+
+  virtual int GetMessagesCount(QMessageBox::Icon icon=QMessageBox::NoIcon);
+  virtual int GetTotalMessagesCount();
+  virtual bool Save(const QString& prefix) { return true; }
+  virtual bool Restore(const QString& prefix) { return true; }
+
+  QPixmap GetIcon(QMessageBox::Icon icon, QWidget* widget);
+
+  ActionList GetActions();
+
+signals:
+  void MessageCountChanged(QMessageBox::Icon);
+  void AllCleared();
+
+public slots:
+  void Clear();
+  void RemoveSelected();
+  void Update();
+
+private slots:
+  void ContextMenuRequested(const QPoint& pos);
+
+private:
+  void Increase(QMessageBox::Icon icon);
+  void Decrease(QMessageBox::Icon icon);
+
+  QStandardItemModel* model_;
+  QListView* view_;
+
+  ActionList actions_;
+  QMap<int,int> count_map_;
+};
+
+}} // ns
+
+#endif
diff --git a/modules/gui/src/panel_bar/tabbed_panel_bar.cc b/modules/gui/src/panel_bar/tabbed_panel_bar.cc
deleted file mode 100644
index fdac9bccd934355b4d59f618e485c02e376a8480..0000000000000000000000000000000000000000
--- a/modules/gui/src/panel_bar/tabbed_panel_bar.cc
+++ /dev/null
@@ -1,84 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-
-#include <QSettings>
-
-#include <ost/gui/widget_registry.hh>
-
-#include "tabbed_panel_bar.hh"
-
-namespace ost { namespace gui {
-
-TabbedPanelBar::TabbedPanelBar(PanelBar* parent):
-  PanelWidgetContainer(parent)
-{
-  layout_ = new QHBoxLayout(this);
-  layout_->setMargin(0);
-  layout_->setSpacing(0);
-  tabWidget_ = new QTabWidget(this);
-  #if QT_VERSION>=0x40503
-    tabWidget_->setDocumentMode(true);
-  #endif
-  layout_->addWidget(tabWidget_);
-}
-
-bool TabbedPanelBar::Save(const QString& prefix)
-{
-  return true;
-}
-
-bool TabbedPanelBar::Restore(const QString& prefix)
-{
-  return true;
-}
-
-void TabbedPanelBar::WidgetMoved(Widget* widget, int index){
-  QString class_name = widget->metaObject()->className();
-  if(tabWidget_->indexOf(widget)>=0){
-    tabWidget_->removeTab(tabWidget_->indexOf(widget));
-  }
-  tabWidget_->insertTab(index,widget,WidgetRegistry::Instance()->GetFullName(class_name));
-}
-
-void TabbedPanelBar::ShowWidget(Widget* widget, int pos, bool show){
-  if(tabWidget_->indexOf(widget)>=0){
-    if(!show){
-      tabWidget_->removeTab(tabWidget_->indexOf(widget));
-    }
-  }
-  else{
-    if(show){
-      WidgetMoved(widget,pos);
-    }
-  }
-}
-
-QString TabbedPanelBar::GetName(){
-  return "Tabbed Mode";
-}
-
-TabbedPanelBar::~TabbedPanelBar(){
-  //Do not destroy widgets
-  for(int i=0; i< tabWidget_->count();i++){
-    tabWidget_->widget(i)->setParent(NULL);
-  }
-}
-
-}}
-
diff --git a/modules/gui/src/panel_bar/bottom_bar.cc b/modules/gui/src/panels/bottom_bar.cc
similarity index 100%
rename from modules/gui/src/panel_bar/bottom_bar.cc
rename to modules/gui/src/panels/bottom_bar.cc
index e5bf3a423fc651d479c66fd0c7e4def320c353db..f3b643aec2a1db820220a8927c2183be901ad618 100644
--- a/modules/gui/src/panel_bar/bottom_bar.cc
+++ b/modules/gui/src/panels/bottom_bar.cc
@@ -17,13 +17,13 @@
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
 
-#include <QAction>
 
 #include "bottom_bar.hh"
 
 #include "splitter_panel_bar.hh"
 #include "tabbed_panel_bar.hh"
 
+#include <QAction>
 namespace ost { namespace gui {
 
 BottomBar::BottomBar(QWidget* parent):
diff --git a/modules/gui/src/panel_bar/bottom_bar.hh b/modules/gui/src/panels/bottom_bar.hh
similarity index 100%
rename from modules/gui/src/panel_bar/bottom_bar.hh
rename to modules/gui/src/panels/bottom_bar.hh
diff --git a/modules/gui/src/panel_bar/button_bar.cc b/modules/gui/src/panels/button_bar.cc
similarity index 100%
rename from modules/gui/src/panel_bar/button_bar.cc
rename to modules/gui/src/panels/button_bar.cc
diff --git a/modules/gui/src/panel_bar/button_bar.hh b/modules/gui/src/panels/button_bar.hh
similarity index 100%
rename from modules/gui/src/panel_bar/button_bar.hh
rename to modules/gui/src/panels/button_bar.hh
index 578769349be20124f66b77b3a7ba2ff2fdb93017..ab36d0570cef9b04d48e2130e1afcd9c338e9be5 100644
--- a/modules/gui/src/panel_bar/button_bar.hh
+++ b/modules/gui/src/panels/button_bar.hh
@@ -19,10 +19,6 @@
 #ifndef OST_GUI_BOTTOM_BAR_BUTTON_BAR
 #define OST_GUI_BOTTOM_BAR_BUTTON_BAR
 
-#include <QWidget>
-#include <QString>
-#include <QHBoxLayout>
-#include <QList>
 
 #include <ost/gui/module_config.hh>
 #include <ost/gui/widget.hh>
@@ -30,6 +26,10 @@
 #include "button_box.hh"
 #include "event_button.hh"
 
+#include <QWidget>
+#include <QString>
+#include <QHBoxLayout>
+#include <QList>
 namespace ost { namespace gui {
 
 /// \brief button box
diff --git a/modules/gui/src/panel_bar/button_box.cc b/modules/gui/src/panels/button_box.cc
similarity index 100%
rename from modules/gui/src/panel_bar/button_box.cc
rename to modules/gui/src/panels/button_box.cc
diff --git a/modules/gui/src/panel_bar/button_box.hh b/modules/gui/src/panels/button_box.hh
similarity index 100%
rename from modules/gui/src/panel_bar/button_box.hh
rename to modules/gui/src/panels/button_box.hh
index a04931aa62662c2ce613a7a53eac088f278f5812..f6525e609b359e97bcc2c462d3fc17f4c969b0ba 100644
--- a/modules/gui/src/panel_bar/button_box.hh
+++ b/modules/gui/src/panels/button_box.hh
@@ -19,17 +19,17 @@
 #ifndef OST_GUI_BOTTOM_BAR_BUTTON_BOX
 #define OST_GUI_BOTTOM_BAR_BUTTON_BOX
 
-#include <QWidget>
-#include <QString>
-#include <QGridLayout>
-#include <QList>
-#include <QLabel>
 
 #include <ost/gui/module_config.hh>
 #include <ost/gui/widget.hh>
 
 #include "event_button.hh"
 
+#include <QWidget>
+#include <QString>
+#include <QGridLayout>
+#include <QList>
+#include <QLabel>
 namespace ost { namespace gui {
 
 /// \brief button box
diff --git a/modules/gui/src/panel_bar/drop_box.cc b/modules/gui/src/panels/drop_box.cc
similarity index 100%
rename from modules/gui/src/panel_bar/drop_box.cc
rename to modules/gui/src/panels/drop_box.cc
index a65dfa2c5df5b6f6bb1b7f552b800e9c52ec63d8..149e0a1a4f1f301071c2275b11b465b018c931ea 100644
--- a/modules/gui/src/panel_bar/drop_box.cc
+++ b/modules/gui/src/panels/drop_box.cc
@@ -17,11 +17,11 @@
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
 
-#include <QHBoxLayout>
-#include <QLabel>
 
 #include "drop_box.hh"
 
+#include <QHBoxLayout>
+#include <QLabel>
 namespace ost { namespace gui {
 
 DropBox::DropBox(QWidget* parent):
diff --git a/modules/gui/src/panel_bar/drop_box.hh b/modules/gui/src/panels/drop_box.hh
similarity index 100%
rename from modules/gui/src/panel_bar/drop_box.hh
rename to modules/gui/src/panels/drop_box.hh
diff --git a/modules/gui/src/panel_bar/event_button.cc b/modules/gui/src/panels/event_button.cc
similarity index 100%
rename from modules/gui/src/panel_bar/event_button.cc
rename to modules/gui/src/panels/event_button.cc
diff --git a/modules/gui/src/panel_bar/event_button.hh b/modules/gui/src/panels/event_button.hh
similarity index 100%
rename from modules/gui/src/panel_bar/event_button.hh
rename to modules/gui/src/panels/event_button.hh
index f1c6d034f7d0b7cf63daf86dd50c5ce87d01a664..0063e5d116db050d67b541f6ffb5dfbe61ace3f9 100644
--- a/modules/gui/src/panel_bar/event_button.hh
+++ b/modules/gui/src/panels/event_button.hh
@@ -19,16 +19,16 @@
 #ifndef OST_GUI_BOTTOM_BAR_EVENT_BUTTON
 #define OST_GUI_BOTTOM_BAR_EVENT_BUTTON
 
+
+#include <ost/gui/module_config.hh>
+#include <ost/gui/widget.hh>
+
 #include <QToolButton>
 #include <QMouseEvent>
 #include <QDragEnterEvent>
 #include <QDropEvent>
 #include <QWidget>
 #include <QString>
-
-#include <ost/gui/module_config.hh>
-#include <ost/gui/widget.hh>
-
 namespace ost { namespace gui {
 
 /// \brief button box
diff --git a/modules/gui/src/panel_bar/panel_bar.cc b/modules/gui/src/panels/panel_bar.cc
similarity index 97%
rename from modules/gui/src/panel_bar/panel_bar.cc
rename to modules/gui/src/panels/panel_bar.cc
index db90f50d33ea08f0a312b020a4f66c20c66b64af..291acc925014285f75b985aa7b77bea865262e13 100644
--- a/modules/gui/src/panel_bar/panel_bar.cc
+++ b/modules/gui/src/panels/panel_bar.cc
@@ -17,20 +17,20 @@
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
 
-#include <QSettings>
-#include <QVariant>
 
 #include <ost/gui/gosty_app.hh>
 #include <ost/gui/perspective.hh>
-#include <ost/gui/panel_bar/panels.hh>
-#include <ost/gui/panel_bar/drop_box.hh>
 #include <ost/gui/widget.hh>
 #include <ost/gui/widget_registry.hh>
 
+#include "drop_box.hh"
 #include "panel_bar.hh"
-#include "tabbed_panel_bar.hh"
+#include "panel_manager.hh"
 #include "splitter_panel_bar.hh"
+#include "tabbed_panel_bar.hh"
 
+#include <QSettings>
+#include <QVariant>
 namespace ost {
 namespace gui {
 
@@ -69,7 +69,7 @@ void PanelBar::AddWidget(Widget* widget, bool is_hidden)
 {
   int index = this->GetIndex(widget);
   if (index == -1) {
-    QString class_name = widget->metaObject()->className();
+    QString class_name = widget->GetUniqueID();
     WidgetState ws = WidgetState(widget, !is_hidden, class_name);
     widget_states_.append(ws);
     if(current_view_mode_){
@@ -221,7 +221,7 @@ void PanelBar::InsertWidget(Widget * widget, int index, bool is_hidden)
       current_view_mode_->WidgetMoved(widget, index);
     }
   } else {
-    QString class_name = widget->metaObject()->className();
+    QString class_name = widget->GetUniqueID();
     WidgetState ws = WidgetState(widget, !is_hidden, class_name);
     widget_states_.insert(index, ws);
     if(current_view_mode_){
diff --git a/modules/gui/src/panel_bar/panel_bar.hh b/modules/gui/src/panels/panel_bar.hh
similarity index 95%
rename from modules/gui/src/panel_bar/panel_bar.hh
rename to modules/gui/src/panels/panel_bar.hh
index 474146b5b75cbdd0dcb780b576167fe39edd73c0..ecf930b1c8b3635f19806431294cb211d6ec446a 100644
--- a/modules/gui/src/panel_bar/panel_bar.hh
+++ b/modules/gui/src/panels/panel_bar.hh
@@ -19,11 +19,6 @@
 #ifndef OST_GUI_PANEL_BAR_PANEL_BAR
 #define OST_GUI_PANEL_BAR_PANEL_BAR
 
-#include <QStackedLayout>
-#include <QWidget>
-#include <QString>
-#include <QAction>
-#include <QActionGroup>
 
 #include <ost/gui/module_config.hh>
 #include <ost/gui/widget_pool.hh>
@@ -33,6 +28,11 @@
 #include "button_box.hh"
 
 
+#include <QStackedLayout>
+#include <QWidget>
+#include <QString>
+#include <QAction>
+#include <QActionGroup>
 namespace ost { namespace gui {
 
 class PanelWidgetContainer;
@@ -80,10 +80,10 @@ public:
   int GetIndex(Widget* widget);
 
   /// \brief Begin with dragging widgets
-  /// This method is called by the \ref Panels class. Read more about this method at \ref Panels::StartDrag() .
+  /// This method is called by the \ref PanelManager class. Read more about this method at \ref PanelManager::StartDrag() .
   void DragEnter();
   /// \brief Stop dragging widgets
-  /// This method is called by the \ref Panels class. Read more about this method at \ref Panels::EndDrag() .
+  /// This method is called by the \ref PanelManager class. Read more about this method at \ref PanelManager::EndDrag() .
   void EndDrag();
 
   /// \brief Get action which changes the visibility of this widget
diff --git a/modules/gui/src/panel_bar/panel_bar_widget_holder.cc b/modules/gui/src/panels/panel_bar_widget_holder.cc
similarity index 78%
rename from modules/gui/src/panel_bar/panel_bar_widget_holder.cc
rename to modules/gui/src/panels/panel_bar_widget_holder.cc
index d017071ccdcd72ea9048eba9ece439dd07587d95..02fc9d181d92207caa82364cb2cc8b118c42016f 100644
--- a/modules/gui/src/panel_bar/panel_bar_widget_holder.cc
+++ b/modules/gui/src/panels/panel_bar_widget_holder.cc
@@ -18,6 +18,18 @@
 //------------------------------------------------------------------------------
 #include <cassert>
 
+
+#include <ost/gui/gosty_app.hh>
+#include <ost/platform.hh>
+
+#include <ost/gui/widget.hh>
+#include <ost/gui/widget_registry.hh>
+#include <ost/gui/perspective.hh>
+
+#include "panel_manager.hh"
+#include "panel_bar.hh"
+#include "panel_bar_widget_holder.hh"
+
 #include <QApplication>
 #include <QMenu>
 #include <QHBoxLayout>
@@ -30,18 +42,6 @@
 #include <QAction>
 #include <QComboBox>
 #include <QDebug>
-
-#include <ost/platform.hh>
-
-#include <ost/gui/widget.hh>
-#include <ost/gui/widget_registry.hh>
-#include <ost/gui/gosty_app.hh>
-#include <ost/gui/perspective.hh>
-#include <ost/gui/panel_bar/panel_bar.hh>
-#include <ost/gui/panel_bar/panels.hh>
-
-#include "panel_bar_widget_holder.hh"
-
 /*
   Author: Marco Biasini, Stefan Scheuber
  */
@@ -49,33 +49,31 @@
 namespace ost { namespace gui {
 
 
-PanelBarWidgetHolder::PanelBarWidgetHolder(Widget* widget,Qt::Orientation orientation,
-                                         QWidget* parent):
+PanelBarWidgetHolder::PanelBarWidgetHolder(Widget* widget, Qt::Orientation orientation,
+                                           QWidget* parent):
   QWidget(parent), toolbar_(new QToolBar(parent)),
   widget_(widget), label_(NULL)
 {
   this->SetupToolBar();
   QVBoxLayout* v_layout=new QVBoxLayout(this);
   this->setLayout(v_layout);
+  widget->setVisible(true);  
   v_layout->setMargin(0);
   v_layout->setSpacing(0);    
-  v_layout->addWidget(toolbar_, 1);
-  v_layout->addWidget(widget, 100);
+  v_layout->addWidget(toolbar_, 0);
+  v_layout->addWidget(widget, 1);
 
-  this->setSizePolicy(widget->sizePolicy());
+  this->setSizePolicy(widget->sizePolicy());  
   if(orientation == Qt::Horizontal){
     if(this->sizePolicy().horizontalPolicy()==QSizePolicy::Fixed){
-      this->setMinimumWidth(widget->minimumWidth());
-      this->setMinimumWidth(widget->maximumWidth());
-    }
-    else if(this->sizePolicy().verticalPolicy()==QSizePolicy::Fixed){
+      this->setFixedWidth(widget->minimumWidth());
+    } else if (this->sizePolicy().verticalPolicy()==QSizePolicy::Fixed) {
       v_layout->addStretch(1);
     }
   }
   if(orientation == Qt::Vertical){
-    if(this->sizePolicy().verticalPolicy()==QSizePolicy::Fixed){
-      this->setMinimumHeight(toolbar_->height()+widget->minimumHeight());
-      this->setMaximumHeight(toolbar_->height()+widget->maximumHeight());
+    if(this->sizePolicy().verticalPolicy()==QSizePolicy::Fixed) {
+      this->setFixedHeight(this->sizeHint().height());
     }
   }
 
@@ -88,12 +86,12 @@ void PanelBarWidgetHolder::SetupToolBar()
   icon_path.cd("gui");
   icon_path.cd("icons");
 
-  QString class_name=widget_->metaObject()->className();
+  QString class_name=widget_->GetUniqueID();
   WidgetRegistry* wf=WidgetRegistry::Instance();
-
+  toolbar_->setAttribute(Qt::WA_MacSmallSize);
   QAction* label_ = toolbar_->addAction(wf->GetFullName(class_name));
   connect(label_, SIGNAL(triggered(bool)), this, SLOT(LabelClick(bool)));
-  toolbar_->addSeparator();
+  //toolbar_->addSeparator();
   QWidget* spacer = new QWidget(this);
   QHBoxLayout* hbox = new QHBoxLayout(spacer);
   spacer->setLayout(hbox);
@@ -104,14 +102,13 @@ void PanelBarWidgetHolder::SetupToolBar()
   toolbar_->setContentsMargins(0, 0, 0, 0);
   toolbar_->setToolButtonStyle(Qt::ToolButtonIconOnly);
   toolbar_->setIconSize(QSize(16,16));
-  if(!actions.isEmpty()){
-    for(int i = 0;i<actions.size();i++){
-      toolbar_->addAction(actions[i]);
-    }
-  }
+  for (int i=0; i<actions.size();i++) {
+    toolbar_->addAction(actions[i]);
+  }  
   QAction* delete_me=toolbar_->addAction(" x ");
   delete_me->setToolTip("Close "+ label_->text());
-  delete_me->setIcon(QIcon(icon_path.absolutePath()+QDir::separator()+QString("close_icon.png")));
+  delete_me->setIcon(QIcon(icon_path.absolutePath()+QDir::separator()+
+                           QString("close_icon.png")));
   connect(delete_me, SIGNAL(triggered()), this, SLOT(Remove()));
 }
 
@@ -125,8 +122,8 @@ void PanelBarWidgetHolder::SetWidget(Widget* widget)
   QBoxLayout* l=dynamic_cast<QBoxLayout*>(layout());
   assert(l);
   l->removeWidget(widget_);
-  l->addWidget(widget, 100);
-  QString class_name=widget->metaObject()->className();
+  l->addWidget(widget, 1);
+  QString class_name=widget->GetUniqueID();
   WidgetRegistry* wf=WidgetRegistry::Instance();
   label_->setText(wf->GetFullName(class_name));
   widget_=widget;
@@ -134,11 +131,11 @@ void PanelBarWidgetHolder::SetWidget(Widget* widget)
 
 void PanelBarWidgetHolder::LabelClick(bool checked)
 {
-  Panels* panels = GostyApp::Instance()->GetPerspective()->GetPanels();
+  PanelManager* panels = GostyApp::Instance()->GetPerspective()->GetPanels();
   QMenu* m = panels->GetAvailableWidgetsMenu();
   if (QAction* a=m->exec(toolbar_->mapToGlobal(QPoint(0, 0)))) {
     QString new_class_name=a->data().toString();
-    if (new_class_name!=widget_->metaObject()->className()) {
+    if (new_class_name!=widget_->GetUniqueID()) {
       panels->ReplaceWidget(widget_,new_class_name);
     }
   }
@@ -172,14 +169,14 @@ void PanelBarWidgetHolder::mouseMoveEvent(QMouseEvent *event)
 
   drag->setMimeData(mime_data);
   drag->exec();
-  Panels* panels = GostyApp::Instance()->GetPerspective()->GetPanels();
+  PanelManager* panels = GostyApp::Instance()->GetPerspective()->GetPanels();
   panels->EndDrag();
 }
 
 void PanelBarWidgetHolder::dragEnterEvent(QDragEnterEvent *event)
 {
   if (event->mimeData()->hasFormat("OpenStructure/Widget")){
-    Panels* panels = GostyApp::Instance()->GetPerspective()->GetPanels();
+    PanelManager* panels = GostyApp::Instance()->GetPerspective()->GetPanels();
     panels->StartDrag();
     event->acceptProposedAction();
   }
diff --git a/modules/gui/src/panel_bar/panel_bar_widget_holder.hh b/modules/gui/src/panels/panel_bar_widget_holder.hh
similarity index 100%
rename from modules/gui/src/panel_bar/panel_bar_widget_holder.hh
rename to modules/gui/src/panels/panel_bar_widget_holder.hh
index e06d6ccec0e137f52fabe4c4c6b2c24c2fc155c3..0b3aca1e81d074c3584fedba2fe2547230571d61 100644
--- a/modules/gui/src/panel_bar/panel_bar_widget_holder.hh
+++ b/modules/gui/src/panels/panel_bar_widget_holder.hh
@@ -19,13 +19,13 @@
 #ifndef OST_GUI_PANEL_BAR_WIDGET_HOLDER_HH
 #define OST_GUI_PANEL_BAR_WIDGET_HOLDER_HH
 
-#include <QWidget>
-#include <QMouseEvent>
 
 #include <ost/gui/module_config.hh>
 
 #include "panel_bar.hh"
 
+#include <QWidget>
+#include <QMouseEvent>
 class QToolBar;
 class QAction;
 
diff --git a/modules/gui/src/panel_bar/panels.cc b/modules/gui/src/panels/panel_manager.cc
similarity index 85%
rename from modules/gui/src/panel_bar/panels.cc
rename to modules/gui/src/panels/panel_manager.cc
index 3f6eedae94617bab6e4bd22284ceb4bfa3c354c7..5a5e3cf6c018f4cbc2005477016c32d4559b5cec 100644
--- a/modules/gui/src/panel_bar/panels.cc
+++ b/modules/gui/src/panels/panel_manager.cc
@@ -17,18 +17,18 @@
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
 
-#include <QSettings>
-#include <QMenu>
-#include <QDebug>
 
 #include <ost/gui/widget_registry.hh>
 
 #include "bottom_bar.hh"
 #include "side_bar.hh"
-#include "panels.hh"
+#include "panel_manager.hh"
 #include "tabbed_panel_bar.hh"
 #include "splitter_panel_bar.hh"
 
+#include <QSettings>
+#include <QMenu>
+#include <QDebug>
 namespace ost { namespace gui {
 
 class ExternalWidgetFactory: public WidgetFactory {
@@ -45,7 +45,7 @@ public:
 };
 
 
-Panels::Panels(QWidget* widget):
+PanelManager::PanelManager(QWidget* widget):
  Widget(NULL, widget->parentWidget()),
      right_panel_splitter_(new ThinSplitter(Qt::Horizontal, this)),
      left_panel_splitter_(new ThinSplitter(Qt::Horizontal, this)),
@@ -97,29 +97,28 @@ Panels::Panels(QWidget* widget):
   this->acceptDrops();
 }
 
-void Panels::AddWidgetToPool(const QString& class_name, int limit){
+void PanelManager::AddWidgetToPool(const QString& class_name, int limit){
   pool_->Add(class_name, limit);
 }
 
-void Panels::AddWidgetToPool(const QString& name, Widget* widget){
-  QString id = widget->metaObject()->className();
-  widget->setParent(this);
-  id.replace(".", "::");
-  ExternalWidgetFactory* ewf = new ExternalWidgetFactory(id,name,widget);
+void PanelManager::AddWidgetToPool(const QString& name, Widget* widget) {
+  //widget->setParent(this);
+  widget->SetUniqueID(name);
+  ExternalWidgetFactory* ewf = new ExternalWidgetFactory(name, name, widget);
   WidgetRegistry::Instance()->RegisterWidgetFactory(ewf);
-  pool_->Add(id, 1);
+  pool_->Add(name, 1);
 }
 
-void Panels::AddWidget(PanelPosition pos, Widget* widget, bool is_hidden){
+void PanelManager::AddWidget(PanelPosition pos, Widget* widget, bool is_hidden){
   if(panels_.contains(pos) && this->GetParentPanel(widget) == NONE){
-    if(pool_->IsAvailable(widget->metaObject()->className())){
+    if(pool_->IsAvailable(widget->GetUniqueID())){
       panels_[pos]->AddWidget(widget,is_hidden);
-      pool_->Take(widget->metaObject()->className());
+      pool_->Take(widget->GetUniqueID());
     }
   }
 }
 
-void Panels::AddWidgetByName(PanelPosition pos, const QString& class_name, 
+void PanelManager::AddWidgetByName(PanelPosition pos, const QString& class_name,
                              bool is_hidden)
 {
   QString n=class_name;
@@ -130,7 +129,7 @@ void Panels::AddWidgetByName(PanelPosition pos, const QString& class_name,
   }
 }
 
-bool Panels::Save(const QString& prefix)
+bool PanelManager::Save(const QString& prefix)
 {
   bool saveok = true;
   QSettings settings;
@@ -172,7 +171,7 @@ bool Panels::Save(const QString& prefix)
   return saveok;
 }
 
-bool Panels::Restore(const QString& prefix)
+bool PanelManager::Restore(const QString& prefix)
 {
   QList<int> sizes = QList<int>();
   QSettings settings;
@@ -214,13 +213,13 @@ bool Panels::Restore(const QString& prefix)
   return restoreok;
 }
 
-void Panels::ToggleViewMode(PanelPosition pos){
+void PanelManager::ToggleViewMode(PanelPosition pos){
   if(panels_.contains(pos)){
    panels_[pos]->ToggleViewMode();
   }
 }
 
-void Panels::ToggleHide(){
+void PanelManager::ToggleHide(){
   QMapIterator<PanelPosition, PanelBar*> i(panels_);
   while (i.hasNext()) {
       i.next();
@@ -228,13 +227,13 @@ void Panels::ToggleHide(){
   }
 }
 
-void Panels::ToggleHide(PanelPosition pos){
+void PanelManager::ToggleHide(PanelPosition pos){
   if(panels_.contains(pos)){
    panels_[pos]->ToggleHide();
   }
 }
 
-void Panels::MoveWidget(Widget * widget, PanelPosition pos, int index){
+void PanelManager::MoveWidget(Widget * widget, PanelPosition pos, int index){
   if(panels_.contains(pos)){
     PanelPosition current_position = this->GetParentPanel(widget);
     if(current_position == pos){
@@ -243,44 +242,44 @@ void Panels::MoveWidget(Widget * widget, PanelPosition pos, int index){
     else{
       if(panels_.contains(current_position)){
         panels_[current_position]->RemoveWidget(widget);
-        pool_->Give(widget->metaObject()->className());
+        pool_->Give(widget->GetUniqueID());
       }
-      if(pool_->IsAvailable(widget->metaObject()->className())){
+      if(pool_->IsAvailable(widget->GetUniqueID())){
         panels_[pos]->InsertWidget(widget,index,false);
-        pool_->Take(widget->metaObject()->className());
+        pool_->Take(widget->GetUniqueID());
       }
     }
   }
 }
 
-void Panels::MoveNextTo(Widget* target, Widget* widget){
+void PanelManager::MoveNextTo(Widget* target, Widget* widget){
   PanelPosition target_position =  this->GetParentPanel(target);
   if(panels_.contains(target_position)){
     this->MoveWidget(widget,target_position,panels_[target_position]->GetIndex(target));
   }
 }
 
-void Panels::ReplaceWidget(Widget* w1, Widget* w2){
-  if(pool_->IsAvailable(w2->metaObject()->className())){
+void PanelManager::ReplaceWidget(Widget* w1, Widget* w2){
+  if(pool_->IsAvailable(w2->GetUniqueID())){
     PanelPosition pos_w1 = this->GetParentPanel(w1);
     PanelPosition pos_w2  = this->GetParentPanel(w2);
     if(panels_.contains(pos_w1) && pos_w2 == NONE){
       int index = panels_[pos_w1]->GetIndex(w1);
       panels_[pos_w1]->RemoveWidget(w1);
-      pool_->Give(w1->metaObject()->className());
+      pool_->Give(w1->GetUniqueID());
       panels_[pos_w1]->InsertWidget(w2,index,false);
-      pool_->Take(w2->metaObject()->className());
+      pool_->Take(w2->GetUniqueID());
     }
   }
 }
 
-void Panels::ReplaceWidget(Widget* w1, QString& class_name){
+void PanelManager::ReplaceWidget(Widget* w1, QString& class_name){
   if(pool_->IsAvailable(class_name)){
     PanelPosition pos = this->GetParentPanel(w1);
     if(panels_.contains(pos)){
       int index = panels_[pos]->GetIndex(w1);
       panels_[pos]->RemoveWidget(w1);
-      pool_->Give(w1->metaObject()->className());
+      pool_->Give(w1->GetUniqueID());
       WidgetRegistry* wf=WidgetRegistry::Instance();
       Widget* widget = wf->Create(class_name,this);
       panels_[pos]->InsertWidget(widget,index,false);
@@ -289,21 +288,21 @@ void Panels::ReplaceWidget(Widget* w1, QString& class_name){
   }
 }
 
-void Panels::RemoveWidget(Widget *widget){
+void PanelManager::RemoveWidget(Widget *widget){
   PanelPosition pos = this->GetParentPanel(widget);
   if(panels_.contains(pos)){
     panels_[pos]->RemoveWidget(widget);
-    pool_->Give(widget->metaObject()->className());
+    pool_->Give(widget->GetUniqueID());
   }
 }
 
-QList<QString> Panels::GetAvailableWidgets()
+QList<QString> PanelManager::GetAvailableWidgets()
 {
   return pool_->GetAvailableWidgets();
 }
 
 
-QMenu* Panels::GetAvailableWidgetsMenu()
+QMenu* PanelManager::GetAvailableWidgetsMenu()
 {
   QMenu* m=new QMenu;
 
@@ -317,7 +316,7 @@ QMenu* Panels::GetAvailableWidgetsMenu()
   return m;
 }
 
-PanelPosition Panels::GetParentPanel(Widget* widget){
+PanelPosition PanelManager::GetParentPanel(Widget* widget){
   QMapIterator<PanelPosition, PanelBar*> i(panels_);
   while (i.hasNext()) {
       i.next();
@@ -329,7 +328,7 @@ PanelPosition Panels::GetParentPanel(Widget* widget){
   return NONE;
 }
 
-void Panels::StartDrag()
+void PanelManager::StartDrag()
 {
   QMapIterator<PanelPosition, PanelBar*> i(panels_);
   while (i.hasNext()) {
@@ -338,7 +337,7 @@ void Panels::StartDrag()
   }
 }
 
-void Panels::EndDrag()
+void PanelManager::EndDrag()
 {
   QMapIterator<PanelPosition, PanelBar*> i(panels_);
   while (i.hasNext()) {
@@ -347,7 +346,7 @@ void Panels::EndDrag()
   }
 }
 
-QMenu* Panels::GetMenu()
+QMenu* PanelManager::GetMenu()
 {
   QMenu* panel_menu = new QMenu(this);
   panel_menu->setTitle("Panels");
@@ -378,7 +377,7 @@ QMenu* Panels::GetMenu()
   return panel_menu;
 }
 
-void Panels::UpdateAddMenu(){
+void PanelManager::UpdateAddMenu(){
   add_menu_->clear();
   WidgetRegistry* wf=WidgetRegistry::Instance();
   QList<QString> available=this->GetAvailableWidgets();
@@ -389,7 +388,7 @@ void Panels::UpdateAddMenu(){
   }
 }
 
-void Panels::AddWidgetFromMenu(QAction* action){
+void PanelManager::AddWidgetFromMenu(QAction* action){
   if(action){
     QString new_class_name=action->data().toString();
     if(panels_.contains(current_menu_)){
@@ -398,7 +397,7 @@ void Panels::AddWidgetFromMenu(QAction* action){
   }
 }
 
-void Panels::UpdateCurrentMenu(){
+void PanelManager::UpdateCurrentMenu(){
   QAction* action = qobject_cast<QAction*>(this->sender());
   if(action){
     current_menu_ = PanelPosition(action->data().toInt());
diff --git a/modules/gui/src/panel_bar/panels.hh b/modules/gui/src/panels/panel_manager.hh
similarity index 93%
rename from modules/gui/src/panel_bar/panels.hh
rename to modules/gui/src/panels/panel_manager.hh
index 1dd71496431162ef92a6968c5e2cfa27b92b9741..d4d505517932134fe957fb53ccd10178ce5504b5 100644
--- a/modules/gui/src/panel_bar/panels.hh
+++ b/modules/gui/src/panels/panel_manager.hh
@@ -16,14 +16,9 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#ifndef OST_GUI_PANEL_BAR_PANELS
-#define OST_GUI_PANEL_BAR_PANELS
+#ifndef OST_GUI_PANEL_BAR_PANEL_MANAGER
+#define OST_GUI_PANEL_BAR_PANEL_MANAGER
 
-#include <QWidget>
-#include <QString>
-#include <QList>
-#include <QMenu>
-#include <QDragEnterEvent>
 
 #include <ost/gui/widget.hh>
 #include <ost/gui/widget_pool.hh>
@@ -32,6 +27,11 @@
 #include "panel_widget_container.hh"
 #include "button_box.hh"
 
+#include <QWidget>
+#include <QString>
+#include <QList>
+#include <QMenu>
+#include <QDragEnterEvent>
 namespace ost { namespace gui {
 
 enum PanelPosition
@@ -45,18 +45,18 @@ enum PanelPosition
 /// \brief Class which organizes all widgets which are in the side panels
 /// This class handles all side bar widgets. It can be used to display, hide or move a widget to a PaneBar. There are three Bars (left, bottom, right) which are organized by this class.
 /// Whenever a widget is being removed or added it checks first if the widget type is known and if there are available instances.
-class DLLEXPORT_OST_GUI Panels : public Widget {
+class DLLEXPORT_OST_GUI PanelManager : public Widget {
   Q_OBJECT
 public:
-  Panels(QWidget* widget);
-  ~Panels(){ }
+  PanelManager(QWidget* widget);
+  ~PanelManager(){ }
   virtual bool Save(const QString& prefix);
   virtual bool Restore(const QString& prefix);
 
   /// \brief Add a widget to the widget pool
   ///
   /// The widget must already be in the WidgetRegistry.
-  /// If you are not sure if the Widget is in the WidgetRegistry, use the \ref Panels::AddWidgetToPool(const QString& name, Widget* widget) Method instead.
+  /// If you are not sure if the Widget is in the WidgetRegistry, use the \ref PanelManager::AddWidgetToPool(const QString& name, Widget* widget) Method instead.
   /// \param class_name class name of class which should be added to WidgetRegistry.
   /// \param limit amount of parallel instances allowed (-1 if infinite)
   virtual void AddWidgetToPool(const QString& class_name, int limit=-1);
@@ -75,11 +75,11 @@ public:
   /// \param is_hidden marks if the class should be displayed in the gui. Default the widget will be shown.
   void AddWidget(PanelPosition pos, Widget* widget, bool is_hidden=false);
   /// \brief Display a Widget in a PanelBar
-  /// Same as \ref Panels::AddWidget(PanelPosition pos, Widget* widget, bool is_hidden)
+  /// Same as \ref PanelManager::AddWidget(PanelPosition pos, Widget* widget, bool is_hidden)
   /// \param pos Indicates which PanelBar is affected
   /// \param class_name the class_name of the widget you would like to add.
   /// \param is_hidden marks if the class should be displayed in the gui. Default the widget will be shown.
-  void AddWidgetByName(PanelPosition pos, const QString& class_name, bool hidden=false);
+  void AddWidgetByName(PanelPosition pos, const QString& class_name, bool is_hidden=false);
 
   /// \brief Replace a Widget with another Widget
   /// With this Method you can replace a Widget which is in a PanelBar with another Widget.
@@ -87,7 +87,7 @@ public:
   /// \param w1 The widget which will be replaced
   /// \param w2 The new Widget which should replace the old one.
   void ReplaceWidget(Widget* w1, Widget* w2);
-  /// Same as \ref Panels::ReplaceWidget(Widget* w1, Widget* w2)
+  /// Same as \ref PanelManager::ReplaceWidget(Widget* w1, Widget* w2)
   /// \param w1 The widget which will be replaced
   /// \param class_name The class_name which from which a instance will be created and then replaces the old one.
   void ReplaceWidget(Widget* w1, QString& class_name);
diff --git a/modules/gui/src/panel_bar/panel_widget_container.cc b/modules/gui/src/panels/panel_widget_container.cc
similarity index 100%
rename from modules/gui/src/panel_bar/panel_widget_container.cc
rename to modules/gui/src/panels/panel_widget_container.cc
diff --git a/modules/gui/src/panel_bar/panel_widget_container.hh b/modules/gui/src/panels/panel_widget_container.hh
similarity index 93%
rename from modules/gui/src/panel_bar/panel_widget_container.hh
rename to modules/gui/src/panels/panel_widget_container.hh
index ea8c3e0679f9781e4232ed6f59bfeb8a287e1b6b..e46ae504421dd6209960175253044542062e29c4 100644
--- a/modules/gui/src/panel_bar/panel_widget_container.hh
+++ b/modules/gui/src/panels/panel_widget_container.hh
@@ -19,17 +19,17 @@
 #ifndef OST_GUI_PANEL_BAR_PANEL_WIDGET_CONTAINER
 #define OST_GUI_PANEL_BAR_PANEL_WIDGET_CONTAINER
 
-#include <QHBoxLayout>
-#include <QWidget>
-#include <QString>
-#include <QAction>
-#include <QMap>
 
 #include <ost/gui/module_config.hh>
 #include <ost/gui/widget.hh>
 
 #include "panel_bar.hh"
 
+#include <QHBoxLayout>
+#include <QWidget>
+#include <QString>
+#include <QAction>
+#include <QMap>
 namespace ost { namespace gui {
 
 /// \brief A PanelWidgetContainer can display various widgets
@@ -54,11 +54,11 @@ public:
   /// \param show if show if false hide the widget even the position is not correct.
   virtual void ShowWidget(Widget* widget,int pos,bool show = true) = 0;
   /// \brief Begin with dragging widgets
-  /// This method is initially called in the \ref Panels class in the \ref Panels::StartDrag() method.
+  /// This method is initially called in the \ref PanelManager class in the \ref PanelManager::StartDrag() method.
 
   virtual void StartDrag();
   /// \brief Stop dragging widgets
-  /// This method is initially called in the \ref Panels class in the \ref Panels::EndDrag() method.
+  /// This method is initially called in the \ref PanelManager class in the \ref PanelManager::EndDrag() method.
   virtual void EndDrag();
 
   /// \brief Get the PanelBar
diff --git a/modules/gui/src/panel_bar/side_bar.cc b/modules/gui/src/panels/side_bar.cc
similarity index 100%
rename from modules/gui/src/panel_bar/side_bar.cc
rename to modules/gui/src/panels/side_bar.cc
index 425a8bb37a3b19fbf09527c6c11cf02a676e2c46..460e8a5641b5bf1658417b00cb17b65dee36d243 100644
--- a/modules/gui/src/panel_bar/side_bar.cc
+++ b/modules/gui/src/panels/side_bar.cc
@@ -17,13 +17,13 @@
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
 
-#include <QAction>
 
 #include "side_bar.hh"
 
 #include "splitter_panel_bar.hh"
 #include "tabbed_panel_bar.hh"
 
+#include <QAction>
 namespace ost { namespace gui {
 
 SideBar::SideBar(QWidget* parent):
diff --git a/modules/gui/src/panel_bar/side_bar.hh b/modules/gui/src/panels/side_bar.hh
similarity index 100%
rename from modules/gui/src/panel_bar/side_bar.hh
rename to modules/gui/src/panels/side_bar.hh
diff --git a/modules/gui/src/panel_bar/splitter_panel_bar.cc b/modules/gui/src/panels/splitter_panel_bar.cc
similarity index 95%
rename from modules/gui/src/panel_bar/splitter_panel_bar.cc
rename to modules/gui/src/panels/splitter_panel_bar.cc
index 7ba19f4fd00b708ddb82e78775d5520e6013c5e5..bfd59c5948d2693717f64cf317ce3daa250ceda4 100644
--- a/modules/gui/src/panel_bar/splitter_panel_bar.cc
+++ b/modules/gui/src/panels/splitter_panel_bar.cc
@@ -17,17 +17,14 @@
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
 
-#include <QSettings>
-
-#include <QPalette>
 #include <ost/gui/widget_registry.hh>
 
 #include "panel_widget_container.hh"
 #include "splitter_panel_bar.hh"
-#include <iostream>
 
-#include <iostream>
+#include <QSettings>
 
+#include <QPalette>
 namespace ost { namespace gui {
 
 SplitterPanelBar::SplitterPanelBar(PanelBar* parent,Qt::Orientation orientation):
@@ -83,7 +80,7 @@ void SplitterPanelBar::WidgetMoved(Widget* widget, int index){
     wh->setVisible(false);
     wh->setParent(NULL);
   }
-  PanelBarWidgetHolder* side_bar_widget_holder = new PanelBarWidgetHolder(widget,splitter_->orientation(),this->GetPanelBar());
+  PanelBarWidgetHolder* side_bar_widget_holder=new PanelBarWidgetHolder(widget,splitter_->orientation(),this->GetPanelBar());
   widget_holders_.insert(index,side_bar_widget_holder);
   splitter_->insertWidget(index, widget_holders_.at(index));
   if(pos>=0 && pos<sizes_.size() && index>=0 && index<sizes_.size()){
@@ -95,7 +92,8 @@ void SplitterPanelBar::WidgetMoved(Widget* widget, int index){
 }
 
 
-QString SplitterPanelBar::GetName(){
+QString SplitterPanelBar::GetName()
+{
   return "Splitter Mode";
 }
 
diff --git a/modules/gui/src/panel_bar/splitter_panel_bar.hh b/modules/gui/src/panels/splitter_panel_bar.hh
similarity index 97%
rename from modules/gui/src/panel_bar/splitter_panel_bar.hh
rename to modules/gui/src/panels/splitter_panel_bar.hh
index a08a1bf1935490433a523bb0aa5feb29194b2f26..b283c9cbfacb429ea83fcbe98f2d5d9bc9e4da22 100644
--- a/modules/gui/src/panel_bar/splitter_panel_bar.hh
+++ b/modules/gui/src/panels/splitter_panel_bar.hh
@@ -19,19 +19,19 @@
 #ifndef OST_GUI_SPLITTER_PANEL_BAR
 #define OST_GUI_SPLITTER_PANEL_BAR
 
-#include <QHBoxLayout>
-#include <QWidget>
-#include <QString>
-#include <QAction>
 
 #include <ost/gui/module_config.hh>
-#include <ost/gui/panel_bar/panel_bar_widget_holder.hh>
 #include <ost/gui/widget_pool.hh>
 #include <ost/gui/widget.hh>
 #include <ost/gui/thin_splitter.hh>
 
 #include "panel_widget_container.hh"
+#include "panel_bar_widget_holder.hh"
 
+#include <QHBoxLayout>
+#include <QWidget>
+#include <QString>
+#include <QAction>
 namespace ost { namespace gui {
 
 /// \brief bottom Bar
diff --git a/modules/gui/src/panels/tabbed_panel_bar.cc b/modules/gui/src/panels/tabbed_panel_bar.cc
new file mode 100644
index 0000000000000000000000000000000000000000..36ec6e2bc5f75db9eec0968ffc8a1c81cb968756
--- /dev/null
+++ b/modules/gui/src/panels/tabbed_panel_bar.cc
@@ -0,0 +1,170 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+//------------------------------------------------------------------------------
+
+
+#include <ost/gui/gosty_app.hh>
+#include <ost/gui/perspective.hh>
+#include <ost/gui/widget_registry.hh>
+
+#include "tabbed_panel_bar.hh"
+
+#include <QApplication>
+#include <QSettings>
+#include <QDir>
+namespace ost { namespace gui {
+
+TabbedPanelBar::TabbedPanelBar(PanelBar* parent):
+  PanelWidgetContainer(parent)
+{
+  layout_ = new QHBoxLayout(this);
+  layout_->setMargin(0);
+  layout_->setSpacing(0);
+  tab_widget_ = new TabbedDragWidget(this);
+  #if QT_VERSION>=0x40503
+    tab_widget_->setDocumentMode(true);
+  #endif
+  layout_->addWidget(tab_widget_);
+
+  toolbar_ = new QToolBar(this);
+  toolbar_->setFloatable(false);
+  toolbar_->setContentsMargins(0, 0, 0, 0);
+  toolbar_->setToolButtonStyle(Qt::ToolButtonIconOnly);
+  toolbar_->setIconSize(QSize(16,16));
+  tab_widget_->setCornerWidget(toolbar_, Qt::TopRightCorner);
+  connect(tab_widget_,SIGNAL(currentChanged(int)),this,SLOT(CurrentChanged(int)));
+  this->setAcceptDrops(true);
+}
+
+bool TabbedPanelBar::Save(const QString& prefix)
+{
+  return true;
+}
+
+bool TabbedPanelBar::Restore(const QString& prefix)
+{
+  return true;
+}
+
+void TabbedPanelBar::WidgetMoved(Widget* widget, int index){
+  QString class_name = widget->GetUniqueID();
+  if(tab_widget_->indexOf(widget)>=0){
+    tab_widget_->removeTab(tab_widget_->indexOf(widget));
+  }
+  tab_widget_->insertTab(index,widget,WidgetRegistry::Instance()->GetFullName(class_name));
+}
+
+void TabbedPanelBar::ShowWidget(Widget* widget, int pos, bool show){
+  if(tab_widget_->indexOf(widget)>=0){
+    if(!show){
+      tab_widget_->removeTab(tab_widget_->indexOf(widget));
+    }
+  }
+  else{
+    if(show){
+      WidgetMoved(widget,pos);
+    }
+  }
+}
+
+QString TabbedPanelBar::GetName(){
+  return "Tabbed Mode";
+}
+
+void TabbedPanelBar::CurrentChanged(int index){
+  if(Widget* widget = qobject_cast<Widget*>(tab_widget_->currentWidget())){
+    ActionList actions = widget->GetActions();
+    toolbar_->clear();
+    if(!actions.isEmpty()){
+      for(int i = 0;i<actions.size();i++){
+        toolbar_->addAction(actions[i]);
+      }
+    }
+  }
+}
+
+void TabbedPanelBar::dragEnterEvent(QDragEnterEvent *event)
+{
+  if (event->mimeData()->hasFormat("OpenStructure/Widget")){
+    PanelManager* panels = GostyApp::Instance()->GetPerspective()->GetPanels();
+    panels->StartDrag();
+    event->acceptProposedAction();
+  }
+}
+
+void TabbedPanelBar::dropEvent(QDropEvent *event)
+{
+  const QMimeData* mime_data = event->mimeData();
+  QVariant variant =  mime_data->property("OpenStructure/Widget");
+  Widget* widget = variant.value<Widget*>();
+  Widget* current_widget = qobject_cast<Widget*>(tab_widget_->currentWidget());
+  if(widget && current_widget && widget != current_widget){
+    GostyApp::Instance()->GetPerspective()->GetPanels()->MoveNextTo(current_widget,widget);
+  }
+  event->acceptProposedAction();
+}
+
+TabbedPanelBar::~TabbedPanelBar(){
+  toolbar_->clear();
+}
+
+//TabbedDragWidget
+TabbedDragWidget::TabbedDragWidget(QWidget* parent):
+  QTabWidget(parent) {
+  setTabBar(new DragTabBar(this));
+}
+
+//DragTabBar
+DragTabBar::DragTabBar(QTabWidget* parent):
+  QTabBar(parent),tab_widget_(parent) {}
+
+void DragTabBar::mousePressEvent(QMouseEvent *event)
+{
+  if (event->button() == Qt::LeftButton){
+    drag_start_pos_ = event->pos();
+  }
+  QTabBar::mousePressEvent(event);
+}
+
+void DragTabBar::mouseMoveEvent(QMouseEvent *event)
+{
+  if (!(event->buttons() & Qt::LeftButton)) return;
+
+  if ((event->pos() - drag_start_pos_).manhattanLength()
+        < QApplication::startDragDistance()) return;
+
+  Widget* widget = qobject_cast<Widget*>(tab_widget_->currentWidget());
+  if(!widget)return;
+
+  QDrag *drag = new QDrag(this);
+  QMimeData *mime_data = new QMimeData;
+  QVariant self;
+  self.setValue(widget);
+  mime_data->setData("OpenStructure/Widget",QByteArray());
+  mime_data->setProperty("OpenStructure/Widget",self);
+
+  drag->setMimeData(mime_data);
+  drag->exec();
+  PanelManager* panels = GostyApp::Instance()->GetPerspective()->GetPanels();
+  panels->EndDrag();
+}
+
+
+
+}}
+
diff --git a/modules/gui/src/panel_bar/tabbed_panel_bar.hh b/modules/gui/src/panels/tabbed_panel_bar.hh
similarity index 71%
rename from modules/gui/src/panel_bar/tabbed_panel_bar.hh
rename to modules/gui/src/panels/tabbed_panel_bar.hh
index 0579c4b6e937d87e990504b53eab7e165270256b..78fb2ab40db4d3920beed0ac4dc03f912451a369 100644
--- a/modules/gui/src/panel_bar/tabbed_panel_bar.hh
+++ b/modules/gui/src/panels/tabbed_panel_bar.hh
@@ -19,11 +19,6 @@
 #ifndef OST_GUI_TABBED_PANEL_BAR
 #define OST_GUI_TABBED_PANEL_BAR
 
-#include <QHBoxLayout>
-#include <QWidget>
-#include <QString>
-#include <QAction>
-#include <QTabWidget>
 
 #include <ost/gui/module_config.hh>
 #include <ost/gui/widget_pool.hh>
@@ -32,9 +27,39 @@
 #include "panel_widget_container.hh"
 #include "button_box.hh"
 
+#include <QHBoxLayout>
+#include <QWidget>
+#include <QString>
+#include <QAction>
+#include <QTabBar>
+#include <QTabWidget>
+#include <QToolBar>
 namespace ost { namespace gui {
 
-/// \brief tabbed bottom Bar
+/// \brief tabbed drag widget
+class DLLEXPORT_OST_GUI DragTabBar : public QTabBar{
+  Q_OBJECT
+public:
+  DragTabBar(QTabWidget* parent);
+
+protected:
+  void mousePressEvent(QMouseEvent *event);
+  void mouseMoveEvent(QMouseEvent *event);
+
+private:
+  QTabWidget* tab_widget_;
+  QPoint drag_start_pos_;
+
+};
+
+/// \brief tabbed drag widget
+class DLLEXPORT_OST_GUI TabbedDragWidget : public QTabWidget{
+  Q_OBJECT
+public:
+  TabbedDragWidget(QWidget* parent);
+};
+
+/// \brief tabbed bar
 class DLLEXPORT_OST_GUI TabbedPanelBar : public PanelWidgetContainer {
   Q_OBJECT
 public:
@@ -46,10 +71,20 @@ public:
 
   void WidgetMoved(Widget* widget, int position);
   QString GetName();
+
+protected:
+  void dragEnterEvent(QDragEnterEvent *event);
+  void dropEvent(QDropEvent *event);
+
 private:
   virtual void ShowWidget(Widget* widget, int pos, bool show);
   QHBoxLayout* layout_;
-  QTabWidget* tabWidget_;
+  QTabWidget* tab_widget_;
+  QToolBar* toolbar_;
+
+private slots:
+  void CurrentChanged(int index);
+
 };
 
 }}
diff --git a/modules/gui/src/perspective.cc b/modules/gui/src/perspective.cc
index 6b59bded294f6a68e70b4f2ed2a93bba01ce8da1..6af76c48090d1bc09529b97906290c34d7fd0272 100644
--- a/modules/gui/src/perspective.cc
+++ b/modules/gui/src/perspective.cc
@@ -16,7 +16,17 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
+
+#include <ost/platform.hh>
+
+#include <ost/gui/widget_registry.hh>
+#include <ost/gui/perspective.hh>
+#include <ost/gui/file_browser.hh>
+#include <ost/gui/main_area.hh>
+#include <ost/gui/messages/message_box_widget.hh>
+
 #include <QTextEdit>
+#include <QSizeGrip>
 #include <QMainWindow>
 #include <QSettings>
 #include <QDebug>
@@ -26,14 +36,7 @@
 #include <QSizeGrip>
 #include <QKeySequence>
 #include <QStatusBar>
-
-#include <ost/platform.hh>
-
-#include <ost/gui/widget_registry.hh>
-#include <ost/gui/perspective.hh>
-#include <ost/gui/file_browser.hh>
-#include <ost/gui/main_area.hh>
-
+#include <QPushButton>
 /*
   Author: Marco Biasini
  */
@@ -53,8 +56,9 @@ Perspective::Perspective(QMainWindow* parent):
   parent->setCentralWidget(central_);
 
   status_bar_ = new QStatusBar(main_area_);
+  status_bar_->setSizeGripEnabled (false);
 
-  panels_ = new Panels(main_area_);
+  panels_ = new PanelManager(main_area_);
   l->addWidget(panels_,1);
   this->SetupQuickAccessBar();
   l->addWidget(quick_access_bar_, 0);
@@ -69,27 +73,35 @@ void Perspective::SetupQuickAccessBar()
   QHBoxLayout* l2=new QHBoxLayout(quick_access_bar_);
   l2->setMargin(0);
   l2->setSpacing(0);
-
-  QToolButton* toggle_side_bar=new QToolButton(quick_access_bar_);
-  toggle_side_bar->setText("A");
+  l2->setContentsMargins(0, 0, 0, 0);
+  QPushButton* toggle_side_bar=new QPushButton(quick_access_bar_);
+  toggle_side_bar->setAttribute(Qt::WA_MacSmallSize);
+  toggle_side_bar->setFlat(true);
   toggle_side_bar->setToolTip("Glory A-Button");
-  toggle_side_bar->setIconSize(QSize(20,20));
-  toggle_side_bar->setIcon(QIcon(icon_path.absolutePath()+QDir::separator()+QString("show_sidebar_icon.png")));
+  toggle_side_bar->setIcon(QIcon(icon_path.absolutePath()+QDir::separator()+
+                                 QString("show_sidebar_icon.png")));
+  toggle_side_bar->setIconSize(QSize(10,10));  
   toggle_side_bar->setCheckable(true);
-  toggle_side_bar->setChecked(true);
+  toggle_side_bar->setFixedSize(QSize(20, 20));  
+  toggle_side_bar->setChecked(false);
   connect(toggle_side_bar, SIGNAL(clicked()), panels_,
           SLOT(ToggleHide()));
   l2->addWidget(toggle_side_bar, 0);
 
-  QToolButton* add_side_bar_widget=new QToolButton(quick_access_bar_);          
-  add_side_bar_widget->setText("+");
+  QPushButton* add_side_bar_widget=new QPushButton(quick_access_bar_);
+  add_side_bar_widget->setAttribute(Qt::WA_MacSmallSize);
+  add_side_bar_widget->setFlat(true);  
+  add_side_bar_widget->setFixedSize(QSize(20, 20));
   add_side_bar_widget->setToolTip("Add widget to left sidebar");
-  add_side_bar_widget->setIconSize(QSize(20,20));
-  add_side_bar_widget->setIcon(QIcon(icon_path.absolutePath()+QDir::separator()+QString("add_icon.png")));
+  add_side_bar_widget->setIcon(QIcon(icon_path.absolutePath()+QDir::separator()+
+                                     QString("add_icon.png")));
+  add_side_bar_widget->setIconSize(QSize(10,10));  
   connect(add_side_bar_widget, SIGNAL(clicked()), this, 
           SLOT(AddSideBarWidget()));          
   l2->addWidget(add_side_bar_widget, 0);
   l2->addWidget(status_bar_);
+  l2->addWidget(new MessageBoxWidget(quick_access_bar_));
+  l2->addWidget(new QSizeGrip(quick_access_bar_));
 }
 
 void Perspective::StatusMessage(const String& m)
@@ -115,7 +127,7 @@ QMenu* Perspective::GetMenu(const QString& name)
   return menu;
 }
 
-Panels* Perspective::GetPanels()
+PanelManager* Perspective::GetPanels()
 {
   return panels_;
 }
diff --git a/modules/gui/src/perspective.hh b/modules/gui/src/perspective.hh
index 533b3d0f11110c384c2a03792449d51fd5f8678b..b52a7c8f0414fc5b759e82300e8fe5c30228a031 100644
--- a/modules/gui/src/perspective.hh
+++ b/modules/gui/src/perspective.hh
@@ -19,21 +19,21 @@
 #ifndef OST_GUI_PERSPECTIVE_HH
 #define OST_GUI_PERSPECTIVE_HH
 
-#include <QObject>
-#include <QMenuBar>
-#include <QMap>
-#include <QString>
-#include <QMenu>
-#include <QStatusBar>
 
 class QMainWindow;
 class QTextEdit;
 
-#include <ost/gui/panel_bar/panels.hh>
-#include <ost/gui/panel_bar/button_bar.hh>
-#include <ost/gui/panel_bar/panel_bar.hh>
+#include <ost/gui/panels/panel_manager.hh>
+#include <ost/gui/panels/button_bar.hh>
+#include <ost/gui/panels/panel_bar.hh>
 #include <ost/gui/module_config.hh>
 
+#include <QObject>
+#include <QMenuBar>
+#include <QMap>
+#include <QString>
+#include <QMenu>
+#include <QStatusBar>
 /*
   Author: Marco Biasini, Stefan Scheuber
  */
@@ -60,9 +60,9 @@ public:
   /// \return The menu with the given name. If it does not exist, it will be created and returned.
   QMenu* GetMenu(const QString& name);
   
-  /// \brief The Panels class organizes all the widgets in the side panels.
-  /// \return The Panels instance which is used in this perspective.
-  Panels* GetPanels();
+  /// \brief The PanelManager class organizes all the widgets in the side panels.
+  /// \return The PanelManager instance which is used in this perspective.
+  PanelManager* GetPanels();
 
   /// \brief Returns the MainArea
   /// \return The main area which is used in this perspective.
@@ -94,7 +94,7 @@ private:
   QMenuBar*        menu_bar_;
   QMap<QString,QMenu*> menus_;
   MainArea*       main_area_;
-  Panels*         panels_;
+  PanelManager*   panels_;
   QWidget*        quick_access_bar_;
   QStatusBar*     status_bar_;
 };
diff --git a/modules/gui/src/plot_viewer/plot_axis_base.cc b/modules/gui/src/plot_viewer/plot_axis_base.cc
deleted file mode 100644
index 95a75cdb5bba3d34a258e3d7f8ccc804b77c96f1..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_axis_base.cc
+++ /dev/null
@@ -1,90 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-/*
-  Author: Andreas Schenk
-*/
-
-#include <QWheelEvent>
-#include <QMouseEvent>
-#include "plot_axis_base.hh"
-
-namespace ost{namespace gui{
-
-PlotAxisBase::PlotAxisBase(QWidget * parent):
-  QWidget(parent),
-  ticker_(),
-  global_mouse_pos_()
-{
-}
-
-PlotAxisBase::~PlotAxisBase()
-{
-}
-
-void PlotAxisBase::wheelEvent ( QWheelEvent * e )
-{
-  emit zoom(e->delta(),e->pos());
-}
-void PlotAxisBase::SetMinimum(Real min)
-{
-  ticker_.SetMinimum(min);
-  update();
-}
-
-void PlotAxisBase::SetMaximum(Real max)
-{
-  ticker_.SetMaximum(max);
-  update();
-}
-
-void PlotAxisBase::SetSeparation(int separation)
-{
-  ticker_.SetSeparation(separation);
-  update();
-}
-int PlotAxisBase::GetSeparation()
-{
-  return ticker_.GetSeparation();
-
-}
-
-void PlotAxisBase::SetStart(int start)
-{
-  ticker_.SetStart(start);
-}
-
-void PlotAxisBase::SetEnd(int end)
-{
-  ticker_.SetEnd(end);
-}
-
-TickList PlotAxisBase::GetTicks()
-{
-  return ticker_.GetTicks();
-}
-
-void PlotAxisBase::mousePressEvent( QMouseEvent * event )
-{
-  if(event->button()== Qt::LeftButton){
-    global_mouse_pos_=event->globalPos();
-  }
-}
-
-
-}}//ns
diff --git a/modules/gui/src/plot_viewer/plot_axis_horizontal.cc b/modules/gui/src/plot_viewer/plot_axis_horizontal.cc
deleted file mode 100644
index 05b13f5519734df82c2681e51134f6921353cdf9..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_axis_horizontal.cc
+++ /dev/null
@@ -1,63 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-/*
-  Author: Andreas Schenk
-*/
-#include <QPainter>
-#include <QMouseEvent>
-
-#include "plot_axis_horizontal.hh"
-
-namespace ost{namespace gui{
-
-PlotAxisHorizontal::PlotAxisHorizontal(QWidget * parent):
-  PlotAxisBase(parent)
-{
-  SetStart(AXISWIDTH);
-  SetSeparation(40);
-}
-
-PlotAxisHorizontal::~PlotAxisHorizontal()
-{
-}
-
-void PlotAxisHorizontal::paintEvent(QPaintEvent* paint_event)
-{
-  SetEnd(width());
-  TickList ticks=GetTicks();
-  QPainter painter(this);
-  painter.setRenderHint(QPainter::Antialiasing);
-  for(int i=0;i<static_cast<int>(ticks.size());++i){
-    if(ticks[i].first<static_cast<int>(AXISWIDTH)){
-      continue;
-    }
-    painter.drawLine(ticks[i].first,0,ticks[i].first,9);
-    painter.drawText(QRect(ticks[i].first-GetSeparation()/2,12,GetSeparation(),20),Qt::AlignCenter,QString("%1").arg(ticks[i].second));
-  }
-}
-
-void PlotAxisHorizontal::mouseMoveEvent( QMouseEvent * event )
-{
-  if(event->buttons() & Qt::LeftButton){
-    emit translate(static_cast<Real>(event->globalPos().x()-global_mouse_pos_.x()),0.0);
-    global_mouse_pos_=event->globalPos();
-  }
-}
-
-}}//ns
diff --git a/modules/gui/src/plot_viewer/plot_axis_vertical.cc b/modules/gui/src/plot_viewer/plot_axis_vertical.cc
deleted file mode 100644
index f6bf01a2c5f772da187f027523f83cb2a6be1418..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_axis_vertical.cc
+++ /dev/null
@@ -1,65 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-/*
-  Author: Andreas Schenk
-*/
-
-#include <QMouseEvent>
-#include <QPainter>
-
-#include "plot_axis_vertical.hh"
-
-namespace ost{namespace gui{
-
-PlotAxisVertical::PlotAxisVertical(QWidget * parent):
-  PlotAxisBase(parent)
-{
-  SetStart(AXISWIDTH);
-  SetSeparation(40);
-}
-
-PlotAxisVertical::~PlotAxisVertical()
-{
-}
-
-void PlotAxisVertical::paintEvent(QPaintEvent* paint_event)
-{
-  SetEnd(height());
-  TickList ticks=GetTicks();
-  QPainter painter(this);
-  painter.setRenderHint(QPainter::Antialiasing);
-  for(int i=0;i<static_cast<int>(ticks.size());++i){
-    Real ypos=height()-ticks[i].first;
-    if(ticks[i].first<static_cast<int>(AXISWIDTH)){
-      continue;
-    }
-    painter.drawLine(AXISWIDTH-10,ypos,AXISWIDTH-1,ypos);
-    painter.drawText(QRect(2,ypos-GetSeparation()/2,AXISWIDTH-14,GetSeparation()),Qt::AlignVCenter,QString("%1").arg(ticks[i].second));
-  }
-}
-
-void PlotAxisVertical::mouseMoveEvent( QMouseEvent * event )
-{
-  if(event->buttons() & Qt::LeftButton){
-    emit translate(0.0,static_cast<Real>(event->globalPos().y()-global_mouse_pos_.y()));
-    global_mouse_pos_=event->globalPos();
-  }
-}
-
-}}//ns
diff --git a/modules/gui/src/plot_viewer/plot_axis_vertical.hh b/modules/gui/src/plot_viewer/plot_axis_vertical.hh
deleted file mode 100644
index e6412b7d0244768cc23395b31179d1c7eb4b43fd..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_axis_vertical.hh
+++ /dev/null
@@ -1,42 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef PLOT_AXIS_VERTICAL_HH_
-#define PLOT_AXIS_VERTICAL_HH_
-
-/*
-  Author: Andreas Schenk
-*/
-
-#include "plot_axis_base.hh"
-
-namespace ost{namespace gui{
-
-class DLLEXPORT_OST_GUI PlotAxisVertical: public PlotAxisBase
-{
-public:
-  PlotAxisVertical(QWidget * parent = 0);
-  virtual ~PlotAxisVertical();
-protected:
-  virtual void paintEvent(QPaintEvent* paint_event);
-  virtual void mouseMoveEvent ( QMouseEvent * event );
-};
-
-}}//ns
-
-#endif /*PLOT_AXIS_VERTICAL_HH_*/
diff --git a/modules/gui/src/plot_viewer/plot_data.cc b/modules/gui/src/plot_viewer/plot_data.cc
deleted file mode 100644
index 2955482a60b310b16d681dc7b46a25852777a2f8..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_data.cc
+++ /dev/null
@@ -1,149 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-/*
-  Author: Andreas Schenk
-*/
-
-#include <limits>
-#include <sstream>
-#include "plot_data.hh"
-
-namespace ost{namespace gui{
-
-PlotData::PlotData():
-  PlotDataBase(),
-  minx_(std::numeric_limits<Real>().max()),
-  maxx_(-std::numeric_limits<Real>().max()),
-  miny_(std::numeric_limits<Real>().max()),
-  maxy_(-std::numeric_limits<Real>().max()),
-  pde_vector_()
-{
-}
-
-PlotData::~PlotData()
-{
-}
-
-void PlotData::AddXYQ(Real x, Real y, Real w, const QString& n)
-{
-  AddXEYEQ(x, 0.0, y, 0.0,w, n);
-}
-void PlotData::AddXYE(Real x, Real y, Real e, const QString& n)
-{
-  AddXEYEQ(x, 0.0, y, e,1.0, n);
-}
-void PlotData::AddXYEQ(Real x, Real y, Real e,Real q, const QString& n)
-{
-  AddXEYEQ(x, 0.0, y, e,q, n);
-}
-void PlotData::AddXEYE(Real x, Real ex, Real y, Real ey, const QString& n)
-{
-  AddXEYEQ(x, ex, y, ey ,1.0, n);
-}
-void PlotData::AddXY(Real x, Real y, const QString& n)
-{
-  AddXEYEQ(x, 0, y, 0,1, n);
-}
-
-void PlotData::AddYQ(Real y, Real w, const QString& n)
-{
-  AddYEQ(y, 0.0,w, n);
-}
-void PlotData::AddYE(Real y, Real e, const QString& n)
-{
-  AddYEQ(y, e,1.0, n);
-}
-void PlotData::AddY(Real y, const QString& n)
-{
-  AddYEQ(y, 0,1, n);
-}
-
-void PlotData::AddYEQ(Real y, Real ey, Real w, const QString& n)
-{
-  static int x=0;
-  AddXEYEQ(x,0,y,ey,w,n);
-  ++x;
-}
-
-void PlotData::AddXEYEQ(Real x, Real ex, Real y, Real ey, Real q, const QString& n)
-{
-  pde_vector_.push_back(PlotDataEntry(x, ex, y, ey,q, n));
-  minx_=std::min(minx_, x);
-  maxx_=std::max(maxx_, x);
-  miny_=std::min(miny_, y);
-  maxy_=std::max(maxy_, y);
-}
-
-void PlotData::Clear()
-{
-  pde_vector_.clear();
-  minx_=std::numeric_limits<Real>().max();
-  maxx_=-std::numeric_limits<Real>().max();
-  miny_=std::numeric_limits<Real>().max();
-  maxy_=-std::numeric_limits<Real>().max();
-}
-Real PlotData::GetMinimumX()
-{
-  if(minx_>maxx_){
-    return 0.0;
-  }else{
-    return minx_;
-  }
-}
-Real PlotData::GetMaximumX()
-{
-  if(minx_>maxx_){
-    return 1.0;
-  }else if(minx_==maxx_){
-    return minx_+1.0;
-  }else{
-    return maxx_;
-  }
-}
-Real PlotData::GetMinimumY()
-{
-  if(miny_>maxy_){
-    return 0.0;
-  }else{
-    return miny_;
-  }
-}
-Real PlotData::GetMaximumY()
-{
-  if(miny_>maxy_){
-    return 1.0;
-  }else if(miny_==maxy_){
-    return miny_+1.0;
-  }else{
-    return maxy_;
-  }
-}
-
-
-PlotDataEntry PlotData::GetPlotDataEntry(unsigned int idx)
-{
-  return pde_vector_[idx];
-}
-
-unsigned int PlotData::GetCount()
-{
- return pde_vector_.size();
-}
-
-}}//ns
diff --git a/modules/gui/src/plot_viewer/plot_data.hh b/modules/gui/src/plot_viewer/plot_data.hh
deleted file mode 100644
index 8790d9b063a8066674004710d4d4c90683e829de..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_data.hh
+++ /dev/null
@@ -1,75 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-
-
-#ifndef PLOT_DATA_HH_
-#define PLOT_DATA_HH_
-
-
-/*
-  Author: Andreas Schenk
-*/
-
-#include <vector>
-#include <boost/shared_ptr.hpp>
-#include <ost/gui/module_config.hh>
-#include "plot_data_base.hh"
-#include "plot_data_entry.hh"
-
-namespace ost{namespace gui{
-
-class DLLEXPORT_OST_GUI PlotData: public PlotDataBase
-{
-public:
-  PlotData();
-  virtual ~PlotData();
-
-  virtual Real GetMinimumX();
-  virtual Real GetMaximumX();
-  virtual Real GetMinimumY();
-  virtual Real GetMaximumY();
-  
-  void AddXY(Real x, Real y, const QString& info = "");
-  void AddXYQ(Real x, Real y, Real Q, const QString& info = "");
-  void AddXYEQ(Real x, Real y,Real e, Real q, const QString& info = "");
-  void AddXYE(Real x, Real y, Real e, const QString& info = "");
-  void AddXEYE(Real x, Real ex, Real y, Real ey, const QString& info = "");
-  void AddXEYEQ(Real x, Real ex, Real y, Real ey,Real Q, const QString& info = "");
-  void AddY(Real y,  const QString& info = "");
-  void AddYQ(Real y, Real Q,  const QString& info = "");
-  void AddYE(Real y, Real e,  const QString& info = "");
-  void AddYEQ(Real y, Real ey,Real Q,  const QString& info = "");
-  void Clear();
-
-  PlotDataEntry GetPlotDataEntry(unsigned int idx);
-  unsigned int GetCount();
-  
-protected:
-  Real minx_;
-  Real maxx_;
-  Real miny_;
-  Real maxy_;
-  std::vector<PlotDataEntry> pde_vector_;
-};
-
-typedef boost::shared_ptr<PlotData> PlotDataPtr;
-
-}}//ns
-
-#endif /*PLOT_DATA_HH_*/
diff --git a/modules/gui/src/plot_viewer/plot_data_base.cc b/modules/gui/src/plot_viewer/plot_data_base.cc
deleted file mode 100644
index 1c1474087b122d32e98be05cb55ad2c48bd15c07..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_data_base.cc
+++ /dev/null
@@ -1,35 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-/*
-  Author: Andreas Schenk
-*/
-
-#include "plot_data_base.hh"
-
-namespace ost{namespace gui{
-
-PlotDataBase::PlotDataBase()
-{
-}
-
-PlotDataBase::~PlotDataBase()
-{
-}
-
-}}//ns
diff --git a/modules/gui/src/plot_viewer/plot_data_entry.hh b/modules/gui/src/plot_viewer/plot_data_entry.hh
deleted file mode 100644
index f6d443eaed51d07ebf22ed4671508273bee20d09..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_data_entry.hh
+++ /dev/null
@@ -1,49 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef PLOT_DATA_POINT_HH_
-#define PLOT_DATA_POINT_HH_
-
-
-/*
-  Author: Andreas Schenk
-*/
-
-#include <QString>
-#include <ost/gui/module_config.hh>
-
-namespace ost{namespace gui{
-
-class DLLEXPORT_OST_GUI PlotDataEntry {
-public:
-    PlotDataEntry(Real x_=0, Real ex_=0, Real y_=0, Real ey_=0, Real q_=1,
-                  const QString& info_ = ""):
-      x(x_), y(y_), ex(ex_), ey(ey_), q(q_), info(info_) {}
-    Real x;
-    Real y;
-    Real ex;
-    Real ey;
-    Real q;
-    QString info;
-};
-
-
-
-}}//ns
-
-#endif /*PLOT_DATA_POINT_HH_*/
diff --git a/modules/gui/src/plot_viewer/plot_data_graphics_item.cc b/modules/gui/src/plot_viewer/plot_data_graphics_item.cc
deleted file mode 100644
index 68f287076de406cc4256840b4eddbbf5858e4962..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_data_graphics_item.cc
+++ /dev/null
@@ -1,141 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-/*
-  Author: Andreas Schenk
-*/
-
-#include <QtAlgorithms>
-
-#include <ost/dyn_cast.hh>
-#include <ost/gui/python_shell/python_interpreter.hh>
-#include "plot_data_info.hh"
-#include "plot_graphics_ellipse_item.hh"
-#include "plot_graphics_rectangle_item.hh"
-#include "plot_graphics_cross_item.hh"
-#include "plot_graphics_diagonal_cross_item.hh"
-#include "plot_data_graphics_item.hh"
-
-
-namespace ost{namespace gui{
-
-PlotDataGraphicsItem::PlotDataGraphicsItem(const PlotDataInfoPtr& info,const PlotDataPtr& dataptr, QGraphicsItem * parent):
-  PlotDataGraphicsItemBase(info,parent),
-  dataptr_(dataptr)
-{
-}
-
-PlotDataGraphicsItem::~PlotDataGraphicsItem()
-{
-}
-
-
-void PlotDataGraphicsItem::Redraw()
-{
-  unsigned int zvalue=0;
-  qDeleteAll(childItems());
-  if(dataptr_->GetCount()==0){
-    return;
-  }
-  PlotDataInfoPtr infoptr=dyn_cast<PlotDataInfo>(infoptr_);
-  switch(infoptr->errormode){
-  case PlotDataInfo::NONE:
-    break;
-  case PlotDataInfo::LINE:
-    break;
-  case PlotDataInfo::BOX:
-    break;
-  case PlotDataInfo::VECTOR:
-    break;
-  default:
-    break;
-  }
-  switch(infoptr->mode){
-  case PlotDataInfo::LINES:
-  case PlotDataInfo::POINTSANDLINES:
-    //draw lines
-  {
-    PlotDataEntry old=dataptr_->GetPlotDataEntry(0);
-    for (unsigned int i=1;i<dataptr_->GetCount();++i) {
-      PlotDataEntry pde=dataptr_->GetPlotDataEntry(i);
-      QGraphicsLineItem* line=new QGraphicsLineItem(old.x,old.y,pde.x,pde.y,this);
-      line->setZValue(++zvalue);
-      line->setPen(infoptr->pen);
-      old=pde;
-    }
-    break;
-  }
-  case PlotDataInfo::AREA:
-  case PlotDataInfo::POINTSANDAREA:
-    //draw area
-    break;
-  default:
-    break;
-  }
-  switch(infoptr->mode){
-  case PlotDataInfo::POINTS:
-  case PlotDataInfo::POINTSANDLINES:
-  case PlotDataInfo::POINTSANDAREA:
-    //draw points
-    switch(infoptr->shape){
-    case PlotDataInfo::CIRCLE:
-      for (unsigned int i=0;i<dataptr_->GetCount();++i) {
-        PlotDataEntry pde=dataptr_->GetPlotDataEntry(i);
-        PlotGraphicsEllipseItem* ellipse=new PlotGraphicsEllipseItem(pde,infoptr,this);
-        ellipse->setZValue(++zvalue);
-      }
-      break;
-    case PlotDataInfo::RECTANGLE:
-      for (unsigned int i=0;i<dataptr_->GetCount();++i) {
-        PlotDataEntry pde=dataptr_->GetPlotDataEntry(i);
-        PlotGraphicsRectangleItem* rect=new PlotGraphicsRectangleItem(pde,infoptr,this);
-        rect->setZValue(++zvalue);
-      }
-      break;
-    case PlotDataInfo::CROSS:
-      for (unsigned int i=0;i<dataptr_->GetCount();++i) {
-        PlotDataEntry pde=dataptr_->GetPlotDataEntry(i);
-        PlotGraphicsCrossItem* cross=new PlotGraphicsCrossItem(pde,infoptr,this);
-        cross->setZValue(++zvalue);
-      }
-      break;
-    case PlotDataInfo::DIAGONALCROSS:
-      for (unsigned int i=0;i<dataptr_->GetCount();++i) {
-        PlotDataEntry pde=dataptr_->GetPlotDataEntry(i);
-        PlotGraphicsDiagonalCrossItem* diagcross=new PlotGraphicsDiagonalCrossItem(pde,infoptr,this);
-        diagcross->setZValue(++zvalue);
-      }
-      break;
-    default:
-      break;
-    }
-    break;
-  default:
-    break;
-  }
-}
-
-void PlotDataGraphicsItem::Callback(const PlotDataEntry& pde)
-{
-  PlotDataInfoPtr infoptr=dyn_cast<PlotDataInfo>(infoptr_);
-  if(infoptr->callback!=boost::python::object()){
-    PythonInterpreter::Instance().CallFunction(infoptr->callback,boost::python::make_tuple(pde.x,pde.y,pde.ex,pde.ey,pde.q,boost::python::str(pde.info.toStdString().c_str())));
-  }
-}
-
-}}//ns
diff --git a/modules/gui/src/plot_viewer/plot_data_graphics_item.hh b/modules/gui/src/plot_viewer/plot_data_graphics_item.hh
deleted file mode 100644
index eda504efe4d547e67865b570b92fd8017968d63d..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_data_graphics_item.hh
+++ /dev/null
@@ -1,41 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef PLOT_DATA_GRAPHICS_ITEM_HH_
-#define PLOT_DATA_GRAPHICS_ITEM_HH_
-
-#include "plot_data_graphics_item_base.hh"
-#include "plot_data.hh"
-
-namespace ost{namespace gui{
-
-class PlotDataGraphicsItem: public PlotDataGraphicsItemBase
-{
-public:
-  PlotDataGraphicsItem (const PlotDataInfoPtr& info,const PlotDataPtr& dataptr, QGraphicsItem * parent = 0 );
-  virtual ~PlotDataGraphicsItem();
-  void Callback(const PlotDataEntry& pde);
-  virtual void Redraw();
-
-protected:
-  PlotDataPtr dataptr_;
-};
-
-}}//ns
-
-#endif /*PLOT_DATA_GRAPHICS_ITEM_HH_*/
diff --git a/modules/gui/src/plot_viewer/plot_data_graphics_item_base.cc b/modules/gui/src/plot_viewer/plot_data_graphics_item_base.cc
deleted file mode 100644
index dff5d4bc88ac9bba5493e9a9df956a9e748eb6fe..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_data_graphics_item_base.cc
+++ /dev/null
@@ -1,78 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-/*
-  Author: Andreas Schenk
-*/
-
-#include "plot_data_info.hh"
-#include "plot_data_graphics_item_base.hh"
-
-namespace ost{namespace gui{
-
-PlotDataGraphicsItemBase::PlotDataGraphicsItemBase(const PlotInfoBasePtr& info, QGraphicsItem * parent):
-  QObject(),
-  QGraphicsItem(parent),
-  infoptr_(info),
-  dirty_(true)
-{  
-  connect(infoptr_.get(),SIGNAL(visibilityChanged()),this,SLOT(OnVisibilityChange()));
-  connect(infoptr_.get(),SIGNAL(appearanceChanged()),this,SLOT(OnAppearanceChange()));
-}
-
-PlotDataGraphicsItemBase::~PlotDataGraphicsItemBase()
-{
-}
-
-
-
-void PlotDataGraphicsItemBase::paint( QPainter * painter, const QStyleOptionGraphicsItem * option, QWidget * widget)
-{
-  
-}
-
-QRectF PlotDataGraphicsItemBase::boundingRect() const
-{
-  return childrenBoundingRect();
-}
-
-void PlotDataGraphicsItemBase::Redraw()
-{
-  dirty_=false;
-}
-void PlotDataGraphicsItemBase::update ( const QRectF & rect)
-{
-  if(dirty_){
-    dirty_=false;
-    Redraw();
-  }
-}
-void PlotDataGraphicsItemBase::OnAppearanceChange()
-{
-  dirty_=true;
-  update();
-}
-
-void PlotDataGraphicsItemBase::OnVisibilityChange()
-{
-  setVisible(infoptr_->visible);
-  update();
-}
-
-
-}}//ns
diff --git a/modules/gui/src/plot_viewer/plot_data_graphics_item_base.hh b/modules/gui/src/plot_viewer/plot_data_graphics_item_base.hh
deleted file mode 100644
index 050bcca2f51f5be23f62077c30ff9cd7ff2d7822..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_data_graphics_item_base.hh
+++ /dev/null
@@ -1,56 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef PLOT_DATA_GRAPHICS_ITEM_BASE_HH_
-#define PLOT_DATA_GRAPHICS_ITEM_BASE_HH_
-
-/*
-  Author: Andreas Schenk
-*/
-
-#include <QGraphicsItem>
-#include <QObject>
-
-#include <ost/gui/module_config.hh>
-#include "plot_info_base.hh"
-
-namespace ost{namespace gui{
-
-class DLLEXPORT_OST_GUI PlotDataGraphicsItemBase: public QObject, public QGraphicsItem
-{
-  Q_OBJECT
-public:
-  PlotDataGraphicsItemBase(const PlotInfoBasePtr& info,QGraphicsItem * parent = 0);
-  virtual ~PlotDataGraphicsItemBase();
-  virtual void paint( QPainter * painter, const QStyleOptionGraphicsItem * option, QWidget * widget = 0 );
-  virtual QRectF boundingRect() const;
-  virtual void Redraw();
-
-public slots:
-  void OnAppearanceChange();
-  void OnVisibilityChange();
-  void update ( const QRectF & rect = QRectF() );
-  
-protected:
-  PlotInfoBasePtr infoptr_;
-  bool dirty_;
-};
-
-}}//ns
-
-#endif /*PLOT_DATA_GRAPHICS_ITEM_BASE_HH_*/
diff --git a/modules/gui/src/plot_viewer/plot_data_info.cc b/modules/gui/src/plot_viewer/plot_data_info.cc
deleted file mode 100644
index d4199295226e4f4de7418f763f88a588d8c33d5b..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_data_info.cc
+++ /dev/null
@@ -1,85 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-/*
-  Author: Andreas Schenk
-*/
-
-#include "plot_data_info.hh"
-
-namespace ost{namespace gui{
-
-PlotDataInfo::PlotDataInfo(PlotViewerPanel * viewer):
-  PlotInfoBase(viewer),
-  shape(CIRCLE),
-  symbolsize(2),
-  errormode(NONE),
-  errorscalex(1),
-  errorscaley(1),
-  use_weights(false)
-{
-  name="Data";
-}
-
-PlotDataInfo::PlotDataInfo(const PlotDataInfo& pdi):
-  PlotInfoBase(pdi),
-  shape(pdi.shape),
-  symbolsize(pdi.symbolsize),
-  errormode(pdi.errormode),
-  errorscalex(pdi.errorscalex),
-  errorscaley(pdi.errorscaley),
-  use_weights(pdi.use_weights)
-{
-}
-
-PlotDataInfo& PlotDataInfo::SetSymbol(unsigned int val)
-{
-  shape=val;
-  emit appearanceChanged();
-  return *this;
-}
-PlotDataInfo& PlotDataInfo::SetSymbolSize(unsigned int val)
-{
-  symbolsize=val;
-  emit appearanceChanged();
-  return *this;
-}
-PlotDataInfo& PlotDataInfo::SetErrorMode(unsigned int val)
-{
-  errormode=val;
-  emit appearanceChanged();
-  return *this;
-}
-
-PlotDataInfo& PlotDataInfo::SetQuality(bool val)
-{
-  use_weights=val;
-  emit appearanceChanged();
-  return *this;
-}
-
-
-
-PlotDataInfo& PlotDataInfo::SetCallback(const boost::python::object& cb)
-{
-  callback=cb;
-  return *this;
-}
-
-
-}}//ns
diff --git a/modules/gui/src/plot_viewer/plot_data_info.hh b/modules/gui/src/plot_viewer/plot_data_info.hh
deleted file mode 100644
index d1f6a44a6da4faadc6d8cbb5f6540d26a1835bb6..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_data_info.hh
+++ /dev/null
@@ -1,60 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef PLOT_DATA_INFO_HH_
-#define PLOT_DATA_INFO_HH_
-
-
-/*
-  Author: Andreas Schenk
-*/
-
-#include <vector>
-#include <boost/python.hpp>
-
-#include <ost/gui/module_config.hh>
-#include <ost/gui/plot_viewer/plot_data_info_fw.hh>
-
-#include "plot_info_base.hh"
-
-
-namespace ost{namespace gui{
-
-class DLLEXPORT_OST_GUI PlotDataInfo : public PlotInfoBase
-{
-public:
-    PlotDataInfo(PlotViewerPanel * viewer=0);
-    PlotDataInfo(const PlotDataInfo&);
-    virtual PlotDataInfo& SetSymbol(unsigned int val);
-    virtual PlotDataInfo& SetSymbolSize(unsigned int val);
-    virtual PlotDataInfo& SetErrorMode(unsigned int val);
-    virtual PlotDataInfo& SetQuality(bool val);
-    virtual PlotDataInfo& SetCallback(const boost::python::object & callback_);
-    unsigned int shape;
-    unsigned int symbolsize;
-    unsigned int errormode;
-    Real errorscalex;
-    Real errorscaley;
-    bool use_weights;
-    boost::python::object callback;
-
-};
-
-typedef std::vector<PlotDataInfoPtr> PlotDataInfoVector;
-}}//ns
-#endif /*PLOT_DATA_INFO_HH_*/
diff --git a/modules/gui/src/plot_viewer/plot_data_info_fw.hh b/modules/gui/src/plot_viewer/plot_data_info_fw.hh
deleted file mode 100644
index 27f32770d60291b5238e5c0ca0b017911a585316..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_data_info_fw.hh
+++ /dev/null
@@ -1,35 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef PLOT_DATA_INFO_FW_HH_
-#define PLOT_DATA_INFO_FW_HH_
-
-/*
-  Author: Andreas Schenk
-*/
-
-#include <boost/shared_ptr.hpp>
-
-namespace ost{namespace gui{
-
-class PlotDataInfo;
-
-typedef boost::shared_ptr<PlotDataInfo> PlotDataInfoPtr;
-
-}}//ns
-#endif /*PLOT_DATA_INFO_FW_HH_*/
diff --git a/modules/gui/src/plot_viewer/plot_function.cc b/modules/gui/src/plot_viewer/plot_function.cc
deleted file mode 100644
index 2b10657a9fc9d8869022f9a79c047b3fd3776965..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_function.cc
+++ /dev/null
@@ -1,37 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-/*
-  Author: Andreas Schenk
-*/
-
-#include "plot_function.hh"
-
-namespace ost{namespace gui{
-
-PlotFunction::PlotFunction():
-  PlotDataBase()
-{
-}
-
-PlotFunction::~PlotFunction()
-{
-}
-
-
-}}//ns
diff --git a/modules/gui/src/plot_viewer/plot_function_graphics_item.cc b/modules/gui/src/plot_viewer/plot_function_graphics_item.cc
deleted file mode 100644
index 5c017ea09a995a8c0a6b8351b28c8f57cdb9785f..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_function_graphics_item.cc
+++ /dev/null
@@ -1,77 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-/*
-  Author: Andreas Schenk
-*/
-
-#include <ost/dyn_cast.hh>
-
-#include "plot_data_info.hh"
-#include "plot_function_graphics_item.hh"
-
-namespace ost{namespace gui{
-
-PlotFunctionGraphicsItem::PlotFunctionGraphicsItem(const PlotFunctionInfoPtr& info,const PlotFunctionPtr& functionptr, QGraphicsItem * parent):
-  PlotDataGraphicsItemBase(info,parent),
-  functionptr_(functionptr)
-{
-}
-
-PlotFunctionGraphicsItem::~PlotFunctionGraphicsItem()
-{
-}
-
-
-
-void PlotFunctionGraphicsItem::Redraw()
-{
-  unsigned int zvalue=0;
-  qDeleteAll(childItems());
-  PlotFunctionInfoPtr infoptr=dyn_cast<PlotFunctionInfo>(infoptr_);
-  switch(infoptr->mode){
-  case PlotInfoBase::LINES:
-  case PlotInfoBase::POINTSANDLINES:
-  case PlotInfoBase::POINTS:
-    //draw lines
-  {
-    Real xold=infoptr->start;
-    Real yold=functionptr_->Func(xold);
-    for (Real x=xold+infoptr->delta;x<=infoptr->end;x+=infoptr->delta) {
-      Real y=functionptr_->Func(x);
-      QGraphicsLineItem* line=new QGraphicsLineItem(xold,yold,x,y,this);
-      line->setZValue(++zvalue);
-      line->setPen(infoptr->pen);
-      xold=x;
-      yold=y;
-    }
-    break;
-  }
-  case PlotInfoBase::AREA:
-  case PlotInfoBase::POINTSANDAREA:
-    //draw area
-    break;
-  default:
-    break;
-  }
-}
-
-
-
-
-}}
diff --git a/modules/gui/src/plot_viewer/plot_function_graphics_item.hh b/modules/gui/src/plot_viewer/plot_function_graphics_item.hh
deleted file mode 100644
index 2c43be23bf5644dbdcb481249fb208242c7d83cf..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_function_graphics_item.hh
+++ /dev/null
@@ -1,47 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef PLOT_FUNCTION_GRAPHICS_ITEM_HH_
-#define PLOT_FUNCTION_GRAPHICS_ITEM_HH_
-
-/*
-  Author: Andreas Schenk
-*/
-
-#include <QGraphicsItem>
-#include "plot_data_graphics_item_base.hh"
-#include "plot_function.hh"
-#include "plot_function_info.hh"
-
-namespace ost{namespace gui{
-
-class DLLEXPORT_OST_GUI PlotFunctionGraphicsItem: public PlotDataGraphicsItemBase
-{
-public:
-  PlotFunctionGraphicsItem (const PlotFunctionInfoPtr& info,const PlotFunctionPtr& functionptr, QGraphicsItem * parent = 0 );
-  virtual ~PlotFunctionGraphicsItem();
-  virtual void Redraw();
-
-
-protected:
-  PlotFunctionPtr functionptr_;
-};
-
-}}
-
-#endif /*PLOT_FUNCTION_GRAPHICS_ITEM_HH_*/
diff --git a/modules/gui/src/plot_viewer/plot_function_info.hh b/modules/gui/src/plot_viewer/plot_function_info.hh
deleted file mode 100644
index 27661bc607f32bf0f3328a9c493d943115ba912f..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_function_info.hh
+++ /dev/null
@@ -1,48 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef PLOT_FUNCTION_INFO_HH_
-#define PLOT_FUNCTION_INFO_HH_
-
-/*
-  Author: Andreas Schenk
-*/
-
-#include <boost/shared_ptr.hpp>
-#include "plot_info_base.hh"
-
-namespace ost{namespace gui{
-
-class DLLEXPORT_OST_GUI PlotFunctionInfo: public PlotInfoBase
-{
-  Q_OBJECT
-public:
-  PlotFunctionInfo(PlotViewerPanel * viewer=0);
-  virtual ~PlotFunctionInfo();
-  Real start;
-  Real end;
-  Real delta;
-public slots:
-  void OnRangeChange(Real start,Real end,Real delta);
-};
-
-typedef boost::shared_ptr<PlotFunctionInfo> PlotFunctionInfoPtr;
-
-}}//ns
-
-#endif /*PLOT_FUNCTION_INFO_HH_*/
diff --git a/modules/gui/src/plot_viewer/plot_graphics_cross_item.cc b/modules/gui/src/plot_viewer/plot_graphics_cross_item.cc
deleted file mode 100644
index 23ebd6cbcc644a51886933a7bb5f63e5c0d8311d..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_graphics_cross_item.cc
+++ /dev/null
@@ -1,76 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-/*
-  Author: Andreas Schenk
-*/
-
-#include <QCursor>
-#include <QToolTip>
-#include "plot_data_info.hh"
-#include "plot_data_graphics_item.hh"
-#include "plot_graphics_cross_item.hh"
-
-namespace ost {namespace gui {
-
-PlotGraphicsCrossItem::PlotGraphicsCrossItem(const PlotDataEntry& entry,const PlotDataInfoPtr& info , QGraphicsItem * parent):
-  QGraphicsPathItem(parent),
-  pde_(entry)
-{
-  setPos(pde_.x,pde_.y);
-  setPen(info->pen);
-  setBrush(info->brush);
-  setFlags(QGraphicsItem::ItemIgnoresTransformations);
-  setAcceptHoverEvents(true);
-  setCursor(Qt::CrossCursor);
-  QPainterPath path;
-  path.moveTo(-static_cast<Real>(info->symbolsize)/2.0, 0.0);
-  path.lineTo(static_cast<Real>(info->symbolsize)/2.0, 0.0);
-  path.moveTo(0.0,-static_cast<Real>(info->symbolsize)/2.0);
-  path.lineTo(0.0,static_cast<Real>(info->symbolsize)/2.0);
-  setPath(path);
-}
-
-PlotGraphicsCrossItem::~PlotGraphicsCrossItem()
-{
-  // TODO Auto-generated destructor stub
-}
-
-void PlotGraphicsCrossItem::hoverEnterEvent ( QGraphicsSceneHoverEvent * event )
-{
-  QToolTip::showText(event->screenPos(),QString("x:  %1\ny:  %2\nex: %3\ney: %4\nq:  %5\ni:  %6")
-                                                .arg(pde_.x)
-                                                .arg(pde_.y)
-                                                .arg(pde_.ex)
-                                                .arg(pde_.ey)
-                                                .arg(pde_.q)
-                                                .arg(pde_.info),
-                                                event->widget());
-}
-
-void PlotGraphicsCrossItem::hoverLeaveEvent ( QGraphicsSceneHoverEvent * event )
-{
-  QToolTip::showText(event->screenPos(),QString(),event->widget());
-}
-
-void PlotGraphicsCrossItem::mousePressEvent( QGraphicsSceneMouseEvent * event )
-{
-  dynamic_cast<PlotDataGraphicsItem*>(parentItem())->Callback(pde_);
-}
-
-}}//ns
diff --git a/modules/gui/src/plot_viewer/plot_graphics_cross_item.hh b/modules/gui/src/plot_viewer/plot_graphics_cross_item.hh
deleted file mode 100644
index d423d1339ee0a424a15b576ed0c0516b41127aa5..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_graphics_cross_item.hh
+++ /dev/null
@@ -1,48 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef PLOT_GRAPHICS_CROSS_ITEM_HH_
-#define PLOT_GRAPHICS_CROSS_ITEM_HH_
-
-/*
-  Author: Andreas Schenk
-*/
-
-#include <QGraphicsItem>
-#include <QGraphicsSceneHoverEvent>
-#include "plot_data_entry.hh"
-#include "plot_data_info_fw.hh"
-
-namespace ost {namespace gui {
-
-class DLLEXPORT_OST_GUI PlotGraphicsCrossItem: public QGraphicsPathItem
-{
-public:
-  PlotGraphicsCrossItem(const PlotDataEntry& entry,const PlotDataInfoPtr& info , QGraphicsItem * parent);
-  virtual ~PlotGraphicsCrossItem();
-protected:
-  virtual void hoverEnterEvent ( QGraphicsSceneHoverEvent * event );
-  virtual void hoverLeaveEvent ( QGraphicsSceneHoverEvent * event );
-  virtual void mousePressEvent ( QGraphicsSceneMouseEvent * event );
-  PlotDataEntry pde_;
-};
-
-
-}}//ns
-
-#endif /* PLOT_GRAPHICS_CROSS_ITEM_HH_ */
diff --git a/modules/gui/src/plot_viewer/plot_graphics_diagonal_cross_item.cc b/modules/gui/src/plot_viewer/plot_graphics_diagonal_cross_item.cc
deleted file mode 100644
index 88e92852ec7c867e1e54ce3f4b3887e19019fdc4..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_graphics_diagonal_cross_item.cc
+++ /dev/null
@@ -1,75 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-/*
-  Author: Andreas Schenk
-*/
-#include <QCursor>
-#include <QToolTip>
-#include "plot_data_info.hh"
-#include "plot_data_graphics_item.hh"
-#include "plot_graphics_diagonal_cross_item.hh"
-
-namespace ost {namespace gui {
-
-PlotGraphicsDiagonalCrossItem::PlotGraphicsDiagonalCrossItem(const PlotDataEntry& entry,const PlotDataInfoPtr& info , QGraphicsItem * parent):
-  QGraphicsPathItem(parent),
-  pde_(entry)
-{
-  setPos(pde_.x,pde_.y);
-  setPen(info->pen);
-  setBrush(info->brush);
-  setFlags(QGraphicsItem::ItemIgnoresTransformations);
-  setAcceptHoverEvents(true);
-  setCursor(Qt::CrossCursor);
-  QPainterPath path;
-  path.moveTo(-static_cast<Real>(info->symbolsize)/2.0, -static_cast<Real>(info->symbolsize)/2.0);
-  path.lineTo(static_cast<Real>(info->symbolsize)/2.0, static_cast<Real>(info->symbolsize)/2.0);
-  path.moveTo(static_cast<Real>(info->symbolsize)/2.0,-static_cast<Real>(info->symbolsize)/2.0);
-  path.lineTo(-static_cast<Real>(info->symbolsize)/2.0,static_cast<Real>(info->symbolsize)/2.0);
-  setPath(path);
-}
-
-PlotGraphicsDiagonalCrossItem::~PlotGraphicsDiagonalCrossItem()
-{
-  // TODO Auto-generated destructor stub
-}
-
-void PlotGraphicsDiagonalCrossItem::hoverEnterEvent ( QGraphicsSceneHoverEvent * event )
-{
-  QToolTip::showText(event->screenPos(),QString("x:  %1\ny:  %2\nex: %3\ney: %4\nq:  %5\ni:  %6")
-                                                .arg(pde_.x)
-                                                .arg(pde_.y)
-                                                .arg(pde_.ex)
-                                                .arg(pde_.ey)
-                                                .arg(pde_.q)
-                                                .arg(pde_.info),
-                                                event->widget());
-}
-
-void PlotGraphicsDiagonalCrossItem::hoverLeaveEvent ( QGraphicsSceneHoverEvent * event )
-{
-  QToolTip::showText(event->screenPos(),QString(),event->widget());
-}
-
-void PlotGraphicsDiagonalCrossItem::mousePressEvent( QGraphicsSceneMouseEvent * event )
-{
-  dynamic_cast<PlotDataGraphicsItem*>(parentItem())->Callback(pde_);
-}
-
-}}//ns
diff --git a/modules/gui/src/plot_viewer/plot_graphics_diagonal_cross_item.hh b/modules/gui/src/plot_viewer/plot_graphics_diagonal_cross_item.hh
deleted file mode 100644
index 01cf3b5643b5a35e097ca0d0e4640b45f3d36a3d..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_graphics_diagonal_cross_item.hh
+++ /dev/null
@@ -1,48 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef PLOT_GRAPHICS_DIAGONAL_CROSS_ITEM_HH_
-#define PLOT_GRAPHICS_DIAGONAL_CROSS_ITEM_HH_
-
-/*
-  Author: Andreas Schenk
-*/
-
-#include <QGraphicsItem>
-#include <QGraphicsSceneHoverEvent>
-#include "plot_data_entry.hh"
-#include "plot_data_info_fw.hh"
-
-namespace ost {namespace gui {
-
-class DLLEXPORT_OST_GUI PlotGraphicsDiagonalCrossItem: public QGraphicsPathItem
-{
-public:
-  PlotGraphicsDiagonalCrossItem(const PlotDataEntry& entry,const PlotDataInfoPtr& info , QGraphicsItem * parent);
-  virtual ~PlotGraphicsDiagonalCrossItem();
-protected:
-  virtual void hoverEnterEvent ( QGraphicsSceneHoverEvent * event );
-  virtual void hoverLeaveEvent ( QGraphicsSceneHoverEvent * event );
-  virtual void mousePressEvent ( QGraphicsSceneMouseEvent * event );
-  PlotDataEntry pde_;
-};
-
-
-}}//ns
-
-#endif /* PLOT_GRAPHICS_DIAGONAL_CROSS_ITEM_HH_ */
diff --git a/modules/gui/src/plot_viewer/plot_graphics_ellipse_item.cc b/modules/gui/src/plot_viewer/plot_graphics_ellipse_item.cc
deleted file mode 100644
index a176d07ff406667715590c57bd4fb59e058fb5c2..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_graphics_ellipse_item.cc
+++ /dev/null
@@ -1,70 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-/*
-  Author: Andreas Schenk
-*/
-
-#include <QCursor>
-#include <QToolTip>
-#include "plot_data_info.hh"
-#include "plot_data_graphics_item.hh"
-#include "plot_graphics_ellipse_item.hh"
-
-namespace ost{namespace gui{
-
-PlotGraphicsEllipseItem::PlotGraphicsEllipseItem(const PlotDataEntry& entry,const PlotDataInfoPtr& info , QGraphicsItem * parent):
-  QGraphicsEllipseItem(-static_cast<Real>(info->symbolsize)/2.0, -static_cast<Real>(info->symbolsize)/2.0, info->symbolsize, info->symbolsize,parent),
-  pde_(entry)
-{
-  setPos(pde_.x,pde_.y);
-  setPen(info->pen);
-  setBrush(info->brush);
-  setFlags(QGraphicsItem::ItemIgnoresTransformations);
-  setAcceptHoverEvents(true);
-  setCursor(Qt::CrossCursor);
-}
-
-PlotGraphicsEllipseItem::~PlotGraphicsEllipseItem()
-{
-}
-
-void PlotGraphicsEllipseItem::hoverEnterEvent ( QGraphicsSceneHoverEvent * event )
-{
-  QToolTip::showText(event->screenPos(),QString("x:  %1\ny:  %2\nex: %3\ney: %4\nq:  %5\ni:  %6")
-                                                .arg(pde_.x)
-                                                .arg(pde_.y)
-                                                .arg(pde_.ex)
-                                                .arg(pde_.ey)
-                                                .arg(pde_.q)
-                                                .arg(pde_.info),
-                                                event->widget());
-}
-
-void PlotGraphicsEllipseItem::hoverLeaveEvent ( QGraphicsSceneHoverEvent * event )
-{
-  QToolTip::showText(event->screenPos(),QString(),event->widget());
-}
-
-void PlotGraphicsEllipseItem::mousePressEvent( QGraphicsSceneMouseEvent * event )
-{
-  dynamic_cast<PlotDataGraphicsItem*>(parentItem())->Callback(pde_);
-}
-
-
-}}//ns
diff --git a/modules/gui/src/plot_viewer/plot_graphics_ellipse_item.hh b/modules/gui/src/plot_viewer/plot_graphics_ellipse_item.hh
deleted file mode 100644
index f9f21c0524ac585635a7e3d3a5fef34ef89456ef..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_graphics_ellipse_item.hh
+++ /dev/null
@@ -1,47 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef PLOT_GRAPHICS_ELLIPSE_ITEM_HH_
-#define PLOT_GRAPHICS_ELLIPSE_ITEM_HH_
-
-/*
-  Author: Andreas Schenk
-*/
-
-#include <QGraphicsItem>
-#include <QGraphicsSceneHoverEvent>
-#include "plot_data_entry.hh"
-#include "plot_data_info_fw.hh"
-
-namespace ost{namespace gui{
-
-class DLLEXPORT_OST_GUI PlotGraphicsEllipseItem: public QGraphicsEllipseItem
-{
-public:
-  PlotGraphicsEllipseItem(const PlotDataEntry& entry,const PlotDataInfoPtr& info , QGraphicsItem * parent);
-  virtual ~PlotGraphicsEllipseItem();
-protected:
-  virtual void hoverEnterEvent ( QGraphicsSceneHoverEvent * event );
-  virtual void hoverLeaveEvent ( QGraphicsSceneHoverEvent * event );
-  virtual void mousePressEvent ( QGraphicsSceneMouseEvent * event );
-  PlotDataEntry pde_;
-};
-
-}}//ns
-
-#endif /*PLOT_GRAPHICS_ELLIPSE_ITEM_HH_*/
diff --git a/modules/gui/src/plot_viewer/plot_graphics_rectangle_item.cc b/modules/gui/src/plot_viewer/plot_graphics_rectangle_item.cc
deleted file mode 100644
index dd61a1b22d0fa897bf31aa1fa9a5a67704e68a5e..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_graphics_rectangle_item.cc
+++ /dev/null
@@ -1,70 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-/*
-  Author: Andreas Schenk
-*/
-
-#include <QCursor>
-#include <QToolTip>
-#include "plot_data_info.hh"
-#include "plot_data_graphics_item.hh"
-#include "plot_graphics_rectangle_item.hh"
-
-namespace ost {namespace gui {
-
-PlotGraphicsRectangleItem::PlotGraphicsRectangleItem(const PlotDataEntry& entry,const PlotDataInfoPtr& info , QGraphicsItem * parent):
-  QGraphicsRectItem(-static_cast<Real>(info->symbolsize)/2.0, -static_cast<Real>(info->symbolsize)/2.0, info->symbolsize, info->symbolsize,parent),
-  pde_(entry)
-{
-  setPos(pde_.x,pde_.y);
-  setPen(info->pen);
-  setBrush(info->brush);
-  setFlags(QGraphicsItem::ItemIgnoresTransformations);
-  setAcceptHoverEvents(true);
-  setCursor(Qt::CrossCursor);
-}
-
-PlotGraphicsRectangleItem::~PlotGraphicsRectangleItem()
-{
-  // TODO Auto-generated destructor stub
-}
-
-void PlotGraphicsRectangleItem::hoverEnterEvent ( QGraphicsSceneHoverEvent * event )
-{
-  QToolTip::showText(event->screenPos(),QString("x:  %1\ny:  %2\nex: %3\ney: %4\nq:  %5\ni:  %6")
-                                                .arg(pde_.x)
-                                                .arg(pde_.y)
-                                                .arg(pde_.ex)
-                                                .arg(pde_.ey)
-                                                .arg(pde_.q)
-                                                .arg(pde_.info),
-                                                event->widget());
-}
-
-void PlotGraphicsRectangleItem::hoverLeaveEvent ( QGraphicsSceneHoverEvent * event )
-{
-  QToolTip::showText(event->screenPos(),QString(),event->widget());
-}
-
-void PlotGraphicsRectangleItem::mousePressEvent( QGraphicsSceneMouseEvent * event )
-{
-  dynamic_cast<PlotDataGraphicsItem*>(parentItem())->Callback(pde_);
-}
-
-}}//ns
diff --git a/modules/gui/src/plot_viewer/plot_graphics_rectangle_item.hh b/modules/gui/src/plot_viewer/plot_graphics_rectangle_item.hh
deleted file mode 100644
index 5d099c6923eaac8115cd68430684481d8d16d19d..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_graphics_rectangle_item.hh
+++ /dev/null
@@ -1,47 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef PLOTGRAPHICSRECTANGLEITEM_H_
-#define PLOTGRAPHICSRECTANGLEITEM_H_
-
-/*
-  Author: Andreas Schenk
-*/
-
-#include <QGraphicsRectItem>
-#include <QGraphicsSceneHoverEvent>
-#include "plot_data_entry.hh"
-#include "plot_data_info_fw.hh"
-
-namespace ost {namespace gui {
-
-class DLLEXPORT_OST_GUI PlotGraphicsRectangleItem: public QGraphicsRectItem
-{
-public:
-  PlotGraphicsRectangleItem(const PlotDataEntry& entry,const PlotDataInfoPtr& info , QGraphicsItem * parent);
-  virtual ~PlotGraphicsRectangleItem();
-protected:
-  virtual void hoverEnterEvent ( QGraphicsSceneHoverEvent * event );
-  virtual void hoverLeaveEvent ( QGraphicsSceneHoverEvent * event );
-  virtual void mousePressEvent ( QGraphicsSceneMouseEvent * event );
-  PlotDataEntry pde_;
-};
-
-}}//ns
-
-#endif /* PLOTGRAPHICSRECTANGLEITEM_H_ */
diff --git a/modules/gui/src/plot_viewer/plot_group.cc b/modules/gui/src/plot_viewer/plot_group.cc
deleted file mode 100644
index d3bcfc410d6bff698c0ed840b2b89dbb4b77e40a..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_group.cc
+++ /dev/null
@@ -1,162 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-/*
-  Author: Andreas Schenk
-*/
-#include <limits>
-
-#include <ost/dyn_cast.hh>
-
-#include "plot_group.hh"
-
-namespace ost{namespace gui{
-
-PlotGroup::PlotGroup():
-  PlotDataBase(),
-  ptr_list_()
-{
-}
-
-PlotGroup::~PlotGroup()
-{
-}
-
-void PlotGroup::Add(PlotDataPtr dataptr)
-{
-  ptr_list_.push_back(dataptr);
-}
-void PlotGroup::Add(PlotFunctionPtr functionptr)
-{
-  ptr_list_.push_back(functionptr);
-}
-void PlotGroup::Add(PlotGroupPtr groupptr)
-{
-  ptr_list_.push_back(groupptr);
-}
-
-unsigned int PlotGroup::GetSize()
-{
-  return ptr_list_.size();
-}
-PlotDataBasePtr PlotGroup::GetChild(unsigned int index)
-{
-  return ptr_list_[index];
-}
-Real PlotGroup::GetMinimumX()
-{
-  Real minx=std::numeric_limits<Real>::max();
-  unsigned int count=0;
-  for(unsigned int i=0;i<GetSize();++i){
-    PlotDataPtr dataptr=dyn_cast<PlotData>(GetChild(i));
-    if(dataptr!=PlotDataPtr()){
-      ++count;
-      minx=std::min<Real>(minx,dataptr->GetMinimumX());
-    }else{
-      PlotGroupPtr groupptr=dyn_cast<PlotGroup>(GetChild(i));
-      if(groupptr!=PlotGroupPtr()){
-        ++count;
-        minx=std::min<Real>(minx,groupptr->GetMinimumX());
-      }else{
-        //ignore
-      }
-    }
-  }
-  if(count==0){
-    return 0.0;
-  }else{
-    return minx;
-  }
-}
-Real PlotGroup::GetMaximumX()
-{
-  Real maxx=-std::numeric_limits<Real>::max();
-  unsigned int count=0;
-  for(unsigned int i=0;i<GetSize();++i){
-    PlotDataPtr dataptr=dyn_cast<PlotData>(GetChild(i));
-    if(dataptr!=PlotDataPtr()){
-      ++count;
-      maxx=std::max<Real>(maxx,dataptr->GetMaximumX());
-    }else{
-      PlotGroupPtr groupptr=dyn_cast<PlotGroup>(GetChild(i));
-      if(groupptr!=PlotGroupPtr()){
-        ++count;
-        maxx=std::max<Real>(maxx,groupptr->GetMaximumX());
-      }else{
-        //ignore
-      }
-    }
-  }
-  if(count==0){
-    return 1.0;
-  }else{
-    return maxx;
-  }
-}
-Real PlotGroup::GetMinimumY()
-{
-  Real miny=std::numeric_limits<Real>::max();
-  unsigned int count=0;
-  for(unsigned int i=0;i<GetSize();++i){
-    PlotDataPtr dataptr=dyn_cast<PlotData>(GetChild(i));
-    if(dataptr!=PlotDataPtr()){
-      ++count;
-      miny=std::min<Real>(miny,dataptr->GetMinimumY());
-    }else{
-      PlotGroupPtr groupptr=dyn_cast<PlotGroup>(GetChild(i));
-      if(groupptr!=PlotGroupPtr()){
-        ++count;
-        miny=std::min<Real>(miny,groupptr->GetMinimumY());
-      }else{
-        //ignore
-      }
-    }
-  }
-  if(count==0){
-    return 0.0;
-  }else{
-    return miny;
-  }
-}
-Real PlotGroup::GetMaximumY()
-{
-  Real maxy=-std::numeric_limits<Real>::max();
-  unsigned int count=0;
-  for(unsigned int i=0;i<GetSize();++i){
-    PlotDataPtr dataptr=dyn_cast<PlotData>(GetChild(i));
-    if(dataptr!=PlotDataPtr()){
-      ++count;
-      maxy=std::max<Real>(maxy,dataptr->GetMaximumY());
-    }else{
-      PlotGroupPtr groupptr=dyn_cast<PlotGroup>(GetChild(i));
-      if(groupptr!=PlotGroupPtr()){
-        ++count;
-        maxy=std::max<Real>(maxy,groupptr->GetMaximumY());
-      }else{
-        //ignore
-      }
-    }
-  }
-  if(count==0){
-    return 1.0;
-  }else{
-    return maxy;
-  }
-}
-
-}}//ns
diff --git a/modules/gui/src/plot_viewer/plot_group_graphics_item.cc b/modules/gui/src/plot_viewer/plot_group_graphics_item.cc
deleted file mode 100644
index 9157f1cbd255b8606e106fc2c9ceabeabd1808b8..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_group_graphics_item.cc
+++ /dev/null
@@ -1,74 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-/*
-  Author: Andreas Schenk
-*/
-
-#include <ost/dyn_cast.hh>
-#include "plot_data_info.hh"
-#include "plot_function_info.hh"
-#include "plot_data_graphics_item.hh"
-#include "plot_function_graphics_item.hh"
-#include "plot_group_graphics_item.hh"
-
-namespace ost{namespace gui{
-
-PlotGroupGraphicsItem::PlotGroupGraphicsItem(const PlotGroupInfoPtr& info,const PlotGroupPtr& groupptr, QGraphicsItem * parent):
-  PlotDataGraphicsItemBase(info,parent),
-  groupptr_(groupptr)
-{
-  for(unsigned int i=0;i<groupptr->GetSize();++i){
-    PlotDataPtr dataptr=dyn_cast<PlotData>(groupptr->GetChild(i));
-    if(dataptr!=PlotDataPtr()){
-      PlotDataInfoPtr plotdatainfoptr(new PlotDataInfo());
-      new PlotDataGraphicsItem(plotdatainfoptr,dataptr,this);
-      info->Add(plotdatainfoptr);
-    }else{
-      PlotFunctionPtr functionptr=dyn_cast<PlotFunction>(groupptr->GetChild(i));
-      if(functionptr!=PlotFunctionPtr()){
-        PlotFunctionInfoPtr plotfunctioninfoptr(new PlotFunctionInfo());
-        new PlotFunctionGraphicsItem(plotfunctioninfoptr,functionptr,this);
-        info->Add(plotfunctioninfoptr);
-      }else{
-        PlotGroupPtr cgroupptr=dyn_cast<PlotGroup>(groupptr->GetChild(i));
-        if(cgroupptr!=PlotGroupPtr()){
-          PlotGroupInfoPtr plotgroupinfoptr(new PlotGroupInfo());
-          new PlotGroupGraphicsItem(plotgroupinfoptr,groupptr);
-          info->Add(plotgroupinfoptr);
-        }else{
-          //should never be reached
-        }
-      }
-    }
-  }
-}
-
-PlotGroupGraphicsItem::~PlotGroupGraphicsItem()
-{
-}
-
-void PlotGroupGraphicsItem::Redraw()
-{
-  QList<QGraphicsItem *> children=childItems();
-  for(int i=0;i<children.size();++i){
-    dynamic_cast<PlotDataGraphicsItemBase*>(children[i])->Redraw();
-  }
-}
-
-}}//ns
diff --git a/modules/gui/src/plot_viewer/plot_group_graphics_item.hh b/modules/gui/src/plot_viewer/plot_group_graphics_item.hh
deleted file mode 100644
index f1f97d615b7e9f948c1c02e2a42ee2989c727bdf..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_group_graphics_item.hh
+++ /dev/null
@@ -1,44 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef PLOT_GROUP_GRAPHICS_ITEM_HH_
-#define PLOT_GROUP_GRAPHICS_ITEM_HH_
-
-/*
-  Author: Andreas Schenk
-*/
-
-#include "plot_group_info.hh"
-#include "plot_group.hh"
-#include "plot_data_graphics_item_base.hh"
-
-namespace ost{namespace gui{
-
-class DLLEXPORT_OST_GUI PlotGroupGraphicsItem: public PlotDataGraphicsItemBase
-{
-public:
-  PlotGroupGraphicsItem(const PlotGroupInfoPtr& info,const PlotGroupPtr& groupptr, QGraphicsItem * parent = 0 );
-  virtual ~PlotGroupGraphicsItem();
-  virtual void Redraw();
-protected:
-  PlotGroupPtr groupptr_;
-};
-
-}}
-
-#endif /*PLOT_GROUP_GRAPHICS_ITEM_HH_*/
diff --git a/modules/gui/src/plot_viewer/plot_group_info.cc b/modules/gui/src/plot_viewer/plot_group_info.cc
deleted file mode 100644
index 25f799d331023a121708ef4960469bb53185badf..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_group_info.cc
+++ /dev/null
@@ -1,166 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#include <ost/dyn_cast.hh>
-
-#include "plot_group_info.hh"
-#include "plot_data_info.hh"
-
-namespace ost{namespace gui{
-
-PlotGroupInfo::PlotGroupInfo(PlotViewerPanel * viewer):
-  PlotInfoBase(viewer),
-  children_()
-{
-  name="Group";
-}
-
-PlotGroupInfo::~PlotGroupInfo()
-{
-}
-
-void PlotGroupInfo::Add(PlotInfoBasePtr info)
-{
-  children_.push_back(info);
-}
-
-unsigned int PlotGroupInfo:: GetSize()
-{
-  return children_.size();
-}
-
-PlotInfoBasePtr PlotGroupInfo::GetChild(unsigned int i)
-{
-  return children_[i];
-}
-
-PlotGroupInfo& PlotGroupInfo::SetSymbol(unsigned int val)
-{
-  for(PlotInfoBasePtrVector::iterator it=children_.begin();it!=children_.end();++it){
-    PlotDataInfoPtr infoptr=dyn_cast<PlotDataInfo>(*it);
-    if(infoptr!=PlotDataInfoPtr()){
-      infoptr->SetSymbol(val);
-    }
-  }
-  return *this;
-}
-
-PlotGroupInfo& PlotGroupInfo::SetSymbolSize(unsigned int val)
-{
-  for(PlotInfoBasePtrVector::iterator it=children_.begin();it!=children_.end();++it){
-    PlotDataInfoPtr infoptr=dyn_cast<PlotDataInfo>(*it);
-    if(infoptr!=PlotDataInfoPtr()){
-      infoptr->SetSymbolSize(val);
-    }
-  }
-  return *this;
-}
-
-PlotGroupInfo& PlotGroupInfo::SetErrorMode(unsigned int val)
-{
-  for(PlotInfoBasePtrVector::iterator it=children_.begin();it!=children_.end();++it){
-    PlotDataInfoPtr infoptr=dyn_cast<PlotDataInfo>(*it);
-    if(infoptr!=PlotDataInfoPtr()){
-      infoptr->SetErrorMode(val);
-    }
-  }
-  return *this;
-}
-
-PlotGroupInfo& PlotGroupInfo::SetQuality(bool val)
-{
-  for(PlotInfoBasePtrVector::iterator it=children_.begin();it!=children_.end();++it){
-    PlotDataInfoPtr infoptr=dyn_cast<PlotDataInfo>(*it);
-    if(infoptr!=PlotDataInfoPtr()){
-      infoptr->SetQuality(val);
-    }
-  }
-  return *this;
-}
-
-PlotGroupInfo& PlotGroupInfo::SetCallback(const boost::python::object & callback_)
-{
-  for(PlotInfoBasePtrVector::iterator it=children_.begin();it!=children_.end();++it){
-    PlotDataInfoPtr infoptr=dyn_cast<PlotDataInfo>(*it);
-    if(infoptr!=PlotDataInfoPtr()){
-      infoptr->SetCallback(callback_);
-    }
-  }
-  return *this;
-}
-
-
-
-PlotGroupInfo& PlotGroupInfo::SetMode(unsigned int val)
-{
-  for(PlotInfoBasePtrVector::iterator it=children_.begin();it!=children_.end();++it){
-    (*it)->SetMode(val);
-  }
-  return *this;
-}
-
-PlotGroupInfo& PlotGroupInfo::SetColor(const QColor& color)
-{
-  for(PlotInfoBasePtrVector::iterator it=children_.begin();it!=children_.end();++it){
-    (*it)->SetColor(color);
-  }
-  return *this;
-}
-
-PlotGroupInfo& PlotGroupInfo::SetColor(int r, int g, int b)
-{
-  for(PlotInfoBasePtrVector::iterator it=children_.begin();it!=children_.end();++it){
-    (*it)->SetColor(r,g,b);
-  }
-  return *this;
-}
-
-PlotGroupInfo& PlotGroupInfo::SetLineColor(int r, int g, int b)
-{
-  for(PlotInfoBasePtrVector::iterator it=children_.begin();it!=children_.end();++it){
-    (*it)->SetLineColor(r,g,b);
-  }
-  return *this;
-}
-
-PlotGroupInfo& PlotGroupInfo::SetFillColor(int r, int g, int b)
-{
-  for(PlotInfoBasePtrVector::iterator it=children_.begin();it!=children_.end();++it){
-    (*it)->SetFillColor(r,g,b);
-  }
-  return *this;
-}
-
-PlotGroupInfo& PlotGroupInfo::SetLineColor(const QColor& color)
-{
-  for(PlotInfoBasePtrVector::iterator it=children_.begin();it!=children_.end();++it){
-    (*it)->SetLineColor(color);
-  }
-  return *this;
-}
-
-PlotGroupInfo& PlotGroupInfo::SetFillColor(const QColor& color)
-{
-  for(PlotInfoBasePtrVector::iterator it=children_.begin();it!=children_.end();++it){
-    (*it)->SetLineColor(color);
-  }
-  return *this;
-}
-
-
-}}//ns
diff --git a/modules/gui/src/plot_viewer/plot_group_info.hh b/modules/gui/src/plot_viewer/plot_group_info.hh
deleted file mode 100644
index 20f6b4c742cc5e20f03a3b2b96a2a8f7302cd429..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_group_info.hh
+++ /dev/null
@@ -1,61 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef PLOT_GROUP_INFO_HH_
-#define PLOT_GROUP_INFO_HH_
-
-#include <vector>
-#include <boost/shared_ptr.hpp>
-#include <boost/python.hpp>
-#include "plot_info_base.hh"
-
-namespace ost{namespace gui{
-
-class DLLEXPORT_OST_GUI PlotGroupInfo: public PlotInfoBase
-{
-  typedef std::vector<PlotInfoBasePtr> PlotInfoBasePtrVector;
-public:
-  PlotGroupInfo(PlotViewerPanel * viewer=0);
-  virtual ~PlotGroupInfo();
-  virtual PlotGroupInfo& SetSymbol(unsigned int val);
-  virtual PlotGroupInfo& SetSymbolSize(unsigned int val);
-  virtual PlotGroupInfo& SetErrorMode(unsigned int val);
-  virtual PlotGroupInfo& SetQuality(bool val);
-  virtual PlotGroupInfo& SetCallback(const boost::python::object & callback_);
-
-  virtual PlotGroupInfo& SetMode(unsigned int val);
-  virtual PlotGroupInfo& SetColor(const QColor& color);
-  virtual PlotGroupInfo& SetColor(int r, int g, int b);
-  virtual PlotGroupInfo& SetLineColor(int r, int g, int b);
-  virtual PlotGroupInfo& SetFillColor(int r, int g, int b);
-  virtual PlotGroupInfo& SetLineColor(const QColor& color);
-  virtual PlotGroupInfo& SetFillColor(const QColor& color);
-  void Add(PlotInfoBasePtr info);
-  unsigned int GetSize();
-  PlotInfoBasePtr GetChild(unsigned int i);
-protected:
-  PlotInfoBasePtrVector children_;
-};
-
-typedef boost::shared_ptr<PlotGroupInfo> PlotGroupInfoPtr;
-
-
-}}//ns
-
-
-#endif /*PLOT_GROUP_INFO_HH_*/
diff --git a/modules/gui/src/plot_viewer/plot_info_base.cc b/modules/gui/src/plot_viewer/plot_info_base.cc
deleted file mode 100644
index aa284a623c524072b8cb448699529e8aa658fd43..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_info_base.cc
+++ /dev/null
@@ -1,109 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-/*
-  Author: Andreas Schenk
-*/
-
-#include "plot_info_base.hh"
-
-namespace ost { namespace gui {
-
-PlotInfoBase::PlotInfoBase(PlotViewerPanel * viewer):
-  QObject(),
-  name(""),
-  pen(QPen(QColor(0,0,0))),
-  brush(QBrush(QColor(255,255,255))),
-  mode(LINE),
-  visible(true)
-{
-}
-
-PlotInfoBase::PlotInfoBase(const PlotInfoBase& pib):
-  QObject(),
-  name(pib.name),
-  pen(pib.pen),
-  brush(pib.brush),
-  mode(pib.mode),
-  visible(pib.visible)
-{
-}
-
-PlotInfoBase::~PlotInfoBase()
-{
-}
-
-
-PlotInfoBase& PlotInfoBase::SetMode(unsigned int val)
-{
-  mode=val; 
-  emit appearanceChanged();
-  return *this;
-}  
-
-PlotInfoBase& PlotInfoBase::SetVisible(bool val)
-{
-  visible=val;
-  emit visibilityChanged();
-  return *this;
-}  
-
-PlotInfoBase& PlotInfoBase::SetColor(const QColor& color)
-{
-  pen.setColor(color); 
-  brush.setColor(color);
-  emit appearanceChanged();
-  return *this;
-}
-
-PlotInfoBase& PlotInfoBase::SetColor(int r, int g, int b)
-{
-  return SetColor(QColor(r,g,b));
-}
-
-PlotInfoBase& PlotInfoBase::SetLineColor(int r, int g, int b)
-{
-  return SetLineColor(QColor(r,g,b));
-}
-
-PlotInfoBase& PlotInfoBase::SetLineColor(const QColor& color)
-{
-  pen.setColor(color); 
-  emit appearanceChanged();
-  return *this;
-}
-
-PlotInfoBase& PlotInfoBase::SetFillColor(int r, int g, int b)
-{
-  return SetFillColor(QColor(r,g,b));
-}
-PlotInfoBase& PlotInfoBase::SetFillColor(const QColor& color)
-{
-  brush.setColor(color);
-  emit appearanceChanged();
-  return *this;
-}
-
-PlotInfoBase& PlotInfoBase::SetName(const QString& n)
-{
-  name=n;
-  emit nameChanged();
-  return *this;
-}
-
-}}//ns
diff --git a/modules/gui/src/plot_viewer/plot_info_base.hh b/modules/gui/src/plot_viewer/plot_info_base.hh
deleted file mode 100644
index 46b21b085fd6416b860b893edc00f2bc0e118b7f..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_info_base.hh
+++ /dev/null
@@ -1,90 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef PLOT_INFO_BASE_HH_
-#define PLOT_INFO_BASE_HH_
-
-/*
-  Author: Andreas Schenk
-*/
-
-#include <boost/shared_ptr.hpp>
-#include <QObject>
-#include <QColor>
-#include <QPen>
-#include <QBrush>
-
-#include <ost/gui/module_config.hh>
-
-namespace ost{namespace gui{
-
-//fw decl
-class PlotViewerPanel;
-
-class DLLEXPORT_OST_GUI PlotInfoBase: public QObject
-{
-  Q_OBJECT  
-public:
-  enum modes{
-    POINTS,
-    LINES,
-    POINTSANDLINES,
-    AREA,
-    POINTSANDAREA
-  };
-  enum shapes{
-    CIRCLE,
-    RECTANGLE,
-    CROSS,
-    DIAGONALCROSS
-  };
-  enum errormodes{
-    NONE,
-    LINE,
-    BOX,
-    VECTOR
-  };
-  PlotInfoBase(PlotViewerPanel * viewer=0);
-  PlotInfoBase(const PlotInfoBase&);
-  virtual ~PlotInfoBase();
-
-  virtual PlotInfoBase& SetName(const QString& n);
-  virtual PlotInfoBase& SetMode(unsigned int val);
-  virtual PlotInfoBase& SetVisible(bool val);
-  virtual PlotInfoBase& SetColor(const QColor& color);
-  virtual PlotInfoBase& SetColor(int r, int g, int b);
-  virtual PlotInfoBase& SetLineColor(int r, int g, int b);
-  virtual PlotInfoBase& SetFillColor(int r, int g, int b);
-  virtual PlotInfoBase& SetLineColor(const QColor& color);
-  virtual PlotInfoBase& SetFillColor(const QColor& color);
-  QString name;    
-  QPen pen;
-  QBrush brush;
-  unsigned int mode;
-  bool visible;
-
-signals:
-  void appearanceChanged();
-  void visibilityChanged();
-  void nameChanged();
-};
-typedef boost::shared_ptr<PlotInfoBase> PlotInfoBasePtr;
-
-}}//ns
-
-#endif /*PLOT_INFO_BASE_HH_*/
diff --git a/modules/gui/src/plot_viewer/plot_legend_panel.cc b/modules/gui/src/plot_viewer/plot_legend_panel.cc
deleted file mode 100644
index 44decfbc9abe01e0eee9df7ef2569d4afb01f857..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_legend_panel.cc
+++ /dev/null
@@ -1,100 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-/*
-  Author: Andreas Schenk
-*/
-
-#include <ost/dyn_cast.hh>
-#include <QMetaType>
-#include "plot_legend_panel.hh"
-
-Q_DECLARE_METATYPE(ost::gui::PlotInfoBasePtr)
-
-
-namespace ost{namespace gui{
-
-
-PlotLegendPanel::PlotLegendPanel(QWidget* parent):
-  QTreeWidget(parent)
-{
-  setColumnCount(3);
-  setHeaderLabels(QStringList() << "Dataset" << "Visible" << "Apprearance");
-  connect(this,SIGNAL(itemChanged(QTreeWidgetItem*, int)),this,SLOT(OnItemChanged(QTreeWidgetItem*, int)));
-}
-
-PlotLegendPanel::~PlotLegendPanel()
-{
-}
-
-QTreeWidgetItem* PlotLegendPanel::create_item_(const PlotInfoBasePtr& info)
-{
-  QTreeWidgetItem* item=new QTreeWidgetItem(QStringList(info->name));
-  item->setCheckState(1,Qt::Checked);
-  item->setData(0,Qt::UserRole,QVariant::fromValue(info));
-  return item;
-}
-
-void PlotLegendPanel::AddData(const PlotDataInfoPtr& info)
-{
-  addTopLevelItem(create_item_(info));
-}
-
-void PlotLegendPanel::AddFunction(const PlotFunctionInfoPtr& info)
-{
-  addTopLevelItem(create_item_(info));
-}
-
-void PlotLegendPanel::AddGroup(const PlotGroupInfoPtr& info)
-{
-  QTreeWidgetItem* item=create_item_(info);
-  generate_group_(info,item);
-  addTopLevelItem(item);
-}
-
-void PlotLegendPanel::generate_group_(const PlotGroupInfoPtr& info, QTreeWidgetItem* parent)
-{
-  for(unsigned int i=0;i<info->GetSize();++i){
-    PlotDataInfoPtr dataptr=dyn_cast<PlotDataInfo>(info->GetChild(i));
-    if(dataptr!=PlotDataInfoPtr()){
-      parent->addChild(create_item_(dataptr));
-    }else{
-      PlotFunctionInfoPtr functionptr=dyn_cast<PlotFunctionInfo>(info->GetChild(i));
-      if(functionptr!=PlotFunctionInfoPtr()){
-        parent->addChild(create_item_(functionptr));
-      }else{
-        PlotGroupInfoPtr groupptr=dyn_cast<PlotGroupInfo>(info->GetChild(i));
-        if(groupptr!=PlotGroupInfoPtr()){
-          QTreeWidgetItem* child=create_item_(groupptr);
-          generate_group_(groupptr,child);
-          parent->addChild(child);
-        }else{
-          //should never be reached
-        }
-      }
-    }
-  }
-}
-void PlotLegendPanel::OnItemChanged(QTreeWidgetItem * item, int column )
-{
-  if(column==1){
-    item->data(0,Qt::UserRole).value<PlotInfoBasePtr>()->SetVisible(item->checkState(1));
-  }
-}
-
-}}//ns
diff --git a/modules/gui/src/plot_viewer/plot_legend_panel.hh b/modules/gui/src/plot_viewer/plot_legend_panel.hh
deleted file mode 100644
index 29a547d5b19564cd5d3227605e18c27e0509850b..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_legend_panel.hh
+++ /dev/null
@@ -1,52 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef PLOT_LEGEND_PANEL_HH_
-#define PLOT_LEGEND_PANEL_HH_
-
-/*
-  Author: Andreas Schenk
-*/
-
-#include <QTreeWidget>
-#include <QTreeWidgetItem>
-#include "plot_data_info.hh"
-#include "plot_group_info.hh"
-#include "plot_function_info.hh"
-
-namespace ost{namespace gui{
-
-class DLLEXPORT_OST_GUI PlotLegendPanel:public  QTreeWidget
-{
-  Q_OBJECT
-public:
-  PlotLegendPanel(QWidget* parent=0);
-  virtual ~PlotLegendPanel();
-  void AddData(const PlotDataInfoPtr& info);
-  void AddFunction(const PlotFunctionInfoPtr& info);
-  void AddGroup(const PlotGroupInfoPtr& info);
-public slots:
-  void OnItemChanged(QTreeWidgetItem * item, int column );  
-protected:
-  void generate_group_(const PlotGroupInfoPtr& info, QTreeWidgetItem* parent);
-  QTreeWidgetItem* create_item_(const PlotInfoBasePtr& info);
-};
-
-}}//ns
-
-#endif /*PLOT_LEGEND_PANEL_HH_*/
diff --git a/modules/gui/src/plot_viewer/plot_ticker.cc b/modules/gui/src/plot_viewer/plot_ticker.cc
deleted file mode 100644
index 9577e6844d495dc1c06c986b00e3dce3b9d29845..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_ticker.cc
+++ /dev/null
@@ -1,93 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-/*
-  Author: Andreas Schenk
-*/
-
-#include <ost/gui/module_config.hh> // for round
-
-#include <cmath>
-#include "plot_ticker.hh"
-
-PlotTickerBase::PlotTickerBase():
-  min_(0.0),
-  max_(1.0),
-  start_(0),
-  end_(100),
-  separation_(20)
-{
-}
-PlotTickerBase::PlotTickerBase(Real min,Real max,int start,int end,unsigned int separation):
-  min_(min),
-  max_(max),
-  start_(start),
-  end_(end),
-  separation_(separation)
-{
-}
-
-PlotTickerBase::~PlotTickerBase()
-{
-}
-
-
-PlotTickerLinear::PlotTickerLinear():
-  PlotTickerBase()
-{
-}
-
-PlotTickerLinear::PlotTickerLinear(Real min,Real max,int start,int end,unsigned int separation):
-  PlotTickerBase(min,max,start,end,separation)
-{
-}
-PlotTickerLinear::~PlotTickerLinear()
-{
-}
-
-TickList PlotTickerLinear::GetTicks()
-{
-  TickList result;
-  Real sampling=static_cast<Real>(end_-start_)/(max_-min_);
-  int exponent=static_cast<int>(floor(log10( 1.0/sampling )));
-  Real prefac=1;
-  while(1){
-    //std::cout << sampling << " " << exponent << std::endl;
-    int prefacs[]={1,2,5};
-    for(int i=0;i<3 && prefac*pow(10.0,exponent)*sampling<separation_;++i){
-      prefac=prefacs[i];
-    }
-    if(prefac*pow(10.0,exponent)*sampling>=separation_){
-      break;
-    }else {
-      prefac=1;
-      ++exponent;
-    }
-  }
-  Real stepsize=prefac*pow(Real(10.0),static_cast<Real>(exponent));
-  Real val=rint(min_/stepsize)*stepsize;
-  while(val<=max_){
-    int pos=static_cast<int>(round(sampling*(val-min_)))+start_;
-    if(pos>=0){
-      result.push_back(Tick(pos,val));
-    }
-    val+=stepsize;
-  }
-  return result;
-}
-
diff --git a/modules/gui/src/plot_viewer/plot_ticker.hh b/modules/gui/src/plot_viewer/plot_ticker.hh
deleted file mode 100644
index da4e379baa520a11876538a56121f9a98f7440a5..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_ticker.hh
+++ /dev/null
@@ -1,72 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef PLOT_TICKER_HH_
-#define PLOT_TICKER_HH_
-
-/*
-  Author: Andreas Schenk
-*/
-
-#include <vector>
-#include <utility>
-
-#include <ost/gui/module_config.hh>
-
-#include "plot_ticker_fw.hh"
-
-typedef std::pair<int,Real> Tick;
-typedef std::vector<Tick> TickList;
-
-class DLLEXPORT_OST_GUI PlotTickerBase
-{
-public:
-  PlotTickerBase();
-  PlotTickerBase(Real min,Real max=1.0,int start=0,int end=100,unsigned int separation=20);
-  virtual ~PlotTickerBase();
-  Real GetMinimum(){return min_;}
-  void SetMinimum(Real min=0.0){min_=min;}
-  Real GetMaximum(){return max_;}
-  void SetMaximum(Real max=1.0){max_=max;}
-  void SetMinMax(Real min=0.0,Real max=1.0){min_=min;max_=max;}
-  int GetStart(){return start_;}
-  void SetStart(int start=0){start_=start;}
-  int GetEnd(){return end_;}
-  void SetEnd(int end=100){end_=end;}
-  void SetStartEnd(int start=0,int end=100){start_=start;end_=end;}
-  unsigned int GetSeparation(){return separation_;}
-  void SetSeparation(unsigned int separation){separation_=separation;}
-  virtual TickList GetTicks()=0;
-protected:
-  Real min_;
-  Real max_;
-  int start_;
-  int end_;
-  unsigned int separation_;
-};
-
-class DLLEXPORT_OST_GUI PlotTickerLinear: public PlotTickerBase
-{
-public:
-  PlotTickerLinear();
-  PlotTickerLinear(Real min,Real max=1.0,int start=0,int end=100,unsigned int separation=20);
-  virtual ~PlotTickerLinear();
-  virtual TickList GetTicks();
-};
-
-#endif /*PLOT_TICKER_HH_*/
diff --git a/modules/gui/src/plot_viewer/plot_types.hh b/modules/gui/src/plot_viewer/plot_types.hh
deleted file mode 100644
index ea773534bc2b870160ab2663e8af5b80d04175d1..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_types.hh
+++ /dev/null
@@ -1,52 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef PLOT_TYPES_HH_
-#define PLOT_TYPES_HH_
-
-
-/*
-  Author: Andreas Schenk
-*/
-
-#include <QStandardItem>
-
-
-namespace ost{namespace gui{
-
-enum PlotTypes{
-  PlotTypeDataPoint=QStandardItem::UserType+1,
-  PlotTypeData,
-  PlotTypeFunction,
-  PlotTypeGroup
-};
-
-enum PlotItemDataRoles{
-  PlotTypeRole=Qt::UserRole+1,
-  PlotPDERole,
-  PlotFunctionDataRole,
-  PlotFunctionMinRole,
-  PlotFunctionMaxRole,
-  PlotFunctionStepRole,
-  PlotSymbolSizeRole,
-  PlotSymbolRole,
-  PlotModeRole
-};
-}}//ns
-
-#endif /*PLOT_TYPES_HH_*/
diff --git a/modules/gui/src/plot_viewer/plot_viewer.cc b/modules/gui/src/plot_viewer/plot_viewer.cc
deleted file mode 100644
index 4ee454836de1c277e9968c7a4c0f42b756819559..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_viewer.cc
+++ /dev/null
@@ -1,126 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-/*
-  Author: Andreas Schenk
-*/
-
-#include <limits>
-#include <QHBoxLayout>
-#include <QVBoxLayout>
-
-#include "plot_viewer.hh"
-#include "plot_viewer_panel.hh"
-#include "plot_legend_panel.hh"
-#include "plot_data_info.hh"
-#include "plot_data_graphics_item.hh"
-#include "plot_function_graphics_item.hh"
-#include "plot_group_graphics_item.hh"
-
-namespace ost { namespace gui {
-
-PlotViewer::PlotViewer(QWidget* parent,const QString& name):
-  QWidget(parent),
-  scene_(),
-  viewer_(new PlotViewerPanel(&scene_,this)),
-  legend_(new PlotLegendPanel(this)),
-  model_(),
-  ptr_list_()
-{
-  scene_.setSceneRect(-std::numeric_limits<Real>::max()/2.0,-std::numeric_limits<Real>::max()/2.0,std::numeric_limits<Real>::max(),std::numeric_limits<Real>::max());
-  setWindowTitle(name);
-  QHBoxLayout *hlayout = new QHBoxLayout;
-  hlayout->addWidget(viewer_,1);
-  hlayout->addWidget(legend_,0);
-  setLayout(hlayout);
-}
-
-PlotViewer::~PlotViewer()
-{
-}
-
-PlotDataInfoPtr PlotViewer::Add(PlotDataPtr dataptr, bool fit)
-{
-  PlotDataInfoPtr infoptr(new PlotDataInfo(viewer_));
-  scene_.addItem(new PlotDataGraphicsItem(infoptr,dataptr));
-  if(fit){
-    viewer_->SetMinMax(dataptr->GetMinimumX(),dataptr->GetMaximumX(),dataptr->GetMinimumY(),dataptr->GetMaximumY());
-  }
-  legend_->AddData(infoptr);
-  viewer_->update();
-  return infoptr;
-}
-
-PlotFunctionInfoPtr PlotViewer::Add(PlotFunctionPtr functionptr)
-{
-  PlotFunctionInfoPtr infoptr(new PlotFunctionInfo(viewer_));
-  scene_.addItem(new PlotFunctionGraphicsItem(infoptr,functionptr));
-  legend_->AddFunction(infoptr);
-  viewer_->update();
-  return infoptr;
-}
-PlotGroupInfoPtr PlotViewer::Add(PlotGroupPtr groupptr,bool fit)
-{
-  PlotGroupInfoPtr infoptr(new PlotGroupInfo(viewer_));
-  scene_.addItem(new PlotGroupGraphicsItem(infoptr,groupptr));
-  if(fit){
-    viewer_->SetMinMax(groupptr->GetMinimumX(),groupptr->GetMaximumX(),groupptr->GetMinimumY(),groupptr->GetMaximumY());
-  }
-  legend_->AddGroup(infoptr);
-  viewer_->update();
-  return infoptr;
-}
-
-void PlotViewer::SetMinimumX(Real x)
-{
-  viewer_->SetMinimumX(x);
-}
-void PlotViewer::SetMaximumX(Real x)
-{
-  viewer_->SetMaximumX(x);
-}
-void PlotViewer::SetMinimumY(Real y)
-{
-  viewer_->SetMinimumY(y);
-}
-void PlotViewer::SetMaximumY(Real y)
-{
-  viewer_->SetMaximumY(y);
-}
-Real PlotViewer::GetMinimumX() const
-{
-  return viewer_->GetMinimumX();
-}
-Real PlotViewer::GetMaximumX() const
-{
-  return viewer_->GetMaximumX();
-}
-Real PlotViewer::GetMinimumY() const
-{
-  return viewer_->GetMinimumY();
-}
-Real PlotViewer::GetMaximumY() const
-{
-  return viewer_->GetMaximumY();
-}
-
-void PlotViewer::SetAutofit(bool fit){
-  viewer_->SetAutofit(fit);
-}
-
-}}//ns
diff --git a/modules/gui/src/plot_viewer/plot_viewer.hh b/modules/gui/src/plot_viewer/plot_viewer.hh
deleted file mode 100644
index f5a6a4a58976d81447e623d58064a6ce21e43591..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_viewer.hh
+++ /dev/null
@@ -1,74 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef PLOT_VIEWER_HH_
-#define PLOT_VIEWER_HH_
-
-/*
-  Author: Andreas Schenk
-*/
-
-#include <QStandardItemModel>
-#include <QGraphicsScene>
-#include <QWidget>
-#include <QString>
-
-#include "plot_data.hh"
-#include "plot_function.hh"
-#include "plot_group.hh"
-#include "plot_function_info.hh"
-#include "plot_data_info_fw.hh"
-#include "plot_group_info.hh"
-
-namespace ost{namespace gui{
-
-
-//fw decl
-class PlotViewerPanel;
-class PlotLegendPanel;
-
-
-class DLLEXPORT_OST_GUI PlotViewer: public QWidget
-{
-  typedef boost::shared_ptr<QStandardItem> QStandardItemPtr;
-public:
-  PlotViewer(QWidget* parent,const QString& name="");
-  virtual ~PlotViewer();
-  PlotDataInfoPtr Add(PlotDataPtr dataptr, bool fit=false);
-  PlotFunctionInfoPtr Add(PlotFunctionPtr functionptr);
-  PlotGroupInfoPtr Add(PlotGroupPtr groupptr, bool fit=false);
-  void SetMinimumX(Real x);
-  void SetMaximumX(Real x);
-  void SetMinimumY(Real y);
-  void SetMaximumY(Real y);
-  Real GetMinimumX() const;
-  Real GetMaximumX() const;
-  Real GetMinimumY() const;
-  Real GetMaximumY() const;
-  void SetAutofit(bool fit=true);
-private:
-  QGraphicsScene scene_;
-  PlotViewerPanel* viewer_;
-  PlotLegendPanel* legend_;
-  QStandardItemModel model_;
-  std::vector<QStandardItemPtr> ptr_list_;
-};
-
-}}//ns
-
-#endif /*PLOT_VIEWER_HH_*/
diff --git a/modules/gui/src/plot_viewer/plot_viewer_panel.cc b/modules/gui/src/plot_viewer/plot_viewer_panel.cc
deleted file mode 100644
index a440c06803b475b0d90dd3ac2ebf1151ecdf4074..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_viewer_panel.cc
+++ /dev/null
@@ -1,251 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-/*
-  Author: Andreas Schenk
-*/
-
-#include <QtGui>
-#include "plot_viewer_panel.hh"
-#include "plot_types.hh"
-#include "plot_function.hh"
-
-namespace ost{namespace gui{
-
-PlotViewerPanel::PlotViewerPanel(QGraphicsScene * scene, QWidget* parent):
-  QGraphicsView(scene,parent),
-  axis_horizontal_(new PlotAxisHorizontal(this)),
-  axis_vertical_(new PlotAxisVertical(this)),
-  global_mouse_pos_(),
-  autofit_(false)
-{
-  setVerticalScrollBarPolicy(Qt::ScrollBarAlwaysOff);
-  setHorizontalScrollBarPolicy(Qt::ScrollBarAlwaysOff);
-  setDragMode(QGraphicsView::NoDrag);
-  setRenderHint(QPainter::Antialiasing,true);
-  setViewportMargins (PlotAxisBase::AXISWIDTH,0,0,PlotAxisBase::AXISWIDTH);
-  setTransformationAnchor(QGraphicsView::NoAnchor);
-  setResizeAnchor(QGraphicsView::NoAnchor);
-  scale(1.0,-1.0);
-  connect(axis_horizontal_,SIGNAL(zoom(int,QPoint)),this, SLOT(OnZoomX(int,QPoint)));
-  connect(axis_vertical_,SIGNAL(zoom(int,QPoint)),this, SLOT(OnZoomY(int,QPoint)));
-  connect(axis_horizontal_,SIGNAL(translate(Real,Real)),this, SLOT(OnTranslate(Real ,Real)));
-  connect(axis_vertical_,SIGNAL(translate(Real,Real)),this, SLOT(OnTranslate(Real,Real)));
-}
-
-PlotViewerPanel::~PlotViewerPanel()
-{
-}
-
-void PlotViewerPanel::SetMinMax(Real minx,Real maxx,Real miny, Real maxy)
-{
-    QRectF scenerect;
-    scenerect.setCoords(minx,maxy,maxx,miny);
-    QRect viewrect(0,0,viewport()->width(),viewport()->height());
-    setTransform(GetTransform(scenerect,viewrect));
-    UpdateAxes();
-}
-
-void PlotViewerPanel::SetMinimumX(Real x)
-{
-  if(x<GetMaximumX()){
-    QRectF scenerect;
-    scenerect.setCoords(x,GetMaximumY(),GetMaximumX(),GetMinimumY());
-    QRect viewrect(0,0,viewport()->width(),viewport()->height());
-    setTransform(GetTransform(scenerect,viewrect));
-    UpdateAxes();
-  }
-}
-void PlotViewerPanel::SetMaximumX(Real x)
-{
-  if(x>GetMinimumX()){
-    QRectF scenerect;
-    scenerect.setCoords(GetMaximumX(),GetMinimumY(),x,GetMinimumY());
-    QRect viewrect(0,0,viewport()->width(),viewport()->height());
-    setTransform(GetTransform(scenerect,viewrect));
-    UpdateAxes();
-  }
-}
-void PlotViewerPanel::SetMinimumY(Real y)
-{
-  if(y<GetMaximumY()){
-    QRectF scenerect;
-    scenerect.setCoords(GetMinimumX(),GetMaximumY(),GetMaximumX(),y);
-    QRect viewrect(0,0,viewport()->width(),viewport()->height());
-    setTransform(GetTransform(scenerect,viewrect));
-    UpdateAxes();
-  }
-}
-void PlotViewerPanel::SetMaximumY(Real y)
-{
-  if(y>GetMinimumY()){
-    QRectF scenerect;
-    scenerect.setCoords(GetMinimumX(),y,GetMaximumX(),GetMinimumY());
-    QRect viewrect(0,0,viewport()->width(),viewport()->height());
-    setTransform(GetTransform(scenerect,viewrect));
-    UpdateAxes();
-  }
-}
-Real PlotViewerPanel::GetMinimumX() const
-{
-  return mapToScene(QPoint(0,0)).x();
-}
-Real PlotViewerPanel::GetMaximumX() const
-{
-  return mapToScene(QPoint(viewport()->width(),0)).x();
-}
-Real PlotViewerPanel::GetMinimumY() const
-{
-  return mapToScene(QPoint(0,viewport()->height())).y();
-}
-Real PlotViewerPanel::GetMaximumY() const
-{
-  return mapToScene(QPoint(0,0)).y();
-}
-
-Real PlotViewerPanel::GetDelta() const
-{
-  return mapToScene(QPoint(1,0)).x()-mapToScene(QPoint(0,0)).x();
-}
-
-void PlotViewerPanel::wheelEvent ( QWheelEvent * e )
-{
-  QPointF cursorpos=mapToScene(e->pos());
-  Real scalefactor=exp(e->delta()/1000.0);
-  QRectF scenerect;
-  scenerect.setCoords(cursorpos.x()-(cursorpos.x()-GetMinimumX())/scalefactor,
-                      cursorpos.y()+(GetMaximumY()-cursorpos.y())/scalefactor,
-                      cursorpos.x()+(GetMaximumX()-cursorpos.x())/scalefactor,
-                      cursorpos.y()-(cursorpos.y()-GetMinimumY())/scalefactor);
-  QRect viewrect(0,0,viewport()->width(),viewport()->height());
-  setTransform(GetTransform(scenerect,viewrect));
-  UpdateAxes();
-}
-void PlotViewerPanel::OnZoomX(int delta,QPoint pos)
-{
-  QPointF cursorpos=mapToScene(pos+QPoint(-int(PlotAxisBase::AXISWIDTH),0));
-  Real scalefactor=exp(delta/1000.0);
-  QRectF scenerect;
-  scenerect.setCoords(cursorpos.x()-(cursorpos.x()-GetMinimumX())/scalefactor,
-                  GetMaximumY(),
-                  cursorpos.x()+(GetMaximumX()-cursorpos.x())/scalefactor,
-                  GetMinimumY());
-  QRect viewrect(0,0,viewport()->width(),viewport()->height());
-  setTransform(GetTransform(scenerect,viewrect));
-  UpdateAxes();
-}
-
-void PlotViewerPanel::OnZoomY(int delta,QPoint pos)
-{
-  QPointF cursorpos=mapToScene(pos);
-  Real scalefactor=exp(delta/1000.0);
-  QRectF scenerect;
-  scenerect.setCoords(GetMinimumX(),
-                      cursorpos.y()+(GetMaximumY()-cursorpos.y())/scalefactor,
-                      GetMaximumX(),
-                      cursorpos.y()-(cursorpos.y()-GetMinimumY())/scalefactor);
-  QRect viewrect(0,0,viewport()->width(),viewport()->height());
-  setTransform(GetTransform(scenerect,viewrect));
-  UpdateAxes();
-}
-
-void PlotViewerPanel::resizeEvent ( QResizeEvent * event )
-{
-  QGraphicsView::resizeEvent(event);
-  QRect cr=contentsRect();
-  axis_horizontal_->setGeometry(QRect(cr.left(), cr.top()+cr.height()-PlotAxisBase::AXISWIDTH,cr.width(), PlotAxisBase::AXISWIDTH));
-  axis_vertical_->setGeometry(QRect(cr.left(), cr.top(),PlotAxisBase::AXISWIDTH, cr.height()));
-  if(autofit_){
-    QRectF scenerect;
-    scenerect.setCoords(GetMinimumX(),
-                        GetMaximumY(),
-                        mapToScene(QPoint(event->oldSize().width(),0)).x(),
-                        mapToScene(QPoint(0,event->oldSize().height())).y());
-    QRect viewrect(0,0,viewport()->width(),viewport()->height());  QGraphicsView::resizeEvent(event);
-    setTransform(GetTransform(scenerect,viewrect));
-  }else{
-    setTransform(transform().translate(0.0,(event->size().height()-event->oldSize().height())/transform().m22()));
-  }
-  UpdateAxes();
-}
-void PlotViewerPanel::UpdateAxes()
-{
-  axis_horizontal_->SetMinimum(GetMinimumX());
-  axis_horizontal_->SetMaximum(GetMaximumX());
-  axis_vertical_->SetMinimum(GetMinimumY());
-  axis_vertical_->SetMaximum(GetMaximumY());
-  emit rangeChanged(GetMinimumX(),GetMaximumX(),GetDelta());
-}
-
-void PlotViewerPanel::scrollContentsBy ( int dx, int dy )
-{
-  QGraphicsView::scrollContentsBy(dx,dy);
-  UpdateAxes();
-}
-
-void PlotViewerPanel::update()
-{
-  QGraphicsView::update();
-  UpdateAxes();
-}
-
-void PlotViewerPanel::OnTranslate(Real dx, Real dy)
-{
-  translate(dx/transform ().m11(),dy/transform ().m22());
-  update();
-}
-
-void PlotViewerPanel::mousePressEvent( QMouseEvent * event )
-{
-  if(event->button()== Qt::LeftButton){
-    global_mouse_pos_=event->globalPos();
-    return;
-  }
-  QGraphicsView::mousePressEvent(event);
-}
-void PlotViewerPanel::mouseMoveEvent( QMouseEvent * event )
-{
-  if(event->buttons() & Qt::LeftButton){
-    OnTranslate(static_cast<Real>(event->globalPos().x()-global_mouse_pos_.x()),static_cast<Real>(event->globalPos().y()-global_mouse_pos_.y()));
-    global_mouse_pos_=event->globalPos();
-    return;
-  }
-  QGraphicsView::mouseMoveEvent(event);
-}
-
-QTransform PlotViewerPanel::GetTransform(QRectF scenerect, QRect viewrect)
-{
-  qreal vx1,vx2,vy1,vy2;
-  qreal x1,x2,y1,y2;
-  scenerect.getCoords(&x1,&y1,&x2,&y2);;
-  QRectF(viewrect).getCoords(&vx1,&vy1,&vx2,&vy2);
-  Real sx=(vx2-vx1)/(x2-x1);
-  Real sy=(vy2-vy1)/(y2-y1);
-  Real dx=vx1-sx*x1;
-  Real dy=vy1-sy*y1;
-  return QTransform(sx,0.0,0.0,
-                    0.0,sy,0.0,
-                    dx,dy,1.0);
-}
-
-void PlotViewerPanel::SetAutofit(bool fit)
-{
-  autofit_=fit;
-}
-
-}}//ns
diff --git a/modules/gui/src/plot_viewer/plot_viewer_panel.hh b/modules/gui/src/plot_viewer/plot_viewer_panel.hh
deleted file mode 100644
index 535b27534e34e2411aba3c9397b59e11caf8a444..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_viewer_panel.hh
+++ /dev/null
@@ -1,76 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef PLOT_VIEWER_PANEL_HH_
-#define PLOT_VIEWER_PANEL_HH_
-
-
-/*
-  Author: Andreas Schenk
-*/
-
-#include <QWidget>
-#include <QHash>
-#include <QPair>
-#include <QGraphicsView>
-#include "plot_axis_horizontal.hh"
-#include "plot_axis_vertical.hh"
-
-namespace ost{namespace gui{
-
-class DLLEXPORT_OST_GUI PlotViewerPanel:public QGraphicsView
-{
-  Q_OBJECT
-public:
-  PlotViewerPanel(QGraphicsScene * scene, QWidget* parent=0);
-  virtual ~PlotViewerPanel();
-  void SetMinimumX(Real x);
-  void SetMaximumX(Real x);
-  void SetMinimumY(Real x);
-  void SetMaximumY(Real x);
-  void SetMinMax(Real xmin,Real maxx,Real miny, Real maxy);
-  void SetAutofit(bool fit=true);
-  Real GetMinimumX() const;
-  Real GetMaximumX() const;
-  Real GetMinimumY() const;
-  Real GetMaximumY() const;
-  Real GetDelta() const;
-public slots:
-  void OnZoomX(int delta,QPoint pos);
-  void OnZoomY(int delta,QPoint pos);
-  void OnTranslate(Real dx, Real dy);
-  void update();
-signals:
-  void rangeChanged(Real start, Real end, Real delta);
-protected:
-  virtual void wheelEvent ( QWheelEvent * e );
-  virtual void resizeEvent ( QResizeEvent * event );
-  virtual void scrollContentsBy ( int dx, int dy );
-  virtual void mousePressEvent ( QMouseEvent * event );
-  virtual void mouseMoveEvent ( QMouseEvent * event );
-  void UpdateAxes();
-  QTransform GetTransform(QRectF scenerect, QRect viewrect);
-  PlotAxisHorizontal* axis_horizontal_;
-  PlotAxisVertical* axis_vertical_;
-  QPointF global_mouse_pos_;
-  bool autofit_;
-};
-
-}}//ns
-
-#endif /*PLOT_VIEWER_PANEL_HH_*/
diff --git a/modules/gui/src/plot_viewer/plot_viewer_proxy.cc b/modules/gui/src/plot_viewer/plot_viewer_proxy.cc
deleted file mode 100644
index 4f926ce7474e87f8766126a72394824caa6adb0f..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_viewer_proxy.cc
+++ /dev/null
@@ -1,103 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-/*
-  Authors: Andreas Schenk, Johan Hebert, Ansgar Philippsen
-*/
-
-#include "plot_viewer.hh"
-#include "plot_viewer_proxy.hh"
-#include "plot_data_info.hh"
-
-namespace ost{namespace gui{
-
-PlotViewerProxy::PlotViewerProxy():
-  viewer_(0)
-{
-}
-PlotViewerProxy::PlotViewerProxy(PlotViewer* v):
-  viewer_(v)
-{
-}
-
-PlotViewerProxy::~PlotViewerProxy()
-{
-}
-
-
-
-void PlotViewerProxy::Release(PlotViewer* v)
-{
-  if(viewer_==v) {
-    viewer_=0;
-  }
-}
-PlotDataInfoPtr PlotViewerProxy::Add(PlotDataPtr dataptr, bool fit)
-{
-  if(! viewer_) return PlotDataInfoPtr(new PlotDataInfo());
-  return viewer_->Add(dataptr,fit);
-}
-PlotFunctionInfoPtr PlotViewerProxy::Add(PlotFunctionPtr functionptr)
-{
-  if(! viewer_) return PlotFunctionInfoPtr(new PlotFunctionInfo());
-  return viewer_->Add(functionptr);
-}
-PlotGroupInfoPtr PlotViewerProxy::Add(PlotGroupPtr groupptr, bool fit)
-{
-  if(! viewer_) return PlotGroupInfoPtr(new PlotGroupInfo());
-  return viewer_->Add(groupptr,fit);
-}
-
-void PlotViewerProxy::SetMinimumX(Real x)
-{
-  viewer_->SetMinimumX(x);
-}
-void PlotViewerProxy::SetMaximumX(Real x)
-{
-  viewer_->SetMaximumX(x);
-}
-void PlotViewerProxy::SetMinimumY(Real y)
-{
-  viewer_->SetMinimumY(y);
-}
-void PlotViewerProxy::SetMaximumY(Real y)
-{
-  viewer_->SetMaximumY(y);
-}
-Real PlotViewerProxy::GetMinimumX() const
-{
-  return viewer_->GetMinimumX();
-}
-Real PlotViewerProxy::GetMaximumX() const
-{
-  return viewer_->GetMaximumX();
-}
-Real PlotViewerProxy::GetMinimumY() const
-{
-  return viewer_->GetMinimumY();
-}
-Real PlotViewerProxy::GetMaximumY() const
-{
-  return viewer_->GetMaximumY();
-}
-
-void PlotViewerProxy::SetAutofit(bool fit)
-{
-  viewer_->SetAutofit(fit);
-}
-}}//ns
diff --git a/modules/gui/src/plot_viewer/plot_viewer_proxy.hh b/modules/gui/src/plot_viewer/plot_viewer_proxy.hh
deleted file mode 100644
index 3da5b22036454355ee7aa0d39791724ae852fe3a..0000000000000000000000000000000000000000
--- a/modules/gui/src/plot_viewer/plot_viewer_proxy.hh
+++ /dev/null
@@ -1,68 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef PLOT_VEWER_PROXY_HH_
-#define PLOT_VEWER_PROXY_HH_
-
-/*
-  Authors: Andreas Schenk, Johan Hebert, Ansgar Philippsen
-*/
-
-#include <boost/shared_ptr.hpp>
-
-#include "plot_viewer_proxy_fw.hh"
-
-//TODO add forward header to PlotData, etc. and include that
-#include "plot_data.hh"
-#include "plot_function.hh"
-#include "plot_group.hh"
-#include "plot_data_info_fw.hh"
-#include "plot_function_info.hh"
-#include "plot_group_info.hh"
-
-namespace ost{namespace gui{
-
-//fw decl
-class PlotViewer;
-
-class DLLEXPORT_OST_GUI PlotViewerProxy
-{
-public:
-  PlotViewerProxy();
-  PlotViewerProxy(PlotViewer* v);
-  virtual ~PlotViewerProxy();
-  void Release(PlotViewer* v);
-  PlotDataInfoPtr Add(PlotDataPtr dataptr, bool fit=false);
-  PlotFunctionInfoPtr Add(PlotFunctionPtr functionptr);
-  PlotGroupInfoPtr Add(PlotGroupPtr groupptr, bool fit=false);
-  void SetMinimumX(Real x);
-  void SetMaximumX(Real x);
-  void SetMinimumY(Real y);
-  void SetMaximumY(Real y);
-  Real GetMinimumX() const;
-  Real GetMaximumX() const;
-  Real GetMinimumY() const;
-  Real GetMaximumY() const;
-  void SetAutofit(bool fit=true);
-private:
-  PlotViewer* viewer_;
-};
-
-}}//ns
-
-#endif /*PLOT_VEWER_PROXY_HH_*/
diff --git a/modules/gui/src/python_shell/completer_base.cc b/modules/gui/src/python_shell/completer_base.cc
index 1b92a4736ab09b2f5a3c81c7e89d2e4fc4ec2f8d..a63d3b0bac2cddae7edee71b413685f1e803c9c8 100644
--- a/modules/gui/src/python_shell/completer_base.cc
+++ b/modules/gui/src/python_shell/completer_base.cc
@@ -20,6 +20,7 @@
   Authors: Marco Biasini, Andreas Schenk
  */
 
+#include "completer_base.hh"
 
 #include <QStringList>
 #include <QScrollBar>
@@ -27,7 +28,6 @@
 #include <QKeyEvent>
 #include <QApplication>
 
-#include "completer_base.hh"
 
 
 namespace ost { namespace gui {
@@ -61,6 +61,7 @@ void OstCompleterBase::complete(const QRect & rect,bool inline_completion)
                            (popup()->verticalScrollBar()->isVisible() ? 
                             popup()->verticalScrollBar()->width():0);
   popup()->setFixedWidth(popup_width);
+  popup()->move(widget()->mapToGlobal(rect.topLeft()+QPoint(0,-popup()->height())));
 }
 
 QString OstCompleterBase::GetCommonMatch()
@@ -70,7 +71,7 @@ QString OstCompleterBase::GetCommonMatch()
   }
   QStringList matches;
   for(int i=0;i<completionCount();++i){
-  setCurrentRow(i);
+    setCurrentRow(i);
     matches.append(currentCompletion().remove(0,completionPrefix().length()));
   }
   QString common_match;
diff --git a/modules/gui/src/python_shell/dir_model.cc b/modules/gui/src/python_shell/dir_model.cc
index 96c57f61a1c308829fd1f8440a0509d86afd751a..e4d2c049bce398096108d46db00bec0da1ac3579 100644
--- a/modules/gui/src/python_shell/dir_model.cc
+++ b/modules/gui/src/python_shell/dir_model.cc
@@ -20,7 +20,6 @@
   Author: Andreas Schenk
  */
 
-
 #include "dir_model.hh"
 
 
diff --git a/modules/gui/src/python_shell/gutter.cc b/modules/gui/src/python_shell/gutter.cc
index fa952218400a5ab350d62a01238f1d4a90944288..e60b4c4d6b8985535c67ab6fa4d8480a601d5ab4 100644
--- a/modules/gui/src/python_shell/gutter.cc
+++ b/modules/gui/src/python_shell/gutter.cc
@@ -51,17 +51,17 @@ void Gutter::paintEvent(QPaintEvent* paint_event)
   painter.fillRect(paint_event->rect(), QBrush(Qt::lightGray));
   for (GutterBlockList::const_iterator it=blocks.begin(); 
        it!=blocks.end(); ++it) {
-    if (it->type == BLOCKTYPE_ACTIVE) {
+    if (it->type & BLOCKTYPE_ACTIVE) {
       QColor green(Qt::green);
       painter.setPen(QPen(green.darker(), 3));
-    }else  if (it->type == BLOCKTYPE_BLOCKEDIT) {
+    }else  if (it->type & BLOCKTYPE_BLOCKEDIT) {
         painter.setPen(QPen(Qt::yellow, 3));
-    }else  if (it->type == BLOCKTYPE_CODE) {
+    }else  if (it->type & BLOCKTYPE_CODE) {
         QColor green(Qt::green);
         painter.setPen(QPen(green.darker(), 1));
-    } else if (it->type == BLOCKTYPE_OUTPUT) {
+    } else if (it->type & BLOCKTYPE_OUTPUT) {
       painter.setPen(QPen(Qt::blue, 1));
-    } else if (it->type == BLOCKTYPE_ERROR) {
+    } else if (it->type & BLOCKTYPE_ERROR) {
       painter.setPen(QPen(Qt::red, 1));
     } else {
       painter.setPen(QPen(Qt::black, 1));
diff --git a/modules/gui/src/python_shell/main_thread_runner.hh b/modules/gui/src/python_shell/main_thread_runner.hh
index 056dd6165a1be9a3d0d6e6aeb5ddd1c53e4ee61e..399fd8c0328486bce9014d585093da3129ee9640 100644
--- a/modules/gui/src/python_shell/main_thread_runner.hh
+++ b/modules/gui/src/python_shell/main_thread_runner.hh
@@ -25,9 +25,9 @@
   Author: Andreas Schenk
 */
 
-#include <QObject>
 #include <ost/gui/module_config.hh>
 
+#include <QObject>
 namespace ost { namespace gui {
 
 
diff --git a/modules/gui/src/python_shell/output_redirector.cc b/modules/gui/src/python_shell/output_redirector.cc
index 2702b057a74abe66a3e52c8b0f695d7a8bb44f3a..e86879a82307a80a005b5545806ed53cad4366d5 100644
--- a/modules/gui/src/python_shell/output_redirector.cc
+++ b/modules/gui/src/python_shell/output_redirector.cc
@@ -23,22 +23,47 @@
 */
 
 #include "output_redirector.hh"
+#include <QTimer>
 
 
 namespace ost { namespace gui {
 
+OutputRedirector::OutputRedirector():
+ QObject(),
+ buffer_(),
+ timer_()
+{
+}
+
+
 void OutputRedirector::Write( String const& str )
 {
-  buffer_.append(str);
+  if(timer_.isValid()){
+    if(timer_.elapsed()>1000){
+      QString output = buffer_+QString::fromStdString(str);
+      buffer_="";
+      emit OnOutput(output);
+      timer_.restart();
+    }else{
+      buffer_+=QString::fromStdString(str);
+    }
+  }else{
+    buffer_+=QString::fromStdString(str);
+    timer_.start();
+    QTimer::singleShot(0, this, SLOT(Flush()));
+  }
 }
-QString OutputRedirector::GetOutput()
+
+void OutputRedirector::Flush()
 {
-  QString  ret=QString::fromStdString(buffer_);
-  ret.chop(1); // chop off additional newline
-  buffer_.clear();
-  return ret;
+  if(! timer_.isValid()){
+    return;
+  }
+  timer_=QTime();
+  QString output = buffer_;
+  buffer_="";
+  emit OnOutput(output);
 }
-String  OutputRedirector::buffer_; 
 
 
 
diff --git a/modules/gui/src/python_shell/output_redirector.hh b/modules/gui/src/python_shell/output_redirector.hh
index 664c696cbdb1bbe87c9e807cbbb0c0223db89572..2d13948a268c80f985b692c7e5acc7478b40abf4 100644
--- a/modules/gui/src/python_shell/output_redirector.hh
+++ b/modules/gui/src/python_shell/output_redirector.hh
@@ -26,17 +26,26 @@
   Author: Andreas Schenk
 */
 
-#include <QString>
 #include <ost/gui/module_config.hh>
+#include <QTime>
+#include <QString>
+#include <QObject>
 
 namespace ost { namespace gui {
 
-class DLLEXPORT_OST_GUI OutputRedirector {
+class DLLEXPORT_OST_GUI OutputRedirector: public QObject {
+Q_OBJECT
+
 public:
+  OutputRedirector();
   void Write(const String& str);
-  static QString GetOutput();
+public slots:
+  void Flush();
+signals:
+  void OnOutput(const QString& output);
 private:
-    static String  buffer_; 
+    QString  buffer_;
+    QTime timer_;
 };
 
 }}//ns
diff --git a/modules/gui/src/python_shell/python_completer.cc b/modules/gui/src/python_shell/python_completer.cc
index 4618fb74500a69845b530aa27a70f363519d1cc8..d0346397201149c88fb9acb5dc72adaa7db7a244 100644
--- a/modules/gui/src/python_shell/python_completer.cc
+++ b/modules/gui/src/python_shell/python_completer.cc
@@ -22,9 +22,9 @@
 
 #include <iostream>
 
-#include <QStringList>
 #include "python_completer.hh"
 #include "python_namespace_tree_model.hh"
+#include <QStringList>
 
 
 namespace ost { namespace gui {
diff --git a/modules/gui/src/python_shell/python_interpreter.cc b/modules/gui/src/python_shell/python_interpreter.cc
index 2ac697de50880e3081905be5b4eae14bd0d65520..3dea745a5cdc9265fed41ffe9abbdb8aed624856 100644
--- a/modules/gui/src/python_shell/python_interpreter.cc
+++ b/modules/gui/src/python_shell/python_interpreter.cc
@@ -30,13 +30,12 @@
 #include <fstream>
 
 #include <boost/filesystem/convenience.hpp>
+#include <ost/log.hh>
 
 #include <QFile>
 #include <QDebug>
-#include <QApplication>
-#include <QThread>
+#include <QFile>
 #include <QStringList>
-#include <ost/log.hh>
 
 namespace ost { namespace gui {
 
@@ -44,246 +43,78 @@ PythonInterpreter::PythonInterpreter():
   QObject(),
   main_module_(),
   main_namespace_(),
-#ifndef _MSC_VER
-  sig_act_(),
-#endif
-  output_redirector_(),
-  main_thread_runner_(),
   running_(false),
-  mutex_(),
-  gstate_(),
-  main_thread_state_(NULL),
-  proxy_(this),
   compile_command_(),
-  exec_wait_(false),
-  exec_queue_(),
-  parse_expr_cmd_()  
-{
-}
-
-PythonInterpreter::~PythonInterpreter()
-{
- PyGILState_Release(gstate_);
- PyEval_RestoreThread(main_thread_state_);
-}
-
-PythonInterpreter& PythonInterpreter::Instance(bool register_sighandler, 
-                                               bool multithreaded)
-{
-  //todo handle register_sighandler;
-  static bool initialized=false;
-  static PythonInterpreter instance;
-  static QThread thread;
-  if(!initialized){
-    initialized=true;
-    if(multithreaded){
-      instance.moveToThread(&thread);
-      thread.start();
-      instance.Init(true);
-    }else{
-      instance.Init(false);
-    }
-  }
-  return instance;
-}
-
-void PythonInterpreter::Init(bool multithreaded)
+  worker_()
 {
-  if(multithreaded){
-    //initialize over a blocking queued connection to get the correct thread context
-  /*  connect(this, SIGNAL(InitSignal(bool)),this, SLOT(InitSlot(bool)),Qt::BlockingQueuedConnection);
-    emit InitSignal(true);*/
-  }else{
-    // direct initalization
-    InitSlot(false);
-  }
-}
-
-void PythonInterpreter::RedirectOutput()
-{
-  main_namespace_["sys"].attr("stderr") = output_redirector_;
-  main_namespace_["sys"].attr("stdout") = output_redirector_;
-}
-
-void PythonInterpreter::InitSlot(bool multithreaded)
-{
-  if(multithreaded){
-    //main_thread_runner_.moveToThread(QApplication::instance()->thread());
-    //connect(this,SIGNAL(RunInMainThreadSignal(const QString&)),&main_thread_runner_,SLOT(Run(const QString&)),Qt::BlockingQueuedConnection);
-  }else{
-    connect(this,SIGNAL(RunInMainThreadSignal(const QString&)),&main_thread_runner_,SLOT(Run(const QString&)),Qt::DirectConnection);
-  }
-  Py_InitializeEx(1);
-  PyEval_InitThreads();
-  main_thread_state_ = PyEval_SaveThread();
-  gstate_ = PyGILState_Ensure();
-  //store signal handler
-  #ifndef _MSC_VER
-  sigaction(SIGINT,0,&sig_act_);
-  #endif
+  connect(this,SIGNAL(WakeWorker()),&worker_,SLOT(Wake()),Qt::QueuedConnection);
+  connect(&worker_,SIGNAL(Output(unsigned int,const QString&)),this,SIGNAL(Output(unsigned int,const QString&)));
+  connect(&worker_,SIGNAL(ErrorOutput(unsigned int,const QString&)),this,SIGNAL(ErrorOutput(unsigned int,const QString&)));
+  connect(&worker_,SIGNAL(Finished(unsigned int, bool)),this,SIGNAL(Finished(unsigned int, bool)));
   main_module_ = bp::import("__main__");
-  main_module_.attr("in_gui_mode")=true;  
   main_namespace_ = bp::extract<bp::dict>(main_module_.attr("__dict__"));
-  parse_expr_cmd_=bp::import("parser").attr("expr");  
-  main_namespace_["OutputRedirector"] = bp::class_<OutputRedirector>("OutputRedirector", bp::init<>())
-                                          .def("write", &OutputRedirector::Write);
-  main_namespace_["PythonInterpreterProxy"] = bp::class_<PythonInterpreterProxy>("PythonInterpreterProxy", bp::init<PythonInterpreter*>())
-                                          .def("Run", &PythonInterpreterProxy::Run);
-
   main_namespace_["os"]=bp::import("os");
   main_namespace_["__builtin__"]=bp::import("__builtin__");
   main_namespace_["keyword"]=bp::import("keyword");
-
-  parse_expr_cmd_=bp::import("parser").attr("expr");  
-
-  main_namespace_["sys"]=bp::import("sys");  
-
-  main_module_.attr("Proxy")=proxy_;
   bp::object code=bp::import("code");
   compile_command_=code.attr("compile_command");
-
 }
 
-namespace {
-#ifndef _MSC_VER
-  class SigIntHandler {
-  public:
-    SigIntHandler(const struct sigaction& act) {
-      sigaction(SIGINT,&act,&old_);
-    }
-    ~SigIntHandler() {
-      sigaction(SIGINT,&old_,0);
-    }
-  private:
-    struct sigaction old_;
-  };
-#endif
-}
-void PythonInterpreter::RunInitRC()
+PythonInterpreter::~PythonInterpreter()
 {
-  if(!getenv("HOME")) return;
-  String fname=String(getenv("HOME"))+"/.dngrc";
-  try {
-    if (boost::filesystem::exists(fname)) {
-      try {
-        bp::exec_file(bp::str(fname), main_module_.attr("__dict__"), 
-                      main_module_.attr("__dict__"));      
-      } catch(bp::error_already_set&) {
-        PyErr_Print();
-      }
-    }
-  } catch(std::exception&) {
-    // silently ignore. needed for boost 1.33.1
-  }  
 }
 
-void PythonInterpreter::ExecWait()
+PythonInterpreter& PythonInterpreter::Instance()
 {
-  ++exec_wait_;
+  static PythonInterpreter instance;
+  return instance;
 }
 
-void PythonInterpreter::ExecRelease()
+
+
+void PythonInterpreter::Stop()
 {
-  --exec_wait_;
-  assert(exec_wait_>=0);
-  if(exec_wait_==0) {
-    for(std::vector<QString>::const_iterator it=exec_queue_.begin();
-        it!=exec_queue_.end();++it) {
-      if(!RunCommand(*it)) break;        
-    }
-    exec_queue_.clear();
-  }
+  running_=false;
 }
 
-void PythonInterpreter::RunScript(const String& fname)
+void PythonInterpreter::Start()
 {
-    QFile file(QString::fromStdString(fname));
-  if (!file.open(QIODevice::ReadOnly | QIODevice::Text)){
-    LOGN_ERROR("could not open " << fname);
-    return;
-  }
-  QTextStream in(&file);
-  RunCommand(in.readAll());
+  running_=true;
+    emit WakeWorker();
 }
 
-bool PythonInterpreter::IsSimpleExpression(const QString& expr)
+
+
+unsigned int PythonInterpreter::RunScript(const QString& fname)
 {
-  try {
-    parse_expr_cmd_(bp::str(expr.toStdString()));
-    return true;
-  } catch(bp::error_already_set&) {
-    PyErr_Clear();
-    return false;
+  QFile script(fname);
+  if (!script.open(QIODevice::ReadOnly | QIODevice::Text)){
+    LOG_ERROR("could not open " << fname.toStdString());
+    return RunCommand("");
   }
+  QString command=script.readAll();
+  command.append('\n');
+  command.append('\n');
+  return RunCommand(command);
 }
 
-bool PythonInterpreter::RunCommand(const QString& command)
+unsigned int PythonInterpreter::RunCommand(const QString& command)
 {
-  bool flag=true;
-  if(exec_wait_!=0) {
-    exec_queue_.push_back(command);
-    return flag;
+  unsigned int id=worker_.AddCommand(command);
+  if(running_){
+    emit WakeWorker();
   }
-
-  // becore doing anything give Qt the chance to handle events for 100ms
-  QCoreApplication::processEvents(QEventLoop::ExcludeUserInputEvents,100);
-  mutex_.lock();
-  running_=true;
-  mutex_.unlock();
-#ifndef _MSC_VER
-  SigIntHandler sh(sig_act_);
-#endif
-  try{
-    if(command.indexOf(QString("\n"))==-1){
-      if(command=="exit" || command=="quit"){
-        emit Exit();
-      }
-      if (this->IsSimpleExpression(command)) {
-        bp::object repr=main_module_.attr("__builtins__").attr("repr");
-        bp::object result=bp::eval(bp::str(command.toStdString()),
-                                   main_namespace_, main_namespace_);
-        String rstring=bp::extract<String>(repr(result));
-        if(rstring!="None"){
-          output_redirector_.Write(rstring);
-          output_redirector_.Write("\n");
-        }
-        emit Done(STATUS_OK,output_redirector_.GetOutput());
-        flag=true;
-      } else {
-        bp::exec(bp::str(command.toStdString()),main_namespace_,main_namespace_);
-        flag=true;
-      }
-    }else{
-      bp::exec(bp::str(command.toStdString()),main_namespace_,main_namespace_);
-    }
-    emit Done(STATUS_OK,output_redirector_.GetOutput());
-  }catch(bp::error_already_set){
-    if(PyErr_ExceptionMatches(PyExc_SystemExit)){
-      PyErr_Clear();
-      emit Exit();
-    } else{
-      PyErr_Print();
-      QString output=output_redirector_.GetOutput();
-      std::cout << output.toStdString() << std::endl;
-      emit Done(STATUS_ERROR,output);
-      flag=false;
-    }
-  }
-  mutex_.lock();
-  running_=false;
-  mutex_.unlock();
-  return flag;
+  return id;
 }
 
 CodeBlockStatus PythonInterpreter::GetCodeBlockStatus(const QString& command)
 {
+  // move to pure c++ to avoid clash with running worker
+  // move to worker class
   CodeBlockStatus status=CODE_BLOCK_COMPLETE;
-  mutex_.lock();
-  running_=true;
-  mutex_.unlock();
-#ifndef _MSC_VER
+/*#ifndef _MSC_VER
   SigIntHandler sh(sig_act_);
-#endif
+#endif*/
   QStringList lines=command.split("\n");  
   String cmd;  
   for (int i=0; i<lines.size(); ++i) {
@@ -317,70 +148,9 @@ CodeBlockStatus PythonInterpreter::GetCodeBlockStatus(const QString& command)
       }
     }
   }
-  mutex_.lock();
-  running_=false;
-  mutex_.unlock();
-  return status;
-}
-
-enum returncodes{
-    RC_OK=0,
-    RC_ERROR=2>>1,
-    RC_LOOP=2,
-    RC_EXIT=2<<1,
-};
-
-void PythonInterpreter::CallFunction(const bp::object& func,
-                                     const bp::object& args)
-{
-  unsigned int retcode=RC_OK;
-  bool result;
-  try{
-#ifndef _MSC_VER
-  SigIntHandler sh(sig_act_);
-#endif
-    if (len(args)>0) {
-      result=bp::extract<bool>(func(args));
-    } else {
-      result=bp::extract<bool>(func());
-    }
-    if (!result) {
-      retcode|=RC_ERROR;
-      PyErr_Print();
-    }
-  } catch(bp::error_already_set) {
-    if (PyErr_ExceptionMatches(PyExc_KeyboardInterrupt)){
-      retcode|=RC_EXIT;
-    } else {
-      PyErr_Print();
-      retcode|=RC_ERROR;
-    }
-  }
+   return status;
 }
 
-bool PythonInterpreter::IsRunning()
-{
-  mutex_.lock();
-  bool state=running_;
-  mutex_.unlock();
-  return state;
-}
-
-void PythonInterpreter::Abort()
-{
-  if(IsRunning()){
-    raise(SIGINT);
-  }
-}
-
-bp::object PythonInterpreter::RunInMainThread(const QString& widget)
-{
-  PyGILState_Release(gstate_);
-  emit RunInMainThreadSignal(widget);
-  gstate_ = PyGILState_Ensure();
-  return main_module_.attr("Proxy").attr("_widget_");
-
-}
 
 void PythonInterpreter::AppendModulePath(const QString& entry)
 {
@@ -401,18 +171,6 @@ void PythonInterpreter::AppendCommandlineArgument(const QString& arg)
   RunCommand(init_code);
 }
 
-void PythonInterpreter::SetCommandLineArguments(const QList<QString>& args)
-{
-  QString init_code("");
-  init_code += "\nsys.argv=[]";  
-  for (QList<QString>::const_iterator i=args.begin(), e=args.end(); i!=e; ++i) {
-    init_code += "\nsys.argv.append('" ;
-    init_code += *i;    
-    init_code += "')\n";    
-  }
-
-  RunCommand(init_code);
-}
 bp::object PythonInterpreter::GetMainModule() const
 {
   return main_module_;
diff --git a/modules/gui/src/python_shell/python_interpreter.hh b/modules/gui/src/python_shell/python_interpreter.hh
index bb69f5fe9877054b114426d2ecc78c57edf1860c..ec6639bbb8d10342b657afc43eda2096dea9c67a 100644
--- a/modules/gui/src/python_shell/python_interpreter.hh
+++ b/modules/gui/src/python_shell/python_interpreter.hh
@@ -27,21 +27,18 @@
 #ifndef PYTHON_INTERPRETER_HH
 #define PYTHON_INTERPRETER_HH
 
-#include <csignal>
 #include <vector>
 
-#include <QMutex>
-#include <QMetaType>
-
-#include <boost/python.hpp>
-
 #include <ost/gui/module_config.hh>
 
 #include <ost/gui/module_config.hh>
-#include "python_interpreter_proxy.hh"
+#include "python_interpreter_worker.hh"
 #include "output_redirector.hh"
 #include "main_thread_runner.hh"
 
+#include <QQueue>
+#include <QMetaType>
+
 namespace ost { namespace gui {
 namespace bp = boost::python;
 
@@ -52,34 +49,22 @@ enum InterpreterStatus{
 
 
 typedef enum {
-   CODE_BLOCK_COMPLETE,
-   CODE_BLOCK_ERROR,
-   CODE_BLOCK_INCOMPLETE  
+   CODE_BLOCK_COMPLETE=1,
+   CODE_BLOCK_ERROR=2,
+   CODE_BLOCK_INCOMPLETE=4
 } CodeBlockStatus;
 
 class DLLEXPORT_OST_GUI PythonInterpreter: public QObject
 {
   Q_OBJECT
 public:
-  static PythonInterpreter& Instance(bool set_sigint_handler=true, 
-                                     bool multitreaded=false);
+  static PythonInterpreter& Instance();
 
   ~PythonInterpreter();
   bool IsRunning();
-  bp::object RunInMainThread(const QString& widget);
   void AppendModulePath(const QString& entry);
   
   void AppendCommandlineArgument(const QString& arg);
-  /// \brief set command line arguments
-  /// 
-  /// Sets sys.argv to the given list of arguments
-  /// 
-  /// The method internally uses RunCommand and is thus appended to the command
-  /// list when execution is delayed due to an open ExecWait() ExecRelease() 
-  /// block
-  /// 
-  /// \todo escape arguments
-  void SetCommandLineArguments(const QList<QString>& args);
   
   bp::dict GetMainNamespace() const;
   bp::object GetMainModule() const;
@@ -88,62 +73,34 @@ public:
   /// Determines whether the command contains errors, is incomplete or ready
   /// to be run.
   CodeBlockStatus GetCodeBlockStatus(const QString& command);
-  void RunInitRC();
 
-  void RunScript(const String& script);
   
-  /// \brief delay execution of Python commands
-  /// 
-  /// The execution of Python commands with RunCommand and methods that
-  /// make use of RunCommand is delayed until ExecRelease() is called.
-  /// ExecWait(), ExecRelease() calls can be nested.
+  /// \brief stop execution of Python commands
+  /// \sa Start
+  void Stop();
+  /// \brief start/continue execution of Python commands
   /// 
-  /// \sa ExecRelease
-  void ExecWait();
-  /// \brief execute pending Python commands
-  /// 
-  /// \sa ExecWait
-  void ExecRelease();
+  /// \sa Stop
+  void Start();
   
-  /// \brief turn on output redirection
-  void RedirectOutput();
-  /// \brief whether the string can be interpreted as a simple expression
-  /// 
-  /// import and any kind of control structures don't count as simple 
-  /// expressions and will return false.
-  bool IsSimpleExpression(const QString& expr);
 
 public slots:
   /// \brief execute python command
-  bool RunCommand(const QString& command);
-  void CallFunction(const bp::object& func,const bp::object& args);
-  void Abort();
-protected slots:
-  void InitSlot(bool multitreaded);
+  unsigned int RunScript(const QString& script);
+  unsigned int RunCommand(const QString& command);
 signals:
-  void Done(int status,const QString& output);
+  void Output(unsigned int id,const QString& output);
+  void ErrorOutput(unsigned int id,const QString& output);
+  void Finished(unsigned int id, bool error_state);
   void Exit();
-  void InitSignal(bool multitreaded);
-  void RunInMainThreadSignal(const QString& widget);
+  void WakeWorker();
 protected:
-  void Init(bool multitreaded);
   PythonInterpreter();
   bp::object main_module_;
   bp::dict main_namespace_;
-#ifndef _MSC_VER
-  struct sigaction sig_act_;
-#endif
-  OutputRedirector  output_redirector_;
-  MainThreadRunner main_thread_runner_;
   bool running_;
-  QMutex mutex_;
-  PyGILState_STATE gstate_;
-  PyThreadState* main_thread_state_;
-  PythonInterpreterProxy proxy_;
   bp::object compile_command_;
-  int exec_wait_;
-  std::vector<QString>      exec_queue_;
-  bp::object parse_expr_cmd_;  
+  PythonInterpreterWorker worker_;
 };
 
 }} // ns
diff --git a/modules/gui/src/python_shell/python_interpreter_proxy.hh b/modules/gui/src/python_shell/python_interpreter_proxy.hh
index 1cb54fa0b0113ab35d8dbbbed0712d62064dff30..30ba00be194fcc2bf97bc75a5f843fc30ea90ba6 100644
--- a/modules/gui/src/python_shell/python_interpreter_proxy.hh
+++ b/modules/gui/src/python_shell/python_interpreter_proxy.hh
@@ -25,6 +25,7 @@
   Author: Andreas Schenk
 */
 
+#include <boost/python.hpp>
 #include <ost/gui/module_config.hh>
 
 namespace ost { namespace gui {
diff --git a/modules/gui/src/python_shell/python_interpreter_worker.cc b/modules/gui/src/python_shell/python_interpreter_worker.cc
new file mode 100644
index 0000000000000000000000000000000000000000..494df6c0bca61cd5b4a67791d55128c7d27a5ab9
--- /dev/null
+++ b/modules/gui/src/python_shell/python_interpreter_worker.cc
@@ -0,0 +1,136 @@
+#include "python_interpreter_worker.hh"
+#include "python_interpreter.hh"
+
+namespace ost { namespace gui {
+
+    namespace {
+#ifndef _MSC_VER
+  class SigIntHandler {
+  public:
+    SigIntHandler(const struct sigaction& act) {
+      sigaction(SIGINT,&act,&old_);
+    }
+    ~SigIntHandler() {
+      sigaction(SIGINT,&old_,0);
+    }
+  private:
+    struct sigaction old_;
+  };
+#endif
+}
+
+
+
+PythonInterpreterWorker::PythonInterpreterWorker():
+  exec_queue_(),
+  command_id_(0),
+  output_redirector_(new OutputRedirector),
+  error_redirector_(new OutputRedirector),
+  #ifndef _MSC_VER
+  sig_act_(),
+  #endif
+  parse_expr_cmd_(),
+  repr_(),
+  main_namespace_(),
+  current_id_()
+{
+  Py_InitializeEx(1);
+  parse_expr_cmd_=bp::import("parser").attr("expr");
+  main_namespace_ = bp::extract<bp::dict>(bp::import("__main__").attr("__dict__"));
+  repr_=bp::import("__main__").attr("__builtins__").attr("repr");
+  #ifndef _MSC_VER
+  sigaction(SIGINT,0,&sig_act_);
+  #endif
+  main_namespace_["OutputRedirector"] = bp::class_<OutputRedirector,boost::shared_ptr<OutputRedirector>, boost::noncopyable >("OutputRedirector", bp::init<>())
+                                          .def("write", &OutputRedirector::Write);
+  connect(output_redirector_.get(),SIGNAL(OnOutput(const QString&)),this,SLOT(handle_redirector_output(const QString&)));
+  connect(error_redirector_.get(),SIGNAL(OnOutput(const QString&)),this,SLOT(handle_redirector_error(const QString&)));
+  main_namespace_["sys"]=bp::import("sys");
+  main_namespace_["sys"].attr("stderr") = error_redirector_;
+  main_namespace_["sys"].attr("stdout") = output_redirector_;
+}
+
+void PythonInterpreterWorker::Wake()
+{
+  while (!exec_queue_.isEmpty()){
+    std::pair<unsigned int, QString> pair=exec_queue_.dequeue();
+    run_command_(pair);
+  }
+}
+
+unsigned int PythonInterpreterWorker::AddCommand(const QString& command)
+{
+  exec_queue_.enqueue(std::pair<unsigned int, QString>(++command_id_,command)); //wrap around in command_id_ intended
+  return command_id_;
+}
+
+bool PythonInterpreterWorker::is_simple_expression_(const QString& expr)
+{
+  try {
+    parse_expr_cmd_(bp::str(expr.toStdString()));
+    return true;
+  } catch(bp::error_already_set&) {
+    PyErr_Clear();
+    return false;
+  }
+}
+void PythonInterpreterWorker::run_command_(std::pair<unsigned int,QString> pair)
+{
+  #ifndef _MSC_VER
+  SigIntHandler sh(sig_act_);
+  #endif
+  try{
+    // todo handle quit and exit without parantheses
+    current_id_=pair.first;
+    QString command=pair.second;
+    if(is_simple_expression(command)){
+      bp::object result=bp::eval(bp::str(command.toStdString()),
+                                 main_namespace_, main_namespace_);
+      String rstring=bp::extract<String>(repr_(result));
+      if(rstring!="None"){
+        handle_redirector_output(QString::fromStdString(rstring)+"\n");
+      }
+    } else {
+      bp::exec(bp::str(command.toStdString()),main_namespace_,main_namespace_);
+    }
+    output_redirector_->Flush();
+    error_redirector_->Flush();
+    emit Finished(pair.first,true);
+    return;
+  }catch(bp::error_already_set){
+    if(PyErr_ExceptionMatches(PyExc_SystemExit)){
+      PyErr_Clear();
+      //emit Exit();
+    } else{
+      PyErr_Print();
+    }
+  }
+  output_redirector_->Flush();
+  error_redirector_->Flush();
+  emit Finished(pair.first,false);
+  return;
+}
+
+bool PythonInterpreterWorker::is_simple_expression(const QString& expr)
+{
+  try {
+    parse_expr_cmd_(bp::str(expr.toStdString()));
+    return true;
+  } catch(bp::error_already_set&) {
+    PyErr_Clear();
+    return false;
+  }
+}
+
+void PythonInterpreterWorker::handle_redirector_output(const QString& output)
+{
+  emit Output(current_id_,output);
+}
+
+void PythonInterpreterWorker::handle_redirector_error(const QString& output)
+{
+  emit ErrorOutput(current_id_,output);
+}
+
+}} //ns
+
diff --git a/modules/gui/src/python_shell/python_interpreter_worker.hh b/modules/gui/src/python_shell/python_interpreter_worker.hh
new file mode 100644
index 0000000000000000000000000000000000000000..77295ca8612f5877555408774a41f1a945f56de9
--- /dev/null
+++ b/modules/gui/src/python_shell/python_interpreter_worker.hh
@@ -0,0 +1,53 @@
+#ifndef PYTHON_INTERPRETER_WORKER_HH
+#define PYTHON_INTERPRETER_WORKER_HH
+
+#include <csignal>
+#include <utility>
+#include <boost/python.hpp>
+#include <boost/shared_ptr.hpp>
+#include "output_redirector.hh"
+#include <QObject>
+#include <QQueue>
+
+namespace ost { namespace gui {
+namespace bp = boost::python;
+
+class PythonInterpreterWorker: public QObject
+{
+Q_OBJECT
+public:
+  PythonInterpreterWorker();
+  unsigned int AddCommand(const QString& command);
+
+signals:
+  void Finished(unsigned int id, bool error_state);
+  void Output(unsigned int id,const QString& output);
+  void ErrorOutput(unsigned int id,const QString& output);
+
+public slots:
+  void Wake();
+
+protected slots:
+  void handle_redirector_output(const QString& output);
+  void handle_redirector_error(const QString& output);
+
+protected:
+  bool is_simple_expression(const QString& expr);
+  void run_command_(std::pair<unsigned int,QString> pair);
+  bool is_simple_expression_(const QString& expr);
+  QQueue<std::pair<unsigned int,QString> > exec_queue_;
+  unsigned int command_id_;
+  boost::shared_ptr<OutputRedirector>  output_redirector_;
+  boost::shared_ptr<OutputRedirector>  error_redirector_;
+#ifndef _MSC_VER
+  struct sigaction sig_act_;
+#endif
+  bp::object parse_expr_cmd_;
+  bp::object repr_;
+  bp::dict main_namespace_;
+  unsigned int current_id_;
+};
+
+}} //ns
+
+#endif // PYTHON_INTERPRETER_WORKER_HH
diff --git a/modules/gui/src/python_shell/python_namespace_tree_item.cc b/modules/gui/src/python_shell/python_namespace_tree_item.cc
index c4af0f2072b88e1574ee746e0083fdb85dfc06f8..065eeab4197ca201c9c1133fcc8e436e9fe748d0 100644
--- a/modules/gui/src/python_shell/python_namespace_tree_item.cc
+++ b/modules/gui/src/python_shell/python_namespace_tree_item.cc
@@ -89,6 +89,8 @@ bool PythonNamespaceTreeItem::CanFetchMore() const
 
 void PythonNamespaceTreeItem::FetchMore()
 {
+  // todo should imediately return if worker thread is working
+  // todo fix completion for builtins
   initialized_=true;  
   bp::object dir=bp::import("__main__").attr("__builtins__").attr("dir");  
   bp::list keys=bp::extract<bp::list>(dir(namespace_)); 
diff --git a/modules/gui/src/python_shell/python_namespace_tree_model.cc b/modules/gui/src/python_shell/python_namespace_tree_model.cc
index c5b66e03d70a5243d8104199c67ea688494964da..1427a425d2a67d6a17519a92646167336700d8a0 100644
--- a/modules/gui/src/python_shell/python_namespace_tree_model.cc
+++ b/modules/gui/src/python_shell/python_namespace_tree_model.cc
@@ -26,7 +26,7 @@ PythonNamespaceTreeModel::PythonNamespaceTreeModel():
   QAbstractItemModel(),
   root_item_(new PythonNamespaceTreeItem(PythonInterpreter::Instance().GetMainModule(),"main"))
 {
-  connect(&PythonInterpreter::Instance(), SIGNAL(Done(int,const QString&)),
+  connect(&PythonInterpreter::Instance(), SIGNAL(Finished(unsigned int,bool)),
           this, SLOT(NamespaceChanged(void)));
 }
 
@@ -37,6 +37,7 @@ PythonNamespaceTreeModel::~PythonNamespaceTreeModel()
 
 void PythonNamespaceTreeModel::NamespaceChanged()
 {
+  // todo should only be called after all commands are executed
   delete root_item_;
   root_item_=new PythonNamespaceTreeItem(PythonInterpreter::Instance().GetMainModule(),"main");
   dataChanged(QModelIndex(),QModelIndex());
diff --git a/modules/gui/src/python_shell/python_shell.cc b/modules/gui/src/python_shell/python_shell.cc
index ae3030b8a4fa871fc75221eba5826b1069c029a8..6cfdc94aaa49a4ee648b814326857b73b52f2772 100644
--- a/modules/gui/src/python_shell/python_shell.cc
+++ b/modules/gui/src/python_shell/python_shell.cc
@@ -20,14 +20,14 @@
 /* 
   Author: Marco Biasini
  */
-#include <QVBoxLayout>
 
-#include <ost/gui/widget_registry.hh>
 #include <ost/gui/gosty_app.hh>
+#include <ost/gui/widget_registry.hh>
 
 #include "python_shell.hh"
 #include "python_shell_widget.hh"
 
+#include <QVBoxLayout>
 namespace ost { namespace gui {
 
 class PythonShellFactory: public WidgetFactory {
@@ -63,10 +63,6 @@ bool PythonShell::Save(const QString& prefix)
   return true;  
 }
 
-void PythonShell::AddLogger(TextLogger* logger)
-{
-  this->PyShell()->AddLogger(logger);
-}
 
 PythonShellWidget* PythonShell::PyShell()
 {
diff --git a/modules/gui/src/python_shell/python_shell.hh b/modules/gui/src/python_shell/python_shell.hh
index c9246f076de3f2f00a716c9384befecaec37ac0b..84f8929ce04c93d0a15c89f2c9766fa1d952dc8c 100644
--- a/modules/gui/src/python_shell/python_shell.hh
+++ b/modules/gui/src/python_shell/python_shell.hh
@@ -40,7 +40,6 @@ public:
   virtual bool Save(const QString& prefix);
   
 public:
-  void AddLogger(TextLogger* logger);  
   PythonShellWidget* PyShell();
 };
  
diff --git a/modules/gui/src/python_shell/python_shell_fw.hh b/modules/gui/src/python_shell/python_shell_fw.hh
index e86b3804f89f866b451e4cbfde4a21b392f6d877..0d3f1e641d58a946c46f9ed882aada2efd79f928 100644
--- a/modules/gui/src/python_shell/python_shell_fw.hh
+++ b/modules/gui/src/python_shell/python_shell_fw.hh
@@ -35,11 +35,13 @@ enum BlockEditMode {
   EDITMODE_MULTILINE_INACTIVE
 };
 enum BlockType {
-  BLOCKTYPE_OUTPUT,
-  BLOCKTYPE_ERROR,
-  BLOCKTYPE_CODE,
-  BLOCKTYPE_ACTIVE,
-  BLOCKTYPE_BLOCKEDIT
+  BLOCKTYPE_OUTPUT=1,
+  BLOCKTYPE_ERROR=2,
+  BLOCKTYPE_CODE=4,
+  BLOCKTYPE_ACTIVE=8,
+  BLOCKTYPE_BLOCKEDIT=16,
+  BLOCKTYPE_MULTILINE_SQ=32,
+  BLOCKTYPE_MULTILINE_DQ=64
   };
 
 struct GutterBlock{
diff --git a/modules/gui/src/python_shell/python_shell_widget.cc b/modules/gui/src/python_shell/python_shell_widget.cc
index 6d8183bf9a59b0f3e41df1ad3826434e1c9e449e..16d1d4ac2d441c831d345bac845b6ece25955e9d 100644
--- a/modules/gui/src/python_shell/python_shell_widget.cc
+++ b/modules/gui/src/python_shell/python_shell_widget.cc
@@ -16,17 +16,13 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
+/*
+  Authors: Marco Biasini, Andreas Schenk
+ */
+
 #include <iostream>
 
-#include <QDebug>
-#include <QFontMetrics>
-#include <QClipboard>
-#include <QPainter>
-#include <QScrollBar>
-#include <QDirModel>
-#include <QStringList>
 
-#include <ost/gui/python_shell/text_logger.hh>
 #include "python_shell_widget.hh"
 
 #include "gutter.hh"
@@ -37,7 +33,15 @@
 
 #include "python_completer.hh"
 #include "path_completer.hh"
+#include "transition.hh"
 
+#include <QApplication>
+#include <QFontMetrics>
+#include <QClipboard>
+#include <QPainter>
+#include <QScrollBar>
+#include <QDirModel>
+#include <QStringList>
 
 
 /*
@@ -58,9 +62,15 @@ PythonShellWidget::PythonShellWidget(QWidget* parent):
   output_visible_(true),
   completion_start_(0),
   completion_end_(0),
-  mode_(SHELL_INTERACTION_BASH)
+  block_edit_start_(document()->begin()),
+  output_blocks_(),
+  machine_(new StateMachine(this)),
+  readonly_machine_(new StateMachine(this)),
+  readwrite_state_(new State),
+  multiline_active_state_(new State)
 {
-  this->setLineWrapMode(QPlainTextEdit::NoWrap);
+  setLineWrapMode(QPlainTextEdit::WidgetWidth);
+  this->setFrameShape(QFrame::NoFrame);
   document()->setDocumentLayout(new PythonShellTextDocumentLayout(document()));
   setViewportMargins(Gutter::GUTTER_WIDTH, 0, 0, 0);
   setUndoRedoEnabled(false);
@@ -68,14 +78,17 @@ PythonShellWidget::PythonShellWidget(QWidget* parent):
   QFontMetrics metrics(font());
   setTabStopWidth(2*metrics.width(" "));
   setMaximumBlockCount(1000000);
-  connect(this, SIGNAL(updateRequest(QRect, int)) ,gutter_, 
-          SLOT(Update(QRect, int)));
-  connect(this, SIGNAL(Execute(QString)),&PythonInterpreter::Instance(), 
-          SLOT(RunCommand(QString)),Qt::QueuedConnection);
-  connect(&PythonInterpreter::Instance(), SIGNAL(Done(int,const QString&)),this, 
-          SLOT(AppendOutput(int,const QString&)),Qt::QueuedConnection);
+
   textCursor().block().setUserState(BLOCKTYPE_ACTIVE);
   completer_->setWidget(viewport());
+  connect(&PythonInterpreter::Instance(), SIGNAL(Output(unsigned int, const QString &)),
+          this,SLOT(AppendOutput(unsigned int, const QString &)));
+  connect(&PythonInterpreter::Instance(), SIGNAL(Finished(unsigned int, bool)),
+          this,SLOT(OutputFinished(unsigned int,bool)));
+  connect(&PythonInterpreter::Instance(), SIGNAL(ErrorOutput(unsigned int, const QString &)),
+          this,SLOT(AppendError(unsigned int, const QString &)));
+  connect(this,   SIGNAL(updateRequest(QRect, int)) ,
+          gutter_,SLOT(Update(QRect, int)));
   connect(completer_,SIGNAL(activated(const QString&)),this, 
           SLOT(InsertCompletion(const QString&)));
   connect(completer_,SIGNAL(recomplete(const QString&)),this, 
@@ -86,21 +99,393 @@ PythonShellWidget::PythonShellWidget(QWidget* parent):
           SLOT(SetCompletionPrefix(const QString&)));
   path_completer_->setWidget(viewport());
   connect(path_completer_,SIGNAL(activated(const QString&)),this, 
-          SLOT(InsertCompletion(const QString&)));
+          SLOT(InsertPathCompletion(const QString&)));
   connect(path_completer_,SIGNAL(recomplete(const QString&)),this, 
           SLOT(Recomplete(const QString&)));
   connect(this,SIGNAL(RequestPathCompletion(const QRect&,bool)),path_completer_, 
           SLOT(complete(const QRect&,bool)));
   connect(this,SIGNAL(SetPathCompletionPrefix(const QString&)),path_completer_, 
           SLOT(setCompletionPrefix(const QString&)));
-  if (mode_==SHELL_INTERACTION_BASH) {
-    SetBlockEditMode(EDITMODE_SINGLELINE);    
-  } else {
-    SetBlockEditMode(EDITMODE_MULTILINE_INACTIVE);
+  set_block_edit_mode_(EDITMODE_SINGLELINE);
+  setup_readonly_state_machine_();
+  setup_state_machine_();
+}
+
+void PythonShellWidget::setup_readonly_state_machine_()
+{
+  State* readonly=new State;
+  State* mixed=new State;
+  readonly_machine_->addState(mixed);
+  readonly_machine_->addState(readonly);
+  readonly_machine_->addState(readwrite_state_);
+  readonly->addTransition(new SignalTransition(this,
+                                                SIGNAL(cursorPositionChanged()),
+                                                readwrite_state_,
+                                                new EditPositionGuard(this,EditPositionGuard::EQUAL |EditPositionGuard::BIGGER,
+                                                                           EditPositionGuard::ANCHOREQUAL |EditPositionGuard::ANCHORBIGGER)));
+  readonly->addTransition(new SignalTransition(this,
+                                                SIGNAL(cursorPositionChanged()),
+                                                mixed,
+                                                new EditPositionGuard(this,EditPositionGuard::EQUAL |EditPositionGuard::BIGGER,
+                                                                           EditPositionGuard::ANCHORSMALLER)));
+  readonly->addTransition(new SignalTransition(this,
+                                                SIGNAL(cursorPositionChanged()),
+                                                mixed,
+                                                new EditPositionGuard(this,EditPositionGuard::ANCHOREQUAL |EditPositionGuard::ANCHORBIGGER,
+                                                                           EditPositionGuard::SMALLER)));
+
+  readonly->addTransition(new KeyEventTransition(QEvent::KeyPress,
+                                                  Qt::Key_Backspace,
+                                                  Qt::NoModifier,
+                                                  readwrite_state_,
+                                                  true));
+
+  readonly->addTransition(new KeyEventTransition(QEvent::KeyPress,
+                                                  Qt::Key_Any,
+                                                  Qt::NoModifier,
+                                                  readwrite_state_,
+                                                  false));
+
+  readwrite_state_->addTransition(new SignalTransition(this,
+                                                      SIGNAL(cursorPositionChanged()),
+                                                      readonly,
+                                                      new EditPositionGuard(this,EditPositionGuard::SMALLER | EditPositionGuard::EQUAL,
+                                                                                 EditPositionGuard::ANCHORSMALLER)));
+  readwrite_state_->addTransition(new SignalTransition(this,
+                                                      SIGNAL(cursorPositionChanged()),
+                                                      readonly,
+                                                      new EditPositionGuard(this,EditPositionGuard::ANCHORSMALLER | EditPositionGuard::ANCHOREQUAL,
+                                                                                 EditPositionGuard::SMALLER)));
+
+  readwrite_state_->addTransition(new SignalTransition(this,
+                                                        SIGNAL(cursorPositionChanged()),
+                                                        mixed,
+                                                        new EditPositionGuard(this,EditPositionGuard::EQUAL |EditPositionGuard::BIGGER,
+                                                                                   EditPositionGuard::ANCHORSMALLER)));
+  readwrite_state_->addTransition(new SignalTransition(this,
+                                                        SIGNAL(cursorPositionChanged()),
+                                                        mixed,
+                                                        new EditPositionGuard(this,EditPositionGuard::ANCHOREQUAL |EditPositionGuard::ANCHORBIGGER,
+                                                                                   EditPositionGuard::SMALLER)));
+
+  readwrite_state_->addTransition(new KeyEventTransition(QEvent::KeyPress,
+                                                         Qt::Key_Backspace,
+                                                         Qt::NoModifier,
+                                                         readwrite_state_,
+                                                         true,
+                                                         new EditPositionGuard(this,EditPositionGuard::EQUAL,
+                                                                                    EditPositionGuard::ANCHOREQUAL)));
+
+  mixed->addTransition(new SignalTransition(this,
+                                             SIGNAL(cursorPositionChanged()),
+                                             readwrite_state_,
+                                             new EditPositionGuard(this,EditPositionGuard::EQUAL |EditPositionGuard::BIGGER,
+                                                                        EditPositionGuard::ANCHOREQUAL |EditPositionGuard::ANCHORBIGGER)));
+
+  KeyEventTransition* kt1=new KeyEventTransition(QEvent::KeyPress,
+                                                 Qt::Key_Backspace,
+                                                 Qt::NoModifier,
+                                                 readwrite_state_,
+                                                 true);
+  mixed->addTransition(kt1);
+  connect(kt1,SIGNAL(triggered()),this,SLOT(OnMixedToReadwrite()));
+
+  KeyEventTransition* kt2=new KeyEventTransition(QEvent::KeyPress,
+                                                 Qt::Key_Any,
+                                                 Qt::NoModifier,
+                                                 readwrite_state_,
+                                                 false);
+  mixed->addTransition(kt2);
+  connect(kt2,SIGNAL(triggered()),this,SLOT(OnMixedToReadwrite()));
+
+  connect(readonly,SIGNAL(entered()),this,SLOT(OnReadonlyEntered()));
+  connect(readwrite_state_,SIGNAL(entered()),this,SLOT(OnReadwriteEntered()));
+  readonly_machine_->setInitialState(readwrite_state_);
+  readonly_machine_->start();
+}
+
+void PythonShellWidget::setup_state_machine_()
+{
+  #ifdef __APPLE__
+    QFlags<Qt::KeyboardModifier> DNG_ARROW_MODIFIERS = Qt::KeypadModifier;
+    QFlags<Qt::KeyboardModifier> DNG_ENTER_MODIFIERS = Qt::NoModifier;
+  #else
+    QFlags<Qt::KeyboardModifier> DNG_ARROW_MODIFIERS = Qt::NoModifier;
+    QFlags<Qt::KeyboardModifier> DNG_ENTER_MODIFIERS = Qt::KeypadModifier;
+  #endif
+  State* single_line=new State;
+  State* multi_line_inactive=new State;
+  State* completing=new State;
+  State* executing=new State;
+  State* history_up=new State;
+  State* history_down=new State;
+  machine_->addState(single_line);
+  machine_->addState(multiline_active_state_);
+  machine_->addState(multi_line_inactive);
+  machine_->addState(completing);
+  machine_->addState(executing);
+  machine_->addState(history_up);
+  machine_->addState(history_down);
+
+  connect(single_line,SIGNAL(entered()),this,SLOT(OnSingleLineStateEntered()));
+  connect(multiline_active_state_,SIGNAL(entered()),this,SLOT(OnMultiLineActiveStateEntered()));
+  connect(multi_line_inactive,SIGNAL(entered()),this,SLOT(OnMultiLineInactiveStateEntered()));
+  connect(history_up,SIGNAL(entered()),this,SLOT(OnHistoryUpStateEntered()));
+  connect(history_down,SIGNAL(entered()),this,SLOT(OnHistoryDownStateEntered()));
+  connect(executing,SIGNAL(entered()),this,SLOT(OnExecuteStateEntered()));
+
+  KeyEventTransition* tr1=new KeyEventTransition(QEvent::KeyPress,
+                                                 Qt::Key_Return,
+                                                 Qt::NoModifier,
+                                                 executing,
+                                                 true,
+                                                 new BlockStatusGuard(this,CODE_BLOCK_COMPLETE | CODE_BLOCK_ERROR));
+  single_line->addTransition(tr1);
+  KeyEventTransition* tr3=new KeyEventTransition(QEvent::KeyPress,
+                                                 Qt::Key_Return,
+                                                 Qt::NoModifier,
+                                                 multiline_active_state_,
+                                                 true,
+                                                 new BlockStatusGuard(this,CODE_BLOCK_INCOMPLETE));
+  single_line->addTransition(tr3);
+  KeyEventTransition* keypad_enter1=new KeyEventTransition(QEvent::KeyPress,
+                                                           Qt::Key_Enter,
+                                                           DNG_ENTER_MODIFIERS| Qt::NoModifier,
+                                                           multiline_active_state_,
+                                                           true);
+  single_line->addTransition(keypad_enter1);
+  connect(keypad_enter1,SIGNAL(triggered()),this,SLOT(OnKeypadEnterTransition()));
+  KeyEventTransition* keypad_enter2=new KeyEventTransition(QEvent::KeyPress,
+                                                           Qt::Key_Enter,
+                                                           DNG_ENTER_MODIFIERS| Qt::ShiftModifier,
+                                                           multiline_active_state_,
+                                                           true);
+  single_line->addTransition(keypad_enter2);
+  connect(keypad_enter2,SIGNAL(triggered()),this,SLOT(OnKeypadEnterTransition()));
+  KeyEventTransition* keypad_enter3=new KeyEventTransition(QEvent::KeyPress,
+                                                           Qt::Key_Enter,
+                                                           DNG_ENTER_MODIFIERS| Qt::MetaModifier,
+                                                           multiline_active_state_,
+                                                           true);
+  single_line->addTransition(keypad_enter3);
+  connect(keypad_enter3,SIGNAL(triggered()),this,SLOT(OnKeypadEnterTransition()));
+  
+  single_line->addTransition(new KeyEventTransition(QEvent::KeyPress,
+                                                    Qt::Key_Return,
+                                                    Qt::ControlModifier,
+                                                    multiline_active_state_,
+                                                    false));
+  // just to make OSX happy we also add the transitions with Meta (-> Ctrl o OSX)
+  single_line->addTransition(new KeyEventTransition(QEvent::KeyPress,
+                                                    Qt::Key_Return,
+                                                    Qt::MetaModifier,
+                                                    multiline_active_state_,
+                                                    false));
+                                                 
+  connect(tr3,SIGNAL(triggered()),this,SLOT(OnEnterTransition()));
+  single_line->addTransition(new KeyEventTransition(QEvent::KeyPress,Qt::Key_Up,DNG_ARROW_MODIFIERS,history_up));
+  single_line->addTransition(new KeyEventTransition(QEvent::KeyPress,Qt::Key_Down,DNG_ARROW_MODIFIERS,history_down));
+
+  KeyEventTransition* tr4=new KeyEventTransition(QEvent::KeyPress,
+                                                 Qt::Key_Return,
+                                                 Qt::NoModifier,
+                                                 executing,
+                                                 true,
+                                                 new BlockStatusGuard(this,CODE_BLOCK_COMPLETE | CODE_BLOCK_ERROR));
+  multi_line_inactive->addTransition(tr4);
+  KeyEventTransition* tr6=new KeyEventTransition(QEvent::KeyPress,
+                                                 Qt::Key_Return,
+                                                 Qt::NoModifier,
+                                                 multiline_active_state_,
+                                                 true,
+                                                 new BlockStatusGuard(this,CODE_BLOCK_INCOMPLETE));
+  multi_line_inactive->addTransition(tr6);
+  connect(tr6,SIGNAL(triggered()),this,SLOT(OnEnterTransition()));
+  multi_line_inactive->addTransition(new KeyEventTransition(QEvent::KeyPress,Qt::Key_Left,DNG_ARROW_MODIFIERS,multiline_active_state_));
+  multi_line_inactive->addTransition(new KeyEventTransition(QEvent::KeyPress,Qt::Key_Right,DNG_ARROW_MODIFIERS,multiline_active_state_));
+  multi_line_inactive->addTransition(new KeyEventTransition(QEvent::KeyPress,Qt::Key_Return,Qt::ControlModifier,multiline_active_state_));
+  multi_line_inactive->addTransition(new KeyEventTransition(QEvent::KeyPress,Qt::Key_Up,DNG_ARROW_MODIFIERS,history_up));
+  multi_line_inactive->addTransition(new KeyEventTransition(QEvent::KeyPress,Qt::Key_Down,DNG_ARROW_MODIFIERS,history_down));
+  KeyEventTransition* keypad_enter4=new KeyEventTransition(QEvent::KeyPress,
+                                                           Qt::Key_Enter,
+                                                           DNG_ENTER_MODIFIERS| Qt::NoModifier,
+                                                           multiline_active_state_,
+                                                           true);
+  multi_line_inactive->addTransition(keypad_enter4);
+  connect(keypad_enter4,SIGNAL(triggered()),this,SLOT(OnKeypadEnterTransition()));
+  KeyEventTransition* keypad_enter5=new KeyEventTransition(QEvent::KeyPress,
+                                                           Qt::Key_Enter,
+                                                           DNG_ENTER_MODIFIERS| Qt::ShiftModifier,
+                                                           multiline_active_state_,
+                                                           true);
+  multi_line_inactive->addTransition(keypad_enter5);
+  connect(keypad_enter5,SIGNAL(triggered()),this,SLOT(OnKeypadEnterTransition()));
+  KeyEventTransition* keypad_enter6=new KeyEventTransition(QEvent::KeyPress,
+                                                           Qt::Key_Enter,
+                                                           DNG_ENTER_MODIFIERS | Qt::MetaModifier,
+                                                           multiline_active_state_,
+                                                           true);
+  multi_line_inactive->addTransition(keypad_enter6);
+  connect(keypad_enter6,SIGNAL(triggered()),this,SLOT(OnKeypadEnterTransition()));
+  multi_line_inactive->addTransition(new KeyEventTransition(QEvent::KeyPress,
+                                                            Qt::Key_Return,
+                                                            Qt::ControlModifier,
+                                                            multiline_active_state_,
+                                                            false));
+  // just to make OSX happy we also add the transitions with Meta (-> Ctrl o OSX)
+  multi_line_inactive->addTransition(new KeyEventTransition(QEvent::KeyPress,
+                                                            Qt::Key_Return,
+                                                            Qt::MetaModifier,
+                                                            multiline_active_state_,
+                                                            false));
+
+  KeyEventTransition* tr7=new KeyEventTransition(QEvent::KeyPress,
+                                                 Qt::Key_Return,
+                                                 Qt::NoModifier,
+                                                 executing,
+                                                 true,
+                                                 new BlockStatusGuard(this,CODE_BLOCK_COMPLETE | CODE_BLOCK_ERROR));
+  multiline_active_state_->addTransition(tr7);
+  KeyEventTransition* tr8=new KeyEventTransition(QEvent::KeyPress,
+                                                 Qt::Key_Return,
+                                                 Qt::NoModifier,
+                                                 multiline_active_state_,
+                                                 true,
+                                                 new BlockStatusGuard(this,CODE_BLOCK_INCOMPLETE));
+  multiline_active_state_->addTransition(tr8);
+  connect(tr8,SIGNAL(triggered()),this,SLOT(OnEnterTransition()));
+
+  multiline_active_state_->addTransition(new KeyEventTransition(QEvent::KeyPress,Qt::Key_Escape,Qt::NoModifier,multi_line_inactive));
+  multiline_active_state_->addTransition(new KeyEventTransition(QEvent::KeyPress,Qt::Key_Up,Qt::ControlModifier | DNG_ARROW_MODIFIERS,history_up));
+  multiline_active_state_->addTransition(new KeyEventTransition(QEvent::KeyPress,Qt::Key_Down,Qt::ControlModifier | DNG_ARROW_MODIFIERS,history_down));
+  KeyEventTransition* keypad_enter7=new KeyEventTransition(QEvent::KeyPress,
+                                                           Qt::Key_Enter,
+                                                           DNG_ENTER_MODIFIERS | Qt::NoModifier,
+                                                           multiline_active_state_,
+                                                           true);
+  multiline_active_state_->addTransition(keypad_enter7);
+  connect(keypad_enter7,SIGNAL(triggered()),this,SLOT(OnKeypadEnterTransition()));
+  KeyEventTransition* keypad_enter8=new KeyEventTransition(QEvent::KeyPress,
+                                                           Qt::Key_Enter,
+                                                           DNG_ENTER_MODIFIERS | Qt::ShiftModifier,
+                                                           multiline_active_state_,
+                                                           true);
+  multiline_active_state_->addTransition(keypad_enter8);
+  connect(keypad_enter8,SIGNAL(triggered()),this,SLOT(OnKeypadEnterTransition()));
+  KeyEventTransition* keypad_enter9=new KeyEventTransition(QEvent::KeyPress,
+                                                           Qt::Key_Enter,
+                                                           DNG_ENTER_MODIFIERS | Qt::MetaModifier,
+                                                           multiline_active_state_,
+                                                           true);
+  multiline_active_state_->addTransition(keypad_enter9);
+  connect(keypad_enter9,SIGNAL(triggered()),this,SLOT(OnKeypadEnterTransition()));
+
+  history_up->addTransition(new AutomaticTransition(multi_line_inactive,new HistoryGuard(&history_,EDITMODE_MULTILINE_INACTIVE)));
+  history_up->addTransition(new AutomaticTransition(single_line,new HistoryGuard(&history_,EDITMODE_SINGLELINE)));
+  history_down->addTransition(new AutomaticTransition(multi_line_inactive,new HistoryGuard(&history_,EDITMODE_MULTILINE_INACTIVE)));
+  history_down->addTransition(new AutomaticTransition(single_line,new HistoryGuard(&history_,EDITMODE_SINGLELINE)));
+
+  executing->addTransition(new AutomaticTransition(single_line));
+
+  machine_->setInitialState(single_line);
+  machine_->start();
+}
+
+void PythonShellWidget::OnReadonlyEntered()
+{
+  setReadOnly(true);
+  setTextInteractionFlags(textInteractionFlags() | Qt::TextSelectableByKeyboard);
+}
+
+void PythonShellWidget::OnReadwriteEntered()
+{
+  if(textCursor().position()< GetEditStartBlock().position()){
+    moveCursor(QTextCursor::End);
+  }
+  setReadOnly(false);
+}
+void PythonShellWidget::OnMixedToReadwrite()
+{
+  QTextCursor tc=textCursor();
+  if(tc.position()< GetEditStartBlock().position()){
+    tc.setPosition(GetEditStartBlock().position(),QTextCursor::KeepAnchor);
+    setTextCursor(tc);
+  }else{
+    tc.setPosition(GetEditStartBlock().position(),QTextCursor::MoveAnchor);
+    tc.setPosition(textCursor().position(),QTextCursor::KeepAnchor);
+    setTextCursor(tc);
   }
-  PythonInterpreter::Instance().RedirectOutput();
+
 }
 
+void PythonShellWidget::OnKeypadEnterTransition()
+{
+  insertPlainText(QString(QChar::LineSeparator));
+}
+void PythonShellWidget::OnEnterTransition()
+{
+  QTextCursor cursor=textCursor();
+  cursor.movePosition(QTextCursor::EndOfLine, QTextCursor::MoveAnchor);
+  setTextCursor(cursor);
+  cursor.movePosition(QTextCursor::Left, QTextCursor::KeepAnchor);
+  bool new_indent=cursor.selectedText()==":";
+  cursor.movePosition(QTextCursor::StartOfLine);
+  cursor.movePosition(QTextCursor::NextWord, QTextCursor::KeepAnchor);
+  insertPlainText(QString(QChar::ParagraphSeparator));
+  if(cursor.selectedText()[0].isSpace() && ! cursor.atBlockEnd()){
+    insertPlainText(QString(cursor.selectedText()));
+  }
+  if (new_indent){
+    insertPlainText(QString("\t"));
+  }
+}
+void PythonShellWidget::OnSingleLineStateEntered()
+{
+  set_block_edit_mode_(EDITMODE_SINGLELINE);
+}
+void PythonShellWidget::OnMultiLineActiveStateEntered()
+{
+    set_block_edit_mode_(EDITMODE_MULTILINE_ACTIVE);
+}
+void PythonShellWidget::OnMultiLineInactiveStateEntered()
+{
+  set_block_edit_mode_(EDITMODE_MULTILINE_INACTIVE);
+}
+void PythonShellWidget::OnHistoryUpStateEntered()
+{
+  if(history_.AtEnd()){
+    history_.SetCurrentCommand(GetCommand(),get_block_edit_mode_());
+  }
+  history_.MoveToPreviousMatch();
+  set_command_(history_.GetCommand());
+  set_block_edit_mode_(history_.GetCommandMode());
+}
+void PythonShellWidget::OnHistoryDownStateEntered()
+{
+  history_.MoveToNextMatch();
+  set_command_(history_.GetCommand());
+  set_block_edit_mode_(history_.GetCommandMode());
+}
+void PythonShellWidget::OnExecuteStateEntered()
+{
+  QTextCursor cursor=textCursor();
+  cursor.movePosition(QTextCursor::EndOfLine, QTextCursor::MoveAnchor);
+  setTextCursor(cursor);
+  set_block_type_(block_edit_start_,textCursor().block(),BLOCKTYPE_CODE);
+  insertPlainText(QString(QChar::ParagraphSeparator));
+  QString command=GetCommand();
+  QString command_trimmed=command.trimmed();
+  if (command_trimmed.size()>0) {
+    unsigned int id=PythonInterpreter::Instance().RunCommand(command);
+    output_blocks_.insert(id,textCursor().block());
+    history_.AppendCommand(command_trimmed,get_block_edit_mode_());
+    insertPlainText(QString(QChar::ParagraphSeparator));
+  }
+  block_edit_start_=textCursor().block();
+
+}
+
+
 void PythonShellWidget::SetTabWidth(int width) {
   tab_width_=width;
   QFontMetrics metrics(font());
@@ -115,14 +500,14 @@ int PythonShellWidget::GetTabWidth() const {
 
 
 
-void PythonShellWidget::WrapIntoFunction(const QString& command)
+void PythonShellWidget::wrap_into_function_(const QString& command)
 {
   QString tmp_command=command;
   tmp_command.replace(QString(QChar::LineSeparator),
                       QString(QChar::LineSeparator)+QString("\t"));
   QString tmp="def func():"+QString(QChar::LineSeparator)+"\t";
   tmp+=tmp_command;
-  SetCommand(tmp);
+  set_command_(tmp);
   QTextCursor tc=textCursor();
   tc.setPosition(document()->lastBlock().position()+QString("def ").length());
   tc.setPosition(document()->lastBlock().position()+
@@ -144,53 +529,92 @@ void  PythonShellWidget::InsertCompletion(const QString& completion)
   tc.insertText(completion);
   setTextCursor(tc);
 }
+void  PythonShellWidget::InsertPathCompletion(const QString& completion)
+{
+  QString path=QDir::fromNativeSeparators(completion);
+  // append dir separator for directories if none present (Windows adds it already for the inline completion)
+  if(QFileInfo(path).isDir() && ! completion.endsWith("/")){
+    path+="/";
+  }
+  InsertCompletion(path);
+}
 
 
-void PythonShellWidget::AppendOutput(int status,const QString& output)
+void PythonShellWidget::AppendOutput(unsigned int id,const QString& output)
 {
-  QStringList output_list=output.split("\n");
-  if (output_list.size()>=maximumBlockCount ()){
-    QTextCursor cursor=textCursor();
-    cursor.movePosition(QTextCursor::Start);
-    cursor.movePosition(QTextCursor::End,QTextCursor::KeepAnchor);
-    cursor.removeSelectedText();
-    output_list.erase(output_list.begin(),output_list.begin()+
-                      output_list.size()+1-maximumBlockCount());
-  } else if (output_list.size()+blockCount()>maximumBlockCount()){
-    QTextCursor cursor=textCursor();
-    cursor.movePosition(QTextCursor::Start);
-    cursor.movePosition(QTextCursor::NextBlock,QTextCursor::KeepAnchor,
-                        output_list.size()+1+blockCount()-maximumBlockCount());
-    cursor.removeSelectedText();
+  OutputBlockList::iterator it=output_blocks_.find(id);
+  if(it==output_blocks_.end()){
+    return;
   }
-  moveCursor(QTextCursor::End);
-  QTextCursor cursor=textCursor();
-  cursor.beginEditBlock();
-  if (output!="" && output_list.size()>0) {
-    for(int i=0;i<output_list.size();++i){
-      document()->lastBlock().setUserState(status);
-      insertPlainText(output_list[i]);
-      insertPlainText(QString(QChar::ParagraphSeparator));
-    }
+  if(! it->isValid()){
+    return;
   }
-  document()->lastBlock().setUserState(BLOCKTYPE_ACTIVE);
-  cursor.endEditBlock();
+  QTextCursor cursor(*it);
+  cursor.movePosition(QTextCursor::EndOfBlock);
+  cursor.insertText(output);
+  set_block_type_(output_blocks_[id],cursor.block(),BLOCKTYPE_OUTPUT);
+  output_blocks_[id]=cursor.block();
   verticalScrollBar()->triggerAction(QAbstractSlider::SliderToMaximum);
-  this->ensureCursorVisible();  
+  ensureCursorVisible();
+  repaint();
+  QApplication::processEvents();
 }
 
+void PythonShellWidget::AppendError(unsigned int id,const QString& output)
+{
+  OutputBlockList::iterator it=output_blocks_.find(id);
+  if(it==output_blocks_.end()){
+    return;
+  }
+  if(! it->isValid()){
+    return;
+  }
+  QTextCursor cursor(*it);
+  cursor.movePosition(QTextCursor::EndOfBlock);
+  cursor.insertText(output);
+  set_block_type_(output_blocks_[id],cursor.block(),BLOCKTYPE_ERROR);
+  output_blocks_[id]=cursor.block();
+  verticalScrollBar()->triggerAction(QAbstractSlider::SliderToMaximum);
+  ensureCursorVisible();
+  repaint();
+  QApplication::processEvents();
+}
 
+void PythonShellWidget::set_block_type_(const QTextBlock& start, const QTextBlock& end, BlockType type)
+{
+  QTextBlock block=start;
+  while(block!=end){
+    block.setUserState(type);
+    block=block.next();
+  }
+  block.setUserState(type);
+  document()->markContentsDirty(start.position(),end.position()+end.length()-start.position());
+}
 
-void PythonShellWidget::SetCommand(const QString& command)
+void PythonShellWidget::OutputFinished(unsigned int id, bool error)
 {
-  QTextCursor cursor=textCursor();
-  cursor.setPosition(document()->lastBlock().position());
+  OutputBlockList::iterator it=output_blocks_.find(id);
+  if(it==output_blocks_.end()){
+    return;
+  }
+  if(it->isValid()){
+    QTextCursor cursor(*it);
+    cursor.movePosition(QTextCursor::Left,QTextCursor::KeepAnchor);
+    cursor.removeSelectedText();
+  }
+  output_blocks_.erase(it);
+}
+
+void PythonShellWidget::set_command_(const QString& command)
+{
+  QTextCursor cursor(block_edit_start_);
   cursor.movePosition(QTextCursor::End, QTextCursor::KeepAnchor);
-  cursor.beginEditBlock();
   cursor.removeSelectedText();
+  if(block_edit_start_.isValid()){
+    block_edit_start_=document()->lastBlock();
+  }
   cursor.insertText(command);
-  cursor.endEditBlock();
-  QAbstractTextDocumentLayout* layout=document()->documentLayout();  
+  QAbstractTextDocumentLayout* layout=document()->documentLayout();
   dynamic_cast<PythonShellTextDocumentLayout*>(layout)->EmitSizeChange();
   verticalScrollBar()->triggerAction(QAbstractSlider::SliderToMaximum);
   ensureCursorVisible();
@@ -216,7 +640,7 @@ void PythonShellWidget::Complete(bool inline_completion)
     completion_end_=positions->GetEnd(literal_index);
     QTextCursor cp=textCursor();
     QString text=cursor.selectedText();        
-    int sep=text.lastIndexOf(QDir::separator());    
+    int sep=text.lastIndexOf("/");    
     cp.setPosition(positions->GetStart(literal_index));
     if (sep!=-1) {
       cp.movePosition(QTextCursor::NextCharacter,
@@ -225,7 +649,7 @@ void PythonShellWidget::Complete(bool inline_completion)
     if (QDir(text).isAbsolute()) {
       emit SetPathCompletionPrefix(text);
     } else {
-      emit SetPathCompletionPrefix(QDir::currentPath()+QDir::separator()+text);
+      emit SetPathCompletionPrefix(QDir::currentPath()+"/"+text);
     }
     emit RequestPathCompletion(cursorRect(cp), 
                                inline_completion);
@@ -253,69 +677,34 @@ void PythonShellWidget::Complete(bool inline_completion)
   }
 }
 
-bool PythonShellWidget::HandleNav(QKeyEvent* event)
-{
-  if(event->key() == Qt::Key_Up){
-     if (GetBlockEditMode()!=EDITMODE_MULTILINE_ACTIVE) {
-       SanitizeCursorPosition();
-       if(history_.AtEnd()){
-         history_.SetCurrentCommand(textCursor().block().text(),
-                                    GetBlockEditMode());
-       }
-       --history_;
-       SetCommand(history_.GetCommand());
-       this->SetBlockEditMode(history_.GetCommandMode());
-       return true;
-     }else{
-       QTextCursor temporary_cursor=textCursor();
-       int temp_position_before=temporary_cursor.position();
-       temporary_cursor.movePosition(QTextCursor::Up);
-       if (temporary_cursor.position()<document()->lastBlock().position() && 
-           temp_position_before>=document()->lastBlock().position() && 
-           !(event->modifiers() & Qt::ShiftModifier)) {
-         return true;
-       }
-     }
-   }
-   if (event->key() == Qt::Key_Down && 
-       GetBlockEditMode()!=EDITMODE_MULTILINE_ACTIVE) {
-     SanitizeCursorPosition();
-     ++history_;
-     SetCommand(history_.GetCommand());
-     this->SetBlockEditMode(history_.GetCommandMode());     
-     return true;
-   }  
-  return false;
-}
 
-bool PythonShellWidget::HandleCustomCommands(QKeyEvent* event)
+
+bool PythonShellWidget::handle_custom_commands_(QKeyEvent* event)
 {
-  // see ticket #38
-  #if 0
   if ((event->modifiers() == (Qt::ControlModifier | Qt::ShiftModifier)) && 
       event->key() == Qt::Key_H) {
-    SetOutputVisible(!output_visible_);
+    set_output_visible_(!output_visible_);
     return true;
   }
-  #endif
+
   if ((event->modifiers() == (Qt::ControlModifier | Qt::ShiftModifier)) && 
       event->key() == Qt::Key_W) {
-    WrapIntoFunction(textCursor().selectedText());
+    wrap_into_function_(textCursor().selectedText());
     return true;
   }
   // custom handling of CTRL+A to select only text in edit or output section
   if (event->modifiers() == Qt::ControlModifier && 
       event->key() == Qt::Key_A) {
     QTextCursor cursor=textCursor();
-    if(cursor.position()<document()->lastBlock().position()){
+    if(cursor.position()<GetEditStartBlock().position()){
       // select all output
       cursor.setPosition(0);
-      cursor.setPosition(document()->lastBlock().position(),QTextCursor::KeepAnchor);
+      cursor.setPosition(GetEditStartBlock().position(),QTextCursor::KeepAnchor);
       setTextCursor(cursor);
     }else{
       //select whole edit section
-      cursor.movePosition(QTextCursor::StartOfBlock);
-      cursor.movePosition(QTextCursor::EndOfBlock,QTextCursor::KeepAnchor);
+      cursor.setPosition(GetEditStartBlock().position());
+      cursor.movePosition(QTextCursor::End,QTextCursor::KeepAnchor);
       setTextCursor(cursor);
     }
     return true;
@@ -323,81 +712,8 @@ bool PythonShellWidget::HandleCustomCommands(QKeyEvent* event)
   return false;
 }
 
-bool PythonShellWidget::HandleReturnKey(QKeyEvent* event)
-{
-  if(event->key() == Qt::Key_Return || event->key() == Qt::Key_Enter) {
-    QString command=textCursor().block().text();    
-    SanitizeCursorPosition();
-    command.replace(QString(QChar::LineSeparator),QString("\n"));
-    bool execute_cmd=false;
-    bool insert_new_line=false;
-    bool move_to_end=false;
-    if (mode_==SHELL_INTERACTION_MATHEMATICA) {
-      if (event->modifiers() & Qt::ControlModifier ||
-          (command.endsWith("\n") && textCursor().atEnd())) {
-        execute_cmd=true;
-        move_to_end=(event->modifiers() & Qt::ControlModifier)==false;
-      } else {
-        if (textCursor().block().text().trimmed().length()==0) {
-          return true;
-        }
-        insert_new_line=true;
-        move_to_end=true;
-      }
-    } else {
-      if (event->modifiers() & Qt::ControlModifier) {
-        insert_new_line=true;
-        move_to_end=false;
-      } else {
-        PythonInterpreter& pi=PythonInterpreter::Instance();
-        CodeBlockStatus status=pi.GetCodeBlockStatus(command);
-        if (status!=CODE_BLOCK_INCOMPLETE) {
-          execute_cmd=true;
-          move_to_end=true;
-        } else {
-          insert_new_line=true;
-          move_to_end=true;
-        }
-      }
-    }
-    QTextCursor cursor=this->textCursor();      
-    if (move_to_end) {
-      cursor.movePosition(QTextCursor::EndOfLine, QTextCursor::MoveAnchor);
-      this->setTextCursor(cursor);
-    }    
-    if (insert_new_line) {
-      cursor.movePosition(QTextCursor::Left, QTextCursor::KeepAnchor);
-      bool new_indent=cursor.selectedText()==":";
-      cursor.movePosition(QTextCursor::StartOfLine);
-      cursor.movePosition(QTextCursor::NextWord, QTextCursor::KeepAnchor);
-      insertPlainText(QString(QChar::LineSeparator));
-      if(cursor.selectedText()[0].isSpace()){
-        insertPlainText(QString(cursor.selectedText()));
-      }
-      if (new_indent){
-        insertPlainText(QString("\t"));
-      }
-      QAbstractTextDocumentLayout* layout=document()->documentLayout();
-      dynamic_cast<PythonShellTextDocumentLayout*>(layout)->EmitSizeChange();
-      verticalScrollBar()->triggerAction(QAbstractSlider::SliderToMaximum);
-      SetBlockEditMode(EDITMODE_MULTILINE_ACTIVE);
-      return true;
-    }
-    if (execute_cmd) {
-      QKeyEvent new_event(event->type(),event->key(),
-                          Qt::NoModifier,
-                          event->text(),event->isAutoRepeat(),
-                          event->count());
-      QPlainTextEdit::keyPressEvent(&new_event);
-      ExecuteCommand();
-      return true;                          
-    }
-  }
-  return false;
-}
 
-
-bool PythonShellWidget::HandleCompletion(QKeyEvent* event)
+bool PythonShellWidget::handle_completion_(QKeyEvent* event)
 {
   if(event->key() == Qt::Key_Tab){
     QRegExp rx("^\\s*$"); // only white spaces from beginning of line
@@ -413,79 +729,32 @@ bool PythonShellWidget::HandleCompletion(QKeyEvent* event)
   return false;
 }
 
+QTextBlock PythonShellWidget::GetEditStartBlock()
+{
+  return block_edit_start_;
+}
+
 
 void PythonShellWidget::keyPressEvent(QKeyEvent* event)
 {
-  if (this->HandleCustomCommands(event))
-    return;
-    
-  if (this->HandleCompletion(event))
-    return;
-  if (this->HandleNav(event))
-    return;
-
-  if (this->HandleReturnKey(event))
-    return;
-  if ((event->text()!="" && !(event->modifiers() & Qt::ControlModifier)) || 
-      event->matches(QKeySequence::Cut)  ||  event->key()== Qt::Key_Delete){
-    SanitizeCursorPosition();
-    if(GetBlockEditMode()==EDITMODE_MULTILINE_INACTIVE){
-      SetBlockEditMode(EDITMODE_MULTILINE_ACTIVE);
-    }
-  }
-  if (GetBlockEditMode()==EDITMODE_MULTILINE_ACTIVE && event->key()==Qt::Key_Escape){
-    SetBlockEditMode(EDITMODE_MULTILINE_INACTIVE);
-  }
-  
-  if (GetBlockEditMode()==EDITMODE_MULTILINE_INACTIVE && (event->key()==Qt::Key_Right || 
-      event->key() == Qt::Key_Left)) {
-    SetBlockEditMode(EDITMODE_MULTILINE_ACTIVE);
-  }
-  
-  if (event->key()== Qt::Key_Backspace && 
-      textCursor().position()<=document()->lastBlock().position()
-     && !textCursor().hasSelection()){
+  if (this->handle_custom_commands_(event)){
     return;
   }
-  
-
-  if (event->key()== Qt::Key_Left && 
-      textCursor().position()==document()->lastBlock().position() && 
-      !(event->modifiers() & Qt::ShiftModifier)) {
+  if (this->handle_completion_(event)){
     return;
   }
   QPlainTextEdit::keyPressEvent(event);
 }
 
-void PythonShellWidget::ExecuteCommand()
-{
-  QString command=textCursor().block().previous().text();
-  textCursor().block().previous().setUserState(BLOCKTYPE_CODE);
-  document()->markContentsDirty(textCursor().block().previous().position(),
-                                textCursor().block().previous().length());
-  QString cmd=command;
-  cmd.replace(QString(QChar::LineSeparator),QString("\n"));
-  emit Execute(cmd);
-
-  command=command.trimmed();
-  if (command.size()>0) {
-    history_.AppendCommand(command,GetBlockEditMode());
-  }
-  if (mode_==SHELL_INTERACTION_MATHEMATICA) {
-    SetBlockEditMode(EDITMODE_MULTILINE_INACTIVE);
-  } else {
-    SetBlockEditMode(EDITMODE_SINGLELINE);
-  }  
-}
 
 void PythonShellWidget::mouseReleaseEvent(QMouseEvent * event)
 {
   QTextCursor mouse_cursor=cursorForPosition(event->pos());
-  if (GetBlockEditMode()==EDITMODE_MULTILINE_INACTIVE && 
+  if (get_block_edit_mode_()==EDITMODE_MULTILINE_INACTIVE &&
       event->button() == Qt::LeftButton &&
       mouse_cursor.position()>=document()->lastBlock().position()) {
     // switch to active edit mode upon mouse click in edit section
-    SetBlockEditMode(EDITMODE_MULTILINE_ACTIVE);
+    set_block_edit_mode_(EDITMODE_MULTILINE_ACTIVE);
   }
   if (event->button() == Qt::MidButton && 
       mouse_cursor.position()<document()->lastBlock().position()) {
@@ -496,51 +765,35 @@ void PythonShellWidget::mouseReleaseEvent(QMouseEvent * event)
   QPlainTextEdit::mouseReleaseEvent(event);
 }
 
-void PythonShellWidget::SanitizeCursorPosition()
-{
-  if(textCursor().position()<document()->lastBlock().position()){
-    if(textCursor().anchor()<document()->lastBlock().position()){
-      moveCursor(QTextCursor::End);
-    }else{
-      QTextCursor cursor=textCursor();
-      cursor.setPosition(document()->lastBlock().position(),
-                         QTextCursor::KeepAnchor);
-      setTextCursor(cursor);
-    }
-  }else{
-    if(textCursor().anchor()<document()->lastBlock().position()){
-      int current_position=textCursor().position();
-      QTextCursor cursor=textCursor();
-      cursor.setPosition(document()->lastBlock().position());
-      cursor.setPosition(current_position,QTextCursor::KeepAnchor);
-      setTextCursor(cursor);
-    }
-  }
-}
 
-void PythonShellWidget::SetBlockEditMode(BlockEditMode flag)
+
+void PythonShellWidget::set_block_edit_mode_(BlockEditMode flag)
 {
   block_edit_mode_=flag;
   if(flag==EDITMODE_MULTILINE_ACTIVE){
-    document()->lastBlock().setUserState(BLOCKTYPE_BLOCKEDIT);
+    set_block_type_(block_edit_start_,document()->lastBlock(),BLOCKTYPE_BLOCKEDIT);
   }else if(flag==EDITMODE_MULTILINE_INACTIVE){
-    document()->lastBlock().setUserState(BLOCKTYPE_ACTIVE);
+    set_block_type_(block_edit_start_,document()->lastBlock(),BLOCKTYPE_ACTIVE);
   }else {
-    document()->lastBlock().setUserState(BLOCKTYPE_ACTIVE);
+    set_block_type_(block_edit_start_,document()->lastBlock(),BLOCKTYPE_ACTIVE);
   }
   gutter_->update();
-  document()->markContentsDirty(document()->lastBlock().position(),
-                                document()->lastBlock().length());
 }
 
-BlockEditMode PythonShellWidget::GetBlockEditMode()
+BlockEditMode PythonShellWidget::get_block_edit_mode_()
 {
   return block_edit_mode_;
 }
 
 QString PythonShellWidget::GetCommand()
 {
-  return document()->lastBlock().text();
+
+  QTextCursor cursor(block_edit_start_);
+  cursor.movePosition(QTextCursor::End, QTextCursor::KeepAnchor);
+  QString text= cursor.selectedText();
+  text.replace(QChar::LineSeparator,"\n");
+  text.replace(QChar::ParagraphSeparator,"\n");
+  return text;
 }
 
 void PythonShellWidget::insertFromMimeData(const QMimeData * source)
@@ -549,7 +802,7 @@ void PythonShellWidget::insertFromMimeData(const QMimeData * source)
     return;
   }
   QString text=source->text();
-  SanitizeCursorPosition();
+  readonly_machine_->setActive(readwrite_state_);
   text=text.replace("\r\n", QString(1, QChar::LineSeparator))
            .replace('\n', QChar::LineSeparator)
            .replace('\r', QChar::LineSeparator);
@@ -568,19 +821,12 @@ void PythonShellWidget::insertFromMimeData(const QMimeData * source)
     lines[i]=QString(num_spaces, '\t')+right;
   }
   text=lines.join(QString(1, QChar::LineSeparator));
-  int line_sep=text.count(QChar::LineSeparator);
-  if(line_sep>0){
-    QString command=GetCommand();
-    int last_block_start=document()->lastBlock().position();
-    int last_block_end=last_block_start+document()->lastBlock().length();    
-    int shifted_start=textCursor().selectionStart()-last_block_start;
-    int shifted_end=last_block_end-textCursor().selectionEnd();
-    QString rpl_text=command.left(shifted_start)+text+
-                     command.right(shifted_end-1);
-    this->SetCommand(rpl_text);
-    SetBlockEditMode(EDITMODE_MULTILINE_ACTIVE);
-  }else{
-    QPlainTextEdit::insertFromMimeData(source);
+  if(lines.size()>0){
+    machine_->setActive(multiline_active_state_);
+  }
+  QPlainTextEdit::insertFromMimeData(source);
+  if(lines.size()>0){
+    set_block_type_(block_edit_start_,document()->lastBlock(),BLOCKTYPE_BLOCKEDIT);
   }
 }
 
@@ -602,17 +848,22 @@ GutterBlockList PythonShellWidget::GetGutterBlocks(const QRect& rect)
   return result;
 }
 
-void PythonShellWidget::SetOutputVisible(bool flag)
+void PythonShellWidget::set_output_visible_(bool flag)
 {
   output_visible_=flag;
   for (QTextBlock i=document()->begin(); i!=document()->end(); i=i.next()) {
     if(i.userState()==BLOCKTYPE_ERROR || i.userState()==BLOCKTYPE_OUTPUT){
       i.setVisible(flag);
+      i.setLineCount(flag ? qMax(1, i.layout()->lineCount()) : 0);
     }
   }
+  dynamic_cast<PythonShellTextDocumentLayout*>(document()->documentLayout())->requestUpdate();
+  dynamic_cast<PythonShellTextDocumentLayout*>(document()->documentLayout())->EmitSizeChange();
+  ensureCursorVisible();
+  repaint();
   gutter_->update();
-  viewport()->update();  
-  this->update();  
+  viewport()->update();
+  this->update();
 }
 
 void PythonShellWidget::resizeEvent(QResizeEvent* event)
@@ -631,19 +882,5 @@ void PythonShellWidget::showEvent(QShowEvent* event)
   }
 }
 
-void PythonShellWidget::AquireFocus()
-{
-  setFocus(Qt::OtherFocusReason);
-}
-
-void PythonShellWidget::AddLogger(TextLogger* logger)
-{
-  loggers_.push_back(logger);
-  logger->setParent(this);  
-  connect(this,SIGNAL(Execute(const QString&)),
-          logger,SLOT(AppendCode(const QString&)));
-  connect(&PythonInterpreter::Instance(),SIGNAL(Done(int,const QString&)),
-          logger,SLOT(AppendOutput(int,const QString&)));
-}
 
 }}
diff --git a/modules/gui/src/python_shell/python_shell_widget.hh b/modules/gui/src/python_shell/python_shell_widget.hh
index b4c34ce45475b7f4e2f68b5869989866ea6cb399..9ab34b259e1386f6f240f35b918d61112cce586f 100644
--- a/modules/gui/src/python_shell/python_shell_widget.hh
+++ b/modules/gui/src/python_shell/python_shell_widget.hh
@@ -16,55 +16,48 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#ifndef OST_GUI_PYTHON_SHELL_WIDGET_HH
-#define OST_GUI_PYTHON_SHELL_WIDGET_HH
-
 /*
   Authors: Marco Biasini, Andreas Schenk
  */
 
-#include <ost/gui/module_config.hh>
+
+#ifndef OST_GUI_PYTHON_SHELL_WIDGET_HH
+#define OST_GUI_PYTHON_SHELL_WIDGET_HH
 
 
+#include <ost/gui/module_config.hh>
 #include "python_interpreter.hh"
 #include "shell_history.hh"
 #include  "python_shell_fw.hh"
-
 #include "python_syntax_highlighter.hh"
+#include "state_machine.hh"
+#include "state.hh"
 
 #include <QPlainTextEdit>
-
+#include <QHash>
 namespace ost { namespace gui {
 
 // fw decl
 class Gutter;
 class PythonCompleter;
 class PathCompleter;
-class TextLogger;
 
-typedef enum {
-  // to execute a command, the command must end with an empty line, or
-  // Cmd+Return must be pressed
-  SHELL_INTERACTION_MATHEMATICA=0,
-  // to execute a command, a single return key press is sufficient. Cmd+Return
-  // starts newline. This mode is the default
-  SHELL_INTERACTION_BASH=1
-} ShellInteractionMode;
 
 class DLLEXPORT_OST_GUI PythonShellWidget : public QPlainTextEdit {
+
+  typedef QHash<unsigned int,QTextBlock> OutputBlockList;
   Q_OBJECT
+
 public:
   PythonShellWidget(QWidget* parent=NULL);
   GutterBlockList GetGutterBlocks(const QRect& rect);
-  void SetOutputVisible(bool flag=true);
-  
-  void AddLogger(TextLogger* logger);
-  
-  void SetInteractionMode(ShellInteractionMode mode);
-
   void SetTabWidth(int width);
   int GetTabWidth() const;
+  QString GetCommand();
+  QTextBlock GetEditStartBlock();
+
   int tab_width_;
+
 signals:
   void Execute(const QString& command);
   void RequestCompletion(const QRect& rect,bool inline_completion);
@@ -74,30 +67,41 @@ signals:
 
 public slots:
   void InsertCompletion(const QString& completion);
-  void AppendOutput(int status,const QString& output);
-  void AquireFocus();
+  void InsertPathCompletion(const QString& completion);
+  void AppendOutput(unsigned int id,const QString& output);
+  void AppendError(unsigned int id,const QString& output);
+  void OutputFinished(unsigned int id, bool error);
   void Complete(bool inline_completion=true);
   void Recomplete(const QString& completion);
+  // slots for state machine
+  void OnSingleLineStateEntered();
+  void OnMultiLineActiveStateEntered();
+  void OnMultiLineInactiveStateEntered();
+  void OnHistoryUpStateEntered();
+  void OnHistoryDownStateEntered();
+  void OnExecuteStateEntered();
+  void OnEnterTransition();
+  void OnKeypadEnterTransition();
+  void OnReadonlyEntered();
+  void OnReadwriteEntered();
+  void OnMixedToReadwrite();
 
 protected:
   virtual void mouseReleaseEvent (QMouseEvent* event );
   virtual void keyPressEvent (QKeyEvent* event );
   virtual void resizeEvent(QResizeEvent* event);
   virtual void showEvent(QShowEvent* event);
-
-  void WrapIntoFunction(const QString& command);
-  void SetCommand(const QString& command);
-  QString GetCommand();
-  void insertFromMimeData( const QMimeData * source );
-  void SanitizeCursorPosition();
-  void SetBlockEditMode(BlockEditMode flag);
-  
-  bool HandleNav(QKeyEvent* event);
-  bool HandleCompletion(QKeyEvent* event);
-  bool HandleCustomCommands(QKeyEvent* event);
-  bool HandleReturnKey(QKeyEvent* event);
-  BlockEditMode GetBlockEditMode();
-  void ExecuteCommand();
+  virtual void insertFromMimeData( const QMimeData * source );
+  void set_output_visible_(bool flag=true);
+  void setup_readonly_state_machine_();
+  void setup_state_machine_();
+  void wrap_into_function_(const QString& command);
+  void set_command_(const QString& command);
+  void set_block_edit_mode_(BlockEditMode flag);
+  bool handle_completion_(QKeyEvent* event);
+  bool handle_custom_commands_(QKeyEvent* event);
+  BlockEditMode get_block_edit_mode_();
+  void set_block_type_(const QTextBlock& start,const QTextBlock& end, BlockType type);
 
   PythonSyntaxHighlighter highlighter_;
   PythonCompleter* completer_;
@@ -108,8 +112,12 @@ protected:
   bool output_visible_;
   int completion_start_;
   int completion_end_;
-  std::vector<TextLogger*>  loggers_;  
-  ShellInteractionMode mode_;  
+  QTextBlock block_edit_start_;
+  OutputBlockList output_blocks_;
+  StateMachine* machine_;
+  StateMachine* readonly_machine_;
+  State* readwrite_state_;
+  State* multiline_active_state_;
 };
 
 }}//ns
diff --git a/modules/gui/src/python_shell/python_syntax_highlighter.cc b/modules/gui/src/python_shell/python_syntax_highlighter.cc
index c6f16ba6ae99dff924284267fb64b4720a949151..f37eb4d61f866bd097ad8ddfbbce68fa565b23aa 100644
--- a/modules/gui/src/python_shell/python_syntax_highlighter.cc
+++ b/modules/gui/src/python_shell/python_syntax_highlighter.cc
@@ -22,8 +22,6 @@
 
 #include <iostream>
 
-#include <QTextCursor>
-
 #include "python_shell.hh"
 #include "string_literal_positions.hh"
 
@@ -31,6 +29,8 @@
 #include "python_context_parser.hh"
 
 
+#include <QDebug>
+#include <QTextCursor>
 
 namespace ost { namespace gui {    
 
@@ -44,6 +44,8 @@ PythonSyntaxHighlighter::PythonSyntaxHighlighter(QTextDocument* parent):
   formats_[PythonToken::END]=format;  
   format.setForeground(QBrush(QColor(150,0,0)));
   formats_[PythonToken::OPERATOR]=format;  
+  format.setForeground(QBrush(QColor(100,100,100)));  
+  formats_[PythonToken::COMMENT]=format;
   format.setForeground(QBrush(QColor(0,0,150)));
   formats_[PythonToken::GROUPING]=format;  
   format.setForeground(QBrush(QColor(35,107,142)));
@@ -72,11 +74,32 @@ PythonSyntaxHighlighter::PythonSyntaxHighlighter(QTextDocument* parent):
 
 void PythonSyntaxHighlighter::highlightBlock(const QString& text_block) { 
   QTextCursor cursor(currentBlock());
-  cursor.setBlockFormat(block_formats_[static_cast<BlockType>(currentBlockState())]);
-  if (currentBlockState() == BLOCKTYPE_BLOCKEDIT || currentBlockState() == BLOCKTYPE_ACTIVE || currentBlockState() == BLOCKTYPE_CODE){
+  int base_state=-1;  
+  if (currentBlockState() & BLOCKTYPE_OUTPUT) {
+    base_state=BLOCKTYPE_OUTPUT;
+  } else if (currentBlockState() & BLOCKTYPE_ERROR) {
+    base_state=BLOCKTYPE_ERROR;
+  } else if (currentBlockState() & BLOCKTYPE_ACTIVE) {
+    base_state=BLOCKTYPE_ACTIVE;
+  } else if (currentBlockState() & BLOCKTYPE_BLOCKEDIT) {
+    base_state=BLOCKTYPE_BLOCKEDIT;
+  } else if (currentBlockState() & BLOCKTYPE_CODE) {
+    base_state=BLOCKTYPE_CODE;
+  }
+  cursor.setBlockFormat(block_formats_[static_cast<BlockType>(base_state)]);
+  if (currentBlockState() & BLOCKTYPE_BLOCKEDIT || 
+      currentBlockState() & BLOCKTYPE_ACTIVE || 
+      currentBlockState() & BLOCKTYPE_CODE) {
     StringLiteralPositions* positions=new StringLiteralPositions();
     int blockposition=currentBlock().position();
-    PythonTokenizer pt(text_block,0);
+    int string_state=0;
+    int bs=previousBlockState()==-1 ? 0 : previousBlockState();
+    if (bs & BLOCKTYPE_MULTILINE_SQ) {
+      string_state=2;
+    } else if (bs & BLOCKTYPE_MULTILINE_DQ) {
+      string_state=1;
+    }
+    PythonTokenizer pt(text_block,string_state);
     PythonToken t;
     PythonToken last;
     int type_before_last=PythonToken::END;
@@ -84,14 +107,28 @@ void PythonSyntaxHighlighter::highlightBlock(const QString& text_block) {
     while((t = pt.NextToken()).GetType() != PythonToken::END) {
       setFormat(t.GetRange().location,t.GetRange().length,formats_[t.GetType()]);
       if(t.GetType()==PythonToken::STRING_LITERAL){
-        positions->Append(blockposition+t.GetRange().location,blockposition+t.GetRange().location+t.GetRange().length);
+        positions->Append(blockposition+t.GetRange().location,
+                          blockposition+t.GetRange().location+
+                          t.GetRange().length);
       }
       type_before_last=last.GetType();
       last=t;
     }
-    if(last.GetType()==PythonToken::STRING_DELIM && type_before_last!=PythonToken::STRING_LITERAL && type_before_last!=PythonToken::STRING_DELIM){
-      positions->Append(blockposition+last.GetRange().location+1,blockposition+last.GetRange().location+1);
+    if(last.GetType()==PythonToken::STRING_DELIM && 
+       type_before_last!=PythonToken::STRING_LITERAL && 
+       type_before_last!=PythonToken::STRING_DELIM){
+      positions->Append(blockposition+last.GetRange().location+1,
+                        blockposition+last.GetRange().location+1);
+    }
+    int new_state=base_state;
+    if (pt.InString()) {
+      if (pt.GetDelim()=="'''") {
+        new_state|=BLOCKTYPE_MULTILINE_SQ;
+      } else if (pt.GetDelim()=="\"\"\""){
+        new_state|=BLOCKTYPE_MULTILINE_DQ;
+      }
     }
+    setCurrentBlockState(new_state);
     currentBlock().setUserData(positions);
   }
 }
diff --git a/modules/gui/src/python_shell/python_syntax_highlighter.hh b/modules/gui/src/python_shell/python_syntax_highlighter.hh
index dea21746b34d5c6ce76c57070fe7fc62a5d8edbe..e31413678dfaee18e8c17a309fe437e39573e03a 100644
--- a/modules/gui/src/python_shell/python_syntax_highlighter.hh
+++ b/modules/gui/src/python_shell/python_syntax_highlighter.hh
@@ -22,12 +22,12 @@
   Authors: Marco Biasini, Andreas Schenk
  */
 
-#include <QSyntaxHighlighter>
-#include <QTextDocument>
 
 #include "python_shell_fw.hh"
 #include "python_tokenizer.hh"
 
+#include <QSyntaxHighlighter>
+#include <QTextDocument>
 namespace ost { namespace gui {
 
 /** 
diff --git a/modules/gui/src/python_shell/python_tokenizer.cc b/modules/gui/src/python_shell/python_tokenizer.cc
index 1049b3b803d4a40810c7ee75cd2b86b598cd0b36..1cbbc235bea98d9a6879701fd1a77e561b6e556d 100644
--- a/modules/gui/src/python_shell/python_tokenizer.cc
+++ b/modules/gui/src/python_shell/python_tokenizer.cc
@@ -64,6 +64,8 @@ QString PythonToken::GetTypeAsString() const
     return "EOF";
   case GROUPING:
     return "grouping character";
+  case COMMENT:
+    return "comment";
   }
   return "unknown";
 }
@@ -137,11 +139,13 @@ PythonToken PythonTokenizer::GetOperatorToken()
 {
   static QString operators[] = {
     QString("+="), QString("-="), QString("*="), 
+    QString("**"), QString("&="), QString("|="),
     QString("/="), QString("+"), QString("-"), 
     QString("/"), QString("*"), QString("."),
     QString("%"), QString("="), QString("!="), 
     QString("!"), QString("<="), QString(">="), 
-    QString("<"), QString(":"), QString("?"),
+    QString("<"), QString(":"), QString("?"), 
+    QString("|"), QString("&"), QString("^"),
     QString("")
   };
   size_t index = -1;
@@ -205,7 +209,7 @@ PythonToken PythonTokenizer::GetStringDelim()
 {
   Range range(current_pos_,0);
   // Find out which type of delimiters are used for the String. i.e. <">, 
-  // <"""> or <'>
+  // <""">, <'''> or <'>
   QString delimiter = "\"";
   if (command_[current_pos_] == '\'')
     delimiter = "'";
@@ -275,6 +279,15 @@ PythonToken PythonTokenizer::NextToken()
     this->EatWhities();
     if (current_pos_ < command_.size()) {
       QChar current_char = command_[current_pos_];
+      if (current_char=='#') {
+        current_token_=PythonToken(PythonToken::COMMENT, 
+                                   Range(current_pos_, 
+                                         command_.size()-current_pos_),
+                                   command_.mid(current_pos_, 
+                                                command_.size()-current_pos_));
+        current_pos_=command_.size();
+        return current_token_;
+      }
       if (current_char.isDigit()) {
         current_token_ = GetNumberToken();
         return current_token_;
diff --git a/modules/gui/src/python_shell/python_tokenizer.hh b/modules/gui/src/python_shell/python_tokenizer.hh
index 2c398dfbdf673d002c0bf7c484c94c199e2298e3..3e85c89fe899caba8ea57832836534261faccae4 100644
--- a/modules/gui/src/python_shell/python_tokenizer.hh
+++ b/modules/gui/src/python_shell/python_tokenizer.hh
@@ -62,6 +62,7 @@ public:
     NUMBER,
     OPERATOR,
     GROUPING,
+    COMMENT,
     END
   };
   PythonToken();
@@ -86,7 +87,8 @@ public:
   PythonToken NextToken();
   const PythonToken& CurrentToken() const;
   void SetInString(bool in_string);
-  
+  bool InString() const { return in_string_; }
+  const QString& GetDelim() const { return string_delim_; }
 private:
   void EatWhities();
   QString GetSubString(const Range& range);
diff --git a/modules/gui/src/python_shell/shell_history.cc b/modules/gui/src/python_shell/shell_history.cc
index a761cd86f787dd3e9ade0fa997b2abbd492c1a12..01d7e16c329f38b5db15155478f7304e0f9eafa9 100644
--- a/modules/gui/src/python_shell/shell_history.cc
+++ b/modules/gui/src/python_shell/shell_history.cc
@@ -19,7 +19,6 @@
 /*
   Author: Andreas Schenk
  */
-
 #include "shell_history.hh"
 
 namespace ost { namespace gui {
@@ -77,29 +76,33 @@ bool ShellHistory::AtEnd()
   return index_>=history_list_.size();
 }
 
-void ShellHistory::operator--()
+void ShellHistory::MoveToPreviousMatch()
 {
-  if(index_>0){
-    --index_;
+  int newindex=index_-1;
+  while(newindex>=0){
+    if(history_list_[newindex].first.indexOf(current_)==0 || current_.size()==0){
+      index_=newindex;
+      break;
+    }
+    --newindex;
   }
 }
 
-void ShellHistory::operator--(int)
-{
-  operator--();
-}
-
-void ShellHistory::operator++()
+void ShellHistory::MoveToNextMatch()
 {
-  if(index_<history_list_.size()){
-    ++index_;
+  int newindex=index_+1;
+  while(static_cast<unsigned int>(newindex)<history_list_.size()){
+    if(history_list_[newindex].first.indexOf(current_)==0 || current_.size()==0){
+      index_=newindex;
+      break;
+    }
+    ++newindex;
+  }
+  if(static_cast<unsigned int>(newindex)!=index_){
+    index_=history_list_.size();
   }
 }
 
-void ShellHistory::operator++(int)
-{
-  operator++();
-}
 
 }}//ns
 
diff --git a/modules/gui/src/python_shell/shell_history.hh b/modules/gui/src/python_shell/shell_history.hh
index 653650fb2181c4935669e1dabce41a72434cf861..a39d7412901a5dceeef9952353cdd22b9fd9cce2 100644
--- a/modules/gui/src/python_shell/shell_history.hh
+++ b/modules/gui/src/python_shell/shell_history.hh
@@ -23,8 +23,8 @@
  */
 
 #include <vector>
-#include <QString>
 #include "python_shell_fw.hh"
+#include <QString>
 
 namespace ost { namespace gui {
 
@@ -38,10 +38,8 @@ public:
  QString GetCommand();
  BlockEditMode GetCommandMode();
  bool AtEnd();
- void operator--();
- void operator--(int);
- void operator++();
- void operator++(int);
+ void MoveToPreviousMatch();
+ void MoveToNextMatch();
 protected:
  std::vector<std::pair<QString,BlockEditMode> > history_list_;
  QString current_;
diff --git a/modules/gui/src/python_shell/state.cc b/modules/gui/src/python_shell/state.cc
new file mode 100644
index 0000000000000000000000000000000000000000..381fffff4d120cf891fa2b5e552258cdfafc5274
--- /dev/null
+++ b/modules/gui/src/python_shell/state.cc
@@ -0,0 +1,84 @@
+#include <cassert>
+#include "transition.hh"
+#include "state.hh"
+#include "state_machine.hh"
+
+namespace ost { namespace gui {
+
+State::State():
+  QObject(),
+  mouse_event_transitions_(),
+  key_event_transitions_(),
+  automatic_transitions_()
+{
+}
+void State::addTransition(SignalTransition* transition)
+{
+  transition->setParent(this);
+}
+void State::addTransition(MouseEventTransition* transition)
+{
+  transition->setParent(this);
+  mouse_event_transitions_.append(transition);
+}
+void State::addTransition(KeyEventTransition* transition)
+{
+  transition->setParent(this);
+  key_event_transitions_.append(transition);
+}
+void State::addTransition(AutomaticTransition* transition)
+{
+  transition->setParent(this);
+  automatic_transitions_.append(transition);
+}
+bool State::isActive()
+{
+  return parent() && dynamic_cast<StateMachine*>(parent())->isActive(this);
+}
+void State::setActive()
+{
+  assert(parent());
+  dynamic_cast<StateMachine*>(parent())->setActive(this);
+}
+
+bool State::checkEvent(QKeyEvent* event)
+{
+  for(QList<KeyEventTransition*>::iterator it=key_event_transitions_.begin();it!=key_event_transitions_.end();++it){
+    std::pair<bool,bool> pair=(*it)->checkEvent(event);
+    if(pair.first){
+      return pair.second;
+    }
+  }
+  return false;
+}
+
+bool State::checkAutomaticTransitions()
+{
+  for(QList<AutomaticTransition*>::iterator it=automatic_transitions_.begin();it!=automatic_transitions_.end();++it){
+    if((*it)->checkTransition()){
+      return true;
+    }
+  }
+  return false;
+}
+
+bool State::checkEvent(QMouseEvent* event)
+{
+  for(QList<MouseEventTransition*>::iterator it=mouse_event_transitions_.begin();it!=mouse_event_transitions_.end();++it){
+    std::pair<bool,bool> pair=(*it)->checkEvent(event);
+    if(pair.first){
+      return pair.second;
+    }
+  }
+  return false;
+}
+void State::onEntry()
+{
+  emit entered();
+}
+void State::onExit()
+{
+  emit exited();
+}
+
+}}//ns
diff --git a/modules/gui/src/python_shell/state.hh b/modules/gui/src/python_shell/state.hh
new file mode 100644
index 0000000000000000000000000000000000000000..a6c05c36b3b6fc94db8498caf41a0fa71f90323f
--- /dev/null
+++ b/modules/gui/src/python_shell/state.hh
@@ -0,0 +1,45 @@
+#ifndef PYTHON_SHELL_STATE_HH
+#define PYTHON_SHELL_STATE_HH
+
+#include <QObject>
+#include <QList>
+
+//fw decl
+class QKeyEvent;
+class QMouseEvent;
+
+namespace ost { namespace gui {
+
+//fw decl
+class SignalTransition;
+class MouseEventTransition;
+class KeyEventTransition;
+class AutomaticTransition;
+
+class State: public QObject{
+Q_OBJECT
+public:
+  State();
+  void addTransition(SignalTransition * transition);
+  void addTransition(MouseEventTransition * transition);
+  void addTransition(KeyEventTransition* transition);
+  void addTransition(AutomaticTransition* transition);
+  bool isActive();
+  void setActive();
+  bool checkEvent(QKeyEvent* event);
+  bool checkEvent(QMouseEvent* event);
+  bool checkAutomaticTransitions();
+  virtual void onEntry();
+  virtual void onExit();
+signals:
+  void entered();
+  void exited();
+protected:
+  QList<MouseEventTransition*> mouse_event_transitions_;
+  QList<KeyEventTransition*> key_event_transitions_;
+  QList<AutomaticTransition*> automatic_transitions_;
+};
+
+
+}}//ns
+#endif // PYTHON_SHELL_STATE_HH
diff --git a/modules/gui/src/python_shell/state_machine.cc b/modules/gui/src/python_shell/state_machine.cc
new file mode 100644
index 0000000000000000000000000000000000000000..9ce3f37bc85946686bcb1d34f3593b37789336ce
--- /dev/null
+++ b/modules/gui/src/python_shell/state_machine.cc
@@ -0,0 +1,55 @@
+#include <QEvent>
+#include <QKeyEvent>
+#include <QMouseEvent>
+#include "state.hh"
+#include "state_machine.hh"
+
+namespace ost { namespace gui {
+
+StateMachine::StateMachine(QObject* parent):
+  QObject(parent)
+{
+  parent->installEventFilter(this);
+}
+
+bool StateMachine::eventFilter (QObject * watched, QEvent * event)
+{
+  if (event->type() == QEvent::KeyPress || event->type() == QEvent::KeyRelease) {
+    QKeyEvent* key_event = dynamic_cast<QKeyEvent*>(event);
+    return active_state_->checkEvent(key_event);
+  } else if(event->type() == QEvent::MouseButtonDblClick ||
+            event->type() == QEvent::MouseButtonPress ||
+            event->type() == QEvent::MouseButtonRelease ||
+            event->type() == QEvent::MouseMove){
+    QMouseEvent *mouse_event = dynamic_cast<QMouseEvent*>(event);
+    return active_state_->checkEvent(mouse_event);
+  } else {
+    return false;
+  }
+}
+
+void StateMachine::addState(State* state)
+{
+  state->setParent(this);
+}
+void StateMachine::setInitialState(State* state)
+{
+  active_state_=state;
+}
+void StateMachine::start()
+{
+  active_state_->onEntry();
+}
+bool StateMachine::isActive(State* state)
+{
+  return state==active_state_;
+}
+void StateMachine::setActive(State* state)
+{
+  active_state_->onExit();
+  active_state_=state;
+  active_state_->onEntry();
+  active_state_->checkAutomaticTransitions();
+}
+
+}}//ns
diff --git a/modules/gui/src/python_shell/state_machine.hh b/modules/gui/src/python_shell/state_machine.hh
new file mode 100644
index 0000000000000000000000000000000000000000..ac265dfd91e898d3af9ef483de11076a846cafdb
--- /dev/null
+++ b/modules/gui/src/python_shell/state_machine.hh
@@ -0,0 +1,30 @@
+#ifndef PYTHON_SHELL_STATE_MACHINE_HH
+#define PYTHON_SHELL_STATE_MACHINE_HH
+
+#include <QObject>
+
+//fw decl
+class QEvent;
+
+namespace ost { namespace gui {
+
+//fw decl
+class State;
+
+class StateMachine: public QObject{
+Q_OBJECT
+public:
+  StateMachine(QObject* parent);
+  void addState(State* state);
+  void setInitialState(State* state);
+  void start();
+  bool isActive(State* state);
+  void setActive(State* state);
+  bool eventFilter (QObject * watched, QEvent * event);
+protected:
+  State* active_state_;
+};
+
+}}//ns
+
+#endif // PYTHON_SHELL_STATE_MACHINE_HH
diff --git a/modules/gui/src/python_shell/text_logger.cc b/modules/gui/src/python_shell/text_logger.cc
index ef0dee5780eb97e82b61245ba77cc35b21f053bb..04123b9a7c85cee05510df0c93a943f24ec158a5 100644
--- a/modules/gui/src/python_shell/text_logger.cc
+++ b/modules/gui/src/python_shell/text_logger.cc
@@ -70,18 +70,9 @@ void TextLogger::AppendCode(const QString& text)
   operator<<('\n');
   flush();
 }
-void TextLogger::AppendOutput(int status,const QString& text)
+void TextLogger::AppendOutput(unsigned int id,const QString& text)
 {
-  if (text=="\n") {
-    return;
-  }  
-  if(!((log_output_ && status==STATUS_OK) || (log_error_ && status==STATUS_ERROR))
-     || text.size()==0){
-    return;
-  }
-
   operator<<(text);
-  operator<<('\n');
   flush();
 }
 void TextLogger::SetCodeLogging(bool flag)
diff --git a/modules/gui/src/python_shell/text_logger.hh b/modules/gui/src/python_shell/text_logger.hh
index 1be25f652f9f4212e1a9992f33ee00f0001c9d18..9e46fc7401dc73fdbc4f6e2474500c3ef602c8be 100644
--- a/modules/gui/src/python_shell/text_logger.hh
+++ b/modules/gui/src/python_shell/text_logger.hh
@@ -49,7 +49,7 @@ public:
   
 public slots:
   void AppendCode(const QString& text); 
-  void AppendOutput(int status,const QString& text); 
+  void AppendOutput(unsigned int id,const QString& text); 
   
 protected:
   bool log_code_;
diff --git a/modules/gui/src/python_shell/transition.cc b/modules/gui/src/python_shell/transition.cc
new file mode 100644
index 0000000000000000000000000000000000000000..35501292ce99ed4f82cbabe3d3c714748d3d0067
--- /dev/null
+++ b/modules/gui/src/python_shell/transition.cc
@@ -0,0 +1,92 @@
+#include <cassert>
+#include "python_shell_widget.hh"
+#include "transition.hh"
+#include "state.hh"
+#include <QKeyEvent>
+#include <QMouseEvent>
+
+namespace ost { namespace gui {
+
+TransitionBase::TransitionBase(State* target,  TransitionGuard* guard):
+  QObject(),
+  target_(target),
+  guard_(guard)
+{
+  guard_->setParent(this);
+}
+void TransitionBase::trigger_()
+{
+  emit triggered();
+  target_->setActive();
+}
+bool TransitionBase::is_active_()
+{
+  return parent() && dynamic_cast<State*>(parent())->isActive();
+}
+
+AutomaticTransition::AutomaticTransition(State* target,  TransitionGuard*  guard):
+  TransitionBase(target,guard)
+{
+}
+
+bool AutomaticTransition::checkTransition()
+{
+  if(guard_->check()){
+    trigger_();
+    return true;
+  }
+  return false;
+}
+
+SignalTransition::SignalTransition(QObject * sender,const char *  signal, State* target,  TransitionGuard*  guard):
+  TransitionBase(target,guard)
+{
+  connect(sender,signal,this,SLOT(onSignal()));
+}
+void SignalTransition::onSignal()
+{
+  if(is_active_() && guard_->check()){
+    trigger_();
+  }
+}
+
+KeyEventTransition::KeyEventTransition(QEvent::Type type,int key,Qt::KeyboardModifiers modifiers, State* target, bool swallow_event,  TransitionGuard*  guard):
+  TransitionBase(target,guard),
+  type_(type),
+  key_(key),
+  modifiers_(modifiers),
+  swallow_(swallow_event)
+{
+}
+std::pair<bool,bool> KeyEventTransition::checkEvent(QKeyEvent* event)
+{
+  assert(is_active_());
+  if(event->type()==type_ && (event->key()==key_ || 
+     key_==Qt::Key_Any) && event->modifiers() == modifiers_ && guard_->check()){
+    trigger_();
+    return std::pair<bool,bool>(true,swallow_);
+  }
+  return std::pair<bool,bool>(false,false);
+}
+
+MouseEventTransition::MouseEventTransition(QEvent::Type type,Qt::MouseButton button,Qt::KeyboardModifiers modifiers, State* target, bool swallow_event,  TransitionGuard*  guard):
+  TransitionBase(target,guard),
+  type_(type),
+  button_(button),
+  modifiers_(modifiers),
+  swallow_(swallow_event)
+{
+}
+std::pair<bool,bool> MouseEventTransition::checkEvent(QMouseEvent* event)
+{
+// only gets called if active
+  assert(is_active_());
+  if(event->type()==type_ && event->button()==button_ && event->modifiers() == modifiers_ && guard_->check()){
+    trigger_();
+    return std::pair<bool,bool>(true,swallow_);
+  }
+  return std::pair<bool,bool>(false,false);
+}
+
+
+}}//ns
diff --git a/modules/gui/src/python_shell/transition.hh b/modules/gui/src/python_shell/transition.hh
new file mode 100644
index 0000000000000000000000000000000000000000..5c8514cbf95cf00e718ea21c08cdfbabdc029812
--- /dev/null
+++ b/modules/gui/src/python_shell/transition.hh
@@ -0,0 +1,77 @@
+#ifndef PYTHON_SHELL_TRANSITION_HH
+#define PYTHON_SHELL_TRANSITION_HH
+
+#include <utility>
+#include <ost/gui/python_shell/python_interpreter.hh>
+
+#include <QObject>
+#include <QEvent>
+#include "transition_guard.hh"
+//fw decl
+class QKeyEvent;
+class QMouseEvent;
+
+namespace ost { namespace gui {
+
+//fw decl
+class State;
+class PythonShellWidget;
+class ShellHistory;
+
+class TransitionBase: public QObject{
+Q_OBJECT
+public:
+  TransitionBase(State* target, TransitionGuard* guard=new TransitionGuard());
+signals:
+  void triggered();
+protected:
+  void trigger_();
+  bool is_active_();
+  State* target_;
+  TransitionGuard* guard_;
+};
+
+class AutomaticTransition: public TransitionBase{
+Q_OBJECT
+public:
+  AutomaticTransition(State* target, TransitionGuard* guard=new TransitionGuard());
+  bool checkTransition();
+};
+
+class SignalTransition: public TransitionBase{
+Q_OBJECT
+public:
+  SignalTransition(QObject * sender,const char *  signal, State* target, TransitionGuard* guard=new TransitionGuard());
+protected slots:
+  void onSignal();
+};
+
+class KeyEventTransition: public TransitionBase{
+Q_OBJECT
+public:
+  KeyEventTransition(QEvent::Type type,int key,Qt::KeyboardModifiers modifiers, State* target, bool swallow_event=true, TransitionGuard* guard=new TransitionGuard());
+  virtual std::pair<bool,bool> checkEvent(QKeyEvent* event);
+protected:
+  QEvent::Type type_;
+  int key_;
+  Qt::KeyboardModifiers modifiers_;
+  bool swallow_;
+};
+
+class MouseEventTransition: public TransitionBase{
+Q_OBJECT
+public:
+  MouseEventTransition(QEvent::Type type,Qt::MouseButton button,Qt::KeyboardModifiers modifiers, State* target, bool swallow_event=true, TransitionGuard* guard=new TransitionGuard());
+  virtual std::pair<bool,bool> checkEvent(QMouseEvent* event);
+protected:
+  QEvent::Type type_;
+  Qt::MouseButton button_;
+  Qt::KeyboardModifiers modifiers_;
+  bool swallow_;
+};
+
+
+
+
+}}//ns
+#endif // PYTHON_SHELL_TRANSITION_HH
diff --git a/modules/gui/src/python_shell/transition_guard.cc b/modules/gui/src/python_shell/transition_guard.cc
new file mode 100644
index 0000000000000000000000000000000000000000..c32898964cf3a17c7375b5824b9fa0343cd538e1
--- /dev/null
+++ b/modules/gui/src/python_shell/transition_guard.cc
@@ -0,0 +1,86 @@
+#include <iostream>
+#include "transition_guard.hh"
+#include "python_shell_widget.hh"
+#include "shell_history.hh"
+
+namespace ost { namespace gui {
+
+TransitionGuard::TransitionGuard():
+  QObject()
+{
+}
+
+bool TransitionGuard::check()
+{
+  return true;
+}
+
+HistoryGuard::HistoryGuard(ShellHistory* history, BlockEditMode mode):
+  TransitionGuard(),
+  history_(history),
+  mode_(mode)
+{
+}
+
+bool HistoryGuard::check()
+{
+  return history_->GetCommandMode()==mode_;
+}
+
+EditPositionGuard::EditPositionGuard(PythonShellWidget* shell, int flags1, int flags2):
+  TransitionGuard(),
+  shell_(shell),
+  flags1_(flags1),
+  flags2_(flags2)
+{
+}
+
+bool EditPositionGuard::check()
+{
+  return check_flag(flags1_) &&  check_flag(flags2_);
+}
+
+bool EditPositionGuard::check_flag(int flags)
+{
+  if(flags==0){
+    return true;
+  }
+  bool returnflag=false;
+  QTextCursor tc=shell_->textCursor();
+  if(flags & SMALLER){
+    returnflag|=tc.position()<shell_->GetEditStartBlock().position();
+  }
+  if(flags & EQUAL){
+    returnflag|=tc.position()==shell_->GetEditStartBlock().position();
+  }
+  if(flags & BIGGER){
+    returnflag |= tc.position()> shell_->GetEditStartBlock().position();
+  }
+  if(flags & ANCHORSMALLER){
+    returnflag|=tc.anchor()<shell_->GetEditStartBlock().position();
+  }
+  if(flags & ANCHOREQUAL){
+    returnflag|=tc.anchor()==shell_->GetEditStartBlock().position();
+  }
+  if(flags & ANCHORBIGGER){
+    returnflag |= tc.anchor()> shell_->GetEditStartBlock().position();
+  }
+  return returnflag;
+}
+
+BlockStatusGuard::BlockStatusGuard(PythonShellWidget* shell, int status):
+  TransitionGuard(),
+  shell_(shell),
+  status_(status)
+{
+}
+
+bool BlockStatusGuard::check()
+{
+  QString command=shell_->GetCommand();
+  return PythonInterpreter::Instance().GetCodeBlockStatus(command) & status_;
+}
+
+
+
+}} //ns
diff --git a/modules/gui/src/python_shell/transition_guard.hh b/modules/gui/src/python_shell/transition_guard.hh
new file mode 100644
index 0000000000000000000000000000000000000000..5a2906481c36da41fc7ef1d5aefecfc853d76ad9
--- /dev/null
+++ b/modules/gui/src/python_shell/transition_guard.hh
@@ -0,0 +1,73 @@
+#ifndef TRANSITION_GUARD_HH
+#define TRANSITION_GUARD_HH
+
+#include "python_shell_fw.hh"
+#include "python_interpreter.hh"
+#include <QObject>
+
+namespace ost { namespace gui {
+
+
+//fw decl
+  class ShellHistory;
+  class PythonShellWidget;
+
+
+class TransitionGuard: public QObject
+{
+Q_OBJECT
+
+public:
+  TransitionGuard();
+  virtual bool check();
+};
+
+
+
+class HistoryGuard : public TransitionGuard
+{
+public:
+  HistoryGuard(ShellHistory* history, BlockEditMode mode);
+  virtual bool check();
+protected:
+   ShellHistory* history_;
+   BlockEditMode mode_;
+};
+
+class EditPositionGuard : public TransitionGuard
+{
+public:
+  enum FLAGS{
+    ALWAYSTRUE=0,
+    SMALLER=1,
+    EQUAL=2,
+    BIGGER=4,
+    ANCHORSMALLER=8,
+    ANCHOREQUAL=16,
+    ANCHORBIGGER=32
+  };
+    EditPositionGuard(PythonShellWidget* shell,int flags1, int flags2=ALWAYSTRUE);
+    virtual bool check();
+protected:
+    virtual bool check_flag(int flag);
+    PythonShellWidget* shell_;
+    int flags1_;
+    int flags2_;
+};
+
+class BlockStatusGuard : public TransitionGuard
+{
+public:
+    BlockStatusGuard(PythonShellWidget* shell, int status);
+    virtual bool check();
+protected:
+    PythonShellWidget* shell_;
+    int status_;
+};
+
+
+
+}} //ns
+
+
+#endif // TRANSITION_GUARD_HH
diff --git a/modules/gui/src/query_dialog.cc b/modules/gui/src/query_dialog.cc
deleted file mode 100644
index fcaac5755d038a31d5e2d73f89df738b2c1dbab1..0000000000000000000000000000000000000000
--- a/modules/gui/src/query_dialog.cc
+++ /dev/null
@@ -1,105 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#include "query_dialog.hh"
-
-#include <QPushButton>
-#include <QVBoxLayout>
-#include <QHBoxLayout>
-#include <QKeyEvent>
-
-#include <iostream>
-
-#include <ost/mol/query.hh>
-
-namespace ost { namespace gui {
-
-QueryDialog::QueryDialog(QWidget* parent):
-  QDialog(parent), flag_set_(false)
-{
-  error_.setForeground(QBrush(QColor(150,0,0)));
-  default_.setForeground(QBrush(QColor(0,0,0)));  
-  delete layout();
-  QVBoxLayout* vb=new QVBoxLayout(this);  
-  edit_=new QTextEdit(this);
-  edit_->setAcceptRichText(false);
-  edit_->setTabChangesFocus(true);
-  status_=new QLabel(QString(""), this);
-  status_->setWordWrap(true);
-  status_->setMargin(0);
-  QHBoxLayout* hb=new QHBoxLayout();  
-  vb->addWidget(status_);
-  vb->addWidget(edit_);
-  hb->setDirection(QBoxLayout::LeftToRight);
-  QPushButton* select_btn = new QPushButton(tr("Select"), this);
-  QPushButton* cancel_btn = new QPushButton(tr("Cancel"), this);  
-  hb->addWidget(cancel_btn);
-  hb->addWidget(select_btn);
-  vb->addLayout(hb);
-  select_btn->setDefault(true);
-  connect(select_btn, SIGNAL(clicked()), this, SLOT(accept()));
-  connect(cancel_btn, SIGNAL(clicked()), this, SLOT(reject()));  
-  connect(edit_, SIGNAL(textChanged()), this, 
-         SLOT(OnTextChanged()));    
-} 
-
-void QueryDialog::OnTextChanged()
-{
-  if (flag_set_)
-    return;
-  int l=edit_->document()->size().height()/edit_->fontMetrics().lineSpacing();
-  if (l>1) {
-    edit_->document()->undo();
-  }
-  flag_set_=true;
-  this->Colorize();
-  flag_set_=false;
-}
-
-void QueryDialog::Colorize()
-{
-  mol::Query q(edit_->toPlainText().toStdString());
-  QTextCursor c=edit_->textCursor();
-  c.select(QTextCursor::Document);
-  c.setCharFormat(default_);  
-  if (!q.IsValid()) {
-    mol::QueryErrorDesc d=q.GetErrorDescription();
-    c.movePosition(QTextCursor::Start);
-    c.movePosition(QTextCursor::NextCharacter, QTextCursor::MoveAnchor,
-                   d.range.Loc);
-    c.movePosition(QTextCursor::NextCharacter, QTextCursor::KeepAnchor,
-                   d.range.Length);
-    c.setCharFormat(error_);             
-    status_->setText(QString(d.msg.c_str()));    
-  } else {
-    status_->setText(QString(""));
-  }
-}
-
-QString QueryDialog::GetQueryString() const
-{
-  return edit_->toPlainText();
-}
-
-void QueryDialog::keyPressEvent(QKeyEvent* event){
-  if (event->key() == Qt::Key_Return || event->key() == Qt::Key_Enter) {
-    this->accept();
-  }
-}
-
-}}
diff --git a/modules/gui/src/remote_loader.cc b/modules/gui/src/remote_loader.cc
index 559a1c670c8267d48b3d18a001b7ccb26e2209ae..2e07f9ab58490fcb8c02112bfafccf29464e959c 100644
--- a/modules/gui/src/remote_loader.cc
+++ b/modules/gui/src/remote_loader.cc
@@ -18,12 +18,6 @@
 //------------------------------------------------------------------------------
 #include <vector>
 
-#include <QString>
-#include <QSettings>
-#include <QNetworkReply>
-#include <QHBoxLayout>
-#include <QDir>
-
 #include <ost/platform.hh>
 
 #include <ost/gui/file_loader.hh>
@@ -32,6 +26,11 @@
 #include "widget_registry.hh"
 #include "remote_loader.hh"
 
+#include <QString>
+#include <QSettings>
+#include <QNetworkReply>
+#include <QHBoxLayout>
+#include <QDir>
 namespace ost { namespace gui {
 
 RemoteLoader::RemoteLoader(QWidget* parent):
@@ -39,8 +38,10 @@ RemoteLoader::RemoteLoader(QWidget* parent):
 {
   img_support_=OST_IMG_ENABLED;
   line_edit_ = new QLineEdit(this);
-  button_ = new QPushButton("Load",this);
+  button_ = new QToolButton(this);
+  button_->setAttribute(Qt::WA_MacSmallSize);
   progress_bar_ = new QProgressBar(this);
+  progress_bar_->setAttribute(Qt::WA_MacSmallSize);
   progress_bar_->setVisible(false);
   progress_bar_->setRange(0,0);
 
@@ -48,12 +49,9 @@ RemoteLoader::RemoteLoader(QWidget* parent):
   l->addWidget(line_edit_);
   l->addWidget(button_);
   l->addWidget(progress_bar_);
-  l->setMargin(0);
-  l->setSpacing(0);
+  l->setMargin(3);
+  l->setSpacing(2);
 
-  this->setSizePolicy(QSizePolicy::Expanding, QSizePolicy::Fixed);
-  this->setMinimumHeight(progress_bar_->height());
-  this->setMaximumHeight(progress_bar_->height());
   connect(button_, SIGNAL(clicked()), this,
           SLOT(Clicked()));
 
@@ -69,10 +67,14 @@ RemoteLoader::RemoteLoader(QWidget* parent):
   QAction* select_url_action = new QAction(this);
   select_url_action->setText("URL");
   select_url_action->setToolTip("Select remote URL");
-  select_url_action->setIcon(QIcon(icon_path.absolutePath()+QDir::separator()+QString("site_icon.png")));
+  select_url_action->setIcon(QIcon(icon_path.absolutePath()+QDir::separator()+
+                                   QString("site_icon.png")));
   action_list_.append(select_url_action);
-
   connect(select_url_action, SIGNAL(triggered(bool)), this, SLOT(UrlClick()));
+  this->BuildMenu();
+  this->RenameButton();
+  this->setFixedHeight(button_->height());
+  this->setSizePolicy(QSizePolicy::Expanding, QSizePolicy::Fixed);  
 }
 
 void RemoteLoader::UrlClick()
@@ -83,7 +85,7 @@ void RemoteLoader::UrlClick()
 
 void RemoteLoader::BuildMenu(String active_loader)
 {
-  if(active_loader.size()>0){
+  if(!active_loader.empty()){
     selected_site_loader_ = active_loader;
   }
   else if(site_actions_->checkedAction()!=NULL){
@@ -100,9 +102,10 @@ void RemoteLoader::BuildMenu(String active_loader)
     RemoteSiteLoader* loader = FileLoader::GetLoaderManager()->GetRemoteSiteLoader(loader_ident);
     if(loader && ((loader->IsImg() && img_support_) || !loader->IsImg())){
       QAction* action = new QAction(loader_ident,site_loader_menu_);
+      connect(action, SIGNAL(triggered()), this, SLOT(RenameButton()));
       action->setCheckable(true);
       site_actions_->addAction(action);
-      if(site_actions_->checkedAction()==NULL ||selected_site_loader_==loader_ident.toStdString() ){
+      if((site_actions_->checkedAction()==NULL && loader_ident == FileLoader::GetLoaderManager()->GetDefaultRemoteSiteIdent()) ||selected_site_loader_==loader_ident.toStdString() ){
         action->setChecked(true);
       }
       site_loader_menu_->addAction(action);
@@ -132,6 +135,10 @@ bool RemoteLoader::Restore(const QString& prefix)
   if (settings.contains("loader")) {
     this->BuildMenu(settings.value("loader").toString().toStdString());
   }
+  else{
+    this->BuildMenu();
+  }
+  this->RenameButton();
   return true;
 }
 
@@ -141,7 +148,7 @@ void RemoteLoader::Clicked()
   if(!line_edit_->text().isEmpty() && site_actions_->checkedAction()){
     RemoteSiteLoader* loader = FileLoader::GetLoaderManager()->GetRemoteSiteLoader(site_actions_->checkedAction()->text());
 
-    QString text = line_edit_->text();
+    QString text = line_edit_->text().simplified();
     QString id = text;
     QString selection = "";
     int pos = text.indexOf('[');
@@ -187,6 +194,14 @@ void RemoteLoader::DownloadFinished(){
   this->ShowProgressBar(false);
 }
 
+
+void RemoteLoader::RenameButton(){
+  if(site_actions_->checkedAction()){
+    QString text = "Load (" + site_actions_->checkedAction()->text() + ")";
+    button_->setText(text);
+  }
+}
+
 OST_REGISTER_WIDGET_WITH_DEFAULT_FACTORY(ost::gui, RemoteLoader, "Remote Loader");
 
 }}
diff --git a/modules/gui/src/remote_loader.hh b/modules/gui/src/remote_loader.hh
index 441309eee1f70c8db7d6583a77eae552ae8acd25..92c5aa9f8c9d6767cea4d0ea7dc9a1e747010d7f 100644
--- a/modules/gui/src/remote_loader.hh
+++ b/modules/gui/src/remote_loader.hh
@@ -19,16 +19,16 @@
 #ifndef OST_GUI_REMOTE_LOADER_HH
 #define OST_GUI_REMOTE_LOADER_HH
 
-#include <QPushButton>
-#include <QLineEdit>
-#include <QKeyEvent>
-#include <QProgressBar>
-#include <QActionGroup>
 
 #include <ost/gfx/gfx_object.hh>
 #include <ost/gui/module_config.hh>
 #include <ost/gui/widget.hh>
 
+#include <QToolButton>
+#include <QLineEdit>
+#include <QKeyEvent>
+#include <QProgressBar>
+#include <QActionGroup>
 namespace ost { namespace gui {
 
 
@@ -53,10 +53,11 @@ private slots:
   void UrlClick();
   void DownloadFinished();
   void UpdateProgress(qint64 read, qint64 total);
+  void RenameButton();
 
 private:
   QLineEdit* line_edit_;
-  QPushButton* button_;
+  QToolButton* button_;
   QProgressBar* progress_bar_;
   ActionList action_list_;
   QMenu* site_loader_menu_;
diff --git a/modules/gui/src/remote_site_loader.hh b/modules/gui/src/remote_site_loader.hh
index 648850fd5df57578311947545b487e2719ed389c..b00823af7500ea22a295f6d1d858c817744f33f7 100644
--- a/modules/gui/src/remote_site_loader.hh
+++ b/modules/gui/src/remote_site_loader.hh
@@ -24,11 +24,11 @@
 #ifndef OST_GUI_REMOTE_SITE_LOADER_HH
 #define OST_GUI_REMOTE_SITE_LOADER_HH
 
+#include <ost/gui/module_config.hh>
+
 #include <QObject>
 #include <QMenu>
 #include <QNetworkReply>
-#include <ost/gui/module_config.hh>
-
 namespace ost { namespace gui {
 
 class DLLEXPORT_OST_GUI RemoteSiteLoader{
diff --git a/modules/gui/src/scene_menu.cc b/modules/gui/src/scene_menu.cc
index ceba5546acd05db0131eacfb4dc359d14216af6d..7952b8c47ff7eb92cbb1e2d856bf50c5601a0c7a 100644
--- a/modules/gui/src/scene_menu.cc
+++ b/modules/gui/src/scene_menu.cc
@@ -29,8 +29,14 @@ namespace ost { namespace gui {
 SceneMenu::SceneMenu() {
   context_menu_=new QMenu();
   select_menu_=context_menu_->addMenu("Select");
-  QAction* a=select_menu_->addAction("Around Atom");
+  QAction* a=select_menu_->addAction("Atom");
+  connect(a, SIGNAL(triggered()), this, SLOT(SelectAtom()));
+  a=select_menu_->addAction("Residue");
+  connect(a, SIGNAL(triggered()), this, SLOT(SelectResidue()));
+  a=select_menu_->addAction("Around Atom");
   connect(a, SIGNAL(triggered()), this, SLOT(SelectAroundAtom()));
+  a=select_menu_->addAction("Around Residue");
+  connect(a, SIGNAL(triggered()), this, SLOT(SelectAroundResidue()));
   a=select_menu_->addAction("Backbone");
   connect(a, SIGNAL(triggered()), this, SLOT(SelectBackbone()));
   a=select_menu_->addAction("Sidechains");
@@ -76,6 +82,32 @@ void SceneMenu::SelectAroundAtom()
   e->SetSelection(v);
 }
 
+void SceneMenu::SelectAroundResidue()
+{
+  gfx::EntityP e=dyn_cast<gfx::Entity>(picked_.first);
+  mol::EntityView v=e->GetView().CreateEmptyView();
+  v.AddAtom(picked_.second);
+  v=v.ExtendViewToResidues();
+  v=v.ExtendViewToSurrounding(0.5);
+  e->SetSelection(v.ExtendViewToResidues());
+}
+
+void SceneMenu::SelectAtom()
+{
+  gfx::EntityP e=dyn_cast<gfx::Entity>(picked_.first);
+  mol::EntityView v=e->GetView().CreateEmptyView();
+  v.AddAtom(picked_.second);
+  e->SetSelection(v);
+}
+
+void SceneMenu::SelectResidue()
+{
+  gfx::EntityP e=dyn_cast<gfx::Entity>(picked_.first);
+  mol::EntityView v=e->GetView().CreateEmptyView();
+  v.AddAtom(picked_.second);
+  e->SetSelection(v.ExtendViewToResidues());
+}
+
 void SceneMenu::Select(const String& str)
 {
   gfx::EntityP e=dyn_cast<gfx::Entity>(picked_.first);
@@ -102,20 +134,20 @@ void SceneMenu::CenterOnResidue()
 void SceneMenu::CenterOnChain()
 {
   mol::ChainHandle chain=picked_.second.GetResidue().GetChain();
-  gfx::Scene::Instance().SetCenter(chain.GetGeometricCenter());
+  gfx::Scene::Instance().SetCenter(chain.GetBounds().GetCenter());
 }
 
 void SceneMenu::CenterOnView()
 {
   mol::ResidueHandle res=picked_.second.GetResidue();
-  gfx::Scene::Instance().SetCenter(res.GetGeometricCenter());
+  gfx::Scene::Instance().SetCenter(res.GetBounds().GetCenter());
 }
 
 void SceneMenu::CenterOnSelection()
 {
   gfx::EntityP e=dyn_cast<gfx::Entity>(picked_.first);
   if (e->GetSelection() && e->GetSelection().GetAtomCount()>0) {
-    geom::Vec3 center=e->GetSelection().GetGeometricCenter();
+    geom::Vec3 center=e->GetSelection().GetBounds().GetCenter();
     gfx::Scene::Instance().SetCenter(center);
   }
 }
diff --git a/modules/gui/src/scene_menu.hh b/modules/gui/src/scene_menu.hh
index 0b212bad940db904428bcf12ade5357ea2ed8088..9472a6245f46a49bbad0c8bf38d1828b5286bfcc 100644
--- a/modules/gui/src/scene_menu.hh
+++ b/modules/gui/src/scene_menu.hh
@@ -19,15 +19,14 @@
 #ifndef OST_GUI_SCENE_MENU_HH
 #define OST_GUI_SCENE_MENU_HH
 
-#include <QObject>
-#include <QPoint>
-#include <QMenu>
-#include <QString>
 
 #include <ost/mol/mol.hh>
 #include <ost/gfx/gfx_object_fw.hh>
-#include <ost/gui/scene_menu.hh>
 
+#include <QObject>
+#include <QPoint>
+#include <QMenu>
+#include <QString>
 namespace ost { namespace gui {
 
 class SceneMenu : public QObject{
@@ -43,6 +42,9 @@ public slots:
   void SelectSidechains();
   void SelectLigands();
   void SelectAroundAtom();
+  void SelectAroundResidue();
+  void SelectAtom();
+  void SelectResidue();
   void Select(const String& str);
   void UnSelect();
   void CenterOnAtom();
diff --git a/modules/gui/src/scene_selection.cc b/modules/gui/src/scene_selection.cc
index 7beeadc58d7777ca7362424ca03692902d628657..1ef2ee7ce38eab22a77ef5e9501b349c62150b73 100644
--- a/modules/gui/src/scene_selection.cc
+++ b/modules/gui/src/scene_selection.cc
@@ -16,6 +16,7 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
+#include <ost/gui/gosty_app.hh>
 #include <ost/dyn_cast.hh>
 
 #include <ost/geom/vec3.hh>
@@ -35,9 +36,7 @@
 
 #endif
 
-#include <ost/gui/gosty_app.hh>
 #include <ost/gui/scene_win/scene_win.hh>
-#include <ost/gui/query_dialog.hh>
 
 #include "scene_selection.hh"
 
@@ -110,25 +109,20 @@ void SceneSelection::CenterOnObjects() {
     }
   }
   if(changed){
-    gfx::Scene::Instance().SetCenter(geom::Vec3(((max.GetX()+min.GetX())/2),
-                                                ((max.GetY()+min.GetY())/2),
-                                                ((max.GetZ()+min.GetZ())/2)));
+    gfx::Scene::Instance().SetCenter(geom::Vec3(((max.x+min.x)/2),
+                                                ((max.y+min.y)/2),
+                                                ((max.z+min.z)/2)));
   }
 }
 
 void SceneSelection::Delete() {
-  QList<gfx::GfxObjP> selected_objects;
+  QList<gfx::GfxNodeP> selected_objects;
   for(unsigned int i = 0; i < nodes_.size(); i++){
     gfx::GfxNodeP node = nodes_[i];
-    if (node) {
-      gfx::GfxObjP obj = dyn_cast<gfx::GfxObj> (node);
-      if (obj) {
-        selected_objects.append(obj);
-      }
-    }
+    selected_objects.append(node);
   }
   for(int i=0; i < selected_objects.size(); i++){
-      gfx::Scene::Instance().Remove(selected_objects[i]);
+    gfx::Scene::Instance().Remove(selected_objects[i]);
   }
 }
 
@@ -171,26 +165,6 @@ void SceneSelection::ShowOriginalMap()
 
 #endif // OST_IMG_ENABLED
 
-void SceneSelection::Select() {
-  QueryDialog d;
-  if (d.exec() == QDialog::Accepted) {
-    QString query = d.GetQueryString();
-    for(unsigned int i = 0; i < nodes_.size(); i++){
-      gfx::GfxNodeP node = nodes_[i];
-      if (node) {
-        gfx::Entity* obj = dynamic_cast<gfx::Entity*> (node.get());
-        if (obj) {
-          mol::Query q(query.toStdString());
-          if (q.IsValid()) {
-              mol::EntityView ent = obj->GetView().Select(q);
-              obj->SetSelection(ent);
-          }
-        }
-     }
-    }
-  }
-}
-
 void SceneSelection::Deselect(){
   for(unsigned int i = 0; i < nodes_.size(); i++){
     gfx::GfxNodeP node = nodes_[i];
@@ -203,32 +177,6 @@ void SceneSelection::Deselect(){
   }
 }
 
-void SceneSelection::CopyViews() {
-  QueryDialog d;
-  QList<gfx::GfxObjP> objects_to_add;
-  if (d.exec() == QDialog::Accepted) {
-    QString query = d.GetQueryString();
-    for(unsigned int i = 0; i < nodes_.size(); i++){
-      gfx::GfxNodeP node = nodes_[i];
-      if (node) {
-        gfx::Entity* obj = dynamic_cast<gfx::Entity*> (node.get());
-        if (obj) {
-          mol::Query q(query.toStdString());
-          if (q.IsValid()) {
-            mol::EntityView ent = obj->GetView().Select(q);
-            gfx::EntityP new_obj(new gfx::Entity(obj->GetName()
-                                 + " *", ent));
-            objects_to_add.append(new_obj);
-          }
-        }
-      }
-    }
-    for(int i=0; i < objects_to_add.size(); i++){
-      gfx::Scene::Instance().Add(objects_to_add[i]);
-    }
-  }
-}
-
 void SceneSelection::Show() {
   gfx::Scene::Instance().GetRootNode()->Show();
   for(unsigned int i = 0; i < nodes_.size(); i++){
@@ -298,17 +246,6 @@ void SceneSelection::DeselectAllViews(){
   }
 }
 
-void SceneSelection::SelectViews(){
-  QueryDialog d;
-  if (d.exec() == QDialog::Accepted) {
-    QString query = d.GetQueryString();
-    mol::Query q(query.toStdString());
-    mol::EntityView union_view = this->GetViewUnion();
-    if(union_view.IsValid() && q.IsValid()){
-      view_entity_->SetSelection(union_view.Select(q));
-    }
-  }
-}
 
 
 gfx::EntityP SceneSelection::GetViewEntity() const{
diff --git a/modules/gui/src/scene_selection.hh b/modules/gui/src/scene_selection.hh
index 7bbcb2e38416152138f1cd48b2f817ff98174855..ebc2bbfdbca1f44dcc75052e3ef9d766f9f9c6af 100644
--- a/modules/gui/src/scene_selection.hh
+++ b/modules/gui/src/scene_selection.hh
@@ -19,9 +19,6 @@
 #ifndef OST_GUI_SCENE_SELECTION_HH
 #define OST_GUI_SCENE_SELECTION_HH
 
-#include <QObject>
-#include <QMenu>
-#include <QPoint>
 
 #include <ost/mol/query_view_wrapper.hh>
 
@@ -29,6 +26,9 @@
 #include <ost/gfx/gfx_node_fw.hh>
 #include <ost/gui/module_config.hh>
 
+#include <QObject>
+#include <QMenu>
+#include <QPoint>
 namespace ost { namespace gui {
 
 class DLLEXPORT_OST_GUI SceneSelection : public QObject {
@@ -49,14 +49,11 @@ public slots:
   void ShowDownsampledMap();
   void ShowOriginalMap();  
 #endif // OST_IMG_ENABLED
-  void CopyViews();
-  void Select();
   void Deselect();
   void Show();
   void Hide();
   void SelectAllViews();
   void DeselectAllViews();
-  void SelectViews();
   void MakeVisible();
   void MakeHidden();
   void ShowExclusive();
diff --git a/modules/gui/src/scene_win/context_menu.cc b/modules/gui/src/scene_win/context_menu.cc
index afce21203c2508af289a1034a0e6685e4db1c6cc..52b71d38b32f78d3aee6fb0675253aa5b604c766 100644
--- a/modules/gui/src/scene_win/context_menu.cc
+++ b/modules/gui/src/scene_win/context_menu.cc
@@ -21,15 +21,12 @@
 */
 #include <boost/pointer_cast.hpp>
 
-#include <QAction>
-#include <QMenu>
-#include <QItemSelection>
-#include <QItemSelectionModel>
 
 #include <ost/dyn_cast.hh>
 
+#include <ost/gfx/scene.hh>
+
 #include <ost/gui/scene_selection.hh>
-#include <ost/gui/query_dialog.hh>
 
 #if OST_IMG_ENABLED
 #include <ost/gfx/map_iso.hh>
@@ -42,6 +39,10 @@
 
 #include "context_menu.hh"
 
+#include <QAction>
+#include <QMenu>
+#include <QItemSelection>
+#include <QItemSelectionModel>
 namespace ost { namespace gui {
 
 ContextMenu::ContextMenu(QTreeView* view, SceneWinModel* model):
@@ -51,51 +52,39 @@ ContextMenu::ContextMenu(QTreeView* view, SceneWinModel* model):
   connect(action, SIGNAL(triggered()), SceneSelection::Instance(), SLOT(CenterOnObjects()));
   this->AddAction(action, GFX_OBJECT);
 
-  action = new QAction("Copy",this);
-  connect(action, SIGNAL(triggered()), SceneSelection::Instance(), SLOT(CopyViews()));
-  this->AddAction(action, ENTITY);
-  action = new QAction("Create Custom View",this);
-  connect(action, SIGNAL(triggered()), this, SLOT(AddViewFromEntity()));
-  this->AddAction(action, ENTITY);
-  action = new QAction("Select..", this);
-  connect(action, SIGNAL(triggered()), SceneSelection::Instance(), SLOT(Select()));
-  this->AddAction(action, ENTITY);
   action = new QAction("Deselect",this);
   connect(action, SIGNAL(triggered()), SceneSelection::Instance(), SLOT(Deselect()));
   this->AddAction(action, ENTITY);
 
   action = new QAction("Delete",this);
   connect(action, SIGNAL(triggered()), SceneSelection::Instance(), SLOT(Delete()));
-  this->AddAction(action, GFX_OBJECT|NOT_SCENE);
+  this->AddAction(action, GFX_NODE|NOT_SCENE);
 
   action = new QAction("Show",this);
   connect(action, SIGNAL(triggered()), SceneSelection::Instance(), SLOT(Show()));
-  this->AddAction(action, GFX_OBJECT|NOT_VISIBLE);
+  this->AddAction(action, GFX_NODE|NOT_VISIBLE);
   action = new QAction("Hide",this);
   connect(action, SIGNAL(triggered()), SceneSelection::Instance(), SLOT(Hide()));
-  this->AddAction(action, GFX_OBJECT|NOT_HIDDEN);
+  this->AddAction(action, GFX_NODE|NOT_HIDDEN);
 
   action = new QAction("Show",this);
   connect(action, SIGNAL(triggered()), SceneSelection::Instance(), SLOT(MakeVisible()));
-  this->AddAction(action, ENTITY_VIEW);
+  this->AddAction(action, ENTITY_VIEW | VIEWS_SAME_OBJECT);
   action = new QAction("Hide",this);
   connect(action, SIGNAL(triggered()), SceneSelection::Instance(), SLOT(MakeHidden()));
-  this->AddAction(action, ENTITY_VIEW);
+  this->AddAction(action, ENTITY_VIEW | VIEWS_SAME_OBJECT);
   action = new QAction("Show Exclusive",this);
   connect(action, SIGNAL(triggered()), SceneSelection::Instance(), SLOT(ShowExclusive()));
-  this->AddAction(action, ENTITY_VIEW);
+  this->AddAction(action, ENTITY_VIEW | VIEWS_SAME_OBJECT);
   action = new QAction("Hide Exclusive",this);
   connect(action, SIGNAL(triggered()), SceneSelection::Instance(), SLOT(HideExclusive()));
-  this->AddAction(action, ENTITY_VIEW);
+  this->AddAction(action, ENTITY_VIEW | VIEWS_SAME_OBJECT);
   action = new QAction("Select All",this);
   connect(action, SIGNAL(triggered()), SceneSelection::Instance(), SLOT(SelectAllViews()));
-  this->AddAction(action, ENTITY_VIEW);
+  this->AddAction(action, ENTITY_VIEW | VIEWS_SAME_OBJECT);
   action = new QAction("Deselect All",this);
   connect(action, SIGNAL(triggered()), SceneSelection::Instance(), SLOT(DeselectAllViews()));
-  this->AddAction(action, ENTITY_VIEW);
-  action = new QAction("Select..",this);
-  connect(action, SIGNAL(triggered()), SceneSelection::Instance(), SLOT(SelectViews()));
-  this->AddAction(action, ENTITY_VIEW);
+  this->AddAction(action, ENTITY_VIEW | VIEWS_SAME_OBJECT);
   action = new QAction("Create Custom View",this);
   connect(action, SIGNAL(triggered()), this, SLOT(AddView()));
   this->AddAction(action, ENTITY_VIEW);
@@ -134,6 +123,7 @@ void ContextMenu::ShowMenu(const QPoint& pos)
   ContextActionTypes flags;
   flags = ~flags;
 
+  gfx::EntityP view_entity = gfx::EntityP();
   int cnt = 0;
   if(indexes.size()>0){
     for(int i = 0; i < indexes.size(); i++){
@@ -148,7 +138,7 @@ void ContextMenu::ShowMenu(const QPoint& pos)
           else{
             flags &= ~NOT_VISIBLE;
           }
-          if(gfx_node->GetType()==0){flags &= ~NOT_SCENE;}
+          if(gfx::Scene::Instance().GetRootNode() == gfx_node){flags &= ~NOT_SCENE;}
           if(!dyn_cast<gfx::GfxObj> (gfx_node)){flags &= ~GFX_OBJECT;}
           if(!dyn_cast<gfx::Entity> (gfx_node)){flags &= ~ENTITY;}
 #if OST_IMG_ENABLED
@@ -174,7 +164,7 @@ void ContextMenu::ShowMenu(const QPoint& pos)
 #endif // OST_IMG_ENABLED
         }
         else{
-          flags &= ~(GFX_OBJECT | ENTITY
+          flags &= ~(GFX_NODE | GFX_OBJECT | ENTITY
 #if OST_IMG_ENABLED
               | MAP
 #endif
@@ -186,6 +176,14 @@ void ContextMenu::ShowMenu(const QPoint& pos)
           flags &= ~(ENTITY_VIEW | CUSTOM_VIEW);
         }
         else{
+          if(view_entity){
+            if(!(entity_part_node->GetEntity() == view_entity)){
+              flags &= ~VIEWS_SAME_OBJECT;
+            }
+          }
+          else{
+            view_entity = entity_part_node->GetEntity();
+          }
           CustomPartNode* custom_part_node = qobject_cast<CustomPartNode*>(entity_part_node);
           if(!custom_part_node){
             flags &= ~CUSTOM_VIEW;
@@ -221,30 +219,6 @@ void ContextMenu::AddAction(QAction* action,ContextActionTypes type){
   actions_[action] = type;
 }
 
-void ContextMenu::AddViewFromEntity() {
-  QueryDialog d;
-  if (d.exec() == QDialog::Accepted) {
-    QString query = d.GetQueryString();
-    int node_count = SceneSelection::Instance()->GetActiveNodeCount();
-    for(int i = 0; i < node_count; i++){
-      gfx::GfxNodeP node = SceneSelection::Instance()->GetActiveNode(i);
-      if (node) {
-        EntityNode* ent_node = qobject_cast<EntityNode*>(model_->FindGfxNode(node));
-        if (ent_node) {
-          mol::Query q(query.toStdString());
-          if (q.IsValid()) {
-            gfx::EntityP entity = boost::dynamic_pointer_cast<gfx::Entity>(ent_node->GetGfxNode());
-            if(entity){
-              CustomPartNode* child_node = new CustomPartNode("New View", entity, mol::QueryViewWrapper(q,entity->GetView()),ent_node->GetCustomViewNode());
-              model_->AddNode(ent_node->GetCustomViewNode(),child_node);
-            }
-          }
-        }
-     }
-    }
-  }
-}
-
 void ContextMenu::AddView(){
   gfx::EntityP entity = SceneSelection::Instance()->GetViewEntity();
 
diff --git a/modules/gui/src/scene_win/context_menu.hh b/modules/gui/src/scene_win/context_menu.hh
index 1a2501da86e6f7fea9cc09b56b0cd00b67a4f893..03007fc6fcbd4641f881ab29c1bee48eb532cc86 100644
--- a/modules/gui/src/scene_win/context_menu.hh
+++ b/modules/gui/src/scene_win/context_menu.hh
@@ -23,32 +23,34 @@
   Author: Stefan Scheuber
  */
 
-#include <QFlags>
-#include <QMap>
-#include <QAbstractItemModel>
-#include <QTreeView>
 
 #include <ost/gui/module_config.hh>
 #include <ost/gui/scene_win/scene_win_model.hh>
 
+#include <QFlags>
+#include <QMap>
+#include <QAbstractItemModel>
+#include <QTreeView>
 namespace ost { namespace gui {
 
 enum ContextActionType
 {
-  GFX_OBJECT=0x1,
-  ENTITY=0x2,
-  ENTITY_VIEW=0x4,
-  CUSTOM_VIEW=0x8,
-  NOT_VISIBLE=0x10,
-  NOT_HIDDEN=0x20,
-  NOT_SCENE=0x40,
-  SINGLE=0x80,
-  MULTI=0x100
+  GFX_NODE=0x1,
+  GFX_OBJECT=0x2,
+  ENTITY=0x4,
+  ENTITY_VIEW=0x8,
+  CUSTOM_VIEW=0x10,
+  NOT_VISIBLE=0x20,
+  NOT_HIDDEN=0x40,
+  NOT_SCENE=0x80,
+  SINGLE=0x100,
+  MULTI=0x200,
+  VIEWS_SAME_OBJECT=0x400
 #if OST_IMG_ENABLED
-  ,MAP=0x200,
-  MAP_ORIGINAL=0x400,
-  MAP_DOWNSAMPLED=0x800,
-  MAP_DSAMPLED_AVAIL=0x1000
+  ,MAP=0x800,
+  MAP_ORIGINAL=0x1000,
+  MAP_DOWNSAMPLED=0x2000,
+  MAP_DSAMPLED_AVAIL=0x4000
 #endif
 };
 Q_DECLARE_FLAGS(ContextActionTypes, ContextActionType)
@@ -66,7 +68,6 @@ public:
   void AddAction(QAction* action,ContextActionTypes type);
 
 private slots:
-  void AddViewFromEntity();
   void AddView();
   void Rename();
   void DeleteView();
diff --git a/modules/gui/src/scene_win/current_selection_node.cc b/modules/gui/src/scene_win/current_selection_node.cc
index c8b0eb03cff2c81aad85d48a8d94479f533d8ad6..9de4397a43989be2af8d4732e08f0adec8974f02 100644
--- a/modules/gui/src/scene_win/current_selection_node.cc
+++ b/modules/gui/src/scene_win/current_selection_node.cc
@@ -16,18 +16,18 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#include <QFont>
 
+#include <ost/gui/gosty_app.hh>
 #include <ost/mol/query_view_wrapper.hh>
 
 #include <ost/gfx/scene.hh>
 #include <ost/gfx/gfx_node.hh>
 
-#include <ost/gui/gosty_app.hh>
 #include <ost/gui/scene_win/scene_win.hh>
 
 #include "current_selection_node.hh"
 
+#include <QFont>
 namespace ost { namespace gui {
 
 CurrentSelectionNode::CurrentSelectionNode(gfx::EntityP entity, SceneNode* parent):EntityPartNode("Current Selection",entity,mol::QueryViewWrapper(entity->GetSelection()),parent),wrapper_(mol::QueryViewWrapper(entity->GetSelection())){
diff --git a/modules/gui/src/scene_win/current_selection_node.hh b/modules/gui/src/scene_win/current_selection_node.hh
index baedc36040b1f34f54cd87a31b339e8a7db10bca..9a63219d9e63d8a0630e25592aed164fbc43266b 100644
--- a/modules/gui/src/scene_win/current_selection_node.hh
+++ b/modules/gui/src/scene_win/current_selection_node.hh
@@ -19,9 +19,6 @@
 #ifndef OST_GUI_SCENE_WIN_CURRENT_SELECTION_NODE_HH
 #define OST_GUI_SCENE_WIN_CURRENT_SELECTION_NODE_HH
 
-#include <QObject>
-#include <QVariant>
-#include <QModelIndex>
 
 #include <ost/mol/entity_view.hh>
 #include <ost/mol/query_view_wrapper.hh>
@@ -32,6 +29,9 @@
 #include <ost/gui/module_config.hh>
 #include <ost/gui/scene_win/entity_part_node.hh>
 
+#include <QObject>
+#include <QVariant>
+#include <QModelIndex>
 /*
   Author: Stefan Scheuber
  */
diff --git a/modules/gui/src/scene_win/custom_part_node.cc b/modules/gui/src/scene_win/custom_part_node.cc
index f8e5f79db5d70d3ff6d963e0368037301e46dd02..18c9d9972f9646ef64d93b498a7316622eddcc55 100644
--- a/modules/gui/src/scene_win/custom_part_node.cc
+++ b/modules/gui/src/scene_win/custom_part_node.cc
@@ -16,7 +16,6 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#include <QFont>
 
 #include "custom_part_node.hh"
 
@@ -25,6 +24,7 @@
 #include <ost/gfx/entity.hh>
 #include <ost/gfx/gfx_node.hh>
 
+#include <QFont>
 namespace ost { namespace gui {
 
 CustomPartNode::CustomPartNode(QString name, gfx::EntityP entity, mol::QueryViewWrapper part, SceneNode* parent):EntityPartNode(name,entity,part,parent){
diff --git a/modules/gui/src/scene_win/custom_part_node.hh b/modules/gui/src/scene_win/custom_part_node.hh
index b585af4e0ee03dc06445763d6687007dd4fab761..9c9eba9f4bc609178e0e3577a0144657088b3de9 100644
--- a/modules/gui/src/scene_win/custom_part_node.hh
+++ b/modules/gui/src/scene_win/custom_part_node.hh
@@ -19,9 +19,6 @@
 #ifndef OST_GUI_SCENE_WIN_CUSTOM_PART_NODE_HH
 #define OST_GUI_SCENE_WIN_CUSTOM_PART_NODE_HH
 
-#include <QObject>
-#include <QVariant>
-#include <QModelIndex>
 
 #include <ost/mol/query_view_wrapper.hh>
 
@@ -31,6 +28,9 @@
 #include <ost/gui/scene_win/scene_node.hh>
 
 #include "entity_part_node.hh"
+#include <QObject>
+#include <QVariant>
+#include <QModelIndex>
 /*
   Author: Stefan Scheuber
  */
diff --git a/modules/gui/src/scene_win/entity_node.cc b/modules/gui/src/scene_win/entity_node.cc
index 62c646ed85a13146749f3fa7143a6c7a26e4c9a8..3aa51c81ce37a0f9acdeebd6033d4573b008ee73 100644
--- a/modules/gui/src/scene_win/entity_node.cc
+++ b/modules/gui/src/scene_win/entity_node.cc
@@ -16,16 +16,14 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
+#include <ost/gui/gosty_app.hh>
 #include <boost/pointer_cast.hpp>
 
-#include <QFont>
-#include <QString>
 
 #include <ost/mol/query.hh>
 #include <ost/mol/query_view_wrapper.hh>
 #include <ost/mol/view_type_fw.hh>
 
-#include <ost/gui/gosty_app.hh>
 #include <ost/gui/scene_win/scene_win.hh>
 
 #include "current_selection_node.hh"
@@ -35,6 +33,8 @@
 
 #include "entity_node.hh"
 
+#include <QFont>
+#include <QString>
 
 
 namespace ost { namespace gui {
@@ -60,13 +60,13 @@ EntityNode::EntityNode(gfx::EntityP& entity, SceneNode* parent):
   SceneNode* quick_selection = new LabelNode("Quick Selection",this);
   model->AddNode(this, quick_selection);
 
-  SceneNode* node = new EntityPartNode("Backbone", entity, mol::QueryViewWrapper(entity->GetView().Select("aname=CA,C,N,O and peptide=true")), quick_selection);
+  SceneNode* node = new EntityPartNode("Backbone", entity, mol::QueryViewWrapper(mol::Query("aname=CA,C,N,O and peptide=true"),entity->GetView()), quick_selection);
   model->AddNode(quick_selection, node);
-  node = new EntityPartNode("Sidechains", entity, mol::QueryViewWrapper(entity->GetView().Select("aname!=CA,C,N,O and peptide=true",mol::QueryFlag::EXCLUSIVE_BONDS)), quick_selection);
+  node = new EntityPartNode("Sidechains", entity, mol::QueryViewWrapper(mol::Query("aname!=CA,C,N,O and peptide=true"),mol::QueryFlag::EXCLUSIVE_BONDS,entity->GetView()), quick_selection);
   model->AddNode(quick_selection, node);
-  node = new EntityPartNode("Ligands", entity, mol::QueryViewWrapper(entity->GetView().Select("ishetatm=1 and rname!=HOH,WAT")), quick_selection);
+  node = new EntityPartNode("Ligands", entity, mol::QueryViewWrapper(mol::Query("ishetatm=1 and rname!=HOH,WAT"),entity->GetView()), quick_selection);
   model->AddNode(quick_selection, node);
-  node = new EntityPartNode("Water", entity, mol::QueryViewWrapper(entity->GetView().Select("rname=HOH,WAT")), quick_selection);
+  node = new EntityPartNode("Water", entity, mol::QueryViewWrapper(mol::Query("rname=HOH,WAT"),entity->GetView()), quick_selection);
   model->AddNode(quick_selection, node);
 
 
diff --git a/modules/gui/src/scene_win/entity_part_node.cc b/modules/gui/src/scene_win/entity_part_node.cc
index dd56f2484a9a355bed0745c3e9f4524ab652fe10..da8867d8bb6e8c5c03f93d7318de63ee6ef81762 100644
--- a/modules/gui/src/scene_win/entity_part_node.cc
+++ b/modules/gui/src/scene_win/entity_part_node.cc
@@ -16,13 +16,13 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#include <QFont>
 
 #include "entity_part_node.hh"
 
 #include <ost/gfx/entity.hh>
 #include <ost/gfx/gfx_node.hh>
 
+#include <QFont>
 namespace ost { namespace gui {
 
 EntityPartNode::EntityPartNode(QString name, gfx::EntityP entity, mol::QueryViewWrapper part, SceneNode* parent):SceneNode(parent),name_(name),entity_(entity),query_view_(part),visible_(true){
diff --git a/modules/gui/src/scene_win/entity_part_node.hh b/modules/gui/src/scene_win/entity_part_node.hh
index 7f7d3629784aa26e6362011f5f428b03d166ebd7..2eb308cbedae85349e627cc31e9d05abe9b68413 100644
--- a/modules/gui/src/scene_win/entity_part_node.hh
+++ b/modules/gui/src/scene_win/entity_part_node.hh
@@ -19,9 +19,6 @@
 #ifndef OST_GUI_SCENE_WIN_ENTITY_PART_NODE_HH
 #define OST_GUI_SCENE_WIN_ENTITY_PART_NODE_HH
 
-#include <QObject>
-#include <QVariant>
-#include <QModelIndex>
 
 #include <ost/mol/query_view_wrapper.hh>
 
@@ -30,6 +27,9 @@
 #include <ost/gui/module_config.hh>
 #include <ost/gui/scene_win/scene_node.hh>
 
+#include <QObject>
+#include <QVariant>
+#include <QModelIndex>
 /*
   Author: Stefan Scheuber
  */
diff --git a/modules/gui/src/scene_win/gfx_scene_node.cc b/modules/gui/src/scene_win/gfx_scene_node.cc
index 9b8828779f3a85f3e20c726276fe608e64bffdf1..191007aee833f93a9f4e36b2c2e91a39df4eb4b4 100644
--- a/modules/gui/src/scene_win/gfx_scene_node.cc
+++ b/modules/gui/src/scene_win/gfx_scene_node.cc
@@ -16,13 +16,13 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#include <QFont>
 
 #include "gfx_scene_node.hh"
 
 #include <ost/gfx/scene.hh>
 #include <ost/gfx/gfx_node.hh>
 
+#include <QFont>
 namespace ost { namespace gui {
 
 GfxSceneNode::GfxSceneNode(gfx::GfxNodeP gfx_node, SceneNode* parent):SceneNode(parent),gfx_node_(gfx_node){}
@@ -71,10 +71,10 @@ bool GfxSceneNode::SetData(int column, const QVariant& value, int role){
 
 Qt::ItemFlags GfxSceneNode::Flags(int column) const{
   if(column==0){
-    return Qt::ItemIsSelectable|Qt::ItemIsUserCheckable|Qt::ItemIsEnabled;
+    return Qt::ItemIsSelectable|Qt::ItemIsUserCheckable|Qt::ItemIsEnabled|Qt::ItemIsDragEnabled;
   }
   else if(column==1){
-    return Qt::ItemIsSelectable|Qt::ItemIsEnabled|Qt::ItemIsEditable;
+    return Qt::ItemIsSelectable|Qt::ItemIsEnabled|Qt::ItemIsEditable|Qt::ItemIsDragEnabled;
   }
   return Qt::NoItemFlags;
 }
diff --git a/modules/gui/src/scene_win/gfx_scene_node.hh b/modules/gui/src/scene_win/gfx_scene_node.hh
index fb954081514a1ffd585428362d8d79181ebd026b..03100392fa20f685e0b98c81dd22325f62a64048 100644
--- a/modules/gui/src/scene_win/gfx_scene_node.hh
+++ b/modules/gui/src/scene_win/gfx_scene_node.hh
@@ -19,15 +19,15 @@
 #ifndef OST_GUI_SCENE_WIN_GFX_SCENE_NODE_HH
 #define OST_GUI_SCENE_WIN_GFX_SCENE_NODE_HH
 
-#include <QObject>
-#include <QVariant>
-#include <QModelIndex>
 
 #include <ost/gfx/gfx_node_fw.hh>
 
 #include <ost/gui/module_config.hh>
 #include <ost/gui/scene_win/scene_node.hh>
 
+#include <QObject>
+#include <QVariant>
+#include <QModelIndex>
 /*
   Author: Stefan Scheuber
  */
diff --git a/modules/gui/src/scene_win/label_node.cc b/modules/gui/src/scene_win/label_node.cc
index 5cf9b2d95599e76da350026866d4150ad59a606f..8a01e6aec1a27ae35b59a1b3cf0c2f98e3d2fcf1 100644
--- a/modules/gui/src/scene_win/label_node.cc
+++ b/modules/gui/src/scene_win/label_node.cc
@@ -16,13 +16,13 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#include <QFont>
 
 #include "label_node.hh"
 
 #include <ost/gfx/entity.hh>
 #include <ost/gfx/gfx_node.hh>
 
+#include <QFont>
 namespace ost { namespace gui {
 
 LabelNode::LabelNode(QString name, SceneNode* parent):SceneNode(parent),name_(name){
diff --git a/modules/gui/src/scene_win/label_node.hh b/modules/gui/src/scene_win/label_node.hh
index 50d471be0991240d5f99a5becac4be368cc71871..4a9722f7f01ccf09b5afa3609f91f53566f0c5e3 100644
--- a/modules/gui/src/scene_win/label_node.hh
+++ b/modules/gui/src/scene_win/label_node.hh
@@ -19,13 +19,13 @@
 #ifndef OST_GUI_SCENE_WIN_LABEL_NODE_HH
 #define OST_GUI_SCENE_WIN_LABEL_NODE_HH
 
-#include <QObject>
-#include <QVariant>
-#include <QModelIndex>
 
 #include <ost/gui/module_config.hh>
 #include <ost/gui/scene_win/scene_node.hh>
 
+#include <QObject>
+#include <QVariant>
+#include <QModelIndex>
 /*
   Author: Stefan Scheuber
  */
diff --git a/modules/gui/src/scene_win/render_mode_node.cc b/modules/gui/src/scene_win/render_mode_node.cc
index 63789cd3748647cf9b595cc57c2a2826e48defe1..88e67dea8d5990dae5ffe25a885805df462a8ca2 100644
--- a/modules/gui/src/scene_win/render_mode_node.cc
+++ b/modules/gui/src/scene_win/render_mode_node.cc
@@ -16,12 +16,12 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#include <QFont>
 
 #include <ost/mol/query_view_wrapper.hh>
 
 #include "render_mode_node.hh"
 
+#include <QFont>
 namespace ost { namespace gui {
 
 RenderModeNode::RenderModeNode(gfx::EntityP entity, gfx::RenderMode::Type render_mode, SceneNode* parent):EntityPartNode(entity->GetRenderModeName(render_mode).c_str(),entity,mol::QueryViewWrapper(entity->GetRenderView(render_mode)),parent),
@@ -77,9 +77,9 @@ gfx::RenderMode::Type RenderModeNode::GetRenderMode() const {
   return render_mode_;
 }
 
-void RenderModeNode::SetQueryView(mol::QueryViewWrapper part)
+void RenderModeNode::Update()
 {
-  //Do Nothing
+  this->SetQueryView(mol::QueryViewWrapper(entity_->GetRenderView(this->GetRenderMode())));
 }
 
 }}
diff --git a/modules/gui/src/scene_win/render_mode_node.hh b/modules/gui/src/scene_win/render_mode_node.hh
index 68bf5300ee720a5becd74a2e0b07e890d4801d68..fb7304379c7cc18dc97229fa4a80aab0cad44e3b 100644
--- a/modules/gui/src/scene_win/render_mode_node.hh
+++ b/modules/gui/src/scene_win/render_mode_node.hh
@@ -19,9 +19,6 @@
 #ifndef OST_GUI_SCENE_WIN_RENDER_MODE_NODE_HH
 #define OST_GUI_SCENE_WIN_RENDER_MODE_NODE_HH
 
-#include <QObject>
-#include <QVariant>
-#include <QModelIndex>
 
 #include <ost/mol/entity_view.hh>
 #include <ost/mol/query_view_wrapper.hh>
@@ -36,6 +33,9 @@
 #include <ost/gui/module_config.hh>
 #include <ost/gui/scene_win/entity_part_node.hh>
 
+#include <QObject>
+#include <QVariant>
+#include <QModelIndex>
 /*
   Author: Stefan Scheuber
  */
@@ -54,8 +54,7 @@ public:
 
   gfx::RenderMode::Type GetRenderMode() const;
 
-  virtual void SetQueryView(mol::QueryViewWrapper part);
-
+  virtual void Update();
 private:
   gfx::EntityP entity_;
   gfx::RenderMode::Type render_mode_;
diff --git a/modules/gui/src/scene_win/render_modes_node.cc b/modules/gui/src/scene_win/render_modes_node.cc
index 0e46a1a03ea6ef71b9d8a1f2d352cf0542547071..a343490b894a21123cd97e353433db66dee27562 100644
--- a/modules/gui/src/scene_win/render_modes_node.cc
+++ b/modules/gui/src/scene_win/render_modes_node.cc
@@ -16,18 +16,18 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
+#include <ost/gui/gosty_app.hh>
 #include <boost/pointer_cast.hpp>
 
-#include <QFont>
 
 #include <ost/gfx/scene.hh>
 #include <ost/gfx/gfx_node.hh>
 
-#include <ost/gui/gosty_app.hh>
 #include <ost/gui/scene_win/scene_win.hh>
 
 #include "render_modes_node.hh"
 #include "render_mode_node.hh"
+#include <QFont>
 
 namespace ost { namespace gui {
 
@@ -54,6 +54,9 @@ void RenderModesNode::Update(){
       model->AddNode(this, node);
       render_types_.insert(render_modes[i],node);
     }
+    else{
+      render_types_[render_modes[i]]->Update();
+    }
   }
   QSet<gfx::RenderMode::Type> types_to_delete;
   QMap<gfx::RenderMode::Type,RenderModeNode*>::iterator type;
diff --git a/modules/gui/src/scene_win/render_modes_node.hh b/modules/gui/src/scene_win/render_modes_node.hh
index 231bf41bf62a81fad869aebdfde1063a8fd42740..dbb5c1c2bce9d5a4f2eba02c4d2505cd1f6ef751 100644
--- a/modules/gui/src/scene_win/render_modes_node.hh
+++ b/modules/gui/src/scene_win/render_modes_node.hh
@@ -19,9 +19,6 @@
 #ifndef OST_GUI_SCENE_WIN_RENDER_MODES_NODE_HH
 #define OST_GUI_SCENE_WIN_RENDER_MODES_NODE_HH
 
-#include <QObject>
-#include <QVariant>
-#include <QSet>
 
 #include <ost/gfx/entity.hh>
 #include <ost/gfx/entity_fw.hh>
@@ -36,6 +33,9 @@
 
 #include "render_mode_node.hh"
 
+#include <QObject>
+#include <QVariant>
+#include <QSet>
 /*
   Author: Stefan Scheuber
  */
diff --git a/modules/gui/src/scene_win/root_node.cc b/modules/gui/src/scene_win/root_node.cc
index e883f4b69f46b7e554acb8970fc91ed31ac2f185..98fc34dc9dc0da63138b6529309cd91478310ad9 100644
--- a/modules/gui/src/scene_win/root_node.cc
+++ b/modules/gui/src/scene_win/root_node.cc
@@ -16,12 +16,12 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#include <QFont>
 
 #include "root_node.hh"
 
 #include <ost/gfx/scene.hh>
 #include <ost/gfx/gfx_node.hh>
+#include <QFont>
 
 namespace ost { namespace gui {
 
diff --git a/modules/gui/src/scene_win/root_node.hh b/modules/gui/src/scene_win/root_node.hh
index 2738a90f50c856bddb26858f426e3eb6099697a2..4775e6246e269c86d414a5ec705599673bf8b227 100644
--- a/modules/gui/src/scene_win/root_node.hh
+++ b/modules/gui/src/scene_win/root_node.hh
@@ -19,12 +19,12 @@
 #ifndef OST_GUI_SCENE_WIN_ROOT_NODE_HH
 #define OST_GUI_SCENE_WIN_ROOT_NODE_HH
 
-#include <QObject>
-#include <QVariant>
-#include <QModelIndex>
 
 #include <ost/gui/module_config.hh>
 #include <ost/gui/scene_win/scene_node.hh>
+#include <QObject>
+#include <QVariant>
+#include <QModelIndex>
 
 /*
   Author: Stefan Scheuber
diff --git a/modules/gui/src/scene_win/scene_node.hh b/modules/gui/src/scene_win/scene_node.hh
index 926c16f75440e241c1610207cb2033913c0cc64b..9fbdd7cda10e8e8539160d1ddbe816877d3ec846 100644
--- a/modules/gui/src/scene_win/scene_node.hh
+++ b/modules/gui/src/scene_win/scene_node.hh
@@ -19,12 +19,12 @@
 #ifndef OST_GUI_SCENE_WIN_SCENE_NODE_HH
 #define OST_GUI_SCENE_WIN_SCENE_NODE_HH
 
+#include <ost/gui/module_config.hh>
+
 #include <QObject>
 #include <QVariant>
 #include <QModelIndex>
 
-#include <ost/gui/module_config.hh>
-
 /*
   Author: Stefan Scheuber
  */
diff --git a/modules/gui/src/scene_win/scene_win.cc b/modules/gui/src/scene_win/scene_win.cc
index 213582ff632aa1e697fbd193e528a1caccfbf7b3..ba685c3f62a4d58a6babb74dd65c3c8942428806 100644
--- a/modules/gui/src/scene_win/scene_win.cc
+++ b/modules/gui/src/scene_win/scene_win.cc
@@ -19,15 +19,15 @@
 /*
  Authors: Marco Biasini, Ansgar Philippsen, Stefan Scheuber
  */
-#include <QVBoxLayout>
-#include <QHeaderView>
 
-#include <ost/gui/widget_registry.hh>
 #include <ost/gui/gosty_app.hh>
+#include <ost/gui/widget_registry.hh>
 #include <ost/gui/scene_selection.hh>
 
 #include "scene_win.hh"
 
+#include <QVBoxLayout>
+#include <QHeaderView>
 namespace ost { namespace gui {
 
 class SceneWinFactory: public WidgetFactory {
@@ -52,12 +52,15 @@ SceneWin::SceneWin(QWidget* parent) :
   view_ = new QTreeView(this);
   context_menu_ = new ContextMenu(view_,model_);
   view_->setAttribute(Qt::WA_MacShowFocusRect, false);
+  view_->setAttribute(Qt::WA_MacSmallSize, true);
+  view_->setFrameShape(QFrame::NoFrame);
   view_->header()->hide();
   view_->setContextMenuPolicy(Qt::CustomContextMenu);
   view_->setModel(model_);
   view_->setSelectionBehavior(QAbstractItemView::SelectRows);
   view_->setSelectionMode(QAbstractItemView::ExtendedSelection);
   view_->setEditTriggers(QAbstractItemView::EditKeyPressed);
+  view_->setDragEnabled(true);
   view_->expandAll();
 
   layout->addWidget(view_);
diff --git a/modules/gui/src/scene_win/scene_win.hh b/modules/gui/src/scene_win/scene_win.hh
index 9761bb1f1924d01adafc8862c7b1fb0c7566bf2e..612198db622f03e3e82bb138eb3ce9d2b85dc164 100644
--- a/modules/gui/src/scene_win/scene_win.hh
+++ b/modules/gui/src/scene_win/scene_win.hh
@@ -19,8 +19,6 @@
 #ifndef OST_GUI_SCENE_WIN_SCENE_WIN_HH
 #define OST_GUI_SCENE_WIN_SCENE_WIN_HH
 
-#include <QTreeView>
-#include <QItemSelection>
 
 #include <ost/mol/query_view_wrapper.hh>
 
@@ -31,6 +29,8 @@
 #include <ost/gui/scene_win/scene_win_model.hh>
 #include <ost/gui/scene_win/context_menu.hh>
 
+#include <QTreeView>
+#include <QItemSelection>
 /*
   Authors: Marco Biasini, Ansgar Philippsen, Stefan Scheuber
 */
diff --git a/modules/gui/src/scene_win/scene_win_model.cc b/modules/gui/src/scene_win/scene_win_model.cc
index 12df1534d79e3ac9ed4d2dc609773a1cb88ad8e8..9e7542b0815c2a73267820ad1fa1b1991cf8cce9 100644
--- a/modules/gui/src/scene_win/scene_win_model.cc
+++ b/modules/gui/src/scene_win/scene_win_model.cc
@@ -198,6 +198,36 @@ bool SceneWinModel::setData(const QModelIndex& index,
   return false;
 }
 
+QStringList SceneWinModel::mimeTypes() const
+{
+    QStringList types;
+    types << "text/plain";
+    return types;
+}
+
+Qt::DropActions SceneWinModel::supportedDragActions() const
+{
+    return Qt::MoveAction;
+}
+
+QMimeData* SceneWinModel::mimeData(const QModelIndexList &indexes) const
+{
+  QMimeData *mimeData = new QMimeData();
+  QByteArray encoded_data;
+
+  QDataStream stream(&encoded_data, QIODevice::WriteOnly);
+
+
+  foreach (QModelIndex index, indexes) {
+    if (index.isValid() && index.column()==1) {
+      QString text = "scene['"+data(index, Qt::DisplayRole).toString()+"']";
+      encoded_data.append(text);
+    }
+  }
+  mimeData->setData("text/plain", encoded_data);
+  return mimeData;
+}
+
 void SceneWinModel::NodeAdded(const gfx::GfxNodeP& node)
 {
   gfx::EntityP e=boost::dynamic_pointer_cast<gfx::Entity>(node);
diff --git a/modules/gui/src/scene_win/scene_win_model.hh b/modules/gui/src/scene_win/scene_win_model.hh
index 996f7b640de20d1e9fea7303a7f162649757524c..060b148816aaadb7b9734b8a3333589f97788d17 100644
--- a/modules/gui/src/scene_win/scene_win_model.hh
+++ b/modules/gui/src/scene_win/scene_win_model.hh
@@ -23,8 +23,6 @@
   Author: Stefan Scheuber, Marco Biasini, Ansgar Philippsen
  */
 
-#include <QMap>
-#include <QAbstractItemModel>
 
 #include <ost/mol/view_type_fw.hh>
 #include <ost/mol/query_view_wrapper.hh>
@@ -36,6 +34,10 @@
 #include <ost/gui/scene_win/scene_node.hh>
 #include <ost/gui/scene_win/render_modes_node.hh>
 
+#include <QStringList>
+#include <QMimeData>
+#include <QMap>
+#include <QAbstractItemModel>
 namespace ost { namespace gui {
 
 
@@ -88,6 +90,10 @@ public:
                        const QVariant& value=QVariant(), 
                        int role=Qt::DisplayRole);
 
+  virtual QStringList mimeTypes() const;
+  Qt::DropActions supportedDragActions() const;
+  virtual QMimeData* mimeData(const QModelIndexList& indexes) const;
+
   // scene observer interface
   virtual void NodeAdded(const gfx::GfxNodeP& node);
   virtual void NodeRemoved(const gfx::GfxNodeP& node);
diff --git a/modules/gui/src/sequence/sequence_search_bar.cc b/modules/gui/src/sequence/sequence_search_bar.cc
deleted file mode 100644
index 9ae88675e2468dbe5083cbb642df653fd563c67a..0000000000000000000000000000000000000000
--- a/modules/gui/src/sequence/sequence_search_bar.cc
+++ /dev/null
@@ -1,125 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-/*
-  Author: Marco Biasini
- */
-
-#include "sequence_search_bar.hh"
-
-#include <QHBoxLayout>
-#include <QLineEdit>
-#include <QPainter>
-#include <QPaintEvent>
-#include <QLabel>
-#include <QKeyEvent>
-
-namespace ost { namespace gui { 
-
-SeqSearchBar::SeqSearchBar(QWidget* parent):
-  QWidget(parent)
-{
-  subject_=new QLineEdit(this);
-  search_all_=new QCheckBox("search in all sequences", this);
-  search_in_=new QComboBox(this);
-  QHBoxLayout* l= new QHBoxLayout(this);
-  l->addSpacing(2);
-  l->addWidget(subject_, 0);
-  l->setStretch(0,1);
-  l->addWidget(search_all_, 0);
-  QLabel* label=new QLabel("search in:", this);
-  l->addSpacing(10);
-  l->addWidget(label, 0);
-  l->addWidget(search_in_, 0);
-  //subject_->setMaximumWidth(200);
-  setLayout(l);
-  l->setSizeConstraint(QLayout::SetMaximumSize);
-  l->setMargin(1);  
-  search_all_->setCheckState(Qt::Checked);  
-  search_in_->setEnabled(false);  
-#if defined(__APPLE__)
-  subject_->setAttribute(Qt::WA_MacSmallSize, true);
-  search_all_->setAttribute(Qt::WA_MacSmallSize, true);
-  search_in_->setAttribute(Qt::WA_MacSmallSize, true);    
-  label->setAttribute(Qt::WA_MacSmallSize, true);
-#endif  
-  connect(subject_, SIGNAL(textChanged(const QString&)), this, 
-          SLOT(OnSubjectChanged(const QString&)));
-  connect(search_all_, SIGNAL(stateChanged(int)), this, 
-          SLOT(OnSearchAllChanged(int)));
-  connect(search_in_, SIGNAL(currentIndexChanged(int)), this,
-          SLOT(OnSearchInChanged(int)));
-}
-  
-void SeqSearchBar::UpdateItems(const QStringList& sequences)
-{
-  search_in_->clear();
-
-  for(int i=0;i< sequences.size(); i++){
-  search_in_->addItem(sequences[i]);
-  }
-
-  if (sequences.empty()) {
-    search_all_->setCheckState(Qt::Checked);  
-    search_in_->setEnabled(false);
-  }
-  subject_->setFocus(Qt::ActiveWindowFocusReason);  
-  subject_->selectAll();  
-}
-void SeqSearchBar::OnSearchAllChanged(int state)
-{
-  if (state==Qt::Unchecked) {
-    search_in_->setEnabled(true);
-  } else {
-    search_in_->setEnabled(false);
-  }
-  emit Changed(subject_->text(), search_all_->checkState()==Qt::Checked, 
-               search_in_->currentText());
-}
-
-void SeqSearchBar::OnSearchInChanged(int index)
-{
-  emit Changed(subject_->text(), search_all_->checkState()==Qt::Checked, 
-               search_in_->currentText());
-}
-
-void SeqSearchBar::OnSubjectChanged(const QString& str)
-{
-  emit Changed(str, search_all_->checkState()==Qt::Checked, 
-               search_in_->currentText());
-}
-
-void SeqSearchBar::paintEvent(QPaintEvent* paint_event)
-{
-  QPainter p(this);
-  p.setBrush(QBrush(QColor(Qt::blue).lighter(300)));
-  p.setPen(QPen(QColor(Qt::blue).lighter(200)));  
-  p.drawRect(rect());
-  paint_event->accept();
-}
-
-void SeqSearchBar::keyPressEvent(QKeyEvent* key_event)
-{
-  if (key_event->key()==Qt::Key_Escape) {
-    this->hide();
-    key_event->accept(); 
-  }
-  QWidget::keyPressEvent(key_event);
-}
-
-}}
diff --git a/modules/gui/src/sequence/sequence_viewer.cc b/modules/gui/src/sequence/sequence_viewer.cc
deleted file mode 100644
index d00a1b07bbd756a59067afe1c0467605e425f0ee..0000000000000000000000000000000000000000
--- a/modules/gui/src/sequence/sequence_viewer.cc
+++ /dev/null
@@ -1,273 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-
-/*
-  Author: Stefan Scheuber
- */
-#include <boost/pointer_cast.hpp>
-
-#include <QAbstractItemView>
-#include <QApplication>
-#include <QClipboard>
-#include <QHeaderView>
-#include <QPushButton>
-#include <QShortcut>
-#include <QVBoxLayout>
-#include <QVarLengthArray>
-
-#include <ost/mol/chain_view.hh>
-#include <ost/mol/entity_view.hh>
-
-#include <ost/seq/sequence_handle.hh>
-
-#include <ost/gfx/entity.hh>
-#include <ost/gfx/scene.hh>
-#include <ost/gfx/gfx_node_visitor.hh>
-
-#include <ost/gui/widget_registry.hh>
-#include <ost/gui/gosty_app.hh>
-
-#include "sequence_model.hh"
-#include "sequence_viewer.hh"
-
-namespace ost { namespace gui {
-
-class SequenceViewerV2Factory: public WidgetFactory {
-public:
-  SequenceViewerV2Factory() :
-    WidgetFactory("ost::gui::SequenceViewerV2", "Sequence Viewer V2") {
-  }
-
-  virtual Widget* Create(QWidget* parent) {
-    return GostyApp::Instance()->GetSequenceViewerV2();
-  }
-};
-
-OST_REGISTER_WIDGET(SequenceViewerV2, SequenceViewerV2Factory);
-
-struct GetNodesVisitor: public gfx::GfxNodeVisitor {
-  GetNodesVisitor(): nodes_() {}
-  virtual void VisitObject(gfx::GfxObj* o, const Stack& st) {
-    nodes_.push_back(o->shared_from_this());
-  }
-  gfx::NodePtrList nodes_;
-  gfx::NodePtrList GetNodes(){return nodes_;}
-};
-
-SequenceViewerV2::SequenceViewerV2(QWidget* parent): Widget(NULL,parent)
-{
-  gfx::Scene::Instance().AttachObserver(this);
-  model_ = new SequenceModel(this);
-
-  QVBoxLayout* layout = new QVBoxLayout(this);
-  layout->setMargin(0);
-  layout->setSpacing(0);
-
-  seq_search_bar_ = new SeqSearchBar(this);
-  seq_search_bar_->hide();
-  layout->addWidget(seq_search_bar_);
-  QShortcut* shortcut=new QShortcut(QKeySequence(tr("Ctrl+F")), this);
-  connect(shortcut, SIGNAL(activated()), this, SLOT(FindInSequence()));
-  connect(seq_search_bar_, SIGNAL(Changed(const QString&, bool, const QString&)), this, SLOT(OnSearchBarUpdate(const QString&, bool, const QString&)));
-
-  seq_table_view_ = new SequenceTableView(model_);
-  layout->addWidget(seq_table_view_);
-  this->setLayout(layout);
-  connect(model_,SIGNAL(columnsInserted(const QModelIndex&, int, int)),seq_table_view_,SLOT(columnCountChanged(const QModelIndex&, int, int)));
-  connect(model_,SIGNAL(rowsInserted(const QModelIndex&, int, int)),seq_table_view_,SLOT(rowCountChanged(const QModelIndex&, int, int)));
-
-  seq_table_view_->horizontalHeader()->setMinimumSectionSize(2);
-  seq_table_view_->verticalHeader()->setMinimumSectionSize(2);
-  seq_table_view_->setSelectionMode(QAbstractItemView::ExtendedSelection);
-  connect(seq_table_view_->selectionModel(), SIGNAL(selectionChanged(const QItemSelection&, const QItemSelection&)), this, SLOT(SelectionModelChanged(const QItemSelection&, const QItemSelection&)));
-  connect(seq_table_view_,SIGNAL(doubleClicked(const QModelIndex&)),model_,SLOT(DoubleClicked(const QModelIndex&)));
-  connect(seq_table_view_->GetStaticColumn(),SIGNAL(doubleClicked(const QModelIndex&)),this,SLOT(DoubleClicked(const QModelIndex&)));
-  connect(seq_table_view_->GetStaticRow(),SIGNAL(doubleClicked(const QModelIndex&)),this,SLOT(DoubleClicked(const QModelIndex&)));
-  connect(seq_table_view_,SIGNAL(CopyEvent(QKeyEvent*)),this,SLOT(CopyEvent(QKeyEvent*)));
-  connect(seq_table_view_,SIGNAL(MouseWheelEvent(QWheelEvent*)),this,SLOT(MouseWheelEvent(QWheelEvent*)));
-
-  gfx::GfxNodeP root_node = gfx::Scene::Instance().GetRootNode();
-  GetNodesVisitor gnv;
-  gfx::Scene::Instance().Apply(gnv);
-  gfx::NodePtrList list = gnv.GetNodes();
-  for(unsigned int i=0; i<list.size();i++){
-    this->NodeAdded(list[i]);
-  }
-}
-
-void SequenceViewerV2::NodeAdded(const gfx::GfxNodeP& n)
-{
-  if (gfx::EntityP o=boost::dynamic_pointer_cast<gfx::Entity>(n)) {
-    model_->InsertGfxEntity(o);
-    seq_table_view_->resizeColumnsToContents();
-    seq_table_view_->resizeRowsToContents();
-  }
-  this->UpdateSearchBar();
-}
-
-void SequenceViewerV2::NodeRemoved(const gfx::GfxNodeP& node)
-{
-  if (gfx::EntityP o=boost::dynamic_pointer_cast<gfx::Entity>(node)) {
-    model_->RemoveGfxEntity(o);
-  }
-}
-
-void SequenceViewerV2::UpdateSearchBar()
-{
-  QStringList sequence_names_;
-  for(int i = 1; i< model_->rowCount(); i++){
-    QString name = model_->data(model_->index(i,0),Qt::DisplayRole).toString();
-    sequence_names_.append(name);
-  }
-  seq_search_bar_->UpdateItems(sequence_names_);
-}
-
-void SequenceViewerV2::SelectionModelChanged(const QItemSelection& sel, const QItemSelection& desel)
-{
-  gfx::Scene::Instance().DetachObserver(this);
-  model_->SelectionChanged(sel, desel);
-  gfx::Scene::Instance().AttachObserver(this);
-}
-
-void SequenceViewerV2::SelectionChanged(const gfx::GfxObjP& o,
-                                      const mol::EntityView& view)
-{
-  disconnect(seq_table_view_->selectionModel(), SIGNAL(selectionChanged(const QItemSelection&, const QItemSelection&)), this, SLOT(SelectionModelChanged(const QItemSelection&, const QItemSelection&)));
-  gfx::EntityP entity=boost::dynamic_pointer_cast<gfx::Entity>(o);
-  if(entity){
-    const QModelIndexList& list = model_->GetModelIndexes(entity, view);
-    this->SelectList(list);
-  }
-  connect(seq_table_view_->selectionModel(), SIGNAL(selectionChanged(const QItemSelection&, const QItemSelection&)), this, SLOT(SelectionModelChanged(const QItemSelection&, const QItemSelection&)));
-}
-
-void SequenceViewerV2::DoubleClicked(const QModelIndex& index)
-{
-  disconnect(seq_table_view_->selectionModel(), SIGNAL(selectionChanged(const QItemSelection&, const QItemSelection&)), this, SLOT(SelectionModelChanged(const QItemSelection&, const QItemSelection&)));
-  model_->DoubleClicked(index);
-  connect(seq_table_view_->selectionModel(), SIGNAL(selectionChanged(const QItemSelection&, const QItemSelection&)), this, SLOT(SelectionModelChanged(const QItemSelection&, const QItemSelection&)));
-}
-
-void SequenceViewerV2::MouseWheelEvent(QWheelEvent* event)
-{
-  int delta = event->delta();
-  if (event->orientation() == Qt::Vertical) {
-    if(delta>0){
-      model_->ZoomIn();
-      seq_table_view_->viewport()->update();
-      seq_table_view_->resizeColumnsToContents();
-      seq_table_view_->resizeRowsToContents();
-    }
-    else if(delta<0){
-      model_->ZoomOut();
-      seq_table_view_->viewport()->update();
-      seq_table_view_->resizeColumnsToContents();
-      seq_table_view_->resizeRowsToContents();
-    }
-  }
-  event->accept();
-}
-
-void SequenceViewerV2::CopyEvent(QKeyEvent* event)
-{
-  QItemSelectionModel* model = seq_table_view_->selectionModel();
-  const QModelIndexList& list = model->selectedIndexes();
-  if(list.size()>0){
-    QString clipboard_string;
-    QSet<int> rows;
-    int min_col=model_->columnCount();
-    int max_col=0;
-    for(int i = 0; i < list.size(); i++){
-      if(list[i].column()>max_col){
-        max_col = list[i].column();
-      }
-      if(list[i].column()<min_col){
-        min_col = list[i].column();
-      }
-      rows.insert(list[i].row());
-    }
-
-    bool first_row = true;
-    for(int i = 1; i < model_->rowCount(); i++){
-      if(rows.contains(i)){
-        if(!first_row){
-          clipboard_string.append("\n");
-        }
-        for(int j=min_col; j<=max_col; j++){
-          const QModelIndex& index = model_->index(i,j);
-          if(model->isSelected(index)){
-            clipboard_string.append(model_->data(index,Qt::DisplayRole).toString());
-          }
-          else{
-            clipboard_string.append('-');
-          }
-        }
-        first_row = false;
-      }
-    }
-    QApplication::clipboard()->setText(clipboard_string);
-  }
-  event->accept();
-}
-
-void SequenceViewerV2::FindInSequence()
-{
-  if(seq_search_bar_->isHidden()){
-    seq_search_bar_->show();
-  }
-  else{
-    seq_search_bar_->hide();
-  }
-}
-
-void SequenceViewerV2::OnSearchBarUpdate(const QString& subject,
-                                           bool search_in_all, const QString& name)
-{
-  seq_table_view_->selectionModel()->clear();
-  if(search_in_all){
-    const QModelIndexList& list = model_->GetModelIndexes(subject);
-    this->SelectList(list);
-  }
-  else{
-    const QModelIndexList& list = model_->GetModelIndexes(subject,name);
-    this->SelectList(list);
-  }
-}
-
-void SequenceViewerV2::SelectList(const QModelIndexList& list)
-{
-  QItemSelectionModel* model = seq_table_view_->selectionModel();
-  QSet<int> rows_visited;
-  for(int i = 0; i<list.size(); i++){
-    int row =list[i].row();
-    if(!rows_visited.contains(row)){
-      model->select(list[i],QItemSelectionModel::Rows|QItemSelectionModel::Deselect);
-      rows_visited.insert(row);
-    }
-  }
-  for(int i = 0; i<list.size(); i++){
-    model->select(list[i],QItemSelectionModel::Select);
-  }
-}
-
-SequenceViewerV2::~SequenceViewerV2(){
-  gfx::Scene::Instance().DetachObserver(this);
-}
-
-}}
diff --git a/modules/gui/src/sequence/sequence_viewer.hh b/modules/gui/src/sequence/sequence_viewer.hh
deleted file mode 100644
index b04d242dc3c1d3befd3ffda6698e417b3322e2a2..0000000000000000000000000000000000000000
--- a/modules/gui/src/sequence/sequence_viewer.hh
+++ /dev/null
@@ -1,77 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef OST_SEQUENCE_VIEWER_SEQUENCE_VIEWER
-#define OST_SEQUENCE_VIEWER_SEQUENCE_VIEWER
-
-/*
-  Author: Stefan Scheuber
- */
-
-#include <QWidget>
-
-#include <ost/gfx/scene.hh>
-#include <ost/gfx/gfx_object.hh>
-
-#include <ost/gui/widget.hh>
-
-#include <ost/gui/module_config.hh>
-
-#include "sequence_search_bar.hh"
-#include "sequence_model.hh"
-#include "sequence_table_view.hh"
-
-namespace ost { namespace gui {
-
-/// \brief QTableView with first column not moving
-class DLLEXPORT_OST_GUI SequenceViewerV2 : public Widget, public gfx::SceneObserver  {
-  Q_OBJECT
-public:
-  SequenceViewerV2(QWidget* parent=NULL);
-  ~SequenceViewerV2();
-
-  virtual void NodeAdded(const gfx::GfxNodeP& node);
-  virtual void NodeRemoved(const gfx::GfxNodeP& node);
-  virtual void SelectionChanged(const gfx::GfxObjP& o, const mol::EntityView& view);
-
-  virtual bool Restore(const QString&){return true;};
-  virtual bool Save(const QString&){return true;};
-
-public slots:
-/// \internal
-void OnSearchBarUpdate(const QString&, bool, const QString&);
-
-private:
-  void UpdateSearchBar();
-  void SelectList(const QModelIndexList& list);
-  SeqSearchBar* seq_search_bar_;
-  SequenceModel* model_;
-  SequenceTableView* seq_table_view_;
-
-private slots:
-  /// \brief show sequence search bar
-  void FindInSequence();
-  void SelectionModelChanged(const QItemSelection&, const QItemSelection&);
-  void DoubleClicked(const QModelIndex& index);
-  void MouseWheelEvent(QWheelEvent* event);
-  void CopyEvent(QKeyEvent* event);
-};
-
-}}
-
-#endif
diff --git a/modules/gui/src/sequence_viewer/align_properties_painter.cc b/modules/gui/src/sequence_viewer/align_properties_painter.cc
new file mode 100644
index 0000000000000000000000000000000000000000..0dd51f36d33b62bd1e4ca6759fb5008509b6d81f
--- /dev/null
+++ b/modules/gui/src/sequence_viewer/align_properties_painter.cc
@@ -0,0 +1,78 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+//------------------------------------------------------------------------------
+
+/*
+  Author: Stefan Scheuber
+ */
+
+
+
+#include "align_properties_painter.hh"
+
+#include <QtGui>
+namespace ost { namespace gui {
+
+namespace {
+
+QMap<QString,QColor> GetColorMap(){
+  QMap<QString,QColor> map;
+  map["G"]=QColor(175,175,175,100);
+  map["A"]=QColor(175,175,175,100);
+  map["V"]=QColor(175,175,175,100);
+  map["L"]=QColor(175,175,175,100);
+  map["I"]=QColor(175,175,175,100);
+  map["F"]=QColor(255,165,100);
+  map["Y"]=QColor(255,165,100);
+  map["W"]=QColor(255,165,100);
+  map["C"]=QColor(255,255,0,100);
+  map["M"]=QColor(255,255,0,100);
+  map["S"]=QColor(0,255,0,100);
+  map["T"]=QColor(0,255,0,100);
+  map["K"]=QColor(255,0,0,100);
+  map["R"]=QColor(255,0,0,100);
+  map["H"]=QColor(255,0,0,100);
+  map["D"]=QColor(0,0,255,100);
+  map["E"]=QColor(0,0,255,100);
+  map["N"]=QColor(0,0,255,100);
+  map["Q"]=QColor(0,0,255,100);
+  map["P"]=QColor(0,255,255,100);
+  return map;
+}
+
+}
+
+QMap<QString,QColor> AlignPropertiesPainter::color_map_ = GetColorMap();
+
+
+AlignPropertiesPainter::AlignPropertiesPainter(QObject* parent)
+    : Painter(parent)
+{}
+
+void AlignPropertiesPainter::Paint(QPainter* painter, const QStyleOptionViewItem& option, const QModelIndex& index){
+  painter->save();
+  if (index.column()>0){
+    QString text = index.data(Qt::DisplayRole).toString();
+    if(color_map_.contains(text)){
+      painter->fillRect(option.rect, color_map_[text]);
+    }
+  }
+  painter->restore();
+}
+
+}}
diff --git a/modules/gui/src/plot_viewer/plot_axis_horizontal.hh b/modules/gui/src/sequence_viewer/align_properties_painter.hh
similarity index 71%
rename from modules/gui/src/plot_viewer/plot_axis_horizontal.hh
rename to modules/gui/src/sequence_viewer/align_properties_painter.hh
index 7522695e0bd1a98b58183eaf7a97825c9673b6f1..13bda8babfa5d599f836cd2d8da00ac2cbfe9844 100644
--- a/modules/gui/src/plot_viewer/plot_axis_horizontal.hh
+++ b/modules/gui/src/sequence_viewer/align_properties_painter.hh
@@ -16,29 +16,31 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#ifndef PLOT_AXIS_HORIZONTAL_HH_
-#define PLOT_AXIS_HORIZONTAL_HH_
+#ifndef OST_SEQUENCE_VIEWER_ALIGN_PROPERTIES_PAINTER
+#define OST_SEQUENCE_VIEWER_ALIGN_PROPERTIES_PAINTER
 
 /*
-  Author: Andreas Schenk
-*/
+  Author: Stefan Scheuber
+ */
 
-#include "plot_axis_base.hh"
+
+#include "painter.hh"
+#include <QObject>
 
 namespace ost { namespace gui {
 
-class DLLEXPORT_OST_GUI PlotAxisHorizontal: public PlotAxisBase
+
+
+class AlignPropertiesPainter : public Painter
 {
+  Q_OBJECT
 public:
-  PlotAxisHorizontal(QWidget * parent = 0);
-  virtual ~PlotAxisHorizontal();
-protected:
-  virtual void paintEvent(QPaintEvent* paint_event);
-  virtual void mouseMoveEvent ( QMouseEvent * event );
+  AlignPropertiesPainter(QObject* parent = 0);
+  void Paint(QPainter *painter, const QStyleOptionViewItem &option, const QModelIndex &index);
+private:
+  static QMap<QString,QColor> color_map_;
 };
 
-}
-
-}
+}}
 
-#endif /*PLOT_AXIS_HORIZONTAL_HH_*/
+#endif
diff --git a/modules/gui/src/sequence_viewer/alignment_view_object.cc b/modules/gui/src/sequence_viewer/alignment_view_object.cc
new file mode 100644
index 0000000000000000000000000000000000000000..f5a08689be49aed7959370840aa7f2ce89dc79c2
--- /dev/null
+++ b/modules/gui/src/sequence_viewer/alignment_view_object.cc
@@ -0,0 +1,212 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+//------------------------------------------------------------------------------
+
+/*
+  Author: Stefan Scheuber
+ */
+
+
+
+#include <ost/mol/mol.hh>
+#include <ost/mol/view_op.hh>
+
+#include <ost/seq/aligned_region.hh>
+#include <ost/seq/alg/conservation.hh>
+
+#include "sequence_row.hh"
+#include "secstr_row.hh"
+
+#include "painter.hh"
+#include "background_painter.hh"
+#include "seq_secstr_painter.hh"
+#include "seq_selection_painter.hh"
+#include "seq_text_painter.hh"
+
+#include "alignment_view_object.hh"
+
+#include <QtGui>
+namespace ost { namespace gui {
+
+namespace {
+QMap<QString,int> GetGroupMap(){
+  QMap<QString,int> map;
+  map["G"]=1;
+  map["A"]=1;
+  map["V"]=1;
+  map["L"]=1;
+  map["I"]=1;
+  map["F"]=2;
+  map["Y"]=2;
+  map["W"]=2;
+  map["C"]=3;
+  map["M"]=3;
+  map["S"]=4;
+  map["T"]=4;
+  map["K"]=5;
+  map["R"]=5;
+  map["H"]=5;
+  map["D"]=6;
+  map["E"]=6;
+  map["N"]=6;
+  map["Q"]=6;
+  map["P"]=7;
+  return map;
+}
+
+QColor GetColor(int cons){
+  int color = 255 - int((float(cons) / 100) * 200);
+  return QColor(color,color,color);
+}
+
+QColor GetForeGroundColor(QColor background){
+  if(background == Qt::transparent){
+    return Qt::black;
+  }
+  int gray = 255 - background.red();
+  return QColor(gray,gray,gray);
+}
+
+}
+
+QMap<QString,int> AlignmentViewObject::group_map_ = GetGroupMap();
+
+
+const QString AlignmentViewObject::conservation_mode_1 = "Highlight conservation 1";
+const QString AlignmentViewObject::conservation_mode_2 = "Highlight conservation 2";
+
+AlignmentViewObject::AlignmentViewObject(const seq::AlignmentHandle& alignment, QObject* parent): SequenceViewObject(parent), alignment_(alignment)
+{
+  for(int i=0; i<alignment.GetCount(); i++){
+    seq::SequenceHandle seq_handle = alignment.GetSequence(i).Copy();
+    this->AddSequence(seq_handle, seq_handle.GetName().c_str());
+  }
+
+  std::vector<Real> values = seq::alg::Conservation(alignment,false);
+
+  gradient_.SetColorAt(0,gfx::Color(0,0,1));
+  gradient_.SetColorAt(0.5,gfx::Color(1,1,1));
+  gradient_.SetColorAt(1,gfx::Color(1,0,0));
+  //Calculate Conservation Mode 1
+  for(unsigned int i=0; i<values.size(); i++){
+    gfx::Color color = gradient_.GetColorAt(values[i]);
+    conservation_1_[i] = QColor(color.Red()*255,color.Green()*255,color.Blue()*255,100);
+  }
+
+  //Calculate Conservation Mode 2
+  for(int j=0; j<alignment.GetLength(); j++){
+    int group = 0;
+    QString element = "";
+    for(int i=0; i<alignment.GetCount();i++){
+      QString code = QString(alignment.GetOneLetterCode(i,j));
+      if(element.size()==0){
+        element = code;
+      }
+      else if (element != code){
+        element = "  ";
+      }
+      if(group_map_.contains(code) && group>=0){
+        if(group == 0) {
+            group = group_map_[code];
+        }
+        else if(group_map_[code] != group){
+          group = -1;
+        }
+      }
+      else{
+        group = -1;
+      }
+
+    }
+    if(element.size()==1){
+      conservation_2_[j] = QColor(175,175,175);
+    }
+    else if(group > 0){
+      conservation_2_[j] = QColor(200,200,200);
+    }
+    else{
+      conservation_2_[j] = Qt::transparent;
+    }
+  }
+  this->AddDisplayMode(conservation_mode_1);
+  this->AddDisplayMode(conservation_mode_2);
+}
+
+
+QVariant AlignmentViewObject::GetData(int row, int column, int role)
+{
+  if(column > 0){
+    if(this->GetCurrentDisplayMode() == conservation_mode_1){
+      if(role == Qt::UserRole+3 ){
+        if(column -1 < conservation_1_.size()){
+          return QVariant(conservation_1_[column-1]);
+        }
+          return QVariant(Qt::transparent);
+      }
+
+      if(role == Qt::ForegroundRole){
+        if(column -1 < conservation_1_.size()){
+          if(conservation_1_[column-1].red()>128){
+            return QVariant(Qt::black);
+          }
+          else{
+            return QVariant(Qt::white);
+          }
+        }
+        return QVariant(Qt::transparent);
+      }
+    }
+    else if(this->GetCurrentDisplayMode() == conservation_mode_2){
+      if(role == Qt::UserRole+3 ){
+        if(column -1 < conservation_2_.size()){
+          return QVariant(conservation_2_[column-1]);
+        }
+        return QVariant(Qt::transparent);
+      }
+      if(role == Qt::ForegroundRole){
+        if(column -1 < conservation_2_.size()){
+            return QVariant(Qt::black);
+        }
+        return QVariant(Qt::transparent);
+      }
+    }
+  }
+  return BaseViewObject::GetData(row,column,role);
+}
+
+void AlignmentViewObject::SetDisplayMode(const QString& mode)
+{
+  if(this->display_modes_.contains(mode) && mode != this->GetCurrentDisplayMode()){
+    if(mode == conservation_mode_1 || mode == conservation_mode_2){
+      for(int i=0 ; i<this->GetRowCount(); i++){
+        BaseRow* row = this->GetRow(i);
+        row->RemovePainter(seq_secondary_structure_painter);
+        row->RemovePainter(align_properties_painter);
+        row->InsertPainter(conservation_painter,1);
+      }
+    }
+  }
+  SequenceViewObject::SetDisplayMode(mode);
+}
+
+const seq::AlignmentHandle& AlignmentViewObject::GetAlignment()
+{
+  return alignment_;
+}
+
+}}
diff --git a/modules/gui/src/plot_viewer/plot_axis_base.hh b/modules/gui/src/sequence_viewer/alignment_view_object.hh
similarity index 57%
rename from modules/gui/src/plot_viewer/plot_axis_base.hh
rename to modules/gui/src/sequence_viewer/alignment_view_object.hh
index f16b703d1174710e6bacbd060263260954376138..b8fee2800d9e766211590b6b263c3cd02562456e 100644
--- a/modules/gui/src/plot_viewer/plot_axis_base.hh
+++ b/modules/gui/src/sequence_viewer/alignment_view_object.hh
@@ -16,44 +16,46 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#ifndef PLOTAXIS_BASE_HH_
-#define PLOTAXIS_BASE_HH_
+#ifndef OST_SEQUENCE_VIEWER_ALIGNMENT_VIEW_OBJECT
+#define OST_SEQUENCE_VIEWER_ALIGNMENT_VIEW_OBJECT
 
 /*
-  Author: Andreas Schenk
-*/
+  Author: Stefan Scheuber
+ */
 
-#include <QWidget>
+#include <ost/seq/alignment_handle.hh>
 
-#include "plot_ticker.hh"
+#include <ost/gfx/gradient.hh>
+
+#include "sequence_view_object.hh"
 
 namespace ost { namespace gui {
 
-class DLLEXPORT_OST_GUI PlotAxisBase: public QWidget
+class AlignmentViewObject : public SequenceViewObject
 {
   Q_OBJECT
+
 public:
-  PlotAxisBase(QWidget * parent = 0);
-  virtual ~PlotAxisBase();
-  const static unsigned int AXISWIDTH=60;
-  void SetMinimum(Real min);
-  void SetMaximum(Real max);
-signals:
-  void zoom(int delta,QPoint pos);
-  void translate(Real deltax,Real deltay);
-protected:
-  int GetSeparation();
-  void SetSeparation(int separation);
-  void SetStart(int start);
-  void SetEnd(int end);
-  virtual void wheelEvent ( QWheelEvent * e );
-  virtual void mousePressEvent ( QMouseEvent * event );
-  TickList GetTicks();
-  PlotTickerLinear ticker_;
-  QPoint global_mouse_pos_;
+  AlignmentViewObject(const seq::AlignmentHandle& alignment, QObject* parent = 0);
+
+  QVariant GetData(int row, int column, int role);
+  const seq::AlignmentHandle& GetAlignment();
+
+  void SetDisplayMode(const QString& mode);
+
+private:
+  gfx::Gradient gradient_;
+  seq::AlignmentHandle alignment_;
+  QMap<int, QColor> conservation_1_;
+  QMap<int, QColor> conservation_2_;
+
+  static QMap<QString,int> group_map_;
+
+  static const QString conservation_mode_1;
+  static const QString conservation_mode_2;
 };
 
 
-}}//ns
+}}
 
-#endif /*PLOTAXIS_BASE_HH_*/
+#endif
diff --git a/modules/gui/src/sequence/background_painter.cc b/modules/gui/src/sequence_viewer/background_painter.cc
similarity index 100%
rename from modules/gui/src/sequence/background_painter.cc
rename to modules/gui/src/sequence_viewer/background_painter.cc
index 25cf4c65022a3eb0783d7e678d93ca1cabe8e1ff..7e45f62bddcde93345f12bb7925b978f4734002f 100644
--- a/modules/gui/src/sequence/background_painter.cc
+++ b/modules/gui/src/sequence_viewer/background_painter.cc
@@ -22,10 +22,10 @@
  */
 
 
-#include <QtGui>
 
 #include "background_painter.hh"
 
+#include <QtGui>
 namespace ost { namespace gui {
 
 BackgroundPainter::BackgroundPainter(QObject* parent)
diff --git a/modules/gui/src/sequence/background_painter.hh b/modules/gui/src/sequence_viewer/background_painter.hh
similarity index 100%
rename from modules/gui/src/sequence/background_painter.hh
rename to modules/gui/src/sequence_viewer/background_painter.hh
index 942e1dde5bd9b67326862eaf605de1436c962ab7..dc97901d43c69477b6c7a9c63dca51281ae57254 100644
--- a/modules/gui/src/sequence/background_painter.hh
+++ b/modules/gui/src/sequence_viewer/background_painter.hh
@@ -23,9 +23,9 @@
   Author: Stefan Scheuber
  */
 
-#include <QObject>
 
 #include "painter.hh"
+#include <QObject>
 
 namespace ost { namespace gui {
 
diff --git a/modules/gui/src/sequence/base_row.cc b/modules/gui/src/sequence_viewer/base_row.cc
similarity index 100%
rename from modules/gui/src/sequence/base_row.cc
rename to modules/gui/src/sequence_viewer/base_row.cc
index 16dfb0af3831eda02d11e32f964374b5298c5247..2491b765d03adf4982ca5378e7d49bd597b35dbc 100644
--- a/modules/gui/src/sequence/base_row.cc
+++ b/modules/gui/src/sequence_viewer/base_row.cc
@@ -22,10 +22,10 @@
  */
 
 
-#include <QtGui>
 
 #include "base_row.hh"
 
+#include <QtGui>
 namespace ost { namespace gui {
 
 BaseRow::BaseRow(QObject *parent) : QObject(parent)
diff --git a/modules/gui/src/sequence/base_row.hh b/modules/gui/src/sequence_viewer/base_row.hh
similarity index 100%
rename from modules/gui/src/sequence/base_row.hh
rename to modules/gui/src/sequence_viewer/base_row.hh
index 6f20d872b7ff431bb4ba3799e7f5af66c6f52d20..12b86caeb3586d8d56a5ca287a2f2a6f4164ad2d 100644
--- a/modules/gui/src/sequence/base_row.hh
+++ b/modules/gui/src/sequence_viewer/base_row.hh
@@ -23,12 +23,12 @@
   Author: Stefan Scheuber
  */
 
-#include <QObject>
-#include <QModelIndex>
-#include <QList>
 
 #include "painter.hh"
 
+#include <QObject>
+#include <QModelIndex>
+#include <QList>
 namespace ost { namespace gui {
 
 class BaseRow : public QObject
diff --git a/modules/gui/src/sequence/base_view_object.cc b/modules/gui/src/sequence_viewer/base_view_object.cc
similarity index 86%
rename from modules/gui/src/sequence/base_view_object.cc
rename to modules/gui/src/sequence_viewer/base_view_object.cc
index f6292d97bd3a54ff7344666c5d271e7133b98f1b..716cdb8d8ee2d016026bfa9320e1d625d0634784 100644
--- a/modules/gui/src/sequence/base_view_object.cc
+++ b/modules/gui/src/sequence_viewer/base_view_object.cc
@@ -22,10 +22,10 @@
  */
 
 
-#include <QtGui>
 
 #include "base_view_object.hh"
 
+#include <QtGui>
 namespace ost { namespace gui {
 
 BaseViewObject::BaseViewObject(QObject* parent): QObject(parent)
@@ -89,6 +89,30 @@ bool BaseViewObject::SetData(int row, int column, const QVariant& value, int rol
   return rows_[row]->SetData(column, value, role);
 }
 
+const QStringList& BaseViewObject::GetDisplayModes()
+{
+  return display_modes_;
+}
+
+const QString& BaseViewObject::GetCurrentDisplayMode()
+{
+  return current_display_mode_;
+}
+
+void BaseViewObject::SetDisplayMode(const QString& mode)
+{
+  if(display_modes_.contains(mode)){
+    this->current_display_mode_ = mode;
+  }
+}
+
+void BaseViewObject::AddDisplayMode(const QString& mode)
+{
+  if(!display_modes_.contains(mode)){
+    this->display_modes_.append(mode);
+  }
+}
+
 void BaseViewObject::DoubleClicked(int row, int column)
 {
   if(row>=0 || row < rows_.size()){
diff --git a/modules/gui/src/sequence/base_view_object.hh b/modules/gui/src/sequence_viewer/base_view_object.hh
similarity index 74%
rename from modules/gui/src/sequence/base_view_object.hh
rename to modules/gui/src/sequence_viewer/base_view_object.hh
index b751244627216fcddb683cfd1635e44bdbc9e0fa..fc843813d988daefbc0f99a41fb8cd25e29ccb92 100644
--- a/modules/gui/src/sequence/base_view_object.hh
+++ b/modules/gui/src/sequence_viewer/base_view_object.hh
@@ -23,11 +23,11 @@
   Author: Stefan Scheuber
  */
 
-#include <QObject>
-#include <QList>
 
 #include "base_row.hh"
 
+#include <QObject>
+#include <QList>
 
 namespace ost { namespace gui {
 
@@ -45,18 +45,26 @@ public:
   int GetRowCount();
   int GetMaxColumnCount() const;
 
-  void SetSelection(int row, const QSet<int>& added, const QSet<int>& removed);
+  virtual void SetSelection(int row, const QSet<int>& added, const QSet<int>& removed);
+
+  virtual QVariant GetData(int row, int column, int role);
+  virtual bool SetData(int row, int column, const QVariant& value, int role);
+  virtual Qt::ItemFlags Flags(int row, int column) const;
 
-  QVariant GetData(int row, int column, int role);
-  bool SetData(int row, int column, const QVariant& value, int role);
-  Qt::ItemFlags Flags(int row, int column) const;
+  virtual const QStringList& GetDisplayModes();
+  virtual const QString& GetCurrentDisplayMode();
+  virtual void SetDisplayMode(const QString& mode);
 
   void DoubleClicked(int row, int column);
   void ZoomIn();
   void ZoomOut();
 
 protected:
+  virtual void AddDisplayMode(const QString& mode);
+
   QList<BaseRow*> rows_;
+  QString current_display_mode_;
+  QStringList display_modes_;
 };
 
 
diff --git a/modules/gui/pymod/sequence_viewer_proxyV2.hh b/modules/gui/src/sequence_viewer/conservation_painter.cc
similarity index 69%
rename from modules/gui/pymod/sequence_viewer_proxyV2.hh
rename to modules/gui/src/sequence_viewer/conservation_painter.cc
index 7d7e1f269acd559d1cfc6505056ee7aa9c7ca8c7..b5e7085485da45d80c6b6c818e853eda135fa2ce 100644
--- a/modules/gui/pymod/sequence_viewer_proxyV2.hh
+++ b/modules/gui/src/sequence_viewer/conservation_painter.cc
@@ -16,32 +16,30 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#ifndef OST_GUI_SEQUENCE_VIEWER_PROXY_V2_HH
-#define OST_GUI_SEQUENCE_VIEWER_PROXY_V2_HH
 
-#include <ost/gui/sequence/sequence_viewer.hh>
+/*
+  Author: Stefan Scheuber
+ */
 
-#include "sip_handler.hh"
 
+
+#include "conservation_painter.hh"
+
+#include <QtGui>
 namespace ost { namespace gui {
 
-class  SequenceViewerProxyV2 : public SipHandler<SequenceViewerV2> {
 
-public:
-  SequenceViewerProxyV2(SequenceViewerV2* seq_viewer=new SequenceViewerV2()):
-    SipHandler<SequenceViewerV2>(seq_viewer)
-  { }
-  
-  void Show()  
-  {
-    return Me()->show();
-  }
-  void Hide()  
-  {
-    return Me()->hide();
+ConservationPainter::ConservationPainter(QObject* parent)
+    : Painter(parent)
+{}
+
+void ConservationPainter::Paint(QPainter* painter, const QStyleOptionViewItem& option, const QModelIndex& index){
+  painter->save();
+  if (index.column()>0){
+    QColor cons = index.data(Qt::UserRole+3).value<QColor>();
+    painter->fillRect(option.rect, cons);
   }
-};
+  painter->restore();
+}
 
 }}
-
-#endif
diff --git a/modules/gui/src/plot_viewer/plot_viewer_proxy_fw.hh b/modules/gui/src/sequence_viewer/conservation_painter.hh
similarity index 74%
rename from modules/gui/src/plot_viewer/plot_viewer_proxy_fw.hh
rename to modules/gui/src/sequence_viewer/conservation_painter.hh
index e4ac6c8812b8fe6c3b514fc662e57c7a77842b3a..f6cea31597773deb3700cfad553e64f6bcbaeb1c 100644
--- a/modules/gui/src/plot_viewer/plot_viewer_proxy_fw.hh
+++ b/modules/gui/src/sequence_viewer/conservation_painter.hh
@@ -16,21 +16,28 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#ifndef PLOT_VEWER_PROXY_FW_HH_
-#define PLOT_VEWER_PROXY_FW_HH_
+#ifndef OST_SEQUENCE_VIEWER_CONSERVATION_PAINTER
+#define OST_SEQUENCE_VIEWER_CONSERVATION_PAINTER
 
 /*
-  Author: Ansgar Philippsen
-*/
+  Author: Stefan Scheuber
+ */
 
-#include <boost/shared_ptr.hpp>
 
+#include "painter.hh"
+
+#include <QObject>
 namespace ost { namespace gui {
 
-class PlotViewerProxy;
-class PlotViewer;
 
-typedef boost::shared_ptr<PlotViewerProxy> PlotViewerProxyPtr;
+
+class ConservationPainter : public Painter
+{
+  Q_OBJECT
+public:
+  ConservationPainter(QObject* parent = 0);
+  void Paint(QPainter *painter, const QStyleOptionViewItem &option, const QModelIndex &index);
+};
 
 }}
 
diff --git a/modules/gui/src/sequence/painter.hh b/modules/gui/src/sequence_viewer/painter.hh
similarity index 100%
rename from modules/gui/src/sequence/painter.hh
rename to modules/gui/src/sequence_viewer/painter.hh
index 75e601cdabe9adb5e83554eda7d57e5d914a11e8..971c0b1f84f46f4600ec5b954b73cf40aa5d1a84 100644
--- a/modules/gui/src/sequence/painter.hh
+++ b/modules/gui/src/sequence_viewer/painter.hh
@@ -23,15 +23,15 @@
   Author: Stefan Scheuber
  */
 
+
+#include <ost/mol/alg/sec_structure_segments.hh>
+
 #include <QObject>
 #include <QPainter>
 #include <QStyleOptionViewItem>
 #include <QModelIndex>
 #include <QVarLengthArray>
 #include <QList>
-
-#include <ost/mol/alg/sec_structure_segments.hh>
-
 namespace ost { namespace gui {
 
 class Painter : public QObject
diff --git a/modules/gui/src/sequence/secstr_row.cc b/modules/gui/src/sequence_viewer/secstr_row.cc
similarity index 100%
rename from modules/gui/src/sequence/secstr_row.cc
rename to modules/gui/src/sequence_viewer/secstr_row.cc
index 180a47469bc97f931ce713e74574ee20be3083a7..2610fc1a20493f14a50665270736addfb1718f35 100644
--- a/modules/gui/src/sequence/secstr_row.cc
+++ b/modules/gui/src/sequence_viewer/secstr_row.cc
@@ -22,7 +22,6 @@
  */
 
 
-#include <QtGui>
 
 #include <ost/mol/mol.hh>
 #include <ost/mol/view_op.hh>
@@ -31,6 +30,7 @@
 
 #include "secstr_row.hh"
 
+#include <QtGui>
 namespace ost { namespace gui {
 
 SecStrRow::SecStrRow(const QString& name, mol::ChainView& chain, SequenceViewObject* parent) : SequenceRow(name,parent)
diff --git a/modules/gui/src/sequence/secstr_row.hh b/modules/gui/src/sequence_viewer/secstr_row.hh
similarity index 100%
rename from modules/gui/src/sequence/secstr_row.hh
rename to modules/gui/src/sequence_viewer/secstr_row.hh
index 4b6bd2762457b2545807b344f1953362543f0347..7a9d7991dc3e4dbf30f3d646eb4ba0d994591862 100644
--- a/modules/gui/src/sequence/secstr_row.hh
+++ b/modules/gui/src/sequence_viewer/secstr_row.hh
@@ -23,14 +23,14 @@
   Author: Stefan Scheuber
  */
 
-#include <QObject>
-#include <QVarLengthArray>
 
 #include <ost/mol/chain_view.hh>
 #include <ost/mol/alg/sec_structure_segments.hh>
 
 #include "sequence_row.hh"
 
+#include <QObject>
+#include <QVarLengthArray>
 namespace ost { namespace gui {
 
 class SecStrRow : public SequenceRow
diff --git a/modules/gui/src/sequence/seq_secstr_painter.cc b/modules/gui/src/sequence_viewer/seq_secstr_painter.cc
similarity index 100%
rename from modules/gui/src/sequence/seq_secstr_painter.cc
rename to modules/gui/src/sequence_viewer/seq_secstr_painter.cc
index 0929a9527653e2e778316b3dc202962e5797888b..df3a284d8d9c5b281fb7e56e39a1c2dc4fe1a43e 100644
--- a/modules/gui/src/sequence/seq_secstr_painter.cc
+++ b/modules/gui/src/sequence_viewer/seq_secstr_painter.cc
@@ -22,10 +22,10 @@
  */
 
 
-#include <QtGui>
 
 #include "seq_secstr_painter.hh"
 
+#include <QtGui>
 namespace ost { namespace gui {
 
 SeqSecStrPainter::SeqSecStrPainter(QObject* parent)
diff --git a/modules/gui/src/sequence/seq_secstr_painter.hh b/modules/gui/src/sequence_viewer/seq_secstr_painter.hh
similarity index 100%
rename from modules/gui/src/sequence/seq_secstr_painter.hh
rename to modules/gui/src/sequence_viewer/seq_secstr_painter.hh
index a00ebdfd3e0eb83a213f4fce669a19b19e2bfbe4..3dc5fdcb4c112789db41d43cd5528f76b85888a2 100644
--- a/modules/gui/src/sequence/seq_secstr_painter.hh
+++ b/modules/gui/src/sequence_viewer/seq_secstr_painter.hh
@@ -23,10 +23,10 @@
   Author: Stefan Scheuber
  */
 
-#include <QObject>
-#include <QVarLengthArray>
 
 #include "painter.hh"
+#include <QObject>
+#include <QVarLengthArray>
 
 namespace ost { namespace gui {
 
diff --git a/modules/gui/src/sequence/seq_selection_painter.cc b/modules/gui/src/sequence_viewer/seq_selection_painter.cc
similarity index 100%
rename from modules/gui/src/sequence/seq_selection_painter.cc
rename to modules/gui/src/sequence_viewer/seq_selection_painter.cc
index 8473171967a9f398e8e9a9883197ab54ff605146..4cff32d95000b7263c3e45b2c7736bed6ca9b054 100644
--- a/modules/gui/src/sequence/seq_selection_painter.cc
+++ b/modules/gui/src/sequence_viewer/seq_selection_painter.cc
@@ -22,9 +22,9 @@
  */
 
 
-#include <QtGui>
 
 #include "seq_selection_painter.hh"
+#include <QtGui>
 
 namespace ost { namespace gui {
 
diff --git a/modules/gui/src/sequence/seq_selection_painter.hh b/modules/gui/src/sequence_viewer/seq_selection_painter.hh
similarity index 100%
rename from modules/gui/src/sequence/seq_selection_painter.hh
rename to modules/gui/src/sequence_viewer/seq_selection_painter.hh
index a98d5afb6bf0cab9e33e7283ec5e6b80af423aa3..68174501a2edcabbef106bf9556645d7f61a48f3 100644
--- a/modules/gui/src/sequence/seq_selection_painter.hh
+++ b/modules/gui/src/sequence_viewer/seq_selection_painter.hh
@@ -23,9 +23,9 @@
   Author: Stefan Scheuber
  */
 
-#include <QObject>
 
 #include "painter.hh"
+#include <QObject>
 
 namespace ost { namespace gui {
 
diff --git a/modules/gui/src/sequence/seq_text_painter.cc b/modules/gui/src/sequence_viewer/seq_text_painter.cc
similarity index 96%
rename from modules/gui/src/sequence/seq_text_painter.cc
rename to modules/gui/src/sequence_viewer/seq_text_painter.cc
index 30c1e162321fc727a516bb14f582f7f8d4797a29..ea1599e9e5a5e9028e377757ae84bc937424fc1d 100644
--- a/modules/gui/src/sequence/seq_text_painter.cc
+++ b/modules/gui/src/sequence_viewer/seq_text_painter.cc
@@ -22,10 +22,10 @@
  */
 
 
-#include <QtGui>
 
 #include "seq_text_painter.hh"
 
+#include <QtGui>
 namespace ost { namespace gui {
 
 SeqTextPainter::SeqTextPainter(QObject* parent)
@@ -34,7 +34,7 @@ SeqTextPainter::SeqTextPainter(QObject* parent)
 
 void SeqTextPainter::Paint(QPainter* painter, const QStyleOptionViewItem& option, const QModelIndex& index){
   painter->save();
-  painter->setPen(QPen(Qt::black));
+  painter->setPen(index.data(Qt::ForegroundRole).value<QColor>());
   QVariant value = index.data(Qt::DisplayRole);
   if (value.isValid()){
     QString text = value.toString();
diff --git a/modules/gui/src/sequence/seq_text_painter.hh b/modules/gui/src/sequence_viewer/seq_text_painter.hh
similarity index 100%
rename from modules/gui/src/sequence/seq_text_painter.hh
rename to modules/gui/src/sequence_viewer/seq_text_painter.hh
index 429394cb4bca349b3bc67a9269fbda2048954223..89d3190809d49696bc6b6f74d58343f125b8e244 100644
--- a/modules/gui/src/sequence/seq_text_painter.hh
+++ b/modules/gui/src/sequence_viewer/seq_text_painter.hh
@@ -23,9 +23,9 @@
   Author: Stefan Scheuber
  */
 
-#include <QObject>
 
 #include "painter.hh"
+#include <QObject>
 
 namespace ost { namespace gui {
 
diff --git a/modules/gui/src/sequence/sequence_delegate.cc b/modules/gui/src/sequence_viewer/sequence_delegate.cc
similarity index 100%
rename from modules/gui/src/sequence/sequence_delegate.cc
rename to modules/gui/src/sequence_viewer/sequence_delegate.cc
index 6bb36cac4c7ba1dae8af0df6dc2f6e66748feac3..ba2598b85f80556948dbce64d17b15948a3deab4 100644
--- a/modules/gui/src/sequence/sequence_delegate.cc
+++ b/modules/gui/src/sequence_viewer/sequence_delegate.cc
@@ -22,8 +22,8 @@
  */
 
 
-#include <QtGui>
 #include "sequence_delegate.hh"
+#include <QtGui>
 
 namespace ost { namespace gui {
 
diff --git a/modules/gui/src/sequence/sequence_delegate.hh b/modules/gui/src/sequence_viewer/sequence_delegate.hh
similarity index 100%
rename from modules/gui/src/sequence/sequence_delegate.hh
rename to modules/gui/src/sequence_viewer/sequence_delegate.hh
index 3c74fcf54abd4f7604c10b41dde9427fa0e7d54f..4396faafa2d2125e0147d4d03996a31ed5aedbe6 100644
--- a/modules/gui/src/sequence/sequence_delegate.hh
+++ b/modules/gui/src/sequence_viewer/sequence_delegate.hh
@@ -23,10 +23,10 @@
   Author: Stefan Scheuber
  */
 
-#include <QItemDelegate>
-#include <QModelIndex>
 
 #include "sequence_model.hh"
+#include <QItemDelegate>
+#include <QModelIndex>
 
 namespace ost { namespace gui {
 
diff --git a/modules/gui/src/sequence_viewer/sequence_item.cc b/modules/gui/src/sequence_viewer/sequence_item.cc
deleted file mode 100644
index 6200f6c15f6ea86c4ee5f970255cb10be60b1f96..0000000000000000000000000000000000000000
--- a/modules/gui/src/sequence_viewer/sequence_item.cc
+++ /dev/null
@@ -1,494 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-/*
-  Author: Marco Biasini
- */
- 
-#include <ost/mol/mol.hh>
-#include <boost/bind.hpp>
-
-#include "sequence_item.hh"
-#include "sequence_scene.hh"
-
-#include <QPainter>
-#include <QGraphicsSceneMouseEvent>
-#include <QGraphicsSceneContextMenuEvent>
-#include <QGraphicsItem>
-#include <QDebug>
-
-namespace ost { namespace gui {
-
-using boost::bind;
-
-Knob::Knob(const QString& text, const QColor& color, 
-           SequenceItem* parent):
-  QGraphicsItem(parent)
-{
-  
-}
-  
-void Knob::paint(QPainter* painter, const QStyleOptionGraphicsItem*,
-                 QWidget* widget)
-{
-  painter->setBrush(QBrush(color_));
-  painter->setPen(QPen(color_.darker()));
-  painter->drawEllipse(this->boundingRect());
-  if (this->isUnderMouse()) {
-    painter->setPen(QPen(color_.darker()));
-  } else {
-    painter->setPen(QPen(Qt::white));
-  }
-  painter->drawText(this->boundingRect(), Qt::AlignCenter, text_);  
-}
-
-QRectF Knob::boundingRect() const
-{
-  return QRectF(0.0, 0.0, 15.0, 15.0);
-}
-
-
-SequenceHeader::SequenceHeader(SequenceItem* parent):
-  QGraphicsItem(parent)
-{
-  font_=QFont("Courier", 12);
-  font_.setKerning(false);
-  font_.setFixedPitch(true);
-}
-
-  
-void SequenceHeader::paint(QPainter* painter, const QStyleOptionGraphicsItem*,
-                           QWidget* widget)
-{
-  SequenceItem* si=dynamic_cast<SequenceItem*>(this->parentItem());
-  painter->setFont(font_);
-  QFontMetrics m(font_);
-  QString name(si->GetSequence().GetName().c_str());
-  QRectF br=this->boundingRect();
-  name=m.elidedText(name, Qt::ElideMiddle, br.width());
-  painter->drawText(br, Qt::AlignTop, name);
-}
-
-QRectF SequenceHeader::boundingRect() const
-{
-  QFontMetrics metrics(font_);
-  SequenceItem* si=dynamic_cast<SequenceItem*>(this->parentItem());
-  QString name(si->GetSequence().GetName().c_str());
-  QRectF rect(0, -2,name.size()*si->GetCharWidth()*1.1, 
-              si->GetCharHeight()+2);
-  SequenceScene* s=dynamic_cast<SequenceScene*>(this->scene());
-  rect.setWidth(std::min(qreal(s->GetHeaderWidth()), rect.width()));
-  return rect;
-}
-
-SequenceBody::SequenceBody(SequenceItem* parent):
-  QGraphicsItem(parent)
-{
-  
-}
-
-  
-void SequenceBody::paint(QPainter* painter, const QStyleOptionGraphicsItem*,
-                         QWidget* widget)
-{  
-  SequenceItem* si=dynamic_cast<SequenceItem*>(this->parentItem());
-  seq::SequenceHandle seq=si->GetSequence();
-  if (!seq.IsValid()) {
-    return;
-  }
-  QString qstr(seq.GetString().c_str());
-  QColor sel_color(Qt::yellow);  
-  if (si->IsSecStructureVisible()) {
-    sel_color.setAlpha(50);
-    painter->setBrush(QBrush(sel_color));
-    painter->setPen(QPen(QColor(Qt::yellow).darker()));  
-    painter->drawPath(si->GetSecStructPaths());    
-  }
-  painter->setFont(si->GetFont());
-  painter->setPen(QPen(Qt::black));  
-  QString tt("X");
-  QRectF br=this->boundingRect();
-  for (int i=0; i<qstr.size(); ++i) {
-    tt[0]=qstr[i];
-    QRectF rect(br.left()+i*si->GetCharWidth(), br.top(), 
-                br.width(), br.height());    
-    painter->drawText(rect, Qt::AlignLeft|Qt::AlignVCenter, tt);    
-  }
-
-  sel_color=QColor(Qt::green).lighter();
-  painter->setPen(QPen(Qt::green));  
-  sel_color.setAlpha(100);
-  painter->setBrush(QBrush(sel_color));
-  QRectF text_bounds=painter->boundingRect(boundingRect(), 
-                                           Qt::AlignLeft|Qt::AlignVCenter,
-                                           qstr);
-  const SequenceItem::Selection& sel=si->GetSelection();
-  for (size_t i=0; i<sel.size(); ++i) {
-    painter->drawRect(QRectF(sel[i].Loc*si->GetCharWidth(), 0, 
-                             sel[i].Length*si->GetCharWidth(),
-                             si->GetCharHeight()));
-  }
-}
-
-QRectF SequenceBody::boundingRect() const
-{
-  SequenceItem* si=dynamic_cast<SequenceItem*>(this->parentItem());
-  seq::SequenceHandle seq=si->GetSequence();
-  if (!seq.IsValid()) {
-    return QRectF();
-  }
-  return QRectF(0, -2, seq.GetLength()*si->GetCharWidth(), 
-                si->GetCharHeight()+2);  
-}
-
-
-SequenceItem::SequenceItem(const seq::SequenceHandle& seq, 
-                           QGraphicsItem* parent):
-  QGraphicsItem(parent), seq_(seq), show_sec_struct_(true)
-{
-  header_=new SequenceHeader(this);  
-  body_=new SequenceBody(this);
-  body_->translate(120.0, 0.0);
-  font_=QFont("Courier", 12);
-  font_.setKerning(false);
-  font_.setFixedPitch(true);
-  QFontMetrics metrics(font_);
-  advance_=metrics.boundingRect('W').width();
-  height_=metrics.boundingRect('|').height();
-  ascent_=metrics.ascent();
-  this->setAcceptedMouseButtons(Qt::LeftButton);
-  this->ExtractSecStructSegments();
-  selection_change_=false;
-}
-
-SequenceHeader* SequenceItem::GetHeader()
-{
-  return header_;
-}
-
-SequenceBody* SequenceItem::GetBody()
-{
-  return body_;
-}
-
-const seq::SequenceHandle& SequenceItem::GetSequence() const
-{
-  return seq_;
-}
-
-QRectF SequenceItem::GetCharBounds(int pos) const
-{
-  QPointF a(pos*advance_, 0);
-  return QRectF(this->mapToScene(a), QSizeF(advance_, height_));
-}
-
-float SequenceItem::GetCharWidth() const
-{
-  return advance_;
-}
-
-float SequenceItem::GetCharHeight() const
-{
-  return height_;
-}
-
-void SequenceItem::paint(QPainter* painter, const QStyleOptionGraphicsItem*,
-                         QWidget* widget)
-{
-}
-
-QRectF SequenceItem::boundingRect() const
-{
-  QRectF child_r(this->childrenBoundingRect());
-  if (show_sec_struct_) {
-    return QRectF(child_r.topLeft(), 
-                  QSize(child_r.width(), child_r.height()*2.5));    
-  } else {
-    return QRectF(child_r.topLeft(), 
-                  QSize(child_r.width(), child_r.height()));
-  }
-}
-
-void SequenceItem::ExtractSecStructSegments()
-{
-  if (!seq_.HasAttachedView()) {
-    return;
-  }
-  mol::ChainView chain=seq_.GetAttachedView().GetChainList()[0];
-  sec_=mol::alg::ExtractSecStructureSegments(chain);
-  this->SecStructSegmentsToPaths();
-}
-
-void SequenceHeader::contextMenuEvent(QGraphicsSceneContextMenuEvent* event)
-{
-  //...
-}
-void SequenceBody::mousePressEvent(QGraphicsSceneMouseEvent* event)
-{
-  SequenceItem* si=dynamic_cast<SequenceItem*>(this->parentItem());  
-  event->accept();
-  last_index_=-1;
-  good_ole_click_=true;
-  merge_select_=event->modifiers() & Qt::ShiftModifier;
-  si->BeginSelectionChange();
-}
-
-void SequenceBody::mouseDoubleClickEvent(QGraphicsSceneMouseEvent* event)
-{
-  SequenceItem* si=dynamic_cast<SequenceItem*>(this->parentItem());    
-  int index=std::max(0, int(event->pos().x()/si->GetCharWidth()));  
-  // find the secondary structure element -- if any that we are in
-  mol::alg::SecStructureSegments::iterator i=si->GetSecStructSegments().begin(),
-                                           e=si->GetSecStructSegments().end();  
-  for (;i!=e; ++i) {
-    if (i->first<=index && i->last>=index) {
-      si->Select(i->first, i->last+1, !merge_select_);
-      break;
-    }
-  }
-  good_ole_click_=false;
-}
-void SequenceHeader::mousePressEvent(QGraphicsSceneMouseEvent* event)
-{
-  event->accept();
-}
-
-void SequenceHeader::mouseReleaseEvent(QGraphicsSceneMouseEvent* event)
-{
-  SequenceItem* si=dynamic_cast<SequenceItem*>(this->parentItem());
-  if (si->IsEverythingSelected()) {
-    si->ClearSelection();
-  } else {
-    si->SelectAll();
-  }
-
-}
-
-void SequenceBody::mouseReleaseEvent(QGraphicsSceneMouseEvent* event)
-{
-  SequenceItem* si=dynamic_cast<SequenceItem*>(this->parentItem());    
-  if (good_ole_click_) {
-    int index=std::max(0, int(event->pos().x()/si->GetCharWidth()));
-    si->Select(index, index+1, !merge_select_);    
-  }
-  si->EndSelectionChange();
-}
-
-void SequenceBody::mouseMoveEvent(QGraphicsSceneMouseEvent* event)
-{
-  SequenceItem* si=dynamic_cast<SequenceItem*>(this->parentItem());    
-  good_ole_click_=false;  
-  if (!si->GetSequence().IsValid()) {
-    return;
-  }
-  float x=event->pos().x();
-  int index=std::max(0, int(x/si->GetCharWidth()));
-  if (last_index_!=-1 && last_index_!=index) {
-    si->Select(last_index_, index, !merge_select_);
-  } else {
-    last_index_=index;
-  }
-}
-
-void SequenceItem::StackToPath(std::vector<QPointF>& stack)
-{
-  if (!stack.empty()) {
-    sec_paths_.moveTo(QPointF(stack.front().x(), stack.front().y()+.5*ascent_));
-    for (std::vector<QPointF>::iterator j=stack.begin()+1, 
-         e2=stack.end(); j!=e2; ++j) {
-      sec_paths_.lineTo(QPointF(j->x(), j->y()+0.5*ascent_));
-    }
-    for (std::vector<QPointF>::reverse_iterator j=stack.rbegin(), 
-         e2=stack.rend(); j!=e2; ++j) {
-      sec_paths_.lineTo(QPointF(j->x(), -j->y()+.5*ascent_));
-    }        
-    sec_paths_.closeSubpath();
-    stack.clear();
-  }  
-}
-
-void SequenceItem::SecStructSegmentsToPaths()
-{
-  sec_paths_=QPainterPath();
-  
-  sec_paths_.setFillRule(Qt::WindingFill);
-  std::vector<QPointF> stack;
-  int last_end=-2;
-  for (mol::alg::SecStructureSegments::iterator i=sec_.begin(), 
-       e=sec_.end(); i!=e; ++i) {
-    mol::alg::SecStructureSegment s=*i;
-    if (last_end!=s.first-1) {
-      this->StackToPath(stack);
-    }
-    if (s.ss_type.IsCoil()) {
-      stack.push_back(QPointF(s.first*advance_, -.6*height_));
-      stack.push_back(QPointF((s.last+1)*advance_,  -.6*height_));
-    } else if (s.ss_type.IsHelical()) {
-      stack.push_back(QPointF(s.first*advance_, -.6*height_));
-      stack.push_back(QPointF(s.first*advance_, -.9*height_));
-      stack.push_back(QPointF((s.last+1)*advance_, -.9*height_));
-      stack.push_back(QPointF((s.last+1)*advance_, -.6*height_));
-    } else if (s.ss_type.IsExtended()) {
-      stack.push_back(QPointF(s.first*advance_, -.6*height_));
-      stack.push_back(QPointF(s.first*advance_, -.9*height_));
-      stack.push_back(QPointF((s.last-0.5)*advance_, -.9*height_));
-      stack.push_back(QPointF((s.last-0.5)*advance_, -1.3*height_));
-      stack.push_back(QPointF((s.last+1)*advance_, -.6*height_));
-      
-    }
-    last_end=s.last;    
-  }
-  this->StackToPath(stack);  
-}
-
-void SequenceItem::Select(int i1, int i2, bool clear)
-{
-  if (selection_change_>0) {
-    selection_=ref_sel_;    
-  }
-  int a1=std::min(i1, i2);
-  int len=std::abs(i1-i2);
-  Range sel_start(a1, len);
-  Range* sel=&sel_start;
-  bool modified=false;
-  if (clear) {
-    selection_.clear();
-    selection_.push_back(*sel);    
-  } else {
-    for (size_t i=0; i<selection_.size(); ++i) {
-      if (sel->Loc>=selection_[i].Loc && sel->Loc<selection_[i].End()) {
-        int old_end=selection_[i].End();        
-        if (sel->End()<=selection_[i].End()) {
-          selection_[i].Length=int(sel->Loc-selection_[i].Loc);
-          if (old_end-sel->End()>0) {
-            selection_.push_back(Range(sel->End(), old_end-sel->End()));
-          }          
-        } else {
-          selection_[i].Length=int(sel->Loc-selection_[i].Loc);
-          if (sel->End()-old_end>0) {
-            selection_.push_back(Range(old_end, sel->End()-old_end));
-          }
-        }
-        modified=true;
-        break;
-      } else if (sel->End()>selection_[i].Loc && 
-                 sel->End()<=selection_[i].End()) {
-        int nn=selection_[i].Loc;
-        selection_[i].Length-=sel->End()-selection_[i].Loc;
-        selection_[i].Loc=sel->End();
-        modified=true;
-        selection_.push_back(Range(sel->Loc, nn-sel->Loc));
-        break;
-      } else if (sel->Loc<selection_[i].Loc && 
-                 sel->End()>selection_[i].End()) {
-        selection_[i].Length=0;
-      } else if (sel->Loc==selection_[i].End()) {
-        selection_[i].Length+=sel->Length;
-        sel->Length=0;       
-        sel=&selection_[i];
-        modified=true;
-      } else if (sel->End()==selection_[i].Loc) {    
-        selection_[i].Loc-=sel->Length;  
-        selection_[i].Length+=sel->Length;
-        sel->Length=0;
-        sel=&selection_[i];        
-        modified=true;
-      }
-    }
-    if (!modified) {
-      selection_.push_back(Range(a1, len));      
-    }
-  }
-  Selection::iterator i=std::remove_if(selection_.begin(), selection_.end(),
-                                       bind(&Range::Length, _1)==size_t(0));
-  selection_.erase(i, selection_.end());
-  if (!selection_change_) {
-    emit this->SelectionChanged(this);
-  } else {
-    selection_change_=2;
-  }
-  update();
-}
-
-void SequenceItem::ClearSelection()
-{
-  selection_.clear();
-  if (selection_change_>0) {
-    selection_change_=2;
-  } else {
-    emit this->SelectionChanged(this);
-    update();    
-  }
-}
-
-void SequenceItem::SelectAll()
-{
-  if (!seq_.IsValid()) {
-    return;
-  }
-  selection_.clear();
-  selection_.push_back(Range(0, seq_.GetLength()));  
-  if (selection_change_>0) {
-    selection_change_=1;
-  } else {
-    emit this->SelectionChanged(this);  
-    update();
-  }
-}
-
-void SequenceItem::BeginSelectionChange()
-{
-  selection_change_=1;
-  ref_sel_=selection_;
-}
-
-void SequenceItem::EndSelectionChange()
-{
-  if (selection_change_==2) {
-    emit this->SelectionChanged(this);    
-  }
-  selection_change_=0;  
-}
-
-bool SequenceItem::IsEverythingSelected() const
-{
-  return selection_.size()==1 && selection_.front().Loc==0 && 
-         selection_.front().End()>=static_cast<size_t>(seq_.GetLength());
-}
-
-const SequenceItem::Selection& SequenceItem::GetSelection() const
-{
-  return selection_;
-}
-
-mol::alg::SecStructureSegments& SequenceItem::GetSecStructSegments()
-{
-  return sec_;
-}
-
-void SequenceItem::SetShowSecStructure(bool show)
-{
-  show_sec_struct_=show;
-}
-
-bool SequenceItem::IsSecStructureVisible() const
-{
-  return show_sec_struct_;
-}
-
-}}
diff --git a/modules/gui/src/sequence_viewer/sequence_item.hh b/modules/gui/src/sequence_viewer/sequence_item.hh
deleted file mode 100644
index aeaa63d1a9af36e29a925aa5af3b5fc214b2c8be..0000000000000000000000000000000000000000
--- a/modules/gui/src/sequence_viewer/sequence_item.hh
+++ /dev/null
@@ -1,153 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef OST_GUI_SEQUENCE_ITEM_HH
-#define OST_GUI_SEQUENCE_ITEM_HH
-
-#include <ost/gui/module_config.hh>
-#include <ost/mol/sec_structure.hh>
-#include <ost/mol/alg/sec_structure_segments.hh>
-
-#include <ost/seq/sequence_handle.hh>
-
-#include <QGraphicsItem>
-#include <QFont>
-
-namespace ost { namespace gui {
-
-class SequenceItem;
-class SequenceHeader;
-
-class DLLEXPORT_OST_GUI Knob : public QGraphicsItem {
-public:
-  Knob(const QString& text, const QColor& color, 
-       SequenceItem* parent=NULL);
-  
-  virtual void paint(QPainter* painter, const QStyleOptionGraphicsItem* opts,
-                     QWidget* widget=NULL);  
-  virtual QRectF boundingRect() const;
-private:
-  QString text_;
-  QColor  color_;
-};
-
-class DLLEXPORT_OST_GUI SequenceHeader : public QGraphicsItem {
-public:
-  SequenceHeader(SequenceItem* parent=NULL);
-  
-  virtual void paint(QPainter* painter, const QStyleOptionGraphicsItem* opts,
-                     QWidget* widget=NULL);
-  virtual QRectF boundingRect() const;                     
-protected:
-  virtual void mousePressEvent(QGraphicsSceneMouseEvent* event);
-  virtual void mouseReleaseEvent(QGraphicsSceneMouseEvent* event);  
-  virtual void contextMenuEvent(QGraphicsSceneContextMenuEvent* event);
-private:
-  QFont font_;
-};
-
-class DLLEXPORT_OST_GUI SequenceBody : public QGraphicsItem {
-public:
-  SequenceBody(SequenceItem* parent=NULL);
-  
-  virtual void paint(QPainter* painter, const QStyleOptionGraphicsItem* opts,
-                     QWidget* widget=NULL);
-  virtual QRectF boundingRect() const;         
-protected:
-  virtual void mousePressEvent(QGraphicsSceneMouseEvent* event);
-  virtual void mouseReleaseEvent(QGraphicsSceneMouseEvent* event);  
-  virtual void mouseMoveEvent(QGraphicsSceneMouseEvent* event);
-
-  virtual void mouseDoubleClickEvent(QGraphicsSceneMouseEvent* event);    
-private:
-  QFont    font_;
-  bool     merge_select_;
-  bool     good_ole_click_;
-  int      last_index_;  
-};
-
-
-class DLLEXPORT_OST_GUI SequenceItem : public QObject, // required for signals 
-                                       public QGraphicsItem {
-  Q_OBJECT
-public:
-  typedef std::vector<Range> Selection;  
-  
-  SequenceItem(const seq::SequenceHandle& seq, QGraphicsItem* parent=NULL);
-  
-  /// \brief get sequence
-  const seq::SequenceHandle& GetSequence() const;
-  
-  virtual void paint(QPainter* painter, const QStyleOptionGraphicsItem* opts,
-                     QWidget* widget=NULL);
-  virtual QRectF boundingRect() const;                     
-  
-  QRectF GetCharBounds(int pos) const;
-  
-  float GetCharWidth() const;  
-  float GetCharHeight() const;
-  
-  SequenceBody* GetBody();
-  SequenceHeader* GetHeader();
-  QPainterPath& GetSecStructPaths() { return sec_paths_; }
-  QFont GetFont() { return font_; }
-  
-  const Selection& GetSelection() const;
-  void Select(int i1, int i2, bool clear=true);
-    
-  void BeginSelectionChange();
-  void EndSelectionChange();  
-  
-  bool IsEverythingSelected() const;
-  void ClearSelection();
-  void SelectAll();
-  void SetShowSecStructure(bool show=true);
-  bool IsSecStructureVisible() const;
-  
-  mol::alg::SecStructureSegments& GetSecStructSegments();
-signals:
-
-  /// \brief emitted whenever the selection changes
-  /// 
-  /// When using BeginSelectionChange(), no signal is emitted until 
-  /// EndSelectionChange() is called.
-  void SelectionChanged(SequenceItem* item);
-private:
-  void ExtractSecStructSegments();
-  void SecStructSegmentsToPaths();
-  void StackToPath(std::vector<QPointF>& stack);
-  
-  QPainterPath                     sec_paths_;
-  mol::alg::SecStructureSegments   sec_;  
-  SequenceHeader*                  header_;
-  SequenceBody*                    body_;
-  seq::SequenceHandle              seq_;
-  QFont                            font_;
-  Selection                        selection_;
-  Selection                        ref_sel_;
-  float                            advance_;
-  float                            height_; 
-  float                            ascent_;
-  int                              selection_change_;
-  bool                             show_sec_struct_;
-};
-
-typedef std::vector<SequenceItem*> SequenceItemList;
-}}
-
-#endif
diff --git a/modules/gui/src/sequence/sequence_model.cc b/modules/gui/src/sequence_viewer/sequence_model.cc
similarity index 67%
rename from modules/gui/src/sequence/sequence_model.cc
rename to modules/gui/src/sequence_viewer/sequence_model.cc
index dc26ce348841621fa3d330fce38e83d1f9c7a062..342a04e1f258cfe8b87cd0488bb616d46b94ab2c 100644
--- a/modules/gui/src/sequence/sequence_model.cc
+++ b/modules/gui/src/sequence_viewer/sequence_model.cc
@@ -21,12 +21,6 @@
   Author: Stefan Scheuber
  */
 
-#include <QMap>
-#include <QMapIterator>
-
-#include <QtGui>
-
-#include "sequence_view_object.hh"
 
 #include "title_row.hh"
 
@@ -35,6 +29,10 @@
 
 #include "sequence_model.hh"
 
+#include <QMap>
+#include <QMapIterator>
+
+#include <QtGui>
 namespace ost { namespace gui {
 
 SequenceModel::SequenceModel(QObject *parent)
@@ -42,10 +40,10 @@ SequenceModel::SequenceModel(QObject *parent)
 {
   this->beginInsertRows(QModelIndex(),this->rowCount(),this->rowCount());
   BaseViewObject* title = new BaseViewObject(this);
-  TitleRow* title_row = new TitleRow(this);
-  Painter* p = new BackgroundPainter(this);
+  TitleRow* title_row = new TitleRow(title);
+  Painter* p = new BackgroundPainter(title_row);
   title_row->InsertPainter(p);
-  p = new TickPainter(this);
+  p = new TickPainter(title_row);
   title_row->InsertPainter(p);
   title->InsertRow(0,title_row);
   objects_.append(title);
@@ -78,13 +76,26 @@ void SequenceModel::InsertChain(QString& name, mol::ChainView& view){
   this->endInsertRows();
 }
 
+void SequenceModel::InsertAlignment(const seq::AlignmentHandle& alignment){
+  int cols = this->columnCount();
+  int new_cols = alignment.GetLength();
+  this->beginInsertRows(QModelIndex(),this->rowCount(),this->rowCount()+alignment.GetCount()-1);
+  objects_.append(new AlignmentViewObject(alignment, this));
+  if(new_cols > cols){
+    this->max_columns = new_cols;
+    this->beginInsertColumns(QModelIndex(), cols, new_cols);
+    this->endInsertColumns();
+  }
+  this->endInsertRows();
+}
+
 void SequenceModel::InsertSequences(const QList<QString>& names, seq::SequenceList& list){
   this->beginInsertRows(this->index(this->rowCount(),0),this->rowCount(),this->rowCount()+list.GetCount());
   objects_.append(new SequenceViewObject(list, names, this));
   this->endInsertRows();
 }
 
-void SequenceModel::InsertGfxEntity(gfx::EntityP& ent){
+void SequenceModel::InsertGfxEntity(const gfx::EntityP& ent){
   mol::EntityView view=ent->GetView();
   int size = view.GetChainList().size();
   int cols = this->columnCount();
@@ -100,7 +111,7 @@ void SequenceModel::InsertGfxEntity(gfx::EntityP& ent){
   this->endInsertRows();
 }
 
-void SequenceModel::RemoveGfxEntity(gfx::EntityP& entity){
+void SequenceModel::RemoveGfxEntity(const gfx::EntityP& entity){
   if(SequenceViewObject* obj = this->GetItem(entity)){
     int index = this->GetGlobalRow(obj,0);
     this->beginRemoveRows(QModelIndex(),index,index+obj->GetRowCount()-1);
@@ -116,6 +127,22 @@ void SequenceModel::RemoveGfxEntity(gfx::EntityP& entity){
   }
 }
 
+void SequenceModel::RemoveAlignment(const seq::AlignmentHandle& alignment){
+  if(AlignmentViewObject* obj = this->GetItem(alignment)){
+    int index = this->GetGlobalRow(obj,0);
+    this->beginRemoveRows(QModelIndex(),index,index+obj->GetRowCount()-1);
+    int cols_before = this->columnCount();
+    objects_.removeOne(obj);
+    this->endRemoveRows();
+    int cols = this->GetColumnCount();
+    if(cols_before>cols){
+      this->max_columns = cols;
+      this->beginRemoveColumns(QModelIndex(), cols, cols_before);
+      this->endRemoveColumns();
+    }
+  }
+}
+
 int SequenceModel::GetColumnCount() const{
   int cols = 0;
   for(int i = 0; i<objects_.size();i++){
@@ -127,7 +154,7 @@ int SequenceModel::GetColumnCount() const{
   return cols;
 }
 
-SequenceViewObject* SequenceModel::GetItem(gfx::EntityP& entity){
+SequenceViewObject* SequenceModel::GetItem(const gfx::EntityP& entity){
   if(entity != NULL){
     for (int i = 0 ; i< objects_.size(); i++){
       if(SequenceViewObject* seq_view_object = qobject_cast<SequenceViewObject*>(objects_[i])){
@@ -140,12 +167,23 @@ SequenceViewObject* SequenceModel::GetItem(gfx::EntityP& entity){
   return NULL;
 }
 
+AlignmentViewObject* SequenceModel::GetItem(const seq::AlignmentHandle& alignment){
+  for (int i = 0 ; i< objects_.size(); i++){
+    if(AlignmentViewObject* alignment_object = qobject_cast<AlignmentViewObject*>(objects_[i])){
+      if(alignment == alignment_object->GetAlignment()){
+        return alignment_object;
+      }
+    }
+  }
+  return NULL;
+}
+
 const PainterList& SequenceModel::GetPainters(const QModelIndex& index) const{
   QPair<int, BaseViewObject*> pair = this->GetRowWithItem(index);
   if(pair.second){
     return pair.second->GetRow(pair.first)->GetPainters();
   }
-  return empty_list_;
+  return empty_painter_list_;
 }
 
 QPair<int, BaseViewObject*> SequenceModel::GetRowWithItem(int row) const{
@@ -256,6 +294,121 @@ void SequenceModel::DoubleClicked(const QModelIndex& index)
   }
 }
 
+const QStringList& SequenceModel::GetDisplayModes()
+{
+  display_modes_.clear();
+  QMap<QString,int> string_map;
+  for (int i = 0; i<objects_.size(); i++){
+    const QStringList& list = objects_[i]->GetDisplayModes();
+    for(int j=0; j<list.size(); j++){
+      if(!string_map.contains(list.at(j))){
+        string_map.insert(list.at(j),1);
+      }
+      else {
+        string_map[list.at(j)] = string_map[list.at(j)] + 1;
+      }
+    }
+  }
+  bool removed = false;
+  QMapIterator<QString, int> i(string_map);
+  while (i.hasNext()) {
+    i.next();
+    if(objects_.size()-1 <= i.value()){
+      display_modes_.append(i.key());
+    }
+    else{
+      removed = true;
+    }
+  }
+  if(removed){
+    display_modes_.insert(0," ");
+  }
+  return display_modes_;
+}
+
+const QStringList& SequenceModel::GetDisplayModes(const gfx::EntityP& entity)
+{
+  BaseViewObject* item = this->GetItem(entity);
+  if(item){
+    return item->GetDisplayModes();
+  }
+  else{
+    return empty_string_list_;
+  }
+}
+
+const QStringList& SequenceModel::GetDisplayModes(const seq::AlignmentHandle& alignment)
+{
+  BaseViewObject* item = this->GetItem(alignment);
+  if(item){
+    return item->GetDisplayModes();
+  }
+  else{
+    return empty_string_list_;
+  }
+}
+
+const QString& SequenceModel::GetCurrentDisplayMode()
+{
+  current_display_mode_.clear();
+  for (int i = 0; i<objects_.size(); i++){
+    const QString& mode = objects_[i]->GetCurrentDisplayMode();
+    if(current_display_mode_.isEmpty()){
+      current_display_mode_ = mode;
+    }
+    else if(current_display_mode_ != mode){
+      current_display_mode_ = " ";
+      break;
+    }
+  }
+  return current_display_mode_;
+}
+
+const QString& SequenceModel::GetCurrentDisplayMode(const gfx::EntityP& entity)
+{
+  BaseViewObject* item = this->GetItem(entity);
+  if(item){
+    return item->GetCurrentDisplayMode();
+  }
+  else{
+    return empty_string_;
+  }
+}
+
+const QString& SequenceModel::GetCurrentDisplayMode(const seq::AlignmentHandle& alignment)
+{
+  BaseViewObject* item = this->GetItem(alignment);
+  if(item){
+    return item->GetCurrentDisplayMode();
+  }
+  else{
+    return empty_string_;
+  }
+}
+
+void SequenceModel::SetDisplayMode(const QString& mode)
+{
+  for (int i = 0; i<objects_.size(); i++){
+    objects_[i]->SetDisplayMode(mode);
+  }
+}
+
+void SequenceModel::SetDisplayMode(const gfx::EntityP& entity, const QString& mode)
+{
+  BaseViewObject* item = this->GetItem(entity);
+  if(item){
+    return item->SetDisplayMode(mode);
+  }
+}
+
+void SequenceModel::SetDisplayMode(const seq::AlignmentHandle& alignment, const QString& mode)
+{
+  BaseViewObject* item = this->GetItem(alignment);
+  if(item){
+    return item->SetDisplayMode(mode);
+  }
+}
+
 int SequenceModel::rowCount(const QModelIndex& parent) const
 {
   int rows = 0;
diff --git a/modules/gui/src/sequence/sequence_model.hh b/modules/gui/src/sequence_viewer/sequence_model.hh
similarity index 71%
rename from modules/gui/src/sequence/sequence_model.hh
rename to modules/gui/src/sequence_viewer/sequence_model.hh
index 98cbe3aa4d47476f133e7cdcae9592a92246b016..5a105c66fd1b8aa6b95d9dc5883e998191192cba 100644
--- a/modules/gui/src/sequence/sequence_model.hh
+++ b/modules/gui/src/sequence_viewer/sequence_model.hh
@@ -23,18 +23,20 @@
   Author: Stefan Scheuber
  */
 
-#include <QAbstractTableModel>
-#include <QItemSelection>
 
 #include <ost/mol/chain_view.hh>
 
 #include <ost/seq/sequence_list.hh>
+#include <ost/seq/alignment_handle.hh>
 
 #include <ost/gfx/entity.hh>
 
 #include "base_view_object.hh"
+#include "alignment_view_object.hh"
 #include "sequence_view_object.hh"
 
+#include <QAbstractTableModel>
+#include <QItemSelection>
 namespace ost { namespace gui {
 
 class SequenceModel : public QAbstractTableModel
@@ -44,12 +46,14 @@ class SequenceModel : public QAbstractTableModel
 public:
   SequenceModel(QObject *parent = 0);
 
-  void InsertGfxEntity(gfx::EntityP& entity);
+  void InsertAlignment(const seq::AlignmentHandle& alignment);
+  void InsertGfxEntity(const gfx::EntityP& entity);
   void InsertChain(QString& name, mol::ChainView& view);
   void InsertSequence(QString& name, seq::SequenceHandle& seq);
   void InsertSequences(const QList<QString>& names, seq::SequenceList& list);
 
-  void RemoveGfxEntity(gfx::EntityP& entity);
+  void RemoveAlignment(const seq::AlignmentHandle& alignment);
+  void RemoveGfxEntity(const gfx::EntityP& entity);
 
   QModelIndexList GetModelIndexes(gfx::EntityP& entity, const mol::EntityView& view);
   QModelIndexList GetModelIndexes(const QString& subject, const QString& sequence_name=QString());
@@ -57,6 +61,16 @@ public:
   int GetGlobalRow(BaseViewObject* obj, int row) const;
 
 
+  const QStringList& GetDisplayModes();
+  const QStringList& GetDisplayModes(const gfx::EntityP& entity);
+  const QStringList& GetDisplayModes(const seq::AlignmentHandle& alignment);
+  const QString& GetCurrentDisplayMode();
+  const QString& GetCurrentDisplayMode(const gfx::EntityP& entity);
+  const QString& GetCurrentDisplayMode(const seq::AlignmentHandle& alignment);
+  void SetDisplayMode(const QString& mode);
+  void SetDisplayMode(const gfx::EntityP& entity, const QString& mode);
+  void SetDisplayMode(const seq::AlignmentHandle& alignment, const QString& mode);
+
   const PainterList& GetPainters(const QModelIndex& index) const;
 
   // abstract item model interface
@@ -76,17 +90,21 @@ public slots:
   void ZoomOut();
   void DoubleClicked(const QModelIndex& index);
   void SelectionChanged(const QItemSelection& sel, const QItemSelection& desel);
-
 private:
   int GetColumnCount() const;
-  SequenceViewObject* GetItem(gfx::EntityP& entity);
+  SequenceViewObject* GetItem(const gfx::EntityP& entity);
+  AlignmentViewObject* GetItem(const seq::AlignmentHandle& alignment);
   BaseViewObject* GetItem(const QModelIndex& index) const;
   QPair<int, BaseViewObject*> GetRowWithItem(int row) const;
   QPair<int, BaseViewObject*> GetRowWithItem(const QModelIndex& index) const;
 
   QList<BaseViewObject*> objects_;
   int max_columns;
-  PainterList empty_list_;
+  PainterList empty_painter_list_;
+  QString empty_string_;
+  QStringList empty_string_list_;
+  QStringList display_modes_;
+  QString current_display_mode_;
 };
 
 
diff --git a/modules/gui/src/sequence/sequence_row.cc b/modules/gui/src/sequence_viewer/sequence_row.cc
similarity index 98%
rename from modules/gui/src/sequence/sequence_row.cc
rename to modules/gui/src/sequence_viewer/sequence_row.cc
index 517a86eeeb779d7d5cafced51ead05232c61afaf..5537b9f82e51b1c121163147cf9f0edc950bd81b 100644
--- a/modules/gui/src/sequence/sequence_row.cc
+++ b/modules/gui/src/sequence_viewer/sequence_row.cc
@@ -22,7 +22,6 @@
  */
 
 
-#include <QtGui>
 
 #include <ost/mol/mol.hh>
 #include <ost/mol/view_op.hh>
@@ -32,6 +31,7 @@
 #include "sequence_view_object.hh"
 #include "sequence_row.hh"
 
+#include <QtGui>
 namespace ost { namespace gui {
 
 SequenceRow::SequenceRow(const QString& name, seq::SequenceHandle& sequence, SequenceViewObject* parent) : BaseRow(QFont("Courier",11),parent), name_(name), name_font_(QFont("Courier",11)), sequence_(sequence)
@@ -112,7 +112,7 @@ QVariant SequenceRow::GetData(int column, int role) const
 
 Qt::ItemFlags SequenceRow::Flags(int column) const
 {
-  if(column<0 || column > this->GetColumnCount())return Qt::NoItemFlags;
+  if(column<0 || column >= this->GetColumnCount())return Qt::NoItemFlags;
 
   if(column==0){
     return Qt::ItemIsSelectable|Qt::ItemIsEnabled;
diff --git a/modules/gui/src/sequence/sequence_row.hh b/modules/gui/src/sequence_viewer/sequence_row.hh
similarity index 100%
rename from modules/gui/src/sequence/sequence_row.hh
rename to modules/gui/src/sequence_viewer/sequence_row.hh
index 51979f330de1a0c2249816c6eda26784d3f29564..1665366ba447e0121b94a5c9a41fa5919616d291 100644
--- a/modules/gui/src/sequence/sequence_row.hh
+++ b/modules/gui/src/sequence_viewer/sequence_row.hh
@@ -23,11 +23,11 @@
   Author: Stefan Scheuber
  */
 
-#include <QObject>
 
 #include <ost/seq/sequence_handle.hh>
 
 #include "base_row.hh"
+#include <QObject>
 
 namespace ost { namespace gui {
 
diff --git a/modules/gui/src/sequence_viewer/sequence_scene.cc b/modules/gui/src/sequence_viewer/sequence_scene.cc
deleted file mode 100644
index 4b77a71e3e61d610ecfa973a87ae242be634d3d2..0000000000000000000000000000000000000000
--- a/modules/gui/src/sequence_viewer/sequence_scene.cc
+++ /dev/null
@@ -1,134 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#include "sequence_scene.hh"
-#include <boost/bind.hpp>
-#include <QPainter>
-
-namespace ost { namespace gui {
-
-using boost::bind;
-
-void SequenceScene::drawBackground(QPainter* painter, const QRectF& rect)
-{
-  if (sequences_.empty()) {
-    return;
-  }
-  QBrush stripe_brushes[]={
-    QBrush(QColor(Qt::white)),
-    QBrush(QColor(245, 245, 245))
-  };
-  float width=sequences_[0]->GetCharWidth()*5;
-  QRectF stripe(QPointF(((int(rect.left()/width)-1)-1)*width+header_width_,
-                        rect.top()), 
-                QSizeF(width, rect.height()));
-  int n=round(rect.width()/width)+2;
-  int start=std::max(0, int(floor(rect.left()/width)))-1;  
-  for (int i=0; i<n; ++i, stripe.translate(width, 0.0)) {
-    painter->fillRect(stripe, stripe_brushes[(i+start+2) % 2]);
-  }
-  painter->setPen(QPen(Qt::gray));
-  const static int STEP_SIZE=10;
-  float s=sequences_[0]->GetCharWidth()*STEP_SIZE;
-  int n_rulers=round(rect.width()/s);
-  int first=std::max(0, int(floor(rect.left()/s)));
-  painter->fillRect(QRectF(QPointF(0.0, rect.top()), 
-                           QSizeF(header_width_, rect.height())),
-                    QBrush(Qt::white));  
-  for (int i=first;i<first+n_rulers+2; ++i) {
-    painter->drawText(QRectF(QPointF(i*s-50+header_width_, 
-                                     rect.top()), QSizeF(100, 30)),
-                      Qt::AlignCenter, QString::number(i*STEP_SIZE));
-    painter->drawLine(QPointF(i*s+header_width_, rect.top()+30), 
-                      QPointF(i*s+header_width_, rect.top()+30+rect.height()));
-  }
-
-}
-
-void SequenceScene::SetContextMenu(QMenu* menu)
-{
-  context_menu_=menu;
-}
-
-QMenu* SequenceScene::GetContextMenu()
-{
-  return context_menu_;
-}
-
-SequenceScene::SequenceScene(QObject* parent):
-  QGraphicsScene(parent), header_width_(120.0)
-{
-  connect(this, SIGNAL(sceneRectChanged(const QRectF&)), this, 
-          SLOT(OnSceneRectChange(const QRectF&)));
-  context_menu_=NULL;
-}
-
-void SequenceScene::RepackSequences()
-{
-  if (sequences_.empty()) {
-    return;
-  }
-  sequences_.front()->setPos(0.0, 50.0);
-  for (std::vector<SequenceItem*>::iterator i=sequences_.begin()+1, 
-       e=sequences_.end(); i!=e; ++i) {
-     (*i)->setPos(0.0, (*(i-1))->pos().y()+
-                 (*(i-1))->boundingRect().height());        
-  } 
-}
-
-void SequenceScene::AddSequence(SequenceItem* seq)
-{
-  this->addItem(seq);
-  if (!sequences_.empty()) {
-    seq->setPos(0.0, sequences_.back()->pos().y()+
-                sequences_.back()->boundingRect().height());
-  } else {
-    seq->setPos(0.0, 50.0);
-  }
-  sequences_.push_back(seq);
-  update();
-}
-
-void SequenceScene::RemoveSequence(SequenceItem* seq)
-{
-  this->removeItem(seq);
-  std::vector<SequenceItem*>::iterator f=std::find(sequences_.begin(),
-    sequences_.end(), seq);
-  if(f != sequences_.end())
-  {
-    sequences_.erase(f);
-  }
-  RepackSequences();
-}
-
-void SequenceScene::SetHeaderWidth(float width)
-{
-  header_width_=width;
-  update();
-}
-
-float SequenceScene:: GetHeaderWidth() const
-{
-  return header_width_;
-}
-
-void SequenceScene::OnSceneRectChange(const QRectF& rect)
-{
-}
-
-}}
diff --git a/modules/gui/src/sequence_viewer/sequence_scene.hh b/modules/gui/src/sequence_viewer/sequence_scene.hh
deleted file mode 100644
index 2547d9fbdf27527b2870617058affc08c9e76b2e..0000000000000000000000000000000000000000
--- a/modules/gui/src/sequence_viewer/sequence_scene.hh
+++ /dev/null
@@ -1,67 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef OST_GUI_SEQUENCE_SCENE_HH
-#define OST_GUI_SEQUENCE_SCENE_HH
-
-#include <ost/gui/module_config.hh>
-#include <ost/gui/sequence_viewer/sequence_item.hh>
-
-#include <QGraphicsScene>
-
-namespace ost { namespace gui {
-
-
-class SequenceScene : public QGraphicsScene {
-  Q_OBJECT
-public:
-  typedef std::vector<Range> Selection;
-
-  SequenceScene(QObject* parent=NULL);
-
-  void SetContextMenu(QMenu* menu);
-
-  QMenu* GetContextMenu();
-  std::vector<SequenceItem*>& GetSequences() { return sequences_; }
-  const Selection& GetSelection() const;
-
-  /// \brief get length of longest sequence (including gaps) in the alignment
-  void GetMaxSequenceLength();
-
-  
-  void SetHeaderWidth(float width);
-  float GetHeaderWidth() const;
-  void AddSequence(SequenceItem* seq);
-  void RemoveSequence(SequenceItem* seq);
-  void RepackSequences();
-public slots:
-  void OnSceneRectChange(const QRectF& rect);  
-protected: 
-  virtual void drawBackground(QPainter* painter, const QRectF& rect);
-private:
-  void UpdateAlignment();
-  Selection                  selection_;
-  Selection                  ref_sel_;
-  std::vector<SequenceItem*> sequences_;
-  QMenu*                     context_menu_;
-  float                      header_width_;
-};
-
-}}
-
-#endif
diff --git a/modules/gui/src/sequence_viewer/sequence_search_bar.cc b/modules/gui/src/sequence_viewer/sequence_search_bar.cc
index 808d45904e21293e5360e7bd5e3e8e25de82c132..9ae88675e2468dbe5083cbb642df653fd563c67a 100644
--- a/modules/gui/src/sequence_viewer/sequence_search_bar.cc
+++ b/modules/gui/src/sequence_viewer/sequence_search_bar.cc
@@ -21,7 +21,6 @@
  */
 
 #include "sequence_search_bar.hh"
-#include "sequence_item.hh"
 
 #include <QHBoxLayout>
 #include <QLineEdit>
@@ -32,7 +31,7 @@
 
 namespace ost { namespace gui { 
 
-SequenceSearchBar::SequenceSearchBar(QWidget* parent):
+SeqSearchBar::SeqSearchBar(QWidget* parent):
   QWidget(parent)
 {
   subject_=new QLineEdit(this);
@@ -41,13 +40,13 @@ SequenceSearchBar::SequenceSearchBar(QWidget* parent):
   QHBoxLayout* l= new QHBoxLayout(this);
   l->addSpacing(2);
   l->addWidget(subject_, 0);
+  l->setStretch(0,1);
   l->addWidget(search_all_, 0);
   QLabel* label=new QLabel("search in:", this);
   l->addSpacing(10);
   l->addWidget(label, 0);
   l->addWidget(search_in_, 0);
-  l->addStretch(1);
-  subject_->setMaximumWidth(200);
+  //subject_->setMaximumWidth(200);
   setLayout(l);
   l->setSizeConstraint(QLayout::SetMaximumSize);
   l->setMargin(1);  
@@ -67,23 +66,22 @@ SequenceSearchBar::SequenceSearchBar(QWidget* parent):
           SLOT(OnSearchInChanged(int)));
 }
   
-void SequenceSearchBar::Show(const std::vector<SequenceItem*>& sequences)
+void SeqSearchBar::UpdateItems(const QStringList& sequences)
 {
   search_in_->clear();
-  
-  for (size_t i=0;i<sequences.size(); ++i) {
-    QString name(sequences[i]->GetSequence().GetName().c_str());
-    search_in_->addItem(name);
+
+  for(int i=0;i< sequences.size(); i++){
+  search_in_->addItem(sequences[i]);
   }
+
   if (sequences.empty()) {
     search_all_->setCheckState(Qt::Checked);  
     search_in_->setEnabled(false);
   }
-  this->show();
   subject_->setFocus(Qt::ActiveWindowFocusReason);  
   subject_->selectAll();  
 }
-void SequenceSearchBar::OnSearchAllChanged(int state)
+void SeqSearchBar::OnSearchAllChanged(int state)
 {
   if (state==Qt::Unchecked) {
     search_in_->setEnabled(true);
@@ -91,22 +89,22 @@ void SequenceSearchBar::OnSearchAllChanged(int state)
     search_in_->setEnabled(false);
   }
   emit Changed(subject_->text(), search_all_->checkState()==Qt::Checked, 
-               search_in_->currentIndex());
+               search_in_->currentText());
 }
 
-void SequenceSearchBar::OnSearchInChanged(int index)
+void SeqSearchBar::OnSearchInChanged(int index)
 {
   emit Changed(subject_->text(), search_all_->checkState()==Qt::Checked, 
-               search_in_->currentIndex());
+               search_in_->currentText());
 }
 
-void SequenceSearchBar::OnSubjectChanged(const QString& str)
+void SeqSearchBar::OnSubjectChanged(const QString& str)
 {
   emit Changed(str, search_all_->checkState()==Qt::Checked, 
-               search_in_->currentIndex());
+               search_in_->currentText());
 }
 
-void SequenceSearchBar::paintEvent(QPaintEvent* paint_event)
+void SeqSearchBar::paintEvent(QPaintEvent* paint_event)
 {
   QPainter p(this);
   p.setBrush(QBrush(QColor(Qt::blue).lighter(300)));
@@ -115,7 +113,7 @@ void SequenceSearchBar::paintEvent(QPaintEvent* paint_event)
   paint_event->accept();
 }
 
-void SequenceSearchBar::keyPressEvent(QKeyEvent* key_event)
+void SeqSearchBar::keyPressEvent(QKeyEvent* key_event)
 {
   if (key_event->key()==Qt::Key_Escape) {
     this->hide();
diff --git a/modules/gui/src/sequence_viewer/sequence_search_bar.hh b/modules/gui/src/sequence_viewer/sequence_search_bar.hh
index fae7280dc6d119f47063e29645a5baaa882c95fe..865a42be22c30a828ba24285319f8f6d5bb592cc 100644
--- a/modules/gui/src/sequence_viewer/sequence_search_bar.hh
+++ b/modules/gui/src/sequence_viewer/sequence_search_bar.hh
@@ -16,8 +16,8 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#ifndef OST_SEQUENCE_SEARCH_BAR_HH
-#define OST_SEQUENCE_SEARCH_BAR_HH
+#ifndef OST_SEQUENCE_VIEWER_SEQUENCE_SEARCH_BAR_HH
+#define OST_SEQUENCE_VIEWER_SEQUENCE_SEARCH_BAR_HH
 
 /*
   Author: Marco Biasini
@@ -27,20 +27,19 @@
 #include <QWidget>
 #include <QComboBox>
 #include <QCheckBox>
+#include <QSet>
 
 namespace ost { namespace gui {
 
-class SequenceItem;  
-
 /// \brief search bar to search in multiple sequence alignment
-class DLLEXPORT_OST_GUI SequenceSearchBar : public QWidget {
+class DLLEXPORT_OST_GUI SeqSearchBar : public QWidget {
   Q_OBJECT
 public:
-  SequenceSearchBar(QWidget* parent=NULL);
+  SeqSearchBar(QWidget* parent=NULL);
   
-  void Show(const std::vector<SequenceItem*>& sequences);
+  void UpdateItems(const QStringList& sequences);
 signals:
-  void Changed(const QString&, bool, int);
+  void Changed(const QString&, bool, const QString&);
 public slots:
    void OnSubjectChanged(const QString&);
    void OnSearchInChanged(int);
diff --git a/modules/gui/src/sequence/sequence_table_view.cc b/modules/gui/src/sequence_viewer/sequence_table_view.cc
similarity index 93%
rename from modules/gui/src/sequence/sequence_table_view.cc
rename to modules/gui/src/sequence_viewer/sequence_table_view.cc
index f97bbb3e96636b8d273920f6782f5628c9959f25..a4998dcf3419bd50c4a4b1153b1f78f5fbb8aff9 100644
--- a/modules/gui/src/sequence/sequence_table_view.cc
+++ b/modules/gui/src/sequence_viewer/sequence_table_view.cc
@@ -21,15 +21,14 @@
   Author: Stefan Scheuber
  */
 
+
+#include "sequence_table_view.hh"
+#include "sequence_model.hh"
 #include <QHeaderView>
 #include <QScrollBar>
 #include <QTableWidgetItem>
 #include <QMouseEvent>
 
-#include <iostream>
-#include "sequence_table_view.hh"
-#include "sequence_model.hh"
-
 namespace ost { namespace gui {
 
 
@@ -66,12 +65,14 @@ SequenceTableView::SequenceTableView(QAbstractItemModel * model)
 
   delegate_ = new SequenceDelegate(qobject_cast<SequenceModel*>(this->model()),this);
 
+#if !(defined(__APPLE__) && (QT_VERSION>=0x040600))
   this->InitStaticRow();
   this->InitStaticColumn();
   this->InitStaticField();
   this->viewport()->stackUnder(static_field_);
   this->viewport()->stackUnder(static_column_);
   this->viewport()->stackUnder(static_row_);
+#endif
  }
 
 void SequenceTableView::InitStaticColumn()
@@ -187,33 +188,39 @@ void SequenceTableView::InitStaticField(){
   this->updateStaticField();
 }
 void SequenceTableView::ResizeWidth(int index, int, int size)
-{
+{ 
+#if !(defined(__APPLE__) && (QT_VERSION>=0x040600))  
   if(index == 0){
     static_column_->setColumnWidth(0,size);
+    static_row_->setColumnWidth(0,size);
     static_field_->setColumnWidth(0,size);
     this->updateStaticColumn();
     this->updateStaticField();
   }
-  static_row_->setRowHeight(index,size);
+#endif  
 }
 
 void SequenceTableView::ResizeHeight(int index, int, int size)
 {
-  static_column_->setRowHeight(index, size);
+#if !(defined(__APPLE__) && (QT_VERSION>=0x040600))
   if(index == 0){
+    static_column_->setRowHeight(0,size);
     static_row_->setRowHeight(0,size);
     static_field_->setRowHeight(0,size);
     this->updateStaticRow();
     this->updateStaticField();
   }
+#endif
 }
 
 void SequenceTableView::resizeEvent(QResizeEvent * event)
 {
   QTableView::resizeEvent(event);
+#if !(defined(__APPLE__) && (QT_VERSION>=0x040600))
   this->updateStaticColumn();
   this->updateStaticRow();
   this->updateStaticField();
+#endif  
 }
 
 QModelIndex SequenceTableView::moveCursor(CursorAction action, Qt::KeyboardModifiers modifiers)
@@ -237,9 +244,13 @@ QModelIndex SequenceTableView::moveCursor(CursorAction action, Qt::KeyboardModif
 }
 
 void SequenceTableView::scrollTo(const QModelIndex & index, ScrollHint hint){
+#if !(defined(__APPLE__) && (QT_VERSION>=0x040600))
   if(index.column()>0 && index.row()>0){
     QTableView::scrollTo(index, hint);
   }
+#else
+  QTableView::scrollTo(index, hint);
+#endif
 }
 
 void SequenceTableView::updateStaticColumn()
@@ -268,18 +279,23 @@ void SequenceTableView::updateStaticField(){
 }
 
 void SequenceTableView::columnCountChanged(const QModelIndex& index, int old_count, int new_count){
-  if(old_count >= 0 && old_count <= new_count){
+  if(old_count >= 0 && old_count <= new_count) {
+  
     if(old_count == 0)old_count = 1;
     for(int col=old_count; col<=new_count; col++){
+#if !(defined(__APPLE__) && (QT_VERSION>=0x040600))        
       static_column_->setColumnHidden(col, true);
       static_field_->setColumnHidden(col,true);
+#endif          
       this->setItemDelegateForColumn(col, delegate_);
     }
+
   }
 }
 
 void SequenceTableView::rowCountChanged(const QModelIndex& index, int old_count, int new_count){
   if(old_count >= 0 && old_count <= new_count){
+#if !(defined(__APPLE__) && (QT_VERSION>=0x040600))    
     if(old_count == 0){
       old_count = 1;
     }
@@ -287,23 +303,28 @@ void SequenceTableView::rowCountChanged(const QModelIndex& index, int old_count,
       static_row_->setRowHidden(row, true);
       static_field_->setRowHidden(row,true);
     }
+#endif
   }
 }
 
 
 void SequenceTableView::resizeColumnsToContents(){
   QTableView::resizeColumnsToContents();
+#if !(defined(__APPLE__) && (QT_VERSION>=0x040600))    
   static_column_->setColumnWidth(0,this->columnWidth(0));
   static_field_->setColumnWidth(0,this->columnWidth(0));
   for(int i = 0; i < this->model()->columnCount(); i++){
     static_row_->setColumnWidth(i,this->columnWidth(i));
   }
+
   this->updateStaticColumn();
   this->updateStaticField();
+#endif  
 }
 
 void SequenceTableView::resizeRowsToContents(){
   QTableView::resizeRowsToContents();
+#if !(defined(__APPLE__) && (QT_VERSION>=0x040600))
   static_row_->setRowHeight(0,this->rowHeight(0));
   static_field_->setRowHeight(0,this->rowHeight(0));
   for(int i = 0; i < this->model()->columnCount(); i++){
@@ -311,17 +332,21 @@ void SequenceTableView::resizeRowsToContents(){
   }
   this->updateStaticRow();
   this->updateStaticField();
+#endif  
 }
 
-QTableView* SequenceTableView::GetStaticRow(){
+QTableView* SequenceTableView::GetStaticRow()
+{
   return static_row_;
 }
 
-QTableView* SequenceTableView::GetStaticColumn(){
+QTableView* SequenceTableView::GetStaticColumn()
+{
   return static_column_;
 }
 
-QTableView* SequenceTableView::GetStaticField(){
+QTableView* SequenceTableView::GetStaticField()
+{
   return static_field_;
 }
 
diff --git a/modules/gui/src/sequence/sequence_table_view.hh b/modules/gui/src/sequence_viewer/sequence_table_view.hh
similarity index 100%
rename from modules/gui/src/sequence/sequence_table_view.hh
rename to modules/gui/src/sequence_viewer/sequence_table_view.hh
index e138d07eadc8dc63a4c110b4fbcb2900f82bac44..3114a8f6e8c334cd40f46529f9f05707aa62dcac 100644
--- a/modules/gui/src/sequence/sequence_table_view.hh
+++ b/modules/gui/src/sequence_viewer/sequence_table_view.hh
@@ -23,13 +23,13 @@
   Author: Stefan Scheuber
  */
 
-#include <QTableView>
-#include <QWheelEvent>
 
 #include <ost/gui/module_config.hh>
 
 #include "sequence_delegate.hh"
 
+#include <QTableView>
+#include <QWheelEvent>
 namespace ost { namespace gui {
 
 /// \brief QTableView with first column not moving
diff --git a/modules/gui/src/sequence/sequence_view_object.cc b/modules/gui/src/sequence_viewer/sequence_view_object.cc
similarity index 65%
rename from modules/gui/src/sequence/sequence_view_object.cc
rename to modules/gui/src/sequence_viewer/sequence_view_object.cc
index d3e53093a6e06357b9c2d019e570e0c9c0518b5a..40a46a519d85158584d37338558bd70128fd7f6b 100644
--- a/modules/gui/src/sequence/sequence_view_object.cc
+++ b/modules/gui/src/sequence_viewer/sequence_view_object.cc
@@ -22,7 +22,6 @@
  */
 
 
-#include <QtGui>
 
 #include <ost/mol/mol.hh>
 #include <ost/mol/view_op.hh>
@@ -30,38 +29,50 @@
 #include "sequence_row.hh"
 #include "secstr_row.hh"
 
-#include "painter.hh"
-#include "background_painter.hh"
-#include "seq_secstr_painter.hh"
-#include "seq_selection_painter.hh"
-#include "seq_text_painter.hh"
-
 #include "sequence_view_object.hh"
 
+#include <QtGui>
 namespace ost { namespace gui {
 
+const QString SequenceViewObject::properties_mode = "Highlight properties";
+const QString SequenceViewObject::secondary_structure_mode = "Secondary structure";
+
+AlignPropertiesPainter* SequenceViewObject::align_properties_painter = new AlignPropertiesPainter();
+ConservationPainter* SequenceViewObject::conservation_painter = new ConservationPainter();
+BackgroundPainter* SequenceViewObject::background_painter = new BackgroundPainter();
+SeqSecStrPainter* SequenceViewObject::seq_secondary_structure_painter = new SeqSecStrPainter();
+SeqSelectionPainter* SequenceViewObject::seq_selection_painter = new SeqSelectionPainter();
+SeqTextPainter* SequenceViewObject::seq_text_painter = new SeqTextPainter();
+
 SequenceViewObject::SequenceViewObject(seq::SequenceList& sequences, const QList<QString>& names, QObject *parent): BaseViewObject(parent), entity_(gfx::EntityP())
 {
+  this->Init();
   if(names.size() == sequences.GetCount()){
     for(int i=0; i<sequences.GetCount(); i++){
       seq::SequenceHandle seq = sequences[i];
       this->AddSequence(seq, names[i]);
     }
   }
+  this->SetDisplayMode(properties_mode);
 }
 
 SequenceViewObject::SequenceViewObject(seq::SequenceHandle& sequence, const QString& name, QObject *parent): BaseViewObject(parent), entity_(gfx::EntityP())
 {
+  this->Init();
   this->AddSequence(sequence, name);
+  this->SetDisplayMode(properties_mode);
 }
 
 SequenceViewObject::SequenceViewObject(mol::ChainView& chain, const QString& name, QObject *parent): BaseViewObject(parent), entity_(gfx::EntityP())
 {
+  this->Init();
   this->AddChain(chain, name);
+  this->SetDisplayMode(properties_mode);
 }
 
-SequenceViewObject::SequenceViewObject(gfx::EntityP& entity, QObject* parent): BaseViewObject(parent), entity_(entity)
+SequenceViewObject::SequenceViewObject(const gfx::EntityP& entity, QObject* parent): BaseViewObject(parent), entity_(entity)
 {
+  this->Init();
   mol::EntityView view =entity->GetView();
   for (mol::ChainViewList::const_iterator c=view.GetChainList().begin(),
        e1=view.GetChainList().end(); c!=e1; ++c) {
@@ -72,31 +83,40 @@ SequenceViewObject::SequenceViewObject(gfx::EntityP& entity, QObject* parent): B
     }
     this->AddChain(chain, name);
   }
+  this->SetDisplayMode(secondary_structure_mode);
+}
+
+SequenceViewObject::SequenceViewObject(QObject* parent): BaseViewObject(parent), entity_(gfx::EntityP())
+{
+  this->Init();
+  this->SetDisplayMode(properties_mode);
+}
+
+void SequenceViewObject::Init()
+{
+  this->AddDisplayMode(properties_mode);
+  if(entity_){
+    this->AddDisplayMode(secondary_structure_mode);
+  }
 }
 
 void SequenceViewObject::AddSequence(seq::SequenceHandle& sequence, const QString& name)
 {
   SequenceRow* new_row = new SequenceRow(name, sequence, this);
-  Painter* p = new BackgroundPainter(this);
-  new_row->InsertPainter(p);
-  p = new SeqSelectionPainter(this);
-  new_row->InsertPainter(p);
-  p = new SeqTextPainter(this);
-  new_row->InsertPainter(p);
+  new_row->InsertPainter(background_painter);
+  new_row->InsertPainter(align_properties_painter);
+  new_row->InsertPainter(seq_text_painter);
+  new_row->InsertPainter(seq_selection_painter);
   rows_.append(new_row);
 }
 
 void SequenceViewObject::AddChain(mol::ChainView& chain, const QString& name)
 {
   SecStrRow* new_row = new SecStrRow(name, chain, this);
-  Painter* p = new BackgroundPainter(this);
-  new_row->InsertPainter(p);
-  p = new SeqSecStrPainter(this);
-  new_row->InsertPainter(p);
-  p = new SeqTextPainter(this);
-  new_row->InsertPainter(p);
-  p = new SeqSelectionPainter(this);
-  new_row->InsertPainter(p);
+  new_row->InsertPainter(background_painter);
+  new_row->InsertPainter(seq_secondary_structure_painter);
+  new_row->InsertPainter(seq_text_painter);
+  new_row->InsertPainter(seq_selection_painter);
   rows_.append(new_row);
 }
 
@@ -110,6 +130,29 @@ gfx::EntityP& SequenceViewObject::GetGfxObject()
   return entity_;
 }
 
+void SequenceViewObject::SetDisplayMode(const QString& mode)
+{
+  if(this->display_modes_.contains(mode) &&  mode != this->GetCurrentDisplayMode()){
+    if(mode == properties_mode){
+      for(int i=0 ; i<this->GetRowCount(); i++){
+        BaseRow* row = this->GetRow(i);
+        row->RemovePainter(seq_secondary_structure_painter);
+        row->RemovePainter(conservation_painter);
+        row->InsertPainter(align_properties_painter,1);
+      }
+    }
+    else if(mode == secondary_structure_mode){
+      for(int i=0 ; i<this->GetRowCount(); i++){
+        BaseRow* row = this->GetRow(i);
+        row->RemovePainter(align_properties_painter);
+        row->RemovePainter(conservation_painter);
+        row->InsertPainter(seq_secondary_structure_painter,1);
+      }
+    }
+  }
+  BaseViewObject::SetDisplayMode(mode);
+}
+
 QMap<int, QList<int> > SequenceViewObject::GetIndexesForView(const mol::EntityView& view)
 {
   if(view.GetChainCount()==0){
diff --git a/modules/gui/src/sequence/sequence_view_object.hh b/modules/gui/src/sequence_viewer/sequence_view_object.hh
similarity index 72%
rename from modules/gui/src/sequence/sequence_view_object.hh
rename to modules/gui/src/sequence_viewer/sequence_view_object.hh
index 9d85f85b839908c2ae469087e4f06cce2bd47aca..ba862c724efba112968fdc735f0f1cc1271a4492 100644
--- a/modules/gui/src/sequence/sequence_view_object.hh
+++ b/modules/gui/src/sequence_viewer/sequence_view_object.hh
@@ -30,8 +30,16 @@
 
 #include <ost/seq/sequence_list.hh>
 
+#include "align_properties_painter.hh"
+#include "conservation_painter.hh"
+#include "background_painter.hh"
+#include "seq_secstr_painter.hh"
+#include "seq_selection_painter.hh"
+#include "seq_text_painter.hh"
+
 #include "base_view_object.hh"
 
+
 namespace ost { namespace gui {
 
 class SequenceViewObject : public BaseViewObject
@@ -42,7 +50,10 @@ public:
   SequenceViewObject(seq::SequenceList& sequences, const QList<QString>& names, QObject* parent = 0);
   SequenceViewObject(seq::SequenceHandle& sequence, const QString& name, QObject* parent = 0);
   SequenceViewObject(mol::ChainView& chain, const QString& name, QObject* parent = 0);
-  SequenceViewObject(gfx::EntityP& entity, QObject* parent = 0);
+  SequenceViewObject(const gfx::EntityP& entity, QObject* parent = 0);
+  SequenceViewObject(QObject* parent = 0);
+
+  void Init();
 
   void AddSequence(seq::SequenceHandle& sequence, const QString& name=QString());
   void AddChain(mol::ChainView& chain, const QString& name=QString());
@@ -50,11 +61,26 @@ public:
   void AttachGfxObject(gfx::EntityP& ent);
   gfx::EntityP& GetGfxObject();
 
+  virtual void SetDisplayMode(const QString& mode);
+
   QMap<int, QList<int> > GetIndexesForView(const mol::EntityView& view);
   QMap<int, QList<int> > GetIndexesForSubject(const QString& subject, const QString& sequence_name=QString());
 
+protected:
+  static const QString properties_mode;
+  static const QString secondary_structure_mode;
+
+  static AlignPropertiesPainter* align_properties_painter;
+  static ConservationPainter* conservation_painter;
+  static BackgroundPainter* background_painter;
+  static SeqSecStrPainter* seq_secondary_structure_painter;
+  static SeqSelectionPainter* seq_selection_painter;
+  static SeqTextPainter* seq_text_painter;
+
 private:
   gfx::EntityP entity_;
+
+
 };
 
 
diff --git a/modules/gui/src/sequence_viewer/sequence_viewer.cc b/modules/gui/src/sequence_viewer/sequence_viewer.cc
index 05d5d03cf1c64f68a374105eee97fe1bafb3b979..79c13057f9e85b248bfc9590d3f5bc1af19929ad 100644
--- a/modules/gui/src/sequence_viewer/sequence_viewer.cc
+++ b/modules/gui/src/sequence_viewer/sequence_viewer.cc
@@ -16,25 +16,54 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#include <QMenu>
 
-#include <ost/dyn_cast.hh>
-#include <ost/mol/view_op.hh>
+/*
+  Author: Stefan Scheuber
+ */
+#include <ost/gui/gosty_app.hh>
+#include <boost/pointer_cast.hpp>
+
+
+#include <ost/platform.hh>
+#include <ost/mol/chain_view.hh>
+#include <ost/mol/entity_view.hh>
+
+#include <ost/seq/sequence_handle.hh>
 
 #include <ost/gfx/entity.hh>
 #include <ost/gfx/scene.hh>
 #include <ost/gfx/gfx_node_visitor.hh>
-#include <ost/gfx/gfx_node.hh>
-#include <ost/gfx/gfx_object.hh>
 
 #include <ost/gui/widget_registry.hh>
-#include <ost/gui/gosty_app.hh>
 
+#include "sequence_model.hh"
 #include "sequence_viewer.hh"
 
-
+#include <QAbstractItemView>
+#include <QApplication>
+#include <QClipboard>
+#include <QDir>
+#include <QHeaderView>
+#include <QMenu>
+#include <QPushButton>
+#include <QShortcut>
+#include <QVBoxLayout>
+#include <QVarLengthArray>
 namespace ost { namespace gui {
 
+class SequenceViewerFactory: public WidgetFactory {
+public:
+  SequenceViewerFactory() :
+    WidgetFactory("ost::gui::SequenceViewer", "Sequence Viewer") {
+  }
+
+  virtual Widget* Create(QWidget* parent) {
+    return GostyApp::Instance()->GetSequenceViewer();
+  }
+};
+
+OST_REGISTER_WIDGET(SequenceViewer, SequenceViewerFactory);
+
 struct GetNodesVisitor: public gfx::GfxNodeVisitor {
   GetNodesVisitor(): nodes_() {}
   virtual void VisitObject(gfx::GfxObj* o, const Stack& st) {
@@ -44,199 +73,364 @@ struct GetNodesVisitor: public gfx::GfxNodeVisitor {
   gfx::NodePtrList GetNodes(){return nodes_;}
 };
 
-class SequenceViewerFactory: public WidgetFactory {
-public:
-	SequenceViewerFactory() :
-    WidgetFactory("ost::gui::SequenceViewer", "Sequence Viewer") {
+SequenceViewer::SequenceViewer(bool stand_alone, QWidget* parent): Widget(NULL,parent)
+{
+  model_ = new SequenceModel(this);
+
+  QVBoxLayout* layout = new QVBoxLayout(this);
+  layout->setMargin(0);
+  layout->setSpacing(0);
+  this->setLayout(layout);
+
+  this->InitActions();
+
+
+  if(stand_alone){
+    this->InitMenuBar();
   }
+  this->InitSearchBar();
+  this->InitView();
 
-  virtual Widget* Create(QWidget* parent) {
-    return GostyApp::Instance()->GetSequenceViewer();
+  if(!stand_alone){
+    gfx::Scene::Instance().AttachObserver(this);
+    gfx::GfxNodeP root_node = gfx::Scene::Instance().GetRootNode();
+    GetNodesVisitor gnv;
+    gfx::Scene::Instance().Apply(gnv);
+    gfx::NodePtrList list = gnv.GetNodes();
+    for(unsigned int i=0; i<list.size();i++){
+      this->NodeAdded(list[i]);
+    }
   }
-};
+}
 
-OST_REGISTER_WIDGET(SequenceViewer, SequenceViewerFactory);
+void SequenceViewer::InitMenuBar()
+{
+  toolbar_ = new QToolBar(this);
+  toolbar_->setToolButtonStyle(Qt::ToolButtonIconOnly);
+  toolbar_->setIconSize(QSize(16,16));
+  toolbar_->addActions(action_list_);
+  layout()->addWidget(toolbar_);
+}
 
-SequenceViewer::SequenceViewer(QWidget* parent):
-  SequenceViewerBase(parent), we_are_changing_the_selection_(false)
+void SequenceViewer::InitSearchBar()
 {
-  gfx::Scene::Instance().AttachObserver(this);
-  this->SetDisplayStyle(SequenceViewer::LOOSE);
+  seq_search_bar_ = new SeqSearchBar(this);
+  seq_search_bar_->hide();
+  layout()->addWidget(seq_search_bar_);
+  connect(seq_search_bar_, SIGNAL(Changed(const QString&, bool, const QString&)), this, SLOT(OnSearchBarUpdate(const QString&, bool, const QString&)));
+}
 
-  gfx::GfxNodeP root_node = gfx::Scene::Instance().GetRootNode();
-  GetNodesVisitor gnv;
-  gfx::Scene::Instance().Apply(gnv);
-  gfx::NodePtrList list = gnv.GetNodes();
-  for(unsigned int i=0; i<list.size();i++){
-    this->NodeAdded(list[i]);
-  }
+void SequenceViewer::InitView()
+{
+  seq_table_view_ = new SequenceTableView(model_);
+  seq_table_view_->setFrameShape(QFrame::NoFrame);
+  seq_table_view_->setTextElideMode(Qt::ElideRight);  
+  layout()->addWidget(seq_table_view_);
+
+  connect(model_,SIGNAL(columnsInserted(const QModelIndex&, int, int)),seq_table_view_,SLOT(columnCountChanged(const QModelIndex&, int, int)));
+  connect(model_,SIGNAL(rowsInserted(const QModelIndex&, int, int)),seq_table_view_,SLOT(rowCountChanged(const QModelIndex&, int, int)));
+
+  seq_table_view_->horizontalHeader()->setMinimumSectionSize(2);
+  seq_table_view_->verticalHeader()->setMinimumSectionSize(2);
+  seq_table_view_->setSelectionMode(QAbstractItemView::ExtendedSelection);
+  connect(seq_table_view_->selectionModel(), SIGNAL(selectionChanged(const QItemSelection&, const QItemSelection&)), this, SLOT(SelectionModelChanged(const QItemSelection&, const QItemSelection&)));
+  connect(seq_table_view_,SIGNAL(doubleClicked(const QModelIndex&)),model_,SLOT(DoubleClicked(const QModelIndex&)));
+#if !(defined(__APPLE__) && (QT_VERSION>=0x040600))  
+  connect(seq_table_view_->GetStaticColumn(),SIGNAL(doubleClicked(const QModelIndex&)),this,SLOT(DoubleClicked(const QModelIndex&)));
+  connect(seq_table_view_->GetStaticRow(),SIGNAL(doubleClicked(const QModelIndex&)),this,SLOT(DoubleClicked(const QModelIndex&)));
+#endif
+  connect(seq_table_view_,SIGNAL(CopyEvent(QKeyEvent*)),this,SLOT(CopyEvent(QKeyEvent*)));
+  connect(seq_table_view_,SIGNAL(MouseWheelEvent(QWheelEvent*)),this,SLOT(MouseWheelEvent(QWheelEvent*)));
 }
 
-SequenceViewer::~SequenceViewer()
+void SequenceViewer::InitActions()
 {
-  gfx::Scene::Instance().DetachObserver(this);
+  QDir icon_path(GetSharedDataPath().c_str());
+  icon_path.cd("gui");
+  icon_path.cd("icons");
+
+  QAction* find_action = new QAction(this);
+  find_action->setText("Find Dialog");
+  find_action->setShortcut(QKeySequence(tr("Ctrl+F")));
+  find_action->setCheckable(true);
+  find_action->setToolTip("Display Find-Dialog (Ctrl+F)");
+  find_action->setIcon(QIcon(icon_path.absolutePath()+QDir::separator()+QString("find_icon.png")));
+  action_list_.append(find_action);
+  connect(find_action, SIGNAL(triggered(bool)), this, SLOT(FindInSequence()));
+
+  display_mode_actions_ = new QActionGroup(this);
+  QAction* menu_action = new QAction(this);
+  menu_action->setText("Menubar");
+  menu_action->setShortcut(QKeySequence(tr("Ctrl+M")));
+  menu_action->setToolTip("Display Options (Ctrl+M)");
+  menu_action->setIcon(QIcon(icon_path.absolutePath()+QDir::separator()+QString("menubar_icon.png")));
+  action_list_.append(menu_action);
+  connect(menu_action, SIGNAL(triggered(bool)), this, SLOT(DisplayMenu()));
+}
+
+void SequenceViewer::AddEntity(const gfx::EntityP& entity)
+{
+  model_->InsertGfxEntity(entity);
+  this->FitToContents();
+  this->UpdateSearchBar();
+}
+
+void SequenceViewer::RemoveEntity(const gfx::EntityP& entity)
+{
+  model_->RemoveGfxEntity(entity);
 }
 
 void SequenceViewer::NodeAdded(const gfx::GfxNodeP& n)
 {
-  if (gfx::EntityP o=dyn_cast<gfx::Entity>(n)) {
-    // extract all chains 
-    mol::EntityView v=o->GetView();
-    for (mol::ChainViewList::const_iterator c=v.GetChainList().begin(),
-         e1=v.GetChainList().end(); c!=e1; ++c) {
-      mol::ChainView chain=*c;
-      String seq_str;
-      seq_str.reserve(chain.GetResidueCount());
-      for (mol::ResidueViewList::const_iterator r=chain.GetResidueList().begin(),
-           e2=chain.GetResidueList().end(); r!=e2; ++r) {
-        mol::ResidueView res=*r;
-        seq_str.append(1, res.GetOneLetterCode());
-      }
-      if (seq_str.empty()) {
-        continue;
-      }      
-      String name=o->GetName();
-      if (chain.GetName()!="" && chain.GetName()!=" ") {
-        name+=" ("+chain.GetName()+")";
-      }
-      seq::SequenceHandle seq=seq::CreateSequence(name, seq_str);
-      mol::EntityView v_one_chain=v.GetHandle().CreateEmptyView();
-      v_one_chain.AddChain(chain, mol::ViewAddFlag::INCLUDE_ALL);
-      seq.AttachView(v_one_chain);
-      SequenceItem* item=new SequenceItem(seq);
-      connect(item, SIGNAL(SelectionChanged(SequenceItem*)),
-              this, SLOT(ItemSelectionChanged(SequenceItem*)));
-      this->AddSequence(item);
-      obj_map_.insert(std::make_pair(item, o));      
-    }
+  if (gfx::EntityP o=boost::dynamic_pointer_cast<gfx::Entity>(n)) {
+    this->AddEntity(o);
   }
 }
 
-void SequenceViewer::ItemSelectionChanged(SequenceItem* item)
+void SequenceViewer::NodeRemoved(const gfx::GfxNodeP& node)
 {
-  if (we_are_changing_the_selection_==true) {
-    return;
+  if (gfx::EntityP o=boost::dynamic_pointer_cast<gfx::Entity>(node)) {
+    this->RemoveEntity(o);
   }
-  we_are_changing_the_selection_=true;
-  // map sequence item back to graphical object
-  if (gfx::GfxObjP p=this->GfxObjForSeqItem(item)) {
-    gfx::EntityP ec=dyn_cast<gfx::Entity>(p);
-    seq::SequenceHandle seq=item->GetSequence();
-    mol::EntityView att_v=seq.GetAttachedView();
-    if (!att_v) {
-      we_are_changing_the_selection_=false;      
-      return;
+}
+
+void SequenceViewer::AddAlignment(const seq::AlignmentHandle& alignment)
+{
+  if(alignment.GetCount()>0 && alignment.GetLength()>0){
+    model_->InsertAlignment(alignment);
+    this->FitToContents();
+  }
+}
+
+void SequenceViewer::RemoveAlignment(const seq::AlignmentHandle& alignment)
+{
+  model_->RemoveAlignment(alignment);
+}
+
+void SequenceViewer::UpdateSearchBar()
+{
+  QStringList sequence_names_;
+  for(int i = 1; i< model_->rowCount(); i++){
+    QString name = model_->data(model_->index(i,0),Qt::DisplayRole).toString();
+    sequence_names_.append(name);
+  }
+  seq_search_bar_->UpdateItems(sequence_names_);
+}
+
+void SequenceViewer::SelectionModelChanged(const QItemSelection& sel, const QItemSelection& desel)
+{
+  gfx::Scene::Instance().DetachObserver(this);
+  model_->SelectionChanged(sel, desel);
+  gfx::Scene::Instance().AttachObserver(this);
+}
+
+void SequenceViewer::SelectionChanged(const gfx::GfxObjP& o,
+                                      const mol::EntityView& view)
+{
+  disconnect(seq_table_view_->selectionModel(), SIGNAL(selectionChanged(const QItemSelection&, const QItemSelection&)), this, SLOT(SelectionModelChanged(const QItemSelection&, const QItemSelection&)));
+  gfx::EntityP entity=boost::dynamic_pointer_cast<gfx::Entity>(o);
+  if(entity){
+    const QModelIndexList& list = model_->GetModelIndexes(entity, view);
+    this->SelectList(list);
+  }
+  connect(seq_table_view_->selectionModel(), SIGNAL(selectionChanged(const QItemSelection&, const QItemSelection&)), this, SLOT(SelectionModelChanged(const QItemSelection&, const QItemSelection&)));
+}
+
+void SequenceViewer::DoubleClicked(const QModelIndex& index)
+{
+  disconnect(seq_table_view_->selectionModel(), SIGNAL(selectionChanged(const QItemSelection&, const QItemSelection&)), this, SLOT(SelectionModelChanged(const QItemSelection&, const QItemSelection&)));
+  model_->DoubleClicked(index);
+  connect(seq_table_view_->selectionModel(), SIGNAL(selectionChanged(const QItemSelection&, const QItemSelection&)), this, SLOT(SelectionModelChanged(const QItemSelection&, const QItemSelection&)));
+}
+
+void SequenceViewer::FitToContents()
+{
+  seq_table_view_->resizeColumnsToContents();
+  seq_table_view_->resizeRowsToContents();
+  seq_table_view_->setColumnWidth(0, 150);  
+}
+
+void SequenceViewer::MouseWheelEvent(QWheelEvent* event)
+{
+  int delta = event->delta();
+  if (event->orientation() == Qt::Vertical) {
+    if(delta>0){
+      model_->ZoomIn();
+      this->FitToContents();
+      seq_table_view_->viewport()->update();      
     }
-    const SequenceItem::Selection& sel=item->GetSelection();
-    // reset selection of "our" chain
-    mol::EntityView sel_v=ec->GetSelection();
-    if (mol::ChainView c=sel_v.FindChain(att_v.GetChainList().front().GetHandle())) {
-      sel_v.RemoveChain(c);
+    else if(delta<0){
+      model_->ZoomOut();
+      this->FitToContents();
+      seq_table_view_->viewport()->update();      
     }
-    if (sel.empty()) {
-      try {
-        ec->SetSelection(sel_v);        
-      } catch(...) {
+  }
+  event->accept();
+}
+
+void SequenceViewer::CopyEvent(QKeyEvent* event)
+{
+  QItemSelectionModel* model = seq_table_view_->selectionModel();
+  const QModelIndexList& list = model->selectedIndexes();
+  if(list.size()>0){
+    QString clipboard_string;
+    QSet<int> rows;
+    int min_col=model_->columnCount();
+    int max_col=0;
+    for(int i = 0; i < list.size(); i++){
+      if(list[i].column()>max_col){
+        max_col = list[i].column();
+      }
+      if(list[i].column()<min_col){
+        min_col = list[i].column();
       }
-      we_are_changing_the_selection_=false;      
-      return;
-    }   
-    for (SequenceItem::Selection::const_iterator j=sel.begin(),
-         e=sel.end(); j!=e; ++j) {
-      for (size_t k=j->Loc; k<j->End(); ++k) {
-        if (int(k)>seq.GetLength() || seq.GetOneLetterCode(k)=='-') {
-          continue;
+      rows.insert(list[i].row());
+    }
+
+    bool first_row = true;
+    for(int i = 1; i < model_->rowCount(); i++){
+      if(rows.contains(i)){
+        if(!first_row){
+          clipboard_string.append("\n");
         }
-        if (mol::ResidueView rv=seq.GetResidue(k)) {
-          sel_v.AddResidue(rv, mol::ViewAddFlag::INCLUDE_ATOMS);
+        for(int j=min_col; j<=max_col; j++){
+          const QModelIndex& index = model_->index(i,j);
+          if(model->isSelected(index)){
+            clipboard_string.append(model_->data(index,Qt::DisplayRole).toString());
+          }
+          else{
+            clipboard_string.append('-');
+          }
         }
+        first_row = false;
       }
     }
-    sel_v.AddAllInclusiveBonds();
-    try {
-      ec->SetSelection(sel_v);      
-    } catch(...) {
-    }
+    QApplication::clipboard()->setText(clipboard_string);
+  }
+  event->accept();
+}
 
+void SequenceViewer::FindInSequence()
+{
+  if(seq_search_bar_->isHidden()){
+    seq_search_bar_->show();
+  }
+  else{
+    seq_search_bar_->hide();
   }
-  we_are_changing_the_selection_=false;
 }
 
-void SequenceViewer::NodeRemoved(const gfx::GfxNodeP& node)
+void SequenceViewer::OnSearchBarUpdate(const QString& subject,
+                                           bool search_in_all, const QString& name)
 {
-  if (gfx::EntityP o=dyn_cast<gfx::Entity>(node)) {
-    SequenceItemList seq_items=this->SeqItemsForGfxObj(o);
-    for (SequenceItemList::iterator i=seq_items.begin(),
-     e=seq_items.end(); i!=e; ++i) {
-    SequenceItem* seq_item=*i;
-    this->RemoveSequence(seq_item);
-    delete seq_item;
-    }
+  seq_table_view_->selectionModel()->clear();
+  if(search_in_all){
+    const QModelIndexList& list = model_->GetModelIndexes(subject);
+    this->SelectList(list);
+  }
+  else{
+    const QModelIndexList& list = model_->GetModelIndexes(subject,name);
+    this->SelectList(list);
   }
 }
 
-void SequenceViewer::SelectionChanged(const gfx::GfxObjP& o, 
-                                      const mol::EntityView& view)
+void SequenceViewer::SelectList(const QModelIndexList& list)
 {
-  if (we_are_changing_the_selection_) {
-    return;
+  QItemSelectionModel* model = seq_table_view_->selectionModel();
+  QSet<int> rows_visited;
+  for(int i = 0; i<list.size(); i++){
+    int row =list[i].row();
+    if(!rows_visited.contains(row)){
+      model->select(list[i],QItemSelectionModel::Rows|QItemSelectionModel::Deselect);
+      rows_visited.insert(row);
+    }
   }
-  we_are_changing_the_selection_=true;
-  gfx::EntityP ec=dyn_cast<gfx::Entity>(o);
-  
+  for(int i = 0; i<list.size(); i++){
+    model->select(list[i],QItemSelectionModel::Select);
+  }
+}
 
-  std::vector<bool> selected_cols;
-  selected_cols.resize(this->GetLongestSequenceLength(), false);
+const QStringList& SequenceViewer::GetDisplayModes()
+{
+  return model_->GetDisplayModes();
+}
+const QStringList& SequenceViewer::GetDisplayModes(const seq::AlignmentHandle& alignment)
+{
+  return model_->GetDisplayModes(alignment);
+}
+const QStringList& SequenceViewer::GetDisplayModes(const gfx::EntityP& entity)
+{
+  return model_->GetDisplayModes(entity);
+}
 
-  // get affected sequence items
-  SequenceItemList seq_items=this->SeqItemsForGfxObj(o);
+const QString& SequenceViewer::GetCurrentDisplayMode()
+{
+  return model_->GetCurrentDisplayMode();
+}
+const QString& SequenceViewer::GetCurrentDisplayMode(const seq::AlignmentHandle& alignment)
+{
+  return model_->GetCurrentDisplayMode(alignment);
+}
+const QString& SequenceViewer::GetCurrentDisplayMode(const gfx::EntityP& entity)
+{
+  return model_->GetCurrentDisplayMode(entity);
+}
 
-  for (SequenceItemList::iterator i=seq_items.begin(), 
-       e=seq_items.end(); i!=e; ++i) {
-    SequenceItem* seq_item=*i;
+void SequenceViewer::ChangeDisplayMode(const QString& string)
+{
+  model_->SetDisplayMode(string);
+  seq_table_view_->viewport()->update();
+}
 
-    if(view.GetChainCount()==0){
-        this->SelectColumns(seq_item, selected_cols);
-    }
-    else
-    {
-    seq::SequenceHandle seq=seq_item->GetSequence();
-    mol::ChainView dst_chain=(seq.GetAttachedView().GetChainList())[0];
-    if (mol::ChainView src_chain=view.FindChain(dst_chain.GetName())) {
-        // for each residue in the selection deduce index in sequence
-        for (mol::ResidueViewList::const_iterator j=src_chain.GetResidueList().begin(),
-           e2=src_chain.GetResidueList().end(); j!=e2; ++j) {
-        mol::ResidueView dst_res=dst_chain.FindResidue(j->GetHandle());
-        assert(dst_res.IsValid());
-        int p=seq.GetPos(dst_res.GetIndex());
-        assert(p>=0 && p<=seq.GetLength());
-        selected_cols[p]=true;
-        }
-        this->SelectColumns(seq_item, selected_cols);
-        std::fill(selected_cols.begin(), selected_cols.end(), false);
-      }
-    }
-  }
-  we_are_changing_the_selection_=false;  
+void SequenceViewer::ChangeDisplayMode(const seq::AlignmentHandle& alignment, const QString& string)
+{
+  model_->SetDisplayMode(alignment, string);
+  seq_table_view_->viewport()->update();
+}
+
+void SequenceViewer::ChangeDisplayMode(const gfx::EntityP& entity, const QString& string)
+{
+  model_->SetDisplayMode(entity, string);
+  seq_table_view_->viewport()->update();
 }
 
-SequenceItemList SequenceViewer::SeqItemsForGfxObj(const gfx::GfxObjP& obj)
+ActionList SequenceViewer::GetActions()
 {
-  SequenceItemList seq_items;
-  gfx::EntityP ec=dyn_cast<gfx::Entity>(obj);
-  std::map<SequenceItem*, gfx::EntityP>::iterator i,e;
-  for (i=obj_map_.begin(), e=obj_map_.end(); i!=e; ++i) {
-    if (i->second==ec) {
-      seq_items.push_back(i->first);
+  return action_list_;
+}
+
+void SequenceViewer::DisplayMenu()
+{
+  QMenu* menu = new QMenu();
+  QList<QAction*> actions = display_mode_actions_->actions();
+  for(int i=0;i<actions.size();i++){
+    display_mode_actions_->removeAction(actions[i]);
+  }
+  const QStringList& display_modes = this->GetDisplayModes();
+  for(int i=0; i<display_modes.size(); i++){
+    QString ident(display_modes[i]);
+    QAction* action = new QAction(ident,menu);
+    action->setCheckable(true);
+    connect(action,SIGNAL(triggered(bool)),this,SLOT(ChangeDisplayMode()));
+    display_mode_actions_->addAction(action);
+    if(display_modes[i] == this->GetCurrentDisplayMode() ){
+      action->setChecked(true);
     }
+    menu->addAction(action);
   }
-  return seq_items;
+  menu->exec(QCursor::pos());
 }
 
-gfx::GfxObjP SequenceViewer::GfxObjForSeqItem(SequenceItem* item)
+void SequenceViewer::ChangeDisplayMode()
 {
-  std::map<SequenceItem*, gfx::EntityP>::iterator i=obj_map_.find(item);
-  return (i!=obj_map_.end()) ? i->second : gfx::EntityP();
+  QAction* action = display_mode_actions_->checkedAction();
+  if(action){
+    this->ChangeDisplayMode(action->text());
+  }
+}
+
+SequenceViewer::~SequenceViewer(){
+  gfx::Scene::Instance().DetachObserver(this);
 }
 
 }}
diff --git a/modules/gui/src/sequence_viewer/sequence_viewer.hh b/modules/gui/src/sequence_viewer/sequence_viewer.hh
index 0b5811dc1fb17fd7905501845b01a77d592d75c8..6a3c49efcabf852bf39a1bf47d6f503f75c2c5ea 100644
--- a/modules/gui/src/sequence_viewer/sequence_viewer.hh
+++ b/modules/gui/src/sequence_viewer/sequence_viewer.hh
@@ -16,45 +16,97 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#ifndef OST_SEQUENCE_VIEWER_HH
-#define OST_SEQUENCE_VIEWER_HH
+#ifndef OST_SEQUENCE_VIEWER_SEQUENCE_VIEWER
+#define OST_SEQUENCE_VIEWER_SEQUENCE_VIEWER
 
 /*
-  Author: Marco Biasini
+  Author: Stefan Scheuber
  */
 
-#include <map>
 
-#include <ost/gfx/scene_observer.hh>
-#include <ost/gui/sequence_viewer/sequence_viewer_base.hh>
-#include <ost/gfx/entity.hh>
+#include <ost/seq/alignment_handle.hh>
 
-namespace ost { namespace gui {
+#include <ost/gfx/scene.hh>
+#include <ost/gfx/gfx_object.hh>
+
+#include <ost/gui/widget.hh>
+
+#include <ost/gui/module_config.hh>
 
-class SequenceItem;
+#include "sequence_search_bar.hh"
+#include "sequence_model.hh"
+#include "sequence_table_view.hh"
 
-/// \brief sequence view
-class DLLEXPORT_OST_GUI SequenceViewer : public SequenceViewerBase, 
-                                         public gfx::SceneObserver {
+#include <QWidget>
+#include <QActionGroup>
+#include <QToolBar>
+namespace ost { namespace gui {
+
+/// \brief QTableView with first column not moving
+class DLLEXPORT_OST_GUI SequenceViewer : public Widget, public gfx::SceneObserver  {
   Q_OBJECT
 public:
-  SequenceViewer(QWidget* parent=NULL);
+  SequenceViewer(bool stand_alone=true, QWidget* parent=NULL);
   ~SequenceViewer();
-  
-  virtual void NodeAdded(const gfx::GfxNodeP& node);
-  
-  virtual void NodeRemoved(const gfx::GfxNodeP& node);
-  
-  virtual void SelectionChanged(const gfx::GfxObjP& obj, const mol::EntityView& sel);
+
+  virtual void SelectionChanged(const gfx::GfxObjP& o, const mol::EntityView& view);
+
+  virtual void AddEntity(const gfx::EntityP& entity);
+  virtual void RemoveEntity(const gfx::EntityP& entity);
+
+  virtual void AddAlignment(const seq::AlignmentHandle& alignment);
+  virtual void RemoveAlignment(const seq::AlignmentHandle& alignment);
+
+  virtual bool Restore(const QString&){return true;};
+  virtual bool Save(const QString&){return true;};
+
+  virtual const QStringList& GetDisplayModes();
+  virtual const QStringList& GetDisplayModes(const seq::AlignmentHandle& alignment);
+  virtual const QStringList& GetDisplayModes(const gfx::EntityP& entity);
+
+  virtual const QString& GetCurrentDisplayMode();
+  virtual const QString& GetCurrentDisplayMode(const seq::AlignmentHandle& alignment);
+  virtual const QString& GetCurrentDisplayMode(const gfx::EntityP& entity);
+
+  virtual ActionList GetActions();
+
 public slots:
-  void ItemSelectionChanged(SequenceItem* item);
+  void ChangeDisplayMode(const QString&);
+  void ChangeDisplayMode(const seq::AlignmentHandle&, const QString&);
+  void ChangeDisplayMode(const gfx::EntityP&, const QString&);
+  void DisplayMenu();
+  //internal
+  void OnSearchBarUpdate(const QString&, bool, const QString&);
+
 private:
-  SequenceItemList SeqItemsForGfxObj(const gfx::GfxObjP& obj);
-  gfx::GfxObjP GfxObjForSeqItem(SequenceItem* seq_item);  
-  std::map<SequenceItem*, gfx::EntityP>  obj_map_;
-  bool we_are_changing_the_selection_;
+  virtual void NodeAdded(const gfx::GfxNodeP& node);
+  virtual void NodeRemoved(const gfx::GfxNodeP& node);
+  void FitToContents();
+  void InitActions();
+  void InitView();
+  void InitSearchBar();
+  void InitMenuBar();
+  void UpdateSearchBar();
+  void SelectList(const QModelIndexList& list);
+  QToolBar* toolbar_;
+  SeqSearchBar* seq_search_bar_;
+  SequenceModel* model_;
+  SequenceTableView* seq_table_view_;
+
+  ActionList action_list_;
+
+  QActionGroup* display_mode_actions_;
+
+private slots:
+  void ChangeDisplayMode();
+  void FindInSequence();
+  void SelectionModelChanged(const QItemSelection&, const QItemSelection&);
+  void DoubleClicked(const QModelIndex& index);
+  void MouseWheelEvent(QWheelEvent* event);
+  void CopyEvent(QKeyEvent* event);
+
 };
- 
+
 }}
 
 #endif
diff --git a/modules/gui/src/sequence_viewer/sequence_viewer_base.cc b/modules/gui/src/sequence_viewer/sequence_viewer_base.cc
deleted file mode 100644
index 61cae9aac9015f3c3db6a27741a12c7f84da109a..0000000000000000000000000000000000000000
--- a/modules/gui/src/sequence_viewer/sequence_viewer_base.cc
+++ /dev/null
@@ -1,237 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#include "sequence_viewer_base.hh"
-#include "sequence_search_bar.hh"
-#include <QShortcut>
-#include <QVBoxLayout>
-#include <QPainter>
-
-namespace ost { namespace gui {
-
-SequenceViewerBase::SequenceViewerBase(QWidget* parent):
-  Widget(NULL, parent),  style_(DENSE), sel_mode_(ROW),
-  scene_(new SequenceScene(this)), search_bar_(new SequenceSearchBar(this)),
-  view_(new QGraphicsView(NULL, this))
-{
-  QVBoxLayout* l=new QVBoxLayout;
-  this->setLayout(l);
-  l->setMargin(0);
-  l->setSpacing(0);
-  view_->setScene(scene_);
-  l->addWidget(search_bar_, 0);  
-  l->addWidget(view_, 1);  
-  view_->setScene(scene_);
-  view_->setRenderHints(QPainter::Antialiasing|QPainter::TextAntialiasing);
-  view_->setViewportUpdateMode(QGraphicsView::FullViewportUpdate);  
-  QShortcut* shortcut=new QShortcut(QKeySequence(tr("Ctrl+F")), this);  
-  connect(shortcut, SIGNAL(activated()), this, SLOT(FindInSequence()));    
-  connect(search_bar_, SIGNAL(Changed(const QString&, bool, int)), this,
-          SLOT(OnSearchBarUpdate(const QString&, bool, int)));  
-  search_bar_->hide();
-  view_->setAlignment(Qt::AlignLeft|Qt::AlignTop);
-}
-
-namespace {
-  
-size_t update_select_state(seq::SequenceHandle seq, const String& subject,
-                           std::vector<bool>& sel_state)
-{
-  size_t pos=0;
-  size_t first=String::npos;
-  String seq_str=seq.GetString();
-  while ((pos=seq_str.find(subject, pos))!=String::npos) {
-    if (first==String::npos) {
-      first=pos;
-    }
-    std::fill_n(sel_state.begin()+pos, subject.length(), true);
-    pos+=subject.length();
-  }
-  return first;
-}
-
-
-void set_sel(std::vector<bool>& selected, SequenceItem* item)
-{
-  std::vector<bool>::iterator c=selected.begin();
-  item->ClearSelection();
-  while (c!=selected.end()) {
-    std::vector<bool>::iterator e=c;
-    while ((*(++e))==*c && e!=selected.end()) {}
-    if (*c) {
-      // this is really ugly!
-      item->BeginSelectionChange();      
-      item->Select(c-selected.begin(), e-selected.begin(), false);
-    }
-    c=e;
-  }
-  item->EndSelectionChange();
-}
-
-}
-
-void SequenceViewerBase::FindInSequence()
-{
-  if (scene_->GetSequences().empty()) {
-    return;
-  }
-  search_bar_->Show(scene_->GetSequences());
-}
-
-int SequenceViewerBase::GetLongestSequenceLength() const
-{
-  std::vector<SequenceItem*>::iterator i=scene_->GetSequences().begin(),
-                                       e=scene_->GetSequences().end();  
-  int longest=0;
-  for (; i!=e; ++i) {
-    longest=std::max(longest, (*i)->GetSequence().GetLength());
-  }
-  return longest;
-}
-
-void SequenceViewerBase::SelectColumns(std::vector<bool>& selected_cols)
-{
-  std::vector<SequenceItem*>::iterator i=scene_->GetSequences().begin(),
-                                       e=scene_->GetSequences().end();
-  for (; i!=e; ++i) {
-    set_sel(selected_cols, *i);
-  }
-}
-
-void SequenceViewerBase::SelectColumns(SequenceItem* seq_item,
-                                       std::vector<bool>& selected_cols)
-{
-  set_sel(selected_cols, seq_item);
-}
-
-void SequenceViewerBase::ClearSelection()
-{
-  std::vector<SequenceItem*>::iterator i=scene_->GetSequences().begin(),
-                                       e=scene_->GetSequences().end();
-  for (; i!=e; ++i) {
-    (*i)->ClearSelection();
-  }
-}
-
-void SequenceViewerBase::OnSearchBarUpdate(const QString& subject, 
-                                           bool search_in_all, int seq_id)
-{
-  String std_subj=subject.toStdString();
-  this->ClearSelection();  
-  if (scene_->GetSequences().empty() || (seq_id==-1 && !search_in_all)) {
-    return;
-  }  
-  if (subject.size()==0) {
-    return;
-  }  
-  
-  std::vector<bool> selected;
-  selected.resize(GetLongestSequenceLength(), false);
-  /// \todo implement selection for SelMode==COLUMN
-  std::pair<int, size_t> first(0, String::npos);
-  if (search_in_all) {
-    for (size_t i=0; i<scene_->GetSequences().size(); ++i) {
-      (scene_->GetSequences())[i]->ClearSelection();
-      seq::SequenceHandle s=(scene_->GetSequences())[i]->GetSequence();
-      size_t pos=update_select_state(s, std_subj, selected);
-      if (pos!=String::npos && first.second==String::npos) {
-        first.second=pos;
-        first.first=i;
-      }
-      if (sel_mode_==ROW) {
-        set_sel(selected, (scene_->GetSequences())[i]); 
-        std::fill_n(selected.begin(), selected.size(), false);        
-      }
-    }
-  } else {
-    first.first=seq_id;
-    SequenceItem* s=(scene_->GetSequences())[seq_id];
-    size_t pos=update_select_state(s->GetSequence(), std_subj, selected);
-    if (pos!=String::npos) {
-      first.second=pos;
-    }
-    if (sel_mode_==ROW) {
-      set_sel(selected, s);
-    }
-  } 
-  if (sel_mode_==COLUMN) {
-    this->SelectColumns(selected);
-  }
-  if (first.second!=String::npos) {
-    QRectF r=(scene_->GetSequences()[first.first]->GetCharBounds(first.second));
-
-    view_->ensureVisible(r);
-  }
-  scene_->update();
-}
-
-void SequenceViewerBase::SetDisplayStyle(Style style)
-{
-  style_=style;
-  for (std::vector<SequenceItem*>::iterator i=scene_->GetSequences().begin(),
-       e=scene_->GetSequences().end(); i!=e; ++i) {
-    (*i)->SetShowSecStructure(style_==LOOSE);
-  }
-  scene_->RepackSequences();
-}
-
-void SequenceViewerBase::SetSelMode(SelMode mode)
-{
-  sel_mode_=mode;
-}
-
-SequenceViewerBase::SelMode SequenceViewerBase::GetSelMode() const
-{
-  return sel_mode_;
-}
-
-SequenceViewerBase::Style SequenceViewerBase::GetDisplayStyle() const
-{
-  return style_;
-}
-
-void SequenceViewerBase::AddSequence(SequenceItem* seq)
-{
-  seq->SetShowSecStructure(style_==LOOSE);
-  scene_->AddSequence(seq);
-  QRectF rect=scene_->itemsBoundingRect();
-  view_->setSceneRect(QRectF(0, 0, +rect.left()+rect.width(), 
-                             rect.height()+rect.top()));
-}
-
-void SequenceViewerBase::RemoveSequence(SequenceItem* seq)
-{
-  scene_->RemoveSequence(seq);
-}
-
-void SequenceViewerBase::Clear()
-{
-
-}
-
-bool SequenceViewerBase::Restore(const QString& prefix)
-{
-  return true;
-}
-
-bool SequenceViewerBase::Save(const QString& prefix)
-{
-  return true;
-}
-
-}}
diff --git a/modules/gui/src/sequence_viewer/sequence_viewer_base.hh b/modules/gui/src/sequence_viewer/sequence_viewer_base.hh
deleted file mode 100644
index 6bc183765c54a9f3b3b4f20f33eb0a0cd20a6e73..0000000000000000000000000000000000000000
--- a/modules/gui/src/sequence_viewer/sequence_viewer_base.hh
+++ /dev/null
@@ -1,99 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef OST_GUI_SEQUENCE_VIEWER_BASE_HH
-#define OST_GUI_SEQUENCE_VIEWER_BASE_HH
-/*
-  Author: Marco Biasini
- */
-
-#include <ost/gui/sequence_viewer/sequence_item.hh>
-#include <ost/gui/sequence_viewer/sequence_scene.hh>
-
-#include <ost/gui/widget.hh>
-
-#include <QGraphicsView>
-
-namespace ost { namespace gui {
-
-class SequenceSearchBar;
-
-/// \brief base class for sequence viewers
-/// 
-/// subclassed by AlignmentViewer and SequenceViewer
-class DLLEXPORT_OST_GUI SequenceViewerBase : public Widget {
-  Q_OBJECT
-public:
-  typedef enum {
-    DENSE,
-    LOOSE,
-  } Style;
-  
-  typedef enum {
-    COLUMN,
-    ROW
-  } SelMode;
-public:
-  SequenceViewerBase(QWidget* parent=NULL);
-  void SetDisplayStyle(Style style);
-  
-  void SetSelMode(SelMode mode);
-  
-  SelMode GetSelMode() const;
-  Style GetDisplayStyle() const;
-  
-  /// \brief add sequence
-  /// 
-  /// issue: should we copy the sequence object to avoid weird side-effects?
-  void AddSequence(SequenceItem* seq);
-  
-  /// \brief remove sequence
-  void RemoveSequence(SequenceItem* seq);
-  
-  /// \brief select columns in all sequences
-  void SelectColumns(std::vector<bool>& selected_cols);
-  
-  /// \brief select columns in sequence
-  void SelectColumns(SequenceItem* seq, std::vector<bool>& selected_cols);
-  /// \brief get length of longest sequence including gaps
-  int GetLongestSequenceLength() const;
-  /// \brief remove all sequences
-  void Clear();
-
-  virtual bool Restore(const QString& prefix);
-  virtual bool Save(const QString& prefix);
-public slots:
-  /// \brief clear selection
-  void ClearSelection();
-  
-  /// \internal
-  void OnSearchBarUpdate(const QString&, bool, int);
-  
-  /// \brief show sequence search bar
-  void FindInSequence();
-
-private:
-  Style               style_;  
-  SelMode             sel_mode_;
-  SequenceScene*      scene_;
-  SequenceSearchBar*  search_bar_;  
-  QGraphicsView*      view_;
-};
-
-}}
-#endif
diff --git a/modules/gui/src/sequence/tick_painter.cc b/modules/gui/src/sequence_viewer/tick_painter.cc
similarity index 100%
rename from modules/gui/src/sequence/tick_painter.cc
rename to modules/gui/src/sequence_viewer/tick_painter.cc
diff --git a/modules/gui/src/sequence/tick_painter.hh b/modules/gui/src/sequence_viewer/tick_painter.hh
similarity index 100%
rename from modules/gui/src/sequence/tick_painter.hh
rename to modules/gui/src/sequence_viewer/tick_painter.hh
index d5c6c4fff05c68214c3f012b26b046f29bbfeedd..11ff679bb183e91fa8cb92ffa08176c8ca2f418d 100644
--- a/modules/gui/src/sequence/tick_painter.hh
+++ b/modules/gui/src/sequence_viewer/tick_painter.hh
@@ -23,9 +23,9 @@
   Author: Stefan Scheuber
  */
 
-#include <QObject>
 
 #include "painter.hh"
+#include <QObject>
 
 namespace ost { namespace gui {
 
diff --git a/modules/gui/src/sequence/title_row.cc b/modules/gui/src/sequence_viewer/title_row.cc
similarity index 89%
rename from modules/gui/src/sequence/title_row.cc
rename to modules/gui/src/sequence_viewer/title_row.cc
index 39013b3d7fda9a5df35d377ed3411220c24e2800..b8b05fbcaaa9089b7b73727ffe4dfc59b68bbda0 100644
--- a/modules/gui/src/sequence/title_row.cc
+++ b/modules/gui/src/sequence_viewer/title_row.cc
@@ -22,11 +22,11 @@
  */
 
 
-#include <QtGui>
 
 #include "sequence_model.hh"
 #include "title_row.hh"
 
+#include <QtGui>
 namespace ost { namespace gui {
 
 TitleRow::TitleRow(QObject* parent) : BaseRow(QFont("Courier",10),parent), font_("Verdana",9), small_font_("Verdana",7)
@@ -77,10 +77,11 @@ Qt::ItemFlags TitleRow::Flags(int column) const
 void TitleRow::DoubleClicked(int column)
 {
  if(this->parent()){
-   SequenceModel* model = qobject_cast<SequenceModel*>(this->parent()->parent());
-   int rows = model->rowCount()-1;
-   QItemSelection add = QItemSelection(model->index(1,column),model->index(rows,column));
-   model->SelectionChanged(add,QItemSelection());
+   if(SequenceModel* model = qobject_cast<SequenceModel*>(this->parent()->parent())){
+     int rows = model->rowCount()-1;
+     QItemSelection add = QItemSelection(model->index(1,column),model->index(rows,column));
+     model->SelectionChanged(add,QItemSelection());
+   }
  }
 }
 
diff --git a/modules/gui/src/sequence/title_row.hh b/modules/gui/src/sequence_viewer/title_row.hh
similarity index 100%
rename from modules/gui/src/sequence/title_row.hh
rename to modules/gui/src/sequence_viewer/title_row.hh
index 6274d3c13dd322ef63a1c7ce87253d2bb4776b5e..409d62e5033fd46bcb313061541e3fa191dd0957 100644
--- a/modules/gui/src/sequence/title_row.hh
+++ b/modules/gui/src/sequence_viewer/title_row.hh
@@ -23,9 +23,9 @@
   Author: Stefan Scheuber
  */
 
-#include <QObject>
 
 #include "base_row.hh"
+#include <QObject>
 
 namespace ost { namespace gui {
 
diff --git a/modules/gui/src/test_code.cc b/modules/gui/src/test_code.cc
deleted file mode 100644
index ac01ef1a1542b3a17c4a321941807cd15c95cb01..0000000000000000000000000000000000000000
--- a/modules/gui/src/test_code.cc
+++ /dev/null
@@ -1,71 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#include <cstdlib>
-
-#include "test_code.hh"
-
-#include <ost/log.hh>
-#include <ost/entity.hh>
-#include <ost/gfx/scene.hh>
-#include <ost/gfx/entity_connect.hh>
-
-using namespace ost;
-using namespace ost::gfx;
-
-namespace {
-
-mol::EntityHandle build_entity()
-{
-  mol::EntityHandle e = CreateEntity();
-
-  mol::ChainHandle chain = e.InsertChain("");
-
-  mol::ResidueHandle res = chain.AppendResidue("");
-
-  mol::AtomHandle a0 = res.InsertAtom("X",geom::Vec3(0.0,0.0,0.0));
-  mol::AtomHandle a1 = res.InsertAtom("X",geom::Vec3(0.0,0.0,10.0));
-  mol::AtomHandle a2 = res.InsertAtom("X",geom::Vec3(10.0,0.0,10.0));
-  mol::AtomHandle a3 = res.InsertAtom("X",geom::Vec3(10.0,-10.0,10.0));
-  mol::AtomHandle a4 = res.InsertAtom("X",geom::Vec3(10.0,0.0,10.0));
-  mol::AtomHandle a5 = res.InsertAtom("X",geom::Vec3(10.0,0.0,20.0));
-  //mol::AtomHandle a6 = res.InsertAtom(geom::Vec3(10.0,-10.0,20.0));
-  //mol::AtomHandle a7 = res.InsertAtom(geom::Vec3(20.0,0.0,20.0));
-  e.Connect(a0,a1);
-  e.Connect(a1,a2);
-  e.Connect(a2,a3);
-  e.Connect(a1,a4);
-  e.Connect(a2,a5);
-  //e.Connect(a5,a6);
-  //e.Connect(a5,a7);
-
-  e.RebuildICS();
-
-  return e;
-}
-
-} // anon ns
-
-void test_code()
-{
-  mol::EntityHandle eh = build_entity();
-
-  GfxObjP go (new EntityConnect("test",eh));
-  Scene::Instance().Add(go);
-  Scene::Instance().SetCenter(go->GetCenter());
-}
diff --git a/modules/gui/src/test_code.hh b/modules/gui/src/test_code.hh
deleted file mode 100644
index 0cd9a36b0b2c740e7488f013c92ba8ab01aad9a3..0000000000000000000000000000000000000000
--- a/modules/gui/src/test_code.hh
+++ /dev/null
@@ -1,24 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef OST_TEST_CODE_HH
-#define OST_TEST_CODE_HH
-
-void test_code();
-
-#endif
diff --git a/modules/gui/src/thin_splitter.cc b/modules/gui/src/thin_splitter.cc
index 78051b1f99421758c058de5dfaf757774044ef62..aed72b937e8b11a0dde1b48ad31d0ded48a252ea 100644
--- a/modules/gui/src/thin_splitter.cc
+++ b/modules/gui/src/thin_splitter.cc
@@ -16,6 +16,9 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
+
+#include "thin_splitter.hh"
+
 #include <QRegion>
 #include <QPainter>
 #include <QResizeEvent>
@@ -23,9 +26,6 @@
 #include <QSplitterHandle>
 #include <QApplication>
 #include <QPalette>
-
-#include "thin_splitter.hh"
-
 /*
    Author: Marco Biasini
  */
@@ -47,9 +47,17 @@ public:
   virtual void resizeEvent(QResizeEvent *event)
   {
     if (this->orientation()==Qt::Horizontal) {
+#if defined(__APPLE__)
+      this->setContentsMargins(1, 0, 0, 0);
+#else
       this->setContentsMargins(1, 0, 1, 0);
+#endif
     } else {
+#if defined(__APPLE__)
+      this->setContentsMargins(0, 1, 0, 0);
+#else                          
       this->setContentsMargins(0, 1, 0, 1);
+#endif
     }
     this->setMask(QRegion());
   }
@@ -58,8 +66,8 @@ public:
   {
     QPainter p(this);
     QPalette palette=qApp->palette();
-    p.setBrush(QBrush(palette.color(QPalette::Active, QPalette::Shadow)));
-    p.setPen(Qt::black);
+    p.setBrush(QBrush(QColor(120,120,120)));
+    p.setPen(QColor(120,120,120));
     p.drawRect(this->contentsRect());
   }
 };
diff --git a/modules/gui/src/tools/manipulator.cc b/modules/gui/src/tools/manipulator.cc
index ac50e4dd20db637ae8d5851e615291244e7514be..29fe8b703e6710f025f0ae6cfe83b3c389686819 100644
--- a/modules/gui/src/tools/manipulator.cc
+++ b/modules/gui/src/tools/manipulator.cc
@@ -16,7 +16,7 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#include <QDir>
+#include <ost/gui/gosty_app.hh>
 
 #include <ost/platform.hh>
 
@@ -24,11 +24,11 @@
 #include <ost/gfx/gfx_object.hh>
 #include <ost/gfx/gfx_node.hh>
 
-#include <ost/gui/gosty_app.hh>
 #include <ost/gui/scene_selection.hh>
 
 #include "manipulator.hh"
 
+#include <QDir>
 namespace ost { namespace gui {
 
 Manipulator::Manipulator():
diff --git a/modules/gui/src/tools/manipulator.hh b/modules/gui/src/tools/manipulator.hh
index 2fb4cbbe4c209f29a3a6c25605d890f68ef3811e..2affc6628e104c971f8b9b749edf894ef510973c 100644
--- a/modules/gui/src/tools/manipulator.hh
+++ b/modules/gui/src/tools/manipulator.hh
@@ -22,13 +22,14 @@
 /*
   Author: Marco Biasini
  */
-#include <QList>
 
 #include <ost/gui/module_config.hh>
 #include <ost/gfx/input.hh>
 
 #include <ost/gui/tools/tool.hh>
 
+#include <QList>
+
 namespace ost { namespace gui {
 
 class Manipulator;
diff --git a/modules/gui/src/tools/map_tool.cc b/modules/gui/src/tools/map_tool.cc
index 58b67d3e77ccb474fa129663ac7515ce29272bc7..ef2a784412153df6b475a8a74404ae0f99ee4aff 100644
--- a/modules/gui/src/tools/map_tool.cc
+++ b/modules/gui/src/tools/map_tool.cc
@@ -16,17 +16,17 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#include <QDir>
 
+#include <ost/gui/gosty_app.hh>
 #include <ost/platform.hh>
 #include <ost/gfx/map_iso.hh>
 #include <ost/gfx/map_slab.hh>
 #include <ost/gfx/scene.hh>
 
 #include <ost/gui/scene_selection.hh>
-#include <ost/gui/gosty_app.hh>
 #include "map_tool.hh"
 
+#include <QDir>
 namespace ost { namespace gui {
 
 MapTool::MapTool():
diff --git a/modules/gui/src/tools/map_tool.hh b/modules/gui/src/tools/map_tool.hh
index 2d1257cb81dd029518207cd137aa7f0be25d2ed5..35547b51525f85ec4d89532c480979b09b413f20 100644
--- a/modules/gui/src/tools/map_tool.hh
+++ b/modules/gui/src/tools/map_tool.hh
@@ -22,10 +22,10 @@
 /*
   Author: Ansgar Philippsen
 */
-#include <QList>
 
 #include <ost/gui/tools/tool.hh>
 
+#include <QList>
 namespace ost { namespace gui {
 
 class DLLEXPORT_OST_GUI MapTool : public Tool {
diff --git a/modules/gui/src/tools/measure_tool.cc b/modules/gui/src/tools/measure_tool.cc
index ac8c2951478fa3c4ad59002cfac65066d8c4c8bf..4247e2f830d7f859a03666693c522e530cfc88ae 100644
--- a/modules/gui/src/tools/measure_tool.cc
+++ b/modules/gui/src/tools/measure_tool.cc
@@ -27,7 +27,6 @@
 #include <iostream>
 #include <sstream>
 
-#include <QDir>
 
 #include <ost/platform.hh>
 #include <ost/gfx/scene.hh>
@@ -36,6 +35,7 @@
 
 #include <ost/geom/vec3.hh>
 
+#include <QDir>
 namespace ost { namespace gui {
 
 MeasureTool::MeasureTool()
diff --git a/modules/gui/src/tools/measure_tool.hh b/modules/gui/src/tools/measure_tool.hh
index 77b5f627f117ec072404837e49b6267a4c5fb5a8..d1eedcef7c44652865c6de1c10c42771b4eaa79c 100644
--- a/modules/gui/src/tools/measure_tool.hh
+++ b/modules/gui/src/tools/measure_tool.hh
@@ -22,12 +22,12 @@
 /*
   Author: Tobias Schmidt
  */
-#include <QList>
 
 #include <ost/gui/tools/tool.hh>
 #include <ost/mol/atom_handle.hh>
 #include <ost/gfx/color.hh>
 
+#include <QList>
 namespace ost { namespace gui {
 
 class DLLEXPORT_OST_GUI Measurement {
diff --git a/modules/gui/src/tools/mouse_event.hh b/modules/gui/src/tools/mouse_event.hh
index 28f1e04450215344ea7abcd1326d8b3785360e87..234ee6d4ce63b333b17ac940f5f38108716404db 100644
--- a/modules/gui/src/tools/mouse_event.hh
+++ b/modules/gui/src/tools/mouse_event.hh
@@ -34,7 +34,7 @@ public:
   typedef enum {
     LeftButton=Qt::LeftButton,
     RightButton=Qt::RightButton,
-    MiddleButton=Qt::MidButton,
+    MiddleButton=Qt::MidButton
   } Button;
   typedef int Buttons;
 public:
diff --git a/modules/gui/src/tools/selection_tool.cc b/modules/gui/src/tools/selection_tool.cc
index 047577a62fa5adb03df4e795877aa6071f215097..dfc45ca8f0aa55cc979336f8a54c0d9cbaf42730 100644
--- a/modules/gui/src/tools/selection_tool.cc
+++ b/modules/gui/src/tools/selection_tool.cc
@@ -21,13 +21,13 @@
  */
 #include "selection_tool.hh"
 
-#include <QDir>
 
 #include <ost/platform.hh>
 #include <ost/gfx/scene.hh>
 
 #include <ost/gui/gl_canvas.hh>
 
+#include <QDir>
 namespace ost { namespace gui {
 
 SelectionTool::SelectionTool()
diff --git a/modules/gui/src/tools/selection_tool.hh b/modules/gui/src/tools/selection_tool.hh
index d805ced221a8b663f8c16ef7e6371e774d68aea2..a02102fdb55924d6f40a64e784a6a2a121378657 100644
--- a/modules/gui/src/tools/selection_tool.hh
+++ b/modules/gui/src/tools/selection_tool.hh
@@ -22,10 +22,10 @@
 /*
   Author: Marco Biasini
  */
-#include <QList>
 
 #include <ost/gui/tools/tool.hh>
 
+#include <QList>
 
 namespace ost { namespace gui {
 
diff --git a/modules/gui/src/tools/tool.hh b/modules/gui/src/tools/tool.hh
index 24f4536901c87d6c08e2738c85c2d46e5b520f66..0be85bc7daaa514f2d0965095c13919ac1fc0a82 100644
--- a/modules/gui/src/tools/tool.hh
+++ b/modules/gui/src/tools/tool.hh
@@ -24,13 +24,14 @@
  */
 #include <vector>
 
-#include <QIcon>
 
 #include <ost/gui/module_config.hh>
 #include <ost/gfx/gfx_node.hh>
 #include <ost/gui/tools/mouse_event.hh>
 #include <ost/gui/tools/tool_options.hh>
 
+#include <QIcon>
+
 namespace ost { namespace gui {
 
 class ToolOptions;
diff --git a/modules/gui/src/tools/tool_bar.cc b/modules/gui/src/tools/tool_bar.cc
index 11621af0f4f07980bf0be1755bbbd54cb7009dd5..e4babc0ed2b85be84a2113f3f30a127a74e35bc8 100644
--- a/modules/gui/src/tools/tool_bar.cc
+++ b/modules/gui/src/tools/tool_bar.cc
@@ -16,15 +16,15 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#include <QAction>
-#include <QDebug>
-#include <QActionGroup>
 
+#include <ost/gui/gosty_app.hh>
 #include <ost/mol/query_view_wrapper.hh>
 #include <ost/gui/tools/tool_manager.hh>
-#include <ost/gui/gosty_app.hh>
 #include "tool_bar.hh"
 
+#include <QAction>
+#include <QDebug>
+#include <QActionGroup>
 namespace ost { namespace gui {
 
 ToolBar::ToolBar(QWidget* parent):
diff --git a/modules/gui/src/tools/tool_bar.hh b/modules/gui/src/tools/tool_bar.hh
index 1e95d5bbf4f27c0c6fa808bf862a6c36a05aaded..f58594cc5b899436ed92e811d6cc161b8274025b 100644
--- a/modules/gui/src/tools/tool_bar.hh
+++ b/modules/gui/src/tools/tool_bar.hh
@@ -23,13 +23,13 @@
   Author: Marco Biasini
  */
 
-#include <QToolBar>
-#include <QList>
 
 #include <ost/gfx/gfx_node.hh>
 #include <ost/gui/module_config.hh>
 #include <ost/gui/tools/tool.hh>
 
+#include <QToolBar>
+#include <QList>
 
 class QActionGroup;
 
diff --git a/modules/gui/src/tools/tool_manager.hh b/modules/gui/src/tools/tool_manager.hh
index 5fa48b05e0a619f7e6a4d4fd56486b46a146546d..d571f00151995a7e10ed5f86cb51ee5e8170803e 100644
--- a/modules/gui/src/tools/tool_manager.hh
+++ b/modules/gui/src/tools/tool_manager.hh
@@ -20,10 +20,10 @@
 #define OST_GUI_TOOL_MANAGER_HH
 
 #include <ost/gui/module_config.hh>
-#include <QObject>
 
 #include <ost/gui/tools/tool.hh>
 
+#include <QObject>
 /*
   Author: Marco Biasini
  */
diff --git a/modules/gui/src/tools/tool_option.cc b/modules/gui/src/tools/tool_option.cc
index d29197f26c27101f89e6a6022c0d5453e249dbb0..699a4e60d6f5f939dc1862c70b65a26b60e49f86 100644
--- a/modules/gui/src/tools/tool_option.cc
+++ b/modules/gui/src/tools/tool_option.cc
@@ -20,8 +20,8 @@
 
 namespace ost { namespace gui {
 
-template class DLLEXPORT_OST_GUI ToolOptionNum<int,ToolOption::INT>;
-template class DLLEXPORT_OST_GUI ToolOptionNum<float,ToolOption::FLOAT>;
+template class TEMPLATE_DEF_EXPORT ToolOptionNum<int,ToolOption::INT>;
+template class TEMPLATE_DEF_EXPORT ToolOptionNum<float,ToolOption::FLOAT>;
 
 ToolOption::ToolOption(const String& key, const String& verbose_name, 
                        Type type):
diff --git a/modules/gui/src/tools/tool_option.hh b/modules/gui/src/tools/tool_option.hh
index ac75253517cf1ac3381f76ab817086e282bca03e..ff08fad0df6dd5dcfe84e4ea39135d3de1927531 100644
--- a/modules/gui/src/tools/tool_option.hh
+++ b/modules/gui/src/tools/tool_option.hh
@@ -26,9 +26,10 @@
 #include <limits>
 #include <vector>
 
-#include <QObject>
 
 #include <ost/gui/module_config.hh>
+#include <QObject>
+
 
 namespace ost { namespace gui {
 
@@ -54,7 +55,7 @@ private:
 
 
 template <typename T, ToolOption::Type C>
-class DLLEXPORT_OST_GUI ToolOptionNum : public ToolOption {
+class DLLEXPORT ToolOptionNum : public ToolOption {
 public:
   ToolOptionNum(const String& key, const String& verbose_name, T default_v, 
                 T min_value=std::numeric_limits<T>::min(),
@@ -87,11 +88,14 @@ private:
 typedef ToolOptionNum<int, ToolOption::INT> ToolOptionInt;
 typedef ToolOptionNum<float, ToolOption::FLOAT> ToolOptionFloat;
 
-#ifndef _MSC_VER
-extern template class ToolOptionNum<int,ToolOption::INT>;
-extern template class ToolOptionNum<float,ToolOption::FLOAT>;
+
+#if !defined(_MSC_VER)
+  extern template class ToolOptionNum<int,ToolOption::INT>;
+  extern template class ToolOptionNum<float,ToolOption::FLOAT>;
 #endif
 
+
+
 class DLLEXPORT_OST_GUI ToolOptionEnum : public ToolOption {
 public:
   struct Tuple {
diff --git a/modules/gui/src/tools/tool_option_group.hh b/modules/gui/src/tools/tool_option_group.hh
index 6b47d0ed6ea46f20e368d328a0c52dfdd3292984..ead9a57e3bdde25cb17ed698f5f996fba3931afe 100644
--- a/modules/gui/src/tools/tool_option_group.hh
+++ b/modules/gui/src/tools/tool_option_group.hh
@@ -23,11 +23,11 @@
   Author: Marco Biasini
  */
 
-#include <QObject>
 
 #include <ost/gui/module_config.hh>
 #include <ost/gui/tools/tool_option.hh>
 
+#include <QObject>
 namespace ost { namespace gui {
 
 
diff --git a/modules/gui/src/tools/tool_options.hh b/modules/gui/src/tools/tool_options.hh
index fd7d20d2c7841cf78e31df57b481be0cde760ae8..f4c9adeda925bbd66ab6b01a907ef0232f852689 100644
--- a/modules/gui/src/tools/tool_options.hh
+++ b/modules/gui/src/tools/tool_options.hh
@@ -23,11 +23,11 @@
   Author: Marco Biasini
  */
  
-#include <QObject>
 
 #include <ost/gui/module_config.hh>
 #include <ost/gui/tools/tool_option_group.hh>
 
+#include <QObject>
 namespace ost { namespace gui {
 
 
diff --git a/modules/gui/src/tools/tool_options_win.cc b/modules/gui/src/tools/tool_options_win.cc
index ecc1c1e4087154e71ab8e1d307faa5ac2b5607f6..56b2f551df416f841882869a75c8ba0edec790ed 100644
--- a/modules/gui/src/tools/tool_options_win.cc
+++ b/modules/gui/src/tools/tool_options_win.cc
@@ -16,14 +16,14 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#include <QVBoxLayout>
 
+#include <ost/gui/gosty_app.hh>
 #include <ost/gui/tools/tool_options_win.hh>
 #include <ost/gui/widget_registry.hh>
 #include <ost/gui/tools/tool_options_widget.hh>
 #include <ost/gui/tools/tool_manager.hh>
-#include <ost/gui/gosty_app.hh>
 
+#include <QVBoxLayout>
 namespace ost { namespace gui {
 
 
diff --git a/modules/gui/src/tools/tool_options_win.hh b/modules/gui/src/tools/tool_options_win.hh
index 08347ac994cfef1ff0cf0fc348cfe37e2c967e4e..9c1d7900c89d5d37fc435d2b88fceb0cb8e18f72 100644
--- a/modules/gui/src/tools/tool_options_win.hh
+++ b/modules/gui/src/tools/tool_options_win.hh
@@ -21,13 +21,13 @@
 
 #include <map>
 
-#include <QStackedWidget>
  
 #include <ost/gui/module_config.hh>
 
 #include <ost/gui/tools/tool.hh>
 #include <ost/gui/widget.hh>
 
+#include <QStackedWidget>
 
 /*
   Author: Marco Biasini
diff --git a/modules/gui/src/widget.hh b/modules/gui/src/widget.hh
index f8bdbd7767e90a01cf6f0100a5bf7d626b0581e7..45252b0475925e5e038a4d1a1d4f143adfc0c0fb 100644
--- a/modules/gui/src/widget.hh
+++ b/modules/gui/src/widget.hh
@@ -19,11 +19,11 @@
 #ifndef OST_GUI_WIDGET_HH
 #define OST_GUI_WIDGET_HH
 
-#include <QWidget>
-#include <QMetaType>
 
 #include <ost/gui/module_config.hh>
 
+#include <QWidget>
+#include <QMetaType>
 /*
   Author: Marco Biasini
  */
@@ -56,11 +56,26 @@ public:
   QWidget* GetInternalWidget();
   void SetInternalWidget(QWidget* widget);
   
+  
+  const QString& GetUniqueID() const
+  {
+    if (unique_id_.size()==0) {
+      unique_id_=this->metaObject()->className();
+    }
+    return unique_id_;
+  }
+  
+  void SetUniqueID(const QString& id)
+  {
+    unique_id_=id;
+  }
+  
   virtual bool Restore(const QString& prefix)=0;
   
   virtual bool Save(const QString& prefix)=0;
   
 private:
+  mutable QString  unique_id_;
   QWidget* internal_;
   bool     destroy_on_close_;
 };
diff --git a/modules/gui/src/widget_geom_handler.cc b/modules/gui/src/widget_geom_handler.cc
index 6b9914157b5317033815f605b8aeed12fbe9973b..aa2acd8d9e9a371cba22b83d5cdf0d5f8f8783ca 100644
--- a/modules/gui/src/widget_geom_handler.cc
+++ b/modules/gui/src/widget_geom_handler.cc
@@ -16,10 +16,10 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#include <QSettings>
 #include <iostream>
 #include "widget_geom_handler.hh"
 
+#include <QSettings>
 namespace ost { namespace gui {
 
 WidgetGeomHandler::WidgetGeomHandler(const QString& name, QWidget* widget, QWidget* parent)
diff --git a/modules/gui/src/widget_geom_handler.hh b/modules/gui/src/widget_geom_handler.hh
index 070a7ae7fa57c651380f0196895dc22fbadb2d41..164719ba4ae35222ceb4b60992a8465d7deed7bc 100644
--- a/modules/gui/src/widget_geom_handler.hh
+++ b/modules/gui/src/widget_geom_handler.hh
@@ -19,10 +19,10 @@
 #ifndef OST_GUI_WIDGET_GEOM_HANDLER_HH
 #define OST_GUI_WIDGET_GEOM_HANDLER_HH
 
-#include <QWidget>
 
 #include <ost/gui/module_config.hh>
 
+#include <QWidget>
 namespace ost { namespace gui {
 
 class DLLEXPORT_OST_GUI WidgetGeomHandler: public QObject{
diff --git a/modules/gui/src/widget_pool.hh b/modules/gui/src/widget_pool.hh
index 7555a2116318202d38001f8e385d6baed3312061..8a938c63506a94db3200a753ce39a3d01ead03a0 100644
--- a/modules/gui/src/widget_pool.hh
+++ b/modules/gui/src/widget_pool.hh
@@ -19,8 +19,8 @@
 #ifndef OST_GUI_WIDGET_POOL_HH
 #define OST_GUI_WIDGET_POOL_HH
 
-#include <QSettings>
 #include <ost/gui/widget.hh>
+#include <QSettings>
 /*
   Author: Marco Biasini, Stefan Scheuber
  */
diff --git a/modules/gui/src/widget_registry.cc b/modules/gui/src/widget_registry.cc
index d528f701d694a41cf5c3a6a6f79cab6b5177de89..965545f127358b4c88dce4ddcf044f5eb433b9e0 100644
--- a/modules/gui/src/widget_registry.cc
+++ b/modules/gui/src/widget_registry.cc
@@ -16,10 +16,10 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#include <QDebug>
 
 #include "widget_registry.hh"
 
+#include <QDebug>
 namespace ost { namespace gui {
   
 
diff --git a/modules/gui/src/xpm/angle_transform.svg b/modules/gui/src/xpm/angle_transform.svg
deleted file mode 100644
index b6298dec768698e96ce75e1a53e6d1673ef18e63..0000000000000000000000000000000000000000
--- a/modules/gui/src/xpm/angle_transform.svg
+++ /dev/null
@@ -1,167 +0,0 @@
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-   sodipodi:version="0.32"
-   inkscape:version="0.42.2"
-   sodipodi:docbase="/home/ansgar/projects/dng/modules/gui/src/xpm"
-   sodipodi:docname="angle_transform.svg"
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diff --git a/modules/gui/src/xpm/angle_transform.xpm b/modules/gui/src/xpm/angle_transform.xpm
deleted file mode 100644
index 4acf8c79989c8cbaafa0cd3e629f2af0d802257b..0000000000000000000000000000000000000000
--- a/modules/gui/src/xpm/angle_transform.xpm
+++ /dev/null
@@ -1,289 +0,0 @@
-/* XPM */
-static const char * angle_transform_xpm[] = {
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diff --git a/modules/gui/src/xpm/ost_small.xpm b/modules/gui/src/xpm/ost_small.xpm
deleted file mode 100644
index 3a9e8ea213534c7d96046533d68442431199db51..0000000000000000000000000000000000000000
--- a/modules/gui/src/xpm/ost_small.xpm
+++ /dev/null
@@ -1,370 +0,0 @@
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index 4e91390c5834c446c0741a42868f1112838fd5ea..0000000000000000000000000000000000000000
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-". . . . . . . . . . . . . ( _ : < [ } | . . . . 1 ^ ^ 2 3 . . . ",
-". . . . . . . . . . . . . 4 5 6 . 7 8 9 . . . 0 a b ^ c . . . . ",
-". . . . . . . . . . . . . d e 6 . . f g . . . h i j k l . . . . ",
-". . . . . . . . . . . . . m n o . . p q < . . r s t u v . . . . ",
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-". . . . . . . . . . . . . F G . . . | ! H . I J K L M . . . . . ",
-". . . . . . . . . . . . . N . . . . @ O P Q R S T U . . . . . . ",
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-". . . . . . M.N.O.P.Q.. . R.S.. . . T.q U.. . . . . . . . . . . ",
-". . . . . V.^ ^ N.W.. . . X.q Y.. . Z.`.. . . . . . . . . . . . ",
-". . . . .  +^ ^ .+C.. . . ++! @+. o } #+. . . . . . . . . . . . ",
-". . . . .  +^ ^ $+. . . . . %+: &+*+8 =+. . . . . . . . . . . . ",
-". . . . . -+;+>+. . . . . . ,+' ) ! d . . . . . . . . . . . . . ",
-". . . . . . . . . . . . . . . '+$ )+& . . . . . . . . . . . . . ",
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deleted file mode 100644
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diff --git a/modules/img/alg/doc/alg.rst b/modules/img/alg/doc/alg.rst
new file mode 100644
index 0000000000000000000000000000000000000000..e9f5fb0f2b0d8f6bc43a509989365d5ad2ce108c
--- /dev/null
+++ b/modules/img/alg/doc/alg.rst
@@ -0,0 +1,499 @@
+:mod:`img.alg <ost.img.alg>` - Image Processing Algorithms
+================================================================================
+
+.. module:: ost.img.alg
+  :synopsis: Image processing algorithms
+  
+Applying algorithms
+-------------------
+
+While image properties are usually manipulated using method of the 
+:class:`~ost.img.ImageHandle` class, their data content is manipulated using 
+image algorithms. Image algorithms are objects. Each of them is a class, and its 
+methods are used to handle the algorithm parameters. Applying an algorithm to an 
+image is then conceptually a two-step process. First, an instance of an 
+algorithm class is created, yielding an algorithm object. In a second step, the 
+algorithm object is applied to an image. An algorithm can be applied in-place 
+(using the :meth:`~ost.img.ImageHandle.Apply` method), modifying the image, or 
+out-of-place, (using :meth:`~ost.img.ImageHandle.ApplyIP` ), leaving the original image 
+untouched, and returning the result as a new image. 
+
+Here is an example. All the algorithms used in the following are described in the :ref:`algorithms` section.
+
+.. code-block:: python
+ 
+  # creates an algorithm object
+  rand_alg = img.alg.Randomize() 
+  # applies algorithm object in place, overwriting the image
+  im.ApplyIP( rand_alg )
+
+Sometimes, there is no need to create a permanent instance of an algorithm 
+object. A temporary object enough:
+
+.. code-block:: python
+
+  # applies temporary algorithm object in-place
+  im.ApplyIP( img.alg.GaussianFilter(4.0) )
+
+When used this way, the algorithm class will cease to exist as soon as the 
+algorithm is applied. However, some algorithm are stateful and store 
+information. One good example is the :class:`Stat` algorithm, which does not
+modify the image when applied, but change its internal state to store 
+information extracted from the image, which can be recovered later. For example:
+
+.. code-block:: python
+
+  # creates and applies an algorithm object
+  stat=img.alg.Stat()
+  im.ApplyIP(stat)
+  # extracts information from the algorithm
+  mean=stat.GetMean()
+
+It is important to remember that when the algorithms ceases to exist, all information it stores is lost.
+
+Fourier Transforming Images
+----------------------------
+
+An image can be Fourier-transformed using either the :class:`FFT` algorithm or 
+the :class:`DFT` algorithm. The difference between the two is that the 
+:class:`DFT` algorithm honors the :ref:`spatial-origin` of the image, and 
+applies the corresponding phase shift in Fourier space. The :class:`FFT` does 
+not follow this behavior. 
+
+.. code-block:: python
+
+  # create an instance of the Dft algorithm object
+  dft=img.alg.DFT() 
+  # do the actual Fourier transformation
+  im_ft=im.Apply(dft) 
+  # back-transform
+  im2 = im_ft.Apply(dft) 
+
+The :class:`FFT` and :class:`DFT` algorithms do not require a direction to be 
+given (forward or back transform). This is implicitly determined by the current 
+:ref:`data-domain` of the image being transformed. The following rules apply. 
+
+* :obj:`SPATIAL` -> :obj:`HALF_FREQUENCY`
+* :obj:`HALF_FREQUENCY` -> :obj:`SPATIAL`
+* :obj:`FREQUENCY` -> :obj:`COMPLEX_SPATIAL`
+* :obj:`COMPLEX_SPATIAL` -> :obj:`FREQUENCY`
+
+.. _filters:
+
+Filters
+-------
+
+OpenStructure makes several image filters available. Most of them are Fourier 
+space filters, others are real space ones. However, since the 
+:class:`~ost.img.ImagerHandle` class is aware of its own :ref:`data-domain`, 
+the user does not need to convert the image to Fourier space or to real space. 
+Irrespective of which domain the filter applies to, OpenStructure  will 
+internally convert the image to the appropriate domain, apply the filter, and 
+then return the image to its original conditions.
+
+The following filters are available (their are described in the :ref:`algorithms` section below)
+
+Fourier space filters:
+
+* :class:`LowPassFilter`
+* :class:`HighPassFilter`
+* :class:`GaussianLowPassFilter`
+* :class:`GaussianHighPassFilter`
+* :class:`FermiLowPassFilter`
+* :class:`FermiHighPassFilter`
+* :class:`ButterworthLowPassFilter`
+* :class:`ButterworthHighPassFilter`
+* :class:`FermiLowPassFilter`
+
+Real space filters:
+
+* :class:`GaussianFilter`
+
+.. _algorithms:
+
+Selected Algorithms
+--------------------------------------------------------------------------------
+
+Many algorithms are available for image manipulation. What follows is a description of the 
+most important ones.
+
+.. class:: DFT()
+
+   This algorithm performs a Fourier Transform of the image, honoring its 
+   :ref:`spatial-origin`, thus applying the corresponding phase shift in Fourier 
+   space.
+
+.. class:: DiscreteShrink(block_size)
+
+   The algorithm performs a scaling of the original image by merging adjacent 
+   blocks of pixels. The block size is passed in the constructor in the form of 
+   a :class:`~ost.img.Size` but can be changed later using the relevant method. 
+   The :class:`~ost.img.Size` and the :class:`~ost.img.Extent` of the image are 
+   changed when the algorithm is applied. The :ref:`pixel-sampling` of the image 
+   is also adjusted according to the scaling, so that the size of the image in 
+   the absolute reference system used by OpenStructure stays constant.
+   
+   :param block_size: Size of the blocks to be merged
+   :type block_size: :class:`~ost.img.Size`
+
+   .. method:: GetBlocksize()
+
+     Returns the current size of the blocks to be merged
+
+     :rtype: :class:`~ost.img.Size`
+
+   .. method:: SetBlocksize(block size)
+
+    Sets the size of the blocks to be shrunk to the specified value
+
+    :param block_size:
+    :type  block_size: :class:`~ost.img.Size`
+ 
+.. class:: FFT()
+
+    This algorithm performs a Fourier Transform of the image, without honoring 
+    its :ref:`spatial-origin` (See :class:`DFT`)
+	
+.. class:: LowPassFilter(cutoff=1.0)
+
+   This algorithm applies a Fourier low pass filter to the image. The filter cutoff frequency needs
+   to be provided in sampling units (for example 8 Angstrom). Please notice that this filter features a sharp dropoff.
+
+   :param cutoff: Frequency cutoff in sampling units
+   :type  cutoff: float
+
+   .. method:: GetLimit()
+     
+     Returns the current value of the filter cutoff frequency  (in sampling units).
+
+     :rtype: float
+
+   .. method:: SetLimit(cutoff)
+
+     Sets the value of the filter cutoff frequency to the specified value (in sampling units).
+
+     :param cutoff: Frequency cutoff in sampling units
+     :type  cutoff: float
+
+.. class:: HighPassFilter(cutoff=1.0)
+
+   This algorithm applies a Fourier high pass filter to the image. The filter cutoff frequency needs
+   to be provided in sampling units (for example 8 Angstrom). Please notice that this filter features a sharp dropoff.
+
+   :param cutoff: Frequency cutoff in sampling units
+   :type  cutoff: float
+
+   .. method:: GetLimit()
+     
+     Returns the current value of the filter cutoff frequency  (in sampling units).
+
+     :rtype: float
+
+   .. method:: SetLimit(cutoff)
+
+     Sets the value of the filter cutoff frequency to the specified value (in sampling units).
+
+     :param cutoff: Frequency cutoff in sampling units
+     :type  cutoff: float
+
+
+.. class:: GaussianLowPassFilter(cutoff=1.0)
+
+   This algorithm applies a Fourier `Gaussian low pass filter <http://en.wikipedia.org/wiki/Gaussian_filter>`_ to the
+   image. The filter cutoff frequency needs to be provided in sampling units (for example 8 Angstrom). 
+
+   :param cutoff: Frequency cutoff in sampling units
+   :type  cutoff: float
+
+   .. method:: GetLimit()
+  
+     Returns the current value of the filter cutoff frequency (in sampling units).
+
+     :rtype: float
+
+   .. method:: SetLimit(cutoff)
+
+	 Sets the value of the filter cutoff frequency to the specified value (in sampling units).
+
+	 :param cutoff: Frequency cutoff in sampling units
+	 :type  cutoff: float
+
+.. class:: GaussianHighPassFilter(cutoff=1.0)
+
+   This algorithm applies a Fourier `Gaussian High pass filter <http://en.wikipedia.org/wiki/Gaussian_filter>`_ to the
+   image. The filter cutoff frequency needs to be provided in sampling units (for example 8 Angstrom). 
+
+   :param cutoff: Frequency cutoff in sampling units
+   :type  cutoff: float
+
+   .. method:: GetLimit()
+  
+     Returns the current value of the filter cutoff frequency (in sampling units).
+
+     :rtype: float
+
+   .. method:: SetLimit(cutoff)
+
+	 Sets the value of the filter cutoff frequency to the specified value (in sampling units).
+
+	 :param cutoff: Frequency cutoff in sampling units
+	 :type  cutoff: float
+	
+.. class:: FermiLowPassFilter(cutoff=1.0,t=1.0)
+
+   This algorithm applies a Fourier `Fermi low pass filter <http://en.wikipedia.org/wiki/Fermi_filter>`_ to the
+   image. The filter cutoff frequency and the temperature parameter T need to be provided in sampling units 
+   (for example 8 Angstrom). 
+
+   :param cutoff: Frequency cutoff in sampling units
+   :type  cutoff: float
+   :param t: Temperature factor in sampling units
+   :type  t: float
+
+   .. method:: GetLimit()
+  
+     Returns the current value of the filter cutoff frequency in sampling units.
+
+     :rtype: float
+
+   .. method:: SetLimit(cutoff)
+
+	 Sets the value of the filter cutoff frequency to the specified value (in sampling units).
+
+	 :param cutoff: Frequency cutoff in sampling units
+	 :type  cutoff: float
+	
+   .. method:: GetT()
+  
+     Returns the current value of the filter's T factor (in sampling units).
+
+     :rtype: float
+
+   .. method:: SetT(t_factor)
+
+	 Sets the value of the filter's T factor to the specified value (in sampling units).
+
+	 :param t_factor: Frequency cutoff in sampling units
+	 :type  t_factor: float
+
+.. class:: FermiHighPassFilter(cutoff=1.0,t=1.0)
+
+   This algorithm applies a Fourier `Fermi high pass filter <http://en.wikipedia.org/wiki/Fermi_filter>`_ to the
+   image. The filter cutoff frequency and the temperature parameter T need to be provided in sampling units 
+   (for example 8 Angstrom). 
+
+   :param cutoff: Frequency cutoff in sampling units
+   :type  cutoff: float
+   :param t: Temperature factor in sampling units
+   :type  t: float
+
+   .. method:: GetLimit()
+  
+     Returns the current value of the filter cutoff frequency in sampling units.
+
+     :rtype: float
+
+   .. method:: SetLimit(cutoff)
+
+	 Sets the value of the filter cutoff frequency to the specified value (in sampling units).
+
+	 :param cutoff: Frequency cutoff in sampling units
+	 :type  cutoff: float
+	
+   .. method:: GetT()
+  
+     Returns the current value of the filter's T factor (in sampling units).
+
+     :rtype: float
+
+   .. method:: SetT(t_factor)
+
+	 Sets the value of the filter's T factor to the specified value (in sampling units).
+
+	 :param t_factor: Frequency cutoff in sampling units
+	 :type  t_factor: float
+	
+.. class:: ButterworthLowPassFilter(passband=1.0,stopband=1.0)
+
+   This algorithm applies a Fourier `Butterworth low pass filter <http://en.wikipedia.org/wiki/Butterworth_filter>`_ to
+   the image. The filter passband and stopband frequencies need to be provided in sampling units (for example 8 Angstrom). 
+   The default values of the Epsilon and Maximum Passband Gain parameters are set to 0.882 and 10.624 respectively.
+
+   :param passband: Passband frequency in sampling units
+   :type  passband: float
+   :param stopband: Stopband frequency in sampling units
+   :type  stopband: float
+
+   .. method:: GetLimit()
+  
+     Returns the current value of the filter passband frequency in sampling units.
+
+     :rtype: float
+
+   .. method:: SetLimit(passband)
+
+	 Sets the value of the filter passband frequency to the specified value (in sampling units).
+
+	 :param passband: Frequency cutoff in sampling units
+	 :type  passband: float
+	
+   .. method:: GetStop()
+  
+     Returns the current value of the filter's stopband frequency (in sampling units).
+
+     :rtype: float
+
+   .. method:: SetStop(stopband)
+
+	 Sets the value of the filter's stopband frequency to the specified value (in sampling units).
+
+	 :param stopband: Frequency cutoff in sampling units
+	 :type  stopband: float	
+	
+   .. method:: GetEps()
+  
+     Returns the current value of the filter's Epsilon parameter.
+
+     :rtype: float
+
+   .. method:: SetEps(epsilon)
+
+	 Sets the value of the filter's epsilon parameter to the specified value.
+
+	 :param eps: Epsilon parameter
+	 :type  eps: float
+	
+   .. method:: GetA()
+  
+     Returns the current value of the filter's Maximum Passband Gain parameter.
+
+     :rtype: float
+
+   .. method:: SetA(gain)
+
+	 Sets the value of the filter's Maximum Passband Gain parameter to the specified value.
+
+	 :param gain: Maximum Passband Gain parameter
+	 :type  gain: float			
+	
+.. class:: ButterworthHighPassFilter(passband=1.0,stopband=1.0)
+
+   This algorithm applies a Fourier `Butterworth high pass filter <http://en.wikipedia.org/wiki/Butterworth_filter>`_ 
+   to the image. The filter passband and stopband frequencies need to be provided in sampling units (for example 8
+   Angstrom). The default values of the Epsilon and Maximum Passband Gain parameters are set to 0.882 and 10.624
+   respectively.
+
+   :param passband: Passband frequency in sampling units
+   :type  passband: float
+   :param stopband: Stopband frequency in sampling units
+   :type  stopband: float
+
+   .. method:: GetLimit()
+  
+     Returns the current value of the filter passband frequency in sampling units.
+
+     :rtype: float
+
+   .. method:: SetLimit(passband)
+
+	 Sets the value of the filter passband frequency to the specified value (in sampling units).
+
+	 :param passband: Frequency cutoff in sampling units
+	 :type  passband: float
+	
+   .. method:: GetStop()
+  
+     Returns the current value of the filter's stopband frequency (in sampling units).
+
+     :rtype: float
+
+   .. method:: SetStop(stopband)
+
+	 Sets the value of the filter's stopband frequency to the specified value (in sampling units).
+
+	 :param stopband: Frequency cutoff in sampling units
+	 :type  stopband: float	
+	
+   .. method:: GetEps()
+  
+     Returns the current value of the filter's Epsilon parameter.
+
+     :rtype: float
+
+   .. method:: SetEps(epsilon)
+
+	 Sets the value of the filter's epsilon parameter to the specified value.
+
+	 :param eps: Epsilon parameter
+	 :type  eps: float
+	
+   .. method:: GetA()
+   
+     Returns the current value of the filter's Maximum Passband Gain parameter.
+
+     :rtype: float
+
+   .. method:: SetA(gain)
+
+	 Sets the value of the filter's Maximum Passband Gain parameter to the specified value.
+
+	 :param gain: Maximum Passband Gain parameter
+	 :type  gain: float	
+	
+.. class:: GaussianFilter(sigma=1.0)
+
+	 This algorithm applies a real space Gaussian filter to the image, as defined in the following publication:
+	
+	 I.T.Young, L.J. van Vliet,"Recursive implementation of the Gaussian filter",Signal Processing, 44(1995), 139-151
+	
+	 :param sigma: Width of the Gaussian filter
+	 :type  sigma: float
+
+	 .. method:: GetSigma()
+
+	   Returns the current value of the filter's width.
+
+	   :rtype: float
+
+	 .. method:: SetSigma(width)
+
+	   Sets the value of the filter's width to the specified value.
+
+	   :param sigma: Width of the Gaussian filter
+	   :type  sigma: float			
+	
+	 .. method:: SetQ(q_param)
+
+	   Sets the value of the filter's Q parameter (see publication) to the specified value.
+
+	   :param q_param: Filter's Q parameter
+	   :type  q_param: float			
+
+.. class:: Histogram(bins, minimum, maximum)
+
+   This algorithm performs an histogram analysis of the image. The minimum and 
+   maximum pixel values of the histogram representation must be provided when 
+   the algorithm object is created, as well as the number of bins in the 
+   histogram. Bins are equally spaced and minimum and maximum values for each 
+   bin are automatically computed.
+   
+   When the algorithm is applied to an image, the analysis is carried out. A 
+   python 'list' object containing in sequence the pixel counts for all the bins 
+   can the be recovered from the algorithm object.
+
+   :param bins: Number of bins in the histogram
+   :type  bins: int
+   :param minimum: Minimum value in the histogram
+   :type  minimum: float
+   :param maximum: Maximum value in the histogram
+
+   .. method:: GetBins()
+
+     Returns the bins of the histogram representation
+
+     :rtype: list of ints 
+
+   :type  maximum: float
+
+   .. method:: GetBins()
+
diff --git a/modules/img/alg/src/alg_transform.hh b/modules/img/alg/src/alg_transform.hh
index be066cf1ca3839bb13f38faddc8e0fff61310994..436e3a25748afb5a2bbbccb9a7d824613874ab7a 100644
--- a/modules/img/alg/src/alg_transform.hh
+++ b/modules/img/alg/src/alg_transform.hh
@@ -50,15 +50,15 @@ struct DLLEXPORT_IMG_ALG TransformFnc {
 
     if(offset_==Vec3(0.0,0.0,0.0)) {
       for(ExtentIterator it(nisi->GetExtent()); !it.AtEnd(); ++it) {
-	Point p(it);
-	Vec3 vold_norm=Vec3(imat * Vec4(p.ToVec3()));
-	nisi->Value(it) = isi.CalcIntpolValue(vold_norm);
+        Point p(it);
+        Vec3 vold_norm=Vec3(imat * Vec4(p.ToVec3()));
+        nisi->Value(it) = isi.CalcIntpolValue(vold_norm);
       }
     } else {
       for(ExtentIterator it(nisi->GetExtent()); !it.AtEnd(); ++it) {
-	Point p(it);
-	Vec3 vold_norm=Vec3(imat * Vec4(p.ToVec3()-offset_))+offset_;
-	nisi->Value(it) = isi.CalcIntpolValue(vold_norm);
+        Point p(it);
+        Vec3 vold_norm=Vec3(imat * Vec4(p.ToVec3()-offset_))+offset_;
+        nisi->Value(it) = isi.CalcIntpolValue(vold_norm);
       }
     }
     
diff --git a/modules/img/alg/src/discrete_shrink.cc b/modules/img/alg/src/discrete_shrink.cc
index 3398c820b8f05e528f6bcdfd5aa26ab47d328121..3bc1fa2d11432a015a0fe4e9963d25c4244b7d58 100644
--- a/modules/img/alg/src/discrete_shrink.cc
+++ b/modules/img/alg/src/discrete_shrink.cc
@@ -72,8 +72,10 @@ ImageStateBasePtr DiscreteShrinkFnc::VisitState(const ImageStateImpl<T,D>& isi)
 
   Extent new_ext(newsize);
 
-  LOG_VERBOSE("ds: " << isi.GetExtent() << " " << new_ext << std::endl);
+  LOG_DEBUG("extent of shrunken image" << isi.GetExtent() << " " << new_ext);
 
+
+  geom::Vec3 ao = isi.GetAbsoluteOrigin();
   PixelSampling new_ps = isi.GetSampling();
   new_ps.SetExtent(new_ext);
 
@@ -95,8 +97,7 @@ ImageStateBasePtr DiscreteShrinkFnc::VisitState(const ImageStateImpl<T,D>& isi)
   dt = div(start[1],bs_[1]);  newstart[1] = dt.quot;
   dt = div(start[2],bs_[2]);  newstart[2] = dt.quot;
 
-  LOG_VERBOSE("ds: newstart: " << newstart << std::endl);
-
+  ni->SetAbsoluteOrigin(ao);
   ni->SetSpatialOrigin(newstart);
   ni->GetSampling().SetPixelSampling(CompMultiply(ni->GetSampling().GetPixelSampling(),Vec3(bs_[0],bs_[1],bs_[2])));
 
diff --git a/modules/img/alg/src/highest_peak_search_3d.cc b/modules/img/alg/src/highest_peak_search_3d.cc
index aaedb099410dbf3e292d3430037ee32c1fd9158a..c8e884577be8e601c78c58eecaf1221cb461283e 100644
--- a/modules/img/alg/src/highest_peak_search_3d.cc
+++ b/modules/img/alg/src/highest_peak_search_3d.cc
@@ -74,42 +74,43 @@ namespace detail {
         bool insert=true;
         bool remove_smaller=false;
         img::PeakList::iterator min_it;
+
         if(!list_.empty()) {
           min_it = list_.begin();
-        }
 
-        for(img::PeakList::iterator it=list_.begin();it!=list_.end();++it)
-        {
-          if(it->GetValue() < min_it->GetValue()) min_it = it;
-          if (it->GetValue() >= cand_peak.GetValue() && detail::is_within(cand_peak, *it, exclusion_radius_)) {
-            insert=false;
-          } else if (cand_peak.GetValue() >= it->GetValue() && detail::is_within(cand_peak, *it, exclusion_radius_)) {
-            remove_smaller=true;
+          for(img::PeakList::iterator it=list_.begin();it!=list_.end();++it)
+          {
+            if(it->GetValue() < min_it->GetValue()) min_it = it;
+            if (it->GetValue() >= cand_peak.GetValue() && detail::is_within(cand_peak, *it, exclusion_radius_)) {
+              insert=false;
+            } else if (cand_peak.GetValue() >= it->GetValue() && detail::is_within(cand_peak, *it, exclusion_radius_)) {
+              remove_smaller=true;
+            }
           }
-        }
 
-        if (!insert) return false;
+          if (!insert) return false;
 
-        if (cand_peak.GetValue() < min_it->GetValue()) {
-          return false;
-        }
+          if (cand_peak.GetValue() < min_it->GetValue()) {
+            return false;
+          }
 
-        if (remove_smaller)
-        {
-          img::PeakList::iterator new_end = remove_if(list_.begin(),list_.end(),
-          detail::is_smaller_and_within_radius(cand_peak,exclusion_radius_));
-          list_.erase(new_end,list_.end());
-        }
+          if (remove_smaller)
+          {
+            img::PeakList::iterator new_end = remove_if(list_.begin(),list_.end(),
+            detail::is_smaller_and_within_radius(cand_peak,exclusion_radius_));
+            list_.erase(new_end,list_.end());
+          }
 
-        if (list_.size() == max_num_peaks_) {
-          list_.erase(min_it);
+          if (list_.size() == max_num_peaks_) {
+            list_.erase(min_it);
+          }
         }
 
         list_.push_back(cand_peak);
         return true;
       }
 
-      //! Gets list of peaks from collector
+       //! Gets list of peaks from collector
       img::PeakList GetPeakList() const { return list_; }
 
       //! Clears the peak list removing all peaks in the list
@@ -117,7 +118,7 @@ namespace detail {
 
     private:
 
-      img::PeakList list_;
+      img::PeakList list_;      
       unsigned int max_num_peaks_;
       int exclusion_radius_;
 
@@ -129,22 +130,28 @@ template <typename T, class D>
   void HighestPeakSearch3DBase::VisitState(const ImageStateImpl<T,D>& isi)
   {
 
-    LOG_VERBOSE("highest peak search with the parameters" << std::endl);
-    LOG_VERBOSE(" max number of peaks: " << max_num_peaks_ << std::endl);
-    LOG_VERBOSE(" exclusion radius: " << exclusion_radius_ << std::endl);
-    LOG_VERBOSE(" threshold: " << threshold_ << std::endl);
- 
-    if(ext_list_.size()==0) 
+    LOG_DEBUG("highest peak search (" 
+              << "max number of peaks: " << max_num_peaks_ << ", "
+              << "exclusion radius: " << exclusion_radius_ << ", "
+              << "threshold: " << threshold_ << ")");
+
+    if (max_num_peaks_ < 1)
+    {
+      throw Error("Error: Maximum number of peaks smaller than 1. Cannot create peak list");
+    }
+
+    if(ext_list_.size()==0)
     {
-      LOG_VERBOSE(" excluded regions: none" << std::endl);
+      LOG_DEBUG(" excluded regions: none");
     } 
     else 
     {
-      LOG_VERBOSE(" excluded regions:" << std::endl);
+      std::stringstream ss;
       for(ExtList::const_iterator it=ext_list_.begin();it!=ext_list_.end();++it) 
       {
-       LOG_VERBOSE("  " << (*it) << std::endl);
+        ss << " " << (*it);
       }
+      LOG_DEBUG("exluded regions:" << ss.str());
     }
 
     detail::PeakCollector peak_collector(max_num_peaks_,exclusion_radius_);
diff --git a/modules/img/alg/src/histogram.hh b/modules/img/alg/src/histogram.hh
index f974247da64b4f51f1c8d5d87afc1e59b608f022..7805d40fcb86740c0d85eadc35d97111f17eed75 100644
--- a/modules/img/alg/src/histogram.hh
+++ b/modules/img/alg/src/histogram.hh
@@ -17,6 +17,8 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
+#ifndef OST_IMG_ALG_HISTOGRAM_HH
+#define OST_IMG_ALG_HISTOGRAM_HH
 
 /*
   Author: Ansgar Philippsen
@@ -75,3 +77,5 @@ typedef ImageStateNonModAlgorithm<HistogramBase> Histogram;
 OST_IMG_ALG_EXPLICIT_INST_DECL(class,ImageStateNonModAlgorithm<alg::HistogramBase>)
 
 }} // namespaces
+
+#endif
diff --git a/modules/img/base/doc/img.rst b/modules/img/base/doc/img.rst
new file mode 100644
index 0000000000000000000000000000000000000000..89670946546e1c6427206e0451abc0520933040e
--- /dev/null
+++ b/modules/img/base/doc/img.rst
@@ -0,0 +1,461 @@
+:mod:`~ost.img` - Images and Density Maps
+================================================================================
+
+.. toctree::
+  :hidden:
+
+  point-size-extent
+
+.. module:: ost.img
+   :synopsis: Images and density maps
+              
+Introduction : The ImageHandle
+--------------------------------------------------------------------------------
+
+OpenStructure offers extensive processing capabilities for planar 2d images and
+3d maps using the :mod:`img` module. The main datastructure for images is the 
+:class:`ImageHandle` class.
+
+ImageHandles provide a clean and efficient interface to interact with images and 
+maps. An :class:`ImageHandle` can store an image in either real (:obj:`SPATIAL`) 
+or Fourier (:obj:`FREQUENCY`) space and always keep track of the currently 
+active  domain. This means,for example that one can apply a Fourier 
+transformation to an :class:`ImageHandle` containing a :obj:`SPATIAL` image and 
+the image will correctly  identify the new active domain as  :obj:`FREQUENCY`. 
+The :class:`ImageHandle` also understands, for example, that applying a 
+Fourier Transform to a centrosymmetric :obj:`FREQUENCY` image results in a real 
+:obj:`SPATIAL` image, but applying it to a non-centrosymmetric one results in a 
+complex :obj:`SPATIAL` image.
+
+Furthermore, the image will make sure that real and Fourier space 
+information about the image are always in sync. If, for example, the pixel 
+sampling is changed while the current active domain is real space, the pixel 
+sampling in Fourier space will be adjusted accordingly, and vice versa.
+
+Creating and visualizing ImageHandles
+--------------------------------------------------------------------------------
+
+As a first step, enter the following lines in the OpenStructure python console:
+
+.. code-block:: python
+  
+  im=img.CreateImage(img.Size(200,200))
+
+This will create an empty, 2D image, with a height and width of 200 pixels, 
+whose origin (ie the pixel with the coordinates <0,0>) is in the top-left 
+corner.
+
+.. code-block:: python
+  
+  v=gui.CreateDataViewer(im)
+
+A viewer window will pop up (see below), showing a white frame on a black 
+background. The inner area of the white frame is the image, which is empty.
+
+Reading and writing into an image
+-------------------------------------------------------------------------------
+
+Data can be read and written from and into an image using the following 
+commands:
+
+.. code-block:: python
+
+  # writes the real value 23.4 into pixel 10,10
+  im.SetReal(img.Point(10,10),23.4)
+  # reads the value in pixel 10,10
+  val=im.GetReal(img.Point(10,10))
+    
+The complex equivalents are also available    
+
+.. code-block:: python
+
+  # writes the complex value value 2+3j into pixel 10,10
+  im.SetComplex(img.Point(10,10),2+3j)
+  # reads the value in pixel 10,10
+  val=im.GetComplex(img.Point(10,10))
+
+The image knows in which domain it is, and will adjust the type of data being 
+written accordingly. For example, if one writes a complex value in a 
+:obj:`SPATIAL` image, the value will be automatically converted to a real one by 
+taking the amplitude of the complex number. On the other hand, if one writes a 
+real value in a :obj:`FREQUENCY` image, the value is automatically
+converted to complex by setting the imaginary part to 0.
+
+Image properties
+-----------------
+
+.. _data-domain:
+
+The data domain
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The data domain of an image specifies wether the image contains data in the 
+spatial or frequency domain. A :obj:`HALF_FREQUENCY` domain also exists, 
+representing centrosymmetric frequency data (such as the data coming from the 
+Fourier transform of an image from the real spatial domain)
+
+.. data:: SPATIAL
+
+  Real-valued spatial images
+
+.. data:: COMPLEX_SPATIAL
+
+  Complex-valued spatial images, i.e. resulting from a Fourier transform of
+  the :obj:`FREQUENCY` domain.
+  
+.. data:: FREQUENCY
+  
+  Complex frequeny domain.
+  
+.. data:: HALF_FREQUENCY
+
+  Centrosymmetric frequency images
+    
+
+
+.. _spatial-origin:
+
+The spatial origin
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The spatial origin of an image is the first pixel of its extent. Specifically, 
+this is the top left pixel for 2D images and the top-front-left  corner for 3D
+images.
+
+.. _absolute-origin:
+
+The absolute origin
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The absolute origin of an image describes the coordinates, in the absolute 
+reference system used by OpenStructure, of the pixel in with all indexes equal 
+to 0. Please note that the pixel does not necessarily need to belong to the 
+extent of the image.
+
+.. _pixel-sampling:
+
+Pixel sampling
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+
+The pixel sampling property of an image describes the size of its pixels. For
+the same image, the size of pixels in the :obj:`SPATIAL` and in the
+:obj:`FREQUENCY` :ref:`data-domain` are obviously interdependent.
+OpenStructure takes care of the transformation and allows access to both pixel 
+sampling irrespective of the current image domain.
+
+The ImageHandle class
+--------------------------------------------------------------------------------
+
+The public interface of the ImageHandle class provides many ways to manipulate 
+image properties. What follows is a brief description of the most important 
+methods and attributes of the ImageHandle class.
+
+.. class:: ImageHandle
+
+  .. attribute:: size
+  
+    The size of the image. Read-only.
+    
+    :type: :class:`Size`
+    
+  .. attribute:: extent
+  
+    The extent of the image. Read-only.
+    
+    :type: :class:`Extent`
+  
+  .. attribute:: type
+  
+    The DataType of an image represents the nature of the data it contains. An
+    image can contain :obj`REAL` or :obj:`COMPLEX` values.
+  
+  .. attribute:: absolute_origin
+  
+    The absolute origin of an image describes the coordinates, in the absolute 
+    reference system used by OpenStructure, of the pixel in with all indexes 
+    equal to 0. Please note that the pixel does not necessarily need to belong 
+    to the extent of the image. Read-write.
+    
+    :type: :class:`~ost.geom.Vec3`
+    
+
+  .. attribute:: spatial_origin
+  
+    The spatial origin of an image is the first pixel of its extent. 
+    Specifically, this is the top left pixel for 2D images and the 
+    top-front-left  corner for 3Dimages.
+    
+    :type: :class:`Point`
+
+  .. attribute:: domain
+  
+    The current domain of the image. See :ref:`data-domain`. Read-only.
+    
+
+  .. method:: Apply(algorithm)
+
+     Applies an algorithm on an image and returns a new ImageHandle containing 
+     the modified image. See :doc:`../alg/alg` 
+
+     :param algorithm: algorithm
+     :type  algorithm: Instance of an algorithm class - See :doc:`../alg/alg`.
+     :rtype: :class:`ImageHandle`
+
+  .. method:: ApplyIP(algorithm)
+
+     Applies an algorithm on an image, overwriting the current content. See 
+     `:doc:`../alg/alg`
+
+     :param algorithm: algorithm
+     :type  algorithm: Instance of an algorithm class - See: doc:`../alg/alg`.
+
+  .. method:: CenterSpatialOrigin()
+
+     Sets the :ref:`spatial-origin` of an image in such a way that the central 
+     pixel has all 0 indexes, e.g. (0,0) or (0,0,0) for 3d images.
+    
+  .. method:: CoordToIndex(coord)
+
+     Returns the indexes of an image corresponding to the specified absolute 
+     coordinates. (See :ref:`absolute-origin`). A given set of absolute 
+     coordinates will almost never fall exactly at the center of a pixel, so 
+     this method return fractional indexes. 
+
+     :param coord: Absolute coordinates
+     :type  coord: :class:`~ost.geom.Vec3`
+     :rtype: Vec3
+
+  .. method:: Copy()
+     
+     Creates a and returns a copy of the ImageHandle. The new handle does not 
+     point to the same underlying data as the old one, but to a complete and 
+     separate copy of the original data.
+
+     :rtype: :class:`ImageHandle`
+
+  .. method:: Extract(extent)
+     
+     Creates and returns a new image that contains a copy of a portion of the 
+     original image. The extracted image keeps the same :ref:`data-type` of the 
+     original image, but extractions from images in the 'FREQEUNCY' or 
+     'HALF FREQUENCY' domains result in :obj:`COMPLEX ` :obj:`SPATIAL` images. 
+     This transformation is necessary, since the there is no guarantee that the 
+     extracted :obj:`FREQUENCY` sub-image is centered around the origin and 
+     hence back-transformable to :obj:`SPATIAL`.
+
+     :param extent: Portion of the image to extract
+     :type  extent: :class:`Extent`
+     :rtype: :class:`ImageHandle`
+
+  .. method:: FractionalIndexToCoord(frac_pixel)
+
+     Same as :meth:`IndexToCoord`, but introduces subpixel precision by 
+     accepting fractional numbers for pixel indexes.
+     
+     :param frac_pixel: Fractional pixel indexes
+     :type  frac_pixel: :class:`~ost.geom.Vec3`
+     :rtype: :class:`~ost.geom.Vec3`
+
+  .. method:: GetAbsoluteOrigin()
+    
+     Returns the :ref:`absolute-origin` of an image
+
+     :rtype: :class:`~ost.geom.Vec3`
+
+  .. method:: GetComplex(pixel)
+
+     Returns the complex value of the specified image pixel. If the image holds 
+     data of the 'REAL' :ref:`data-type`, the method return s complex value with 
+     the pixel content as real part and a null imaginary part.
+
+     :param pixel: Image pixel
+     :type  pixel: :class:`Point`
+     :rtype: complex
+
+  .. method:: GetDomain()
+    
+     See :attr:`domain`
+
+  .. method:: GetExtent()
+
+    See :attr:`extent`
+
+
+  .. method:: GetFrequencySampling()
+     
+     Returns the :ref:`pixel-sampling` of the image in the :obj:`FREQUENCY` 
+     :ref:`data-domain`
+       
+     :rtype: :class:`~ost.geom.Vec3`
+
+  .. method:: GetIntpolComplex(frac_pixel)
+
+     Returns the interpolated complex value of the virtual pixel corresponding 
+     to the specified fractional indexes. This is computed by calculating a 
+     weighted vector sum of the values of the surrounding pixels. If the image 
+     holds data of the 'REAL' :ref:`data-type`, the method computes the 
+     interpolated value using bilinear interpolation (trilinear for 3D images), 
+     then returns a complex value with the interpolated value as real part and a 
+     null imaginary part.
+
+     :param frac_pixel: Fractional pixel indexes
+     :type  frac_pixel: :class:`~ost.geom.Vec3`
+     :rtype: complex
+
+  .. method:: GetIntpolReal(frac_pixel)
+
+     Returns the interpolated value of the virtual pixel corresponding to the 
+     specified fractional indexes. This is computed by using bilinear 
+     interpolation (trilinear for 3D images). If the image holds data of the 
+     :obj:`COMPLEX ` :ref:`data-type`, the method computes the interpolated 
+     value as a weighted vector sum of the values of the surrounding pixels, 
+     then returns the amplitude of the interpolated value. 
+
+     :param frac_pixel: Fractional pixel indexes
+     :type  frac_pixel: :class:`~ost.geom.Vec3` 
+     :rtype: float
+
+  .. method:: GetPixelSampling()
+   
+     Returns the :ref:`pixel-sampling` of the image in the current 
+     :ref:`data-domain`.
+
+     :rtype: :class:`~ost.geom.Vec3`
+
+  .. method:: GetReal(pixel)
+
+     Returns the value of the specified image pixel. If the image holds data of 
+     the :obj:`COMPLEX ` :ref:`data-type`, the method return the amplitude of 
+     the pixel content.
+
+     :param pixel: Image pixel
+     :type  pixel: :class:`Point`
+     :rtype: float
+
+  .. method:: GetSize()
+
+     Returns the :class:`Size` of the image.
+
+     :rtype: :class:`Size`
+
+  .. method:: GetSpatialOrigin()
+
+     Returns the :ref:`spatial-origin` of the image.
+
+     :rtype: :class:`Point`
+
+  .. method:: GetSpatialSampling()
+
+     Return the :ref:`pixel-sampling` of the image in the :obj:`SPATIAL`
+     :ref:`data-domain`.
+
+     :rtype: :class:`~ost.geom.Vec3`
+
+  .. method:: GetType()
+     
+     Returns the :ref:`data-type` of the image (:obj:`REAL` or :obj:`COMPLEX`)
+  
+     :rtype: DataType  ???????????
+
+  .. method:: IndexToCoord(pixel)
+ 
+     Returns the absolute coordinates (See :ref:`absolute-origin`) corresponding 
+     to the pixel with the specified indexes. Please note this method always
+     returns the coordinates corresponding to the center of the pixel. When 
+     sub-pixel precision is needed, the method :meth:`FractionalIndexToCoord` 
+     can be used.
+    
+     :param pixel:
+     :type  pixel: :class:`Point`
+     :rtype: :class:`~ost.geom.Vec3`
+
+  .. method:: IsFrequency()
+
+     Returns true if the :ref:`data-domain` of the image is `FREQUENCY` or 
+     `HALF-FREQUENCY`     
+
+     :rtype: bool
+
+  .. method:: IsSpatial()
+
+     Returns true if the :ref:`data-domain` of the image is :obj:`SPATIAL`.  
+
+     :rtype: bool
+
+  .. method:: IsValid()
+
+     Returns true, when the image handle is valid, false if not. It is an error 
+     to call any method on the image handle other than `IsValid` when this 
+     method returns false.
+
+     :rtype: bool
+
+  .. method:: Paste(source_image)
+   
+     Copies the content of a different image into the current one, overwriting 
+     pre-existing data . The values of pixels with given indexes in the source 
+     image are copied into pixels with the same indexes in the target image. If 
+     the two images have different extents (see :class:`Extent`), pixels that do 
+     not exist in both are ignored. Please notice that this method only copies 
+     the pixel content: all other properties of the image are left untouched. 
+
+     :param source_image: Source image that gets pasted into the current one
+     :type  source_image: :class:`ImageHandle`
+
+  .. method:: SetAbsoluteOrigin(coord)
+  
+     Sets the :ref:`absolute-origin` of the image to the specified coordinates  
+  
+     :param coord: Absolute coordinates
+     :type  coord: :class:`~ost.geom.Vec3`
+ 
+  .. method:: SetComplex(pixel, value)
+
+     Sets the content of the specified pixel to the provided value.  If the 
+     image holds data of the 'REAL' :ref:`data-type`, the method sets the pixel 
+     to the amplitude of the provided.
+     value.
+
+     :param pixel: Image pixel
+     :type  pixel: :class:`Point`
+     :param value: Value 
+     :type  value: complex
+ 
+  .. method:: SetPixelSampling(sampling)
+
+     Sets the :ref:`pixel-sampling` of the image to the provided values in the 
+     current :ref:`data-domain`. 
+
+     :param sampling: Size of a pixel in x,y and z direction respectively
+     :type  sampling: :class:`~ost.geom.Vec3`
+
+  .. method:: SetReal(pixel, value)
+
+     Sets the content of the specified pixel to the provided value.  If the 
+     image holds data of the :obj:`COMPLEX` :ref:`data-type`, the method sets 
+     the pixel to a value has a real part equal to the provided value and a null 
+     complex part.
+ 
+     :param pixel: Image pixel
+     :type  pixel: :class:`Point`
+     :param value: Value
+     :type  value: float
+
+  .. method:: SetSpatialOrigin(pixel_indexes)
+
+     Sets the :ref:`spatial-origin` of the image to the provided indexes.
+
+     :param pixel_indexes: Indexes of the first pixel of the image
+     :type  pixel_indexes: :class:`Point`
+     :rtype: None
+
+  .. method:: SetSpatialSampling(sampl)
+
+     Sets the :ref:`pixel-sampling` if the image to the provided values in the 
+     spatial :ref:`data-domain`
+
+     :param sampl: Size of a pixel in x,y and z direction respectively
+     :type  sampl: :class:`~ost.geom.Vec3`
+ 
+  
diff --git a/modules/img/base/doc/point-size-extent.rst b/modules/img/base/doc/point-size-extent.rst
new file mode 100644
index 0000000000000000000000000000000000000000..af2731adb21d7ffae75bb859d78f16835b392965
--- /dev/null
+++ b/modules/img/base/doc/point-size-extent.rst
@@ -0,0 +1,143 @@
+Point, Size, Extent
+================================================================================
+
+.. currentmodule:: ost.img
+
+
+This document describes some of the classes used in the :mod`~ost.img` module to describe image properties such as size, pixel coordinates and extents.
+
+
+Point
+--------------------------------------------------------------------------------
+
+.. class:: Point(x=0, y=0, z=0)
+           Point(vec)
+           Point(size)
+           Point(point)
+
+  :param x: integral x coordinate
+  :type  x: int
+  :param y: integral y coordinate
+  :type  y: int
+  :param z: integral z coordinate
+  :type  z: int 
+  :param vec: The vectors coordinates will be rounded to the next 
+     integral value. In case of a :class:`~ost.geom.Vec4`, the coordinates will
+     be divided by the homogenous coordinate.
+  :type vec: :class:`~ost.geom.Vec3`, :class:`~ost.geom.Vec4`
+  :param point:
+  :type point: Initialize from point
+
+  This class represents an image pixel. It is defined using three integer 
+  numbers, corresponding to the pixel’s indexes along the width, height and 
+  depth dimensions respectively. 
+  
+  .. method:: __getitem__(index)
+    
+    Read-write access to the coordinates.
+    
+    ..code-block:: python
+    
+      p=img.Point(1,2,3)
+      print p
+      p[1]=5
+
+  .. method:: ToVec3()
+    
+    Converts the point to a :class:`~ost.geom.Vec3`
+  
+  .. method:: ToVec2()
+  
+    Converts the point to a :class:`~ost.geom.Vec2`. The z coordinate of the
+    point is ommitted.
+ 
+  .. method:: ToVec4()
+  
+    Converts the point to a :class:`~ost.geom.Vec4`, with the homogenous
+    coordinate set to 1.
+  
+  
+
+
+Size
+--------------------------------------------------------------------------------
+
+.. class:: Size(width, height, depth)
+           Size(width, height)
+
+  This property describes the size of an image. It is defined using three 
+  integer numbers: When depth is not specified, the size is assumed to refer to 
+  a 2D image two-dimensional (depth=1).
+
+  The :class:`Size` class can be passed to the :func:`CreateImage` function to
+  define the size of the image being created.
+
+  .. code-block:: python 
+
+    # uses the size class to create an image
+    s=img.Size(40,20,30)
+    i=img.CreateImage(s)
+    # uses a temporary instance of the Size class
+    i=img.CreateImage(img.Size(40,20,30))
+
+Extent
+--------------------------------------------------------------------------------
+
+.. class:: Extent(first_point, last_point)
+           Extent(first_point, size)
+           Extent(size, center_point)
+
+  This class describes the extent of an image in pixels. The image extent is 
+  a rectangle in 2d and a cuboid in 3d, and can be defined in a number of ways: 
+  giving the first and the last point of the extent, specifying the first point 
+  and the size of the extent, or listing the size of the extent and its central 
+  point.
+
+
+  **Some examples:**
+
+  .. code-block:: python 
+
+    # defines a rectangular extent that goes from pixel (2,4) to pixel (5,10)  
+    s=img.Extent(img.Point(2,4),img.Point(5,10))
+    # defines the same extent using its first point and its size
+    s=img.Extent(img.Point(2,4),img.Size(4,7))
+    # again the same extent using its size and central pixel
+    s=img.Extent(img.Size(4,7),img.Point(3,7))
+
+  The :class:`Extent` class can be passed to the :func:`CreateImage` function to
+  create an image with a specific extent.
+
+  .. code-block:: python 
+
+    # uses the Extent class to create an image
+    e=img.Extent(img.Point(2,4),img.Size(4,7))
+    i=img.CreateImage(e)
+    # uses a temporary instance of the Extent class
+    i=img.CreateImage(img.Extent(img.Point(2,4),img.Size(4,7)))
+
+  Given an :class:`Extent`, is it possible to recover its full size, and also
+  the length of each of its dimensions separately.
+
+  **Examples:**
+
+  .. code-block:: python 
+
+    # gets the size of an extent (e is a 3D extent)
+    s=e.GetSize()
+    # gets the three dimensions separately
+    w=e.GetWidth()
+    h=e.GetHeight()
+    d=e.GetDepth()
+
+  When one needs to visit all the image pixels belonging to an :class:`Extent`
+  in sequence, one can use an :class:`ExtentIterator`:
+
+  .. code-block:: python 
+
+    # defines an iterator over an extent e
+    ei=ExtentIterator(e)
+    # visits all the pixels in the extent and
+    # prints out their values
+    for pixel in ei:
+      print i.GetReal(pixel)
\ No newline at end of file
diff --git a/modules/img/base/pymod/__init__.py b/modules/img/base/pymod/__init__.py
index b4564fed2d007d7957fa620303a744768fb417ab..488406e2d19e82c01c1e202c4bc328782dfba8e0 100644
--- a/modules/img/base/pymod/__init__.py
+++ b/modules/img/base/pymod/__init__.py
@@ -18,3 +18,4 @@
 #------------------------------------------------------------------------------
 from _img import *
 MapHandle=ImageHandle
+from ost.img import alg
diff --git a/modules/img/base/pymod/export_data.cc b/modules/img/base/pymod/export_data.cc
index a58f780d0b3ec657d85aa5885d651c3cb7de9e7f..b9f2cf3c18946b88461fff4d939452db33dad876 100644
--- a/modules/img/base/pymod/export_data.cc
+++ b/modules/img/base/pymod/export_data.cc
@@ -38,13 +38,15 @@ void export_Data()
     .value("REAL",REAL)
     .value("COMPLEX",COMPLEX)
     .value("WORD",WORD)
-    ;
+    .export_values()
+  ;
 
   enum_<DataDomain>("DataDomain")
     .value("SPATIAL",SPATIAL)
     .value("FREQUENCY",FREQUENCY)
     .value("HALF_FREQUENCY",HALF_FREQUENCY)
-    ;
+    .export_values()
+  ;
 
   // data wrapper
   void (ConstData::*apply1)(NonModAlgorithm&) const = &ConstData::Apply;
@@ -59,6 +61,7 @@ void export_Data()
 
   class_<ConstData, boost::noncopyable>("ConstData", no_init )
     .def("GetType",&ConstData::GetType)
+    .add_property("type", &ConstData::GetType)
     .def("GetDomain",&ConstData::GetDomain)
     .def("GetExtent",&ConstData::GetExtent)
     .def("GetReal",&ConstData::GetReal)
@@ -66,9 +69,18 @@ void export_Data()
     .def("Apply",apply1)
     .def("GetSize",&ConstData::GetSize)
     .def("IsSpatial",&ConstData::IsSpatial)
+    .add_property("is_spatial", &ConstData::IsSpatial)
+    .add_property("is_frequency", &ConstData::IsSpatial)
+    .add_property("size", &ConstData::GetSize)
+    .add_property("domain", &ConstData::GetDomain)
+    .add_property("extent", &ConstData::GetExtent)
+    .add_property("pixel_sampling", &ConstData::GetPixelSampling)
+    .add_property("spatial_sampling", &ConstData::GetSpatialSampling)
+    .add_property("frequency_sampling", &ConstData::GetFrequencySampling)    
     .def("IsFrequency",&ConstData::IsFrequency)
     .def("GetPixelSampling",&ConstData::GetPixelSampling)
     .def("GetSpatialSampling",&ConstData::GetSpatialSampling)
+
     .def("GetFrequencySampling",&ConstData::GetFrequencySampling)
     //.def("IndexToCoord",&ConstData::IndexToCoord)
     //.def("CoordToindex",&ConstData::CoordToIndex)
@@ -91,5 +103,7 @@ void export_Data()
     .def("SetPixelSampling",setpixelsampling1)
     .def("SetSpatialSampling",setspatialsampling0)
     .def("SetSpatialSampling",setspatialsampling1)
-    ;
+    .add_property("spatial_origin", &Data::GetSpatialOrigin, 
+                  &Data::SetSpatialOrigin)
+  ;
 }
diff --git a/modules/img/base/pymod/export_image_handle.cc b/modules/img/base/pymod/export_image_handle.cc
index 942e7b61cd427ab7b6b4a5c5f13bd9a824fb6b6a..379a4cde2c2c3337d5d762567ef8648e10675c8b 100644
--- a/modules/img/base/pymod/export_image_handle.cc
+++ b/modules/img/base/pymod/export_image_handle.cc
@@ -84,7 +84,6 @@ inline ImageHandle g2a(const Data& d,const Extent& e)
 
 inline ImageHandle ih_copy1(ImageHandle& h) {return h.Copy();}
 inline ImageHandle ih_copy2(ImageHandle& h, bool cc) {return h.Copy(cc);}
-inline ImageHandle ih_copy3(ImageHandle& h, const Extent& e) {return h.Copy(e);}
 
 } // anon ns
 
@@ -112,7 +111,6 @@ void export_ImageHandle()
   class_<ImageHandle, bases<Data> >("ImageHandle", no_init )
     .def("Copy",ih_copy1) 
     .def("Copy",ih_copy2,args("content_flag")) 
-    .def("Copy",ih_copy3,args("extent")) 
     .def("Extract",&ImageHandle::Extract,args("extent"))
     .def("Paste",&ImageHandle::Paste,args("data"))
     .def("Set",&ImageHandle::Set,args("image"))
diff --git a/modules/img/base/pymod/export_mask.cc b/modules/img/base/pymod/export_mask.cc
index 6db4cf05e80dd066460fed2215a83c58444a0396..3385d8ffc69061639aa221442dc24f9d3da4d988 100644
--- a/modules/img/base/pymod/export_mask.cc
+++ b/modules/img/base/pymod/export_mask.cc
@@ -26,6 +26,7 @@
 using namespace boost::python;
 
 #include <ost/img/mask.hh>
+#include <ost/img/mask_info_convert.hh>
 
 namespace ost { namespace img {
 
@@ -100,5 +101,7 @@ void export_Mask()
   def("Mask",mask2);
   def("Mask",mask3);
   def("Mask",mask4);
+  def("InfoToMask",InfoToMask);
+  def("MaskToInfo",MaskToInfo);
 
 }
diff --git a/modules/img/base/pymod/wrap_img.cc b/modules/img/base/pymod/wrap_img.cc
index 20576672d9578fbb56341c5a458bde8138835005..e98a158530546283f4e60e6c6bceb496a62222da 100644
--- a/modules/img/base/pymod/wrap_img.cc
+++ b/modules/img/base/pymod/wrap_img.cc
@@ -54,18 +54,9 @@ void export_Phase();
 void export_Progress();
 void export_Map();
 
-// exception translator
-void translator(const ost::Message& x) {
-  PyErr_SetString(PyExc_UserWarning, x.what() );
-}
-
 // actual module definitions
 BOOST_PYTHON_MODULE(_img)
 {
-  // exception translators
-  register_exception_translator<ost::Message>(&translator);
-  register_exception_translator<ost::Error>(&translator);
-
   export_Data();
   export_DataAlgorithm();
   export_Extent();
diff --git a/modules/img/base/src/CMakeLists.txt b/modules/img/base/src/CMakeLists.txt
index 0d0e7e47a5b42c6e028275471a66928d34d54c2c..97ea2ed0b32297cf7e5298ec975d221a956da806 100644
--- a/modules/img/base/src/CMakeLists.txt
+++ b/modules/img/base/src/CMakeLists.txt
@@ -29,6 +29,7 @@ extent_mask.cc
 spherical_mask.cc
 mask_op.cc
 circle_mask.cc
+mask_info_convert.cc
 image_list.cc
 physical_units.cc
 progress.cc
@@ -86,6 +87,7 @@ spherical_mask.hh
 mask_op.hh
 mask.hh
 circle_mask.hh
+mask_info_convert.hh
 image_list.hh
 physical_units.hh
 progress.hh
@@ -105,4 +107,4 @@ module(NAME img SOURCES "${OST_IMG_SOURCES}"
        HEADERS ${OST_IMG_RASTER_IMAGE_HEADERS} IN_DIR raster_image
                 ${OST_IMG_IMAGE_STATE_HEADERS} IN_DIR image_state
                 ${OST_IMG_HEADERS}
-       DEPENDS_ON geom base)
+       DEPENDS_ON geom base info)
diff --git a/modules/img/base/src/image_handle.cc b/modules/img/base/src/image_handle.cc
index 712868a3181ed0fa47d7989748b759abb18a5dc1..3490869b5a1cc11a804a6fd68aeae6798ba62798 100644
--- a/modules/img/base/src/image_handle.cc
+++ b/modules/img/base/src/image_handle.cc
@@ -93,12 +93,6 @@ ImageHandle ImageHandle::Copy(bool cc) const
   return ImageHandle(StatePtrPtr(new ImageStateBasePtr(ImageStatePtr()->Clone(cc))));
 }
 
-ImageHandle ImageHandle::Copy(const Extent& e) const
-{
-  LOG_MESSAGE("ImageHandle::Copy(Extent) ist deprecated, use Extract() instead" << std::endl);
-  return Extract(e);
-}
-
 ImageHandle ImageHandle::Extract(const Extent& e) const
 {
 #if 0
@@ -662,12 +656,6 @@ ImageHandle ConstImageHandle::Copy(bool cc) const
   return handle_.Copy(cc);
 }
 
-ImageHandle ConstImageHandle::Copy(const Extent& e) const
-{
-  LOG_MESSAGE("ConstImageHandle::Copy(Extent) ist deprecated, use Extract() instead" << std::endl);
-  return handle_.Extract(e);
-}
-
 ImageHandle ConstImageHandle::Extract(const Extent& e) const
 {
   return handle_.Extract(e);
diff --git a/modules/img/base/src/image_handle.hh b/modules/img/base/src/image_handle.hh
index d85bbc5831b8c1d5e7bb1fb095bbcc749367a87a..ef0493487ad8fee82e50572a9b9a2e71ded37b1f 100644
--- a/modules/img/base/src/image_handle.hh
+++ b/modules/img/base/src/image_handle.hh
@@ -153,9 +153,6 @@ public:
   */
   ImageHandle Copy(bool cc=true) const;
 
-  //! DEPRECATED
-  ImageHandle Copy(const Extent& e) const;
-
   //! return a handle to a new image containing a partial copy
   /*!
     The returning domain will match the type (ie REAL or COMPLEX), 
@@ -561,9 +558,6 @@ public:
   //! see ImageHandle::Copy(bool)
   ImageHandle Copy(bool cc=true) const;
 
-  //! DEPRECATED
-  ImageHandle Copy(const Extent& e) const;
-
   //! see ImageHandle::Copy(const Extent&)
   ImageHandle Extract(const Extent& e) const;
 
diff --git a/modules/img/base/src/image_impl.cc b/modules/img/base/src/image_impl.cc
index 09ec52126be57a338f8ce8dc83febd2a60928910..e9280ba48ec15c778e136f193c3852b38d0a5287 100644
--- a/modules/img/base/src/image_impl.cc
+++ b/modules/img/base/src/image_impl.cc
@@ -29,5 +29,4 @@ ImageImpl CreateImageImpl(const Extent& e, DataType type, DataDomain dom)
   return ImageImpl(new ImageStateBasePtr(CreateState(e,type,dom)));
 }
 
-
 }} // ns
diff --git a/modules/img/base/src/image_state/image_state_algorithm.hh b/modules/img/base/src/image_state/image_state_algorithm.hh
index bd1e1f3f17e422335e17bf20f45756671e793ff4..9717dbf1ce1d770a22b8241282cdb6a07fc5002b 100644
--- a/modules/img/base/src/image_state/image_state_algorithm.hh
+++ b/modules/img/base/src/image_state/image_state_algorithm.hh
@@ -331,7 +331,7 @@ public:
 private:
   template <typename T, class D>
   void T_Visit_(ImageStateImpl<T,D>& isi) {
-    VisitState(isi);
+    this->VisitState(isi);
   }
 };
 
@@ -376,7 +376,7 @@ public:
 private:
   template <typename T, class D>
   void T_Visit_(ImageStateImpl<T,D>& isi) const {
-    VisitState(isi);
+    this->VisitState(isi);
   }
 };
 
@@ -402,7 +402,7 @@ public:
 private:
   template <typename T, class D>
   ImageStateBasePtr T_Visit_(const ImageStateImpl<T,D>& isi) {
-    return VisitState(isi);
+    return this->VisitState(isi);
   }
 };
 
@@ -430,7 +430,7 @@ public:
 private:
   template <typename T, class D>
   ImageStateBasePtr T_Visit_(const ImageStateImpl<T,D>& isi) const {
-    return VisitState(isi);
+    return this->VisitState(isi);
   }
 };
 
@@ -457,7 +457,7 @@ public:
 private:
   template <typename T, class D>
   ImageStateBasePtr T_Visit_(ImageStateImpl<T,D>& isi) {
-    return VisitState(isi);
+    return this->VisitState(isi);
   }
 };
 
diff --git a/modules/img/base/src/image_state/image_state_impl.cc b/modules/img/base/src/image_state/image_state_impl.cc
index 190728a105dd5977f6d85640a8f80ff83584c7bb..ca8834fe87fca3199c9018644266d4b5cf6f2539 100644
--- a/modules/img/base/src/image_state/image_state_impl.cc
+++ b/modules/img/base/src/image_state/image_state_impl.cc
@@ -72,7 +72,8 @@ template <typename T, class D>
 ImageStateImpl<T,D>::ImageStateImpl(const ImageStateImpl<T,D>& s):
   domain_(s.domain_),
   data_(s.data_),
-  sampling_(s.sampling_)
+  sampling_(s.sampling_),
+  absolute_origin_(s.absolute_origin_)
 {
   sampling_.SetDomain(domain_.GetDomain());
 }
@@ -85,6 +86,7 @@ ImageStateImpl<T,D>& ImageStateImpl<T,D>::operator=(const ImageStateImpl<T,D>& s
     domain_=s.domain_;
     data_=s.data_; // copy
     sampling_=s.sampling_;
+    absolute_origin_=s.absolute_origin_;
     sampling_.SetDomain(domain_.GetDomain());
   }
   return *this;
@@ -103,7 +105,7 @@ boost::shared_ptr<ImageStateImpl<T,D> > ImageStateImpl<T,D>::CloneState(bool cc)
   if(cc) {
     return SharedPtrType(new ImageStateImpl<T,D>(*this));
   } else {
-    return SharedPtrType(new ImageStateImpl<T,D>(domain_.GetLogicalExtent(),sampling_));
+    return SharedPtrType(new ImageStateImpl<T,D>(domain_.GetLogicalExtent(),sampling_,this->absolute_origin_));
   }
 }
 
diff --git a/modules/img/base/src/mask_info_convert.cc b/modules/img/base/src/mask_info_convert.cc
new file mode 100644
index 0000000000000000000000000000000000000000..de40f80a4733b605be1543f61dee6fec88d0ad56
--- /dev/null
+++ b/modules/img/base/src/mask_info_convert.cc
@@ -0,0 +1,227 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 by the OpenStructure authors
+// Copyright (C) 2003-2010 by the IPLT authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+//------------------------------------------------------------------------------
+
+/*
+  Authors: Andreas Schenk, Ansgar Philippsen
+*/
+
+#include <stack>
+
+#include <ost/info/info_visitor.hh>
+#include <ost/info/info.hh>
+#include "mask_info_convert.hh"
+#include "polygon_mask.hh"
+#include "circle_mask.hh"
+#include "extent_mask.hh"
+#include "composite_mask.hh"
+#include "inverted_mask.hh"
+#include "spherical_mask.hh"
+#include "mask_visitor.hh"
+
+namespace ost{ namespace img {
+
+namespace {
+
+
+
+class PolygonInfoVisitor: public info::InfoConstVisitor
+{
+public:
+  PolygonInfoVisitor():
+    p_()
+  {}
+
+  Polygon2 GetPolygon() const {return p_;}
+
+  virtual bool VisitGroup(const info::InfoGroup& group)
+  {
+    if(group.GetName()=="Polygon"){
+      return true;
+    } else if(group.GetName()=="Node"){
+      p_.AddNode(geom::Vec2(group.GetItem("x").AsFloat(),
+			    group.GetItem("y").AsFloat()));
+      return false;
+    }
+    return true;
+  }
+
+  virtual void VisitGroupFinish(const info::InfoGroup& group)
+  {}
+
+private:
+  Polygon2 p_;  
+};
+
+// this is used recursively
+class MaskInfoVisitor: public info::InfoConstVisitor
+{
+public:
+  MaskInfoVisitor():
+    mask_list_()
+  {}
+
+  std::vector<MaskPtr> GetMaskList() const {return mask_list_;}
+
+  virtual bool VisitGroup(const info::InfoGroup& group) 
+  {
+    String name=group.GetName();
+    if(name=="Composite"){
+      String opname=group.GetItem("Operator").GetValue();
+      MaskInfoVisitor miv;
+      group.Apply(miv,false); // subgroups
+      std::vector<MaskPtr> mpl = miv.GetMaskList();
+      mask_list_.push_back(MaskPtr(new CompositeMask(mpl[0],mpl[1],opname)));
+      return false;
+    }else if(name=="Invert"){
+      MaskInfoVisitor miv;
+      group.Apply(miv,false); // subgroups
+      std::vector<MaskPtr> mpl = miv.GetMaskList();
+      mask_list_.push_back(MaskPtr(new InvertedMask(mpl[0])));
+      return false;
+    }else if(name=="Circle"){
+      Circle2 c;
+      c.SetRadius(group.GetItem("Radius").AsFloat());
+      c.SetCenter(geom::Vec2(group.GetItem("Center/x").AsFloat(),
+			     group.GetItem("Center/y").AsFloat()));
+      mask_list_.push_back(MaskPtr(new CircleMask(c)));
+      return false;
+    }else if(name=="Polygon"){
+      PolygonInfoVisitor pvis;
+      group.Apply(pvis);
+      mask_list_.push_back(MaskPtr(new PolygonMask(pvis.GetPolygon())));
+      return false;
+    }else if(name=="Extent"){
+      Extent e(Point(group.GetItem("Start/x").AsInt(),
+		     group.GetItem("Start/y").AsInt()),
+	       Point(group.GetItem("End/x").AsInt(),
+		     group.GetItem("End/y").AsInt()));
+      mask_list_.push_back(MaskPtr(new ExtentMask(e)));
+      return false;
+    }else if(name=="Sphere"){
+      Sphere s;
+      s.SetRadius(group.GetItem("Radius").AsFloat());
+      s.SetOrigin(geom::Vec3(group.GetItem("Origin/x").AsFloat(),
+			     group.GetItem("Origin/y").AsFloat(),
+			     group.GetItem("Origin/z").AsFloat()));
+      mask_list_.push_back(MaskPtr(new SphericalMask(s)));
+      return false;
+    }
+    return true;    
+  }
+
+  virtual void VisitGroupFinish(const info::InfoGroup& group)
+  {
+  }
+
+private:
+  std::vector<MaskPtr> mask_list_;
+};
+
+
+// mask visitor for mask->info conversion
+class MaskToInfoVisitor: public MaskVisitor
+{
+  typedef std::stack<info::InfoGroup> InfoGroupStack;
+public:
+  MaskToInfoVisitor(info::InfoGroup& g):
+    igs_()
+  {
+    igs_.push(g);
+  }
+  virtual void VisitCircleMask(CircleMask& m) 
+  {
+    info::InfoGroup cg=igs_.top().CreateGroup("Circle");
+    info::InfoGroup centerg=cg.CreateGroup("Center");
+    centerg.CreateItem("x","").SetFloat(m.GetCenter()[0]);
+    centerg.CreateItem("y","").SetFloat(m.GetCenter()[1]);
+    cg.CreateItem("Radius","").SetFloat(m.GetRadius());
+  }
+  virtual void VisitCompositeMask(CompositeMask& m) 
+  {
+    info::InfoGroup compg=igs_.top().CreateGroup("Composite");
+    compg.CreateItem("Operator",m.GetOperatorName());
+    igs_.push(compg);
+  }
+  virtual void VisitCompositeMaskFinish(CompositeMask& m) 
+  {
+    igs_.pop();
+  }
+  virtual void VisitExtentMask(ExtentMask& m) 
+  {
+    info::InfoGroup extg=igs_.top().CreateGroup("Extent");
+    info::InfoGroup startg=extg.CreateGroup("Start");
+    startg.CreateItem("x","").SetInt(m.GetStart()[0]);
+    startg.CreateItem("y","").SetInt(m.GetStart()[1]);
+    info::InfoGroup endg=extg.CreateGroup("End");
+    endg.CreateItem("x","").SetInt(m.GetEnd()[0]);
+    endg.CreateItem("y","").SetInt(m.GetEnd()[1]);
+  }
+  virtual void VisitInvertedMask(InvertedMask& m) 
+  {
+    info::InfoGroup invertg=igs_.top().CreateGroup("Invert");
+    igs_.push(invertg);
+  }
+  virtual void VisitInvertedMaskFinish(InvertedMask& m) 
+  {
+    igs_.pop();
+  }
+  virtual void VisitPolygonMask(PolygonMask& m) 
+  {
+    info::InfoGroup polyg=igs_.top().CreateGroup("Polygon");
+    for(unsigned int nn=0;nn<m.GetNodeCount();++nn) {
+      info::InfoGroup nodeg=polyg.CreateGroup("Node");
+      geom::Vec2 node=m.GetNode(nn);
+      nodeg.CreateItem("x","").SetFloat(node[0]);
+      nodeg.CreateItem("y","").SetFloat(node[1]);
+    }
+  }
+  virtual void VisitSphericalMask(SphericalMask& m) 
+  {
+    info::InfoGroup cg=igs_.top().CreateGroup("Sphere");
+    info::InfoGroup centerg=cg.CreateGroup("Origin");
+    centerg.CreateItem("x","").SetFloat(m.GetOrigin()[0]);
+    centerg.CreateItem("y","").SetFloat(m.GetOrigin()[1]);
+    centerg.CreateItem("z","").SetFloat(m.GetOrigin()[2]);
+    cg.CreateItem("Radius","").SetFloat(m.GetRadius());
+  }
+private:
+  InfoGroupStack igs_;
+};
+
+} // anon ns
+
+MaskPtr DLLEXPORT InfoToMask(const info::InfoGroup& g)
+{
+  MaskInfoVisitor vis;
+  g.Apply(vis);
+  std::vector<MaskPtr> mlist = vis.GetMaskList();
+  if(!mlist.empty()) {
+    return mlist[0];
+  }
+  return MaskPtr();
+}
+
+void MaskToInfo(const MaskPtr& mptr ,info::InfoGroup& g)
+{
+  MaskToInfoVisitor vis(g);
+  mptr->Apply(vis);
+}
+
+}} //ns
diff --git a/modules/gui/src/plot_viewer/plot_ticker_fw.hh b/modules/img/base/src/mask_info_convert.hh
similarity index 71%
rename from modules/gui/src/plot_viewer/plot_ticker_fw.hh
rename to modules/img/base/src/mask_info_convert.hh
index 46e54a3067b85ccf4cec527e7419dba2c4ce6f5b..04a01eac42e211c08a18bc2f28c6897fce371bfb 100644
--- a/modules/gui/src/plot_viewer/plot_ticker_fw.hh
+++ b/modules/img/base/src/mask_info_convert.hh
@@ -2,6 +2,7 @@
 // This file is part of the OpenStructure project <www.openstructure.org>
 //
 // Copyright (C) 2008-2010 by the OpenStructure authors
+// Copyright (C) 2003-2010 by the IPLT authors
 //
 // This library is free software; you can redistribute it and/or modify it under
 // the terms of the GNU Lesser General Public License as published by the Free
@@ -16,18 +17,22 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#ifndef PLOT_TICKER_FW_HH_
-#define PLOT_TICKER_FW_HH_
 
 /*
-  Author: Andreas Schenk
+  Authors: Andreas Schenk, Ansgar Philippsen
 */
 
-#include <boost/shared_ptr.hpp>
+#ifndef MASK_INFO_CONVERT_HH_
+#define MASK_INFO_CONVERT_HH_
 
+#include <ost/info/info_group.hh>
+#include "mask_base_fw.hh"
 
-class PlotTickerBase;
+namespace ost { namespace img {
 
-typedef boost::shared_ptr<PlotTickerBase> PlotTickerPtr;
+MaskPtr DLLEXPORT InfoToMask(const info::InfoGroup& g);
+void DLLEXPORT MaskToInfo(const MaskPtr& mptr, info::InfoGroup& g);
 
-#endif /*PLOT_TICKER_FW_HH_*/
+}} //ns
+
+#endif /*MASK_INFO_CONVERT_HH_*/
diff --git a/modules/img/base/src/module_config.hh b/modules/img/base/src/module_config.hh
index 0205ffc00c9d9acde7e9c65737cf74f52392f5fc..ad9f913a3be6f400661e7973b61d59d4c735970e 100644
--- a/modules/img/base/src/module_config.hh
+++ b/modules/img/base/src/module_config.hh
@@ -25,9 +25,9 @@
 #if defined(OST_MODULE_OST_IMG)
 #  define DLLEXPORT_OST_IMG_BASE DLLEXPORT
 #  if defined(_MSC_VER)
-#    define OST_IMG_ALG_EXPLICIT_INST_DECL(c, t)
+#    define OST_IMG_BASE_EXPLICIT_INST_DECL(c, t)
 #  else
-#    define OST_IMG_ALG_EXPLICIT_INST_DECL(c, t) extern template c TEMPLATE_EXPORT t;
+#    define OST_IMG_BASE_EXPLICIT_INST_DECL(c, t) extern template c TEMPLATE_EXPORT t;
 #  endif
 #else
 #  define DLLEXPORT_OST_IMG_BASE DLLIMPORT
diff --git a/modules/img/base/src/paste_impl.hh b/modules/img/base/src/paste_impl.hh
index 91ae6c4d86a87927596a8ae71a6744cb0fd95658..689f9a59f3111e4780b9c890eb1a525c10e0ca27 100644
--- a/modules/img/base/src/paste_impl.hh
+++ b/modules/img/base/src/paste_impl.hh
@@ -47,6 +47,8 @@ typedef image_state::ImageStateNonModAlgorithm<PasteFnc> PasteImpl;
 
 }
 
+OST_IMG_BASE_EXPLICIT_INST_DECL(class,image_state::ImageStateNonModAlgorithm<detail::PasteFnc>)
+
 }} // ns
 
 #endif
diff --git a/modules/img/base/src/pixel_sampling.cc b/modules/img/base/src/pixel_sampling.cc
index 5cff35235abfc6c634b2632b422d7ef7e1afe005..0ba2c608d7ad5ef7233d2a3fa3a0ca8a9067e3b5 100644
--- a/modules/img/base/src/pixel_sampling.cc
+++ b/modules/img/base/src/pixel_sampling.cc
@@ -122,7 +122,7 @@ Vec3 PixelSampling::Vec2Coord(const Vec3& p) const
 void PixelSampling::set_spat_scale(const Vec3& dim)
 {
   if(dim[0]<=0.0 || dim[1]<0.0 || dim[2]<0.0) {
-    LOG_ERROR("invalid spatial pixel sampling, must be >0" << std::endl);
+    LOG_ERROR("invalid spatial pixel sampling, must be >0");
     return;
   }
   spat_scale_=dim;
diff --git a/modules/img/base/src/value_util.hh b/modules/img/base/src/value_util.hh
index b17e42cff6c9277e74cec1b73498d5fbeb7cd2a9..44247eda7d3779af0721d1a8e18c89a8e9c2135e 100644
--- a/modules/img/base/src/value_util.hh
+++ b/modules/img/base/src/value_util.hh
@@ -69,7 +69,16 @@ T Random() {
   return UniformRandom();
 }
  
-  
+typedef boost::variate_generator<boost::mt19937&, boost::uniform_int<> > UniformIntGenerator;
+
+inline
+UniformIntGenerator GetUniformIntGenerator(int min, int max)
+{
+  boost::uniform_int<> dist(min,max);
+  return UniformIntGenerator(RandomGenerator, dist);
+}
+
+
 // value to value conversion
   
 // declaration
diff --git a/modules/index.rst b/modules/index.rst
index 52dcde170b022e7824aa2cedd23d3a5c3c65332d..147274735b6617024bf345b5d88c6ce4b031c8fa 100644
--- a/modules/index.rst
+++ b/modules/index.rst
@@ -2,7 +2,93 @@ OpenStructure documentation
 ================================================================================
 
 .. toctree::
+  :hidden:
+  :maxdepth: 1
+  
+  install
+  intro
+  base/generic
+  base/base
+  geom/geom
+  mol/base/mol
+  mol/alg/molalg
+  conop/conop
+  img/base/img
+  img/alg/alg
+  seq/base/seq
+  io/io
+  gfx/gfx
+  gui/gui
+  newmodule
+  external
+  
+For Starters
+--------------------------------------------------------------------------------
 
-  geom/doc/geom
-  conop/doc/conop
-  mol/base/doc/mol
\ No newline at end of file
+**Installation**: `install from binary <http://www.openstructure.org/download/>`_ | :doc:`install from source <install>`
+
+**Tutorial Style**: :doc:`introduction <intro>` | :doc:`molecules intro <intro-01>` | :doc:`images intro <intro-02>` | :doc:`graphics intro <intro-03>`
+
+
+
+
+Molecules
+--------------------------------------------------------------------------------
+
+**Overview**: :doc:`molecules intro <intro-01>` | :doc:`mol overview <mol/base/mol>` | :doc:`graphical entity<gfx/entity>` | :doc:`entity <mol/base/entity>`
+
+**Input/Output**: :ref:`loading and saving molecules <mol-io>`
+
+**Connectivity**: :doc:`the conop module <conop/conop>`
+
+
+
+
+Density Maps and Images
+--------------------------------------------------------------------------------
+
+**Overview**: :doc:`images intro <intro-02>` | :doc:`img module <img/base/img>` | :doc:`img.alg module <img/alg/alg>`
+
+
+
+
+Sequences and Alignments
+--------------------------------------------------------------------------------
+
+**Overview**: :doc:`sequence module <seq/base/seq>`
+
+**Input/Output**: :ref:`loading and saving sequences <seq-io>`
+
+
+
+
+Graphics
+--------------------------------------------------------------------------------
+
+**Overview** :doc:`graphics intro <intro-03>`
+
+**Main Classes**: :doc:`the scene <gfx/scene>` | :doc:`graphical entity <gfx/entity>`
+
+
+
+
+Graphical User Interface
+--------------------------------------------------------------------------------
+
+**Overview**: :doc:`module overview <gui/gui>` | :doc:`organization <gui/layout>` :doc:`tools <gui/tools>`
+
+**Widgets**: :doc:`python shell <gui/python_shell>` | :doc:`sequence viewer <gui/sequence_viewer>`
+
+
+
+
+Extending OpenStructure
+--------------------------------------------------------------------------------
+
+**Howto:** :doc:`write new modules <newmodule>` | :doc:`integrate third-party tools <external>` | :doc:`logging <base/logging>`
+
+
+
+
+
+  
\ No newline at end of file
diff --git a/modules/info/pymod/wrap_info.cc b/modules/info/pymod/wrap_info.cc
index a449095327199007bef05ecf95b0290f60d1d4e9..0f80c9522eddb2362449998df8ccb156175f2a5e 100644
--- a/modules/info/pymod/wrap_info.cc
+++ b/modules/info/pymod/wrap_info.cc
@@ -36,9 +36,6 @@ using namespace ost::info;
 
 namespace {
 
-void info_error_translator(const InfoError& x) {
-  PyErr_SetString(PyExc_UserWarning, x.what());
-}
 
 InfoHandle (*CreateInfoPtr1)()=CreateInfo;
 InfoHandle (*CreateInfoPtr2)(const String&)=CreateInfo;
@@ -63,7 +60,7 @@ void info_group_apply2b(InfoGroup* g, InfoConstVisitor& v, bool b)
   g->Apply(v,b);
 }
 
-void info_group_remove1(InfoGroup* g, InfoPath& path )
+void info_group_remove1(InfoGroup* g, const String& path )
 {
   g->Remove(path);
 }
@@ -72,7 +69,7 @@ void info_group_remove2(InfoGroup* g, InfoGroup& group )
 {
   g->Remove(group);
 }
-void info_group_remove3(InfoGroup* g, InfoPath& path, bool use_defaults )
+void info_group_remove3(InfoGroup* g, const String& path, bool use_defaults )
 {
   g->Remove(path,use_defaults);
 }
@@ -160,7 +157,6 @@ BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(retrieveitem_overloads, RetrieveItem, 1,
 
 BOOST_PYTHON_MODULE(_info)
 {
-  register_exception_translator<InfoError>(&info_error_translator);
 
   enum_<Type>("ItemType")
     .value("STRING",IT_STRING)
diff --git a/modules/info/src/info_group.cc b/modules/info/src/info_group.cc
index de5d158a0ba2943257fdb3a37ae81cdc19cb7e75..fcc6fb7083789d5ae58c7e05336defabfd5a291b 100644
--- a/modules/info/src/info_group.cc
+++ b/modules/info/src/info_group.cc
@@ -169,16 +169,25 @@ bool InfoGroup::do_group_lookup(std::vector<String>::const_iterator& pos,
 } 
 
 bool InfoGroup::do_group_lookup(std::vector<String>::const_iterator& pos,
-                                const std::vector<String>::const_iterator& end,
-                                InfoGroup& subgroup) const
+				const std::vector<String>::const_iterator& end,
+				InfoGroup& subgroup) const
 {
-  InfoGroupList subgroups;
-  if (this->do_group_lookup(pos, end, subgroups)) {
-    subgroup.Swap(subgroups.front());
+  if(pos==end) {
     return true;
   }
+  if(impl_->HasSub(*pos)) {
+    InfoGroup subgrp(root_,impl_->GetSub(*pos));
+    // remember last valid group
+    subgroup = subgrp;
+    ++pos;
+    if(pos==end) {
+      return true;
+    } else {
+      return subgrp.do_group_lookup(pos,end,subgroup);
+    }
+  }
   return false;
-}
+} 
 
 bool InfoGroup::HasGroup(const InfoPath& path, bool use_defaults) const
 {
@@ -210,6 +219,7 @@ InfoGroup InfoGroup::RetrieveGroup(const InfoPath& path, bool use_defaults)
     return GetGroup(path);
   } else {
     std::vector<String> plist=path.GetList();
+    if(plist.empty()) return *this;
     InfoGroup last_group(*this);
     std::vector<String>::const_iterator pos=plist.begin();
     bool ret=do_group_lookup(pos,plist.end(),last_group);
diff --git a/modules/info/src/info_handle.hh b/modules/info/src/info_handle.hh
index f7677a73618e218b3ec56e06c98414611d2f2693..aa3a7f3ce7c5b19a6b099283d0d81e75169ec345 100644
--- a/modules/info/src/info_handle.hh
+++ b/modules/info/src/info_handle.hh
@@ -51,7 +51,7 @@ DLLEXPORT InfoHandle LoadInfo(const String& file);
   to an underlying info class, which is shared among copies of InfoHandles
   unless the Copy() method is used.
 */
-class DLLEXPORT InfoHandle {
+class DLLEXPORT_OST_INFO InfoHandle {
   friend InfoHandle CreateInfo();
   friend InfoHandle CreateInfo(const String& text);
   friend InfoHandle LoadInfo(const String&);
diff --git a/modules/info/src/info_impl.cc b/modules/info/src/info_impl.cc
index a9726b11d4de4cfdbe2547ce488a92d7302f869c..de1aeaa1f430e32caec03cd2f0e89835314dac7a 100644
--- a/modules/info/src/info_impl.cc
+++ b/modules/info/src/info_impl.cc
@@ -97,12 +97,7 @@ InfoImpl::InfoImpl(const String& fname):
   document_("EMDataInfo"),
   def_list_()
 {
-  QFile file(QS(fname));
-  if (!document_.setContent(&file)) {
-    file.close();
-    throw(InfoError("QDomDocument.setContent failed"));
-  }
-  file.close();
+  Import(fname);
 }
 
 RootPtr InfoImpl::Copy() const
@@ -117,9 +112,34 @@ void InfoImpl::Import(const String& fname)
 {
   document_=QDomDocument("EMDataInfo");
   QFile file(QS(fname));
-  if (!document_.setContent(&file)) {
+  if(!file.exists()){
     file.close();
-    throw(InfoError("QDomDocument.setContent failed"));
+    throw(InfoError("File: "+fname+" doesn't exist."));
+  }
+  QString errormessage;
+  int errorline,errorcolumn;
+  if (!document_.setContent(&file,&errormessage,&errorline,&errorcolumn)) {
+    file.close();
+    if(file.error()){
+      switch(file.error()){
+      case QFile::ReadError:
+        throw(InfoError("Error while reading file: "+fname));
+        break;
+      case QFile::OpenError:
+        throw(InfoError("File: "+fname+" could not be opened."));
+        break;
+      case QFile::PermissionsError:
+        throw(InfoError("Permission error accessing file: "+fname));
+        break;
+      default:
+        throw(InfoError("Unspecified error while accessing file: "+fname));
+        break;
+      }
+    }else{
+      std::ostringstream stream;
+      stream << "Error while accessing file " << fname << ": " << errormessage.toStdString() << " in line " << errorline << " column " << errorcolumn;
+      throw(InfoError(stream.str()));
+    }
   }
   file.close();
 }
diff --git a/modules/info/src/info_set.hh b/modules/info/src/info_set.hh
index 43dda09edcf1bf7fab7a56a8ee3954ec161229a7..54562c975cad15de01b4c7ad9a270e77cf3fcfb3 100644
--- a/modules/info/src/info_set.hh
+++ b/modules/info/src/info_set.hh
@@ -25,12 +25,12 @@
 #include <map>
 
 #include <ost/base.hh>
-
+#include "module_config.hh"
 #include "info_group.hh"
 
 namespace ost { namespace info {
 
-class DLLEXPORT InfoSet {
+class DLLEXPORT_OST_INFO InfoSet {
 public:
   InfoSet(const String& name="");
 
diff --git a/modules/info/src/info_verbose_visitor.hh b/modules/info/src/info_verbose_visitor.hh
index dd387db69dd77bcf83317ed0f269273a65a84b54..210b82d3655cbd47fea6913eb37f478ef0d8f6ab 100644
--- a/modules/info/src/info_verbose_visitor.hh
+++ b/modules/info/src/info_verbose_visitor.hh
@@ -31,7 +31,7 @@
 
 namespace ost { namespace info {
 
-class DLLEXPORT VerboseInfoVisitor: public InfoVisitor {
+class DLLEXPORT_OST_INFO VerboseInfoVisitor: public InfoVisitor {
 public:
   virtual void VisitItem(InfoItem& item);
   virtual bool VisitGroup(InfoGroup& group);
diff --git a/modules/info/src/info_visitor.hh b/modules/info/src/info_visitor.hh
index c408a85df626f2a35ce3ec0b19ead2ecbb24970f..f677546b8bc58b6448c855a535ae1395c72525d5 100644
--- a/modules/info/src/info_visitor.hh
+++ b/modules/info/src/info_visitor.hh
@@ -28,11 +28,12 @@
 #define OST_INFO_VISITOR_HH
 
 #include <ost/base.hh>
+#include "module_config.hh"
 #include "info_fw.hh"
 
 namespace ost { namespace info {
 
-class DLLEXPORT InfoVisitor {
+class DLLEXPORT_OST_INFO InfoVisitor {
 public:
   virtual ~InfoVisitor();
 
@@ -54,7 +55,7 @@ public:
   virtual void VisitGroupFinish(InfoGroup& group);
 };
 
-class DLLEXPORT InfoConstVisitor {
+class DLLEXPORT_OST_INFO InfoConstVisitor {
 public:
   virtual ~InfoConstVisitor();
 
diff --git a/modules/io/doc/formats.rst b/modules/io/doc/formats.rst
new file mode 100644
index 0000000000000000000000000000000000000000..3912141d21a5a59de7aeb94306e7e014890c1069
--- /dev/null
+++ b/modules/io/doc/formats.rst
@@ -0,0 +1,73 @@
+Supported File Formats
+================================================================================
+
+Structure File Formats
+--------------------------------------------------------------------------------
+
+The following file formats are supported by :func:`~ost.io.LoadEntity`. 
+
+
+
+CRD - CARD format file used by CHARMM
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+This trajectory file format is used by the CHARMM program suite (Molecular Modelling).
+
+*Recognized File Extensions*
+  crd
+
+PDB - Brookhaven PDB File
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Fine grained control over PDB file import is available via the 
+:func:`~ost.io.LoadPDB` function. The PDB importer supports loading gzipped PDB 
+files, which are auto-detected by the .gz file extension.
+
+*Recognized File Extensions*
+  ent, pdb, ent.gz, pdb.gz
+
+*Format Name*
+  pdb
+
+PQR
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+  pqr
+
+*Format Name*
+  pqr
+  
+SDF - Structured Data File
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+  sdf
+  
+Sequence File Formats
+--------------------------------------------------------------------------------
+
+FASTA
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+  fasta, fna, fas, fa, fsa
+  
+*Format Name*
+  fasta
+
+ClustalW
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+  aln
+  
+*Format Name*
+  clustal
+
+Promod
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+  ali
+  
+*Format Name*
+  promod
diff --git a/modules/io/doc/io.rst b/modules/io/doc/io.rst
new file mode 100644
index 0000000000000000000000000000000000000000..b2037b3addfce4c660774d6177e33c261db729a6
--- /dev/null
+++ b/modules/io/doc/io.rst
@@ -0,0 +1,224 @@
+:mod:`~ost.io` - Input and Output of Sequences, Structures and Maps
+================================================================================
+
+.. toctree::
+  :hidden:
+  
+  formats
+
+.. module:: ost.io
+  :synopsis: Input and output of sequences, alignments, structures, images and density maps.
+
+The io module deals with input and output of :class:`entities 
+<ost.mol.EntityHandle>`, :class:`alignments <ost.seq.AlignmentHandle>`, 
+:class:`sequences <ost.seq.SequenceHandle>`, :class:`images 
+<ost.img.ImageHandle>`. Importers for common file formats containing molecules 
+such as PDB, SDF and CHARMM trajectory files are available. Sequence and 
+alignment file formats such as FASTA and CLUSTALW are supported as well as  
+various image data (e.g. png, dm3) and density map files (e.g. CCP4, MRC). 
+
+.. _mol-io:
+
+Molecular Structures
+--------------------------------------------------------------------------------
+
+Loading Molecular Structures
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The :mod:`~ost.io` modules offers several ways to load molecular structures 
+depending on your requirements. The most general way is offered by 
+:func:`~ost.io.LoadEntity`, which will automatically detect the file format based 
+on the file extension.
+
+.. function:: LoadEntity(filename, format='auto')
+
+  Load entity from disk. If format is set to 'auto', the function guesses the 
+  filetype based on the extension of the file. Files ending in '.pdb', '.ent', 
+  '.ent.gz', '.pdb.gz' will automatically be loaded as PDB files, for example. 
+  For files without or exotic extensions, the format can be set explicitly as 
+  the second parameter. 
+  
+  .. code-block:: python
+
+    # recognizes SDF file by file extension
+    ent=io.LoadEntity('file.sdf')
+
+    # In this case, there is no file extensions, so you have to say it's a 
+    # SDF file explicitly
+    ent=io.LoadEntity('file', 'sdf')
+
+  For a list of file formats supported by :func:`LoadEntity`, see :doc:`formats`.
+  
+  :raises: :exc:`~ost.io.IOUnknownFormatException` if the format string supplied 
+      is not recognized or the file format can not be detected based on the 
+      file extension
+      
+      :exc:`~ost.io.IOException` if the import fails due to an erroneous or 
+      inexistent file
+
+Some of the formats have a dedicated function that allows you to tweak many 
+parameters that affect the import. PDB files can be loaded with 
+:func:`~ost.io.LoadPDB`. It offers a tighter control over the exact loading 
+behaviour.
+
+.. autofunction:: ost.io.LoadPDB
+
+
+Saving Molecular Structures
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Saving a complete entity or a view is a matter of calling 
+:func:`~ost.io.SaveEntity`.
+
+.. code-block:: python
+  
+  ent=io.LoadEntity('protein.pdb')
+  # save full entity
+  io.SaveEntity(ent, 'full.pdb')
+  # only save C-alpha atoms
+  io.SaveEntity(ent.Select('aname=CA and peptide=true'), 'calpha.pdb')
+  
+:func:`~ost.io.SavePDB` provides a simple way to save several entities into one 
+file:
+
+
+.. code-block:: python
+  
+  ent=io.LoadEntity('protein.pdb')
+  # Save complete entity
+  io.SavePDB(ent, 'full.pdb')
+  # Save chain A and chain B separately
+  io.SavePDB([ent.Select('cname=A'), ent.Select('cname=B')], 'split.pdb')
+
+
+.. function:: SaveEntity(ent, filename, format='auto')
+  
+  Save entity to disk. If format is set to 'auto', the function guesses the 
+  filetype based on the file extension, otherwise the supplied format is checked 
+  against the available export plugins.
+  
+  :param ent: The entity to be saved
+  :type  ent: :class:`~ost.mol.EntityHandle` or :class:`~ost.mol.EntityView`
+  :param filename: The filename
+  :type  filename: string
+  :param format: Name of the format
+  :type  format: string
+  
+  :raises: :exc:`~ost.io.IOUnknownFormatException` if the format string supplied 
+      is not recognized or the file format can not be detected based on the 
+      file extension
+      
+.. autofunction:: ost.io.SavePDB
+
+
+
+.. _seq-io:
+
+Sequences and Alignments
+--------------------------------------------------------------------------------
+
+Loading sequence or alignment files
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. function:: LoadSequence(filename, format='auto')
+
+  Load sequence data from disk. If format is set to 'auto', the function guesses 
+  the filetype based on the extension of the file. Files ending in '.fasta', 
+  '.aln' will automatically be loaded.
+  
+  For files with non-standard extensions, the format can be set explicitly 
+  specifying the `format` parameter. 
+  
+  .. code-block:: python
+
+    # recognizes FASTA file by file extension
+    myseq=io.LoadSequence('seq.fasta')
+    # for obtaining a SequenceList
+    seqlist=io.LoadSequenceList('seqs.fasta')
+    # or for multiple aligned fasta files use
+    aln=io.LoadAlignment('algnm.aln',format="clustal")
+    
+  For a list of file formats supported by :func:`LoadSequence` see
+  :doc:`formats`.
+  
+  :raises: :exc:`~ost.io.IOUnknownFormatException` if the format string supplied 
+      is not recognized or the file format can not be detected based on the 
+      file extension
+      
+      :exc:`~ost.io.IOException` if the import fails due to an erroneous or 
+      inexistent file
+
+.. function:: LoadSequenceList(filename, format='auto')
+
+  For a desription of how to use :func:`LoadSequenceList` please refer to 
+  :func:`LoadSequence`. For a list of file formats supported by
+  :func:`LoadSequenceList` see :doc:`formats`.
+
+.. function:: LoadAlignment(filename, format='auto')
+
+  For a desription of how to use :func:`LoadAlignment` please refer to 
+  :func:`LoadSequence`. For a list of file formats supported by 
+  :func:`LoadAlignment` see :doc:`formats`.
+      
+Saving Sequence Data
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. function:: SaveSequence(filename, format='auto')
+
+  Saving sequence data is performed by calling :func:`SaveSequence`.
+  For files with non-standard extensions, the format can be set explicitly 
+  specifying the 'format' parameter. 
+  
+  .. code-block:: python
+
+    # recognizes FASTA file by file extension
+    io.SaveSequence(myseq,'seq.fasta')
+    # for saving a SequenceList
+    io.SaveSequenceList(seqlist,'seqlist.fasta')
+    # or multiple aligned fasta files
+    io.SaveAlignment(aln,'algnm.aln',format="clustal")
+    
+  For a list of file formats supported by :func:`SaveSequence` see
+  :doc:`formats`.
+  
+  :raises: :exc:`~ost.io.IOUnknownFormatException` if the format string supplied 
+      is not recognized or the file format can not be detected based on the 
+      file extension
+      
+      :exc:`~ost.io.IOException` if the import fails due to an erroneous or 
+      inexistent file
+
+.. function:: SaveSequenceList(filename, format='auto')
+
+  For a desription of how to use :func:`SaveSequenceList` please refer to 
+  :func:`SaveSequence`. For a list of file formats supported by 
+  :func:`SaveSequenceList` see :doc:`formats`.
+
+.. function:: SaveAlignment(filename, format='auto')
+
+  For a desription of how to use :func:`SaveAlignment` please refer to 
+  :func:`SaveSequence`.
+  
+  For a list of file formats supported by :func:`SaveAlignment` see 
+  :doc:`formats`.
+
+
+.. testsetup:: io
+  from ost import io
+
+.. testcode:: io
+  :hide:
+
+  from ost import io,seq
+  ent=io.LoadPDB('./examples/entity/fragment.pdb')
+  print ent.atom_count 
+  myseq=seq.SequenceFromChain('t',ent.chains[0])
+  print myseq.GetLength()
+
+.. testoutput:: io
+  :hide:
+
+  81
+  12
+
+
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index 344f971292b41d79cddbb61925c71d5296d0d474..2cf6900a10edd878f78a2b748830d33f2f102afe 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -16,35 +16,98 @@
 # along with this library; if not, write to the Free Software Foundation, Inc.,
 # 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #------------------------------------------------------------------------------
+import os, tempfile, ftplib, httplib
+
 from _io import *
-from ost import mol,conop
+from ost import mol, conop
+
+def __GetModelFromPDB(model_id, output_dir, file_pattern='pdb%s.ent.gz'):
+  file_name = file_pattern % model_id
+  file_path = os.path.join(output_dir,file_name)
+  try:
+    server="ftp.wwpdb.org"
+    ftp=ftplib.FTP(server,"anonymous","user@")
+    ftp.cwd("pub/pdb/data/structures/all/pdb")
+    ftp_retrfile=open(file_path,"wb")
+    ftp.retrbinary("RETR "+file_name,ftp_retrfile.write)
+    ftp_retrfile.close()
+  except:
+    conn=httplib.HTTPConnection('www.pdb.org')
+    conn.request('GET', '/pdb/files/%s.pdb.gz' % model_id )
+    response=conn.getresponse()
+    if response.status==200:
+      data=response.read()
+      f=open(os.path.join(output_dir, file_pattern % model_id), 'w+')
+      f.write(data)
+      f.close()
+    else:
+      conn.close()
+      return False
+  return os.path.getsize(file_path) > 0
 
 def LoadPDB(filename, restrict_chains="", no_hetatms=False,
             fault_tolerant=False, load_multi=False,
-            join_spread_atom_records=False, calpha_only=False):
+            join_spread_atom_records=False, calpha_only=False, 
+            remote=False, dialect='PDB', strict_hydrogens=False):
   """
-  Load PDB file from disk.
+  Load PDB file from disk and returns one or more entities. Several options 
+  allow to customize the exact behaviour of the PDB import.
 
-  If restrict_chains is not an empty string, only chains listed in the
-  string will be imported.
+  :param restrict_chains: If not an empty string, only chains listed in the
+     string will be imported.
 
-  If fault_tolerant is set to true, the import will succeed, even if the
-  PDB contains faulty records. The faulty records will be ignored in that
-  case.
+  :param fault_tolerant: If True, the import will succeed, even if the
+     PDB contains faulty records. The faulty records will be ignored and import 
+     continues as if the records haven't been present.
 
-  If not_hetatms is set to True, HETATM records will be ignored
+  :param no_hetatms: If set to True, HETATM records will be ignored
 
-  If load_multi is set to true, a list of entities will be returned instead
-  of only the first.
+  :param load_multi: If set to True, a list of entities will be returned instead
+     of only the first. This is useful when dealing with multi-PDB files.
 
-  If join_spread_atom_records is set to true, atom records belonging to the
-  same residue are joined, even if they do not appear sequentially in the PDB
-  file.
+  :param join_spread_atom_records: If set to true, atom records belonging to the
+     same residue are joined, even if they do not appear sequentially in the PDB
+     file.
+  
+  :param remote: If set to true, the method tries to load the pdb from the remote
+     pdb repository www.pdb.org.
+  :rtype: :class:`~ost.mol.EntityHandle` or a list thereof if `load_multi` is 
+      True.
+  :param dialect: Specifies the particular dialect to use. By default, the 
+     official PDB format is used. Alternatively, by setting the dialect to 
+     CHARMM, the loading is optimized for CHARMM PDB files.
+  :type dialect: :class:`str`
+  
+  :param strict_hydrogens: whether hydrogen names should be strictly checked.  
+      It is very common for PDB files to not follow the correct naming 
+      conventions for hydrogen atoms. That's why by default, the names of the 
+      hydrogens are not required to be correct. Rather, the connectivity is 
+      inferred with distance-based checks. By turning this flag on, the names 
+      of the hydrogen atoms are checked against the names in the database like 
+      all other atom types.
+
+  :raises: :exc:`~ost.io.IOException` if the import fails due to an erroneous or 
+      inexistent file
   """
+  
+  if dialect not in ('PDB', 'CHARMM',):
+    raise ValueError('dialect must be PDB or CHARMM')
+
+  if remote:
+    output_dir = tempfile.gettempdir()
+    if __GetModelFromPDB(filename, output_dir):
+      filename = os.path.join(output_dir, 'pdb%s.ent.gz' % filename)
+    else:
+      raise IOError('Can not load PDB %s from www.pdb.org'%filename) 
+  
   conop_inst=conop.Conopology.Instance()
   builder=conop_inst.GetBuilder("DEFAULT")
+  if dialect=='PDB':
+    builder.dialect=conop.PDB_DIALECT
+  elif dialect=='CHARMM':
+    builder.dialect=conop.CHARMM_DIALECT
+  builder.strict_hydrogens=strict_hydrogens
   reader=PDBReader(filename)
-
   flags=0
   if calpha_only:
     flags|=PDB.CALPHA_ONLY
@@ -54,6 +117,8 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=False,
     flags|=PDB.NO_HETATMS
   if join_spread_atom_records:
     flags|=PDB.JOIN_SPREAD_ATOM_RECORDS
+  if dialect=='CHARMM':
+    flags|=PDB.CHARMM_FORMAT
   try:
     PDB.PushFlags(PDB.Flags() | flags)
     if load_multi:
@@ -63,6 +128,8 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=False,
         reader.Import(ent, restrict_chains)
         conop_inst.ConnectAll(builder, ent, 0)
         ent_list.append(ent)
+      if len(ent_list)==0:
+        raise IOError("File doesn't contain any entities")
       PDB.PopFlags()
       return ent_list
     else:
@@ -70,6 +137,8 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=False,
       if reader.HasNext():
         reader.Import(ent, restrict_chains)
         conop_inst.ConnectAll(builder, ent, 0)
+      else:
+        raise IOError("File doesn't contain any entities")
       PDB.PopFlags()
       return ent
   except:
@@ -78,7 +147,13 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=False,
 
 def SavePDB(models, filename):
   """
-  Save entity or list of entities to disk
+  Save entity or list of entities to disk. If a list of entities is supplied the 
+  PDB file will be saved as a multi PDB file. Each of the entities is wrapped 
+  into a MODEL/ENDMDL pair.
+  
+  :param models: The entity or list of entities (handles or views) to be saved
+  :param filename: The filename
+  :type  filename: string
   """
   if not getattr(models, '__len__', None):
     models=[models]
diff --git a/modules/io/pymod/export_map_io.cc b/modules/io/pymod/export_map_io.cc
index 6f30e29616033f81e30b91c2cc4dbdb147895118..e2b10e158a946cb5c1a768eb843766fe14b25aaf 100644
--- a/modules/io/pymod/export_map_io.cc
+++ b/modules/io/pymod/export_map_io.cc
@@ -132,6 +132,8 @@ void export_map_io()
     .def("GetFormat", &TIF::GetFormat)
     .def("SetSigned", &TIF::SetSigned)
     .def("GetSigned", &TIF::GetSigned)
+    .def("SetBitDepth", &TIF::SetBitDepth)
+    .def("GetBitDepth", &TIF::GetBitDepth)
     .def("GetPhasecolor", &TIF::GetPhasecolor)
     .def("SetPhasecolor", &TIF::SetPhasecolor)
     .def("SetSubimage", &TIF::SetSubimage)
@@ -143,9 +145,13 @@ void export_map_io()
     .def("GetNormalizeOnSave", &PNG::GetNormalizeOnSave)
   ;
 
-  class_<DAT, bases<ImageFormatBase> >("DAT", init<bool,Endianess>((arg("normalize_on_save") = false,arg("endianess") = OST_LOCAL_ENDIAN)))
-    .def("SetNormalizeOnSave", &PNG::SetNormalizeOnSave)
-    .def("GetNormalizeOnSave", &PNG::GetNormalizeOnSave)
+  class_<DAT, bases<ImageFormatBase> >("DAT", init<bool,Format,bool,Endianess>((arg("normalize_on_save") = false,arg("format")=OST_DEFAULT_FORMAT,arg("signed")=false,arg("endianess") = OST_LOCAL_ENDIAN)))
+    .def("SetNormalizeOnSave", &DAT::SetNormalizeOnSave)
+    .def("GetNormalizeOnSave", &DAT::GetNormalizeOnSave)
+    .def("SetSigned", &DAT::SetSigned)
+    .def("GetSigned", &DAT::GetSigned)
+    .def("SetBitDepth", &DAT::SetBitDepth)
+    .def("GetBitDepth", &DAT::GetBitDepth)
   ;
 
   class_<JPK, bases<TIF> >("JPK", init<boost::logic::tribool,Format,bool,bool,int>
diff --git a/modules/io/pymod/export_pdb_io.cc b/modules/io/pymod/export_pdb_io.cc
index 1aec7e6fe5415aea60d813955b924b271c3159db..1275ea7a62fdc15025c646046d468a80ac1f6dd6 100644
--- a/modules/io/pymod/export_pdb_io.cc
+++ b/modules/io/pymod/export_pdb_io.cc
@@ -54,6 +54,7 @@ void export_pdb_io()
     pdb_scope.attr("WRITE_MULTIPLE_MODELS")=PDB::WRITE_MULTIPLE_MODELS;
     pdb_scope.attr("JOIN_SPREAD_ATOM_RECORDS")=PDB::JOIN_SPREAD_ATOM_RECORDS;
     pdb_scope.attr("CALPHA_ONLY")=PDB::CALPHA_ONLY;    
+    pdb_scope.attr("CHARMM_FORMAT")=PDB::CHARMM_FORMAT;
   }
 
   class_<PDBReader, boost::noncopyable>("PDBReader", init<String>())
diff --git a/modules/io/pymod/wrap_io.cc b/modules/io/pymod/wrap_io.cc
index b04d3ac78ab729a8125fd258f9b7de89c2f15653..dc5ce987c38cb9dd4f2cd692cc306b8b2dd567a4 100644
--- a/modules/io/pymod/wrap_io.cc
+++ b/modules/io/pymod/wrap_io.cc
@@ -104,15 +104,14 @@ BOOST_PYTHON_MODULE(_io)
   def("LoadSequence", &LoadSequence, arg("format")="auto");
   def("SequenceListFromString", &SequenceListFromString);
   def("SequenceFromString", &SequenceFromString);  
-  def("SaveAlignment", &SaveAlignment, 
-      save_alignment_ov(args("alignment", "filename", "format")));
+  def("SaveAlignment", &SaveAlignment, arg("format")="auto");
   def("LoadSurface",LoadSurface,load_surface_ov());
   def("LoadManagedSurface",LoadManagedSurface,load_msurface_ov());
 
   def("SequenceToString", &SequenceToString);
   def("SequenceListToString", &SequenceListToString); 
-  def("SaveSequenceList", &SaveSequenceList);
-  def("SaveSequence", &SaveSequence);
+  def("SaveSequenceList", &SaveSequenceList, arg("format")="auto");
+  def("SaveSequence", &SaveSequence, arg("format")="auto");
   def("LoadSDF", &LoadSDF);
 
   def("LoadCRD", &LoadCRD);
diff --git a/modules/io/src/convert.cc b/modules/io/src/convert.cc
index 0d9ac88658ee3fb8d1ed8730317ef488633d27c7..8cc6a83ea13ccf742633694c8e8f301787c8319c 100644
--- a/modules/io/src/convert.cc
+++ b/modules/io/src/convert.cc
@@ -226,7 +226,7 @@ void to_vax_converter_float_helper(const unsigned int* in, unsigned int * out)
   if ( e == EXPONENT_MASK ) {
     // VAX's have no equivalents for IEEE +-Infinity and +-NaN [e=all-1's] 
     // Fixup to VAX +-extrema [e=all-1's] with zero mantissa [m=0] 
-    LOGN_ERROR("IEEE Infinity or NaN encountered. Fixup to VAX extrema");
+    LOG_ERROR("IEEE Infinity or NaN encountered. Fixup to VAX extrema");
     *out = (*in & SIGN_BIT) | EXPONENT_MASK;
   }else{
     e >>= MANTISSA_SIZE;   // Obtain the biased IEEE exponent 
@@ -243,7 +243,7 @@ void to_vax_converter_float_helper(const unsigned int* in, unsigned int * out)
       // Silent underflow 
       *out=0;;                                  
     }else if( e > ( 2 * VAX_F_EXPONENT_BIAS - 1 ) ){
-      LOGN_ERROR("Overflow. Fixup to VAX extrema");
+      LOG_ERROR("Overflow. Fixup to VAX extrema");
        *out = ( *in & SIGN_BIT ) | ~SIGN_BIT;
     }else{
       // VAX normalized form [e>0] (both mantissas are 23 bits) 
@@ -259,7 +259,7 @@ void from_vax_converter_float_helper(const unsigned int* in, unsigned int * out)
     // If the biased VAX exponent is zero [e=0] 
     if ( ( *in & SIGN_BIT ) == SIGN_BIT ){
       // If negative [s=1] 
-      LOGN_ERROR("VAX reserved operand fault; fixup to IEEE zero");
+      LOG_ERROR("VAX reserved operand fault; fixup to IEEE zero");
     }
     // Set VAX dirty [m<>0] or true [m=0] zero to IEEE +zero [s=e=m=0] 
     *out = 0;
diff --git a/modules/io/src/img/CMakeLists.txt b/modules/io/src/img/CMakeLists.txt
index 4ed3e1999b5be767123770d113d215c8bbe70b39..8fa9a30ffd45564867fef83e5b17ef7bee0250b0 100644
--- a/modules/io/src/img/CMakeLists.txt
+++ b/modules/io/src/img/CMakeLists.txt
@@ -10,6 +10,7 @@ map_io_dat_handler.cc
 map_io_jpk_handler.cc
 map_io_nanoscope_handler.cc
 map_io_png_handler.cc
+map_io_df3_handler.cc
 convert_vax_data.c
 image_format.cc
 tiff_util.cc
@@ -18,6 +19,7 @@ PARENT_SCOPE
 
 set(OST_IO_IMG_HEADERS
 load_map.hh
+map_io_df3_handler.hh
 image_format.hh
 image_format_conversion.cc
 map_io_dx_handler.hh
diff --git a/modules/io/src/img/load_map.cc b/modules/io/src/img/load_map.cc
index f700d37368aef23e6c0570bfdb8bf732b7447392..c120c6e354c00299260e14e78b176a898a368612 100644
--- a/modules/io/src/img/load_map.cc
+++ b/modules/io/src/img/load_map.cc
@@ -27,19 +27,19 @@
 
 namespace ost { namespace io {
 
-DLLEXPORT_OST_IO img::ImageHandle LoadImage(const boost::filesystem::path& loc)
+img::ImageHandle LoadImage(const boost::filesystem::path& loc)
 {
   UndefinedImageFormat undefined;
   return LoadImage(loc,undefined);
 }
 
-DLLEXPORT_OST_IO img::ImageHandle LoadImage(const boost::filesystem::path& loc, const ImageFormatBase& formatstruct)
+img::ImageHandle LoadImage(const boost::filesystem::path& loc, const ImageFormatBase& formatstruct)
 {
   if(!boost::filesystem::exists(loc)){
     throw IOException("file not found: " + loc.string());
   }
 
-  LOG_DUMP("creating MapIOHandler for " << loc.string() << std::endl);
+  LOG_DEBUG("creating MapIOHandler for " << loc.string());
 
   MapIOHandlerPtr map_io = IOManager::Instance().FindMapImportHandlerFile(loc,formatstruct);
 
@@ -49,7 +49,7 @@ DLLEXPORT_OST_IO img::ImageHandle LoadImage(const boost::filesystem::path& loc,
 
   img::ImageHandle ih = CreateImage(img::Extent(),img::REAL,img::SPATIAL);
 
-  LOG_DUMP("calling import on map io handle" << std::endl);
+  LOG_DEBUG("calling import on map io handle");
   map_io->Import(ih,loc,formatstruct);
 
   // TODO: fix this in regard to automatic copy of ConstData info obj
@@ -59,40 +59,40 @@ DLLEXPORT_OST_IO img::ImageHandle LoadImage(const boost::filesystem::path& loc,
   return ih;
 }
 
-DLLEXPORT_OST_IO void SaveImage(const img::ImageHandle& image, const boost::filesystem::path& loc)
+void SaveImage(const img::ImageHandle& image, const boost::filesystem::path& loc)
 {
   UndefinedImageFormat undefined;
   SaveImage(image,loc,undefined);
 }
 
-DLLEXPORT_OST_IO void SaveImage(const img::ImageHandle& image, const boost::filesystem::path& loc,const ImageFormatBase& formatstruct)
+void SaveImage(const img::ImageHandle& image, const boost::filesystem::path& loc,const ImageFormatBase& formatstruct)
 {
   MapIOHandlerPtr map_io = IOManager::Instance().FindMapExportHandlerFile(loc,formatstruct);
 
   if(!map_io) {
     throw IOUnknownFormatException("could not find io-plugin for " + loc.string());
   }
-  LOG_DUMP("calling export on map io handle" << std::endl);
+  LOG_DEBUG("calling export on map io handle");
   map_io->Export(image, loc,formatstruct);
 }
 
 
-DLLEXPORT_OST_IO img::MapHandle LoadMap(const boost::filesystem::path& loc, const ImageFormatBase& formatstruct)
+img::MapHandle LoadMap(const boost::filesystem::path& loc, const ImageFormatBase& formatstruct)
 {
   return LoadImage(loc,formatstruct);
 }
 
-DLLEXPORT_OST_IO img::MapHandle LoadMap(const boost::filesystem::path& loc)
+img::MapHandle LoadMap(const boost::filesystem::path& loc)
 {
   return LoadImage(loc);
 }
 
-DLLEXPORT_OST_IO void SaveMap(const img::ImageHandle& image, const boost::filesystem::path& loc,const ImageFormatBase& formatstruct )
+void SaveMap(const img::ImageHandle& image, const boost::filesystem::path& loc,const ImageFormatBase& formatstruct )
 {
   SaveImage(image,loc,formatstruct);
 }
 
-DLLEXPORT_OST_IO void SaveMap(const img::ImageHandle& image, const boost::filesystem::path& loc)
+void SaveMap(const img::ImageHandle& image, const boost::filesystem::path& loc)
 {
   SaveImage(image,loc);
 }
diff --git a/modules/io/src/img/map_io_dat_handler.cc b/modules/io/src/img/map_io_dat_handler.cc
index 988d590e5a333a8ab9a6d9ac17c175f17833d549..c2503261e5cd59aa257818b3da27d8e0e6cadfa2 100644
--- a/modules/io/src/img/map_io_dat_handler.cc
+++ b/modules/io/src/img/map_io_dat_handler.cc
@@ -17,6 +17,7 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
+#include <ost/stdint.hh>
 #include <boost/shared_array.hpp>
 #include <boost/filesystem/operations.hpp>
 #include <boost/filesystem/fstream.hpp>
@@ -34,11 +35,33 @@ namespace ost { namespace io {
 
 String DAT::FORMAT_STRING = "defined_dat";
 
-DAT::DAT(bool normalize_on_save, Endianess end):
-    ImageFormatBase(FORMAT_STRING)
+DAT::DAT(bool normalize_on_save, Format bit_depth, bool sign, Endianess end):
+    ImageFormatBase(FORMAT_STRING),
+    normalize_on_save_(normalize_on_save),
+    bit_depth_(bit_depth),
+    signed_(sign),
+    endianness_(end)
 {
-    normalize_on_save_ = normalize_on_save;
-    endianness_ = end;
+}
+
+Format DAT::GetBitDepth() const
+{
+  return bit_depth_;
+}
+
+void DAT::SetBitDepth (Format bitdepth)
+{
+  bit_depth_ = bitdepth;
+}
+
+bool DAT::GetSigned () const
+{
+  return signed_;
+}
+
+void DAT::SetSigned (bool sign)
+{
+  signed_ = sign;
 }
 
 Endianess DAT::GetEndianess() const
@@ -92,7 +115,7 @@ void MapIODatHandler::Import(img::MapHandle& sh, const boost::filesystem::path&
   infile.close();
 }
 
-template <int CONVERSIONTYPE>
+template <int CONVERSIONTYPE,typename DATATYPE>
 void real_filler(img::MapHandle& sh, std::istream& file)
 {
   BinaryIStream<CONVERSIONTYPE> file_bin(file);
@@ -101,7 +124,7 @@ void real_filler(img::MapHandle& sh, std::istream& file)
   img::Progress::Instance().Register(&this_dummy,size[1],100);
   for(unsigned int row=0;row<size[1];row++) {
     for(unsigned int column=0;column<size[0];column++) {
-      short value;
+      DATATYPE value;
       file_bin >> value;
       sh.SetReal(img::Point(column,row),static_cast<Real>(value));
     }
@@ -110,7 +133,7 @@ void real_filler(img::MapHandle& sh, std::istream& file)
   img::Progress::Instance().DeRegister(&this_dummy);
 }
 
-template <int CONVERSIONTYPE>
+template <int CONVERSIONTYPE,typename DATATYPE>
 void real_dumper(const img::MapHandle& sh, std::ostream& file, const DAT& formatdat)
 {
   BinaryOStream<CONVERSIONTYPE> file_bin(file);
@@ -124,7 +147,7 @@ void real_dumper(const img::MapHandle& sh, std::ostream& file, const DAT& format
     for(unsigned int row=0;row<size[1];row++) {
       for(unsigned int column=0;column<size[0];column++)
       {
-        file_bin << static_cast<short>(norm.Convert(sh.GetReal(img::Point(column,row))));
+        file_bin << static_cast<DATATYPE>(norm.Convert(sh.GetReal(img::Point(column,row))));
       }
       img::Progress::Instance().AdvanceProgress(&this_dummy);
     }
@@ -151,21 +174,168 @@ void MapIODatHandler::Import(img::MapHandle& sh, std::istream& file, const Image
   uint  filesize = end-start;
   file.seekg(curr_pos,std::ios::beg);
 
-  unsigned int size=static_cast<unsigned int>(sqrt(filesize/2.0));
-   // default origin is top-left
-  sh.Reset(img::Extent(img::Point(0,0),img::Size(size,size)), img::REAL, img::SPATIAL);
-
-  switch(formatdat.GetEndianess()) {
-  case OST_BIG_ENDIAN:
-    real_filler<OST_BIG_ENDIAN>(sh,file);
+  double datasize=1.0;
+  switch(formatdat.GetBitDepth()){
+  case OST_BIT8_FORMAT:
+  case OST_DEFAULT_FORMAT:
+    datasize=1.0;
+    break;
+  case OST_BIT16_FORMAT:
+    datasize=2.0;
     break;
-  case OST_LITTLE_ENDIAN:
-    real_filler<OST_LITTLE_ENDIAN>(sh,file);
+  case OST_BIT32_FORMAT:
+    datasize=4.0;
     break;
-  case OST_VAX_DATA:
-    real_filler<OST_VAX_DATA>(sh,file);
+  case OST_FLOAT_FORMAT:
+    datasize=sizeof(float);
     break;
- }
+  case OST_DOUBLE_FORMAT:
+    datasize=sizeof(double);
+    break;
+  }
+  unsigned int size=static_cast<unsigned int>(sqrt(filesize/datasize));
+   // default origin is top-left
+  sh.Reset(img::Extent(img::Point(0,0),img::Size(size,size)), img::REAL, img::SPATIAL);
+
+  if(formatdat.GetSigned()){
+    switch(formatdat.GetBitDepth()){
+    case OST_BIT8_FORMAT:
+    case OST_DEFAULT_FORMAT:
+      switch(formatdat.GetEndianess()) {
+      case OST_BIG_ENDIAN:
+        real_filler<OST_BIG_ENDIAN,int8_t>(sh,file);
+        break;
+      case OST_LITTLE_ENDIAN:
+        real_filler<OST_LITTLE_ENDIAN,int8_t>(sh,file);
+        break;
+      case OST_VAX_DATA:
+        real_filler<OST_VAX_DATA,int8_t>(sh,file);
+        break;
+      }
+      break;
+    case OST_BIT16_FORMAT:
+      switch(formatdat.GetEndianess()) {
+      case OST_BIG_ENDIAN:
+        real_filler<OST_BIG_ENDIAN,int16_t>(sh,file);
+        break;
+      case OST_LITTLE_ENDIAN:
+        real_filler<OST_LITTLE_ENDIAN,int16_t>(sh,file);
+        break;
+      case OST_VAX_DATA:
+        real_filler<OST_VAX_DATA,int16_t>(sh,file);
+        break;
+      }
+      break;
+    case OST_BIT32_FORMAT:
+      switch(formatdat.GetEndianess()) {
+      case OST_BIG_ENDIAN:
+        real_filler<OST_BIG_ENDIAN,int32_t>(sh,file);
+        break;
+      case OST_LITTLE_ENDIAN:
+        real_filler<OST_LITTLE_ENDIAN,int32_t>(sh,file);
+        break;
+      case OST_VAX_DATA:
+        real_filler<OST_VAX_DATA,int32_t>(sh,file);
+        break;
+      }
+      break;
+    case OST_FLOAT_FORMAT:
+      switch(formatdat.GetEndianess()) {
+      case OST_BIG_ENDIAN:
+        real_filler<OST_BIG_ENDIAN,float>(sh,file);
+        break;
+      case OST_LITTLE_ENDIAN:
+        real_filler<OST_LITTLE_ENDIAN,float>(sh,file);
+        break;
+      case OST_VAX_DATA:
+        real_filler<OST_VAX_DATA,float>(sh,file);
+        break;
+      }
+      break;
+    case OST_DOUBLE_FORMAT:
+      switch(formatdat.GetEndianess()) {
+      case OST_BIG_ENDIAN:
+        real_filler<OST_BIG_ENDIAN,double>(sh,file);
+        break;
+      case OST_LITTLE_ENDIAN:
+        real_filler<OST_LITTLE_ENDIAN,double>(sh,file);
+        break;
+      case OST_VAX_DATA:
+        real_filler<OST_VAX_DATA,double>(sh,file);
+        break;
+      }
+      break;
+    }
+  }else{
+    switch(formatdat.GetBitDepth()){
+    case OST_BIT8_FORMAT:
+    case OST_DEFAULT_FORMAT:
+      switch(formatdat.GetEndianess()) {
+      case OST_BIG_ENDIAN:
+        real_filler<OST_BIG_ENDIAN,uint8_t>(sh,file);
+        break;
+      case OST_LITTLE_ENDIAN:
+        real_filler<OST_LITTLE_ENDIAN,uint8_t>(sh,file);
+        break;
+      case OST_VAX_DATA:
+        real_filler<OST_VAX_DATA,uint8_t>(sh,file);
+        break;
+      }
+      break;
+    case OST_BIT16_FORMAT:
+      switch(formatdat.GetEndianess()) {
+      case OST_BIG_ENDIAN:
+        real_filler<OST_BIG_ENDIAN,uint16_t>(sh,file);
+        break;
+      case OST_LITTLE_ENDIAN:
+        real_filler<OST_LITTLE_ENDIAN,uint16_t>(sh,file);
+        break;
+      case OST_VAX_DATA:
+        real_filler<OST_VAX_DATA,uint16_t>(sh,file);
+        break;
+      }
+      break;
+    case OST_BIT32_FORMAT:
+      switch(formatdat.GetEndianess()) {
+      case OST_BIG_ENDIAN:
+        real_filler<OST_BIG_ENDIAN,uint32_t>(sh,file);
+        break;
+      case OST_LITTLE_ENDIAN:
+        real_filler<OST_LITTLE_ENDIAN,uint32_t>(sh,file);
+        break;
+      case OST_VAX_DATA:
+        real_filler<OST_VAX_DATA,uint32_t>(sh,file);
+        break;
+      }
+      break;
+    case OST_FLOAT_FORMAT:
+      switch(formatdat.GetEndianess()) {
+      case OST_BIG_ENDIAN:
+        real_filler<OST_BIG_ENDIAN,float>(sh,file);
+        break;
+      case OST_LITTLE_ENDIAN:
+        real_filler<OST_LITTLE_ENDIAN,float>(sh,file);
+        break;
+      case OST_VAX_DATA:
+        real_filler<OST_VAX_DATA,float>(sh,file);
+        break;
+      }
+      break;
+    case OST_DOUBLE_FORMAT:
+      switch(formatdat.GetEndianess()) {
+      case OST_BIG_ENDIAN:
+        real_filler<OST_BIG_ENDIAN,double>(sh,file);
+        break;
+      case OST_LITTLE_ENDIAN:
+        real_filler<OST_LITTLE_ENDIAN,double>(sh,file);
+        break;
+      case OST_VAX_DATA:
+        real_filler<OST_VAX_DATA,double>(sh,file);
+        break;
+      }
+      break;
+    }
+  }
 }
 
 void MapIODatHandler::Export(const img::MapHandle& mh2,
@@ -197,17 +367,145 @@ void MapIODatHandler::Export(const img::MapHandle& sh, std::ostream& file,const
     throw IOException("DAT IO: Dat format only supports square 2D images");
   }
 
-  switch(formatdat.GetEndianess()) {
-  case OST_BIG_ENDIAN:
-    real_dumper<OST_BIG_ENDIAN>(sh,file,formatdat);
-    break;
-  case OST_LITTLE_ENDIAN:
-    real_dumper<OST_LITTLE_ENDIAN>(sh,file,formatdat);
-    break;
-  case OST_VAX_DATA:
-    real_dumper<OST_VAX_DATA>(sh,file,formatdat);
-    break;
- }
+  if(formatdat.GetSigned()){
+    switch(formatdat.GetBitDepth()){
+    case OST_BIT8_FORMAT:
+    case OST_DEFAULT_FORMAT:
+      switch(formatdat.GetEndianess()) {
+      case OST_BIG_ENDIAN:
+        real_dumper<OST_BIG_ENDIAN,int8_t>(sh,file,formatdat);
+        break;
+      case OST_LITTLE_ENDIAN:
+        real_dumper<OST_LITTLE_ENDIAN,int8_t>(sh,file,formatdat);
+        break;
+      case OST_VAX_DATA:
+        real_dumper<OST_VAX_DATA,int8_t>(sh,file,formatdat);
+        break;
+      }
+      break;
+    case OST_BIT16_FORMAT:
+      switch(formatdat.GetEndianess()) {
+      case OST_BIG_ENDIAN:
+        real_dumper<OST_BIG_ENDIAN,int16_t>(sh,file,formatdat);
+        break;
+      case OST_LITTLE_ENDIAN:
+        real_dumper<OST_LITTLE_ENDIAN,int16_t>(sh,file,formatdat);
+        break;
+      case OST_VAX_DATA:
+        real_dumper<OST_VAX_DATA,int16_t>(sh,file,formatdat);
+        break;
+      }
+      break;
+    case OST_BIT32_FORMAT:
+      switch(formatdat.GetEndianess()) {
+      case OST_BIG_ENDIAN:
+        real_dumper<OST_BIG_ENDIAN,int32_t>(sh,file,formatdat);
+        break;
+      case OST_LITTLE_ENDIAN:
+        real_dumper<OST_LITTLE_ENDIAN,int32_t>(sh,file,formatdat);
+        break;
+      case OST_VAX_DATA:
+        real_dumper<OST_VAX_DATA,int32_t>(sh,file,formatdat);
+        break;
+      }
+      break;
+    case OST_FLOAT_FORMAT:
+      switch(formatdat.GetEndianess()) {
+      case OST_BIG_ENDIAN:
+        real_dumper<OST_BIG_ENDIAN,float>(sh,file,formatdat);
+        break;
+      case OST_LITTLE_ENDIAN:
+        real_dumper<OST_LITTLE_ENDIAN,float>(sh,file,formatdat);
+        break;
+      case OST_VAX_DATA:
+        real_dumper<OST_VAX_DATA,float>(sh,file,formatdat);
+        break;
+      }
+      break;
+    case OST_DOUBLE_FORMAT:
+      switch(formatdat.GetEndianess()) {
+      case OST_BIG_ENDIAN:
+        real_dumper<OST_BIG_ENDIAN,double>(sh,file,formatdat);
+        break;
+      case OST_LITTLE_ENDIAN:
+        real_dumper<OST_LITTLE_ENDIAN,double>(sh,file,formatdat);
+        break;
+      case OST_VAX_DATA:
+        real_dumper<OST_VAX_DATA,double>(sh,file,formatdat);
+        break;
+      }
+      break;
+    }
+  }else{
+    switch(formatdat.GetBitDepth()){
+    case OST_BIT8_FORMAT:
+    case OST_DEFAULT_FORMAT:
+      switch(formatdat.GetEndianess()) {
+      case OST_BIG_ENDIAN:
+        real_dumper<OST_BIG_ENDIAN,int8_t>(sh,file,formatdat);
+        break;
+      case OST_LITTLE_ENDIAN:
+        real_dumper<OST_LITTLE_ENDIAN,int8_t>(sh,file,formatdat);
+        break;
+      case OST_VAX_DATA:
+        real_dumper<OST_VAX_DATA,int8_t>(sh,file,formatdat);
+        break;
+      }
+      break;
+    case OST_BIT16_FORMAT:
+      switch(formatdat.GetEndianess()) {
+      case OST_BIG_ENDIAN:
+        real_dumper<OST_BIG_ENDIAN,int16_t>(sh,file,formatdat);
+        break;
+      case OST_LITTLE_ENDIAN:
+        real_dumper<OST_LITTLE_ENDIAN,int16_t>(sh,file,formatdat);
+        break;
+      case OST_VAX_DATA:
+        real_dumper<OST_VAX_DATA,int16_t>(sh,file,formatdat);
+        break;
+      }
+      break;
+    case OST_BIT32_FORMAT:
+      switch(formatdat.GetEndianess()) {
+      case OST_BIG_ENDIAN:
+        real_dumper<OST_BIG_ENDIAN,int32_t>(sh,file,formatdat);
+        break;
+      case OST_LITTLE_ENDIAN:
+        real_dumper<OST_LITTLE_ENDIAN,int32_t>(sh,file,formatdat);
+        break;
+      case OST_VAX_DATA:
+        real_dumper<OST_VAX_DATA,int32_t>(sh,file,formatdat);
+        break;
+      }
+      break;
+    case OST_FLOAT_FORMAT:
+      switch(formatdat.GetEndianess()) {
+      case OST_BIG_ENDIAN:
+        real_dumper<OST_BIG_ENDIAN,float>(sh,file,formatdat);
+        break;
+      case OST_LITTLE_ENDIAN:
+        real_dumper<OST_LITTLE_ENDIAN,float>(sh,file,formatdat);
+        break;
+      case OST_VAX_DATA:
+        real_dumper<OST_VAX_DATA,float>(sh,file,formatdat);
+        break;
+      }
+      break;
+    case OST_DOUBLE_FORMAT:
+      switch(formatdat.GetEndianess()) {
+      case OST_BIG_ENDIAN:
+        real_dumper<OST_BIG_ENDIAN,double>(sh,file,formatdat);
+        break;
+      case OST_LITTLE_ENDIAN:
+        real_dumper<OST_LITTLE_ENDIAN,double>(sh,file,formatdat);
+        break;
+      case OST_VAX_DATA:
+        real_dumper<OST_VAX_DATA,double>(sh,file,formatdat);
+        break;
+      }
+      break;
+    }
+  }
 }
 
 }} // namespaces
diff --git a/modules/io/src/img/map_io_dat_handler.hh b/modules/io/src/img/map_io_dat_handler.hh
index 92335aa170b08ef1ac32b36b25436471810c0746..9244c705be6870ddd82f74d3a06c4127c22d0143 100644
--- a/modules/io/src/img/map_io_dat_handler.hh
+++ b/modules/io/src/img/map_io_dat_handler.hh
@@ -34,7 +34,13 @@ class DLLEXPORT_OST_IO DAT: public ImageFormatBase
 
  public:
 
-  DAT(bool normalize_on_save = true,Endianess endianness = OST_LOCAL_ENDIAN);
+  DAT(bool normalize_on_save = true, Format bit_depth = OST_DEFAULT_FORMAT, bool sign = false,Endianess endianness = OST_LOCAL_ENDIAN);
+
+  Format GetBitDepth() const;
+  void SetBitDepth ( Format bitdepth);
+
+  bool GetSigned () const;
+  void SetSigned (bool sign);
 
   Endianess GetEndianess() const;
   void SetEndianess(Endianess end);
@@ -45,6 +51,8 @@ class DLLEXPORT_OST_IO DAT: public ImageFormatBase
  private:
 
   bool normalize_on_save_;
+  Format bit_depth_;
+  bool signed_;
   Endianess endianness_;
 };
 
diff --git a/modules/io/src/img/map_io_df3_handler.cc b/modules/io/src/img/map_io_df3_handler.cc
new file mode 100644
index 0000000000000000000000000000000000000000..b6f637eab3943f0a1d85fecec851a2217585af72
--- /dev/null
+++ b/modules/io/src/img/map_io_df3_handler.cc
@@ -0,0 +1,144 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 by the OpenStructure authors
+// Copyright (C) 2003-2010 by the IPLT authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+//------------------------------------------------------------------------------
+/*
+  Author: Marco Biasini
+*/
+
+#include <cstdio>
+#include <cstring>
+#include <iomanip>
+#include <limits>
+#include <sstream>
+#include <fstream>
+#include <ost/log.hh>
+#include <boost/filesystem/fstream.hpp>
+#include <boost/algorithm/string.hpp>
+#include <ost/io/swap_util.hh>
+#include <ost/img/alg/normalizer_factory.hh>
+#include <ost/io/io_exception.hh>
+#include <ost/io/converting_streams.hh>
+#include <ost/img/progress.hh>
+
+#include "map_io_df3_handler.hh"
+
+namespace bf = boost::filesystem;
+
+namespace ost { namespace io {
+
+String DF3::FORMAT_STRING="defined_df3";
+
+DF3::DF3(bool normalize_on_save):
+    ImageFormatBase(FORMAT_STRING),
+    normalize_on_save_(normalize_on_save)
+{
+}
+
+bool DF3::GetNormalizeOnSave() const
+{
+  return normalize_on_save_;
+}
+
+void DF3::SetNormalizeOnSave(bool normalize_on_save)
+{
+  normalize_on_save_ = normalize_on_save;
+}
+
+void DF3MapIOHandler::Import(img::MapHandle& mh, const bf::path& loc,
+                             const ImageFormatBase& formatstruct)
+{
+}
+
+void DF3MapIOHandler::Import(img::MapHandle& mh, std::istream& infile,
+                             const ImageFormatBase& formatstruct)
+{
+}
+
+
+void DF3MapIOHandler::Export(const img::MapHandle& mh2,
+                             const bf::path& loc,
+                             const ImageFormatBase& format) const
+{
+  boost::filesystem::ofstream outfile(loc, std::ios::binary);
+  if(!outfile)
+  {
+    throw IOException("could not open "+loc.string());
+  }
+  BinaryOStream<OST_BIG_ENDIAN> big_endian_stream(outfile);
+  this->Export(mh2, big_endian_stream, format);
+  outfile.close();
+
+}  
+  
+void DF3MapIOHandler::Export(const img::MapHandle& mh2,
+                             std::ostream& outfile,
+                             const ImageFormatBase& format) const
+{  
+  static unsigned short max_val=std::numeric_limits<unsigned short>::max();
+  DF3 default_df3;
+  DF3& fmt=default_df3;
+  if (format.GetFormatString()==DF3::FORMAT_STRING) {
+    fmt=format.As<DF3>();
+  } else {
+    assert(format.GetFormatString()==UndefinedImageFormat::FORMAT_STRING);
+  }
+  if (mh2.GetType()==img::COMPLEX) {
+    throw IOException("DF3 doesn't support complex-valued maps");
+  }
+  img::alg::Normalizer norm=img::alg::CreateNoOpNormalizer();
+  if (fmt.GetNormalizeOnSave() == true) {
+    
+    norm=img::alg::CreateLinearRangeNormalizer(mh2, format.GetMinimum(), 
+                                               format.GetMaximum());
+  }
+  img::Size size=mh2.GetSize();
+  for (size_t i=0; i<3; ++i) {
+    unsigned short v=size[i];
+    Convert<OST_BIG_ENDIAN,unsigned short>::FromIP(&v);
+    outfile.write(reinterpret_cast<const char*>(&v), sizeof(unsigned short));
+  }
+  for (img::ExtentIterator i(mh2.GetExtent()); !i.AtEnd(); ++i) {
+    Real norm_value=norm.Convert(mh2.GetReal(i))*max_val;
+    unsigned short v=static_cast<unsigned short>(norm_value);
+    Convert<OST_BIG_ENDIAN,unsigned short>::FromIP(&v);
+    outfile.write(reinterpret_cast<const char*>(&v), sizeof(unsigned short));
+  }
+}
+
+bool DF3MapIOHandler::MatchContent(unsigned char* header)
+{
+  return false;
+}
+
+bool DF3MapIOHandler::MatchType(const ImageFormatBase& type)
+{
+  if(type.GetFormatString()==DF3::FORMAT_STRING) {
+    return true;
+  }
+  return false;
+}
+
+bool DF3MapIOHandler::MatchSuffix(const String& loc)
+{
+  return detail::FilenameEndsWith(loc,".df3");
+}
+
+
+
+}} //namespaces
diff --git a/modules/io/src/img/map_io_df3_handler.hh b/modules/io/src/img/map_io_df3_handler.hh
new file mode 100644
index 0000000000000000000000000000000000000000..c6f3afd2f7f07bcbb4ad53d65d9be0afca3b95dc
--- /dev/null
+++ b/modules/io/src/img/map_io_df3_handler.hh
@@ -0,0 +1,69 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 by the OpenStructure authors
+// Copyright (C) 2003-2010 by the IPLT authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+//------------------------------------------------------------------------------
+#ifndef OST_IO_DF3_HANDLER_HH
+#define OST_IO_DF3_HANDLER_HH
+
+/*
+  Author: Marco Biasini
+ */
+#include "map_io_handler.hh"
+
+namespace ost { namespace io {
+
+class DLLEXPORT_OST_IO DF3: public ImageFormatBase
+{
+ public:
+
+  DF3(bool normalize_on_save = false);
+
+  bool GetNormalizeOnSave() const;
+  void SetNormalizeOnSave(bool normalize_on_save);
+  static String FORMAT_STRING;
+  static String FORMAT_NAME_STRING;
+  static String FORMAT_ALIGNMENT_STRING;
+
+ private:
+
+  bool normalize_on_save_;
+};
+
+class DLLEXPORT_OST_IO DF3MapIOHandler: public MapIOHandler
+{
+ public:
+  virtual void Import(img::MapHandle& sh, const boost::filesystem::path& loc,
+                      const ImageFormatBase& formatstruct);
+  virtual void Import(img::MapHandle& sh, std::istream& loc,
+                      const ImageFormatBase& formatstruct);
+  virtual void Export(const img::MapHandle& sh, const boost::filesystem::path& loc, 
+                      const ImageFormatBase& formatstruct) const;
+  virtual void Export(const img::MapHandle& sh, std::ostream& loc,
+                      const ImageFormatBase& formatstruct) const;
+  static bool MatchContent(unsigned char* header);
+  static bool MatchType(const ImageFormatBase& type);
+  static bool MatchSuffix(const String& loc);
+  static String GetFormatName() { return "DF3"; };
+  static String GetFormatDescription() { return "PovRay Density file format"; };
+};
+
+typedef MapIOHandlerFactory<DF3MapIOHandler> MapIODF3HandlerFactory;
+
+}} // ns
+
+#endif
diff --git a/modules/io/src/img/map_io_dm3_handler.cc b/modules/io/src/img/map_io_dm3_handler.cc
index b53c6b1b2fa95b86747156d8bd1a60c3b8de60bd..359d396f22324da37312038063770ce29c8595dc 100644
--- a/modules/io/src/img/map_io_dm3_handler.cc
+++ b/modules/io/src/img/map_io_dm3_handler.cc
@@ -74,9 +74,9 @@ void value_convert(void* src_ptr, DEST* dest_ptr, size_t count)
 {
   SOURCE* r_src_ptr = reinterpret_cast<SOURCE*>(src_ptr);
   for(uint c=0;c<count;++c) {
-    LOG_VERBOSE(" " << c << " / " << count << " .");
+    LOG_TRACE(" " << c << " / " << count << " .");
     DEST val=static_cast<DEST>(r_src_ptr[c]);
-    LOG_VERBOSE(" ." << std::endl);
+    LOG_TRACE(" ." << std::endl);
     dest_ptr[c] = val;
   }
 }
@@ -216,7 +216,7 @@ void DM3Collector::ParseFile(const bf::path& loc)
   {
     throw IOException("could not open "+loc.string());
   }
-  LOG_VERBOSE("Starting DM3 Parsing" << std::endl);
+  LOG_DEBUG("Starting DM3 Parsing" << std::endl);
   this->ParseStream(ifile);
   ifile.close();
 }
@@ -231,16 +231,16 @@ void DM3Collector::ParseStream(std::istream& fp)
   uint endianess;
   file_read(&endianess,sizeof(uint),1,fp);
 
-  LOG_MESSAGE("version: " << version << std::endl);
-  LOG_MESSAGE("bytecount: " << bytecount << std::endl);
-  LOG_MESSAGE("endianess: " << endianess << std::endl);
+  LOG_INFO("version: " << version);
+  LOG_INFO("bytecount: " << bytecount);
+  LOG_INFO("endianess: " << endianess);
 
   parse_tag_group(0,"ROOT",fp);
   img::Progress::Instance().DeRegister(this);
   if(fp.eof()==0) {
-    LOG_ERROR("file not parsed completely" << std::endl);
+    LOG_ERROR("file not parsed completely");
   } else {
-    LOG_VERBOSE("file parsed completely" << std::endl);
+    LOG_INFO("file parsed completely");
   }
 
 }
@@ -320,7 +320,9 @@ void DM3Collector::check_image()
 
       image_handle_list_.push_back(ih);
     } else {
-      LOG_ERROR("missmatch in byte size of data (" << data_size*type_sizeof(image_number_type_) << " != " << image_data_byte_size_ << "), ignoring this image entry" << std::endl);
+      LOG_ERROR("missmatch in byte size of data (" 
+                << data_size*type_sizeof(image_number_type_) << " != " 
+                << image_data_byte_size_ << "), ignoring this image entry");
     }
 
     image_width_=0;
@@ -348,7 +350,7 @@ size_t DM3Collector::type_sizeof(uint n)
 
 void DM3Collector::parse_tag_group(int depth, const String& name,std::istream& fp)
 {
-  LOG_VERBOSE(String(depth,' ') << "parsing tag group [" << name << "]" << std::endl);
+  LOG_TRACE(String(depth,' ') << "parsing tag group [" << name << "]");
 
   uchar sorted;
   file_read(&sorted,sizeof(uchar),1,fp);
@@ -356,13 +358,14 @@ void DM3Collector::parse_tag_group(int depth, const String& name,std::istream& f
   uchar open;
   file_read(&open,sizeof(uchar),1,fp);
 
-  LOG_VERBOSE(String(depth,' ') << "s,o: " << static_cast<int>(sorted) << "," << static_cast<int>(open) << std::endl);
+  LOG_TRACE(String(depth,' ') << "s,o: " << static_cast<int>(sorted) << "," 
+            << static_cast<int>(open));
 
   uint tag_count;
   file_read(&tag_count,sizeof(uint),1,fp);
   if(swap_tag_) swap_uint(&tag_count,1);
 
-  LOG_VERBOSE(String(depth,' ') << "tag_count: " << tag_count << std::endl);
+  LOG_TRACE(String(depth,' ') << "tag_count: " << tag_count);
 
   handle_tag_group(name);
 
@@ -373,12 +376,12 @@ void DM3Collector::parse_tag_group(int depth, const String& name,std::istream& f
 
 void DM3Collector::parse_tag_entry(int depth,std::istream& fp)
 {
-  LOG_VERBOSE(String(depth,' ') << "parsing tag entry" << std::endl);
+  LOG_TRACE(String(depth,' ') << "parsing tag entry");
 
   uchar id;
   file_read(&id,sizeof(uchar),1,fp);
 
-  LOG_VERBOSE(String(depth,' ') << "id: " << static_cast<int>(id) << std::endl);
+  LOG_TRACE(String(depth,' ') << "id: " << static_cast<int>(id));
 
   if(!(id==20 || id==21)) {
     std::ostringstream msg("");
@@ -397,7 +400,8 @@ void DM3Collector::parse_tag_entry(int depth,std::istream& fp)
     label=String(&buffer[0],nlabel);
   }
 
-  LOG_MESSAGE(String(depth,' ') << "nlabel: " << nlabel << " label: '" << label << "'" << std::endl);
+  LOG_TRACE(String(depth,' ') << "nlabel: " << nlabel << " label: '" 
+            << label << "'" << std::endl);
 
   if(id==static_cast<uchar>(20)) {
     parse_tag_group(depth+1,label,fp);
@@ -409,7 +413,7 @@ void DM3Collector::parse_tag_entry(int depth,std::istream& fp)
 
 void DM3Collector::parse_tag_type(int depth, const String& name, std::istream& fp)
 {
-  LOG_VERBOSE(String(depth,' ') << "parsing tag type" << std::endl);
+  LOG_TRACE(String(depth,' ') << "parsing tag type");
 
   char dummy[4];
   file_read(dummy,sizeof(char),4,fp);
@@ -417,21 +421,21 @@ void DM3Collector::parse_tag_type(int depth, const String& name, std::istream& f
   if(String(dummy,4)!=String("%%%%")) {
     throw IOException("I/O Dm3: invalid tag_type magic number");
   } else {
-    LOG_VERBOSE(String(depth,' ') << "magic number %%%% found" << std::endl);
+    LOG_TRACE(String(depth,' ') << "magic number %%%% found");
   }
 
   uint ntype;
   file_read(&ntype,sizeof(uint),1,fp);
   if(swap_tag_) swap_uint(&ntype,1);
 
-  LOG_VERBOSE(String(depth,' ') << "ntype: " << ntype << std::endl);
+  LOG_TRACE(String(depth,' ') << "ntype: " << ntype);
 
   std::vector<uint> tag_type_info(ntype);
   file_read(&tag_type_info[0],sizeof(uint),ntype,fp);
   if(swap_tag_) swap_uint(&tag_type_info[0],ntype);
 
   for(uint i=0;i<ntype;++i) {
-    LOG_VERBOSE(String(depth,' ') << "type_info[" << i << "]: " << tag_type_info[i] << std::endl);
+    LOG_TRACE(String(depth,' ') << "type_info[" << i << "]: " << tag_type_info[i]);
   }
 
   if(ntype==1) { // simple type
@@ -452,7 +456,7 @@ void DM3Collector::parse_tag_type(int depth, const String& name, std::istream& f
 
 void DM3Collector::parse_tag_type_single(int depth, const String& name,TagTypeInfo& tag_type_info,std::istream& fp)
 {
-  LOG_VERBOSE(String(depth,' ') << "parsing simple tag [" << name << "]" << std::endl);
+  LOG_TRACE(String(depth,' ') << "parsing simple tag [" << name << "]");
 
   // tag_type_info[0] contains number type
   uint number_type=tag_type_info[0];
@@ -461,7 +465,7 @@ void DM3Collector::parse_tag_type_single(int depth, const String& name,TagTypeIn
     msg << "I/O Dm3: unexpected number type " << number_type << " for simple type";
     throw IOException(msg.str());
   } else {
-    LOG_VERBOSE(String(depth,' ') << "reading simple value of number_type " << number_type << std::endl);
+    LOG_TRACE(String(depth,' ') << "reading simple value of number_type " << number_type);
   }
 
   uchar buffer[16]; // sufficient for all primitive types
@@ -470,14 +474,14 @@ void DM3Collector::parse_tag_type_single(int depth, const String& name,TagTypeIn
   // TODO: swap data
   double tmp;
   tag_value_convert<double>(number_type,buffer,&tmp);
-  LOG_VERBOSE(String(depth,' ') << "value: " << tmp << std::endl);
+  LOG_TRACE(String(depth,' ') << "value: " << tmp);
 
   handle_single_tag(name,number_type,buffer);
 }
 
 void DM3Collector::parse_tag_type_String(int depth, const String& name, TagTypeInfo& tag_type_info,std::istream& fp)
 {
-  LOG_VERBOSE (String(depth,' ') << "parsing String tag [" << name << "]" << std::endl);
+  LOG_TRACE(String(depth,' ') << "parsing String tag [" << name << "]");
   // tag_type_info[0] contains number type 18
   // tag_type_info[1] contains String length
   std::vector<char> buffer(tag_type_info[1]*2);
@@ -486,7 +490,7 @@ void DM3Collector::parse_tag_type_String(int depth, const String& name, TagTypeI
 
 void DM3Collector::parse_tag_type_array(int depth, const String& name, TagTypeInfo& tag_type_info,std::istream& fp)
 {
-  LOG_VERBOSE(String(depth,' ') << "parsing array tag [" << name << "]" << std::endl);
+  LOG_TRACE(String(depth,' ') << "parsing array tag [" << name << "]");
   // tag_type_info[0] contains number type 20
   // tag_type_info[1] contains array number type
   // tag_type_info[2] contains array length
@@ -496,12 +500,12 @@ void DM3Collector::parse_tag_type_array(int depth, const String& name, TagTypeIn
     msg << "I/O Exception: unexpected number type " << number_type << " for array";
     throw IOException(msg.str());
   } else {
-    LOG_VERBOSE(String(depth,' ') << "parsing array of number_type " << number_type << std::endl);
+    LOG_TRACE(String(depth,' ') << "parsing array of number_type " << number_type);
   }
 
   size_t array_type_size = type_sizeof(number_type);
 
-  LOG_VERBOSE(String(depth,' ') << "array byte size: " << array_type_size*tag_type_info[2] << std::endl);
+  LOG_TRACE(String(depth,' ') << "array byte size: " << array_type_size*tag_type_info[2]);
 
   //std::vector<uchar> data(array_type_size*tag_type_info[2]);
   boost::shared_array<uchar> array_data(new uchar[array_type_size*tag_type_info[2]]);
@@ -512,7 +516,7 @@ void DM3Collector::parse_tag_type_array(int depth, const String& name, TagTypeIn
 
 void DM3Collector::parse_tag_type_simple_struct(int depth, const String& name, TagTypeInfo& tag_type_info,std::istream& fp)
 {
-  LOG_VERBOSE(String(depth,' ') << "parsing simple struct tag [" << name << "]" << std::endl);
+  LOG_TRACE(String(depth,' ') << "parsing simple struct tag [" << name << "]");
   // tag_type_info[0] contains number type 15
   if(tag_type_info[0]!=15) {
     std::ostringstream msg("");
@@ -521,7 +525,7 @@ void DM3Collector::parse_tag_type_simple_struct(int depth, const String& name, T
   }
 
   // tag_type_info[2] contains number of entries in struct
-  LOG_VERBOSE(String(depth,' ') << "reading in " << tag_type_info[2] << " values" << std::endl);
+  LOG_TRACE(String(depth,' ') << "reading in " << tag_type_info[2] << " values");
   std::vector<uint> number_types(tag_type_info[2]);
   std::vector<long> buffers(tag_type_info[2]);
   for(uint c=0;c<tag_type_info[2];++c) {
@@ -531,14 +535,14 @@ void DM3Collector::parse_tag_type_simple_struct(int depth, const String& name, T
       msg << "I/O Dm3: unexpected number type " << number_types[c] << " while parsing tag_type_struct";
       throw IOException(msg.str());
     } else {
-      LOG_VERBOSE("reading value of number_type " << number_types[c] << std::endl);
+      LOG_TRACE("reading value of number_type " << number_types[c]);
     }
     size_t bufsize = type_sizeof(number_types[c]);
     void* buffer = &buffers[c];
     file_read(buffer,bufsize,1,fp);
     double tmp;
     tag_value_convert<double>(number_types[c],buffer,&tmp);
-    LOG_VERBOSE(String(depth,' ') << "value " << c << ": " << tmp << std::endl);
+    LOG_TRACE(String(depth,' ') << "value " << c << ": " << tmp);
     // TODO: swap data
   }
   handle_struct_tag(name,number_types,buffers);
@@ -547,7 +551,7 @@ void DM3Collector::parse_tag_type_simple_struct(int depth, const String& name, T
 
 void DM3Collector::parse_tag_type_array_struct(int depth, const String& name, TagTypeInfo& tag_type_info,std::istream& fp)
 {
-  LOG_VERBOSE(String(depth,' ') << "parsing array struct tag [" << name << "]" << std::endl);
+  LOG_DEBUG(String(depth,' ') << "parsing array struct tag [" << name << "]");
   // tag_type_info[0] contains number type 20
   if(tag_type_info[0]!=20) {
     std::ostringstream msg("");
@@ -558,20 +562,22 @@ void DM3Collector::parse_tag_type_array_struct(int depth, const String& name, Ta
   // tag_type_info[size-1] contains length of array!
   uint array_size = tag_type_info[tag_type_info.size()-1];
 
-  LOG_VERBOSE(String(depth,' ') << "looping over " << array_size << " array elements" << std::endl);
+  LOG_TRACE(String(depth,' ') << "looping over " << array_size 
+            << " array elements");
 
   uchar buffer[16]; // sufficient for all primitive types
   for(uint ac=0;ac<array_size;++ac) {
     // tag_type_info[3] contains number of entries in struct
-    LOG_VERBOSE(String(depth,' ') << "reading in " << tag_type_info[3] << " values for array entry " << ac << std::endl);
+    LOG_TRACE(String(depth,' ') << "reading in " << tag_type_info[3] << " values for array entry ");
     for(uint c=0;c<tag_type_info[3];++c) {
       uint number_type=tag_type_info[c*2+5];
       if(number_type>10) {
-  std::ostringstream msg("");
-  msg << "I/O Dm3: unexpected number type " << number_type << " while parsing tag_type_struct";
-  throw IOException(msg.str());
+        std::ostringstream msg;
+        msg << "I/O Dm3: unexpected number type " << number_type 
+            << " while parsing tag_type_struct";
+        throw IOException(msg.str());
       } else {
-        LOG_VERBOSE(String(depth,' ') << "reading value of number_type " << number_type << std::endl);
+        LOG_TRACE(String(depth, ' ') << "reading value of number_type " << number_type);
       }
       size_t bufsize = type_sizeof(number_type);
       file_read(buffer,bufsize,1,fp);
diff --git a/modules/io/src/img/map_io_dx_handler.cc b/modules/io/src/img/map_io_dx_handler.cc
index f8f38fad1440e19503b1dd6560ec96d60e7ffacf..61b0a90e465b8cd5ee9735e60cda9f035a024c70 100644
--- a/modules/io/src/img/map_io_dx_handler.cc
+++ b/modules/io/src/img/map_io_dx_handler.cc
@@ -46,9 +46,9 @@ using boost::format;
 String DX::FORMAT_STRING="defined_dx";
 
 DX::DX (bool normalize_on_save):
-  ImageFormatBase(FORMAT_STRING)
+  ImageFormatBase(FORMAT_STRING),
+  normalize_on_save_(normalize_on_save) 
 {
-  normalize_on_save_ = normalize_on_save;
 }
 
 bool DX::GetNormalizeOnSave() const
diff --git a/modules/io/src/img/map_io_jpk_handler.cc b/modules/io/src/img/map_io_jpk_handler.cc
index 2f36a21ed7504da5c89956479ed2e73d2b2e7780..8f778b3acbcf3d2420b3a5a3d70dad0d0cc9af1f 100644
--- a/modules/io/src/img/map_io_jpk_handler.cc
+++ b/modules/io/src/img/map_io_jpk_handler.cc
@@ -89,8 +89,8 @@ void MapIOJpkHandler::Import(img::ImageHandle& image, const boost::filesystem::p
               }
               image*=(*scale*units_scale);
               image+=(*base*units_scale);
-              LOG_MESSAGE("jpk_plugin: scalefactor: " << *scale << "  offset: "
-                          << *base<< std::endl);
+              LOG_INFO("jpk_plugin: scalefactor: " << *scale 
+                           << "  offset: " << *base);
             } else {
               throw IOException("Missing scaling tags");
             }
@@ -107,7 +107,7 @@ void MapIOJpkHandler::Import(img::ImageHandle& image, const boost::filesystem::p
   }
   char* s;
   TIFFGetField(tfile, jpk_tags::EncoderUnit(newformat.GetSubimage()), &count, &s);
-  LOG_MESSAGE("jpk_plugin: units: " << s << std::endl);
+  LOG_INFO("jpk_plugin: units: " << s);
 
 
   Real* sx;
@@ -118,7 +118,7 @@ void MapIOJpkHandler::Import(img::ImageHandle& image, const boost::filesystem::p
       image.SetPixelSampling(geom::Vec3(*sx/static_cast<Real>(image.GetSize()[0])*Units::m,
                                         *sy/static_cast<Real>(image.GetSize()[1])*Units::m,
                                         1));
-    LOG_MESSAGE("jpk_plugin: sx: " << *sx << "  sy: "<< *sy<< std::endl);
+    LOG_INFO("jpk_plugin: sx: " << *sx << "  sy: "<< *sy);
   }
   else {
     throw IOException("Missing size tags");
@@ -184,8 +184,8 @@ void MapIOJpkHandler::Import(img::MapHandle& image, std::istream& loc,const Imag
               }
               image*=(*scale*units_scale);
               image+=(*base*units_scale);
-              LOG_MESSAGE("jpk_plugin: scalefactor: " << *scale << "  offset: "
-                          << *base<< std::endl);
+              LOG_INFO("jpk_plugin: scalefactor: " << *scale << "  offset: "
+                            << *base);
             }else {
               throw IOException("Missing scaling tags");
             }
@@ -202,7 +202,7 @@ void MapIOJpkHandler::Import(img::MapHandle& image, std::istream& loc,const Imag
   }
   char* s;
   TIFFGetField(tfile, jpk_tags::EncoderUnit(newformat.GetSubimage()), &count, &s);
-  LOG_MESSAGE("jpk_plugin: units: " << s << std::endl);
+  LOG_INFO("jpk_plugin: units: " << s);
 
 
   Real* sx;
@@ -213,7 +213,7 @@ void MapIOJpkHandler::Import(img::MapHandle& image, std::istream& loc,const Imag
       image.SetPixelSampling(geom::Vec3(*sx/static_cast<Real>(image.GetSize()[0])*Units::m,
                                         *sy/static_cast<Real>(image.GetSize()[1])*Units::m,
                                         1));
-    LOG_MESSAGE("jpk_plugin: sx: " << *sx << "  sy: "<< *sy<< std::endl);
+    LOG_INFO("jpk_plugin: sx: " << *sx << "  sy: "<< *sy);
   }
   else {
     throw IOException("Missing size tags");
diff --git a/modules/io/src/img/map_io_mrc_handler.cc b/modules/io/src/img/map_io_mrc_handler.cc
index d5ccdb9fd42dcf9cc050a17a182c2cdb65651d35..aa4a1cf40be7817932edd7662357bb52722f6e73 100644
--- a/modules/io/src/img/map_io_mrc_handler.cc
+++ b/modules/io/src/img/map_io_mrc_handler.cc
@@ -93,11 +93,11 @@ String MRC::FORMAT_STRING = "defined_mrc";
 
 
 MRC::MRC(bool normalize_on_save, Subformat subformat,Endianess endianess_on_save):
-  ImageFormatBase(FORMAT_STRING)
+  ImageFormatBase(FORMAT_STRING),
+  subformat_(subformat),
+  normalize_on_save_(normalize_on_save),
+  endianess_on_save_(endianess_on_save)
 {
-  normalize_on_save_ = normalize_on_save;
-  subformat_ = subformat;
-  endianess_on_save_ = endianess_on_save;
 }
 
 Endianess MRC::GetEndianessOnSave() const
@@ -306,14 +306,14 @@ public:
   }
   void Print()
   {
-    LOG_MESSAGE("ncrs: " << nc << " " << nr << " " << ns << std::endl);
-    LOG_MESSAGE("mode " << mode << std::endl);
-    LOG_MESSAGE("nxyz: " << nx << " " << ny << " " << nz << std::endl);
-    LOG_MESSAGE("cell: " << x << " " << y << " " << z);
-    LOG_MESSAGE(alpha << " " << beta << " " << gamma << std::endl);
-    LOG_MESSAGE("order: " << mapc << mapr << maps << std::endl);
-    LOG_MESSAGE("sg: " << ispg << " " << nsymbt << std::endl);
-    LOG_MESSAGE("nlabel: " << nlabel << std::endl);
+    LOG_INFO("ncrs: " << nc << " " << nr << " " << ns);
+    LOG_INFO("mode " << mode);
+    LOG_INFO("nxyz: " << nx << " " << ny << " " << nz);
+    LOG_INFO("cell: " << x << " " << y << " " << z);
+    LOG_INFO(alpha << " " << beta << " " << gamma);
+    LOG_INFO("order: " << mapc << mapr << maps);
+    LOG_INFO("sg: " << ispg << " " << nsymbt);
+    LOG_INFO("nlabel: " << nlabel);
   }
 
   int nc,nr,ns;
@@ -348,9 +348,9 @@ public:
   }
   void Print()
   {
-    LOG_MESSAGE("mrc header" << std::endl);
+    LOG_INFO("mrc header");
     header_base::Print();
-    LOG_MESSAGE("ori: " << xorigin << " " << yorigin << std::endl);
+    LOG_INFO("ori: " << xorigin << " " << yorigin);
   }
   static int DetermineDataFormat( std::istream& f)
   {
@@ -372,7 +372,7 @@ public:
     }else if(x>0.0 || x<1.0) {
       Convert<OST_VAX_DATA,float>::FromIP(&x);
       if(x<1.0) {
-        LOG_VERBOSE("suspicious floating Point value in mrc header" << std::endl);
+        LOG_VERBOSE("suspicious floating Point value in mrc header");
         return OST_LITTLE_ENDIAN;
       }else{
         return OST_VAX_DATA;
@@ -474,13 +474,13 @@ public:
     f.seekg(0,std::ios::beg); // seek to beginning
     char float_machst= machst[0] & 0x0f;
     if(float_machst == 1){
-      LOGN_DEBUG("CCP4Import: reading big endian data");
+      LOG_DEBUG("CCP4Import: reading big endian data");
       return OST_BIG_ENDIAN;
     }else if(float_machst == 2){
-      LOGN_DEBUG("CCP4Import: reading vax data");
+      LOG_DEBUG("CCP4Import: reading vax data");
       return OST_VAX_DATA;
     }else if(float_machst == 4){
-      LOGN_DEBUG("CCP4Import: reading little endian data");
+      LOG_DEBUG("CCP4Import: reading little endian data");
       return OST_LITTLE_ENDIAN;
     } else{
       throw(IOException("CCP4Import: Cray, Convex native and Fijitsu VP formats are not supported."));
@@ -493,9 +493,9 @@ public:
     using boost::format;
     namespace bf = boost::filesystem;
 
-    LOGN_MESSAGE("ccp4 header:");
+    LOG_INFO("ccp4 header:");
     header_base::Print();
-    LOGN_MESSAGE(" arms: " << arms);
+    LOG_INFO(" arms: " << arms);
   }
 
   int lskflag;
@@ -629,16 +629,16 @@ void complex_filler(img::image_state::ComplexHalfFrequencyImageState& isi,
           // complex conjugate
           fhandle >> real >> imag;
           isi.Value(p)=Complex(Real(real),-Real(imag));
-          LOG_DEBUG(" " << p  << " " << isi.Value(p) << std::endl);
+          LOG_DEBUG(" " << p  << " " << isi.Value(p));
         }
         if(sr==header.nr) {
         // why set point (py,header.ny/2,pz)?
         //  isi.Value(Point(py,header.ny/2,pz))=scale*Complex(Real(real),Real(imag));
-        //  LOG_DEBUG("+" << Point(py,header.ny/2,pz) << " <- " << Point(sx,cy,sz) << " " << " " << isi.Value(Point(py,header.ny/2,pz)) << std::endl);
+        //  LOG_DEBUG("+" << Point(py,header.ny/2,pz) << " <- " << Point(sx,cy,sz) << " " << " " << isi.Value(Point(py,header.ny/2,pz)));
           p[mapc]=p[header.mapr];
           p[mapr]=header.nr/2;
           isi.Value(p)=Complex(Real(real),Real(imag));
-          LOG_DEBUG("+" << p << " " << isi.Value(p) << std::endl);
+          LOG_DEBUG("+" << p << " " << isi.Value(p));
         }
         Progress::Instance().AdvanceProgress(&this_dummy);
       }
@@ -650,11 +650,11 @@ void complex_filler(img::image_state::ComplexHalfFrequencyImageState& isi,
           p[mapc]=sc;
           fhandle >> real >> imag;
           isi.Value(p)=Complex(Real(real),Real(imag));
-          LOG_DEBUG(" " << p << " " << isi.Value(p) << std::endl);
+          LOG_DEBUG(" " << p << " " << isi.Value(p));
         }
         p[mapc]=sc;
         isi.Value(p)=Complex(Real(real),-Real(imag));
-        LOG_DEBUG(" " << p << " " << isi.Value(p) << std::endl);
+        LOG_DEBUG(" " << p << " " << isi.Value(p));
         Progress::Instance().AdvanceProgress(&this_dummy);
       }
       // set second half of r=0 and r=nr/2 line
@@ -663,10 +663,10 @@ void complex_filler(img::image_state::ComplexHalfFrequencyImageState& isi,
         p[mapr]=0;
         p[maps]=ss;
         isi.Value(Point(-p[0],p[1],p[2]))=std::conj(isi.Value(p));
-        LOG_DEBUG(" " << Point(-p[0],p[1],p[2]) << " <- " << p << "**" << std::endl);
+        LOG_DEBUG(" " << Point(-p[0],p[1],p[2]) << " <- " << p << "**");
         p[mapr]=header.nr/2;
         isi.Value(p)=std::conj(isi.Value(Point(-p[0],p[1],p[2])));
-        LOG_DEBUG(" " << p << " <- " << Point(-p[0],p[1],p[2]) << "**" << std::endl);
+        LOG_DEBUG(" " << p << " <- " << Point(-p[0],p[1],p[2]) << "**");
       }
     }
     Progress::Instance().DeRegister(&this_dummy);
@@ -742,7 +742,7 @@ void complex_dumper(BinaryOStream<CONVERSIONTYPE>& f,
         pnt[mapc]=-sc;
         Complex val = conj(norm.Convert(isc->Value(pnt)));
         f << static_cast<B>(val.real()) << static_cast<B>(val.imag());
-        LOG_DEBUG(" " << pnt  << " " << val << std::endl);
+        LOG_DEBUG(" " << pnt  << " " << val);
       }
       f << static_cast<B>(0.0) << static_cast<B>(0.0);
       Progress::Instance().AdvanceProgress(&this_dummy);
@@ -755,12 +755,12 @@ void complex_dumper(BinaryOStream<CONVERSIONTYPE>& f,
         pnt[mapc]=sc;
         Complex  val =norm.Convert(isc->Value(pnt));
         f << static_cast<B>(val.real()) << static_cast<B>(val.imag());
-        LOG_DEBUG(" " << pnt << " " << val << std::endl);
+        LOG_DEBUG(" " << pnt << " " << val);
       }
       pnt[mapc]=sc;
       Complex  val = norm.Convert(conj(isc->Value(pnt)));
       f << static_cast<B>(val.real()) << static_cast<B>(val.imag());
-      LOG_DEBUG(" " << pnt << " " << val << std::endl);
+      LOG_DEBUG(" " << pnt << " " << val);
       Progress::Instance().AdvanceProgress(&this_dummy);
     }
   }
@@ -805,9 +805,9 @@ void import_helper(img::MapHandle& image, std::istream& in,const MRC& formatmrc)
                                           static_cast<Real>(header.y)/static_cast<Real>(header.ny),
                                           static_cast<Real>(header.z)/static_cast<Real>(header.nz)));
     }else{
-      LOG_MESSAGE("Suspicious dell dimensions found. Cannot set sampling.");
+      LOG_INFO("Suspicious dell dimensions found. Cannot set sampling.");
     }
-    LOG_MESSAGE("resulting image extent: " << image.GetExtent() << std::endl);
+    LOG_INFO("resulting image extent: " << image.GetExtent());
     if(img::image_state::RealSpatialImageState *rs=dynamic_cast<img::image_state::RealSpatialImageState*>(image.ImageStatePtr().get())) {
       if(header.mode==0) {
         detail::real_filler<uchar,CONVERSIONTYPE>(*rs,f,header);
@@ -939,22 +939,22 @@ void MapIOMrcHandler::Import(img::MapHandle& sh, std::istream& loc, const ImageF
    std::istream head_str(&head_strbuf);
    head_strbuf.push(boost::iostreams::basic_array_source<char>(headerptr,sizeof(header_)));
    if (formatmrc.GetSubformat()==MRC_OLD_FORMAT) {
-     LOGN_DEBUG("mrc io: importing old style format");
+     LOG_DEBUG("mrc io: importing old style format");
      detail::import_endianess_switcher<detail::mrc_header>(sh,loc,head_str,formatmrc);
    } else if (formatmrc.GetSubformat()==MRC_NEW_FORMAT) {
-     LOGN_DEBUG("mrc io: importing new style format");
+     LOG_DEBUG("mrc io: importing new style format");
      detail::import_endianess_switcher<detail::ccp4_header>(sh,loc,head_str,formatmrc);
    } else if (is_file_ && (detail::FilenameEndsWith(filename_,".ccp4") || detail::FilenameEndsWith(filename_,".map") || detail::FilenameEndsWith(filename_,".map.gz"))) {
-     LOGN_DEBUG("mrc io: importing new style format");
+     LOG_DEBUG("mrc io: importing new style format");
      detail::import_endianess_switcher<detail::ccp4_header>(sh,loc,head_str,formatmrc);
    } else {
 	 unsigned char header_content[256];
 	 memcpy(&header_content[0],&header_,256*sizeof(char));
      if (MatchContent(header_content) == true) {
-       LOGN_DEBUG("mrc io: importing new style format");
+       LOG_DEBUG("mrc io: importing new style format");
        detail::import_endianess_switcher<detail::ccp4_header>(sh,loc,head_str,formatmrc);
      } else {
-       LOGN_DEBUG("mrc io: importing old style format");
+       LOG_DEBUG("mrc io: importing old style format");
        detail::import_endianess_switcher<detail::mrc_header>(sh,loc,head_str,formatmrc);
      }
   }
@@ -985,10 +985,10 @@ void MapIOMrcHandler::Export(const img::MapHandle& sh, std::ostream& loc,const I
     assert (formatstruct.GetFormatString()==UndefinedImageFormat::FORMAT_STRING);
   }
   if (formatmrc.GetSubformat()==MRC_OLD_FORMAT) {
-   LOGN_DEBUG("mrc io: exporting old style format");
+   LOG_DEBUG("mrc io: exporting old style format");
    detail::export_endianess_switcher<detail::mrc_header>(sh,loc,formatmrc);
   } else {
-   LOGN_DEBUG("mrc io: exporting new style format");
+   LOG_DEBUG("mrc io: exporting new style format");
    detail::export_endianess_switcher<detail::ccp4_header>(sh,loc,formatmrc);
   }
 }
diff --git a/modules/io/src/img/map_io_mrc_handler.hh b/modules/io/src/img/map_io_mrc_handler.hh
index 673fac913ec9932fb561bc5211cfa2526208cf74..b73aaf56ea77dbcf7fe8fdee0da19df872f5f554 100644
--- a/modules/io/src/img/map_io_mrc_handler.hh
+++ b/modules/io/src/img/map_io_mrc_handler.hh
@@ -46,7 +46,6 @@ class DLLEXPORT_OST_IO MRC: public ImageFormatBase
   Subformat subformat_;
   bool normalize_on_save_;
   Endianess endianess_on_save_;
-  Subformat subf_;
 };
 
 class DLLEXPORT_OST_IO CCP4: public MRC
diff --git a/modules/io/src/img/map_io_nanoscope_handler.cc b/modules/io/src/img/map_io_nanoscope_handler.cc
index 0019fa320092cd330c9b601181a153559c58dbff..a18a25c56ee5d52050d3ae5637d0b978056836c6 100644
--- a/modules/io/src/img/map_io_nanoscope_handler.cc
+++ b/modules/io/src/img/map_io_nanoscope_handler.cc
@@ -47,9 +47,9 @@ namespace ost { namespace io {
 String Nanoscope::FORMAT_STRING = "defined_nanoscope";
 
 Nanoscope::Nanoscope(int subimage):
-  ImageFormatBase(FORMAT_STRING)
+  ImageFormatBase(FORMAT_STRING),
+  subimage_(subimage)
 {
-  subimage_ = subimage;
 }
 
 int Nanoscope::GetSubimage() const
@@ -179,17 +179,17 @@ void header_filler(NHeader& h, std::istream& in, int inum)
 void print_header (const NHeader& header, int inum)
 {
   if(Logger::Instance().GetLogLevel()>2) {
-    LOG_MESSAGE("io_nanoscope: header dump for image " << inum << std::endl);
-    LOG_MESSAGE(" px      : " << header.px << std::endl);
-    LOG_MESSAGE(" py      : " << header.py << std::endl);
-    LOG_MESSAGE(" nmsize  : " << header.nmsize << std::endl);
-    LOG_MESSAGE(" sampling: " << header.sampling << " nm" << std::endl);
-    LOG_MESSAGE(" zscale  : " << header.zscale << std::endl);
-    LOG_MESSAGE(" multih  : " << header.multih << std::endl);
-    LOG_MESSAGE(" multid  : " << header.multid << std::endl);
-    LOG_MESSAGE(" multi   : " << header.multi << std::endl);
-    LOG_MESSAGE(" doffset : " << header.doffset << std::endl);
-    LOG_MESSAGE(" dlength : " << header.dlength << std::endl);
+    LOG_INFO("io_nanoscope: header dump for image " << inum);
+    LOG_INFO(" px      : " << header.px);
+    LOG_INFO(" py      : " << header.py);
+    LOG_INFO(" nmsize  : " << header.nmsize);
+    LOG_INFO(" sampling: " << header.sampling << " nm");
+    LOG_INFO(" zscale  : " << header.zscale);
+    LOG_INFO(" multih  : " << header.multih);
+    LOG_INFO(" multid  : " << header.multid);
+    LOG_INFO(" multi   : " << header.multi);
+    LOG_INFO(" doffset : " << header.doffset);
+    LOG_INFO(" dlength : " << header.dlength);
   }
 }
 
diff --git a/modules/io/src/img/map_io_png_handler.cc b/modules/io/src/img/map_io_png_handler.cc
index 84b290d2e22214c3ee31a662c30c402fb941358e..9107953aafd55b6aee191ca9c7aedf7f464bc2dd 100644
--- a/modules/io/src/img/map_io_png_handler.cc
+++ b/modules/io/src/img/map_io_png_handler.cc
@@ -46,9 +46,9 @@ namespace ost { namespace io {
 String PNG::FORMAT_STRING="defined_png";
 
 PNG::PNG(bool normalize_on_save):
-    ImageFormatBase(FORMAT_STRING)
+    ImageFormatBase(FORMAT_STRING),
+    normalize_on_save_(normalize_on_save)
 {
-    normalize_on_save_ = normalize_on_save;
     this->SetMinimum(0.0);
     this->SetMaximum(255.0);
 }
diff --git a/modules/io/src/img/map_io_situs_handler.cc b/modules/io/src/img/map_io_situs_handler.cc
index a7e12da30beb181738c49fc71eb2ed9b91a9101f..989c60d71c9fa6e85e07fded9662ae6a661506d7 100644
--- a/modules/io/src/img/map_io_situs_handler.cc
+++ b/modules/io/src/img/map_io_situs_handler.cc
@@ -46,9 +46,9 @@ namespace ost { namespace io {
 String Situs::FORMAT_STRING="defined_situs";
 
 Situs::Situs(bool normalize_on_save):
-    ImageFormatBase(FORMAT_STRING)
+    ImageFormatBase(FORMAT_STRING),
+    normalize_on_save_(normalize_on_save)
 {
-    normalize_on_save_ = normalize_on_save;
 }
 
 bool Situs::GetNormalizeOnSave() const
@@ -89,8 +89,8 @@ void print_header(const situs_header& h)
   s << "situs header: " << std::endl;
   s << format(" voxel width: %1") % h.dwidth << std::endl;
   s << format(" size x y z: %1 %2 %3") % h.extx % h.exty % h.extz << std::endl;
-  s << format(" origin x y z: %1 %2 %3") % h.gridx % h.gridy % h.gridz << std::endl;
-  LOG_MESSAGE(s.str());
+  s << format(" origin x y z: %1 %2 %3") % h.gridx % h.gridy % h.gridz;
+  LOG_INFO(s.str());
 }
 
 
@@ -208,7 +208,7 @@ void MapIOSitusHandler::Import(img::MapHandle& mh, std::istream& infile,const Im
   mh.Reset(msize);
   mh.SetSpatialSampling(geom::Vec3(header.dwidth,header.dwidth,header.dwidth));
 
-  LOG_VERBOSE("resulting image extent: " << mh.GetExtent() << std::endl);
+  LOG_VERBOSE("resulting image extent: " << mh.GetExtent());
 
   detail::real_filler(infile,header,mh,1.0);
 
diff --git a/modules/io/src/img/map_io_spi_handler.cc b/modules/io/src/img/map_io_spi_handler.cc
index 63b5e1e4ca4f88e584a7eceaf1855c29a457876b..6b308f91218053490d1c9c1254ccc3cf5cf1b257 100644
--- a/modules/io/src/img/map_io_spi_handler.cc
+++ b/modules/io/src/img/map_io_spi_handler.cc
@@ -48,10 +48,10 @@ namespace ost { namespace io {
 String Spider::FORMAT_STRING = "defined_spider";
 
 Spider::Spider(bool normalize_on_save,Endianess endianness_on_save):
-  ImageFormatBase(FORMAT_STRING)
+  ImageFormatBase(FORMAT_STRING),
+  normalize_on_save_(normalize_on_save),
+  endianness_on_save_(endianness_on_save)
 {
-  normalize_on_save_ = normalize_on_save;
-  endianness_on_save_ = endianness_on_save;
 }
 
 Endianess Spider::GetEndianessOnSave() const
@@ -201,8 +201,8 @@ void print_header(const spider_header& h)
     s << format(" std dev: %1%") % h.fSig << std::endl;
   }
   s << format(" scale: %1%") %  h.fScale << std::endl;
-  s << format(" header size:  %1%") % h.fLabbyt << std::endl;
-  LOG_MESSAGE(s.str());
+  s << format(" header size:  %1%") % h.fLabbyt;
+  LOG_INFO(s.str());
 }
 
 int determine_byte_order(std::istream& f)
@@ -218,10 +218,10 @@ int determine_byte_order(std::istream& f)
     if (bs_iform<-22.0 ||bs_iform>3.0 ||static_cast<int>(bs_iform)==0) {
       throw(ost::io::IOException("error reading spider file (even tried byte-swapping"));
     }
-    LOG_VERBOSE("Spider IO: reading big endian data" << std::endl);
+    LOG_VERBOSE("Spider IO: reading big endian data");
     return OST_BIG_ENDIAN;
   }
-  LOG_VERBOSE("Spider IO: reading little endian data" << std::endl);
+  LOG_VERBOSE("Spider IO: reading little endian data");
   return OST_LITTLE_ENDIAN;
 }
 
@@ -432,7 +432,7 @@ void MapIOSpiHandler::Import(img::MapHandle& mh, std::istream& infile,const Imag
 
   mh.Reset(msize);
 
-  LOG_MESSAGE("density map extent: " << mh.GetExtent() << std::endl);
+  LOG_INFO("density map extent: " << mh.GetExtent());
 
 
   switch(detail::determine_byte_order(infile)){
@@ -449,7 +449,7 @@ void MapIOSpiHandler::Import(img::MapHandle& mh, std::istream& infile,const Imag
 
   if (header.fScale==0.0)  {
     mh.SetSpatialSampling(geom::Vec3(1.0,1.0,1.0));
-    LOG_MESSAGE("assuming 1 A spatial sampling" << std::endl);
+    LOG_INFO("assuming 1 A spatial sampling");
   } else {
     Real fscale=static_cast<Real>(header.fScale);
     mh.SetSpatialSampling(geom::Vec3(fscale,fscale,fscale));
@@ -457,8 +457,8 @@ void MapIOSpiHandler::Import(img::MapHandle& mh, std::istream& infile,const Imag
 
   mh.SetAbsoluteOrigin(geom::Vec3(0,0,0));
 
-  LOG_MESSAGE("assuming origin at the first voxel" << std::endl);
-  LOG_MESSAGE("assuming absolute origin at (0,0,0)" << std::endl);
+  LOG_INFO("assuming origin at the first voxel");
+  LOG_INFO("assuming absolute origin at (0,0,0)");
 
 }
 
diff --git a/modules/io/src/img/map_io_tiff_handler.cc b/modules/io/src/img/map_io_tiff_handler.cc
index 10c1a5c3f754a2a9b70cfd9da68f704b8e43cb45..a4c3fd191312e5ec94caa4eb11a4dda00a97e2f4 100644
--- a/modules/io/src/img/map_io_tiff_handler.cc
+++ b/modules/io/src/img/map_io_tiff_handler.cc
@@ -47,21 +47,21 @@ namespace ost { namespace io {
 String TIF::FORMAT_STRING="defined_tiff";
 
  TIF::TIF(boost::logic::tribool normalize_on_save, Format bit_depth, bool sign, bool phasecolor, int subimage):
-    ImageFormatBase(FORMAT_STRING)
+  ImageFormatBase(FORMAT_STRING),
+  normalize_on_save_(normalize_on_save),
+  bit_depth_(bit_depth),
+  signed_(sign),
+  phasecolor_(phasecolor)
 {
-  normalize_on_save_ = normalize_on_save;
-  bit_depth_ = bit_depth;
-  signed_ = sign;
-  phasecolor_ = phasecolor;
 }
 
 TIF::TIF(String format_string, boost::logic::tribool  normalize_on_save, Format bit_depth,bool sign, bool phasecolor, int subimage):
-  ImageFormatBase(format_string)
+  ImageFormatBase(FORMAT_STRING),
+  normalize_on_save_(normalize_on_save),
+  bit_depth_(bit_depth),
+  signed_(sign),
+  phasecolor_(phasecolor)
 {
-  normalize_on_save_ = normalize_on_save;
-  bit_depth_ = bit_depth;
-  signed_ = sign;
-  phasecolor_ = phasecolor;
 }
 
 Format TIF::GetBitDepth() const
@@ -134,7 +134,7 @@ void MapIOTiffHandler::Import(img::MapHandle& image, const boost::filesystem::pa
     assert (formatstruct.GetFormatString()==UndefinedImageFormat::FORMAT_STRING);
   }
 
-  LOG_VERBOSE("I/O Tiff: using library version " << TIFFGetVersion() << std::endl);
+  LOG_VERBOSE("I/O Tiff: using library version " << TIFFGetVersion());
   detail::tiff_warning_handler_wrapper twhw;
   TIFF* tfile=open_subimage_file(location,formattif);
   load_image_data(tfile,image,formattif);
@@ -151,7 +151,7 @@ void MapIOTiffHandler::Import(img::ImageHandle& image, std::istream& location, c
     assert (formatstruct.GetFormatString()==UndefinedImageFormat::FORMAT_STRING);
   }
 
-  LOG_VERBOSE("I/O Tiff: using library version " << TIFFGetVersion() << std::endl);
+  LOG_VERBOSE("I/O Tiff: using library version " << TIFFGetVersion());
   detail::tiff_warning_handler_wrapper twhw;
   TIFF* tfile=open_subimage_stream(location,formattif);
   load_image_data(tfile,image,formattif);
@@ -219,18 +219,18 @@ void MapIOTiffHandler::do_export(const img::MapHandle& image,TIFF* tfile,TIF& fo
     case OST_BIT32_FORMAT:
     case OST_DEFAULT_FORMAT:
       norm = img::alg::CreateLinearRangeNormalizer(image,formattif.GetMinimum(),formattif.GetMaximum());
-      LOGN_VERBOSE("Autodetecting normalization for export: normalization on");
+      LOG_VERBOSE("Autodetecting normalization for export: normalization on");
       break;
     case OST_FLOAT_FORMAT:
     case OST_DOUBLE_FORMAT:
-    LOGN_VERBOSE("Autodetecting normalization for export: normalization off");
+    LOG_VERBOSE("Autodetecting normalization for export: normalization off");
       break;
     }
   } else if (formattif.GetNormalizeOnSave() == true) {
-    LOGN_VERBOSE("Normalization used for export.");
+    LOG_VERBOSE("Normalization used for export.");
     norm = img::alg::CreateLinearRangeNormalizer(image,formattif.GetMinimum(),formattif.GetMaximum());
   } else {
-    LOGN_VERBOSE("No normalization used for export.");
+    LOG_VERBOSE("No normalization used for export.");
   }
 
   detail::tiff_warning_handler_wrapper twhw;
@@ -440,9 +440,9 @@ TIFF* MapIOTiffHandler::open_subimage_file(const boost::filesystem::path& locati
   if(formattif.GetSubimage()!=-1){
     directory_number=formattif.GetSubimage();
   }
-  LOG_VERBOSE("I/O Tiff: using directory nr. " << directory_number<< std::endl);
+  LOG_VERBOSE("I/O Tiff: using directory nr. " << directory_number);
   const String& filename = location.string();
-  LOG_VERBOSE("I/O Tiff: calling TIFFOpen with " << filename.c_str() << std::endl);
+  LOG_VERBOSE("I/O Tiff: calling TIFFOpen with " << filename.c_str());
   TIFF* tfile=TIFFOpen(filename.c_str(),"r");
   if(!tfile) {
     throw IOException("could not open " + filename + String(" for reading"));
@@ -462,9 +462,9 @@ TIFF* MapIOTiffHandler::open_subimage_stream(std::istream& location,const TIF& f
   if(formattif.GetSubimage()!=-1){
     directory_number=formattif.GetSubimage();
   }
-  LOG_VERBOSE("I/O Tiff: using directory nr. " << directory_number<< std::endl);
+  LOG_VERBOSE("I/O Tiff: using directory nr. " << directory_number);
   const String& filename = "stream";
-  LOG_VERBOSE("I/O Tiff: calling TIFFClientOpen with " << filename.c_str() << std::endl);
+  LOG_VERBOSE("I/O Tiff: calling TIFFClientOpen with " << filename.c_str());
   TIFF* tfile=TIFFClientOpen(filename.c_str(),
                              "rm",
                              &location,
@@ -508,7 +508,7 @@ void MapIOTiffHandler::load_image_data(TIFF* tfile, img::ImageHandle& image,  co
   }
   TIFFGetField(tfile,TIFFTAG_ROWSPERSTRIP,&rps);
 
-  LOG_MESSAGE ("I/O Tiff: Header: " << width << "x" << height << " " << bpp << "bpp" << std::endl);
+  LOG_INFO("I/O Tiff: Header: " << width << "x" << height << " " << bpp << "bpp");
 
   img::Extent image_extent(img::Point(0,0),img::Size(width,height));
 
@@ -531,19 +531,19 @@ void MapIOTiffHandler::load_image_data(TIFF* tfile, img::ImageHandle& image,  co
   if(!TIFFGetField(tfile,TIFFTAG_SAMPLEFORMAT,&fmt))
   {
     // todo check subtype
-    LOG_MESSAGE("I/O Tiff: Unknown sample format: assuming uint" << std::endl);
+    LOG_INFO("I/O Tiff: Unknown sample format: assuming uint");
     fmt=SAMPLEFORMAT_UINT;
   }
 
-  LOG_MESSAGE("I/O Tiff: Header: spp=" << spp << "; rps=" << rps << "; plc=" << plc << "; ori=" << ori << std::endl);
-  LOG_MESSAGE("I/O Tiff: Header: pos= " << xpos << "," << ypos << "; reso= " << xreso << "," << yreso << ";" << std::endl);
+  LOG_INFO("I/O Tiff: Header: spp=" << spp << "; rps=" << rps << "; plc=" << plc << "; ori=" << ori);
+  LOG_INFO("I/O Tiff: Header: pos= " << xpos << "," << ypos << "; reso= " << xreso << "," << yreso << ";");
 
   if(bpp!=8 && bpp!=16 && bpp!=32 && bpp!=64 && bpp!=128) {
     throw IOException("bits per sample must be 8, 16, 32, 64 or 128");
   }
 
   if(spp==0) {
-    LOG_MESSAGE("I/O Tiff: Samples per pixel is zero, assuming one" << std::endl);
+    LOG_INFO("I/O Tiff: Samples per pixel is zero, assuming one");
     spp=1;
   }
 
@@ -551,7 +551,7 @@ void MapIOTiffHandler::load_image_data(TIFF* tfile, img::ImageHandle& image,  co
     if(spp>4) {
       throw IOException("I/O Tiff: unexpected spp>4 in header");
     }
-    LOG_MESSAGE("I/O Tiff: Samples per pixel>1, reading first channel only" << std::endl);
+    LOG_INFO("I/O Tiff: Samples per pixel>1, reading first channel only");
   }
 
   if(TIFFIsTiled(tfile)) {
@@ -563,12 +563,12 @@ void MapIOTiffHandler::load_image_data(TIFF* tfile, img::ImageHandle& image,  co
   uint stripsize=TIFFStripSize(tfile);
   uint stripcount=TIFFNumberOfStrips(tfile);
 
-  LOG_MESSAGE("I/O Tiff: " << "found " << stripcount << " strips in tiff file" << std::endl);
-  LOG_MESSAGE("I/O Tiff: " << "allocating " << stripsize << " bytes for temporary read buffer" << std::endl);
+  LOG_INFO("I/O Tiff: " << "found " << stripcount << " strips in tiff file");
+  LOG_INFO("I/O Tiff: " << "allocating " << stripsize << " bytes for temporary read buffer");
   buf = _TIFFmalloc(stripsize);
 
   if(image.GetType()==img::WORD) {
-    LOG_MESSAGE("I/O Tiff: " << "reseting target image to WORD " << image_extent << std::endl);
+    LOG_INFO("I/O Tiff: " << "reseting target image to WORD " << image_extent);
     image.Reset(image_extent, img::WORD, img::SPATIAL);
 
     img::image_state::WordSpatialImageState *is =
@@ -579,7 +579,7 @@ void MapIOTiffHandler::load_image_data(TIFF* tfile, img::ImageHandle& image,  co
 
     int current_row = 0;
 
-    LOG_VERBOSE("I/O Tiff: " << "importing data" << std::endl);
+    LOG_VERBOSE("I/O Tiff: " << "importing data");
     img::Progress::Instance().Register(this,stripcount,100);
     for (strip = 0; strip < stripcount; ++strip) {
       int cread=TIFFReadEncodedStrip(tfile, strip, buf, (tsize_t) -1);
@@ -596,7 +596,7 @@ void MapIOTiffHandler::load_image_data(TIFF* tfile, img::ImageHandle& image,  co
       }
       img::Progress::Instance().AdvanceProgress(this);
     }
-    LOG_VERBOSE("I/O Tiff: " << "done" << std::endl);
+    LOG_VERBOSE("I/O Tiff: " << "done");
     img::Progress::Instance().DeRegister(this);
     uint16 photometric;
     if(TIFFGetField(tfile,TIFFTAG_PHOTOMETRIC,&photometric)){
@@ -615,14 +615,14 @@ void MapIOTiffHandler::load_image_data(TIFF* tfile, img::ImageHandle& image,  co
     img::image_state::RealSpatialImageState *isr=0;
     img::image_state::ComplexSpatialImageState *isc=0;
     if(fmt==SAMPLEFORMAT_COMPLEXINT || fmt==SAMPLEFORMAT_COMPLEXIEEEFP){
-      LOG_MESSAGE("I/O Tiff: " << "reseting target image to complex spatial " << image_extent << std::endl);
+      LOG_INFO("I/O Tiff: " << "reseting target image to complex spatial " << image_extent);
       image.Reset(image_extent,img::COMPLEX,img::SPATIAL);
       isc = dynamic_cast<img::image_state::ComplexSpatialImageState*>(image.ImageStatePtr().get());
       if(!isc) {
         throw IOException("unexpected failure of dynamic_cast in tiff io");
       }
     }else{
-      LOG_MESSAGE("I/O Tiff: " << "reseting target image to Real img::SPATIAL" << image_extent << std::endl);
+      LOG_INFO("I/O Tiff: " << "reseting target image to Real img::SPATIAL" << image_extent);
       image.Reset(image_extent, img::REAL, img::SPATIAL);
 
       isr= dynamic_cast<img::image_state::RealSpatialImageState*>(image.ImageStatePtr().get());
@@ -634,7 +634,7 @@ void MapIOTiffHandler::load_image_data(TIFF* tfile, img::ImageHandle& image,  co
 
     int current_row = 0;
 
-    LOG_VERBOSE("I/O Tiff: " << "importing data" << std::endl);
+    LOG_VERBOSE("I/O Tiff: " << "importing data");
     img::Progress::Instance().Register(this,stripcount,100);
     for (strip = 0; strip < stripcount; ++strip) {
       int cread=TIFFReadEncodedStrip(tfile, strip, buf, (tsize_t) -1);
@@ -704,7 +704,7 @@ void MapIOTiffHandler::load_image_data(TIFF* tfile, img::ImageHandle& image,  co
       }
       img::Progress::Instance().AdvanceProgress(this);
     }
-    LOG_VERBOSE("I/O Tiff: " << "done" << std::endl);
+    LOG_VERBOSE("I/O Tiff: " << "done");
 
     img::Progress::Instance().DeRegister(this);
     uint16 photometric;
diff --git a/modules/io/src/img/tiff_util.cc b/modules/io/src/img/tiff_util.cc
index 37f8c322609b991c03d36df02053e86a8c695fbe..0fa8e318621d850990c827c0ad5e26c9d3f3c92c 100644
--- a/modules/io/src/img/tiff_util.cc
+++ b/modules/io/src/img/tiff_util.cc
@@ -19,7 +19,6 @@
 //------------------------------------------------------------------------------
 
 #include <stdarg.h>
-#include <sstream>
 #include <cassert>
 #include <complex>
 #include <ost/log.hh>
@@ -39,10 +38,7 @@ void tiff_warning_handler(const char *mod, const char* fmt, va_list ap)
 #else
   snprintf(message,1024,fmt,ap);
 #endif
-  String msg;
-  std::stringstream msgs(msg);
-  msgs << mod << ": " << message << std::endl;
-  LOG_MESSAGE(msg);
+  LOG_INFO(mod << ": " << message);
 }
 
 int32_t CustomTIFFReadProcIStream(void* thandle, void* tdata, int32_t tsize)
diff --git a/modules/io/src/io_manager.cc b/modules/io/src/io_manager.cc
index 3e61ce59b61e54d72fa11436dcba3614c007a9c7..c97938f907004b7a046d0bf0ae100d43adfbd525 100644
--- a/modules/io/src/io_manager.cc
+++ b/modules/io/src/io_manager.cc
@@ -37,6 +37,7 @@
 #  include  <ost/io/img/map_io_dat_handler.hh>
 #  include  <ost/io/img/map_io_jpk_handler.hh>
 #  include  <ost/io/img/map_io_nanoscope_handler.hh>
+#  include  <ost/io/img/map_io_df3_handler.hh>
 #endif
 namespace ost { namespace io {
 
@@ -62,6 +63,7 @@ IOManager::IOManager()
   RegisterFactory(MapIOHandlerFactoryBasePtr(new MapIOJpkHandlerFactory));
   RegisterFactory(MapIOHandlerFactoryBasePtr(new MapIODatHandlerFactory));
   RegisterFactory(MapIOHandlerFactoryBasePtr(new MapIONanoscopeHandlerFactory));
+  RegisterFactory(MapIOHandlerFactoryBasePtr(new MapIODF3HandlerFactory));  
 #endif
 }
 
diff --git a/modules/io/src/mol/CMakeLists.txt b/modules/io/src/mol/CMakeLists.txt
index 860b4df0d09e6525952e9728389b436f1fe8db5d..8498858451420988e3a4132c6df570b30e35eff0 100644
--- a/modules/io/src/mol/CMakeLists.txt
+++ b/modules/io/src/mol/CMakeLists.txt
@@ -12,12 +12,14 @@ save_entity.cc
 load_entity.cc
 surface_io_msms_handler.cc
 load_surface.cc
+chemdict_parser.cc
 dcd_io.cc
 star_parser.cc
 PARENT_SCOPE
 )
 
 set(OST_IO_MOL_HEADERS
+chemdict_parser.hh
 star_parser.hh
 dcd_io.hh
 entity_io_crd_handler.hh	
diff --git a/modules/io/src/mol/chemdict_parser.cc b/modules/io/src/mol/chemdict_parser.cc
new file mode 100644
index 0000000000000000000000000000000000000000..2668221bafab38c5f682497cbe416906c09756ad
--- /dev/null
+++ b/modules/io/src/mol/chemdict_parser.cc
@@ -0,0 +1,163 @@
+#include <ost/io/mol/chemdict_parser.hh>
+
+namespace ost { namespace io {
+
+using namespace ost::conop;
+  
+bool ChemdictParser::OnBeginData(const StringRef& data_name) 
+{    
+  compound_.reset(new Compound(data_name.str()));
+  compound_->SetDialect(dialect_);
+  if (last_!=data_name[0]) {
+    last_=data_name[0];
+    std::cout << last_ << std::flush;
+  }
+  atom_map_.clear();
+  insert_=true;
+  return true; 
+}
+
+bool ChemdictParser::OnBeginLoop(const StarLoopDesc& header)
+{ 
+  if (header.GetCategory()=="chem_comp_atom") {
+    loop_type_=ATOM_SPEC;
+    indices_[ATOM_NAME]=header.GetIndex("atom_id");
+    indices_[ALT_ATOM_NAME]=header.GetIndex("alt_atom_id");
+    indices_[ELE]=header.GetIndex("type_symbol");      
+    indices_[IS_LEAVING]=header.GetIndex("pdbx_leaving_atom_flag");
+    indices_[IS_AROMATIC]=header.GetIndex("pdbx_aromatic_flag");
+    indices_[ORDINAL]=header.GetIndex("pdbx_ordinal");      
+    return true;
+  } else if (header.GetCategory()=="chem_comp_bond") {
+    loop_type_=BOND_SPEC;
+    indices_[ATOM_ID1]=header.GetIndex("atom_id_1");
+    indices_[ATOM_ID2]=header.GetIndex("atom_id_2");
+    indices_[BOND_ORDER]=header.GetIndex("value_order");
+    return true;
+  }
+  loop_type_=DONT_KNOW;
+  return false;
+}
+
+void ChemdictParser::OnDataRow(const StarLoopDesc& header, 
+                               const std::vector<StringRef>& columns) 
+{                        
+  if (loop_type_==ATOM_SPEC) {
+    AtomSpec atom;
+    atom.is_leaving=columns[indices_[IS_LEAVING]][0]=='Y';
+    atom.name=columns[indices_[ATOM_NAME]].str();
+    atom.alt_name=columns[indices_[ALT_ATOM_NAME]].str();
+    atom.ordinal=columns[indices_[ORDINAL]].to_int().second-1;
+    atom.element=columns[indices_[ELE]].str();
+    atom.is_aromatic=columns[indices_[IS_AROMATIC]][0]=='Y';
+    compound_->AddAtom(atom);
+    atom_map_[atom.name]=atom.ordinal;
+  } else if (loop_type_==BOND_SPEC) {
+    BondSpec bond;
+    String atom_one=columns[indices_[ATOM_ID1]].str();
+    String atom_two=columns[indices_[ATOM_ID2]].str();      
+    bond.atom_one=atom_map_[atom_one];
+    bond.atom_two=atom_map_[atom_two];
+    char b=columns[indices_[BOND_ORDER]][0];
+    bond.order=b=='D' ? 2 : (b=='S' ? 1 : 3);
+    if (bond.atom_one>bond.atom_two) {
+      std::swap(bond.atom_one, bond.atom_two);
+    }
+    compound_->AddBond(bond);
+  }
+}
+
+void ChemdictParser::OnDataItem(const StarDataItem& item)
+{
+  if (item.GetCategory()==StringRef("chem_comp", 9)) {
+    if (item.GetName()==StringRef("type", 4)) {
+      // convert type to uppercase
+      String type=item.GetValue().str();
+      for (String::iterator i=type.begin(), e=type.end(); i!=e; ++i) {
+        *i=toupper(*i);
+      }
+      // The type of water is set to "?". let's change it to water...
+      if (compound_->GetID()=="HOH") {
+        compound_->SetChemClass(mol::ChemClass(mol::ChemClass::Water));
+        compound_->SetOneLetterCode('.');
+      } else {
+        std::map<String, mol::ChemClass>::iterator i=tm_.find(type);
+        if (i!=tm_.end()) {
+          compound_->SetChemClass(i->second);
+        } else {
+          std::cout << "unknown type '" << type << "' for compound "
+                    << compound_->GetID() << std::endl;
+        }
+      }
+
+    } else if (item.GetName()==StringRef("formula", 7)) {
+      compound_->SetFormula(item.GetValue().str());
+    } else if (item.GetName()==StringRef("one_letter_code", 15)) {
+      if (item.GetValue().length()==1) {
+        compound_->SetOneLetterCode(item.GetValue()[0]);   
+      }
+    } else if (item.GetName()==StringRef("pdbx_initial_date", 17)) {        
+      compound_->SetCreationDate(Date::FromString(item.GetValue()));
+    } else if (item.GetName()==StringRef("pdbx_modified_date", 18)) {
+      compound_->SetModificationDate(Date::FromString(item.GetValue()));
+    }
+  } else if (item.GetName()==StringRef("atom_id", 7)) {
+    atom_.name=item.GetValue().str();
+  } else if (item.GetName()==StringRef("alt_atom_id", 11)) {
+    if (compound_->GetID()=="ILE" && item.GetValue()==StringRef("CD1", 3)) {
+      atom_.alt_name="CD";
+    } else {
+      atom_.alt_name=item.GetValue().str();       
+    }
+
+  } else if (item.GetName()==StringRef("type_symbol", 11)) {
+    atom_.element=item.GetValue().str();
+  } else if (item.GetName()==StringRef("pdbx_ordinal", 12)) {
+    atom_.ordinal=item.GetValue().to_int().second-1;
+  }
+}
+
+void ChemdictParser::OnEndData()
+{
+  if (insert_) {
+    if (compound_->GetAtomSpecs().empty()) {
+      compound_->AddAtom(atom_);
+    }
+    lib_->AddCompound(compound_);      
+  }
+}
+
+std::map<String, mol::ChemClass> ChemdictParser::tm_=std::map<String, mol::ChemClass>();
+
+void ChemdictParser::InitTypeMap()
+{
+  if (!tm_.empty())
+    return;
+  tm_["L-PEPTIDE COOH CARBOXY TERMINUS"]=mol::ChemClass(mol::ChemClass::LPeptideLinking);
+  tm_["L-PEPTIDE NH3 AMINO TERMINUS"]=mol::ChemClass(mol::ChemClass::LPeptideLinking);   
+  tm_["D-PEPTIDE NH3 AMINO TERMINUS"]=mol::ChemClass(mol::ChemClass::DPeptideLinking);
+  tm_["L-SACCHARIDE 1,4 AND 1,4 LINKING"]=mol::ChemClass(mol::ChemClass::LSaccharide);
+  tm_["D-SACCHARIDE 1,4 AND 1,4 LINKING"]=mol::ChemClass(mol::ChemClass::DSaccharide);
+  tm_["L-SACCHARIDE"]=mol::ChemClass(mol::ChemClass::LSaccharide);
+  tm_["D-SACCHARIDE"]=mol::ChemClass(mol::ChemClass::DSaccharide);
+  tm_["SACCHARIDE"]=mol::ChemClass(mol::ChemClass::Saccharide);
+  tm_["D-PEPTIDE LINKING"]=mol::ChemClass(mol::ChemClass::DPeptideLinking);
+  tm_["L-PEPTIDE LINKING"]=mol::ChemClass(mol::ChemClass::LPeptideLinking);
+  tm_["L-PEPTIDE-LINKING"]=mol::ChemClass(mol::ChemClass::LPeptideLinking);
+  tm_["DNA LINKING"]=mol::ChemClass(mol::ChemClass::DNALinking);
+  tm_["RNA LINKING"]=mol::ChemClass(mol::ChemClass::RNALinking);
+  tm_["L-DNA LINKING"]=mol::ChemClass(mol::ChemClass::DNALinking);
+  tm_["L-RNA LINKING"]=mol::ChemClass(mol::ChemClass::RNALinking);  
+  tm_["R-DNA LINKING"]=mol::ChemClass(mol::ChemClass::DNALinking);
+  tm_["R-RNA LINKING"]=mol::ChemClass(mol::ChemClass::RNALinking);  
+  tm_["DNA OH 3 PRIME TERMINUS"]=mol::ChemClass(mol::ChemClass::DNALinking);
+  tm_["PEPTIDE-LIKE"]=mol::ChemClass(mol::ChemClass::PeptideLinking);
+  tm_["PEPTIDE LINKING"]=mol::ChemClass(mol::ChemClass::PeptideLinking);
+  tm_["PEPTIDE-LINKING"]=mol::ChemClass(mol::ChemClass::PeptideLinking);  
+  tm_["NON-POLYMER"]=mol::ChemClass(mol::ChemClass::NonPolymer);
+  tm_["RNA OH 3 PRIME TERMINUS"]=mol::ChemClass(mol::ChemClass::RNALinking);
+  tm_["?"]=mol::ChemClass(mol::ChemClass::Unknown);  
+  tm_["WATER"]=mol::ChemClass(mol::ChemClass::Water);
+}
+
+}}
\ No newline at end of file
diff --git a/modules/io/src/mol/chemdict_parser.hh b/modules/io/src/mol/chemdict_parser.hh
new file mode 100644
index 0000000000000000000000000000000000000000..a76ae3c0cc6d58ccdf99356d22960148fc09c75c
--- /dev/null
+++ b/modules/io/src/mol/chemdict_parser.hh
@@ -0,0 +1,93 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+//------------------------------------------------------------------------------
+#ifndef OST_CONOP_CHEMDICT_PARSER_HH
+#define OST_CONOP_CHEMDICT_PARSER_HH
+
+/*
+  Author: Marco Biasini
+ */
+ 
+ 
+#include <ost/mol/mol.hh>
+#include <ost/io/mol/star_parser.hh>
+#include <ost/conop/compound_lib.hh>
+ 
+namespace ost { namespace io {
+
+typedef enum {
+  ATOM_SPEC,
+  BOND_SPEC,
+  DONT_KNOW
+} LoopType;
+
+class DLLEXPORT_OST_IO ChemdictParser : public StarParser {
+public:
+  ChemdictParser(std::istream& stream, conop::Compound::Dialect dialect): 
+    StarParser(stream), compound_(new conop::Compound("UNK")), 
+    last_(0), loop_type_(DONT_KNOW), dialect_(dialect)
+  {
+    this->InitTypeMap();
+  }
+
+  virtual bool OnBeginData(const StringRef& data_name);
+
+  virtual bool OnBeginLoop(const StarLoopDesc& header);
+
+  virtual void OnDataRow(const StarLoopDesc& header, 
+                         const std::vector<StringRef>& columns);
+
+  virtual void OnDataItem(const StarDataItem& item);
+
+  virtual void OnEndData();
+
+  void SetCompoundLib(const conop::CompoundLibPtr& lib) 
+  {
+    lib_=lib;
+  }
+private:
+  void InitTypeMap();  
+  conop::CompoundLibPtr                   lib_;
+  conop::CompoundPtr                      compound_;
+  typedef enum {
+    ATOM_NAME=0,
+    ALT_ATOM_NAME=1,
+    IS_AROMATIC=2,
+    ORDINAL=3,
+    IS_LEAVING=4,
+    ELE=5,
+    STEREO_CONF=6,
+    ATOM_ID1=0,
+    ATOM_ID2=1,
+    BOND_ORDER=2
+  } PropIndex;
+  char                                    last_;
+  int                                     indices_[10];
+  bool                                    insert_;
+  static std::map<String, mol::ChemClass> tm_;  
+  std::map<String, int>                   atom_map_;
+  LoopType                                loop_type_;  
+  conop::AtomSpec                         atom_;
+  conop::Compound::Dialect                dialect_;
+};
+
+
+}}
+
+
+#endif
\ No newline at end of file
diff --git a/modules/io/src/mol/dcd_io.cc b/modules/io/src/mol/dcd_io.cc
index c580ce1b244361b28e85199f2c206f3d8c61c1be..177cd57af0e7a7144d40123c17c091d675f77c7f 100644
--- a/modules/io/src/mol/dcd_io.cc
+++ b/modules/io/src/mol/dcd_io.cc
@@ -78,25 +78,24 @@ mol::CoordGroupHandle load_dcd(const mol::AtomHandleList& alist2,
   bool gap_flag = true;
 
   boost::filesystem::path trj_f(trj_fn);
-  boost::filesystem::ifstream ff(trj_f);
+  boost::filesystem::ifstream ff(trj_f, std::ios::binary);
   
   DCDHeader header;
   char dummy[4];
   bool swap_flag=false;
 
-  LOGN_MESSAGE("importing trajectory data");
+  LOG_INFO("importing trajectory data");
 
   if(gap_flag) ff.read(dummy,sizeof(dummy));
   ff.read(header.hdrr,sizeof(char)*4);
   ff.read(reinterpret_cast<char*>(header.icntrl),sizeof(int)*20);
-
-  if(header.icntrl[1]<0 || header.icntrl[1]>1e6) {
+  if(header.icntrl[1]<0 || header.icntrl[1]>1e8) {
     // nonsense atom count, try swapping
     swap_int(header.icntrl,20);
-    if(header.icntrl[1]<0 || header.icntrl[1]>1e6) {
+    if(header.icntrl[1]<0 || header.icntrl[1]>1e8) {
       throw(IOException("LoadCHARMMTraj: nonsense atom count in header"));
     } else {
-      LOGN_MESSAGE("LoadCHARMMTraj: byte-swapping");
+      LOG_INFO("LoadCHARMMTraj: byte-swapping");
       swap_flag=true;
     }
   }
@@ -106,13 +105,13 @@ mol::CoordGroupHandle load_dcd(const mol::AtomHandleList& alist2,
   if(header.icntrl[19]!=0) { // CHARMM format
     skip_flag=(header.icntrl[10]!=0);
     if(skip_flag) {
-      LOGN_VERBOSE("LoadCHARMMTraj: using CHARMM format with per-frame header");
+      LOG_VERBOSE("LoadCHARMMTraj: using CHARMM format with per-frame header");
     } else {
-      LOGN_VERBOSE("LoadCHARMMTraj: using CHARMM format");
+      LOG_VERBOSE("LoadCHARMMTraj: using CHARMM format");
     }
   } else {
     // XPLOR format
-    LOGN_VERBOSE("LoadCHARMMTraj: using XPLOR format");
+    LOG_VERBOSE("LoadCHARMMTraj: using XPLOR format");
   }
 
   if(gap_flag) ff.read(dummy,sizeof(dummy));
@@ -132,12 +131,12 @@ mol::CoordGroupHandle load_dcd(const mol::AtomHandleList& alist2,
   header.f_atom_count=header.icntrl[8];
   header.atom_count=header.t_atom_count-header.f_atom_count;
 
-  LOGN_DEBUG("LoadCHARMMTraj: " << header.num << " trajectories with " 
+  LOG_DEBUG("LoadCHARMMTraj: " << header.num << " trajectories with " 
                << header.atom_count << " atoms (" << header.f_atom_count 
                << " fixed) each");
 
   if(alist.size() != static_cast<size_t>(header.t_atom_count)) {
-    LOGN_ERROR("LoadCHARMMTraj: atom count missmatch: " << alist.size() 
+    LOG_ERROR("LoadCHARMMTraj: atom count missmatch: " << alist.size() 
                << " in coordinate file, " << header.t_atom_count 
                << " in each traj frame");
     throw(IOException("invalid trajectory"));
@@ -147,13 +146,22 @@ mol::CoordGroupHandle load_dcd(const mol::AtomHandleList& alist2,
   std::vector<geom::Vec3> clist(header.t_atom_count);
   std::vector<float> xlist(header.t_atom_count);
 
+  size_t frame_size=0;
+  if (skip_flag) {
+    frame_size+=14*4;
+  }
+  if (gap_flag) {
+    frame_size+=6*sizeof(dummy);
+  }
+  frame_size+=3*sizeof(float)*xlist.size();
+
   int i=0;
-  for(;i<header.num;++i) {
+  for(;i<header.num;i+=stride) {
     if(skip_flag) ff.seekg(14*4,std::ios_base::cur);
     // read each frame
     if(!ff) {
       /* premature EOF */
-      LOGN_ERROR("LoadCHARMMTraj: premature end of file, " << i 
+      LOG_ERROR("LoadCHARMMTraj: premature end of file, " << i 
                  << " frames read");
       break;
     }
@@ -163,36 +171,40 @@ mol::CoordGroupHandle load_dcd(const mol::AtomHandleList& alist2,
     if(swap_flag) swap_float(&xlist[0],xlist.size());
     if(gap_flag) ff.read(dummy,sizeof(dummy));
     for(uint j=0;j<clist.size();++j) {
-      clist[j].SetX(xlist[j]);
+      clist[j].x=xlist[j];
     }
+
     // y coord
     if(gap_flag) ff.read(dummy,sizeof(dummy));
     ff.read(reinterpret_cast<char*>(&xlist[0]),sizeof(float)*xlist.size());
     if(swap_flag) swap_float(&xlist[0],xlist.size());
     if(gap_flag) ff.read(dummy,sizeof(dummy));
     for(uint j=0;j<clist.size();++j) {
-      clist[j].SetY(xlist[j]);
+      clist[j].y=xlist[j];
     }
+
     // z coord
     if(gap_flag) ff.read(dummy,sizeof(dummy));
     ff.read(reinterpret_cast<char*>(&xlist[0]),sizeof(float)*xlist.size());
     if(swap_flag) swap_float(&xlist[0],xlist.size());
     if(gap_flag) ff.read(dummy,sizeof(dummy));
     for(uint j=0;j<clist.size();++j) {
-      clist[j].SetZ(xlist[j]);
+      clist[j].z=xlist[j];
     }
 
     cg.AddFrame(clist);
 
+    // skip frames (defined by stride)
+    if(stride>1) ff.seekg(frame_size*(stride-1),std::ios_base::cur);
   }
 
   ff.get();
   if(!ff.eof()) {
-    LOGN_VERBOSE("LoadCHARMMTraj: unexpected trailing file data, bytes read: " 
+    LOG_VERBOSE("LoadCHARMMTraj: unexpected trailing file data, bytes read: " 
                  << ff.tellg());
   }
 
-  LOGN_VERBOSE("Loaded " << cg.GetFrameCount() << " frames with " << cg.GetAtomCount() << " atoms each");
+  LOG_VERBOSE("Loaded " << cg.GetFrameCount() << " frames with " << cg.GetAtomCount() << " atoms each");
 
   return cg;
 }
diff --git a/modules/io/src/mol/entity_io_crd_handler.cc b/modules/io/src/mol/entity_io_crd_handler.cc
index 2fd39293ff0fe11c929e97915a59735edb034742..320db5d1d667f81a895096b170ecac51920ca0e4 100644
--- a/modules/io/src/mol/entity_io_crd_handler.cc
+++ b/modules/io/src/mol/entity_io_crd_handler.cc
@@ -81,7 +81,7 @@ void CRDReader::Import(mol::EntityHandle& ent)
   while(std::getline(in_,line)) {
     ParseAndAddAtom(line,ent);
   }
-  LOGN_MESSAGE("imported " << chain_count_ << " chains, " << residue_count_
+  LOG_INFO("imported " << chain_count_ << " chains, " << residue_count_
                 << " residues, " << atom_count_ << " atoms");  
 }
 
@@ -89,7 +89,7 @@ void CRDReader::ParseAndAddAtom(const String& line, mol::EntityHandle& ent)
 {
   mol::XCSEditor editor=ent.RequestXCSEditor(mol::BUFFERED_EDIT);
 
-  LOGN_TRACE( "line: [" << line << "]" );
+  LOG_TRACE( "line: [" << line << "]" );
 
   //int anum = boost::lexical_cast<int>(boost::trim_copy(line.substr(0,5)));
   String aname = boost::trim_copy(line.substr(16,4));
@@ -104,7 +104,7 @@ void CRDReader::ParseAndAddAtom(const String& line, mol::EntityHandle& ent)
   mol::ResidueKey rkey(rname);
   
   // some postprocessing
-  LOGN_TRACE( "s_chain: [" << s_chain << "]" );
+  LOG_TRACE( "s_chain: [" << s_chain << "]" );
 
   mol::ResNum rnum(irnum);
   
@@ -127,21 +127,21 @@ void CRDReader::ParseAndAddAtom(const String& line, mol::EntityHandle& ent)
 
   if(update_chain) {  
     if (!(curr_chain_=ent.FindChain(s_chain))) {
-      LOGN_DUMP("new chain " << s_chain);      
+      LOG_DEBUG("new chain " << s_chain);      
       curr_chain_=editor.InsertChain(s_chain);
       ++chain_count_;      
     }
   }
 
   if(update_residue) {
-    LOGN_DUMP("new residue " << rkey << " " << rnum);
+    LOG_DEBUG("new residue " << rkey << " " << rnum);
     curr_residue_=editor.AppendResidue(curr_chain_, rkey, rnum);
     assert(curr_residue_.IsValid());
     ++residue_count_;
   }
 
   // finally add atom
-  LOGN_DUMP("adding atom " << aname << " (" << ele << ") @" << apos);
+  LOG_DEBUG("adding atom " << aname << " (" << ele << ") @" << apos);
   mol::AtomProp aprop;
   aprop.element=ele;
   aprop.radius=conop::Conopology::Instance().GetDefaultAtomRadius(ele);
@@ -186,9 +186,9 @@ bool CRDWriter::VisitAtom(const mol::AtomHandle& atom)
               << format("%5i") % res.GetNumber() << " "
               << format("%4s") % res.GetKey() << " "
               << format("%-4s") % atom.GetName()
-              << format("%10.5f") % atom.GetPos().GetX()
-              << format("%10.5f") % atom.GetPos().GetY()
-              << format("%10.5f") % atom.GetPos().GetZ() << " "
+              << format("%10.5f") % atom.GetPos().x
+              << format("%10.5f") % atom.GetPos().y
+              << format("%10.5f") % atom.GetPos().z << " "
               << format("%-4s") % e_name << " "
               << format("%-5i") % res.GetNumber() << " "
               << format("%8.5f") % atom.GetBFactor()
diff --git a/modules/io/src/mol/entity_io_mae_handler.cc b/modules/io/src/mol/entity_io_mae_handler.cc
index d002a712035e21f4ab96bc47de7c2785cd6f5999..e810c9089efc13896ce0e418815e846a27ba43cb 100644
--- a/modules/io/src/mol/entity_io_mae_handler.cc
+++ b/modules/io/src/mol/entity_io_mae_handler.cc
@@ -127,16 +127,16 @@ void MAEReader::Import(mol::EntityHandle& ent)
       if(in_atom_block) {
         if(parsing_atoms) {
           if(boost::regex_match(line,r_delim)) {
-            LOGN_DUMP( "stopping atom parsing" );
+            LOG_DEBUG( "stopping atom parsing" );
             parsing_atoms=false;
             prop_list.clear();
           } else {
             // parsing atom line
             std::vector<std::string> tokens=tokenize(line);
             for(size_t i=0;i<tokens.size();++i) {
-              LOG_DUMP( "[" << tokens[i] << "] ");
+              LOG_DEBUG( "[" << tokens[i] << "] ");
             }
-            LOGN_DUMP("");
+            LOG_DEBUG("");
             add_atom(ent,editor,
                      tokens[i_atom_name],
                      tokens[i_atom_xpos],
@@ -157,17 +157,17 @@ void MAEReader::Import(mol::EntityHandle& ent)
                i_chain_name==-1) {
               throw IOException("missing atom prop");
             }
-            LOGN_DUMP( "starting atom parsing" );
+            LOG_DEBUG( "starting atom parsing" );
             parsing_atoms=true;
           } else if(line[0]=='}') {
-            LOGN_DUMP( "exiting atom block" );
+            LOG_DEBUG( "exiting atom block" );
             in_atom_block=false;
           } else {
             // parsing property line
             if(line[0]!='#') {
               int pid=prop_list.size()+1;
               prop_list.push_back(line);
-              LOGN_DUMP( "found property '" << prop_list.back() << "' id=" << pid );
+              LOG_DEBUG( "found property '" << prop_list.back() << "' id=" << pid );
               if(line=="s_m_pdb_atom_name") i_atom_name=pid;
               else if(line=="r_m_x_coord") i_atom_xpos=pid;
               else if(line=="r_m_y_coord") i_atom_ypos=pid;
@@ -180,22 +180,22 @@ void MAEReader::Import(mol::EntityHandle& ent)
         }
       } else { // not in atom block
         if(boost::regex_match(line,r_atom_block)) {
-          LOGN_DUMP( "entering atom block" );
+          LOG_DEBUG( "entering atom block" );
           in_atom_block=true;
         } else if(line[0]=='}') {
-          LOGN_DUMP( "exiting ct block" );
+          LOG_DEBUG( "exiting ct block" );
           in_ct_block=false;
         }
       }
     } else { // not in ct block
       if(boost::regex_match(line,r_ct_block)) {
-        LOGN_DUMP( "entering ct block" );
+        LOG_DEBUG( "entering ct block" );
         in_ct_block=true;
       }
     }
   }
 
-  LOGN_MESSAGE("imported " << chain_count_ << " chains, " << residue_count_
+  LOG_INFO("imported " << chain_count_ << " chains, " << residue_count_
                 << " residues, " << atom_count_ << " atoms");  
 }
 
@@ -245,10 +245,10 @@ void MAEReader::add_atom(mol::EntityHandle ent,
   if(update_chain) {  
     if (!(curr_chain_=ent.FindChain(cname))) {
       curr_chain_=editor.InsertChain(cname);
-      LOGN_DUMP("new chain " << curr_chain_);      
+      LOG_DEBUG("new chain " << curr_chain_);      
       ++chain_count_;      
     } else {
-      LOGN_DUMP("old chain " << curr_chain_);      
+      LOG_DEBUG("old chain " << curr_chain_);      
     }
   }
 
@@ -256,15 +256,15 @@ void MAEReader::add_atom(mol::EntityHandle ent,
     if (!(curr_residue_=curr_chain_.FindResidue(rnum))) {
       curr_residue_=editor.AppendResidue(curr_chain_, rkey, rnum);
       assert(curr_residue_.IsValid());
-      LOGN_DUMP(" new residue " << curr_residue_);
+      LOG_DEBUG(" new residue " << curr_residue_);
       ++residue_count_;
     } else {
-      LOGN_DUMP(" old residue " << curr_residue_);
+      LOG_DEBUG(" old residue " << curr_residue_);
     }
   }
 
   // finally add atom
-  LOGN_DUMP("  atom " << aname << " (" << ele << ") @" << apos);
+  LOG_DEBUG("  atom " << aname << " (" << ele << ") @" << apos);
   mol::AtomProp aprop;
   aprop.element=ele;
   aprop.radius=conop::Conopology::Instance().GetDefaultAtomRadius(ele);
diff --git a/modules/io/src/mol/load_entity.cc b/modules/io/src/mol/load_entity.cc
index 22d0aa9335fb6b1f0a040350b7653e40772bc731..4eda99b4a01acb435819e0a9f3905e5e01db9a39 100644
--- a/modules/io/src/mol/load_entity.cc
+++ b/modules/io/src/mol/load_entity.cc
@@ -32,12 +32,12 @@ namespace {
 void Import(mol::EntityHandle& eh, const String& filename, int flag)
 {
   Profile profile_import("import");
-  LOG_DUMP("creating EntityIOHandle for " << filename << std::endl);
+  LOG_DEBUG("creating EntityIOHandle for " << filename);
   EntityIOHandlerP ent_io = IOManager::Instance().FindEntityImportHandler(filename);
 
   // TODO: proper error handling
 
-  LOG_DUMP("calling import on entity io handle" << std::endl);
+  LOG_DEBUG("calling import on entity io handle");
   /*
     This should probably allow various parameters to be passed
     to adjust the loading behaviour for a particular filter.
@@ -46,7 +46,7 @@ void Import(mol::EntityHandle& eh, const String& filename, int flag)
   */
   ent_io->Import(eh,filename);
 
-  LOG_DUMP("running conopology" << std::endl);
+  LOG_DEBUG("running conopology");
 
   if(ent_io->RequiresBuilder()) {
     conop::BuilderP builder = conop::Conopology::Instance().GetBuilder();
@@ -58,9 +58,7 @@ void Import(mol::EntityHandle& eh, const String& filename, int flag)
 
 mol::EntityHandle LoadEntity(const String& filename, int flag)
 {
-  LOG_DEBUG("entering LoadEntity (unmanaged)" << std::endl);
-
-  LOG_DUMP("creating emtpy entity" << std::endl);
+  LOG_DEBUG("creating emtpy entity");
   mol::EntityHandle eh=mol::CreateEntity();
   mol::XCSEditor xcs_lock=eh.RequestXCSEditor(mol::BUFFERED_EDIT);
   Import(eh,filename,flag);
diff --git a/modules/io/src/mol/load_surface.cc b/modules/io/src/mol/load_surface.cc
index 964ff48b44a1184334175a5098ed3881ea4e6f9f..e3f94f75492a8cc506710e81117742aca8467777 100644
--- a/modules/io/src/mol/load_surface.cc
+++ b/modules/io/src/mol/load_surface.cc
@@ -29,10 +29,9 @@ namespace {
 
 void ImportSurface(mol::SurfaceHandle& sh, const String& fname, const String& type)
 {
-  LOG_DUMP("creating EntityIOHandle for " << fname << std::endl);
+  LOG_DEBUG("creating EntityIOHandle for " << fname);
   SurfaceIOHandlerPtr surf_io = IOManager::Instance().FindSurfaceImportHandler(fname,type);
-
-  LOG_DUMP("calling import on surface io handle" << std::endl);
+  LOG_DEBUG("calling import on surface io handle");
   surf_io->Import(sh,fname);
 }
 
diff --git a/modules/io/src/mol/pdb_io.cc b/modules/io/src/mol/pdb_io.cc
index 30b6dc17eb3dc7012c11afd4b5098be28b9f67be..eba9c8877083eaea23bbb1ad81269269fe8d6d96 100644
--- a/modules/io/src/mol/pdb_io.cc
+++ b/modules/io/src/mol/pdb_io.cc
@@ -31,6 +31,7 @@ namespace ost { namespace io {
   const unsigned int PDB::PQR_FORMAT=0x8;
   const unsigned int PDB::JOIN_SPREAD_ATOM_RECORDS=0x10;
   const unsigned int PDB::CALPHA_ONLY=0x20;
+  const unsigned int PDB::CHARMM_FORMAT=0x40;  
 
   void PDB::PushFlags(unsigned int flags) {PDB::Instance().fstack.push(flags);}
   unsigned int PDB::Flags() {return PDB::Instance().fstack.empty() ? 0 : PDB::Instance().fstack.top();}
diff --git a/modules/io/src/mol/pdb_io.hh b/modules/io/src/mol/pdb_io.hh
index b2d1e00bf32f866a7c917332fd08e4af751140dc..c4fc19e035f2b6bf02d135facf06091cb1c38250 100644
--- a/modules/io/src/mol/pdb_io.hh
+++ b/modules/io/src/mol/pdb_io.hh
@@ -42,28 +42,37 @@ struct DLLEXPORT_OST_IO PDB {
     /// \brief enable for PQR
   static const unsigned int PQR_FORMAT;
 
-    /// \brief Join atom records into one residue, even if the atom records
-    ///     are not sequential.
-    /// 
-    /// This is useful in the following case:
-    /// 
-    /// \verbatim
-    /// ATOM     43  N  AALA P   4
-    /// ATOM     45  CA AALA P   4 
-    /// ATOM     47  C  AALA P   4
-    /// ATOM     48  O  AALA P   4
-    /// ATOM     49  N  APRO P   5
-    /// ATOM     50  CD APRO P   5
-    /// ATOM     53  CA APRO P   5
-    /// ATOM     55  CB APRO P   5
-    /// ATOM     58  CG APRO P   5
-    /// ATOM     61  C  APRO P   5
-    /// ATOM     62  O  APRO P   5
-    /// ATOM    550  CB AALA P   4
-    /// \endverbatim
-    /// 
-    /// By default, the atom 550 will start a new residue instead of being
-    /// joined with atoms 43-48 into one residue.
+  /// \brief enables parsing of charmm-style PDBs
+  /// 
+  /// CHARMM files don't use the chain column to mark different chains, but 
+  /// rather put the name in the last columns that is isually used for the atom 
+  /// element an occupancy. Note that it is perfectly possible to parse CHARRM 
+  /// PDB files without this flag, but the mileage may vary as some of the 
+  /// elements are incorrectly assigned.
+  static const unsigned int CHARMM_FORMAT;
+  
+  /// \brief Join atom records into one residue, even if the atom records
+  ///     are not sequential.
+  /// 
+  /// This is useful in the following case:
+  /// 
+  /// \verbatim
+  /// ATOM     43  N  AALA P   4
+  /// ATOM     45  CA AALA P   4 
+  /// ATOM     47  C  AALA P   4
+  /// ATOM     48  O  AALA P   4
+  /// ATOM     49  N  APRO P   5
+  /// ATOM     50  CD APRO P   5
+  /// ATOM     53  CA APRO P   5
+  /// ATOM     55  CB APRO P   5
+  /// ATOM     58  CG APRO P   5
+  /// ATOM     61  C  APRO P   5
+  /// ATOM     62  O  APRO P   5
+  /// ATOM    550  CB AALA P   4
+  /// \endverbatim
+  /// 
+  /// By default, the atom 550 will start a new residue instead of being
+  /// joined with atoms 43-48 into one residue.
   static const unsigned int JOIN_SPREAD_ATOM_RECORDS;
 
     /// \brief only import C-alpha atoms
diff --git a/modules/io/src/mol/pdb_reader.cc b/modules/io/src/mol/pdb_reader.cc
index 21db6adf023afa1fb733103179b66b4e57188131..909a4ec754a87c82598ff18cfbf2a85ea4c215b4 100644
--- a/modules/io/src/mol/pdb_reader.cc
+++ b/modules/io/src/mol/pdb_reader.cc
@@ -126,7 +126,7 @@ bool PDBReader::HasNext()
 void PDBReader::Import(mol::EntityHandle& ent,
                        const String& restrict_chains)
 {
-  LOGN_DEBUG("PDBReader: current flags: " << PDB::Flags());
+  LOG_DEBUG("PDBReader: current flags: " << PDB::Flags());
 
   Profile profile_import("PDBReader::Import");
   this->ClearState();
@@ -145,12 +145,14 @@ void PDBReader::Import(mol::EntityHandle& ent,
           continue;
         }
         if (IEquals(curr_line.substr(0, 6), StringRef("ATOM  ", 6))) {
-          LOGN_TRACE("processing ATOM entry");
+          LOG_TRACE("processing ATOM entry");
           this->ParseAndAddAtom(curr_line, line_num_, ent, 
                                 StringRef("ATOM", 4));
         } else if (IEquals(curr_line.substr(0, 6), StringRef("ANISOU", 6))) {
-          LOGN_TRACE("processing ANISOU entry");
-          this->ParseAnisou(curr_line, line_num_, ent);
+          if (!(PDB::Flags() & PDB::CHARMM_FORMAT)) {
+            LOG_TRACE("processing ANISOU entry");
+            this->ParseAnisou(curr_line, line_num_, ent);            
+          }
         }
         break;
       case 'E':
@@ -179,11 +181,13 @@ void PDBReader::Import(mol::EntityHandle& ent,
         if (IEquals(curr_line.substr(0, 6), StringRef("HETATM", 6))) {
           if (PDB::Flags() & PDB::NO_HETATMS)
             continue;
-          LOGN_TRACE("processing HETATM entry");
+          LOG_TRACE("processing HETATM entry");
           this->ParseAndAddAtom(curr_line, line_num_, ent, 
                                 StringRef("HETATM", 6));
         } else if (IEquals(curr_line.substr(0, 6), StringRef("HELIX ", 6))) {
-          this->ParseHelixEntry(curr_line);
+          if (!(PDB::Flags() & PDB::CHARMM_FORMAT)) {
+            this->ParseHelixEntry(curr_line);            
+          }
         }
         break;
       case 'M':
@@ -211,14 +215,16 @@ void PDBReader::Import(mol::EntityHandle& ent,
           continue;
         }
         if (IEquals(curr_line.substr(0, 6), StringRef("SHEET ", 6))) {
-          this->ParseStrandEntry(curr_line);
+          if (!(PDB::Flags() & PDB::CHARMM_FORMAT)) {
+            this->ParseStrandEntry(curr_line);
+          }
         }
         break;
       default:
         break;
     }
   }  while (std::getline(in_, curr_line_) && ++line_num_ && go_on);
-  LOGN_MESSAGE("imported "
+  LOG_INFO("imported "
                << chain_count_ << " chains, "
                << residue_count_ << " residues, "
                << atom_count_ << " atoms; with "
@@ -235,7 +241,7 @@ void PDBReader::AssignSecStructure(mol::EntityHandle ent)
        i!=e; ++i) {
     mol::ChainHandle chain=ent.FindChain(i->chain);
     if (!chain.IsValid()) {
-      LOGN_MESSAGE("ignoring helix record for unknown chain "+i->chain);
+      LOG_INFO("ignoring helix record for unknown chain "+i->chain);
       continue;
     }
     mol::SecStructure alpha(mol::SecStructure::ALPHA_HELIX);
@@ -244,7 +250,8 @@ void PDBReader::AssignSecStructure(mol::EntityHandle ent)
     // two secondary structure segments to insert one residue of coil 
     // conformation.
     mol::ResNum start=i->start, end=i->end;
-    if (helix_list_.end()!=i+1 && (*(i+1)).start.GetNum()<=end.GetNum()+1) {
+    if (helix_list_.end()!=i+1 && (*(i+1)).start.GetNum()<=end.GetNum()+1 &&
+        (*(i+1)).end.GetNum()>end.GetNum()) {
       end=mol::ResNum((*(i+1)).start.GetNum()-2);
     }
     chain.AssignSecondaryStructure(alpha, start, end);
@@ -254,13 +261,14 @@ void PDBReader::AssignSecStructure(mol::EntityHandle ent)
        i!=e; ++i) {
     mol::ChainHandle chain=ent.FindChain(i->chain);
     if (!chain.IsValid()) {
-      LOGN_MESSAGE("ignoring strand record for unknown chain "+i->chain);
+      LOG_INFO("ignoring strand record for unknown chain "+i->chain);
       continue;
     }
     mol::SecStructure extended(mol::SecStructure::EXTENDED);
     mol::ResNum start=i->start, end=i->end;
     // see comment for helix assignment
-    if (strand_list_.end()!=i+1 && (*(i+1)).start.GetNum()<=end.GetNum()+1) {
+    if (strand_list_.end()!=i+1 && (*(i+1)).start.GetNum()<=end.GetNum()+1 &&
+        (*(i+1)).end.GetNum()>end.GetNum()) {
       end=mol::ResNum((*(i+1)).start.GetNum()-2);
     }    
     chain.AssignSecondaryStructure(extended, start, end);
@@ -279,27 +287,48 @@ void PDBReader::ClearState()
   strand_list_.clear();
 }
 
+bool PDBReader::EnsureLineLength(const StringRef& line, size_t size)
+{
+  if (line.length()<size) {
+    if (PDB::Flags() & PDB::SKIP_FAULTY_RECORDS) {
+      return false;
+    }    
+    throw IOException(str(format("premature end of line %d") %line_num_));
+  }  
+  return true;
+}
+
 bool PDBReader::ParseAtomIdent(const StringRef& line, int line_num, 
-                               char& chain_name,  StringRef& res_name,
+                               String& chain_name,  StringRef& res_name,
                                mol::ResNum& resnum, StringRef& atom_name, 
                                char& alt_loc, const StringRef& record_type)
 {
-  chain_name=line[21];
-  if (restrict_chains_.size()>0 &&
-    restrict_chains_.find(chain_name)==String::npos) {
+  if (!this->EnsureLineLength(line, 27)) {
     return false;
   }
+  if (PDB::Flags() & PDB::CHARMM_FORMAT) {
+    if (line.size()>73) {
+      size_t width=std::min(line.size()-72, size_t(4));
+      chain_name=line.substr(72, width).trim().str();      
+    }
+  } else {
+    chain_name=String(1, line[21]);    
+    if (restrict_chains_.size()>0 &&
+      restrict_chains_.find(chain_name)==String::npos) {
+      return false;
+    }    
+  }
 
   std::pair<bool, int> a_num=line.substr(6, 5).ltrim().to_int();
   if (!a_num.first) {
-    if (PDB::Flags() & PDB::SKIP_FAULTY_RECORDS) {
-      return false;
+    if (!(PDB::Flags() & PDB::SKIP_FAULTY_RECORDS)) {
+      throw IOException(str(format("invalid atom number on line %d") %line_num));      
     }
-    throw IOException(str(format("invalid atom number on line %d") %line_num));
+    LOG_WARNING("invalid atom number on line " << line_num);
   }
   atom_name=line.substr(12, 4).trim();
   alt_loc=line[16];
-  res_name=line.substr(17, 3).trim();
+  res_name=line.substr(17, (PDB::Flags() & PDB::CHARMM_FORMAT) ? 4 : 3).trim();
   std::pair<bool, int> res_num=line.substr(22, 4).ltrim().to_int();;
   if (!res_num.first) {
     if (PDB::Flags() & PDB::SKIP_FAULTY_RECORDS) {
@@ -325,7 +354,10 @@ bool PDBReader::ParseAtomIdent(const StringRef& line, int line_num,
 void PDBReader::ParseAnisou(const StringRef& line, int line_num, 
                             mol::EntityHandle& ent)
 {
-  char chain_name=0;
+  if (!this->EnsureLineLength(line, 77)) {
+    return;
+  }  
+  String chain_name;
   char alt_loc=0;
   StringRef res_name, atom_name;
   mol::ResNum res_num(0);
@@ -372,16 +404,18 @@ void PDBReader::ParseAnisou(const StringRef& line, int line_num,
   aprop.anisou/=10000;
   aprop.has_anisou=true;
   atom.SetAtomProps(aprop);
-  return;  
 }
 
 void PDBReader::ParseAndAddAtom(const StringRef& line, int line_num,
                                 mol::EntityHandle& ent, 
                                 const StringRef& record_type)
 {
+  if (!this->EnsureLineLength(line, 54)) {
+    return;
+  }
   mol::XCSEditor editor=ent.RequestXCSEditor(mol::BUFFERED_EDIT);
   char alt_loc=0;
-  char chain_name=0;
+  String chain_name;
   StringRef res_name, atom_name;
   mol::ResNum res_num(0);
   if (!this->ParseAtomIdent(line, line_num, chain_name, res_name, res_num, 
@@ -420,35 +454,32 @@ void PDBReader::ParseAndAddAtom(const StringRef& line, int line_num,
       temp=line.substr(60, 6).ltrim().to_float();      
     }
   }
-  LOGN_TRACE( "line: [" << line << "]" );
+  LOG_TRACE( "line: [" << line << "]" );
   String s_ele;
-  String s_chain(1, chain_name);
-  String aname(atom_name.str());
-  // determine element from element column (77-78, right justified) if present
-  // otherwise set to empty String. It is up to the builder to determine the
-  // correct element in that case.
-  if (line.length()>=78) {                          // element column present
-    if(line[76]==' ' && line[77]==' ') {            // both characters are empty
-      s_ele="";
-    } else if(line[76]!=' ' || line[77]!=' ') {     // at least one character not
-                                                    // empty
-      if(line[76]==' ' && line[77]!=' ') {          // single character element,
-                                                    // right justified
-        s_ele=line.substr(77,1).str();
-      } else if(line[76]!=' ' && line[77]==' ') {   // single character element,
-                                                    // left justified
-        s_ele=line.substr(76,1).str();
-      } else {                                      // Real character element
-        s_ele=line.substr(76,2).str();
+  if (!(PDB::Flags() & PDB::CHARMM_FORMAT)) {
+    // determine element from element column (77-78, right justified) if 
+    // present otherwise set to empty String. It is up to the builder to 
+    // determine the correct element in that case.
+    if (line.length()>=78) {                       // element column present
+      if(line[76]==' ' && line[77]==' ') {         // both characters are empty
+        s_ele="";                                  
+      } else if(line[76]!=' ' || line[77]!=' ') {  // at least one character not
+                                                   // empty
+        if(line[76]==' ' && line[77]!=' ') {       // single character element,
+                                                   // right justified
+          s_ele=line.substr(77,1).str();           
+        } else if(line[76]!=' ' && line[77]==' ') {// single character element,
+                                                   // left justified
+          s_ele=line.substr(76,1).str();           
+        } else {                                   // Real character element
+          s_ele=line.substr(76,2).str();            
+        }
       }
-    }
+    }  
   }
-  else {
-    s_ele="";                                       // no element column present
-  }
-
+  String aname(atom_name.str());  
   // some postprocessing
-  LOGN_TRACE( "s_chain: [" << chain_name << "]" );
+  LOG_TRACE( "s_chain: [" << chain_name << "]" );
 
   // determine chain and residue update
   bool update_chain=false;
@@ -456,7 +487,7 @@ void PDBReader::ParseAndAddAtom(const StringRef& line, int line_num,
   if(!curr_chain_) {
     update_chain=true;
     update_residue=true;
-  } else if(curr_chain_.GetName()!=s_chain) {
+  } else if(curr_chain_.GetName()!=chain_name) {
     update_chain=true;
     update_residue=true;
   }
@@ -475,11 +506,11 @@ void PDBReader::ParseAndAddAtom(const StringRef& line, int line_num,
       curr_chain_=ent.FindChain(s_chain);
     }
 #else
-      curr_chain_=ent.FindChain(s_chain);
+      curr_chain_=ent.FindChain(chain_name);
 #endif
     if(!curr_chain_.IsValid()) {
-      LOGN_DUMP("new chain " << s_chain);
-      curr_chain_=editor.InsertChain(s_chain);
+      LOG_DEBUG("new chain " << chain_name);
+      curr_chain_=editor.InsertChain(chain_name);
       ++chain_count_;
     }
     assert(curr_chain_.IsValid());
@@ -490,14 +521,14 @@ void PDBReader::ParseAndAddAtom(const StringRef& line, int line_num,
       curr_residue_=curr_chain_.FindResidue(res_num);
     }
     if (!curr_residue_.IsValid()) {
-      LOGN_DUMP("new residue " << res_name << " " << res_num);
+      LOG_DEBUG("new residue " << res_name << " " << res_num);
       curr_residue_=editor.AppendResidue(curr_chain_, res_name.str(), res_num);
       ++residue_count_; 
     }
     assert(curr_residue_.IsValid());
   }
   // finally add atom
-  LOGN_DUMP("adding atom " << aname << " (" << s_ele << ") @" << apos);
+  LOG_DEBUG("adding atom " << aname << " (" << s_ele << ") @" << apos);
   mol::AtomProp aprop;
   aprop.element=s_ele;
   if(is_pqr_) {
@@ -529,41 +560,35 @@ void PDBReader::ParseAndAddAtom(const StringRef& line, int line_num,
       try {
         editor.AddAltAtomPos(String(1, alt_loc), me, apos);
       } catch (Error) {
-        LOGN_MESSAGE("Ignoring atom alt location since there is already an atom "
+        LOG_INFO("Ignoring atom alt location since there is already an atom "
                      "with name " << aname << ", but without an alt loc");
         return;
       }
     } else {
       mol::AtomHandle ah=editor.InsertAltAtom(curr_residue_, aname,
                                               String(1, alt_loc), apos, aprop);
-      /*
-	for now, this is not needed - the cg will use an global atom id sorted
-	list insteadx
-      if (PDB::Flags() & PDB::SEQUENTIAL_ATOM_IMPORT) {
-        sequential_atom_list_.push_back(ah);
-      }
-      */
       ++atom_count_;
     }
   } else {
     mol::AtomHandle ah = editor.InsertAtom(curr_residue_, aname, apos, aprop);
-    /*
-    if (PDB::Flags() & PDB::SEQUENTIAL_ATOM_IMPORT) {
-      sequential_atom_list_.push_back(ah);
-    }
-    */
     ++atom_count_;
   }
 }
 
 void PDBReader::ParseHelixEntry(const StringRef& line)
 {
+  if (!this->EnsureLineLength(line, 38)) {
+    return;
+  }
   std::pair<bool, int>  start_num=line.substr(21, 4).ltrim().to_int();
   std::pair<bool, int>  end_num=line.substr(33, 4).ltrim().to_int();
   if (!start_num.first || !end_num.first) {
+    if (PDB::Flags() & PDB::SKIP_FAULTY_RECORDS) {
+      return;
+    }    
     throw IOException(str(format("invalid helix entry on line %d") % line_num_));
   }
-  LOGN_DEBUG("making helix entry: " << start_num.second << ", " 
+  LOG_DEBUG("making helix entry: " << start_num.second << ", " 
              << line[25] << " " << end_num.second << " " << line[37]);
   HSEntry hse = {to_res_num(start_num.second, line[25]),
                  to_res_num(end_num.second, line[37]),
@@ -577,12 +602,19 @@ void PDBReader::ParseHelixEntry(const StringRef& line)
 
 void PDBReader::ParseStrandEntry(const StringRef& line)
 {
+  if (!this->EnsureLineLength(line, 38)) {
+    return;
+  }  
   std::pair<bool, int>  start_num=line.substr(22, 4).ltrim().to_int();
   std::pair<bool, int>  end_num=line.substr(33, 4).ltrim().to_int();
   if (!start_num.first || !end_num.first) {
-    throw IOException(str(format("invalid strand entry on line %d") % line_num_));
+    if (PDB::Flags() & PDB::SKIP_FAULTY_RECORDS) {
+      return;
+    }
+    throw IOException(str(format("invalid strand entry on line %d")%line_num_));
   }
-  LOGN_DEBUG("making strand entry: " << start_num.second << ", " << line[26] << " " << end_num.second << " " << line[37]);
+  LOG_DEBUG("making strand entry: " << start_num.second << ", " << line[26] 
+            << " " << end_num.second << " " << line[37] << " chain=" << line[21]);
   HSEntry hse = {to_res_num(start_num.second, line[26]),
                  to_res_num(end_num.second, line[37]),
                  line.substr(21,1).str()};
diff --git a/modules/io/src/mol/pdb_reader.hh b/modules/io/src/mol/pdb_reader.hh
index 41f7ffb21ca4769554d2b5a9fa3e195e5876a126..2c2ca2c1a16eadd110ad79aca78dcf31e8afc06b 100644
--- a/modules/io/src/mol/pdb_reader.hh
+++ b/modules/io/src/mol/pdb_reader.hh
@@ -57,7 +57,7 @@ private:
 
   /// \brief parses the common part of ATOM, HETATM and ANISOU records
   bool ParseAtomIdent(const StringRef& line, int line_num, 
-                      char& chain_name, StringRef& res, 
+                      String& chain_name, StringRef& res, 
                       mol::ResNum& resnum, StringRef& atom_name, char& alt_loc,
                       const StringRef& record_type);
   void ParseAnisou(const StringRef& line, int line_num,
@@ -65,6 +65,7 @@ private:
   void ParseHelixEntry(const StringRef& line);
   void ParseStrandEntry(const StringRef& line);
   void Init(const boost::filesystem::path& loc);
+  bool EnsureLineLength(const StringRef& line, size_t size);
   mol::ChainHandle curr_chain_;
   mol::ResidueHandle curr_residue_;
   int chain_count_;
diff --git a/modules/io/src/mol/pdb_writer.cc b/modules/io/src/mol/pdb_writer.cc
index 7b89e1f09cbfea8857fb9057285fcfd16f515c7f..580c40752b8deaecdb279bdd421c52798e82d567 100644
--- a/modules/io/src/mol/pdb_writer.cc
+++ b/modules/io/src/mol/pdb_writer.cc
@@ -39,12 +39,14 @@ namespace {
 bool shift_left(const String& atom_name, bool is_hetatm, 
                 const String& element, float mass) 
 {
+  if (atom_name.length()==4) {
+    return true;
+  }
   if (is_hetatm==false) {
     return false;
   }
 
-  if (isdigit(atom_name[0]) || atom_name=="UNK" ||
-      atom_name.length()==4) {
+  if (isdigit(atom_name[0]) || atom_name=="UNK") {
     return true;
   }
   if (mass>34) {
@@ -198,6 +200,19 @@ public:
     return true;
   }
   
+  virtual bool VisitChain(const mol::ChainHandle& chain)
+  {
+    if (peptide_) {
+      this->WriteTer(prev_);
+    }
+    return true;
+  }
+  virtual void OnExit()
+  {
+    if (peptide_) {
+      this->WriteTer(prev_);
+    }
+  }
   void WriteTer(mol::ResidueHandle res)
   {
     counter_++;
diff --git a/modules/io/src/mol/save_entity.cc b/modules/io/src/mol/save_entity.cc
index 0bfadfc0b0a917a301dff6e3ab774e8601e37529..2a7a64ef285f3ba8b2cc82b7aa1b928e8527bc0c 100644
--- a/modules/io/src/mol/save_entity.cc
+++ b/modules/io/src/mol/save_entity.cc
@@ -31,7 +31,7 @@ void DLLEXPORT_OST_IO SaveEntity(const mol::EntityHandle& en,
 void DLLEXPORT_OST_IO SaveEntity(const mol::EntityView& en, 
                                 const String& filename,
                                 const String& format) {
-  LOG_DUMP("creating EntityIOHandle for " << filename << std::endl);
+  LOG_DEBUG("creating EntityIOHandle for " << filename);
   IOManager& manager=IOManager::Instance();
   EntityIOHandlerP ent_io=manager.FindEntityExportHandler(filename, format);
 
@@ -39,7 +39,7 @@ void DLLEXPORT_OST_IO SaveEntity(const mol::EntityView& en,
     throw IOUnknownFormatException("No IO handler for file='"+filename+"', format='"+
                       format+"' found.");
   }
-  LOG_DUMP("calling export on entity io handle" << std::endl);
+  LOG_DEBUG("calling export on entity io handle");
 
   ent_io->Export(en, filename);                                    
 }
diff --git a/modules/io/src/mol/sdf_reader.cc b/modules/io/src/mol/sdf_reader.cc
index e2f0fabd24c65e33cf31664f8751d2208f60a096..4427850ea6678b6a9a6cb639e3e92e600c9a30a8 100644
--- a/modules/io/src/mol/sdf_reader.cc
+++ b/modules/io/src/mol/sdf_reader.cc
@@ -82,12 +82,12 @@ void SDFReader::Import(mol::EntityHandle& ent)
       }
       curr_chain_.SetStringProp(data_header, data_value);
     } else if (boost::iequals(line, "$$$$")) {
-      LOGN_MESSAGE("MOLECULE " << curr_chain_.GetName() << " (" << chain_count_ << ") added.")
+      LOG_INFO("MOLECULE " << curr_chain_.GetName() << " (" << chain_count_ << ") added.")
       NextMolecule();
     }
   }
 
-  LOGN_MESSAGE("imported " << chain_count_ << " chains, " << residue_count_
+  LOG_INFO("imported " << chain_count_ << " chains, " << residue_count_
                << " residues, " << atom_count_ << " atoms");
 }
 
@@ -113,7 +113,7 @@ void SDFReader::NextMolecule()
 void SDFReader::ParseAndAddHeader(const String& line, int line_num,
                                   mol::EntityHandle& ent, mol::XCSEditor& editor)
 {
-  LOGN_TRACE( "line: [" << line << "]" );
+  LOG_TRACE( "line: [" << line << "]" );
   format chain_fmter("%05i_%s");
   switch(line_num)
   {
@@ -129,12 +129,12 @@ void SDFReader::ParseAndAddHeader(const String& line, int line_num,
         throw IOException(str(format(msg) % line_num));
       }
       curr_chain_=editor.InsertChain(s_chain);
-      LOGN_DUMP("new chain " << s_chain);
+      LOG_DEBUG("new chain " << s_chain);
 
       mol::ResidueKey rkey=boost::trim_copy(s_title);
       mol::ResNum rnum(++residue_count_);
       curr_residue_=editor.AppendResidue(curr_chain_, rkey, rnum);
-      LOGN_DUMP("new residue " << rkey << "(" << rnum << ")");
+      LOG_DEBUG("new residue " << rkey << "(" << rnum << ")");
       break;
     }
     case 2:  // user information line
@@ -169,7 +169,7 @@ void SDFReader::ParseAndAddAtom(const String& line, int line_num,
                                 mol::XCSEditor& editor)
 {
 
-  LOGN_TRACE( "line: [" << line << "]" );
+  LOG_TRACE( "line: [" << line << "]" );
 
   if(line.length()<48 || line.length()>69) {
     String msg="Bad atom line %d: Not correct number of characters on the"
@@ -214,7 +214,7 @@ void SDFReader::ParseAndAddAtom(const String& line, int line_num,
     throw IOException(str(format(msg) % line_num % s_charge));
   }
 
-  LOGN_DUMP("adding atom " << aname << " (" << s_ele << ") @" << apos);
+  LOG_DEBUG("adding atom " << aname << " (" << s_ele << ") @" << apos);
 
   editor.InsertAtom(curr_residue_, aname,apos,aprop);
 }
@@ -224,7 +224,7 @@ void SDFReader::ParseAndAddBond(const String& line, int line_num,
                                 mol::EntityHandle& ent, mol::XCSEditor& editor)
 {
 
-  LOGN_TRACE( "line: [" << line << "]" );
+  LOG_TRACE( "line: [" << line << "]" );
 
   if(line.length()<18 || line.length()>21) {
     String msg="Bad bond line %d: Not correct number of characters on the"
@@ -269,7 +269,7 @@ void SDFReader::ParseAndAddBond(const String& line, int line_num,
     throw IOException(str(format(msg) % line_num % first % second));
   }
 
-  LOGN_DUMP("adding bond " << s_first_name << " " << s_second_name << " (" << s_type << ") ");
+  LOG_DEBUG("adding bond " << s_first_name << " " << s_second_name << " (" << s_type << ") ");
 }
 
 }}
diff --git a/modules/io/src/mol/star_parser.cc b/modules/io/src/mol/star_parser.cc
index 09ce3af22af08f5b84e4dfe9cf2e50e58775606a..6097262cc78eeec8aa6a2e7fa5dfe93b194ea048 100644
--- a/modules/io/src/mol/star_parser.cc
+++ b/modules/io/src/mol/star_parser.cc
@@ -105,6 +105,7 @@ void StarParser::ParseLoop()
   while (this->GetLine(line)) {
     StringRef tline=line.rtrim();
     if (tline.empty()) {
+      this->ConsumeLine();
       continue;
     }
     switch(tline[0]) {
@@ -137,6 +138,7 @@ void StarParser::ParseLoop()
   while (this->GetLine(line)) {
     StringRef tline=line.rtrim();
     if (tline.empty()) {
+      this->ConsumeLine();
       continue;
     }
     switch (tline[0]) {
@@ -213,6 +215,7 @@ void StarParser::ParseDataItem()
     while (this->NextLine(line)) {
       StringRef tline=line.rtrim();
       if (tline.empty()) {
+        this->ConsumeLine();
         continue;
       }
       if (tline[0]==';') {
diff --git a/modules/io/src/mol/surface_io_msms_handler.cc b/modules/io/src/mol/surface_io_msms_handler.cc
index 48659c0999f96409ce4aa64681e509d8504e1e76..1fe223454386192cb76660ad57cc95d6b501bcf5 100644
--- a/modules/io/src/mol/surface_io_msms_handler.cc
+++ b/modules/io/src/mol/surface_io_msms_handler.cc
@@ -42,16 +42,16 @@ std::pair<bf::path,bf::path> detect_files(const bf::path& loc)
 void SurfaceIOMSMSHandler::Import(mol::SurfaceHandle& sh, const bf::path& loc)
 {
   std::pair<bf::path,bf::path> pp = detect_files(loc);
-  LOGN_DEBUG("loading files " << pp.first.string() << " and " << pp.second.string());
+  LOG_DEBUG("loading files " << pp.first.string() << " and " << pp.second.string());
 
   std::ifstream fvert(pp.first.string().c_str());
   if(!fvert) {
-    LOGN_ERROR("could not open " << pp.first.string());
+    LOG_ERROR("could not open " << pp.first.string());
     return;
   }
   std::ifstream fface(pp.second.string().c_str());
   if(!fface) {
-    LOGN_ERROR("could not open " << pp.second.string());
+    LOG_ERROR("could not open " << pp.second.string());
     return;
   }
 
@@ -100,7 +100,7 @@ void SurfaceIOMSMSHandler::Import(mol::SurfaceHandle& sh, const bf::path& loc)
     sh.AddTri(vertice_map[id1],vertice_map[id2],vertice_map[id3]);
   }
 
-  LOGN_MESSAGE("loaded " << vertice_count << " vertices and " << face_count << " faces");
+  LOG_INFO("loaded " << vertice_count << " vertices and " << face_count << " faces");
 }
 
 void SurfaceIOMSMSHandler::Export(const mol::SurfaceHandle& sh,
diff --git a/modules/io/src/seq/fasta_io_handler.cc b/modules/io/src/seq/fasta_io_handler.cc
index 919902088ea0a312a0acc48a27ca1cb6d996899d..198171208bd563319b3dd710fdcade308e58c5c9 100644
--- a/modules/io/src/seq/fasta_io_handler.cc
+++ b/modules/io/src/seq/fasta_io_handler.cc
@@ -92,17 +92,22 @@ void FastaIOHandler::Import(seq::SequenceList& aln,
       String error=str(format(error_msg) % line);
       throw IOException(error);
     }
-    String identifier=line.substr(1);
-    String sequence_str;
-    while (std::getline(instream, line) && line.size()>0 && line[0]!='>') {
-      if (line.find_first_not_of("\n\t ")==String::npos) {
-        continue;
+    String name=line.substr(1);
+    std::stringstream seq_string;
+    while (std::getline(instream, line)) {
+      if (!line.empty() && line[0]=='>') {
+        break;
       }
-      sequence_str+=line;
-    }
-    if (sequence_str.length()>0) {
+      for (String::iterator i=line.begin(), e=line.end(); i!=e; ++i) {
+        if (isspace(*i)) {
+          continue;
+        }
+        seq_string << *i;
+      }
+    }    
+    if (!seq_string.str().empty()) {
       try {
-        seq::SequenceHandle seq=seq::CreateSequence(identifier, sequence_str);
+        seq::SequenceHandle seq=seq::CreateSequence(name, seq_string.str());
         aln.AddSequence(seq);          
         seq_count+=1;
       } catch (seq::InvalidSequence& e) {
diff --git a/modules/io/src/seq/pir_io_handler.cc b/modules/io/src/seq/pir_io_handler.cc
index a5d07c9ee819ab3fc95c766a0f42c6d45015112c..2974dcd51bf6dc4852bf1badad26d61719aaaf37 100644
--- a/modules/io/src/seq/pir_io_handler.cc
+++ b/modules/io/src/seq/pir_io_handler.cc
@@ -72,50 +72,79 @@ bool PirIOHandler::ProvidesExport(const boost::filesystem::path& loc,
   return PirIOHandler::ProvidesImport(loc, format);
 }
 
-void PirIOHandler::Import(seq::SequenceList& aln,
-                            std::istream& instream)
+void PirIOHandler::Import(seq::SequenceList& aln, std::istream& instream)
 {
-  const char* error_msg="Bad Pir file: Expected '>', but '%1%' found.";  
-  
+  const char* error_msg="Expected %1%, but '%2%' found.";  
+  const char* premature_end="Premature end in PIR file on line %1%";
+  const char* empty_seq="PIR file contains empty sequence on line %1%";
   String line;
-  std::getline(instream, line);    
-  int seq_count=0;
-  //not yet supported
-  throw IOException("Import of PIR format is not yet supported!");
+  int line_num=1, seq_count=0;
+  // we can't use a normal while(std::getline(...)) here, because the PIR format 
+  // requires us to perform a one-line look-ahead. 
+  std::getline(instream, line);  
   while (!instream.eof()) {
-    // parse header information. cut after first "|"
+    // skip empty lines
     if (line.find_first_not_of("\n\t ")==String::npos) {
-      std::getline(instream, line);
       continue;
     }
-    if (line.length()==0 || line[0]!='>') {
-      String error=str(format(error_msg) % line);
+    if (line[0]!='>') {
+      String error=str(format(error_msg) % "'>'" % line);
+      throw IOException(error);
+    }
+    if (line.length()<4) {
+      String error=str(format(error_msg) % "seq-type;identifier" % line);
       throw IOException(error);
     }
-    String identifier=line.substr(1);
-    String sequence_str;
-    while (std::getline(instream, line) && line.size()>0 && line[0]!='>') {
-      if (line.find_first_not_of("\n\t ")==String::npos) {
-        continue;
+    String seq_type=line.substr(1, 2);
+    if (!(seq_type=="P1" || seq_type=="F1" || seq_type=="DL" || 
+          seq_type=="DC" || seq_type=="RL" || seq_type=="RC" || 
+          seq_type=="XX")) {
+      throw IOException("Bad PIR file: Unknown sequence type"/*" '%1%' on line %2%" % seq_type % line_nu*m*/);
+    }
+    String name=line.substr(4);
+    int subject_line_num=line_num;
+    if (!std::getline(instream, line)) {
+      throw IOException(str(format(premature_end) % line_num));
+    }
+    line_num+=1;
+    std::stringstream seq_string;
+    bool end_seq=false;
+    while (!end_seq && std::getline(instream, line)) {
+      line_num+=1;
+      for (String::iterator i=line.begin(), e=line.end(); i!=e; ++i) {
+        if (isspace(*i)) {
+          continue;
+        }
+        if (*i=='*') {
+          end_seq=true;
+          break;
+        }
+        seq_string << *i;
       }
-      sequence_str+=line;
     }
-    if (sequence_str.length()>0) {
-      try {
-        seq::SequenceHandle seq=seq::CreateSequence(identifier, sequence_str);
-        aln.AddSequence(seq);          
-        seq_count+=1;
-      } catch (seq::InvalidSequence& e) {
-        throw e;
+    while (std::getline(instream, line)) {
+      line_num+=1;
+      if (!line.empty() && line[0]=='>') {
+        break;
       }
-    } else {
-      throw IOException("Bad Pir file: Sequence is empty.");
     }
-  }    
+    if (!end_seq) {
+      throw IOException(str(format(premature_end) % line_num));
+    }
+    if (seq_string.str().empty()) {
+      throw IOException(str(format(empty_seq) % subject_line_num));
+    }
+    try {
+      seq::SequenceHandle ss=seq::CreateSequence(name, seq_string.str());
+      aln.AddSequence(ss);          
+      seq_count+=1;
+    } catch (seq::InvalidSequence& e) {
+      throw e;
+    }
+  }
   if (seq_count==0) {
     throw IOException("Bad Pir file: File is empty");
-  }                        
-
+  }
 }
 
 void PirIOHandler::Export(const seq::ConstSequenceList& seqs,
diff --git a/modules/io/tests/CMakeLists.txt b/modules/io/tests/CMakeLists.txt
index f0c230801b3dce77efcb5f3fab4c58f240a57b23..1cb26f5fd45b675c5038de4d6dcb9c1a0fc00b26 100644
--- a/modules/io/tests/CMakeLists.txt
+++ b/modules/io/tests/CMakeLists.txt
@@ -3,6 +3,7 @@ set(OST_IO_UNIT_TESTS
   test_io_pdb.cc
   test_io_crd.cc
   test_io_sdf.cc
+  test_pir.cc
   test_iomanager.cc
   tests.cc
 )
diff --git a/modules/io/tests/test_io_pdb.cc b/modules/io/tests/test_io_pdb.cc
index 3b9b691c31b5299da339a02b4e6d5aaec31d6344..df8ff5295dc686bbcf12c281b649a66a7218ff0c 100644
--- a/modules/io/tests/test_io_pdb.cc
+++ b/modules/io/tests/test_io_pdb.cc
@@ -190,6 +190,17 @@ BOOST_AUTO_TEST_CASE(no_endmdl_record)
   BOOST_CHECK_THROW(reader.Import(ent), IOException);
 }
 
+BOOST_AUTO_TEST_CASE(faulty_lines)
+{
+  String fname("testfiles/pdb/faulty.pdb");
+  PDBReader reader(fname);
+  mol::EntityHandle ent=mol::CreateEntity();
+  BOOST_CHECK_THROW(reader.Import(ent), IOException);
+
+  PDB::PushFlags(PDB::SKIP_FAULTY_RECORDS);
+  reader.Import(ent);
+}
+
 BOOST_AUTO_TEST_CASE(write_atom)
 {
   std::stringstream out;
@@ -294,6 +305,48 @@ BOOST_AUTO_TEST_CASE(write_ter)
                             "testfiles/pdb/ter-out.pdb"));
 }
 
+BOOST_AUTO_TEST_CASE(write_ter2)
+{
+  String fname("testfiles/pdb/ter2.pdb");  
+  // this scope is required to force the writer stream to be closed before 
+  // opening the file again in compare_files. Avoids a race condition.
+  {
+    PDBReader reader(fname);
+    PDBWriter writer(String("testfiles/pdb/ter2-out.pdb"));
+    
+    mol::EntityHandle ent=mol::CreateEntity();
+    reader.Import(ent);
+    // we use conopology to mark amino acids as peptide-linking. this is 
+    // require for proper TER output
+    conop::Conopology& conop_inst=conop::Conopology::Instance();
+    conop_inst.ConnectAll(conop_inst.GetBuilder(), ent);
+    writer.Write(ent);
+  }
+  BOOST_CHECK(compare_files("testfiles/pdb/ter2.pdb", 
+                            "testfiles/pdb/ter2-out.pdb"));
+}
+
+BOOST_AUTO_TEST_CASE(write_ter3)
+{
+  String fname("testfiles/pdb/ter3.pdb");  
+  // this scope is required to force the writer stream to be closed before 
+  // opening the file again in compare_files. Avoids a race condition.
+  {
+    PDBReader reader(fname);
+    PDBWriter writer(String("testfiles/pdb/ter3-out.pdb"));
+    
+    mol::EntityHandle ent=mol::CreateEntity();
+    reader.Import(ent);
+    // we use conopology to mark amino acids as peptide-linking. this is 
+    // require for proper TER output
+    conop::Conopology& conop_inst=conop::Conopology::Instance();
+    conop_inst.ConnectAll(conop_inst.GetBuilder(), ent);
+    writer.Write(ent);
+  }
+  BOOST_CHECK(compare_files("testfiles/pdb/ter3.pdb", 
+                            "testfiles/pdb/ter3-out.pdb"));
+}
+
 BOOST_AUTO_TEST_CASE(write_conect)
 {
   // this scope is required to force the writer stream to be closed before
diff --git a/modules/io/tests/test_pir.cc b/modules/io/tests/test_pir.cc
new file mode 100644
index 0000000000000000000000000000000000000000..1829404cc85498587a98e287a6c88c6a267eb0a7
--- /dev/null
+++ b/modules/io/tests/test_pir.cc
@@ -0,0 +1,73 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+//------------------------------------------------------------------------------
+
+/*
+  Author: Marco Biasini
+ */
+
+#define BOOST_TEST_DYN_LINK
+#include <boost/test/unit_test.hpp>
+#include <ost/seq/invalid_sequence.hh>
+#include <ost/io/seq/pir_io_handler.hh>
+#include <ost/io/seq/load.hh>
+#include <ost/io/io_exception.hh>
+
+
+using namespace ost;
+using namespace ost::io;
+
+
+BOOST_AUTO_TEST_SUITE( io )
+
+
+BOOST_AUTO_TEST_CASE(pir_filetypes) 
+{
+  BOOST_CHECK(PirIOHandler::ProvidesImport("","pir"));
+  BOOST_CHECK(PirIOHandler::ProvidesImport("alignment.pir"));
+}
+
+BOOST_AUTO_TEST_CASE(pir_simple) 
+{
+  seq::SequenceHandle s=LoadSequence("testfiles/pir/simple.pir");
+  BOOST_CHECK_EQUAL(s.GetName(), "name");
+  BOOST_CHECK_EQUAL(s.GetString(), "ABCDEFGHIJKLMNOP");
+}
+
+BOOST_AUTO_TEST_CASE(pir_seq_types) 
+{
+  seq::SequenceList s=LoadSequenceList("testfiles/pir/seq-types.pir");
+}
+
+BOOST_AUTO_TEST_CASE(pir_errors)
+{
+  BOOST_CHECK_THROW(SequenceFromString(">", "pir"), IOException);
+  BOOST_CHECK_THROW(SequenceFromString(">P1", "pir"), IOException);
+  BOOST_CHECK_THROW(SequenceFromString(">P1;", "pir"), IOException);
+  BOOST_CHECK_THROW(SequenceFromString(">P1;name\n", "pir"), IOException);
+  BOOST_CHECK_THROW(SequenceFromString(">P1;name\ndescription\n", "pir"), 
+                    IOException);  
+}
+
+BOOST_AUTO_TEST_CASE(pir_no_star) 
+{
+  BOOST_CHECK_THROW(LoadSequence("testfiles/pir/no-star.pir"),  
+                    seq::InvalidSequence);
+}
+
+BOOST_AUTO_TEST_SUITE_END()
\ No newline at end of file
diff --git a/modules/io/tests/testfiles/pdb/faulty.pdb b/modules/io/tests/testfiles/pdb/faulty.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..5264ddde2c0217f3cba84053c8fa8c2f6b5021ea
--- /dev/null
+++ b/modules/io/tests/testfiles/pdb/faulty.pdb
@@ -0,0 +1,238 @@
+S
+SH
+SHE
+SHEE
+SHEET
+SHEET 
+SHEET  
+SHEET   
+SHEET    
+SHEET    1
+SHEET    1 
+SHEET    1  
+SHEET    1   
+SHEET    1   A
+SHEET    1   A 
+SHEET    1   A 7
+SHEET    1   A 7 
+SHEET    1   A 7 A
+SHEET    1   A 7 AL
+SHEET    1   A 7 ALA
+SHEET    1   A 7 ALA 
+SHEET    1   A 7 ALA A
+SHEET    1   A 7 ALA A 
+SHEET    1   A 7 ALA A  
+SHEET    1   A 7 ALA A  5
+SHEET    1   A 7 ALA A  53
+SHEET    1   A 7 ALA A  53 
+SHEET    1   A 7 ALA A  53  
+SHEET    1   A 7 ALA A  53  A
+SHEET    1   A 7 ALA A  53  AL
+SHEET    1   A 7 ALA A  53  ALA
+SHEET    1   A 7 ALA A  53  ALA 
+SHEET    1   A 7 ALA A  53  ALA A
+SHEET    1   A 7 ALA A  53  ALA A 
+SHEET    1   A 7 ALA A  53  ALA A  
+SHEET    1   A 7 ALA A  53  ALA A  5
+SHEET    1   A 7 ALA A  53  ALA A  57
+SHEET    1   A 7 ALA A  53  ALA A  57 
+SHEET    1   A 7 ALA A  53  ALA A  57  
+SHEET    1   A 7 ALA A  53  ALA A  57  0
+SHEET    1   A 7 ALA A  53  ALA A  57  0 
+SHEET    1   A 7 ALA A  53  ALA A  57  0  
+SHEET    1   A 7 ALA A  53  ALA A  57  0   
+SHEET    1   A 7 ALA A  53  ALA A  57  0    
+SHEET    1   A 7 ALA A  53  ALA A  57  0     
+SHEET    1   A 7 ALA A  53  ALA A  57  0      
+SHEET    1   A 7 ALA A  53  ALA A  57  0       
+SHEET    1   A 7 ALA A  53  ALA A  57  0        
+SHEET    1   A 7 ALA A  53  ALA A  57  0         
+SHEET    1   A 7 ALA A  53  ALA A  57  0          
+SHEET    1   A 7 ALA A  53  ALA A  57  0           
+SHEET    1   A 7 ALA A  53  ALA A  57  0            
+SHEET    1   A 7 ALA A  53  ALA A  57  0             
+SHEET    1   A 7 ALA A  53  ALA A  57  0              
+SHEET    1   A 7 ALA A  53  ALA A  57  0               
+SHEET    1   A 7 ALA A  53  ALA A  57  0                
+SHEET    1   A 7 ALA A  53  ALA A  57  0                 
+SHEET    1   A 7 ALA A  53  ALA A  57  0                  
+SHEET    1   A 7 ALA A  53  ALA A  57  0                   
+SHEET    1   A 7 ALA A  53  ALA A  57  0                    
+SHEET    1   A 7 ALA A  53  ALA A  57  0                     
+SHEET    1   A 7 ALA A  53  ALA A  57  0                      
+SHEET    1   A 7 ALA A  53  ALA A  57  0                       
+SHEET    1   A 7 ALA A  53  ALA A  57  0                        
+SHEET    1   A 7 ALA A  53  ALA A  57  0                         
+SHEET    1   A 7 ALA A  53  ALA A  57  0                          
+SHEET    1   A 7 ALA A  53  ALA A  57  0                           
+SHEET    1   A 7 ALA A  53  ALA A  57  0                            
+SHEET    1   A 7 ALA A  53  ALA A  57  0                             
+SHEET    1   A 7 ALA A  53  ALA A  57  0                              
+SHEET    1   A 7 ALA A  53  ALA A  57  0                               
+SHEET    1   A 7 ALA A  53  ALA A  57  0                                
+SHEET    1   A 7 ALA A  53  ALA A  57  0                                 
+SHEET    1   A 7 ALA A  53  ALA A  57  0                                  
+SHEET    1   A 7 ALA A  53  ALA A  57  0                                   
+SHEET    1   A 7 ALA A  53  ALA A  57  0                                    
+SHEET    1   A 7 ALA A  53  ALA A  57  0                                     
+SHEET    1   A 7 ALA A  53  ALA A  57  0                                      
+SHEET    1   A 7 ALA A  53  ALA A  57  0                                       
+H
+HE
+HEL
+HELI
+HELIX
+HELIX 
+HELIX  
+HELIX   
+HELIX    
+HELIX    1
+HELIX    1 
+HELIX    1  
+HELIX    1   
+HELIX    1   1
+HELIX    1   1 
+HELIX    1   1 A
+HELIX    1   1 AR
+HELIX    1   1 ARG
+HELIX    1   1 ARG 
+HELIX    1   1 ARG A
+HELIX    1   1 ARG A 
+HELIX    1   1 ARG A  
+HELIX    1   1 ARG A   
+HELIX    1   1 ARG A   1
+HELIX    1   1 ARG A   15
+HELIX    1   1 ARG A   15 
+HELIX    1   1 ARG A   15  
+HELIX    1   1 ARG A   15  G
+HELIX    1   1 ARG A   15  GL
+HELIX    1   1 ARG A   15  GLU
+HELIX    1   1 ARG A   15  GLU 
+HELIX    1   1 ARG A   15  GLU A
+HELIX    1   1 ARG A   15  GLU A 
+HELIX    1   1 ARG A   15  GLU A  
+HELIX    1   1 ARG A   15  GLU A   
+HELIX    1   1 ARG A   15  GLU A   2
+HELIX    1   1 ARG A   15  GLU A   28
+HELIX    1   1 ARG A   15  GLU A   28 
+HELIX    1   1 ARG A   15  GLU A   28  
+HELIX    1   1 ARG A   15  GLU A   28  1
+HELIX    1   1 ARG A   15  GLU A   28  1 
+HELIX    1   1 ARG A   15  GLU A   28  1  
+HELIX    1   1 ARG A   15  GLU A   28  1   
+HELIX    1   1 ARG A   15  GLU A   28  1    
+HELIX    1   1 ARG A   15  GLU A   28  1     
+HELIX    1   1 ARG A   15  GLU A   28  1      
+HELIX    1   1 ARG A   15  GLU A   28  1       
+HELIX    1   1 ARG A   15  GLU A   28  1        
+HELIX    1   1 ARG A   15  GLU A   28  1         
+HELIX    1   1 ARG A   15  GLU A   28  1          
+HELIX    1   1 ARG A   15  GLU A   28  1           
+HELIX    1   1 ARG A   15  GLU A   28  1            
+HELIX    1   1 ARG A   15  GLU A   28  1             
+HELIX    1   1 ARG A   15  GLU A   28  1              
+HELIX    1   1 ARG A   15  GLU A   28  1               
+HELIX    1   1 ARG A   15  GLU A   28  1                
+HELIX    1   1 ARG A   15  GLU A   28  1                 
+HELIX    1   1 ARG A   15  GLU A   28  1                  
+HELIX    1   1 ARG A   15  GLU A   28  1                   
+HELIX    1   1 ARG A   15  GLU A   28  1                    
+HELIX    1   1 ARG A   15  GLU A   28  1                     
+HELIX    1   1 ARG A   15  GLU A   28  1                      
+HELIX    1   1 ARG A   15  GLU A   28  1                       
+HELIX    1   1 ARG A   15  GLU A   28  1                        
+HELIX    1   1 ARG A   15  GLU A   28  1                         
+HELIX    1   1 ARG A   15  GLU A   28  1                          
+HELIX    1   1 ARG A   15  GLU A   28  1                           
+HELIX    1   1 ARG A   15  GLU A   28  1                            
+HELIX    1   1 ARG A   15  GLU A   28  1                             
+HELIX    1   1 ARG A   15  GLU A   28  1                              
+HELIX    1   1 ARG A   15  GLU A   28  1                               
+HELIX    1   1 ARG A   15  GLU A   28  1                                
+HELIX    1   1 ARG A   15  GLU A   28  1                                 
+HELIX    1   1 ARG A   15  GLU A   28  1                                  
+HELIX    1   1 ARG A   15  GLU A   28  1                                  1
+HELIX    1   1 ARG A   15  GLU A   28  1                                  14
+HELIX    1   1 ARG A   15  GLU A   28  1                                  14 
+HELIX    1   1 ARG A   15  GLU A   28  1                                  14  
+HELIX    1   1 ARG A   15  GLU A   28  1                                  14
+ATOM    241  O   VAL A  36       7.822 -61.026   0.770  1.00 44.33           O  
+ATOM    242  CB  VAL A  36       6.125 -58.659   0.048  1.00 45.53           C 
+ATOM    243  CG1 VAL A  36       6.258 -58.879  -1.447  1.00 44.30           C
+ATOM    244  CG2 VAL A  36       5.116 -57.557   0.325  1.00 45.44           
+ATOM    245  N   ASP A  37       6.227 -62.030  -0.456  1.00 42.63          
+ATOM    246  CA  ASP A  37       7.078 -63.127  -0.923  1.00 41.05         
+ATOM    247  C   ASP A  37       8.028 -62.602  -2.016  1.00 40.83        
+ATOM    248  O   ASP A  37       7.711 -62.636  -3.207  1.00 39.72       
+ATOM    249  CB  ASP A  37       6.175 -64.253  -1.442  1.00 41.60      
+ATOM    250  CG  ASP A  37       6.935 -65.334  -2.183  1.00 44.07     
+ATOM    251  OD1 ASP A  37       8.126 -65.559  -1.862  1.00 48.04    
+ATOM    252  OD2 ASP A  37       6.336 -65.968  -3.080  1.00 43.40   
+ATOM    253  N   ARG A  38       9.205 -62.135  -1.600  1.00 39.28  
+ATOM    254  CA  ARG A  38      10.178 -61.545  -2.522  1.00 40.53 
+ATOM    255  C   ARG A  38      11.326 -62.389  -3.075  1.00 40.66
+ATOM    256  O   ARG A  38      12.046 -61.932  -3.973  1.00 41.1
+ATOM    257  CB  ARG A  38      10.793 -60.295  -1.879  1.00 39.
+ATOM    258  CG  ARG A  38       9.806 -59.190  -1.589  1.00 39
+ATOM    259  CD  ARG A  38      10.370 -57.874  -2.040  1.00 3
+ATOM    260  NE  ARG A  38      10.326 -57.766  -3.489  1.00 
+ATOM    261  CZ  ARG A  38      11.291 -57.238  -4.231  1.00
+ATOM    262  NH1 ARG A  38      12.391 -56.765  -3.657  1.0
+ATOM    263  NH2 ARG A  38      11.158 -57.194  -5.546  1.
+ATOM    264  N   THR A  39      11.507 -63.593  -2.544  1
+ATOM    265  CA  THR A  39      12.594 -64.480  -2.965  
+ATOM    266  C   THR A  39      12.937 -64.454  -4.445 
+ATOM    267  O   THR A  39      14.001 -63.989  -4.831
+ATOM    268  CB  THR A  39      12.294 -65.939  -2.57
+ATOM    269  OG1 THR A  39      12.098 -66.012  -1.1
+ATOM    270  CG2 THR A  39      13.453 -66.855  -2.
+ATOM    271  N   LEU A  40      12.036 -64.952  -5
+ATOM    272  CA  LEU A  40      12.300 -64.998  -
+ATOM    273  C   LEU A  40      12.491 -63.643  
+ATOM    274  O   LEU A  40      13.243 -63.532 
+ATOM    275  CB  LEU A  40      11.187 -65.765
+ATOM    276  CG  LEU A  40      11.013 -67.20
+ATOM    277  CD1 LEU A  40       9.967 -67.8
+ATOM    278  CD2 LEU A  40      12.344 -67.
+ATOM    279  N   ALA A  41      11.815 -62
+ATOM    280  CA  ALA A  41      11.936 -6
+ATOM    281  C   ALA A  41      13.357 -
+ATOM    282  O   ALA A  41      13.925 
+ATOM    283  CB  ALA A  41      10.962
+ATOM    284  N   LYS A  42      13.92
+ATOM    285  CA  LYS A  42      15.2
+ATOM    286  C   LYS A  42      16.
+ATOM    287  O   LYS A  42      17
+ATOM    288  CB  LYS A  42      1
+ATOM    289  CG  LYS A  42      
+ATOM    290  CD  LYS A  42     
+ATOM    291  CE  LYS A  42    
+ATOM    292  NZ  LYS A  42   
+ATOM    293  N   GLU A  43  
+ATOM    294  CA  GLU A  43 
+ATOM    295  C   GLU A  43
+ATOM    296  O   GLU A  4
+ATOM    297  CB  GLU A  
+ATOM    298  CG  GLU A 
+ATOM    299  CD  GLU A
+ATOM    300  OE1 GLU 
+ATOM    301  OE2 GLU
+ATOM    302  N   GL
+ATOM    303  CA  G
+ATOM    304  C   
+ATOM    305  O  
+ATOM    306  N 
+ATOM    307  C
+ATOM    308  
+ATOM    309 
+ATOM    310
+ATOM    31
+ATOM    3
+ATOM    
+ATOM   
+ATOM  
+ATOM 
+ATOM
+ATO
+AT
+A
diff --git a/modules/io/tests/testfiles/pdb/ter2.pdb b/modules/io/tests/testfiles/pdb/ter2.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..8b460b70eb2e9cb6aab59d21e87dfd8c5801585d
--- /dev/null
+++ b/modules/io/tests/testfiles/pdb/ter2.pdb
@@ -0,0 +1,41 @@
+ATOM      1  N   GLN A 153      27.125  29.174  32.121  1.00 27.40           N  
+ATOM      2  CA  GLN A 153      28.561  29.394  32.241  1.00 30.81           C  
+ATOM      3  C   GLN A 153      29.250  29.251  30.888  1.00 35.59           C  
+ATOM      4  O   GLN A 153      28.979  28.314  30.130  1.00 33.20           O  
+ATOM      5  CB  GLN A 153      29.210  28.461  33.272  1.00 30.18           C  
+ATOM      6  CG  GLN A 153      30.694  28.783  33.468  1.00 34.18           C  
+ATOM      7  CD  GLN A 153      31.213  28.442  34.849  1.00 34.20           C  
+ATOM      8  OE1 GLN A 153      31.095  27.308  35.304  1.00 34.26           O  
+ATOM      9  NE2 GLN A 153      31.808  29.430  35.522  1.00 40.83           N  
+ATOM     10  OXT GLN A 153      30.094  30.079  30.532  1.00 45.02           O  
+TER      11      GLN A 153                                                      
+ATOM     12  N   ALA B   1      13.054  45.273  35.363  1.00 44.31           N  
+ATOM     13  CA  ALA B   1      12.088  44.308  35.884  1.00 39.90           C  
+ATOM     14  C   ALA B   1      11.751  44.590  37.349  1.00 35.09           C  
+ATOM     15  O   ALA B   1      12.633  44.881  38.156  1.00 39.85           O  
+ATOM     16  CB  ALA B   1      12.616  42.890  35.717  1.00 36.61           C  
+TER      17      ALA B   1                                                      
+TER      18      ALA B   1                                                      
+HETATM   19  S   SO4 z   1      25.896  25.925  48.976  0.60 29.86           S  
+HETATM   20  O1  SO4 z   1      25.480  27.268  48.589  0.60 30.25           O  
+HETATM   21  O2  SO4 z   1      25.611  24.961  47.915  0.60 34.83           O  
+HETATM   22  O3  SO4 z   1      27.332  25.943  49.244  0.60 34.94           O  
+HETATM   23  O4  SO4 z   1      25.183  25.525  50.189  0.60 32.47           O  
+HETATM   24 ZN    ZN z   2      23.332  26.722  48.256  0.66 22.52          ZN  
+HETATM   25 ZN    ZN z   3       4.294  31.320  20.337  0.28 33.21          ZN  
+HETATM   26  S   SO4 z   4       0.081  30.633  21.315  0.63 40.84           S  
+HETATM   27  O1  SO4 z   4      -1.116  31.446  21.507  0.63 45.94           O  
+HETATM   28  O2  SO4 z   4       1.268  31.440  21.578  0.63 33.61           O  
+HETATM   29  O3  SO4 z   4       0.032  29.503  22.239  0.63 29.10           O  
+HETATM   30  O4  SO4 z   4       0.115  30.163  19.934  0.63 40.96           O  
+CONECT   19   20   21   22   23
+CONECT   20   19
+CONECT   21   19
+CONECT   22   19
+CONECT   23   19
+CONECT   26   27   28   29   30
+CONECT   27   26
+CONECT   28   26
+CONECT   29   26
+CONECT   30   26
+END   
\ No newline at end of file
diff --git a/modules/io/tests/testfiles/pdb/ter3.pdb b/modules/io/tests/testfiles/pdb/ter3.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..b1c12618a3d7ca8786e99c61e2a6de8c6f4d84d0
--- /dev/null
+++ b/modules/io/tests/testfiles/pdb/ter3.pdb
@@ -0,0 +1,12 @@
+ATOM      1  N   GLN A 153      27.125  29.174  32.121  1.00 27.40           N  
+ATOM      2  CA  GLN A 153      28.561  29.394  32.241  1.00 30.81           C  
+ATOM      3  C   GLN A 153      29.250  29.251  30.888  1.00 35.59           C  
+ATOM      4  O   GLN A 153      28.979  28.314  30.130  1.00 33.20           O  
+ATOM      5  CB  GLN A 153      29.210  28.461  33.272  1.00 30.18           C  
+ATOM      6  CG  GLN A 153      30.694  28.783  33.468  1.00 34.18           C  
+ATOM      7  CD  GLN A 153      31.213  28.442  34.849  1.00 34.20           C  
+ATOM      8  OE1 GLN A 153      31.095  27.308  35.304  1.00 34.26           O  
+ATOM      9  NE2 GLN A 153      31.808  29.430  35.522  1.00 40.83           N  
+ATOM     10  OXT GLN A 153      30.094  30.079  30.532  1.00 45.02           O  
+TER      11      GLN A 153                                                      
+END   
\ No newline at end of file
diff --git a/modules/io/tests/testfiles/pir/no-star.pir b/modules/io/tests/testfiles/pir/no-star.pir
new file mode 100644
index 0000000000000000000000000000000000000000..98bc371aa111536824f099eb9cac42680abc8ee3
--- /dev/null
+++ b/modules/io/tests/testfiles/pir/no-star.pir
@@ -0,0 +1,21 @@
+>P1;name
+description
+ABCD EFGH*
+>F1;name
+description
+ABCD EFGH
+>DL;name*
+description
+ABCD EFGH
+>DC;name*
+description
+ABCD EFGH
+>RL;name*
+description
+ABCD EFGH
+>RC;name*
+description
+ABCD EFGH
+>XX;name*
+description
+ABCD EFGH*
\ No newline at end of file
diff --git a/modules/io/tests/testfiles/pir/seq-types.pir b/modules/io/tests/testfiles/pir/seq-types.pir
new file mode 100644
index 0000000000000000000000000000000000000000..ed8569f439128c459582f226aad1f82adc15961c
--- /dev/null
+++ b/modules/io/tests/testfiles/pir/seq-types.pir
@@ -0,0 +1,21 @@
+>P1;name
+description
+ABCD EFGH*
+>F1;name
+description
+ABCD EFGH*
+>DL;name
+description
+ABCD EFGH*
+>DC;name
+description
+ABCD EFGH*
+>RL;name
+description
+ABCD EFGH*
+>RC;name*
+description
+ABCD EFGH*
+>XX;name
+description
+ABCD EFGH*
\ No newline at end of file
diff --git a/modules/io/tests/testfiles/pir/simple.pir b/modules/io/tests/testfiles/pir/simple.pir
new file mode 100644
index 0000000000000000000000000000000000000000..6e8f03e4e6bda4b3d9a43ec1ed462b9cbb888387
--- /dev/null
+++ b/modules/io/tests/testfiles/pir/simple.pir
@@ -0,0 +1,4 @@
+>P1;name
+description
+ABCD EFGH
+IJKL MNOP*
\ No newline at end of file
diff --git a/modules/io/tests/testfiles/test_in.mae b/modules/io/tests/testfiles/test_in.mae
new file mode 100644
index 0000000000000000000000000000000000000000..5ec85f9ae2709202c55d2171a2ad3286c3bf130a
--- /dev/null
+++ b/modules/io/tests/testfiles/test_in.mae
@@ -0,0 +1,2149 @@
+{ 
+  s_m_m2io_version
+  :::
+  2.0.0 
+} 
+
+f_m_ct { 
+  s_m_title
+  s_m_entry_name
+  r_mmod_Potential_Energy-OPLS-2005
+  b_mmod_Minimization_Converged-OPLS-2005
+  r_mmod_RMS_Derivative-OPLS-2005
+  i_mmod_Times_Found-OPLS-2005
+  r_mmod_Relative_Potential_Energy-OPLS-2005
+  i_mmod_Conformation-OPLS-2005
+  s_m_job_name
+  s_m_entry_id
+  :::
+  "" 
+  mmod_csearch.1 
+     -189.953887939453 
+  1     
+    0.0344047322869301 
+  11    
+                     0 
+  1     
+  mmod_csearch 
+  1 
+  m_depend[7] { 
+    # First column is dependency index #
+    i_m_depend_dependency
+    s_m_depend_property
+    :::
+    1         20 r_mmod_Potential_Energy-OPLS-2005 
+    2         20 b_mmod_Minimization_Converged-OPLS-2005 
+    3         20 r_mmod_RMS_Derivative-OPLS-2005 
+    4         20 i_mmod_Times_Found-OPLS-2005 
+    5         20 r_mmod_Relative_Potential_Energy-OPLS-2005 
+    6         20 i_mmod_Conformation-OPLS-2005 
+    7         30 s_m_job_name 
+    :::
+  } 
+  m_atom[26] { 
+    # First column is atom index #
+    i_m_mmod_type
+    r_m_x_coord
+    r_m_y_coord
+    r_m_z_coord
+    i_m_residue_number
+    s_m_insertion_code
+    s_m_mmod_res
+    s_m_chain_name
+    i_m_color
+    r_m_charge1
+    r_m_charge2
+    s_m_pdb_residue_name
+    s_m_pdb_atom_name
+    s_m_grow_name
+    i_m_atomic_number
+    i_m_formal_charge
+    i_m_representation
+    i_m_visibility
+    s_m_atom_name
+    i_m_template_index
+    i_m_minimize_atom_index
+    :::
+    1        2    0.298444    1.945910   -2.821289     1 " " X " "    2   0.37000   0.37000 "    " "    " "  f1"    6   0    0    1 C2 0     1     
+    2        2    0.291296    1.782334   -4.225485     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "  c3"    6   0    0    1 C3 0     2     
+    3        2   -0.299908    0.641409   -4.792196     1 " " X " "    2   0.17700   0.17700 "    " "    " "  c1"    6   0    0    1 C4 0     3     
+    4        2   -0.879318   -0.302158   -3.930153     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "    "    6   0    0    1 C5 0     4     
+    5        2   -0.838839   -0.074482   -2.546795     1 " " X " "    2   0.66500   0.66500 "    " "    " "  n3"    6   0    0    1 C6 0     5     
+    6       41    0.733220    2.537708   -4.863215     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H9 0     6     
+    7       41   -1.353708   -1.193662   -4.315448     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H11 0     7     
+    8       57   -1.545982   -1.232352   -1.483532     1 " " X " "    9  -0.18000  -0.18000 "    " "    " "    "   17   0    0    1 Cl10 0     8     
+    9        2    1.230564    3.258726   -0.808119     1 " " X " "    2  -0.22090  -0.22090 "    " "    " "  c1"    6   0    0    1 C14 0     9     
+    10       2    1.554525    2.296205    0.127582     1 " " X " "    2   0.43430   0.43430 "    " "    " "  c3"    6   0    0    1 C15 0     10    
+    11       2    1.753033    4.147399    1.437892     1 " " X " "    2   0.18590   0.18590 "    " "    " "  n1"    6   0    0    1 C17 0     11    
+    12      25    1.852079    2.817042    1.389199     1 " " X " "   43  -0.48030  -0.48030 "    " "    " "  c1"    7   0    0    1 N22 0     12    
+    13      49    1.288898    4.859284   -0.098060     1 " " X " "   13   0.00100   0.00100 "    " "    " "  c1"   16   0    0    1 S18 0     13    
+    14       2    0.891516    3.202901   -2.243170     1 " " X " "    2   0.70000   0.70000 "    " "    " "  c1"    6   0    0    1 C19 0     14    
+    15      15    1.090923    4.195878   -2.957147     1 " " X " "   70  -0.47000  -0.47000 "    " "    " "  c3"    8   0    0    1 O20 0     15    
+    16       3   -0.323195    0.442771   -6.293649     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C20 0     16    
+    17      41   -0.366020   -0.616491   -6.548190     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H21 0     17    
+    18      41   -1.194706    0.933901   -6.726603     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H22 0     18    
+    19      41    0.570784    0.862253   -6.755689     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H23 0     19    
+    20       3    2.011604    4.946493    2.668135     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C23 0     20    
+    21      41    2.996371    4.710725    3.071317     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H24 0     21    
+    22      41    1.975117    6.012327    2.442882     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H25 0     22    
+    23      41    1.258842    4.725150    3.424520     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H26 0     23    
+    24      25   -0.256386    1.015035   -2.002566     1 " " X " "   43  -0.67800  -0.67800 "    " "    " "  c1"    7   0    0    1 N25 0     24    
+    25      16    1.631289    0.944593   -0.042652     1 " " X " "   70  -0.58500  -0.58500 "    " "    " "  c1"    8   0    0    1 O25 0     25    
+    26      42    0.987321    0.725684   -0.720518     1 " " X " "   21   0.43500   0.43500 "    " "    " "  n2"    1   0    0    1 H26 0     26    
+    :::
+  } 
+  m_bond[54] { 
+    # First column is bond index #
+    i_m_from
+    i_m_to
+    i_m_order
+    i_m_from_rep
+    i_m_to_rep
+    :::
+    1          1      2   1 1 1 
+    2          1     14   1 1 1 
+    3          1     24   2 1 1 
+    4          2      1   1 1 1 
+    5          2      3   2 1 1 
+    6          2      6   1 1 1 
+    7          3      2   2 1 1 
+    8          3      4   1 1 1 
+    9          3     16   1 1 1 
+    10         4      3   1 1 1 
+    11         4      5   2 1 1 
+    12         4      7   1 1 1 
+    13         5      4   2 1 1 
+    14         5      8   1 1 1 
+    15         5     24   1 1 1 
+    16         6      2   1 1 1 
+    17         7      4   1 1 1 
+    18         8      5   1 1 1 
+    19         9     10   2 1 1 
+    20         9     13   1 1 1 
+    21         9     14   1 1 1 
+    22        10      9   2 1 1 
+    23        10     12   1 1 1 
+    24        10     25   1 1 1 
+    25        11     12   2 1 1 
+    26        11     13   1 1 1 
+    27        11     20   1 1 1 
+    28        12     10   1 1 1 
+    29        12     11   2 1 1 
+    30        13      9   1 1 1 
+    31        13     11   1 1 1 
+    32        14      1   1 1 1 
+    33        14      9   1 1 1 
+    34        14     15   2 1 1 
+    35        15     14   2 1 1 
+    36        16      3   1 1 1 
+    37        16     17   1 1 1 
+    38        16     18   1 1 1 
+    39        16     19   1 1 1 
+    40        17     16   1 1 1 
+    41        18     16   1 1 1 
+    42        19     16   1 1 1 
+    43        20     11   1 1 1 
+    44        20     21   1 1 1 
+    45        20     22   1 1 1 
+    46        20     23   1 1 1 
+    47        21     20   1 1 1 
+    48        22     20   1 1 1 
+    49        23     20   1 1 1 
+    50        24      1   2 1 1 
+    51        24      5   1 1 1 
+    52        25     10   1 1 1 
+    53        25     26   1 1 1 
+    54        26     25   1 1 1 
+    :::
+  } 
+} 
+
+f_m_ct { 
+  s_m_title
+  s_m_entry_name
+  r_mmod_Potential_Energy-OPLS-2005
+  b_mmod_Minimization_Converged-OPLS-2005
+  r_mmod_RMS_Derivative-OPLS-2005
+  i_mmod_Times_Found-OPLS-2005
+  r_mmod_Relative_Potential_Energy-OPLS-2005
+  i_mmod_Conformation-OPLS-2005
+  s_m_job_name
+  s_m_entry_id
+  :::
+  "" 
+  mmod_csearch.2 
+     -189.952606201172 
+  1     
+    0.0418152138590813 
+  6     
+      0.00128173828125 
+  2     
+  mmod_csearch 
+  2 
+  m_depend[7] { 
+    # First column is dependency index #
+    i_m_depend_dependency
+    s_m_depend_property
+    :::
+    1         20 r_mmod_Potential_Energy-OPLS-2005 
+    2         20 b_mmod_Minimization_Converged-OPLS-2005 
+    3         20 r_mmod_RMS_Derivative-OPLS-2005 
+    4         20 i_mmod_Times_Found-OPLS-2005 
+    5         20 r_mmod_Relative_Potential_Energy-OPLS-2005 
+    6         20 i_mmod_Conformation-OPLS-2005 
+    7         30 s_m_job_name 
+    :::
+  } 
+  m_atom[26] { 
+    # First column is atom index #
+    i_m_mmod_type
+    r_m_x_coord
+    r_m_y_coord
+    r_m_z_coord
+    i_m_residue_number
+    s_m_insertion_code
+    s_m_mmod_res
+    s_m_chain_name
+    i_m_color
+    r_m_charge1
+    r_m_charge2
+    s_m_pdb_residue_name
+    s_m_pdb_atom_name
+    s_m_grow_name
+    i_m_atomic_number
+    i_m_formal_charge
+    i_m_representation
+    i_m_visibility
+    s_m_atom_name
+    i_m_template_index
+    :::
+    1        2    0.443727    1.890841   -2.845510     1 " " X " "    2   0.37000   0.37000 "    " "    " "  f1"    6   0    0    1 C2 0     
+    2        2   -0.071454    1.919895   -4.161628     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "  c3"    6   0    0    1 C3 0     
+    3        2   -0.562317    0.740485   -4.745051     1 " " X " "    2   0.17700   0.17700 "    " "    " "  c1"    6   0    0    1 C4 0     
+    4        2   -0.511632   -0.442313   -3.991600     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "    "    6   0    0    1 C5 0     
+    5        2    0.015802   -0.399119   -2.692696     1 " " X " "    2   0.66500   0.66500 "    " "    " "  n3"    6   0    0    1 C6 0     
+    6       41   -0.081010    2.846735   -4.721497     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H9 0     
+    7       41   -0.869280   -1.378464   -4.396498     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H11 0     
+    8       57    0.077092   -1.848665   -1.761940     1 " " X " "    9  -0.18000  -0.18000 "    " "    " "    "   17   0    0    1 Cl10 0     
+    9        2    1.220643    3.262742   -0.806637     1 " " X " "    2  -0.22090  -0.22090 "    " "    " "  c1"    6   0    0    1 C14 0     
+    10       2    0.636680    2.644949    0.281608     1 " " X " "    2   0.43430   0.43430 "    " "    " "  c3"    6   0    0    1 C15 0     
+    11       2    2.072014    4.025996    1.384214     1 " " X " "    2   0.18590   0.18590 "    " "    " "  n1"    6   0    0    1 C17 0     
+    12      25    1.125591    3.093136    1.511077     1 " " X " "   43  -0.48030  -0.48030 "    " "    " "  c1"    7   0    0    1 N22 0     
+    13      49    2.420078    4.429776   -0.288281     1 " " X " "   13   0.00100   0.00100 "    " "    " "  c1"   16   0    0    1 S18 0     
+    14       2    1.011769    3.157398   -2.263570     1 " " X " "    2   0.70000   0.70000 "    " "    " "  c1"    6   0    0    1 C19 0     
+    15      15    1.313214    4.111163   -2.995000     1 " " X " "   70  -0.47000  -0.47000 "    " "    " "  c3"    8   0    0    1 O20 0     
+    16       3   -1.118314    0.744290   -6.154004     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C20 0     
+    17      41   -1.825171   -0.072932   -6.299493     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H21 0     
+    18      41   -1.639283    1.678862   -6.363274     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H22 0     
+    19      41   -0.312207    0.632021   -6.879102     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H23 0     
+    20       3    2.758367    4.663562    2.542381     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C23 0     
+    21      41    2.053861    5.275084    3.105808     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H24 0     
+    22      41    3.170607    3.901299    3.203379     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H25 0     
+    23      41    3.572777    5.300367    2.197026     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H26 0     
+    24      25    0.472401    0.738510   -2.127216     1 " " X " "   43  -0.67800  -0.67800 "    " "    " "  c1"    7   0    0    1 N25 0     
+    25      16   -0.341944    1.694151    0.288704     1 " " X " "   70  -0.58500  -0.58500 "    " "    " "  c1"    8   0    0    1 O25 0     
+    26      42   -0.223854    1.185873   -0.517374     1 " " X " "   21   0.43500   0.43500 "    " "    " "  n2"    1   0    0    1 H26 0     
+    :::
+  } 
+  m_bond[54] { 
+    # First column is bond index #
+    i_m_from
+    i_m_to
+    i_m_order
+    i_m_from_rep
+    i_m_to_rep
+    :::
+    1          1      2   1 1 1 
+    2          1     14   1 1 1 
+    3          1     24   2 1 1 
+    4          2      1   1 1 1 
+    5          2      3   2 1 1 
+    6          2      6   1 1 1 
+    7          3      2   2 1 1 
+    8          3      4   1 1 1 
+    9          3     16   1 1 1 
+    10         4      3   1 1 1 
+    11         4      5   2 1 1 
+    12         4      7   1 1 1 
+    13         5      4   2 1 1 
+    14         5      8   1 1 1 
+    15         5     24   1 1 1 
+    16         6      2   1 1 1 
+    17         7      4   1 1 1 
+    18         8      5   1 1 1 
+    19         9     10   2 1 1 
+    20         9     13   1 1 1 
+    21         9     14   1 1 1 
+    22        10      9   2 1 1 
+    23        10     12   1 1 1 
+    24        10     25   1 1 1 
+    25        11     12   2 1 1 
+    26        11     13   1 1 1 
+    27        11     20   1 1 1 
+    28        12     10   1 1 1 
+    29        12     11   2 1 1 
+    30        13      9   1 1 1 
+    31        13     11   1 1 1 
+    32        14      1   1 1 1 
+    33        14      9   1 1 1 
+    34        14     15   2 1 1 
+    35        15     14   2 1 1 
+    36        16      3   1 1 1 
+    37        16     17   1 1 1 
+    38        16     18   1 1 1 
+    39        16     19   1 1 1 
+    40        17     16   1 1 1 
+    41        18     16   1 1 1 
+    42        19     16   1 1 1 
+    43        20     11   1 1 1 
+    44        20     21   1 1 1 
+    45        20     22   1 1 1 
+    46        20     23   1 1 1 
+    47        21     20   1 1 1 
+    48        22     20   1 1 1 
+    49        23     20   1 1 1 
+    50        24      1   2 1 1 
+    51        24      5   1 1 1 
+    52        25     10   1 1 1 
+    53        25     26   1 1 1 
+    54        26     25   1 1 1 
+    :::
+  } 
+} 
+
+f_m_ct { 
+  s_m_title
+  s_m_entry_name
+  r_mmod_Potential_Energy-OPLS-2005
+  b_mmod_Minimization_Converged-OPLS-2005
+  r_mmod_RMS_Derivative-OPLS-2005
+  i_mmod_Times_Found-OPLS-2005
+  r_mmod_Relative_Potential_Energy-OPLS-2005
+  i_mmod_Conformation-OPLS-2005
+  s_m_job_name
+  s_m_entry_id
+  :::
+  "" 
+  mmod_csearch.3 
+     -186.836090087891 
+  1     
+    0.0473463460803032 
+  21    
+       3.1177978515625 
+  3     
+  mmod_csearch 
+  3 
+  m_depend[7] { 
+    # First column is dependency index #
+    i_m_depend_dependency
+    s_m_depend_property
+    :::
+    1         20 r_mmod_Potential_Energy-OPLS-2005 
+    2         20 b_mmod_Minimization_Converged-OPLS-2005 
+    3         20 r_mmod_RMS_Derivative-OPLS-2005 
+    4         20 i_mmod_Times_Found-OPLS-2005 
+    5         20 r_mmod_Relative_Potential_Energy-OPLS-2005 
+    6         20 i_mmod_Conformation-OPLS-2005 
+    7         30 s_m_job_name 
+    :::
+  } 
+  m_atom[26] { 
+    # First column is atom index #
+    i_m_mmod_type
+    r_m_x_coord
+    r_m_y_coord
+    r_m_z_coord
+    i_m_residue_number
+    s_m_insertion_code
+    s_m_mmod_res
+    s_m_chain_name
+    i_m_color
+    r_m_charge1
+    r_m_charge2
+    s_m_pdb_residue_name
+    s_m_pdb_atom_name
+    s_m_grow_name
+    i_m_atomic_number
+    i_m_formal_charge
+    i_m_representation
+    i_m_visibility
+    s_m_atom_name
+    i_m_template_index
+    :::
+    1        2   -0.425793    1.853960   -2.401206     1 " " X " "    2   0.37000   0.37000 "    " "    " "  f1"    6   0    0    1 C2 0     
+    2        2    0.747056    1.565197   -3.136115     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "  c3"    6   0    0    1 C3 0     
+    3        2    0.730860    0.523813   -4.078351     1 " " X " "    2   0.17700   0.17700 "    " "    " "  c1"    6   0    0    1 C4 0     
+    4        2   -0.467544   -0.183586   -4.265742     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "    "    6   0    0    1 C5 0     
+    5        2   -1.595871    0.174061   -3.510966     1 " " X " "    2   0.66500   0.66500 "    " "    " "  n3"    6   0    0    1 C6 0     
+    6       41    1.650406    2.139268   -2.976223     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H9 0     
+    7       41   -0.533008   -0.990913   -4.981379     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H11 0     
+    8       57   -3.070053   -0.688531   -3.745467     1 " " X " "    9  -0.18000  -0.18000 "    " "    " "    "   17   0    0    1 Cl10 0     
+    9        2    0.747499    3.200282   -0.606635     1 " " X " "    2  -0.22090  -0.22090 "    " "    " "  c1"    6   0    0    1 C14 0     
+    10       2    1.650644    2.317976   -0.060846     1 " " X " "    2   0.43430   0.43430 "    " "    " "  c3"    6   0    0    1 C15 0     
+    11       2    2.572801    4.272719    0.644630     1 " " X " "    2   0.18590   0.18590 "    " "    " "  n1"    6   0    0    1 C17 0     
+    12      25    2.684533    2.940216    0.639179     1 " " X " "   43  -0.48030  -0.48030 "    " "    " "  c1"    7   0    0    1 N22 0     
+    13      49    1.158697    4.854330   -0.224311     1 " " X " "   13   0.00100   0.00100 "    " "    " "  c1"   16   0    0    1 S18 0     
+    14       2   -0.456372    2.973132   -1.408107     1 " " X " "    2   0.70000   0.70000 "    " "    " "  c1"    6   0    0    1 C19 0     
+    15      15   -1.456188    3.689998   -1.258329     1 " " X " "   70  -0.47000  -0.47000 "    " "    " "  c3"    8   0    0    1 O20 0     
+    16       3    1.971232    0.181008   -4.876999     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C20 0     
+    17      41    1.958322   -0.862335   -5.193159     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H21 0     
+    18      41    2.033185    0.807286   -5.767027     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H22 0     
+    19      41    2.871722    0.339744   -4.283175     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H23 0     
+    20       3    3.545252    5.174055    1.323217     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C23 0     
+    21      41    3.547570    4.984392    2.396416     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H24 0     
+    22      41    4.549164    5.006530    0.933439     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H25 0     
+    23      41    3.277084    6.217054    1.155104     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H26 0     
+    24      25   -1.579865    1.171163   -2.605431     1 " " X " "   43  -0.67800  -0.67800 "    " "    " "  c1"    7   0    0    1 N25 0     
+    25      16    1.609226    0.956222   -0.120720     1 " " X " "   70  -0.58500  -0.58500 "    " "    " "  c1"    8   0    0    1 O25 0     
+    26      42    2.371750    0.636660    0.349677     1 " " X " "   21   0.43500   0.43500 "    " "    " "  n2"    1   0    0    1 H26 0     
+    :::
+  } 
+  m_bond[54] { 
+    # First column is bond index #
+    i_m_from
+    i_m_to
+    i_m_order
+    i_m_from_rep
+    i_m_to_rep
+    :::
+    1          1      2   1 1 1 
+    2          1     14   1 1 1 
+    3          1     24   2 1 1 
+    4          2      1   1 1 1 
+    5          2      3   2 1 1 
+    6          2      6   1 1 1 
+    7          3      2   2 1 1 
+    8          3      4   1 1 1 
+    9          3     16   1 1 1 
+    10         4      3   1 1 1 
+    11         4      5   2 1 1 
+    12         4      7   1 1 1 
+    13         5      4   2 1 1 
+    14         5      8   1 1 1 
+    15         5     24   1 1 1 
+    16         6      2   1 1 1 
+    17         7      4   1 1 1 
+    18         8      5   1 1 1 
+    19         9     10   2 1 1 
+    20         9     13   1 1 1 
+    21         9     14   1 1 1 
+    22        10      9   2 1 1 
+    23        10     12   1 1 1 
+    24        10     25   1 1 1 
+    25        11     12   2 1 1 
+    26        11     13   1 1 1 
+    27        11     20   1 1 1 
+    28        12     10   1 1 1 
+    29        12     11   2 1 1 
+    30        13      9   1 1 1 
+    31        13     11   1 1 1 
+    32        14      1   1 1 1 
+    33        14      9   1 1 1 
+    34        14     15   2 1 1 
+    35        15     14   2 1 1 
+    36        16      3   1 1 1 
+    37        16     17   1 1 1 
+    38        16     18   1 1 1 
+    39        16     19   1 1 1 
+    40        17     16   1 1 1 
+    41        18     16   1 1 1 
+    42        19     16   1 1 1 
+    43        20     11   1 1 1 
+    44        20     21   1 1 1 
+    45        20     22   1 1 1 
+    46        20     23   1 1 1 
+    47        21     20   1 1 1 
+    48        22     20   1 1 1 
+    49        23     20   1 1 1 
+    50        24      1   2 1 1 
+    51        24      5   1 1 1 
+    52        25     10   1 1 1 
+    53        25     26   1 1 1 
+    54        26     25   1 1 1 
+    :::
+  } 
+} 
+
+f_m_ct { 
+  s_m_title
+  s_m_entry_name
+  r_mmod_Potential_Energy-OPLS-2005
+  b_mmod_Minimization_Converged-OPLS-2005
+  r_mmod_RMS_Derivative-OPLS-2005
+  i_mmod_Times_Found-OPLS-2005
+  r_mmod_Relative_Potential_Energy-OPLS-2005
+  i_mmod_Conformation-OPLS-2005
+  s_m_job_name
+  s_m_entry_id
+  :::
+  "" 
+  mmod_csearch.4 
+     -186.815521240234 
+  1     
+    0.0335310250520706 
+  8     
+      3.13836669921875 
+  4     
+  mmod_csearch 
+  4 
+  m_depend[7] { 
+    # First column is dependency index #
+    i_m_depend_dependency
+    s_m_depend_property
+    :::
+    1         20 r_mmod_Potential_Energy-OPLS-2005 
+    2         20 b_mmod_Minimization_Converged-OPLS-2005 
+    3         20 r_mmod_RMS_Derivative-OPLS-2005 
+    4         20 i_mmod_Times_Found-OPLS-2005 
+    5         20 r_mmod_Relative_Potential_Energy-OPLS-2005 
+    6         20 i_mmod_Conformation-OPLS-2005 
+    7         30 s_m_job_name 
+    :::
+  } 
+  m_atom[26] { 
+    # First column is atom index #
+    i_m_mmod_type
+    r_m_x_coord
+    r_m_y_coord
+    r_m_z_coord
+    i_m_residue_number
+    s_m_insertion_code
+    s_m_mmod_res
+    s_m_chain_name
+    i_m_color
+    r_m_charge1
+    r_m_charge2
+    s_m_pdb_residue_name
+    s_m_pdb_atom_name
+    s_m_grow_name
+    i_m_atomic_number
+    i_m_formal_charge
+    i_m_representation
+    i_m_visibility
+    s_m_atom_name
+    i_m_template_index
+    :::
+    1        2    0.765436    1.631022   -2.858208     1 " " X " "    2   0.37000   0.37000 "    " "    " "  f1"    6   0    0    1 C2 0     
+    2        2   -0.614523    1.822604   -2.617422     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "  c3"    6   0    0    1 C3 0     
+    3        2   -1.544670    0.953721   -3.210825     1 " " X " "    2   0.17700   0.17700 "    " "    " "  c1"    6   0    0    1 C4 0     
+    4        2   -1.060705   -0.073384   -4.037182     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "    "    6   0    0    1 C5 0     
+    5        2    0.323233   -0.188242   -4.242815     1 " " X " "    2   0.66500   0.66500 "    " "    " "  n3"    6   0    0    1 C6 0     
+    6       41   -0.954314    2.629516   -1.981347     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H9 0     
+    7       41   -1.734711   -0.769441   -4.516160     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H11 0     
+    8       57    0.918422   -1.442944   -5.264439     1 " " X " "    9  -0.18000  -0.18000 "    " "    " "    "   17   0    0    1 Cl10 0     
+    9        2    1.543216    3.051072   -0.911799     1 " " X " "    2  -0.22090  -0.22090 "    " "    " "  c1"    6   0    0    1 C14 0     
+    10       2    0.989559    2.442396    0.190502     1 " " X " "    2   0.43430   0.43430 "    " "    " "  c3"    6   0    0    1 C15 0     
+    11       2    1.432039    4.486692    1.081800     1 " " X " "    2   0.18590   0.18590 "    " "    " "  n1"    6   0    0    1 C17 0     
+    12      25    0.925834    3.270480    1.311372     1 " " X " "   43  -0.48030  -0.48030 "    " "    " "  c1"    7   0    0    1 N22 0     
+    13      49    2.034242    4.689659   -0.558074     1 " " X " "   13   0.00100   0.00100 "    " "    " "  c1"   16   0    0    1 S18 0     
+    14       2    1.785533    2.552641   -2.266867     1 " " X " "    2   0.70000   0.70000 "    " "    " "  c1"    6   0    0    1 C19 0     
+    15      15    2.802849    2.890624   -2.888820     1 " " X " "   70  -0.47000  -0.47000 "    " "    " "  c3"    8   0    0    1 O20 0     
+    16       3   -3.029075    1.122486   -2.961776     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C20 0     
+    17      41   -3.618315    0.619984   -3.729188     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H21 0     
+    18      41   -3.299860    0.701759   -1.993314     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H22 0     
+    19      41   -3.303614    2.177571   -2.965404     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H23 0     
+    20       3    1.487238    5.559904    2.113177     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C23 0     
+    21      41    2.191283    5.288325    2.899477     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H24 0     
+    22      41    1.810850    6.499660    1.665793     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H25 0     
+    23      41    0.502901    5.707876    2.557097     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H26 0     
+    24      25    1.215419    0.645811   -3.674683     1 " " X " "   43  -0.67800  -0.67800 "    " "    " "  c1"    7   0    0    1 N25 0     
+    25      16    0.544656    1.156680    0.283590     1 " " X " "   70  -0.58500  -0.58500 "    " "    " "  c1"    8   0    0    1 O25 0     
+    26      42    0.219159    1.041451    1.169947     1 " " X " "   21   0.43500   0.43500 "    " "    " "  n2"    1   0    0    1 H26 0     
+    :::
+  } 
+  m_bond[54] { 
+    # First column is bond index #
+    i_m_from
+    i_m_to
+    i_m_order
+    i_m_from_rep
+    i_m_to_rep
+    :::
+    1          1      2   1 1 1 
+    2          1     14   1 1 1 
+    3          1     24   2 1 1 
+    4          2      1   1 1 1 
+    5          2      3   2 1 1 
+    6          2      6   1 1 1 
+    7          3      2   2 1 1 
+    8          3      4   1 1 1 
+    9          3     16   1 1 1 
+    10         4      3   1 1 1 
+    11         4      5   2 1 1 
+    12         4      7   1 1 1 
+    13         5      4   2 1 1 
+    14         5      8   1 1 1 
+    15         5     24   1 1 1 
+    16         6      2   1 1 1 
+    17         7      4   1 1 1 
+    18         8      5   1 1 1 
+    19         9     10   2 1 1 
+    20         9     13   1 1 1 
+    21         9     14   1 1 1 
+    22        10      9   2 1 1 
+    23        10     12   1 1 1 
+    24        10     25   1 1 1 
+    25        11     12   2 1 1 
+    26        11     13   1 1 1 
+    27        11     20   1 1 1 
+    28        12     10   1 1 1 
+    29        12     11   2 1 1 
+    30        13      9   1 1 1 
+    31        13     11   1 1 1 
+    32        14      1   1 1 1 
+    33        14      9   1 1 1 
+    34        14     15   2 1 1 
+    35        15     14   2 1 1 
+    36        16      3   1 1 1 
+    37        16     17   1 1 1 
+    38        16     18   1 1 1 
+    39        16     19   1 1 1 
+    40        17     16   1 1 1 
+    41        18     16   1 1 1 
+    42        19     16   1 1 1 
+    43        20     11   1 1 1 
+    44        20     21   1 1 1 
+    45        20     22   1 1 1 
+    46        20     23   1 1 1 
+    47        21     20   1 1 1 
+    48        22     20   1 1 1 
+    49        23     20   1 1 1 
+    50        24      1   2 1 1 
+    51        24      5   1 1 1 
+    52        25     10   1 1 1 
+    53        25     26   1 1 1 
+    54        26     25   1 1 1 
+    :::
+  } 
+} 
+
+f_m_ct { 
+  s_m_title
+  s_m_entry_name
+  r_mmod_Potential_Energy-OPLS-2005
+  b_mmod_Minimization_Converged-OPLS-2005
+  r_mmod_RMS_Derivative-OPLS-2005
+  i_mmod_Times_Found-OPLS-2005
+  r_mmod_Relative_Potential_Energy-OPLS-2005
+  i_mmod_Conformation-OPLS-2005
+  s_m_job_name
+  s_m_entry_id
+  :::
+  "" 
+  mmod_csearch.5 
+      -186.51448059082 
+  1     
+    0.0293420907109976 
+  15    
+      3.43940734863281 
+  5     
+  mmod_csearch 
+  5 
+  m_depend[7] { 
+    # First column is dependency index #
+    i_m_depend_dependency
+    s_m_depend_property
+    :::
+    1         20 r_mmod_Potential_Energy-OPLS-2005 
+    2         20 b_mmod_Minimization_Converged-OPLS-2005 
+    3         20 r_mmod_RMS_Derivative-OPLS-2005 
+    4         20 i_mmod_Times_Found-OPLS-2005 
+    5         20 r_mmod_Relative_Potential_Energy-OPLS-2005 
+    6         20 i_mmod_Conformation-OPLS-2005 
+    7         30 s_m_job_name 
+    :::
+  } 
+  m_atom[26] { 
+    # First column is atom index #
+    i_m_mmod_type
+    r_m_x_coord
+    r_m_y_coord
+    r_m_z_coord
+    i_m_residue_number
+    s_m_insertion_code
+    s_m_mmod_res
+    s_m_chain_name
+    i_m_color
+    r_m_charge1
+    r_m_charge2
+    s_m_pdb_residue_name
+    s_m_pdb_atom_name
+    s_m_grow_name
+    i_m_atomic_number
+    i_m_formal_charge
+    i_m_representation
+    i_m_visibility
+    s_m_atom_name
+    i_m_template_index
+    :::
+    1        2    0.182516    2.027644   -2.871495     1 " " X " "    2   0.37000   0.37000 "    " "    " "  f1"    6   0    0    1 C2 0     
+    2        2    0.380164    1.686182   -4.227610     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "  c3"    6   0    0    1 C3 0     
+    3        2   -0.236777    0.535382   -4.745401     1 " " X " "    2   0.17700   0.17700 "    " "    " "  c1"    6   0    0    1 C4 0     
+    4        2   -1.037707   -0.232269   -3.884325     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "    "    6   0    0    1 C5 0     
+    5        2   -1.198196    0.181068   -2.552043     1 " " X " "    2   0.66500   0.66500 "    " "    " "  n3"    6   0    0    1 C6 0     
+    6       41    1.005888    2.306715   -4.856805     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H9 0     
+    7       41   -1.530995   -1.128770   -4.232408     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H11 0     
+    8       57   -2.188499   -0.754939   -1.495981     1 " " X " "    9  -0.18000  -0.18000 "    " "    " "    "   17   0    0    1 Cl10 0     
+    9        2    1.191667    3.271459   -0.914998     1 " " X " "    2  -0.22090  -0.22090 "    " "    " "  c1"    6   0    0    1 C14 0     
+    10       2    1.752743    2.293398   -0.127504     1 " " X " "    2   0.43430   0.43430 "    " "    " "  c3"    6   0    0    1 C15 0     
+    11       2    1.553676    3.947394    1.420305     1 " " X " "    2   0.18590   0.18590 "    " "    " "  n1"    6   0    0    1 C17 0     
+    12      25    1.947091    2.688987    1.196517     1 " " X " "   43  -0.48030  -0.48030 "    " "    " "  c1"    7   0    0    1 N22 0     
+    13      49    0.916151    4.741479   -0.013762     1 " " X " "   13   0.00100   0.00100 "    " "    " "  c1"   16   0    0    1 S18 0     
+    14       2    0.818851    3.268805   -2.330130     1 " " X " "    2   0.70000   0.70000 "    " "    " "  c1"    6   0    0    1 C19 0     
+    15      15    1.020534    4.266575   -3.035895     1 " " X " "   70  -0.47000  -0.47000 "    " "    " "  c3"    8   0    0    1 O20 0     
+    16       3   -0.038694    0.131225   -6.191634     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C20 0     
+    17      41   -0.900338   -0.422993   -6.564603     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H21 0     
+    18      41    0.096072    1.007357   -6.826373     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H22 0     
+    19      41    0.843479   -0.501447   -6.290070     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H23 0     
+    20       3    1.653141    4.613192    2.748989     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C23 0     
+    21      41    1.189678    5.599136    2.714967     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H24 0     
+    22      41    1.146369    4.017543    3.508089     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H25 0     
+    23      41    2.698864    4.730178    3.032740     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H26 0     
+    24      25   -0.612813    1.288673   -2.058294     1 " " X " "   43  -0.67800  -0.67800 "    " "    " "  c1"    7   0    0    1 N25 0     
+    25      16    2.153537    1.049124   -0.518319     1 " " X " "   70  -0.58500  -0.58500 "    " "    " "  c1"    8   0    0    1 O25 0     
+    26      42    2.480479    0.609292    0.259056     1 " " X " "   21   0.43500   0.43500 "    " "    " "  n2"    1   0    0    1 H26 0     
+    :::
+  } 
+  m_bond[54] { 
+    # First column is bond index #
+    i_m_from
+    i_m_to
+    i_m_order
+    i_m_from_rep
+    i_m_to_rep
+    :::
+    1          1      2   1 1 1 
+    2          1     14   1 1 1 
+    3          1     24   2 1 1 
+    4          2      1   1 1 1 
+    5          2      3   2 1 1 
+    6          2      6   1 1 1 
+    7          3      2   2 1 1 
+    8          3      4   1 1 1 
+    9          3     16   1 1 1 
+    10         4      3   1 1 1 
+    11         4      5   2 1 1 
+    12         4      7   1 1 1 
+    13         5      4   2 1 1 
+    14         5      8   1 1 1 
+    15         5     24   1 1 1 
+    16         6      2   1 1 1 
+    17         7      4   1 1 1 
+    18         8      5   1 1 1 
+    19         9     10   2 1 1 
+    20         9     13   1 1 1 
+    21         9     14   1 1 1 
+    22        10      9   2 1 1 
+    23        10     12   1 1 1 
+    24        10     25   1 1 1 
+    25        11     12   2 1 1 
+    26        11     13   1 1 1 
+    27        11     20   1 1 1 
+    28        12     10   1 1 1 
+    29        12     11   2 1 1 
+    30        13      9   1 1 1 
+    31        13     11   1 1 1 
+    32        14      1   1 1 1 
+    33        14      9   1 1 1 
+    34        14     15   2 1 1 
+    35        15     14   2 1 1 
+    36        16      3   1 1 1 
+    37        16     17   1 1 1 
+    38        16     18   1 1 1 
+    39        16     19   1 1 1 
+    40        17     16   1 1 1 
+    41        18     16   1 1 1 
+    42        19     16   1 1 1 
+    43        20     11   1 1 1 
+    44        20     21   1 1 1 
+    45        20     22   1 1 1 
+    46        20     23   1 1 1 
+    47        21     20   1 1 1 
+    48        22     20   1 1 1 
+    49        23     20   1 1 1 
+    50        24      1   2 1 1 
+    51        24      5   1 1 1 
+    52        25     10   1 1 1 
+    53        25     26   1 1 1 
+    54        26     25   1 1 1 
+    :::
+  } 
+} 
+
+f_m_ct { 
+  s_m_title
+  s_m_entry_name
+  r_mmod_Potential_Energy-OPLS-2005
+  b_mmod_Minimization_Converged-OPLS-2005
+  r_mmod_RMS_Derivative-OPLS-2005
+  i_mmod_Times_Found-OPLS-2005
+  r_mmod_Relative_Potential_Energy-OPLS-2005
+  i_mmod_Conformation-OPLS-2005
+  s_m_job_name
+  s_m_entry_id
+  :::
+  "" 
+  mmod_csearch.6 
+     -186.510955810547 
+  1     
+    0.0454494766891003 
+  18    
+      3.44293212890625 
+  6     
+  mmod_csearch 
+  6 
+  m_depend[7] { 
+    # First column is dependency index #
+    i_m_depend_dependency
+    s_m_depend_property
+    :::
+    1         20 r_mmod_Potential_Energy-OPLS-2005 
+    2         20 b_mmod_Minimization_Converged-OPLS-2005 
+    3         20 r_mmod_RMS_Derivative-OPLS-2005 
+    4         20 i_mmod_Times_Found-OPLS-2005 
+    5         20 r_mmod_Relative_Potential_Energy-OPLS-2005 
+    6         20 i_mmod_Conformation-OPLS-2005 
+    7         30 s_m_job_name 
+    :::
+  } 
+  m_atom[26] { 
+    # First column is atom index #
+    i_m_mmod_type
+    r_m_x_coord
+    r_m_y_coord
+    r_m_z_coord
+    i_m_residue_number
+    s_m_insertion_code
+    s_m_mmod_res
+    s_m_chain_name
+    i_m_color
+    r_m_charge1
+    r_m_charge2
+    s_m_pdb_residue_name
+    s_m_pdb_atom_name
+    s_m_grow_name
+    i_m_atomic_number
+    i_m_formal_charge
+    i_m_representation
+    i_m_visibility
+    s_m_atom_name
+    i_m_template_index
+    :::
+    1        2    0.554977    1.881312   -2.934618     1 " " X " "    2   0.37000   0.37000 "    " "    " "  f1"    6   0    0    1 C2 0     
+    2        2   -0.199984    1.911978   -4.127854     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "  c3"    6   0    0    1 C3 0     
+    3        2   -0.684396    0.709183   -4.667890     1 " " X " "    2   0.17700   0.17700 "    " "    " "  c1"    6   0    0    1 C4 0     
+    4        2   -0.384001   -0.487516   -3.997168     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "    "    6   0    0    1 C5 0     
+    5        2    0.385664   -0.437585   -2.823838     1 " " X " "    2   0.66500   0.66500 "    " "    " "  n3"    6   0    0    1 C6 0     
+    6       41   -0.403382    2.856823   -4.616033     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H9 0     
+    7       41   -0.731586   -1.439754   -4.372167     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H11 0     
+    8       57    0.761991   -1.906390   -2.003427     1 " " X " "    9  -0.18000  -0.18000 "    " "    " "    "   17   0    0    1 Cl10 0     
+    9        2    1.245251    3.250255   -0.923786     1 " " X " "    2  -0.22090  -0.22090 "    " "    " "  c1"    6   0    0    1 C14 0     
+    10       2    0.438453    2.806830    0.097990     1 " " X " "    2   0.43430   0.43430 "    " "    " "  c3"    6   0    0    1 C15 0     
+    11       2    2.117347    3.728609    1.323906     1 " " X " "    2   0.18590   0.18590 "    " "    " "  n1"    6   0    0    1 C17 0     
+    12      25    0.949063    3.079148    1.367827     1 " " X " "   43  -0.48030  -0.48030 "    " "    " "  c1"    7   0    0    1 N22 0     
+    13      49    2.668729    4.056818   -0.313611     1 " " X " "   13   0.00100   0.00100 "    " "    " "  c1"   16   0    0    1 S18 0     
+    14       2    1.091782    3.161453   -2.376431     1 " " X " "    2   0.70000   0.70000 "    " "    " "  c1"    6   0    0    1 C19 0     
+    15      15    1.407589    4.114465   -3.101922     1 " " X " "   70  -0.47000  -0.47000 "    " "    " "  c3"    8   0    0    1 O20 0     
+    16       3   -1.502004    0.703323   -5.942904     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C20 0     
+    17      41   -2.185087   -0.146123   -5.965947     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H21 0     
+    18      41   -2.096358    1.613263   -6.029082     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H22 0     
+    19      41   -0.847059    0.639020   -6.811894     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H23 0     
+    20       3    2.876039    4.136247    2.539174     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C23 0     
+    21      41    3.618571    4.892767    2.285505     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H24 0     
+    22      41    2.200451    4.550997    3.287207     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H25 0     
+    23      41    3.388588    3.274635    2.966393     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H26 0     
+    24      25    0.853061    0.715420   -2.308703     1 " " X " "   43  -0.67800  -0.67800 "    " "    " "  c1"    7   0    0    1 N25 0     
+    25      16   -0.774641    2.192926   -0.016349     1 " " X " "   70  -0.58500  -0.58500 "    " "    " "  c1"    8   0    0    1 O25 0     
+    26      42   -1.067056    1.996197    0.867082     1 " " X " "   21   0.43500   0.43500 "    " "    " "  n2"    1   0    0    1 H26 0     
+    :::
+  } 
+  m_bond[54] { 
+    # First column is bond index #
+    i_m_from
+    i_m_to
+    i_m_order
+    i_m_from_rep
+    i_m_to_rep
+    :::
+    1          1      2   1 1 1 
+    2          1     14   1 1 1 
+    3          1     24   2 1 1 
+    4          2      1   1 1 1 
+    5          2      3   2 1 1 
+    6          2      6   1 1 1 
+    7          3      2   2 1 1 
+    8          3      4   1 1 1 
+    9          3     16   1 1 1 
+    10         4      3   1 1 1 
+    11         4      5   2 1 1 
+    12         4      7   1 1 1 
+    13         5      4   2 1 1 
+    14         5      8   1 1 1 
+    15         5     24   1 1 1 
+    16         6      2   1 1 1 
+    17         7      4   1 1 1 
+    18         8      5   1 1 1 
+    19         9     10   2 1 1 
+    20         9     13   1 1 1 
+    21         9     14   1 1 1 
+    22        10      9   2 1 1 
+    23        10     12   1 1 1 
+    24        10     25   1 1 1 
+    25        11     12   2 1 1 
+    26        11     13   1 1 1 
+    27        11     20   1 1 1 
+    28        12     10   1 1 1 
+    29        12     11   2 1 1 
+    30        13      9   1 1 1 
+    31        13     11   1 1 1 
+    32        14      1   1 1 1 
+    33        14      9   1 1 1 
+    34        14     15   2 1 1 
+    35        15     14   2 1 1 
+    36        16      3   1 1 1 
+    37        16     17   1 1 1 
+    38        16     18   1 1 1 
+    39        16     19   1 1 1 
+    40        17     16   1 1 1 
+    41        18     16   1 1 1 
+    42        19     16   1 1 1 
+    43        20     11   1 1 1 
+    44        20     21   1 1 1 
+    45        20     22   1 1 1 
+    46        20     23   1 1 1 
+    47        21     20   1 1 1 
+    48        22     20   1 1 1 
+    49        23     20   1 1 1 
+    50        24      1   2 1 1 
+    51        24      5   1 1 1 
+    52        25     10   1 1 1 
+    53        25     26   1 1 1 
+    54        26     25   1 1 1 
+    :::
+  } 
+} 
+
+f_m_ct { 
+  s_m_title
+  s_m_entry_name
+  r_mmod_Potential_Energy-OPLS-2005
+  b_mmod_Minimization_Converged-OPLS-2005
+  r_mmod_RMS_Derivative-OPLS-2005
+  i_mmod_Times_Found-OPLS-2005
+  r_mmod_Relative_Potential_Energy-OPLS-2005
+  i_mmod_Conformation-OPLS-2005
+  s_m_job_name
+  s_m_entry_id
+  :::
+  "" 
+  mmod_csearch.7 
+     -179.586654663086 
+  0     
+      11.5642328262329 
+  1     
+      10.3672332763672 
+  7     
+  mmod_csearch 
+  7 
+  m_depend[7] { 
+    # First column is dependency index #
+    i_m_depend_dependency
+    s_m_depend_property
+    :::
+    1         20 r_mmod_Potential_Energy-OPLS-2005 
+    2         20 b_mmod_Minimization_Converged-OPLS-2005 
+    3         20 r_mmod_RMS_Derivative-OPLS-2005 
+    4         20 i_mmod_Times_Found-OPLS-2005 
+    5         20 r_mmod_Relative_Potential_Energy-OPLS-2005 
+    6         20 i_mmod_Conformation-OPLS-2005 
+    7         30 s_m_job_name 
+    :::
+  } 
+  m_atom[26] { 
+    # First column is atom index #
+    i_m_mmod_type
+    r_m_x_coord
+    r_m_y_coord
+    r_m_z_coord
+    i_m_residue_number
+    s_m_insertion_code
+    s_m_mmod_res
+    s_m_chain_name
+    i_m_color
+    r_m_charge1
+    r_m_charge2
+    s_m_pdb_residue_name
+    s_m_pdb_atom_name
+    s_m_grow_name
+    i_m_atomic_number
+    i_m_formal_charge
+    i_m_representation
+    i_m_visibility
+    s_m_atom_name
+    i_m_template_index
+    :::
+    1        2   -0.501074    1.649623   -2.219350     1 " " X " "    2   0.37000   0.37000 "    " "    " "  f1"    6   0    0    1 C2 0     
+    2        2    0.695806    1.555975   -2.972343     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "  c3"    6   0    0    1 C3 0     
+    3        2    0.712871    0.790463   -4.151366     1 " " X " "    2   0.17700   0.17700 "    " "    " "  c1"    6   0    0    1 C4 0     
+    4        2   -0.477479    0.164725   -4.557617     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "    "    6   0    0    1 C5 0     
+    5        2   -1.629805    0.313812   -3.768718     1 " " X " "    2   0.66500   0.66500 "    " "    " "  n3"    6   0    0    1 C6 0     
+    6       41    1.596617    2.068291   -2.655131     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H9 0     
+    7       41   -0.512566   -0.425110   -5.465153     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H11 0     
+    8       57   -3.089719   -0.467810   -4.250003     1 " " X " "    9  -0.18000  -0.18000 "    " "    " "    "   17   0    0    1 Cl10 0     
+    9        2    0.692442    2.961336   -0.420574     1 " " X " "    2  -0.22090  -0.22090 "    " "    " "  c1"    6   0    0    1 C14 0     
+    10       2    1.756658    2.298492    0.144035     1 " " X " "    2   0.43430   0.43430 "    " "    " "  c3"    6   0    0    1 C15 0     
+    11       2    2.554061    4.434865    0.204489     1 " " X " "    2   0.18590   0.18590 "    " "    " "  n1"    6   0    0    1 C17 0     
+    12      25    2.800280    3.151137    0.504968     1 " " X " "   43  -0.48030  -0.48030 "    " "    " "  c1"    7   0    0    1 N22 0     
+    13      49    0.981665    4.680272   -0.542961     1 " " X " "   13   0.00100   0.00100 "    " "    " "  c1"   16   0    0    1 S18 0     
+    14       2   -0.569685    2.447225   -0.943758     1 " " X " "    2   0.70000   0.70000 "    " "    " "  c1"    6   0    0    1 C19 0     
+    15      15   -1.631124    2.684315   -0.346872     1 " " X " "   70  -0.47000  -0.47000 "    " "    " "  c3"    8   0    0    1 O20 0     
+    16       3    1.965219    0.632264   -4.981755     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C20 0     
+    17      41    1.835800    1.110862   -5.955288     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H21 0     
+    18      41    2.834087    1.068711   -4.491485     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H22 0     
+    19      41    2.170259   -0.427514   -5.147254     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H23 0     
+    20       3    3.515429    5.545135    0.485256     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C23 0     
+    21      41    4.534661    5.158390    0.516459     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H24 0     
+    22      41    3.452578    6.313237   -0.287776     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H25 0     
+    23      41    3.287545    6.005553    1.444841     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H26 0     
+    24      25   -1.638606    1.031981   -2.631126     1 " " X " "   43  -0.67800  -0.67800 "    " "    " "  c1"    7   0    0    1 N25 0     
+    25      16    1.859540    0.953323    0.388405     1 " " X " "   70  -0.58500  -0.58500 "    " "    " "  c1"    8   0    0    1 O25 0     
+    26      42    2.741385    0.785540    0.716768     1 " " X " "   21   0.43500   0.43500 "    " "    " "  n2"    1   0    0    1 H26 0     
+    :::
+  } 
+  m_bond[54] { 
+    # First column is bond index #
+    i_m_from
+    i_m_to
+    i_m_order
+    i_m_from_rep
+    i_m_to_rep
+    :::
+    1          1      2   1 1 1 
+    2          1     14   1 1 1 
+    3          1     24   2 1 1 
+    4          2      1   1 1 1 
+    5          2      3   2 1 1 
+    6          2      6   1 1 1 
+    7          3      2   2 1 1 
+    8          3      4   1 1 1 
+    9          3     16   1 1 1 
+    10         4      3   1 1 1 
+    11         4      5   2 1 1 
+    12         4      7   1 1 1 
+    13         5      4   2 1 1 
+    14         5      8   1 1 1 
+    15         5     24   1 1 1 
+    16         6      2   1 1 1 
+    17         7      4   1 1 1 
+    18         8      5   1 1 1 
+    19         9     10   2 1 1 
+    20         9     13   1 1 1 
+    21         9     14   1 1 1 
+    22        10      9   2 1 1 
+    23        10     12   1 1 1 
+    24        10     25   1 1 1 
+    25        11     12   2 1 1 
+    26        11     13   1 1 1 
+    27        11     20   1 1 1 
+    28        12     10   1 1 1 
+    29        12     11   2 1 1 
+    30        13      9   1 1 1 
+    31        13     11   1 1 1 
+    32        14      1   1 1 1 
+    33        14      9   1 1 1 
+    34        14     15   2 1 1 
+    35        15     14   2 1 1 
+    36        16      3   1 1 1 
+    37        16     17   1 1 1 
+    38        16     18   1 1 1 
+    39        16     19   1 1 1 
+    40        17     16   1 1 1 
+    41        18     16   1 1 1 
+    42        19     16   1 1 1 
+    43        20     11   1 1 1 
+    44        20     21   1 1 1 
+    45        20     22   1 1 1 
+    46        20     23   1 1 1 
+    47        21     20   1 1 1 
+    48        22     20   1 1 1 
+    49        23     20   1 1 1 
+    50        24      1   2 1 1 
+    51        24      5   1 1 1 
+    52        25     10   1 1 1 
+    53        25     26   1 1 1 
+    54        26     25   1 1 1 
+    :::
+  } 
+} 
+
+f_m_ct { 
+  s_m_title
+  s_m_entry_name
+  r_mmod_Potential_Energy-OPLS-2005
+  b_mmod_Minimization_Converged-OPLS-2005
+  r_mmod_RMS_Derivative-OPLS-2005
+  i_mmod_Times_Found-OPLS-2005
+  r_mmod_Relative_Potential_Energy-OPLS-2005
+  i_mmod_Conformation-OPLS-2005
+  s_m_job_name
+  s_m_entry_id
+  :::
+  "" 
+  mmod_csearch.8 
+     -177.446502685547 
+  1     
+    0.0390108413994312 
+  14    
+      12.5073852539062 
+  8     
+  mmod_csearch 
+  8 
+  m_depend[7] { 
+    # First column is dependency index #
+    i_m_depend_dependency
+    s_m_depend_property
+    :::
+    1         20 r_mmod_Potential_Energy-OPLS-2005 
+    2         20 b_mmod_Minimization_Converged-OPLS-2005 
+    3         20 r_mmod_RMS_Derivative-OPLS-2005 
+    4         20 i_mmod_Times_Found-OPLS-2005 
+    5         20 r_mmod_Relative_Potential_Energy-OPLS-2005 
+    6         20 i_mmod_Conformation-OPLS-2005 
+    7         30 s_m_job_name 
+    :::
+  } 
+  m_atom[26] { 
+    # First column is atom index #
+    i_m_mmod_type
+    r_m_x_coord
+    r_m_y_coord
+    r_m_z_coord
+    i_m_residue_number
+    s_m_insertion_code
+    s_m_mmod_res
+    s_m_chain_name
+    i_m_color
+    r_m_charge1
+    r_m_charge2
+    s_m_pdb_residue_name
+    s_m_pdb_atom_name
+    s_m_grow_name
+    i_m_atomic_number
+    i_m_formal_charge
+    i_m_representation
+    i_m_visibility
+    s_m_atom_name
+    i_m_template_index
+    :::
+    1        2   -0.351380    1.883809   -2.378188     1 " " X " "    2   0.37000   0.37000 "    " "    " "  f1"    6   0    0    1 C2 0     
+    2        2    0.809806    1.506223   -3.091108     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "  c3"    6   0    0    1 C3 0     
+    3        2    0.758510    0.393016   -3.947519     1 " " X " "    2   0.17700   0.17700 "    " "    " "  c1"    6   0    0    1 C4 0     
+    4        2   -0.455516   -0.303655   -4.058286     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "    "    6   0    0    1 C5 0     
+    5        2   -1.567818    0.138412   -3.324532     1 " " X " "    2   0.66500   0.66500 "    " "    " "  n3"    6   0    0    1 C6 0     
+    6       41    1.721011    2.086685   -3.010063     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H9 0     
+    7       41   -0.546642   -1.164928   -4.705018     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H11 0     
+    8       57   -3.061079   -0.711348   -3.468056     1 " " X " "    9  -0.18000  -0.18000 "    " "    " "    "   17   0    0    1 Cl10 0     
+    9        2    0.836723    3.242118   -0.601442     1 " " X " "    2  -0.22090  -0.22090 "    " "    " "  c1"    6   0    0    1 C14 0     
+    10       2    1.771745    2.351568   -0.112074     1 " " X " "    2   0.43430   0.43430 "    " "    " "  c3"    6   0    0    1 C15 0     
+    11       2    2.535289    4.262452    0.866003     1 " " X " "    2   0.18590   0.18590 "    " "    " "  n1"    6   0    0    1 C17 0     
+    12      25    2.723150    2.948302    0.718501     1 " " X " "   43  -0.48030  -0.48030 "    " "    " "  c1"    7   0    0    1 N22 0     
+    13      49    1.141845    4.863292   -0.017745     1 " " X " "   13   0.00100   0.00100 "    " "    " "  c1"   16   0    0    1 S18 0     
+    14       2   -0.338250    3.068119   -1.466881     1 " " X " "    2   0.70000   0.70000 "    " "    " "  c1"    6   0    0    1 C19 0     
+    15      15   -1.288120    3.862137   -1.418520     1 " " X " "   70  -0.47000  -0.47000 "    " "    " "  c3"    8   0    0    1 O20 0     
+    16       3    1.976651   -0.037107   -4.738457     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C20 0     
+    17      41    1.992557    0.460622   -5.708064     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H21 0     
+    18      41    2.895824    0.215389   -4.209352     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H22 0     
+    19      41    1.972288   -1.114258   -4.906909     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H23 0     
+    20       3    3.415944    5.130000    1.697111     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C23 0     
+    21      41    4.414188    5.177618    1.262384     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H24 0     
+    22      41    3.011534    6.140772    1.750588     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H25 0     
+    23      41    3.490827    4.732372    2.709130     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H26 0     
+    24      25   -1.518010    1.206470   -2.504546     1 " " X " "   43  -0.67800  -0.67800 "    " "    " "  c1"    7   0    0    1 N25 0     
+    25      16    1.856357    1.001859   -0.319590     1 " " X " "   70  -0.58500  -0.58500 "    " "    " "  c1"    8   0    0    1 O25 0     
+    26      42    1.492016    0.807006   -1.177194     1 " " X " "   21   0.43500   0.43500 "    " "    " "  n2"    1   0    0    1 H26 0     
+    :::
+  } 
+  m_bond[54] { 
+    # First column is bond index #
+    i_m_from
+    i_m_to
+    i_m_order
+    i_m_from_rep
+    i_m_to_rep
+    :::
+    1          1      2   1 1 1 
+    2          1     14   1 1 1 
+    3          1     24   2 1 1 
+    4          2      1   1 1 1 
+    5          2      3   2 1 1 
+    6          2      6   1 1 1 
+    7          3      2   2 1 1 
+    8          3      4   1 1 1 
+    9          3     16   1 1 1 
+    10         4      3   1 1 1 
+    11         4      5   2 1 1 
+    12         4      7   1 1 1 
+    13         5      4   2 1 1 
+    14         5      8   1 1 1 
+    15         5     24   1 1 1 
+    16         6      2   1 1 1 
+    17         7      4   1 1 1 
+    18         8      5   1 1 1 
+    19         9     10   2 1 1 
+    20         9     13   1 1 1 
+    21         9     14   1 1 1 
+    22        10      9   2 1 1 
+    23        10     12   1 1 1 
+    24        10     25   1 1 1 
+    25        11     12   2 1 1 
+    26        11     13   1 1 1 
+    27        11     20   1 1 1 
+    28        12     10   1 1 1 
+    29        12     11   2 1 1 
+    30        13      9   1 1 1 
+    31        13     11   1 1 1 
+    32        14      1   1 1 1 
+    33        14      9   1 1 1 
+    34        14     15   2 1 1 
+    35        15     14   2 1 1 
+    36        16      3   1 1 1 
+    37        16     17   1 1 1 
+    38        16     18   1 1 1 
+    39        16     19   1 1 1 
+    40        17     16   1 1 1 
+    41        18     16   1 1 1 
+    42        19     16   1 1 1 
+    43        20     11   1 1 1 
+    44        20     21   1 1 1 
+    45        20     22   1 1 1 
+    46        20     23   1 1 1 
+    47        21     20   1 1 1 
+    48        22     20   1 1 1 
+    49        23     20   1 1 1 
+    50        24      1   2 1 1 
+    51        24      5   1 1 1 
+    52        25     10   1 1 1 
+    53        25     26   1 1 1 
+    54        26     25   1 1 1 
+    :::
+  } 
+} 
+
+f_m_ct { 
+  s_m_title
+  s_m_entry_name
+  r_mmod_Potential_Energy-OPLS-2005
+  b_mmod_Minimization_Converged-OPLS-2005
+  r_mmod_RMS_Derivative-OPLS-2005
+  i_mmod_Times_Found-OPLS-2005
+  r_mmod_Relative_Potential_Energy-OPLS-2005
+  i_mmod_Conformation-OPLS-2005
+  s_m_job_name
+  s_m_entry_id
+  :::
+  "" 
+  mmod_csearch.9 
+     -177.424072265625 
+  0     
+     0.081668309867382 
+  12    
+      12.5298156738281 
+  9     
+  mmod_csearch 
+  9 
+  m_depend[7] { 
+    # First column is dependency index #
+    i_m_depend_dependency
+    s_m_depend_property
+    :::
+    1         20 r_mmod_Potential_Energy-OPLS-2005 
+    2         20 b_mmod_Minimization_Converged-OPLS-2005 
+    3         20 r_mmod_RMS_Derivative-OPLS-2005 
+    4         20 i_mmod_Times_Found-OPLS-2005 
+    5         20 r_mmod_Relative_Potential_Energy-OPLS-2005 
+    6         20 i_mmod_Conformation-OPLS-2005 
+    7         30 s_m_job_name 
+    :::
+  } 
+  m_atom[26] { 
+    # First column is atom index #
+    i_m_mmod_type
+    r_m_x_coord
+    r_m_y_coord
+    r_m_z_coord
+    i_m_residue_number
+    s_m_insertion_code
+    s_m_mmod_res
+    s_m_chain_name
+    i_m_color
+    r_m_charge1
+    r_m_charge2
+    s_m_pdb_residue_name
+    s_m_pdb_atom_name
+    s_m_grow_name
+    i_m_atomic_number
+    i_m_formal_charge
+    i_m_representation
+    i_m_visibility
+    s_m_atom_name
+    i_m_template_index
+    :::
+    1        2    0.832070    1.584627   -2.750743     1 " " X " "    2   0.37000   0.37000 "    " "    " "  f1"    6   0    0    1 C2 0     
+    2        2   -0.553806    1.850629   -2.662395     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "  c3"    6   0    0    1 C3 0     
+    3        2   -1.464010    0.954474   -3.248886     1 " " X " "    2   0.17700   0.17700 "    " "    " "  c1"    6   0    0    1 C4 0     
+    4        2   -0.952588   -0.178123   -3.902349     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "    "    6   0    0    1 C5 0     
+    5        2    0.437360   -0.368467   -3.955504     1 " " X " "    2   0.66500   0.66500 "    " "    " "  n3"    6   0    0    1 C6 0     
+    6       41   -0.913588    2.752430   -2.181595     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H9 0     
+    7       41   -1.611312   -0.895794   -4.370723     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H11 0     
+    8       57    1.065492   -1.754394   -4.766256     1 " " X " "    9  -0.18000  -0.18000 "    " "    " "    "   17   0    0    1 Cl10 0     
+    9        2    1.529316    3.067376   -0.819578     1 " " X " "    2  -0.22090  -0.22090 "    " "    " "  c1"    6   0    0    1 C14 0     
+    10       2    0.734752    2.613830    0.214697     1 " " X " "    2   0.43430   0.43430 "    " "    " "  c3"    6   0    0    1 C15 0     
+    11       2    1.546636    4.512086    1.178425     1 " " X " "    2   0.18590   0.18590 "    " "    " "  n1"    6   0    0    1 C17 0     
+    12      25    0.759876    3.444453    1.337445     1 " " X " "   43  -0.48030  -0.48030 "    " "    " "  c1"    7   0    0    1 N22 0     
+    13      49    2.330391    4.563262   -0.392123     1 " " X " "   13   0.00100   0.00100 "    " "    " "  c1"   16   0    0    1 S18 0     
+    14       2    1.830482    2.520361   -2.149963     1 " " X " "    2   0.70000   0.70000 "    " "    " "  c1"    6   0    0    1 C19 0     
+    15      15    2.885047    2.808181   -2.733152     1 " " X " "   70  -0.47000  -0.47000 "    " "    " "  c3"    8   0    0    1 O20 0     
+    16       3   -2.956113    1.208405   -3.188426     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C20 0     
+    17      41   -3.508807    0.270007   -3.137525     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H21 0     
+    18      41   -3.218453    1.799627   -2.310765     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H22 0     
+    19      41   -3.283253    1.750339   -4.075812     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H23 0     
+    20       3    1.740999    5.553403    2.225818     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C23 0     
+    21      41    2.593060    6.186192    1.977480     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H24 0     
+    22      41    0.852351    6.179845    2.300372     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H25 0     
+    23      41    1.925966    5.087497    3.193662     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H26 0     
+    24      25    1.309312    0.491808   -3.394053     1 " " X " "   43  -0.67800  -0.67800 "    " "    " "  c1"    7   0    0    1 N25 0     
+    25      16   -0.025069    1.477545    0.273216     1 " " X " "   70  -0.58500  -0.58500 "    " "    " "  c1"    8   0    0    1 O25 0     
+    26      42   -0.312282    1.263214   -0.608694     1 " " X " "   21   0.43500   0.43500 "    " "    " "  n2"    1   0    0    1 H26 0     
+    :::
+  } 
+  m_bond[54] { 
+    # First column is bond index #
+    i_m_from
+    i_m_to
+    i_m_order
+    i_m_from_rep
+    i_m_to_rep
+    :::
+    1          1      2   1 1 1 
+    2          1     14   1 1 1 
+    3          1     24   2 1 1 
+    4          2      1   1 1 1 
+    5          2      3   2 1 1 
+    6          2      6   1 1 1 
+    7          3      2   2 1 1 
+    8          3      4   1 1 1 
+    9          3     16   1 1 1 
+    10         4      3   1 1 1 
+    11         4      5   2 1 1 
+    12         4      7   1 1 1 
+    13         5      4   2 1 1 
+    14         5      8   1 1 1 
+    15         5     24   1 1 1 
+    16         6      2   1 1 1 
+    17         7      4   1 1 1 
+    18         8      5   1 1 1 
+    19         9     10   2 1 1 
+    20         9     13   1 1 1 
+    21         9     14   1 1 1 
+    22        10      9   2 1 1 
+    23        10     12   1 1 1 
+    24        10     25   1 1 1 
+    25        11     12   2 1 1 
+    26        11     13   1 1 1 
+    27        11     20   1 1 1 
+    28        12     10   1 1 1 
+    29        12     11   2 1 1 
+    30        13      9   1 1 1 
+    31        13     11   1 1 1 
+    32        14      1   1 1 1 
+    33        14      9   1 1 1 
+    34        14     15   2 1 1 
+    35        15     14   2 1 1 
+    36        16      3   1 1 1 
+    37        16     17   1 1 1 
+    38        16     18   1 1 1 
+    39        16     19   1 1 1 
+    40        17     16   1 1 1 
+    41        18     16   1 1 1 
+    42        19     16   1 1 1 
+    43        20     11   1 1 1 
+    44        20     21   1 1 1 
+    45        20     22   1 1 1 
+    46        20     23   1 1 1 
+    47        21     20   1 1 1 
+    48        22     20   1 1 1 
+    49        23     20   1 1 1 
+    50        24      1   2 1 1 
+    51        24      5   1 1 1 
+    52        25     10   1 1 1 
+    53        25     26   1 1 1 
+    54        26     25   1 1 1 
+    :::
+  } 
+} 
+
+f_m_ct { 
+  s_m_title
+  s_m_entry_name
+  r_mmod_Potential_Energy-OPLS-2005
+  b_mmod_Minimization_Converged-OPLS-2005
+  r_mmod_RMS_Derivative-OPLS-2005
+  i_mmod_Times_Found-OPLS-2005
+  r_mmod_Relative_Potential_Energy-OPLS-2005
+  i_mmod_Conformation-OPLS-2005
+  s_m_job_name
+  s_m_entry_id
+  :::
+  "" 
+  mmod_csearch.10 
+     -175.367752075195 
+  0     
+      1.88610029220581 
+  1     
+      14.5861358642578 
+  10    
+  mmod_csearch 
+  10 
+  m_depend[7] { 
+    # First column is dependency index #
+    i_m_depend_dependency
+    s_m_depend_property
+    :::
+    1         20 r_mmod_Potential_Energy-OPLS-2005 
+    2         20 b_mmod_Minimization_Converged-OPLS-2005 
+    3         20 r_mmod_RMS_Derivative-OPLS-2005 
+    4         20 i_mmod_Times_Found-OPLS-2005 
+    5         20 r_mmod_Relative_Potential_Energy-OPLS-2005 
+    6         20 i_mmod_Conformation-OPLS-2005 
+    7         30 s_m_job_name 
+    :::
+  } 
+  m_atom[26] { 
+    # First column is atom index #
+    i_m_mmod_type
+    r_m_x_coord
+    r_m_y_coord
+    r_m_z_coord
+    i_m_residue_number
+    s_m_insertion_code
+    s_m_mmod_res
+    s_m_chain_name
+    i_m_color
+    r_m_charge1
+    r_m_charge2
+    s_m_pdb_residue_name
+    s_m_pdb_atom_name
+    s_m_grow_name
+    i_m_atomic_number
+    i_m_formal_charge
+    i_m_representation
+    i_m_visibility
+    s_m_atom_name
+    i_m_template_index
+    :::
+    1        2   -0.399684    1.306140   -2.115241     1 " " X " "    2   0.37000   0.37000 "    " "    " "  f1"    6   0    0    1 C2 0     
+    2        2    0.601349    1.611990   -3.068706     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "  c3"    6   0    0    1 C3 0     
+    3        2    0.406459    1.254396   -4.413370     1 " " X " "    2   0.17700   0.17700 "    " "    " "  c1"    6   0    0    1 C4 0     
+    4        2   -0.788262    0.603841   -4.761883     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "    "    6   0    0    1 C5 0     
+    5        2   -1.734032    0.333705   -3.762150     1 " " X " "    2   0.66500   0.66500 "    " "    " "  n3"    6   0    0    1 C6 0     
+    6       41    1.516496    2.109656   -2.775632     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H9 0     
+    7       41   -0.986975    0.308211   -5.782819     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H11 0     
+    8       57   -3.203487   -0.461824   -4.188094     1 " " X " "    9  -0.18000  -0.18000 "    " "    " "    "   17   0    0    1 Cl10 0     
+    9        2    0.828319    2.589130   -0.323566     1 " " X " "    2  -0.22090  -0.22090 "    " "    " "  c1"    6   0    0    1 C14 0     
+    10       2    2.048814    2.368307    0.261281     1 " " X " "    2   0.43430   0.43430 "    " "    " "  c3"    6   0    0    1 C15 0     
+    11       2    2.178233    4.616218   -0.044112     1 " " X " "    2   0.18590   0.18590 "    " "    " "  n1"    6   0    0    1 C17 0     
+    12      25    2.809842    3.527593    0.412933     1 " " X " "   43  -0.48030  -0.48030 "    " "    " "  c1"    7   0    0    1 N22 0     
+    13      49    0.582255    4.273344   -0.699875     1 " " X " "   13   0.00100   0.00100 "    " "    " "  c1"   16   0    0    1 S18 0     
+    14       2   -0.239476    1.658927   -0.665288     1 " " X " "    2   0.70000   0.70000 "    " "    " "  c1"    6   0    0    1 C19 0     
+    15      15   -0.978207    1.205666    0.219643     1 " " X " "   70  -0.47000  -0.47000 "    " "    " "  c3"    8   0    0    1 O20 0     
+    16       3    1.463071    1.551745   -5.458026     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C20 0     
+    17      41    1.007406    1.910381   -6.381659     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H21 0     
+    18      41    2.161001    2.313924   -5.109032     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H22 0     
+    19      41    2.029668    0.648308   -5.685297     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H23 0     
+    20       3    2.759526    5.985773   -0.006072     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C23 0     
+    21      41    2.207816    6.604226    0.702064     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H24 0     
+    22      41    3.806620    5.953697    0.297070     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H25 0     
+    23      41    2.695681    6.442727   -0.993360     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H26 0     
+    24      25   -1.544306    0.672080   -2.472743     1 " " X " "   43  -0.67800  -0.67800 "    " "    " "  c1"    7   0    0    1 N25 0     
+    25      16    2.550189    1.168890    0.674031     1 " " X " "   70  -0.58500  -0.58500 "    " "    " "  c1"    8   0    0    1 O25 0     
+    26      42    3.397262    1.346749    1.068713     1 " " X " "   21   0.43500   0.43500 "    " "    " "  n2"    1   0    0    1 H26 0     
+    :::
+  } 
+  m_bond[54] { 
+    # First column is bond index #
+    i_m_from
+    i_m_to
+    i_m_order
+    i_m_from_rep
+    i_m_to_rep
+    :::
+    1          1      2   1 1 1 
+    2          1     14   1 1 1 
+    3          1     24   2 1 1 
+    4          2      1   1 1 1 
+    5          2      3   2 1 1 
+    6          2      6   1 1 1 
+    7          3      2   2 1 1 
+    8          3      4   1 1 1 
+    9          3     16   1 1 1 
+    10         4      3   1 1 1 
+    11         4      5   2 1 1 
+    12         4      7   1 1 1 
+    13         5      4   2 1 1 
+    14         5      8   1 1 1 
+    15         5     24   1 1 1 
+    16         6      2   1 1 1 
+    17         7      4   1 1 1 
+    18         8      5   1 1 1 
+    19         9     10   2 1 1 
+    20         9     13   1 1 1 
+    21         9     14   1 1 1 
+    22        10      9   2 1 1 
+    23        10     12   1 1 1 
+    24        10     25   1 1 1 
+    25        11     12   2 1 1 
+    26        11     13   1 1 1 
+    27        11     20   1 1 1 
+    28        12     10   1 1 1 
+    29        12     11   2 1 1 
+    30        13      9   1 1 1 
+    31        13     11   1 1 1 
+    32        14      1   1 1 1 
+    33        14      9   1 1 1 
+    34        14     15   2 1 1 
+    35        15     14   2 1 1 
+    36        16      3   1 1 1 
+    37        16     17   1 1 1 
+    38        16     18   1 1 1 
+    39        16     19   1 1 1 
+    40        17     16   1 1 1 
+    41        18     16   1 1 1 
+    42        19     16   1 1 1 
+    43        20     11   1 1 1 
+    44        20     21   1 1 1 
+    45        20     22   1 1 1 
+    46        20     23   1 1 1 
+    47        21     20   1 1 1 
+    48        22     20   1 1 1 
+    49        23     20   1 1 1 
+    50        24      1   2 1 1 
+    51        24      5   1 1 1 
+    52        25     10   1 1 1 
+    53        25     26   1 1 1 
+    54        26     25   1 1 1 
+    :::
+  } 
+} 
+
+f_m_ct { 
+  s_m_title
+  s_m_entry_name
+  r_mmod_Potential_Energy-OPLS-2005
+  b_mmod_Minimization_Converged-OPLS-2005
+  r_mmod_RMS_Derivative-OPLS-2005
+  i_mmod_Times_Found-OPLS-2005
+  r_mmod_Relative_Potential_Energy-OPLS-2005
+  i_mmod_Conformation-OPLS-2005
+  s_m_job_name
+  s_m_entry_id
+  :::
+  "" 
+  mmod_csearch.11 
+     -170.199645996094 
+  1     
+    0.0474016517400742 
+  6     
+      19.7542419433594 
+  11    
+  mmod_csearch 
+  11 
+  m_depend[7] { 
+    # First column is dependency index #
+    i_m_depend_dependency
+    s_m_depend_property
+    :::
+    1         20 r_mmod_Potential_Energy-OPLS-2005 
+    2         20 b_mmod_Minimization_Converged-OPLS-2005 
+    3         20 r_mmod_RMS_Derivative-OPLS-2005 
+    4         20 i_mmod_Times_Found-OPLS-2005 
+    5         20 r_mmod_Relative_Potential_Energy-OPLS-2005 
+    6         20 i_mmod_Conformation-OPLS-2005 
+    7         30 s_m_job_name 
+    :::
+  } 
+  m_atom[26] { 
+    # First column is atom index #
+    i_m_mmod_type
+    r_m_x_coord
+    r_m_y_coord
+    r_m_z_coord
+    i_m_residue_number
+    s_m_insertion_code
+    s_m_mmod_res
+    s_m_chain_name
+    i_m_color
+    r_m_charge1
+    r_m_charge2
+    s_m_pdb_residue_name
+    s_m_pdb_atom_name
+    s_m_grow_name
+    i_m_atomic_number
+    i_m_formal_charge
+    i_m_representation
+    i_m_visibility
+    s_m_atom_name
+    i_m_template_index
+    :::
+    1        2    0.071694    1.051899   -2.232556     1 " " X " "    2   0.37000   0.37000 "    " "    " "  f1"    6   0    0    1 C2 0     
+    2        2    0.385295    1.896279   -3.321898     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "  c3"    6   0    0    1 C3 0     
+    3        2   -0.369402    1.805612   -4.503024     1 " " X " "    2   0.17700   0.17700 "    " "    " "  c1"    6   0    0    1 C4 0     
+    4        2   -1.405185    0.859105   -4.557679     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "    "    6   0    0    1 C5 0     
+    5        2   -1.644822    0.043846   -3.440134     1 " " X " "    2   0.66500   0.66500 "    " "    " "  n3"    6   0    0    1 C6 0     
+    6       41    1.201127    2.603989   -3.248762     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H9 0     
+    7       41   -2.012521    0.747450   -5.444757     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H11 0     
+    8       57   -2.911371   -1.123854   -3.509130     1 " " X " "    9  -0.18000  -0.18000 "    " "    " "    "   17   0    0    1 Cl10 0     
+    9        2    1.283824    2.408279   -0.444954     1 " " X " "    2  -0.22090  -0.22090 "    " "    " "  c1"    6   0    0    1 C14 0     
+    10       2    2.411385    2.758193    0.260672     1 " " X " "    2   0.43430   0.43430 "    " "    " "  c3"    6   0    0    1 C15 0     
+    11       2    1.377436    4.785208    0.201612     1 " " X " "    2   0.18590   0.18590 "    " "    " "  n1"    6   0    0    1 C17 0     
+    12      25    2.459193    4.111536    0.604062     1 " " X " "   43  -0.48030  -0.48030 "    " "    " "  c1"    7   0    0    1 N22 0     
+    13      49    0.210445    3.778539   -0.643144     1 " " X " "   13   0.00100   0.00100 "    " "    " "  c1"   16   0    0    1 S18 0     
+    14       2    0.867593    1.101627   -0.966067     1 " " X " "    2   0.70000   0.70000 "    " "    " "  c1"    6   0    0    1 C19 0     
+    15      15    1.192370    0.072014   -0.360081     1 " " X " "   70  -0.47000  -0.47000 "    " "    " "  c3"    8   0    0    1 O20 0     
+    16       3   -0.066991    2.698598   -5.688330     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C20 0     
+    17      41   -0.963513    2.876958   -6.282562     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H21 0     
+    18      41    0.315037    3.665556   -5.360120     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H22 0     
+    19      41    0.682083    2.234574   -6.330000     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H23 0     
+    20       3    1.178274    6.241206    0.445077     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C23 0     
+    21      41    1.439687    6.493294    1.472761     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H24 0     
+    22      41    1.805103    6.822710   -0.230655     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H25 0     
+    23      41    0.136796    6.514395    0.275529     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H26 0     
+    24      25   -0.922787    0.133317   -2.306188     1 " " X " "   43  -0.67800  -0.67800 "    " "    " "  c1"    7   0    0    1 N25 0     
+    25      16    3.444467    1.945858    0.637896     1 " " X " "   70  -0.58500  -0.58500 "    " "    " "  c1"    8   0    0    1 O25 0     
+    26      42    3.176445    1.045410    0.481342     1 " " X " "   21   0.43500   0.43500 "    " "    " "  n2"    1   0    0    1 H26 0     
+    :::
+  } 
+  m_bond[54] { 
+    # First column is bond index #
+    i_m_from
+    i_m_to
+    i_m_order
+    i_m_from_rep
+    i_m_to_rep
+    :::
+    1          1      2   1 1 1 
+    2          1     14   1 1 1 
+    3          1     24   2 1 1 
+    4          2      1   1 1 1 
+    5          2      3   2 1 1 
+    6          2      6   1 1 1 
+    7          3      2   2 1 1 
+    8          3      4   1 1 1 
+    9          3     16   1 1 1 
+    10         4      3   1 1 1 
+    11         4      5   2 1 1 
+    12         4      7   1 1 1 
+    13         5      4   2 1 1 
+    14         5      8   1 1 1 
+    15         5     24   1 1 1 
+    16         6      2   1 1 1 
+    17         7      4   1 1 1 
+    18         8      5   1 1 1 
+    19         9     10   2 1 1 
+    20         9     13   1 1 1 
+    21         9     14   1 1 1 
+    22        10      9   2 1 1 
+    23        10     12   1 1 1 
+    24        10     25   1 1 1 
+    25        11     12   2 1 1 
+    26        11     13   1 1 1 
+    27        11     20   1 1 1 
+    28        12     10   1 1 1 
+    29        12     11   2 1 1 
+    30        13      9   1 1 1 
+    31        13     11   1 1 1 
+    32        14      1   1 1 1 
+    33        14      9   1 1 1 
+    34        14     15   2 1 1 
+    35        15     14   2 1 1 
+    36        16      3   1 1 1 
+    37        16     17   1 1 1 
+    38        16     18   1 1 1 
+    39        16     19   1 1 1 
+    40        17     16   1 1 1 
+    41        18     16   1 1 1 
+    42        19     16   1 1 1 
+    43        20     11   1 1 1 
+    44        20     21   1 1 1 
+    45        20     22   1 1 1 
+    46        20     23   1 1 1 
+    47        21     20   1 1 1 
+    48        22     20   1 1 1 
+    49        23     20   1 1 1 
+    50        24      1   2 1 1 
+    51        24      5   1 1 1 
+    52        25     10   1 1 1 
+    53        25     26   1 1 1 
+    54        26     25   1 1 1 
+    :::
+  } 
+} 
+
+f_m_ct { 
+  s_m_title
+  s_m_entry_name
+  r_mmod_Potential_Energy-OPLS-2005
+  b_mmod_Minimization_Converged-OPLS-2005
+  r_mmod_RMS_Derivative-OPLS-2005
+  i_mmod_Times_Found-OPLS-2005
+  r_mmod_Relative_Potential_Energy-OPLS-2005
+  i_mmod_Conformation-OPLS-2005
+  s_m_job_name
+  s_m_entry_id
+  :::
+  "" 
+  mmod_csearch.12 
+     -170.198547363281 
+  1     
+    0.0486599691212177 
+  7     
+      19.7553405761719 
+  12    
+  mmod_csearch 
+  12 
+  m_depend[7] { 
+    # First column is dependency index #
+    i_m_depend_dependency
+    s_m_depend_property
+    :::
+    1         20 r_mmod_Potential_Energy-OPLS-2005 
+    2         20 b_mmod_Minimization_Converged-OPLS-2005 
+    3         20 r_mmod_RMS_Derivative-OPLS-2005 
+    4         20 i_mmod_Times_Found-OPLS-2005 
+    5         20 r_mmod_Relative_Potential_Energy-OPLS-2005 
+    6         20 i_mmod_Conformation-OPLS-2005 
+    7         30 s_m_job_name 
+    :::
+  } 
+  m_atom[26] { 
+    # First column is atom index #
+    i_m_mmod_type
+    r_m_x_coord
+    r_m_y_coord
+    r_m_z_coord
+    i_m_residue_number
+    s_m_insertion_code
+    s_m_mmod_res
+    s_m_chain_name
+    i_m_color
+    r_m_charge1
+    r_m_charge2
+    s_m_pdb_residue_name
+    s_m_pdb_atom_name
+    s_m_grow_name
+    i_m_atomic_number
+    i_m_formal_charge
+    i_m_representation
+    i_m_visibility
+    s_m_atom_name
+    i_m_template_index
+    :::
+    1        2   -0.159087    1.223987   -2.228355     1 " " X " "    2   0.37000   0.37000 "    " "    " "  f1"    6   0    0    1 C2 0     
+    2        2    0.520994    1.796266   -3.327407     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "  c3"    6   0    0    1 C3 0     
+    3        2    0.615599    1.076114   -4.529570     1 " " X " "    2   0.17700   0.17700 "    " "    " "  c1"    6   0    0    1 C4 0     
+    4        2    0.010197   -0.189253   -4.594483     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "    "    6   0    0    1 C5 0     
+    5        2   -0.663096   -0.682762   -3.465689     1 " " X " "    2   0.66500   0.66500 "    " "    " "  n3"    6   0    0    1 C6 0     
+    6       41    0.962821    2.781066   -3.245346     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H9 0     
+    7       41    0.051269   -0.781748   -5.497527     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H11 0     
+    8       57   -1.413036   -2.233037   -3.546884     1 " " X " "    9  -0.18000  -0.18000 "    " "    " "    "   17   0    0    1 Cl10 0     
+    9        2    0.846929    2.731981   -0.434328     1 " " X " "    2  -0.22090  -0.22090 "    " "    " "  c1"    6   0    0    1 C14 0     
+    10       2    0.879427    3.891829    0.304247     1 " " X " "    2   0.43430   0.43430 "    " "    " "  c3"    6   0    0    1 C15 0     
+    11       2    3.115811    3.495457    0.153832     1 " " X " "    2   0.18590   0.18590 "    " "    " "  n1"    6   0    0    1 C17 0     
+    12      25    2.171957    4.321705    0.614605     1 " " X " "   43  -0.48030  -0.48030 "    " "    " "  c1"    7   0    0    1 N22 0     
+    13      49    2.461728    2.109568   -0.706557     1 " " X " "   13   0.00100   0.00100 "    " "    " "  c1"   16   0    0    1 S18 0     
+    14       2   -0.300433    1.969011   -0.938063     1 " " X " "    2   0.70000   0.70000 "    " "    " "  c1"    6   0    0    1 C19 0     
+    15      15   -1.360001    1.967212   -0.297645     1 " " X " "   70  -0.47000  -0.47000 "    " "    " "  c3"    8   0    0    1 O20 0     
+    16       3    1.343783    1.654272   -5.725140     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C20 0     
+    17      41    1.724088    0.863751   -6.372525     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H21 0     
+    18      41    0.671641    2.281927   -6.310309     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H22 0     
+    19      41    2.190548    2.262983   -5.407103     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H23 0     
+    20       3    4.574327    3.722076    0.354028     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C23 0     
+    21      41    4.810533    3.734897    1.417910     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H24 0     
+    22      41    5.150384    2.927494   -0.120175     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H25 0     
+    23      41    4.870728    4.674794   -0.084469     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H26 0     
+    24      25   -0.750534    0.006834   -2.311553     1 " " X " "   43  -0.67800  -0.67800 "    " "    " "  c1"    7   0    0    1 N25 0     
+    25      16   -0.183832    4.632383    0.740828     1 " " X " "   70  -0.58500  -0.58500 "    " "    " "  c1"    8   0    0    1 O25 0     
+    26      42   -0.972869    4.119030    0.595611     1 " " X " "   21   0.43500   0.43500 "    " "    " "  n2"    1   0    0    1 H26 0     
+    :::
+  } 
+  m_bond[54] { 
+    # First column is bond index #
+    i_m_from
+    i_m_to
+    i_m_order
+    i_m_from_rep
+    i_m_to_rep
+    :::
+    1          1      2   1 1 1 
+    2          1     14   1 1 1 
+    3          1     24   2 1 1 
+    4          2      1   1 1 1 
+    5          2      3   2 1 1 
+    6          2      6   1 1 1 
+    7          3      2   2 1 1 
+    8          3      4   1 1 1 
+    9          3     16   1 1 1 
+    10         4      3   1 1 1 
+    11         4      5   2 1 1 
+    12         4      7   1 1 1 
+    13         5      4   2 1 1 
+    14         5      8   1 1 1 
+    15         5     24   1 1 1 
+    16         6      2   1 1 1 
+    17         7      4   1 1 1 
+    18         8      5   1 1 1 
+    19         9     10   2 1 1 
+    20         9     13   1 1 1 
+    21         9     14   1 1 1 
+    22        10      9   2 1 1 
+    23        10     12   1 1 1 
+    24        10     25   1 1 1 
+    25        11     12   2 1 1 
+    26        11     13   1 1 1 
+    27        11     20   1 1 1 
+    28        12     10   1 1 1 
+    29        12     11   2 1 1 
+    30        13      9   1 1 1 
+    31        13     11   1 1 1 
+    32        14      1   1 1 1 
+    33        14      9   1 1 1 
+    34        14     15   2 1 1 
+    35        15     14   2 1 1 
+    36        16      3   1 1 1 
+    37        16     17   1 1 1 
+    38        16     18   1 1 1 
+    39        16     19   1 1 1 
+    40        17     16   1 1 1 
+    41        18     16   1 1 1 
+    42        19     16   1 1 1 
+    43        20     11   1 1 1 
+    44        20     21   1 1 1 
+    45        20     22   1 1 1 
+    46        20     23   1 1 1 
+    47        21     20   1 1 1 
+    48        22     20   1 1 1 
+    49        23     20   1 1 1 
+    50        24      1   2 1 1 
+    51        24      5   1 1 1 
+    52        25     10   1 1 1 
+    53        25     26   1 1 1 
+    54        26     25   1 1 1 
+    :::
+  } 
+} 
+
+f_m_ct { 
+  s_m_title
+  s_m_entry_name
+  r_mmod_Potential_Energy-OPLS-2005
+  b_mmod_Minimization_Converged-OPLS-2005
+  r_mmod_RMS_Derivative-OPLS-2005
+  i_mmod_Times_Found-OPLS-2005
+  r_mmod_Relative_Potential_Energy-OPLS-2005
+  i_mmod_Conformation-OPLS-2005
+  s_m_job_name
+  s_m_entry_id
+  :::
+  "" 
+  mmod_csearch.13 
+     -170.071914672852 
+  1     
+     0.035539023578167 
+  3     
+      19.8819732666016 
+  13    
+  mmod_csearch 
+  13 
+  m_depend[7] { 
+    # First column is dependency index #
+    i_m_depend_dependency
+    s_m_depend_property
+    :::
+    1         20 r_mmod_Potential_Energy-OPLS-2005 
+    2         20 b_mmod_Minimization_Converged-OPLS-2005 
+    3         20 r_mmod_RMS_Derivative-OPLS-2005 
+    4         20 i_mmod_Times_Found-OPLS-2005 
+    5         20 r_mmod_Relative_Potential_Energy-OPLS-2005 
+    6         20 i_mmod_Conformation-OPLS-2005 
+    7         30 s_m_job_name 
+    :::
+  } 
+  m_atom[26] { 
+    # First column is atom index #
+    i_m_mmod_type
+    r_m_x_coord
+    r_m_y_coord
+    r_m_z_coord
+    i_m_residue_number
+    s_m_insertion_code
+    s_m_mmod_res
+    s_m_chain_name
+    i_m_color
+    r_m_charge1
+    r_m_charge2
+    s_m_pdb_residue_name
+    s_m_pdb_atom_name
+    s_m_grow_name
+    i_m_atomic_number
+    i_m_formal_charge
+    i_m_representation
+    i_m_visibility
+    s_m_atom_name
+    i_m_template_index
+    :::
+    1        2    0.227912    1.693951   -2.781976     1 " " X " "    2   0.37000   0.37000 "    " "    " "  f1"    6   0    0    1 C2 0     
+    2        2    0.322570    1.568399   -4.185273     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "  c3"    6   0    0    1 C3 0     
+    3        2    0.014691    0.338593   -4.790274     1 " " X " "    2   0.17700   0.17700 "    " "    " "  c1"    6   0    0    1 C4 0     
+    4        2   -0.384095   -0.725264   -3.964783     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "    "    6   0    0    1 C5 0     
+    5        2   -0.467914   -0.519028   -2.578599     1 " " X " "    2   0.66500   0.66500 "    " "    " "  n3"    6   0    0    1 C6 0     
+    6       41    0.632395    2.414845   -4.785410     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H9 0     
+    7       41   -0.628478   -1.692773   -4.380033     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H11 0     
+    8       57   -0.962472   -1.821677   -1.563451     1 " " X " "    9  -0.18000  -0.18000 "    " "    " "    "   17   0    0    1 Cl10 0     
+    9        2    1.087714    3.039095   -0.791256     1 " " X " "    2  -0.22090  -0.22090 "    " "    " "  c1"    6   0    0    1 C14 0     
+    10       2    0.845021    3.903717    0.250024     1 " " X " "    2   0.43430   0.43430 "    " "    " "  c3"    6   0    0    1 C15 0     
+    11       2    2.399473    2.568440    1.240948     1 " " X " "    2   0.18590   0.18590 "    " "    " "  n1"    6   0    0    1 C17 0     
+    12      25    1.583465    3.614844    1.400395     1 " " X " "   43  -0.48030  -0.48030 "    " "    " "  c1"    7   0    0    1 N22 0     
+    13      49    2.312434    1.861537   -0.365850     1 " " X " "   13   0.00100   0.00100 "    " "    " "  c1"   16   0    0    1 S18 0     
+    14       2    0.528782    3.016717   -2.147200     1 " " X " "    2   0.70000   0.70000 "    " "    " "  c1"    6   0    0    1 C19 0     
+    15      15    0.293126    4.085238   -2.725145     1 " " X " "   70  -0.47000  -0.47000 "    " "    " "  c3"    8   0    0    1 O20 0     
+    16       3    0.115206    0.164959   -6.291597     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C20 0     
+    17      41   -0.554465   -0.621096   -6.641355     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H21 0     
+    18      41   -0.152011    1.086960   -6.808475     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H22 0     
+    19      41    1.133419   -0.102800   -6.573996     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H23 0     
+    20       3    3.299400    2.058116    2.312656     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C23 0     
+    21      41    2.739787    1.905634    3.235454     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H24 0     
+    22      41    3.742485    1.107817    2.014909     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H25 0     
+    23      41    4.101121    2.772044    2.500530     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H26 0     
+    24      25   -0.176974    0.662157   -2.000225     1 " " X " "   43  -0.67800  -0.67800 "    " "    " "  c1"    7   0    0    1 N25 0     
+    25      16   -0.011101    4.969812    0.267481     1 " " X " "   70  -0.58500  -0.58500 "    " "    " "  c1"    8   0    0    1 O25 0     
+    26      42   -0.289374    5.133066   -0.628399     1 " " X " "   21   0.43500   0.43500 "    " "    " "  n2"    1   0    0    1 H26 0     
+    :::
+  } 
+  m_bond[54] { 
+    # First column is bond index #
+    i_m_from
+    i_m_to
+    i_m_order
+    i_m_from_rep
+    i_m_to_rep
+    :::
+    1          1      2   1 1 1 
+    2          1     14   1 1 1 
+    3          1     24   2 1 1 
+    4          2      1   1 1 1 
+    5          2      3   2 1 1 
+    6          2      6   1 1 1 
+    7          3      2   2 1 1 
+    8          3      4   1 1 1 
+    9          3     16   1 1 1 
+    10         4      3   1 1 1 
+    11         4      5   2 1 1 
+    12         4      7   1 1 1 
+    13         5      4   2 1 1 
+    14         5      8   1 1 1 
+    15         5     24   1 1 1 
+    16         6      2   1 1 1 
+    17         7      4   1 1 1 
+    18         8      5   1 1 1 
+    19         9     10   2 1 1 
+    20         9     13   1 1 1 
+    21         9     14   1 1 1 
+    22        10      9   2 1 1 
+    23        10     12   1 1 1 
+    24        10     25   1 1 1 
+    25        11     12   2 1 1 
+    26        11     13   1 1 1 
+    27        11     20   1 1 1 
+    28        12     10   1 1 1 
+    29        12     11   2 1 1 
+    30        13      9   1 1 1 
+    31        13     11   1 1 1 
+    32        14      1   1 1 1 
+    33        14      9   1 1 1 
+    34        14     15   2 1 1 
+    35        15     14   2 1 1 
+    36        16      3   1 1 1 
+    37        16     17   1 1 1 
+    38        16     18   1 1 1 
+    39        16     19   1 1 1 
+    40        17     16   1 1 1 
+    41        18     16   1 1 1 
+    42        19     16   1 1 1 
+    43        20     11   1 1 1 
+    44        20     21   1 1 1 
+    45        20     22   1 1 1 
+    46        20     23   1 1 1 
+    47        21     20   1 1 1 
+    48        22     20   1 1 1 
+    49        23     20   1 1 1 
+    50        24      1   2 1 1 
+    51        24      5   1 1 1 
+    52        25     10   1 1 1 
+    53        25     26   1 1 1 
+    54        26     25   1 1 1 
+    :::
+  } 
+} 
+
+f_m_ct { 
+  s_m_title
+  s_m_entry_name
+  r_mmod_Potential_Energy-OPLS-2005
+  b_mmod_Minimization_Converged-OPLS-2005
+  r_mmod_RMS_Derivative-OPLS-2005
+  i_mmod_Times_Found-OPLS-2005
+  r_mmod_Relative_Potential_Energy-OPLS-2005
+  i_mmod_Conformation-OPLS-2005
+  s_m_job_name
+  s_m_entry_id
+  :::
+  "" 
+  mmod_csearch.14 
+      -170.06770324707 
+  1     
+    0.0452518649399281 
+  9     
+      19.8861846923828 
+  14    
+  mmod_csearch 
+  14 
+  m_depend[7] { 
+    # First column is dependency index #
+    i_m_depend_dependency
+    s_m_depend_property
+    :::
+    1         20 r_mmod_Potential_Energy-OPLS-2005 
+    2         20 b_mmod_Minimization_Converged-OPLS-2005 
+    3         20 r_mmod_RMS_Derivative-OPLS-2005 
+    4         20 i_mmod_Times_Found-OPLS-2005 
+    5         20 r_mmod_Relative_Potential_Energy-OPLS-2005 
+    6         20 i_mmod_Conformation-OPLS-2005 
+    7         30 s_m_job_name 
+    :::
+  } 
+  m_atom[26] { 
+    # First column is atom index #
+    i_m_mmod_type
+    r_m_x_coord
+    r_m_y_coord
+    r_m_z_coord
+    i_m_residue_number
+    s_m_insertion_code
+    s_m_mmod_res
+    s_m_chain_name
+    i_m_color
+    r_m_charge1
+    r_m_charge2
+    s_m_pdb_residue_name
+    s_m_pdb_atom_name
+    s_m_grow_name
+    i_m_atomic_number
+    i_m_formal_charge
+    i_m_representation
+    i_m_visibility
+    s_m_atom_name
+    i_m_template_index
+    :::
+    1        2    0.401687    1.565048   -2.785479     1 " " X " "    2   0.37000   0.37000 "    " "    " "  f1"    6   0    0    1 C2 0     
+    2        2    0.216623    1.646561   -4.183007     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "  c3"    6   0    0    1 C3 0     
+    3        2   -0.884921    1.003671   -4.771723     1 " " X " "    2   0.17700   0.17700 "    " "    " "  c1"    6   0    0    1 C4 0     
+    4        2   -1.763181    0.294314   -3.936486     1 " " X " "    2  -0.44700  -0.44700 "    " "    " "    "    6   0    0    1 C5 0     
+    5        2   -1.504627    0.247187   -2.557355     1 " " X " "    2   0.66500   0.66500 "    " "    " "  n3"    6   0    0    1 C6 0     
+    6       41    0.919033    2.202823   -4.791137     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H9 0     
+    7       41   -2.627507   -0.214574   -4.339216     1 " " X " "   21   0.15500   0.15500 "    " "    " "    "    1   0    0    1 H11 0     
+    8       57   -2.578118   -0.627322   -1.530318     1 " " X " "    9  -0.18000  -0.18000 "    " "    " "    "   17   0    0    1 Cl10 0     
+    9        2    1.488887    2.742230   -0.799366     1 " " X " "    2  -0.22090  -0.22090 "    " "    " "  c1"    6   0    0    1 C14 0     
+    10       2    2.414499    2.744034    0.217473     1 " " X " "    2   0.43430   0.43430 "    " "    " "  c3"    6   0    0    1 C15 0     
+    11       2    0.709829    3.818932    1.275728     1 " " X " "    2   0.18590   0.18590 "    " "    " "  n1"    6   0    0    1 C17 0     
+    12      25    1.952958    3.342292    1.392700     1 " " X " "   43  -0.48030  -0.48030 "    " "    " "  c1"    7   0    0    1 N22 0     
+    13      49    0.015871    3.558306   -0.317905     1 " " X " "   13   0.00100   0.00100 "    " "    " "  c1"   16   0    0    1 S18 0     
+    14       2    1.594877    2.227989   -2.168993     1 " " X " "    2   0.70000   0.70000 "    " "    " "  c1"    6   0    0    1 C19 0     
+    15      15    2.669802    2.327500   -2.773938     1 " " X " "   70  -0.47000  -0.47000 "    " "    " "  c3"    8   0    0    1 O20 0     
+    16       3   -1.120765    1.078362   -6.266027     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C20 0     
+    17      41   -1.664826    0.202771   -6.621024     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H21 0     
+    18      41   -1.703162    1.966061   -6.513014     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H22 0     
+    19      41   -0.175765    1.127537   -6.807494     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H23 0     
+    20       3   -0.013315    4.506258    2.381836     1 " " X " "    2  -0.06500  -0.06500 "    " "    " "  c1"    6   0    0    1 C23 0     
+    21      41    0.592941    5.318922    2.781782     1 " " X " "   21   0.06000   0.06000 "    " "    " "  n2"    1   0    0    1 H24 0     
+    22      41   -0.954074    4.921025    2.019881     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H25 0     
+    23      41   -0.230156    3.800697    3.183648     1 " " X " "   21   0.06000   0.06000 "    " "    " "    "    1   0    0    1 H26 0     
+    24      25   -0.445251    0.860001   -1.994748     1 " " X " "   43  -0.67800  -0.67800 "    " "    " "  c1"    7   0    0    1 N25 0     
+    25      16    3.684803    2.238685    0.190626     1 " " X " "   70  -0.58500  -0.58500 "    " "    " "  c1"    8   0    0    1 O25 0     
+    26      42    3.898203    2.038623   -0.715541     1 " " X " "   21   0.43500   0.43500 "    " "    " "  n2"    1   0    0    1 H26 0     
+    :::
+  } 
+  m_bond[54] { 
+    # First column is bond index #
+    i_m_from
+    i_m_to
+    i_m_order
+    i_m_from_rep
+    i_m_to_rep
+    :::
+    1          1      2   1 1 1 
+    2          1     14   1 1 1 
+    3          1     24   2 1 1 
+    4          2      1   1 1 1 
+    5          2      3   2 1 1 
+    6          2      6   1 1 1 
+    7          3      2   2 1 1 
+    8          3      4   1 1 1 
+    9          3     16   1 1 1 
+    10         4      3   1 1 1 
+    11         4      5   2 1 1 
+    12         4      7   1 1 1 
+    13         5      4   2 1 1 
+    14         5      8   1 1 1 
+    15         5     24   1 1 1 
+    16         6      2   1 1 1 
+    17         7      4   1 1 1 
+    18         8      5   1 1 1 
+    19         9     10   2 1 1 
+    20         9     13   1 1 1 
+    21         9     14   1 1 1 
+    22        10      9   2 1 1 
+    23        10     12   1 1 1 
+    24        10     25   1 1 1 
+    25        11     12   2 1 1 
+    26        11     13   1 1 1 
+    27        11     20   1 1 1 
+    28        12     10   1 1 1 
+    29        12     11   2 1 1 
+    30        13      9   1 1 1 
+    31        13     11   1 1 1 
+    32        14      1   1 1 1 
+    33        14      9   1 1 1 
+    34        14     15   2 1 1 
+    35        15     14   2 1 1 
+    36        16      3   1 1 1 
+    37        16     17   1 1 1 
+    38        16     18   1 1 1 
+    39        16     19   1 1 1 
+    40        17     16   1 1 1 
+    41        18     16   1 1 1 
+    42        19     16   1 1 1 
+    43        20     11   1 1 1 
+    44        20     21   1 1 1 
+    45        20     22   1 1 1 
+    46        20     23   1 1 1 
+    47        21     20   1 1 1 
+    48        22     20   1 1 1 
+    49        23     20   1 1 1 
+    50        24      1   2 1 1 
+    51        24      5   1 1 1 
+    52        25     10   1 1 1 
+    53        25     26   1 1 1 
+    54        26     25   1 1 1 
+    :::
+  } 
+} 
+
diff --git a/modules/mol/alg/molalg.rst b/modules/mol/alg/molalg.rst
new file mode 100644
index 0000000000000000000000000000000000000000..00735f6def328ed899de4005fb2f803cd23f0206
--- /dev/null
+++ b/modules/mol/alg/molalg.rst
@@ -0,0 +1,25 @@
+:mod:`mol.alg <ost.mol.alg>` -- Algorithms for Structures
+================================================================================
+
+.. module:: ost.mol.alg
+   :synopsis: Algorithms operating on molecular structures
+
+.. function:: LocalDistTest(model, reference, tolerance, radius)
+  
+  This function calculates the agreement of local contacts between the model and 
+  the reference structure. The overlap is a number between zero and one, where 
+  one indicates complete agreement, zero indicates no agreement at all. This 
+  score is similar to the GDT, but does not require any superposition of the 
+  model and the reference.
+  
+  The distance of atom pairs in the reference structure that are closer than a 
+  certain distance (radius) to each other is compared to the distance found in 
+  the model. If the difference between these two distances is smaller than a 
+  threshold value (tolerance), the model and the reference agree. Missing atoms 
+  in the model are treated disagreement and thus lower the score.
+  
+  For residue with symmetric sidechains (GLU, ASP, ARG, VAL, PHE, TYR), the 
+  naming of the atoms is ambigous. For these residues, the overlap of both 
+  possible solutions to the fixed atoms, that is, everything that is not 
+  ambigous is calculated. The solution that gives higher overlap is then used to 
+  calculate the actual overlap score.
\ No newline at end of file
diff --git a/modules/mol/alg/pymod/export_svd_superpose.cc b/modules/mol/alg/pymod/export_svd_superpose.cc
index 3acdc6f6b7d0bef234d00cde96a0e14b76b02a91..b10a4b7c1df864db313d2d4c18066c555ee0fd07 100644
--- a/modules/mol/alg/pymod/export_svd_superpose.cc
+++ b/modules/mol/alg/pymod/export_svd_superpose.cc
@@ -43,8 +43,8 @@ void export_svdSuperPose()
                &SuperpositionResult::entity_view2)
   ;
   def("SuperposeAtoms", &SuperposeAtoms,(arg("apply_transform")=true));
-  def("SuperposeSVD", sup1);
-  def("SuperposeSVD", sup2);
+  def("SuperposeSVD", sup1, (arg("apply_transform")=true));
+  def("SuperposeSVD", sup2, (arg("apply_transform")=true));
   def("CalculateRMSD", &CalculateRMSD, (arg("transformation")=geom::Mat4()));
   def("IterativeSuperposition", &IterativeSuperposition, (arg("ncycles")=200,
                                                           arg("dist_thres")=4.0,
diff --git a/modules/mol/alg/pymod/views.py b/modules/mol/alg/pymod/views.py
index 7086e792809fae30838fe2c0b85b62e3d32a852e..f4a20307724c6b814183ad242637a9852f714ebb 100644
--- a/modules/mol/alg/pymod/views.py
+++ b/modules/mol/alg/pymod/views.py
@@ -69,14 +69,12 @@ def RepresentativeAtoms(ent, chain=None, alpha_and_beta=False):
   If chain is not equal to None, only atoms of the chain with that chain name
   will be added to the view.
   """
-  if isinstance(ent,mol.EntityHandle):
-    e_view = ent.CreateEmptyView()
-  elif isinstance(ent,mol.EntityView):
-    e_view = ent.GetHandle().CreateEmptyView()
+  e_view=ent.CreateEmptyView()
   if ent.IsValid():
     # all chains:
     if chain==None:
       for res in ent.residues:
+        res=res.handle
         if res.IsPeptideLinking():
           atom =  res.FindAtom('CB')
           if atom.IsValid():
@@ -99,7 +97,8 @@ def RepresentativeAtoms(ent, chain=None, alpha_and_beta=False):
 
     elif chain != "" and ent.FindChain(chain).IsValid():
       for res in ent.FindChain(chain).GetResidueList():
-       if res.IsPeptideLinking():
+        res=res.handle
+        if res.IsPeptideLinking():
           atom =  res.FindAtom('CB')
           if atom.IsValid():
             e_view.AddAtom(atom)
diff --git a/modules/mol/alg/pymod/wrap_mol_alg.cc b/modules/mol/alg/pymod/wrap_mol_alg.cc
index ce0be429c6afb0afd5b6b55b2252cc79d446dbbd..240a029a42dd523e8a4dfab72be40fe77bd74fa7 100644
--- a/modules/mol/alg/pymod/wrap_mol_alg.cc
+++ b/modules/mol/alg/pymod/wrap_mol_alg.cc
@@ -22,6 +22,8 @@
  */
 #include <boost/python.hpp>
 #include <ost/config.hh>
+#include <ost/mol/alg/local_dist_test.hh>
+
 using namespace boost::python;
 
 void export_svdSuperPose();
@@ -36,4 +38,6 @@ BOOST_PYTHON_MODULE(_mol_alg)
   #if OST_IMG_ENABLED
   export_entity_to_density();
   #endif
+  
+  def("LocalDistTest", &ost::mol::alg::LocalDistTest);
 }
diff --git a/modules/mol/alg/src/CMakeLists.txt b/modules/mol/alg/src/CMakeLists.txt
index 242eea3d8f3a4c80f29909b3ecad313df10753f7..17dc9acbf2a5d32ac17e62b0e50af18f35122b2f 100644
--- a/modules/mol/alg/src/CMakeLists.txt
+++ b/modules/mol/alg/src/CMakeLists.txt
@@ -2,11 +2,13 @@ set(OST_MOL_ALG_HEADERS
   svd_superpose.hh
   module_config.hh
   sec_structure_segments.hh
+  local_dist_test.hh
 )
 
 set(OST_MOL_ALG_SOURCES
   svd_superpose.cc
   sec_structure_segments.cc
+  local_dist_test.cc
 )
 
 set(MOL_ALG_DEPS mol)
diff --git a/modules/mol/alg/src/local_dist_test.cc b/modules/mol/alg/src/local_dist_test.cc
new file mode 100644
index 0000000000000000000000000000000000000000..bd88902b0e181bb29f62da86ae41367137b23ded
--- /dev/null
+++ b/modules/mol/alg/src/local_dist_test.cc
@@ -0,0 +1,165 @@
+#include <ost/mol/mol.hh>
+#include "local_dist_test.hh"
+
+namespace ost { namespace mol { namespace alg {
+
+namespace {
+
+String swapped_name(const String& name)
+{
+  if (name=="OE1") return "OE2";
+  if (name=="OE2") return "OE1";
+
+  if (name=="OD1") return "OD2";
+  if (name=="OD2") return "OD1";
+
+  if (name=="CG1") return "CG2";
+  if (name=="CG2") return "CG1";
+
+  if (name=="CE1") return "CE2";
+  if (name=="CE2") return "CE1";  
+
+  if (name=="CD1") return "CD2";
+  if (name=="CD2") return "CD1";
+
+  if (name=="NH1") return "NH2";
+  if (name=="NH2") return "NH1";
+
+  return name;
+}
+
+bool swappable(const String& rname, const String& aname)
+{
+  if (rname=="GLU") {
+    return (aname=="OE1" || aname=="OE2");
+  }
+  if (rname=="ASP") {
+    return (aname=="OD1" || aname=="OD2");
+  }
+  if (rname=="VAL") {
+    return (aname=="CG1" || aname=="CG2");
+  }
+  if (rname=="TYR" || rname=="PHE") {
+    return (aname=="CD1" || aname=="CD2" || aname=="CE1" || aname=="CE2");
+  }
+  if (rname=="ARG") {
+    return (aname=="NH1" || aname=="NH2");
+  }  
+  return false;
+}
+
+std::pair<Real, Real> calc_overlap(ResidueView ref_res, 
+                                   EntityView ref,
+                                   ChainView mdl_chain, 
+                                   Real tol, Real max_dist, bool only_fixed, 
+                                   bool swap)
+{
+  std::pair<Real, Real> overlap(0.0, 0.0);
+  AtomViewList ref_atoms=ref_res.GetAtomList();
+
+  ResidueView mdl_res=mdl_chain.FindResidue(ref_res.GetNumber());
+  AtomViewList within;
+  if (max_dist<0){
+      within=ref.GetAtomList();
+  }
+  for (AtomViewList::iterator ai=ref_atoms.begin(),
+       ae=ref_atoms.end(); ai!=ae; ++ai) {
+    if (ai->GetElement()=="H") { continue; }
+    String name=swap ? swapped_name(ai->GetName()) : ai->GetName();
+    AtomView av1=mdl_res ? mdl_res.FindAtom(name) : AtomView();
+    if (max_dist>=0){ 
+      within=ref.FindWithin(ai->GetPos(), max_dist);
+    }
+    for (AtomViewList::iterator aj=within.begin(),
+         ae2=within.end(); aj!=ae2; ++aj) {
+      if (aj->GetElement()=="H") { continue; }
+      if (only_fixed) {
+        if (aj->GetResidue().GetNumber()==ref_res.GetNumber()) {
+          continue;
+        }
+        if (swappable(aj->GetResidue().GetName(), aj->GetName())) {
+          continue;
+        }
+        AtomView av2=mdl_chain.FindAtom(aj->GetResidue().GetNumber(), 
+                                             aj->GetName());
+        overlap.second+=1.0;
+        if (!(av1 && av2)) {
+          continue;
+        }
+        Real mdl_dist=geom::Length(av1.GetPos()-av2.GetPos());
+        Real ref_dist=geom::Length(ai->GetPos()-aj->GetPos());
+        if (std::abs(mdl_dist-ref_dist)<tol) {
+          overlap.first+=1;
+        }
+        continue;
+      }
+      if (aj->GetResidue().GetNumber()>ref_res.GetNumber()) {
+        AtomView av2=mdl_chain.FindAtom(aj->GetResidue().GetNumber(), 
+                                             aj->GetName());
+        overlap.second+=1.0;
+        if (!(av1 && av2)) {
+          continue;
+        }
+        Real mdl_dist=geom::Length(av1.GetPos()-av2.GetPos());
+        Real ref_dist=geom::Length(ai->GetPos()-aj->GetPos());
+        if (std::abs(mdl_dist-ref_dist)<tol) {
+          overlap.first+=1;
+        }
+      }
+    }      
+  }
+  return overlap;
+}
+
+}
+
+Real LocalDistTest(const EntityView& mdl, const EntityView& ref,
+                   Real cutoff, Real max_dist)
+{
+  ResidueViewList ref_residues=ref.GetResidueList();
+  ChainView mdl_chain=mdl.GetChainList()[0];  
+  // Residues with symmetric side-chains require special treatment as there are 
+  // two possible ways to name the atoms. We calculate the overlap with the 
+  // fixed atoms and take the solution that gives bigger scores.
+  XCSEditor edi=ref.GetHandle().RequestXCSEditor(BUFFERED_EDIT);
+  for (ResidueViewList::iterator
+       i=ref_residues.begin(), e=ref_residues.end(); i!=e; ++i) {
+    const String rname=i->GetName();
+    ResidueView mdl_res=mdl_chain.FindResidue(i->GetNumber());
+    if (!mdl_res) {
+     continue;
+    }     
+    if (!(rname=="GLU" || rname=="ASP" || rname=="VAL" || rname=="TYR" || 
+         rname=="PHE" || rname=="LYS" || rname=="ARG")) {
+      continue;
+    }
+
+    std::pair<Real, Real> ov1=calc_overlap(*i, ref, mdl_chain, 
+                                          cutoff, max_dist, true, 
+                                          false);
+    std::pair<Real, Real> ov2=calc_overlap(*i, ref, mdl_chain, 
+                                          cutoff, max_dist, true, 
+                                          true); 
+    if (ov1.first/ov1.second<ov2.first/ov2.second) {
+     AtomViewList atoms=mdl_res.GetAtomList();
+     for (AtomViewList::iterator j=atoms.begin(), 
+          e2=atoms.end(); j!=e2; ++j) {
+       if (swappable(rname, j->GetName())) {
+         edi.RenameAtom(j->GetHandle(), swapped_name(j->GetName()));
+       }
+     }
+
+    }
+  }
+  std::pair<Real, Real> total_ov(0.0, 0.0);
+  for (ResidueViewList::iterator
+       i=ref_residues.begin(), e=ref_residues.end(); i!=e; ++i) {
+     std::pair<Real, Real> ov1=calc_overlap(*i, ref, mdl_chain, cutoff, 
+                                            max_dist, false, false);
+     total_ov.first+=ov1.first;
+     total_ov.second+=ov1.second;
+  }
+  return total_ov.first/total_ov.second;
+}
+
+}}}
diff --git a/modules/mol/alg/src/local_dist_test.hh b/modules/mol/alg/src/local_dist_test.hh
new file mode 100644
index 0000000000000000000000000000000000000000..f0ba3ebea20a6138a0cf14f2a34d24839abe3ef4
--- /dev/null
+++ b/modules/mol/alg/src/local_dist_test.hh
@@ -0,0 +1,15 @@
+#ifndef OST_MOL_ALG_LOCAL_DIST_TEST_HH
+#define OST_MOL_ALG_LOCAL_DIST_TEST_HH
+
+#include <ost/mol/entity_view.hh>
+#include <ost/mol/alg/module_config.hh>
+
+namespace ost { namespace mol { namespace alg {
+  
+Real DLLEXPORT_OST_MOL_ALG LocalDistTest(const EntityView& mdl,
+                                         const EntityView& ref,
+                                         Real cutoff, Real max_dist);
+}}}
+
+#endif
+
diff --git a/modules/mol/base/doc/editors.rst b/modules/mol/base/doc/editors.rst
index aaed57b35ea03c395926d4cf745c2483c80cf6a7..f224b2e1fd2290db8be073dda9d18fc36bf052db 100644
--- a/modules/mol/base/doc/editors.rst
+++ b/modules/mol/base/doc/editors.rst
@@ -1,7 +1,7 @@
 Editors
 ================================================================================
 
-.. currentmodule:: mol
+.. currentmodule:: ost.mol
 
 The structure, topology and connectivity of entities is edited via editors. This 
 includes operations such as changing atom positions, connecting atoms with bonds 
@@ -118,7 +118,7 @@ euclidian space.
      transform.
      
      :param atom: must be a valid atom handle
-     :type  atom: :class:`mol.AtomHandle`
+     :type  atom: :class:`ost.mol.AtomHandle`
      :param pos: The new position
      :type  pos: :class:`geom.Vec3`
      
@@ -129,7 +129,7 @@ euclidian space.
      the original pos.
      
      :param atom: must be a valid atom handle
-     :type  atom: :class:`mol.AtomHandle`
+     :type  atom: :class:`ost.mol.AtomHandle`
      :param pos: The new untransformed position
      :type  pos: :class:`geom.Vec3`
   
diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst
index 75e5c6fdea49ec877259a013762b3126c82c6e92..e6bebee7c94e7f83b8fba0c83685cc930e039002 100644
--- a/modules/mol/base/doc/entity.rst
+++ b/modules/mol/base/doc/entity.rst
@@ -1,23 +1,25 @@
 The Molecular Entity
 ================================================================================
 
-.. currentmodule:: mol
+.. currentmodule:: ost.mol
 
-This document describes the :class:`EntityHandle` and related classes.
+This document describes the :class:`EntityHandle` and the related classes.
 
+The Handle Classes
+--------------------------------------------------------------------------------
 
 .. function:: CreateEntity()
 
    Creates a new entity. The created entity is empty, that is, it does not
    contain any atoms, residues, chains, bonds or torsions. To populate the
-   entity, create a new editor.
+   entity, use an :doc:`entity editor <editors>`.
    
    :returns: The newly created :class:`EntityHandle`
    
 .. class:: EntityHandle
 
   The entity class represents a molecular structure. Such a structure is in
-  general made up of one or more linear chains of residues, which in turn are
+  general made up of one or more chains of residues, which in turn are
   formed by one or more atoms.
 
   The interface of entities is tailored to biological macromolecules, but this
@@ -25,132 +27,197 @@ This document describes the :class:`EntityHandle` and related classes.
   represent a ligand or a collection of water molecules - hence the rather
   generic name.
 
-  .. method:: FindChain(chain_name)
-
-     Get chain by name. See also :meth:`GetChainList`
-
-     :param chain_name:  Chain identifier, e.g. "A"
-     :type  chain_name:  string
-     :returns:           A valid :class:`ChainHandle`, if the entity contains a
-                         chain with the given name, an invalid
-                         :class:`ChainHandle` otherwise.
-                         
-  .. method:: GetChainList()
-     
-     Get list of all chains of this entity. To access a single chain, use
-     :meth:`FindChain`.
-     
-     :returns: A list of :class:`ChainHandles<ChainHandle>`
+  .. attribute:: chains
     
-  .. method:: FindResidue(chain_name, res_num)
-     
-     Get residue by chain name and residue number. See also 
-     :meth:`GetResidueList`
-     
-     :param chain_name:  Chain identifier, e.g. "A"
-     :type  chain_name:  string
-     :param    res_num:  residue number
-     :type     res_num:  mol.ResNum
-     
-     :returns:           A valid :class:`ResidueHandle` if the chain exists and
-                         the chain contains a residue of the given residue
-                         number, an invalid :class:`ResidueHandle` otherwise.
-
-  .. method:: GetResidueList()
+    List of all chains of this entity. The chains are in the same 
+    order they have been added, for example the order they have been listed 
+    in a PDB file.
+    
+    Also available as :meth:`GetChainList`. To access a single chain, use 
+    :meth:`FindChain`.
+    
+    This property is read-only.
+    
+  .. attribute:: residues
+    
+    List of all residues of this entity. The returned residues are first 
+    sorted by chain and then from N- to C-terminus.
+    
+    This property is read-only.
+    
+    **Example usage:**
+    
+    .. code-block:: python
+    
+      for res in ent.residues:
+        print res.name, res.atom_count
+    
+    Also available as :meth:`GetResidueList`. To access a single residue, use 
+    :meth:`FindResidue`. 
   
-     Get list of all residues of this entity. To access a single residue, use
-     :meth:`FindResidue`.
+     :returns: A list of :class:`residue handles<ResidueHandle>`
   
-     :returns: A list of :class:`ResidueHandles<ResidueHandle>`
-     
-  .. method:: FindAtom(chain_name, res_num, atom_name)
+  .. attribute:: atoms
   
-     Get atom by chain name, residue number and atom name. See also
-     :meth:`GetAtomList`
-     
-     :param chain_name:  Chain identifier, e.g. "A"
-     :type  chain_name:  string
-     :param    res_num:  residue number
-     :type     res_num:  mol.ResNum
-     :param  atom_name:  atom name, e.g. CA
-     :type   atom_name:  string
+     Get list of all atoms of this entity. To access a single atom, use
+     :meth:`FindAtom`.
      
-     :returns:           A valid :class:`AtomHandle` if an atom matching the
-                         parameters could be found, an invalid
-                         :class:`AtomHandle` otherwise
-
-  .. method:: GetAtomList()
+     This property is read-only. Also available as :meth:`GetAtomList`
   
-     Get list of all atoms of this entity. To access a single atom, use
-     :meth:`FindAtom`
+     :type: A list of :class:`atom handles<AtomHandle>`
+  
+  .. attribute:: bounds
   
-     :returns: A list of :class:`AtomHandles<AtomHandle>`
+    Axis-aligned bounding box of the entity. Read-only
+    
+    :type: :class:`ost.geom.AlignedCuboid`
 
-  .. method:: RequestXCSEditor([edit_mode=mol.EditMode.BUFFERED_EDIT])
+  .. attribute:: mass
+    
+    The total mass of the entity in Dalton. Also available as :meth:`GetMass`.
+    
+    :type: float
 
-     Request :class:`XCSEditor` for editing the external coordinate system. This
-     call will fail when there are pending changes of the internal coordinate
-     system.
-     
-     :param edit_mode: Must be EditMode.BUFFERED_EDIT or
-                       EditMode.UNBUFFERED_EDIT. For more details, see the
-                       editor documentation.
-     :type edit_mode: mol.EditMode
-     
-     :returns: :class:`XCSEditor`
-  .. method:: RequestICSEditor([edit_mode=mol.EditMode.BUFFERED_EDIT])
+  .. attribute:: center_of_mass
   
-     Request :class:`ICSEditor` for editing the internal coordinate system, such
-     as torsions, bond lengths and angle between two bonds. This call will fail
-     when there are pending changes of the external coordinate system.
-     
-     :param edit_mode: Must be EditMode.BUFFERED_EDIT or
-                       EditMode.UNBUFFERED_EDIT. For more details, see the
-                       editor documentation.
-     :type edit_mode: mol.EditMode
-     
-     :returns: :class:`ICSEditor`
-     
-  .. method:: Select(query, flags)
+    Center of mass. Also available as :meth:`GetCenterOfMass`
+    
+    :type: :class:`~ost.geom.Vec3`
+    
+  .. attribute:: center_of_atoms
   
-     Perform a selection on the entity. The result of the selection is an 
-     :class:`EntityView` which contains usually only a subset of chains,
-     residues, atoms and bonds of the original entity.
-     
-     :param query: The query to be executed. See :class:`Query` for details.
-     :type  query: string or :class:`Query`
-     :param flags: An ORed combination of :class:`QueryFlags`.
-     :type  flags: int
-     :returns:     An :class:`entity view <EntityView>`.
-     :raises:      :class:`QueryError` when the query could not be executed due
-                   to syntactic errors.
+    Center of atoms (not mass-weighted). Also available as 
+    :meth:`GetCenterOfAtoms`.
+    
+    :type: :class:`~ost.geom.Vec3`
   
+  .. method:: FindChain(chain_name)
+    
+    Get chain by name. See also :attr:`chains`
+    
+    :param chain_name:  Chain identifier, e.g. "A"
+    :type  chain_name:  str
+    :returns:           A valid :class:`ChainHandle`, if the entity contains a
+                        chain with the given name, an invalid
+                        :class:`ChainHandle` otherwise.
+                        
+  .. method:: GetChainList()
+    
+    See :attr:`chains`
+    
+  .. method:: FindResidue(chain_name, res_num)
+    
+    Get residue by chain name and residue number. See also 
+    :meth:`GetResidueList`
+    
+    :param chain_name:  Chain identifier, e.g. "A"
+    :type  chain_name:  str
+    :param    res_num:  residue number
+    :type     res_num:  mol.ResNum
+    
+    :returns:           A valid :class:`ResidueHandle` if the chain exists and
+                        the chain contains a residue of the given residue
+                        number, an invalid :class:`ResidueHandle` otherwise.
+    
+  .. method:: GetResidueList()
+    
+    See :attr:`residues`
+    
+  .. method:: FindAtom(chain_name, res_num, atom_name)
+    
+    Get atom by chain name, residue number and atom name. See also
+    :attr:`atoms`
+    
+    :param chain_name:  Chain identifier, e.g. "A"
+    :type  chain_name:  str
+    :param    res_num:  residue number
+    :type     res_num:  mol.ResNum
+    :param  atom_name:  atom name, e.g. CA
+    :type   atom_name:  str
+    
+    :returns:           A valid :class:`AtomHandle` if an atom matching the
+                        parameters could be found, an invalid
+                        :class:`AtomHandle` otherwise
+    
+  .. method:: GetAtomList()
+    
+    See :attr:`atoms`
+    
+  .. method:: RequestXCSEditor([edit_mode=mol.EditMode.BUFFERED_EDIT])
+    
+    Request :class:`XCSEditor` for editing the external coordinate system. This
+    call will fail when there are pending changes of the internal coordinate
+    system.
+    
+    :param edit_mode: Must be EditMode.BUFFERED_EDIT or
+                      EditMode.UNBUFFERED_EDIT. For more details, see the
+                      editor documentation.
+    :type edit_mode: mol.EditMode
+    
+    :returns: :class:`XCSEditor`
+    
+  .. method:: RequestICSEditor([edit_mode=mol.EditMode.BUFFERED_EDIT])
+    
+    Request :class:`ICSEditor` for editing the internal coordinate system, such
+    as torsions, bond lengths and angle between two bonds. This call will fail
+    when there are pending changes of the external coordinate system.
+    
+    :param edit_mode: Must be EditMode.BUFFERED_EDIT or
+                      EditMode.UNBUFFERED_EDIT. For more details, see the
+                      editor documentation.
+    :type edit_mode: mol.EditMode
+    
+    :returns: :class:`ICSEditor`
+    
+  .. method:: Select(query, flags=0)
+    
+    Perform a selection on the entity. The result of the selection is an 
+    :class:`EntityView` which (usually) contains only a subset of chains,
+    residues, atoms and bonds of the original entity.
+    
+    **Example Usage:**
+    
+    .. code-block::python
+      # select calpha atoms of peptides
+      calphas=ent.Select('aname=CA and peptide=true')
+      
+      # select atoms in a box of size 10, centered at the origin
+      in_box=ent.Select('x=-5:5 and y=-5:5 and z=-5:5')
+    
+    :param query: The query to be executed. See :class:`Query` for details.
+    :type  query: string or :class:`Query`
+    :param flags: An ORed combination of :class:`QueryFlags`.
+    :type  flags: int
+    :returns:     An :class:`entity view <EntityView>`.
+    :raises:      :class:`QueryError` when the query could not be executed due
+                  to syntactic errors.
+    
   .. method:: CreateFullView()
-  
-     Creates  an entity view containing all chains, residues, atoms and bonds of
-     this entity.
-     
-     .. code-block:: python
-     
-       # these two lines are identical
-       full=ent.Select('')
-       full=ent.CreateFullView()
-
-     :returns: :class:`EntityView`
-  
+    
+    Creates  an entity view containing all chains, residues, atoms and bonds of
+    this entity.
+    
+    .. code-block:: python
+    
+      # these two lines are identical
+      full=ent.Select('')
+      full=ent.CreateFullView()
+    
+    :returns: :class:`EntityView`
+    
   .. method:: CreateEmptyView()
-  
-     Creates an entity view pointing to this entity, but otherwise empty. This
-     method is usually the starting point for manual entity view creation, e.g.
-     
-     .. code-block:: python
-     
-       view=ent.CreateEmtpyView()
-       for atom in ent.atoms:
-         if ComplicatedPredicate(atom):
-            view.AddAtom(atom)
-
-     :returns: :class:`EntityView`
+    
+    Creates an entity view pointing to this entity, but otherwise empty. This
+    method is usually the starting point for manual entity view creation, e.g.:
+    
+    .. code-block:: python
+    
+      view=ent.CreateEmtpyView()
+      for atom in ent.atoms:
+        if ComplicatedPredicate(atom):
+           view.AddAtom(atom)
+    
+    :returns: :class:`EntityView`
 
   .. method:: Copy()
     
@@ -167,53 +234,129 @@ This document describes the :class:`EntityHandle` and related classes.
     Get center of atoms, that is the average atom position of the entity. Use
     :meth:`GetCenterOfMass` to calculate the mass-weighted center of the entity.
     
-    :returns: :class:`geom.Vec3`
+    :returns: :class:`~ost.geom.Vec3`
     
   .. method:: GetCenterOfMass()
-     
-     Calculates the center of mass of the entity. Use :meth:`GetCenterOfAtoms`
-     to calculate the non-mass-weighted center of the entity.
-     
-     :returns: :class:`geom.Vec3`
-     
+    
+    Calculates the center of mass of the entity. Use :meth:`GetCenterOfAtoms`
+    to calculate the non-mass-weighted center of the entity.
+    
+    :returns: :class:`~ost.geom.Vec3`
+    
   .. method:: GetGeometricCenter()
   
     Calculates the mid-point of the axis aligned bounding box of the entity.
     
-    :returns: :class:`geom.Vec3`
+    :returns: :class:`~ost.geom.Vec3`
     
   .. method:: GetMass()
   
-    Calculates the total mass of the entity by summing up the masses of all
-    atoms.
+    See :attr:`mass`
     
-    :returns: The mass in Dalton
     
-  .. method:: Apply(visitor)
-  
-     Apply EntityVisitor to the entity. In Python, you shouldn't bother using
-     this function. EntityVisitory are mainly used in C++ to implement
-     algorithms that operate are able to operate on EntityViews or
-     EntityHandles.
-     
   .. method:: FindWithin(pos, radius)
   
-     Find all atoms in sphere of given radius centered at *pos*. To turn the
-     returned list of atoms into an :class:`EntityView`, use
-     :func:`CreateViewFromAtomList`.
+    Find all atoms in sphere of given radius centered at *pos*. To turn the
+    returned list of atoms into an :class:`EntityView`, use
+    :func:`CreateViewFromAtomList`.
+    
+    :param pos: Center of sphere
+    :type pos: :class:`~ost.geom.Vec3`
+    :param radius: The radius of the sphere
+    :type radius: float
+    
+    :returns: A list of :class:`atom handles<AtomHandle>`
+    
+.. class:: ChainHandle
+
+  A chain of one or more :class:`residues <ResidueHandle>`. Chains are always 
+  part of an entity.
+  
+  .. attribute:: name
+  
+     The chain name. The name uniquely identifies the chain in the entity. In 
+     most cases, the chain name is one character. This is restriction of the PDB 
+     file format. However, you are free to use longer names as long as you don't 
+     want to save them as PDB files
      
-     :param pos: Center of sphere
-     :type pos: :class:`geom.Vec3`
-     :param radius: The radius of the sphere
-     :type radius: float
+     This property is read-only. To change the name, use an :class:`XCSEditor`. 
      
-     :returns: A list of :class:`AtomHandles<AtomHandle>`
+     Also available as :meth:`GetName`
      
-.. class:: ChainHandle
+     :type: str
+
+  .. attribute:: residues
+   
+     List of all residues of this chain. The residues are sorted from N- to 
+     C-terminus. Usually the residue numbers are in ascending order 
+     (see :attr:`in_sequence`).
+   
+     This property is read-only.
+   
+     **Example usage:**
+   
+     .. code-block:: python
+     
+       chain=ent.FindChain("A")
+       for res in chain.residues:
+         print res.name, res.atom_count
+   
+     Also available as :meth:`GetResidueList`. To access a single residue, use 
+     :meth:`FindResidue`. 
+
+     :returns: A list of :class:`residue handles<ResidueHandle>`
+  
+  .. attribute:: in_sequence
+  
+     Whether the residue numbers are in ascending order. For example:
+     
+     .. code-block:: python
+     
+       chain=ent.FindChain("A")
+       print chain.residues # [A.GLY1, A.GLY2, A.GLY4A, A.GLY4B]
+       print chain.in_sequence # prints true
+       
+       chain=ent.FindChain("B")
+       print chain.residues # [B.GLY1, B.GLY4, B.GLY3]
+       print chain.in_sequence # prints false
+
+  .. attribute:: atoms
+
+     Get list of all atoms of this chain. To access a single atom, use
+     :meth:`FindAtom`.
+   
+     This property is read-only. Also available as :meth:`GetAtomList`
 
+     :type: A list of :class:`atom handles<AtomHandle>`
+
+  .. attribute:: bounds
+
+    Axis-aligned bounding box of the chain. Read-only
+
+    :type: :class:`ost.geom.AlignedCuboid`
+          
+  .. attribute:: mass
+  
+    The total mass of this chain in Dalton. Also available as :meth:`GetMass`
+  
+    :type: float
+
+  .. attribute:: center_of_mass
+
+    Center of mass. Also available as :meth:`GetCenterOfMass`
+  
+    :type: :class:`~ost.geom.Vec3`
+  
+  .. attribute:: center_of_atoms
+    
+    Center of atoms (not mass weighted). Also available as 
+    :meth:`GetCenterOfAtoms`.
+    
+    :type: :class:`~ost.geom.Vec3`
+    
   .. method:: FindResidue(res_num)
    
-    Get residue by residue number. See also :meth:`GetResidueList`
+    Get residue by residue number. See also :attr:`residues`
     
     :param    res_num:  residue number
     :type     res_num:  mol.ResNum
@@ -228,52 +371,1078 @@ This document describes the :class:`EntityHandle` and related classes.
     are usually ordered from N- to C-terminus.To access a single residue, use     
     :meth:`FindResidue`.
     
-    :returns: A list of :class:`ResidueHandles<ResidueHandle>`
+    :returns: A list of :class:`residue handles<ResidueHandle>`
 
   .. method:: FindAtom(res_num, atom_name)
 
-    Get atom by residue number and atom name. See also :meth:`GetAtomList`
+    Get atom by residue number and atom name. See also :attr:`atoms`
 
     :param    res_num:  residue number
     :type     res_num:  mol.ResNum
     :param  atom_name:  atom name, e.g. CA
-    :type   atom_name:  string
+    :type   atom_name:  str
 
     :returns:           A valid :class:`AtomHandle` if an atom matching the
                         parameters could be found, an invalid
                         :class:`AtomHandle` otherwise
 
   .. method:: GetAtomList()
+    
+    See :attr:`atoms`
+    
+  .. method:: GetName()
+  
+    See :attr:`name`
 
-    Get list of all atoms of this chain. To access a single atom, use
-    :meth:`FindAtom`
-
-    :returns: A list of :class:`AtomHandles<AtomHandle>`
 
 .. class:: ResidueHandle
 
+  The residue is either used to represent complete molecules or building blocks 
+  in a polymer, e.g. in a protein, DNA or RNA. A residue consists of one or 
+  more :class:`atoms <AtomHandle>`. Residues are always part of a 
+  :class:`ChainHandle`, even if they are ligands or water molecules where the 
+  concept of a chain does not apply.
+  
+  .. attribute:: name
+  
+    The residue name is usually a str of 3 characters, e.g. `GLY` for 
+    glycine or `ALA` for alanine, but may be shorter, e.g. `G` for guanosine, 
+    or longer for structures loaded from formats other than PDB.
+    
+    This property is read-only. To change the name of the residue, use
+    :meth:`EditorBase.SetResidueName`.
+  
+  .. attribute:: number
+  
+    The number of this residue. The residue number has a numeric part and an
+    insertion-code. This property is read-only. Also available as 
+    :meth:`GetNumber`.
+    
+    :type: :class:`ResNum`
+  
+  .. attribute:: one_letter_code
+  
+    For amino acids, and nucleotides the `one_letter_code` is an alpha-numeric 
+    character. For unknown or more *exotic* residues, the one letter code is set 
+    to '?'.
+    
+    **Example**
+    
+    This code-snippet shows how to get the sequence string from a list of 
+    residues.
+    
+    .. code-block:: python
+    
+      print ''.join([r.one_letter_code for r in chain.residues])
+    
+    :type: str
+    
+  .. attribute:: bounds
+  
+    Axis-aligned bounding box of the residue. Read-only.
+    
+    :type: :class:`ost.geom.AlignedCuboid`
+    
+  .. attribute:: mass
+  
+    The total mass of this residue in Dalton. Also available as :meth:`GetMass`.
+  
+    :type: float
+
+  .. attribute:: center_of_mass
+
+    Center of mass. Also available as :meth:`GetCenterOfMass`
+  
+    :type: :class:`~ost.geom.Vec3`
+  
+  .. attribute:: center_of_atoms
+    
+    Center of atoms (not mass weighted). Also available as 
+    :meth:`GetCenterOfAtoms`.
+    
+    :type: :class:`~ost.geom.Vec3`
+
+  .. attribute:: chain
+  
+    The chain this residue belongs to. Read-only. Also available as 
+    :meth:`GetChain`
+    
+    :type: :class:`ChainHandle`
+  
+  .. attribute:: phi_torsion
+  
+    The PHI dihedral angle between this residue and the next. For residues 
+    that are not amino acids, residues that do not have all atoms required or 
+    residues that do not have bonds between the four atoms involved in the 
+    torsion, the PHI torsion is an invalid handle.
+    
+    Read-only. Also available as :meth:`GetPhiTorsion`
+    
+    :type: :class:`TorsionHandle`
+  
+  .. attribute:: psi_torsion
+  
+    The PSI dihedral angle between this residue and the previous. For residues 
+    that are not amino acids, residues that do not have all atoms required or 
+    residues that do not have bonds between the four atoms involved in the 
+    torsion, the PSI torsion is an invalid handle.
+    
+    Read-only. Also available as :meth:`GetPsiTorsion`
+    
+    :type: :class:`TorsionHandle`
+  
+  .. attribute:: chem_class
+  
+    The chemical class of a residue is used to broadly categorize residues based 
+    on their chemical properties. For example, peptides belong  to the 
+    `LPeptideLinking` or `DPeptideLinking` classes.
+  
+  .. attribute:: sec_structure
+  
+    The secondary structure of the residue.
+    
   .. method:: FindAtom(atom_name)
 
-   Get atom by atom name. See also :meth:`GetAtomList`
+    Get atom by atom name. See also :attr:`atoms`
 
-   :param  atom_name:  atom name, e.g. CA
-   :type   atom_name:  string
+    :param  atom_name:  atom name, e.g. CA
+    :type   atom_name:  str
 
-   :returns:           A valid :class:`AtomHandle` if an atom with the given
-                       name could be found, an invalid :class:`AtomHandle`
-                       otherwise
+    :returns:           A valid :class:`AtomHandle` if an atom with the given
+                        name could be found, an invalid :class:`AtomHandle`
+                        otherwise
 
   .. method:: GetAtomList()
 
-   Get list of all atoms of this residue. To access a single atom, use
-   :meth:`FindAtom`.
+    Get list of all atoms of this residue. To access a single atom, use
+    :meth:`FindAtom`.
+    
+  .. method:: GetChain()
+  
+    See :attr:`chain`
+  
+  .. method:: GetCenterOfAtoms()
+    
+    See :attr:`center_of_atoms`
+    
+  .. method:: GetCenterOfMass()
+  
+    See :attr:`center_of_mass`
+  
+  .. method:: GetPhiTorsion()
+    
+    See :attr:`phi_torsion`
+  
+  .. method:: GetPsiTorsion()
+  
+    See :attr:`psi_torsion`
+  
+  
 
 .. class:: AtomHandle
 
-.. class:: EntityView
-   
-   Represents a subpart of an :class:`EntityHandle`.
-   
+  Represents an atom in a molecular structure. Atoms are always part of a 
+  residue.
+  
+  .. attribute:: name
+  
+    The atom name, usually a capitalized string consisting of the element and
+    an position indicator, e.g. `G1`. In general, the atom name uniquely 
+    identifies an atom within a residue. However, this is not enforced and there
+    may be more than one atoms with the same name. 
+    
+    :type: str
+  
+  .. attribute:: qualified_name
+  
+     The qualified name consists of the atom name as well as a unique residue
+     identifier and chain name. For CA of a glycine with residue number 2 of
+     chain A, the qualified name is "A.GLY2.CA".
+     
+     :type: str
+     
+  .. attribute:: element
+  
+    The atom's element. Note that this may return an empty string. Also 
+    available as :meth:`GetElement`. Read-only.
+    
+    :type: str
+    
+  .. attribute:: mass
+  
+    The atom's mass in Dalton. Also available as :meth:`GetMass`. Read-only.
+    
+    :type: float
+    
+  .. attribute:: pos
+  
+    The atom's position in global coordinates. Also available as :meth:`GetPos`.
+    Read-only.
+    
+    :type: :class:`~ost.geom.Vec3`
+    
+  .. attribute:: radius
+  
+    The van-der-Waals radius of the atom. Also available as :meth:`GetRadius`. 
+    Read-only.
+    
+    :type: float
+  
+  .. attribute:: occupancy
+  
+    The atom's occupancy in the range 0 to 1. Also available as 
+    :meth:`GetOccupancy`. Read-only.
+    
+    :type: float
+  .. attribute:: charge
+    
+    The atom's charge
+    
+    :type: float
+
+  .. attribute:: residue
+  
+    The residue this atom belongs to.
+    
+    :type: :class:`ResidueHandle`
+  
+  .. attribute:: is_hetatm
+  
+    Indicates whether this atom is a hetatm.
+    
+  .. attribute:: bonds
+    
+    List of bonds this atom is involved in. The bonds are  in no particular 
+    order. Also available as :meth:`GetBondList`.
+    
+    :type: list of :class:`bond handles<BondHandle>`
+  
+  .. method:: FindBondToAtom(other_atom)
+
+    Finds and returns the bond formed between this atom and `other_atom`. If no 
+    bond exists between the two atoms, an invalid :class:`BondHandle` is 
+    returned.
+    
+    :param other_atom: The other atom
+    :type  other_atom: :class:`AtomHandle`
+    :rtype: :class:`BondHandle`
+
+  .. method:: GetAtomProps()
+    
+    Get atom properties such as mass, charge, element and occupancy.
+    
+    :rtype: :class:`AtomProp`
+
+  .. method:: GetBondCount()
+    
+    :rtype: int
+
+  .. method:: GetBondList()
+    
+    See :attr:`bonds`
+    
+    :rtype: :class:`BondHandleList`
+
+  .. method:: GetBondPartners()
+    
+    Get list of atoms this atom is bonded with. This method exists as a shortcut 
+    to determine all the bonding partners of an atom and avoids code like this: 
+    
+    .. code-block:: python
+    
+      bond_parters=[]
+      for bond in atom.bonds:
+        if bond.first==atom:
+          bond_partners.append(bond.second)
+        else:
+          bond_partners.append(bond.first)
+
+    :rtype: :class:`AtomHandleList`
+
+  .. method:: GetCharge()
+  
+    See :attr:`charge`
+  
+    :rtype: float
+
+  .. method:: GetElement()
+    
+    See :attr:`element`
+    
+    :rtype: str
+
+  .. method:: GetEntity()
+    
+    The entity this atom belongs to
+    
+    :rtype: :class:`EntityHandle`
+
+  .. method:: GetHashCode()
+    
+    Returns a unique identifier for this atom.
+    :rtype: int
+
+  .. method:: GetIndex()
+    
+    Returns the index of the atom.
+    
+    :rtype: int
+
+  .. method:: GetMass()
+    
+    See :attr:`mass`
+    
+    :rtype: float
+
+  .. method:: GetName()
+
+    See :attr:`name`
+    
+    :rtype: str
+
+  .. method:: GetOriginalPos()
+
+    :rtype: :class:`~ost.geom.Vec3`
+
+  .. method:: GetPos()
+
+    See :attr:`pos`
+    
+    :rtype: :class:`~ost.geom.Vec3`
+
+  .. method:: GetQualifiedName()
+    
+    See :attr:`qualified_name`
+    
+    :rtype: str
+
+  .. method:: GetRadius()
+    
+    See :attr:`radius`
+    
+    :rtype: float
+
+  .. method:: GetResidue()
+    
+    See :attr:`residue`
+    
+    :rtype: :class:`ResidueHandle`
+
+  .. method:: IsHetAtom()
+    
+    See :attr:`is_hetatm`
+    
+    :rtype: bool
+
+  .. method:: IsValid()
+  
+    See :attr:`valid`
+  
+    :rtype: bool
+  
+The View Classes
+--------------------------------------------------------------------------------
+
+.. class:: EntityView
+
+  An entity view represents a structural subset of an :class:`EntityHandle`. For 
+  an introduction ,see :doc:`../../intro-01`.
+  
+  .. attribute:: chains
+   
+    List of all chains of this entity. The chains are in the same 
+    order they have been added.
+    
+    Also available as :meth:`GetChainList`. To access a single chain, use 
+    :meth:`FindChain`.
+    
+    This property is read-only.
+    
+  .. attribute:: residues
+    
+    List of all residues of this entity. The returned residues are first 
+    sorted by chain and then from N- to C-terminus.
+    
+    This property is read-only.
+    
+    **Example usage:**
+    
+    .. code-block:: python
+    
+      for res in ent.residues:
+        print res.name, res.atom_count
+    
+    Also available as :meth:`GetResidueList`. To access a single residue, use 
+    :meth:`FindResidue`. 
+    
+    :type: A list of :class:`ResidueViews <ResidueView>`
+
+  .. attribute:: atoms
+
+    Get list of all atoms of this entity. To access a single atom, use
+    :meth:`FindAtom`.
+    
+    This property is read-only. Also available as :meth:`GetAtomList`
+    
+    :type: A list of :class:`AtomViews <AtomView>`
+
+  .. attribute:: bounds
+  
+    Axis-aligned bounding box of the entity view. Read-only.
+    
+    :type: :class:`ost.geom.AlignedCuboid`
+
+  .. attribute:: handle
+  
+     The underlying :class:`handle <EntityHandle>` of the entity view. Also 
+     available as :meth:`GetHandle`.
+     
+     :type: :class:`EntityHandle`
+
+  .. method:: CreateEmptyView()
+  
+    See :meth:`EntityHandle.CreateEmptyView`
+
+    :rtype: EntityView
+
+  .. method:: CreateFullView()
+
+    Returns a copy of this entity. Provided for `duck-typing <http://en.wikipedia.org/wiki/Duck_typing>` purposes.
+    
+    :rtype: EntityView
+  
+  .. method:: AddChain(chain_handle[, view_add_flags])
+
+    Add chain to view. By default, only the chain is added to the view, but not 
+    its residues and atoms. This behavior can be changed by passing in an
+    appropriate set of `view_add_flags`
+    
+    :param chain_handle:
+    :type  chain_handle: ChainHandle
+    :param view_add_flags: An ORed together combination of `view_add_flags`.
+    :type  view_add_flags: int
+    :rtype: class:`ChainView`
+
+  .. method:: AddResidue(residue_handle[, view_add_flags])
+
+    Add residue to view. If the residue's chain is not already part of the view, 
+    it will be added. By default, only the residue is added, but not its atoms. 
+    This behaviour can be modified by passing in an appropriate combination of 
+    `view_add_flags`.
+    
+    :param residue_handle:
+    :type  residue_handle: ResidueHandle
+    :param view_add_flags:
+    :type  view_add_flags: int
+    :rtype: class:`ResidueView`
+
+  .. method:: AddAtom(atom_handle[, view_add_flags])
+
+    Add the atom to view. The chain and residue of the atom are added to the 
+    view if they haven't already been added.
+    
+    
+    :param atom_handle: The atom handle
+    :type  atom_handle: AtomHandle
+    :param view_add_flags: An ORed together combination of ViewAddFlags
+    :type  view_add_flags: int
+    :rtype: class:`AtomView`
+
+  .. method:: AddBond(bond_handle)
+
+    Add bond to the view.
+    
+    :param bond_handle: Bond to be added
+    :type  bond_handle: BondHandle
+    :returns: True if the bond has been added, false if the bond was already 
+       present in the view.
+    :rtype: bool
+
+  .. method:: AddAllInclusiveBonds()
+  
+     Convenience method to add all bonds to the view for which both of the bond 
+     partners are in the view. This method is useful when manually assembling 
+     views.
+     
+  .. method:: RemoveChain(chain)
+    
+    Remove chain and all its residues from the entity view.
+    
+    :param chain: The chain to be removed. May be invalid
+    :type  chain: ChainView
+
+  .. method:: RemoveResidue(residue)
+
+    Remove residue from view. 
+    
+    :param residue: The residue to be removed. May be invalid
+    
+    :type  residue: ResidueView
+    
+  .. method:: RemoveAtom(atom)
+  
+    Remove atom from view
+
+    :param atom: The atom to be removed. May be invalid
+    
+    :type  atom: AtomView
+
+  .. method:: GetAngle(atom1, atom2, atom3)
+
+    :param atom1:
+    :type  atom1: AtomHandle
+    :param atom2:
+    :type  atom2: AtomHandle
+    :param atom3:
+    :type  atom3: AtomHandle
+    :rtype: float
+
+  .. method:: FindWithin(pos, radius)
+
+    Find all atoms that are within radius of the given position. See 
+    :meth:`EntityHandle.FindWithin`.
+    
+    :param pos:
+    :type  pos: :class:`~ost.geom.Vec3`
+    :param radius:
+    :type  radius: float
+    :rtype: class:`AtomViewList`
+
+  .. method:: FindChain(chain_name)
+
+    Find chain by name.
+    
+    :param chain_name:
+    :type  chain_name: str
+    :returns: The chain if present in the view, an invalid :class:`ChainView` 
+       otherwise
+    :rtype: class:`ChainView`
+
+  .. method:: FindResidue(residue)
+    
+    Find residue view of pointing to the given handle.
+      
+    :param residue: Residue handle
+    :type  residue: ResidueHandle
+    :returns: The residue view pointing the the handle, or an invalid handle if  the residue is not part of the view
+    :rtype: class:`ResidueView`
+
+  .. method:: FindAtom(chain_name, res_num, atom_name)
+
+    :param chain_name: The chain name
+    :type  chain_name: str
+    :param res_num: The residue number
+    :type  res_num: ResNum or int
+    :param atom_name: The name of the atom
+    :type  atom_name: str
+    :rtype: class:`AtomView`
+
+  .. method:: Select(query[, flags])
+
+    Perform selection on entity view. See :meth:`EntityHandle.Select`.
+    
+    :param query: The query
+    :type  query: (:class:`Query` or str)
+    :param flags: An ORed together combination of ViewAddFlags
+    :type  flags: int
+    
+    :rtype: EntityView
+
+  .. method:: Copy()
+    
+    Returns a deep copy of the entity view. The effect is identical to calling
+    
+    .. code-block:: python
+      
+      the_copy=view.Select(')
+    
+    :rtype: EntityView
+
+  .. method:: GetMass()
+
+    Get total mass of view.
+
+    :rtype: float
+
+  .. method:: GetCenterOfMass()
+
+    Get the center of mass. For a non-mass-weighted center, see 
+    :meth:`GetCenterOfAtoms`.
+    
+    :rtype: :class:`~ost.geom.Vec3`
+
+  .. method:: GetGeometricCenter()
+    
+    Get the geometric center (the center of the axis-aligned 
+    bounding box).
+    
+    :rtype: :class:`~ost.geom.Vec3`
+
+  .. method:: GetGeometricStart()
+    
+    :rtype: :class:`~ost.geom.Vec3`
+
+  .. attribute:: chain_count
+    
+    Number of chains. Read-only. See :meth:`GetChainCount`.
+    
+    :type: int
+    
+  .. attribute:: residue_count
+    
+    Number of residues. Read-only. See :meth:`GetResidueCount`.
+    
+    :type: int
+    
+  .. attribute:: atom_count
+    
+    Number of atoms. Read-only. See :meth:`GetAtomCount`.
+    
+    :type: int
+    
+  .. method:: GetCenterOfAtoms()
+    
+    Calculates the center of atoms. For a mass-weighted center, use 
+    :meth:`GetCenterOfMass`.
+    
+    :rtype: :class:`~ost.geom.Vec3`
+
+  .. method:: GetAtomList()
+
+    See :attr:`atoms`
+    
+    :rtype: class:`AtomViewList`
+
+  .. method:: GetBondCount()
+
+    Get number of bonds
+    :rtype: int
+
+  .. method:: GetChainCount()
+
+    Get number chains. See :attr:`chain_count`
+    
+    :rtype: int
+
+  .. method:: GetResidueCount()
+    
+    See :attr:`residue_count`
+    
+    :rtype: int
+
+  .. method:: GetBondList()
+
+    See :attr:`bonds`
+    
+    :rtype: :class:`BondHandleList`
+
+  .. method:: GetHandle()
+  
+    See :attr:`handle`
+
+    :rtype: class:`EntityHandle`
+
+  .. method:: GetResidueList()
+
+    :rtype: class:`ResidueViewList`
+
+  .. method:: GetGeometricEnd()
+
+    :rtype: :class:`~ost.geom.Vec3`
+
+  .. method:: GetChainList()
+
+    See :attr:`chains`
+    
+    :rtype: class:`ChainViewList`
+    
+  .. method:: GetAtomCount()
+    
+    Get number of atoms. See :attr`atom_count`.
+    :rtype: int
+
+.. class:: ChainView
+
+  .. attribute:: name
+  
+     The chain name. The name uniquely identifies the chain in the entity. In 
+     most cases, the chain name is one character. This is restriction of the PDB 
+     file format. However, you are free to use longer names as long as you don't 
+     want to save them as PDB files
+     
+     This property is read-only. To change the name, use an :class:`XCSEditor`. 
+     
+     Also available as :meth:`GetName`
+     
+     :type: str
+
+  .. attribute:: residues
+   
+     List of all residues of this chain. The residues are sorted from N- to 
+     C-terminus. Usually the residue numbers are in ascending order 
+     (see :attr:`in_sequence`).
+   
+     This property is read-only.
+   
+     **Example usage:**
+   
+     .. code-block:: python
+     
+       chain=ent.FindChain("A")
+       for res in chain.residues:
+         print res.name, res.atom_count
+   
+     Also available as :meth:`GetResidueList`. To access a single residue, use 
+     :meth:`FindResidue`. 
+
+     :type: A list of :class:`residue views<residueView>`
+  
+  .. attribute:: in_sequence
+  
+     Whether the residue numbers are in ascending order. For example:
+     
+     .. code-block:: python
+     
+       chain=ent.FindChain("A")
+       print chain.residues # [A.GLY1, A.GLY2, A.GLY4A, A.GLY4B]
+       print chain.in_sequence # prints true
+       
+       chain=ent.FindChain("B")
+       print chain.residues # [B.GLY1, B.GLY4, B.GLY3]
+       print chain.in_sequence # prints false
+
+  .. attribute:: atoms
+
+     Get list of all atoms of this chain. To access a single atom, use
+     :meth:`FindAtom`.
+   
+     This property is read-only. Also available as :meth:`GetAtomList`
+
+     :type: A list of :class:`atom handles<AtomHandle>`
+
+  .. attribute:: bounds
+
+    Axis-aligned bounding box of the chain. Read-only
+ 
+    :type: :class:`ost.geom.AlignedCuboid`
+    
+  .. attribute:: mass
+  
+    The total mass of this chain in Dalton. Also available as :meth:`GetMass`
+  
+    :type: float
+
+  .. attribute:: center_of_mass
+
+    Center of mass. Also available as :meth:`GetCenterOfMass`
+  
+    :type: :class:`~ost.geom.Vec3`
+  
+  .. attribute:: center_of_atoms
+    
+    Center of atoms (not mass weighted). Also available as 
+    :meth:`GetCenterOfAtoms`.
+    
+    :type: :class:`~ost.geom.Vec3`
+
+  .. attribute:: handle
+
+    The chain handle this view points to. Also available as :meth:`GetHandle`.
+ 
+    :type: :class:`ChainHandle`
+   
+  .. attribute:: in_sequence
+  
+    Whether the residue numbers are in ascending order. Note that the value of 
+    `in_sequence` is independent from the value of 
+    :attr:`ChainHandle.in_sequence`.
+    
+    :type: bool
+
+  .. method:: AddAtom(atom_handle[, view_add_flags])
+
+    Add atom to the view. If the residue of the atom is not already part of the 
+    view, it will be added. If the atom does not belong to chain, the result is
+    undefined. 
+    
+    :param atom_handle: The atom to be added
+    :type  atom_handle: :class:`AtomHandle`
+    :param view_add_flags: An ORed together combination of ViewAddFlags
+    :type  view_add_flags: int
+    :rtype: :class:`AtomView`
+
+  .. method:: AddResidue(residue_handle[, view_add_flags])
+
+    Add residue to the view. If the atom does not belong to chain, the result is
+    undefined. By default, only the residue, but no atoms are added to the view. 
+    To change the behavior, pass in a suitable combination of `view_add_flags`.
+    
+    :param residue_handle:
+    :type  residue_handle: :class:`ResidueHandle`
+    :param view_add_flags:
+    :type  view_add_flags: int
+    :rtype: :class:`ResidueView`
+
+  .. method:: FindAtom(res_num, atom_name)
+
+    Find atom with the given residue number and atom name. 
+    
+    :param res_num: The residue number
+    :type  res_num: :class:`ResNum`
+    :param atom_name: The atom name
+    :type  atom_name: str
+    :returns: The atom view, or an invalid atom view if no atom with the given 
+       parameters is part of the view.
+    
+    :rtype: :class:`AtomView`
+
+  .. method:: FindResidue(res_num)
+
+    Find residue by residue number.
+    
+    :param res_num:
+    :type  res_num: :class:`ResNum`
+    :rtype: :class:`ResidueView`
+    :returns: The residue view, or an invalid residue view if no residue with 
+       the given residue number is in the view.
+
+  .. method:: GetCenterOfAtoms()
+
+    See :attr:`center_of_atoms`
+    
+  .. method:: GetCenterOfMass()
+
+    See :attr:`center_of_mass`
+    
+  .. method:: GetEntity()
+    
+    See :attr:`entity`
+
+  .. method:: GetGeometricCenter()
+    
+    See :attr:`geometric_center`
+
+  .. method:: GetHandle()
+
+    See :attr:`handle`
+
+  .. method:: GetMass()
+
+    See :attr:`mass`
+
+  .. method:: GetName()
+
+    See :attr:`name`
+
+  .. method:: GetResidueByIndex(index)
+    
+    Returns the residue view at `index`. If index is negative or bigger than 
+    the number of residues minus one, an invalid ResidueView is returned.
+    
+    :param index: The index
+    :type  index: int
+    :rtype: :class:`ResidueView`
+
+  .. method:: GetResidueList()
+
+    See :attr:`residues`
+
+    :rtype: bool
+
+  .. method:: InSequence()
+  
+    See :attr:`in_sequence`
+
+  .. method:: IsValid()
+
+    See :attr:`valid`
+
+  .. method:: RemoveResidue(residue)
+
+    Remove residue from chain. If the residue is not part of the view, the 
+    chain is left unchanged.
+    
+    :param residue: The residue view. May be invalid
+    :type  residue: :class:`ResidueView`
+    :rtype: None
+
+  .. method:: RemoveResidues()
+   
+    Remove all residues from this chain view
+
+  .. method:: Select(query[, flags])
+
+    Perform query on chain. This will return an entity view containing atoms 
+    and bonds of the residue view that match the residue. In case no atom 
+    matches the predicate, an empty view is returned.
+    
+    :param query: The query
+    :type  query: :class:`Query` or str
+    :param flags: An ORed together combination of query flags
+    :type  flags: int
+    :rtype: :class:`EntityView`
+
+.. class:: ResidueView
+
+  .. attribute:: handle
+
+    The residue handle this view points to. Also available as 
+    :meth:`GetHandle`.
+
+    :type: :class:`ResidueHandle`
+
+  .. attribute:: name
+
+    The residue name is usually a str of 3 characters, e.g. `GLY` for 
+    glycine or `ALA` for alanine, but may be shorter, e.g. `G` for guanosine, 
+    or longer for structures loaded from formats other than PDB.
+  
+    This property is read-only. To change the name of the residue, use
+    :meth:`EditorBase.SetResidueName`.
+
+  .. attribute:: number
+
+    The number of this residue. The residue number has a numeric part and an
+    insertion-code. This property is read-only. Also available as 
+    :meth:`GetNumber`.
+  
+    :type: :class:`ResNum`
+
+  .. attribute:: one_letter_code
+
+    For amino acids, and nucleotides the `one_letter_code` is an alpha-numeric 
+    character. For unknown or more *exotic* residues, the one letter code is set 
+    to '?'.
+  
+    **Example**
+  
+    This code-snippet shows how to get the sequence string from a list of 
+    residues.
+  
+    .. code-block:: python
+  
+      print ''.join([r.one_letter_code for r in chain.residues])
+  
+    :type: str
+  
+  .. attribute:: bounds
+
+    Axis-aligned bounding box of the residue view. Read-only
+
+    :type: :class:`ost.geom.AlignedCuboid`
+
+  .. attribute:: mass
+
+    The total mass of this residue in Dalton. Also available as :meth:`GetMass`.
+
+    :type: float
+
+  .. attribute:: center_of_mass
+
+    Center of mass. Also available as :meth:`GetCenterOfMass`
+
+    :type: :class:`~ost.geom.Vec3`
+
+  .. attribute:: center_of_atoms
+  
+    Center of atoms (not mass weighted). Also available as 
+    :meth:`GetCenterOfAtoms`.
+  
+    :type: :class:`~ost.geom.Vec3`
+
+  .. attribute:: chain
+
+    The chain this residue belongs to. Read-only. Also available as 
+    :meth:`GetChain`
+  
+    :type: :class:`ChainView`
+
+  .. attribute:: handle
+  
+    The residue handle this view points to
+    
+    :type: :class:`ResidueHandle`
+    
+  .. method:: RemoveAtom(atom_view)
+  
+    Remove atom from residue and all associated bonds. If the atom is not part 
+    of the view, the residue view is left unchanged.
+    
+    :param atom_view: The atom to be removed. May be an invalid handle
+    :type  atom_view: :class:`AtomView`
+    :rtype: None
+
+  .. method:: GetHandle()
+
+    See :attr:`handle`
+
+  .. method:: GetMass()
+
+    See :attr:`mass`
+
+  .. method:: GetChain()
+
+    See :attr:`chain`
+
+  .. method:: FindAtom(atom_name)
+    
+    Find atom by name. Returns the atom, or an invalid atom if no atoms with 
+    the given name is part of the view.
+    
+    :param atom_name:
+    :type  atom_name: str
+    :rtype: :class:`AtomView`
+
+  .. method:: GetIndex()
+    
+    See :attr:`index`
+
+  .. method:: GetCenterOfMass()
+
+    See :attr:`center_of_mass`
+
+  .. method:: IsAtomIncluded(atom_handle)
+
+    Returns true if the given atom is part of the view, false if not.
+    
+    :param atom_handle:
+    :type  atom_handle: :class:`AtomHandle`
+    :rtype: bool
+
+  .. method:: GetGeometricCenter()
+
+    See :attr:`geometric_center`
+
+  .. method:: AddAtom(atom_handle[, flags])
+
+    Add atom to the view. 
+    :param atom_handle:
+    :type  atom_handle: :class:`AtomHandle`
+    :param flags: An ORed together combination of ViewAddFlags.
+    :type  flags: int
+    :rtype: :class:`AtomView`
+
+  .. method:: GetCenterOfAtoms()
+
+    See :attr:`center_of_atoms`
+
+  .. method:: GetAtomList()
+
+    See :attr:`atoms`
+    
+  .. method:: Select(query[, flags])
+   
+    Perform selection on residue view. This method will return an entity view 
+    containing all atoms and bonds of the residue matching the predicate. In 
+    case no atom matches the predicate, this will return an empty view.
+    
+    :param query: The query
+    :type  query: :class:`Query` or str
+    :param flags: An ORed together combination of query flags
+    :type  flags: int
+    :rtype: :class:`EntityView`
+
+
 Functions
 --------------------------------------------------------------------------------
 
diff --git a/modules/mol/base/doc/mol.rst b/modules/mol/base/doc/mol.rst
index e4de24691c513680a2c512e652cb3085301c4d6a..1ac7e3f2691b0a28cd299f7176ffa43e8bb4451b 100644
--- a/modules/mol/base/doc/mol.rst
+++ b/modules/mol/base/doc/mol.rst
@@ -1,14 +1,15 @@
-:mod:`mol` -- Molecular structures and surfaces
+:mod:`~ost.mol` -- Molecular structures and surfaces
 ================================================================================
 
-.. module:: mol
+.. module:: ost.mol
    :synopsis: Contains classes and functions to deal with molecular structures
               and surfaces
 
-The mol module implement data structure to work with molecular datasets. At its heart lie the :class:`EntityHandle` and :class:`EntityView` classes which represent molecular structures such as proteins, DNA, RNA and small molecules. There are also classes to deal with molecular surfaces.
+The mol module implements data structures to work with molecular datasets. At its heart lie the :class:`EntityHandle` and :class:`EntityView` classes which represent molecular structures such as proteins, DNA, RNA and small molecules. There are also classes to deal with molecular surfaces.
 
 .. toctree::
   
   entity
   editors
-  query
\ No newline at end of file
+  query
+  surface
\ No newline at end of file
diff --git a/modules/mol/base/doc/query.rst b/modules/mol/base/doc/query.rst
index 20c4b711a2a0e9c190efce278af82df16ac84ee1..156a91b065fa6ea08effb64767b0afdf970b4a9a 100644
--- a/modules/mol/base/doc/query.rst
+++ b/modules/mol/base/doc/query.rst
@@ -1,93 +1,137 @@
 Queries
 ================================================================================
 
-.. class:: Query
+.. currentmodule:: ost.mol
 
-  Blabla
+OpenStructure includes a powerful query system that allows you to perform custom 
+selections on a molecular entity in a convenient way.
+
+
+The Basics
+--------------------------------------------------------------------------------
 
 It is often convenient to highlight or focus certain parts of the structure. 
 OpenStructure includes a powerful query system that allows you to perform custom 
-selections in a convenient way.
+selections in a convenient way. Selections are carried out mainly by calling the Select method made available by EntityHandle and :class:`EntityView` objects while providing a query string. Queries are written using a dedicated mini-language. For example, to select all arginine residues of a given structure, one would write:
 
-Please refer to the tutorial on the query language for an introduction.
+.. code-block:: python
 
-The query language reference
---------------------------------------------------------------------------------
+  arginines=model.Select('rname=ARG')
+
+A simple selection query (called a predicate) consists in a property (here, 
+`rname`), a comparison operator (here, `=`) and an argument (here, `ARG`).  The 
+return value of a call to the :meth:`EntityHandle.Select` method is always an 
+:class:`EntityView`. The :class:`EntityView` always contains a full hierarchy of 
+elements, never standalone separated elements. In the above example, the 
+:class:`EntityView` called `arginines` will contain all chains from the 
+structure called 'model' that have at least one arginine. In turn these chains 
+will contain all residues that have been identified as arginines. The residues 
+themselves will contain references to all of their atoms. Of course, queries are 
+not limited to selecting residues based on their type, it is also possible to 
+select atom by name:
+
+.. code-block:: python
+
+  c_betas=model.Select('aname=CB') 
+
+As before, c`betas is an instance of an :class:`EntityView` object and contains 
+a full hierarchy. The main difference to the previous example is that the 
+selected residues do not contain a list of all of their atoms but only the 
+C-beta. These examples clarify why the name 'view' was chosen for this result of 
+a :meth:`~EntityHandle.Select` statement. It represents a reduced, restrained 
+way of looking at the original structure.
+
+Both the selection statements that have been used so far take strings as their arguments. However, selection properties such as `rnum` (residue number), take numeric arguments. With numeric arguments it is possible to use identity operators ( `!=` and `=`). It is also possible to compare them using the `>`, `<`, `>=` and `<=` operators. For example, the 20 N-terminal residues of a protein can be selected with:
 
-The query consists of one or more predicates combined with boolean 
-operators. A predicate takes the form *prop op value*. Operators are
-one of `` =, !=, >, >=, <=`` and ``<``. A predicate has the following form:
-*PROPERTY - OPERATOR - ARGUMENT*.
-
-The following properties may be used in predicates. The supported type of the
-value is given for each property.
-
- *      ``rname`` residue name. type: string
- *      ``rnum`` residue number. currently only numeric part is honored. 
-        type: int
- *      ``rtype`` residue type as given by the DSSP code, i.e. H for helix, E
-        for extended. type: string
- *      ``aname`` atom name. type: string
- *      ``ele`` element of atom. type: string
- *      ``cname`` chain name. type: string
- *      ``occ`` occupancy, between 0 and 1. type: float
- *      ``abfac`` B (temperature) factor of atom. type: float
- *      ``rbfac`` average B (temperature) factor of residue. type: float. 
-        Note that this does not work for views as expected. When running a 
-        second selection statement on a view, all atoms of the residue handle 
-        and not the view are considered in the calculation
- *      ``ishetatm`` whether the atom is a hetorogenous atom. type: bool or int
-        (0 for false, 1 for true)
- *      ``peptide`` whether the residue is peptide linking. type: bool or int
-        (0 for false, 1 for true)        
- *      ``x``  X coordinate of atom. type: float
- *      ``y``  Y coordinate of atom. type: float
- *      ``z``  Z coordinate of atom. type: float
- *      ``rindex`` index of residue in chain. This index is the same for views 
-        and handles
- *      For :ref:`generic properties in queries <genprop-in-queries>` see below.
-
-Distance-based selections within a given atom position are supported by
-the within statement. To select atoms within 5 Angstrom of the point
-``{1, 2, 3}``, one would write:
-
-``5 <> {1,2,3}``
-
-Negation of this expression is possible with the not operator, i.e.
-
-``not 5 <> {1,2,3}``
-will select atoms that are further than five Angstrom apart from ``{1, 2 , 3}``
-
-Abbreviations
+.. code-block:: python
+
+  n_term=model.Select('rnum<=20')
+  
+Combining predicates
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Two abbreviations exist for convenience:
+Selection predicates can be combined with boolean operators. For example , you might want to select all C atoms with crystallographic occupancy higher than 50. These atoms must match the predicate `ele=C` in addition to the predicate `occ>50`. In the query language this can be written as:
 
-Instead of writing 
+.. code-block:: python
 
-``aname=CA or aname=C or aname=O or aname=N``, 
+  model.Select('ele=C and occ>50')
+  
+Compact forms are available for several selection statements. For example, to select all arginines and aspargines, one could use a statement like:
 
-one can write 
+.. code-block:: python
+  
+  arg_and_asn=model.Select('rname=ARG or rname=ASN')
 
-``aname=CA,N,C,O``. 
+However, this is rather cumbersome as it requires the word `rname` to be typed  twice. Since the only difference between the two parts of the selection is the argument that follows  the word `rname`, the statement can also be written in an abbreviated form:
 
-For integral value ranges, one can use the colon syntax: instead of  
+.. code-block:: python
+  
+  arg_and_asn=model.Select('rname=ARG,ASN')
 
-``rnum>=10 and rnum<=20`` 
+Another example: to select residues with numbers in the range 130 to 200, one could use the following statement
 
-one can write 
+.. code-block:: python
+  
+  center=model.Select('rnum>=130 and rnum<=200')
 
-``rnum=10:20``
+or alternatively use the much nicer syntax:
+
+.. code-block:: python
+
+  center=model.Select('rnum=130:200')
+
+This last statement is completely equivalent to the previous one. This syntax  
+can be used when the selection statement requires a range of integer values 
+within a closed interval.
+
+Distance Queries
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The query
+
+.. code-block:: python
+
+  around_center=model.Select('5 <> {0,0,0}')
+  
+selects all chains, residues and atoms that lie with 5 Å to the origin of the reference system ({0,0,0}). The `<>` operator is called the ‘within’ operator. 
+Instead of a point, the within statements can also be used to return a view containing all chains, residues and atoms within a radius of another selection statement applied to the same entity.  Square brackets are used to delimit the inner query statement. 
+
+.. code-block:: python
+
+  around_hem=model.Select('5 <> [rname=HEM]')
+  model.Select('5 <> [rname=HEM and ele=C] and rname!=HEM')
+
+Bonds and Queries
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+When an :class:`EntityView` is generated by a selection, it includes by default only bonds for which both connected atoms  satisfy the query statement. This can be changed by passing the parameters `EXCLUSIVE_BONDS` or `NO_BONDS` when calling the Select method. `EXCLUSIVE_BONDS` adds bonds to the :class:`EntityView` when at least one of the two atoms falls within the boundary of the selection. `NO_BONDS` suppresses the bond inclusion step completely. 
+
+Whole Residue Queries
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+If the parameter `MATCH_RESIDUES` is passed when the Select method is called, the resulting :class:`EntityView` will include whole residues for which at least one atom satisfies the query. This means that if at least one atom in the residue  falls within the boundaries of the selection, all atoms of the residue will be included in the View.
+
+More Query Usage
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The high level interface for queries are the Select methods of the 
+EntityHandle and :class:`EntityView` classes. By passing in a query string, a view
+consisting of a subset of the elements is returned. 
+
+Queries also offer a second interface: `IsAtomSelected()`, 
+`IsResidueSelected()` and `IsChainSelected()` take an atom, residue or 
+chain as their argument and return true or false, depending on whether the 
+element fulfills the predicates.
 
 .. _genprop-in-queries:
 
 Generic Properties in Queries
---------------------------------------------------------------------------------
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The query language can also be used for numeric generic properties (i.e.
 float and int), but the syntax is slightly different. To access any generic
 properties, it needs to be specified that they are generic and at which level 
-they are defined. Therefore, all generic properties start with a ``g``, followed by an ``a``, ``r`` or ``c`` for atom, residue or chain level respectively. 
+they are defined. Therefore, all generic properties start with a `g`, followed by an `a`, `r` or `c` for atom, residue or chain level respectively. 
 
 .. code-block:: python
    
@@ -122,3 +166,95 @@ statement which can be done using a ':' character:
 Using this method, you will be warned if a generic property is not set for all
 atoms, residues or chains unless you specify a default value. So, be careful
 when you do.
+
+Available Properties
+--------------------------------------------------------------------------------
+
+The following properties may be used in predicates. The type is given for each property.
+
+Properties of Chains
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+
+**cname/chain** (str) :attr:`Chain name<ChainHandle.name>` 
+  
+Properties of Residues
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+
+**rname** (str): :attr:`Residue name<ResidueHandle.name>`
+ 
+**rnum** (int): :attr:`Residue number<ResidueHandle.number>`. Currently only the numeric part is honored.
+ 
+**rtype** (str): Residue type as given by the DSSP code, i.e. H for helix, E for extended.
+  
+**rindex** (int): :attr:`Index<ResidueHandle.index>` of residue in chain. This 
+index is the same for views and handles.
+  
+**ishetatm** (bool): Whether the atom is a :attr:`heterogenous<AtomHandle.is_hetatm>` atom.
+  
+**peptide** (bool): Whether the residue is a :meth:`peptide <ResidueHandle.IsPeptideLinking>`.
+
+**rbfac** (float): average B (temperature) factor of residue
+
+Properties of Atoms
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+
+**aname** (str): :attr:`Atom name<AtomHandle.name>`
+  
+**ele** (str): :attr:`Atom element<AtomHandle.element>`
+
+**occ** (float): :attr:`Atom occupancy<AtomHandle.occupancy>`
+
+**abfac** (float): :attr:`Atom B-factor<AtomHandle.b_factor>`
+
+**x** (float): :attr:`X<AtomHandle.pos>` coordinate of atom.
+
+**y** (float): :attr:`Y<AtomHandle.pos>` coordinate of atom.
+
+**z** (float): :attr:`Z<AtomHandle.pos>` coordinate of atom.
+
+Query API documentation
+--------------------------------------------------------------------------------
+
+In the following, the interface of the query class is described. In general, you will not have to use this interface but will pass the query as string directly. 
+
+.. class:: Query(string='')
+  
+  Create a new query from the given string. The constructor does not throw any
+  error in case the query contains syntax errors. Use :attr:`valid` to check
+  whether the query was valid.
+
+
+  .. attribute:: string
+  
+    The string used to create the query.
+  
+    :type: str
+    
+  .. attribute:: valid
+  
+    True, when the query could be compiled without syntax errors.
+    
+    :type: bool
+
+  .. attribute:: error
+    
+    If :attr:`valid` is false, this attribute contains the error message.
+    Otherwise it is set to an empty string
+    
+    :type: str
+  .. method:: IsAtomSelected(atom)
+  
+    Returns true, when the given atom handle fulfills the predicates, false if
+    not.
+
+  .. method::  IsChainSelected(chain)
+  
+    Return true if at least one of the atomso of the chain matches the
+    predicates.
+    
+  .. method:: IsResidueSelected(residue)
+  
+    Returns true, when at least one atom of the residue matches the predicates.
diff --git a/modules/mol/base/doc/surface.rst b/modules/mol/base/doc/surface.rst
new file mode 100644
index 0000000000000000000000000000000000000000..1520054f9772b163514ea5e10af05eb3687c617e
--- /dev/null
+++ b/modules/mol/base/doc/surface.rst
@@ -0,0 +1,144 @@
+Surfaces
+================================================================================
+
+.. currentmodule:: ost.mol
+
+.. class:: SurfaceHandle
+
+  TODO
+
+  .. method:: Attach(entity, cutoff)
+    
+    Attach an :class:`EntityHandle` or :class:`EntityView` to a molecular
+    surface. For each vertex of the surface, the atom which is closest to this
+    vertex and within the cutoff distance is attached. Like this, the atom and
+    its properties can be retrieved efficiently, which is e.g. used for coloring
+    a surface according to the underlying entity (see
+    :meth:`gfx.Surface.ColorBy`).
+    
+    Be aware that increasing the cutoff distance will significantly increase the
+    time needed to attach an entity to the surface.
+    
+    :param entity: entity to be attached to the surface
+    :type  entity: :class:`EntityHandle`, :class:`EntityView`
+    :param cutoff: distance cutoff
+    :type  cutoff: float
+    :rtype: None
+
+  .. method:: FindWithin(position, cutoff)
+
+    Returns all :class:`surface vertices<SurfaceVertex>` within a certain cutoff 
+    distance of a specified position.
+     
+    :param position: position
+    :type  position: :class:`~ost.geom.Vec3`
+    :param cutoff:   distance cutoff
+    :type  cutoff:   float
+    :rtype:          :class:`SurfaceVertexList`
+
+  .. method:: GetTriIDList()
+  
+    Returns a list containing all IDs of all triangles of a surface.
+
+    :rtype: list of ints
+
+  .. method:: GetVertex(id)
+
+    Returns a :class:`SurfaceVertex` with the specified ID.
+
+    :param id: vertex id
+    :type  id: int
+    :rtype: :class:`SurfaceVertex`
+
+  .. method:: GetVertexIDList()
+
+    Returns a list containing all IDs of all vertices of a surface.
+    
+    :rtype: list of ints
+
+  .. method:: Invert()
+
+    Does an in place inversion of all vertex normal vectors.
+     
+    :rtype: None
+
+.. class:: SurfaceVertex
+
+  TODO
+  
+  .. method:: SurfaceVertex()
+              SurfaceVertex(pos, norm, type, atom)
+              
+    Creates a new SurfaceVertex.
+              
+    :param pos:  vertex position
+    :type  pos:  :class:`geom.Vec3`
+    :param norm: vertex normal vector
+    :type  norm: :class:`geom.Vec3`
+    :param type: vertex type
+    :type  type: int
+    :param atom: attached atom
+    :type  atom: :class:`AtomHandle` 
+              
+  .. attribute:: Atom
+    
+    :class:`AtomHandle` attached to the surface vertex.
+    
+    The AtomHandle is invalid, if no :class:`~ost.mol.EntityHandle` has been
+    attached or if no atom was found within the cutoff distance.
+    
+    See :meth:`SurfaceHandle.Attach` for further details.
+    
+    :type: :class:`AtomHandle`
+  
+  .. attribute:: Normal
+    
+    Normal vector of the surface vertex.
+  
+    :type: :class:`~ost.geom.Vec3`
+  
+  .. attribute:: Position
+  
+    Spatial position of the surface vertex.
+  
+    :type: :class:`~ost.geom.Vec3`
+
+.. class:: SurfaceVertexList
+
+  .. method:: append(vertex)
+
+    Add a single surface vertex.
+
+    :param vertex: surface vertex
+    :type  vertex: :class:`SurfaceVertex`
+    :rtype: None
+
+  .. method:: extend(list)
+  
+    Add a list of surface vertices.
+
+    :param list: list of surface vertices
+    :type  list: :class:`SurfaceVertexList`
+    :rtype: None
+
+.. class:: SurfaceTriIDList
+
+  .. method:: append(id)
+  
+    Add a single triangle ID.
+
+    :param id: trinangle vertex id
+    :type  id: int
+    :rtype: None
+
+  .. method:: extend(list)
+
+    Add a list of triangle IDs.
+
+    :param list: list of triangle vertex ids
+    :type  list: list of ints
+    :rtype: None
+
+
+
+
diff --git a/modules/mol/base/pymod/CMakeLists.txt b/modules/mol/base/pymod/CMakeLists.txt
index 590af690986b9c300a28917bdbc0aea48f6f0cd9..29c336dca643d9bbafac80ad9fb5e3959e6ef48c 100644
--- a/modules/mol/base/pymod/CMakeLists.txt
+++ b/modules/mol/base/pymod/CMakeLists.txt
@@ -18,6 +18,7 @@ export_query_view_wrapper.cc
 export_torsion.cc
 export_visitor.cc
 wrap_mol.cc
+export_entity_property_mapper.cc
 )
 
 pymod(NAME mol CPP ${OST_BASE_PYMOD_SOURCES} PY __init__.py)
diff --git a/modules/mol/base/pymod/__init__.py b/modules/mol/base/pymod/__init__.py
index 0665094dc7b47ae4acf5301041957f089246018c..6431ae0ce891d8e3b8fdbc2dd1ff42c60e90d046 100644
--- a/modules/mol/base/pymod/__init__.py
+++ b/modules/mol/base/pymod/__init__.py
@@ -16,4 +16,6 @@
 # along with this library; if not, write to the Free Software Foundation, Inc.,
 # 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #------------------------------------------------------------------------------
-from _mol import *
\ No newline at end of file
+from _mol import *
+import ost.geom as _geom
+from ost.mol import alg
\ No newline at end of file
diff --git a/modules/mol/base/pymod/bounds.hh b/modules/mol/base/pymod/bounds.hh
new file mode 100644
index 0000000000000000000000000000000000000000..80010c15a69da2909c301685e33b4c3d01efc94d
--- /dev/null
+++ b/modules/mol/base/pymod/bounds.hh
@@ -0,0 +1,36 @@
+#ifndef OST_MOL_EXPORT_BOUNDS_HH
+#define OST_MOL_EXPORT_BOUNDS_HH
+
+#include <ost/log.hh>
+  
+template <typename H>
+geom::Vec3 geom_center(const H& h)
+{
+  return h.GetBounds().GetCenter();
+}
+
+template <typename H>
+geom::Vec3 geom_size(const H& h)
+{
+  WARN_DEPRECATED("GetBoundarySize()/boundary_size is deprecated. Use "
+                  "bounds.size instead")
+  return h.GetBounds().GetSize();
+}
+
+template <typename H>
+geom::Vec3 geom_start(const H& h)
+{
+  WARN_DEPRECATED("GetGeometricStart()/geometric_start is deprecated. Use "
+                  "bounds.min instead")
+  return h.GetBounds().GetMin();
+}
+
+template <typename H>
+geom::Vec3 geom_end(const H& h)
+{
+  WARN_DEPRECATED("GetGeometricEnd()/geometric_end is deprecated. Use "
+                  "bounds.max instead")
+  return h.GetBounds().GetMax();
+}
+
+#endif
diff --git a/modules/mol/base/pymod/export_atom.cc b/modules/mol/base/pymod/export_atom.cc
index c2133beb95fcc8cf280db30c176a075824eedf68..13fc2ee554980d1941bb074db842f2364653bac4 100644
--- a/modules/mol/base/pymod/export_atom.cc
+++ b/modules/mol/base/pymod/export_atom.cc
@@ -27,7 +27,7 @@ using namespace ost;
 using namespace ost::mol;
 
 #include <ost/export_helper/generic_property_def.hh>
-
+#include <ost/export_helper/vector.hh>
 void export_Atom()
 {
   class_<AtomBase> atom_base("AtomBase", no_init);
@@ -76,9 +76,9 @@ void export_Atom()
   class_<AtomHandle, bases<AtomBase> >("AtomHandle", init<>())
     .def("GetResidue",&AtomHandle::GetResidue)
     .add_property("residue",&AtomHandle::GetResidue)
-    .def("Apply", &AtomHandle::Apply, args("visitor"))
     .def("GetBondList", &AtomHandle::GetBondList)
     .def("GetBondCount", &AtomHandle::GetBondCount)
+    .add_property("valid", &AtomHandle::IsValid)    
     .def("GetEntity", &AtomHandle::GetEntity)
     .def("GetHandle", &AtomHandle::GetHandle)
     .add_property("handle", &AtomHandle::GetHandle)
@@ -94,6 +94,7 @@ void export_Atom()
 
   class_<AtomHandleList>("AtomHandleList", no_init)
     .def(vector_indexing_suite<AtomHandleList>())
+    .def(ost::VectorAdditions<AtomHandleList>())
   ;
   class_<AtomProp>("AtomProp", init<>())
     .def_readwrite("element", &AtomProp::element)
diff --git a/modules/mol/base/pymod/export_atom_view.cc b/modules/mol/base/pymod/export_atom_view.cc
index 036a87ae056ded83b3f30b4803315aa9f3295a89..d8bc4a0eeb9e4aaf72a7d083d2b03d3e375767f2 100644
--- a/modules/mol/base/pymod/export_atom_view.cc
+++ b/modules/mol/base/pymod/export_atom_view.cc
@@ -22,26 +22,23 @@
 using namespace boost::python;
 
 #include <ost/mol/mol.hh>
-
+#include <ost/export_helper/vector.hh>
 using namespace ost;
 using namespace ost::mol;
 
 void export_AtomView()
 {
-  void (AtomView::* apply1)(EntityVisitor&) = &AtomView::Apply;
-  void (AtomView::* apply2)(EntityViewVisitor&) = &AtomView::Apply;
 
   class_<AtomView, bases<AtomBase> >("AtomView", init<>())
     .def("GetResidue",&AtomView::GetResidue)
     .add_property("residue",&AtomView::GetResidue)
-    .def("Apply", apply1, args("visitor"))
-    .def("Apply", apply2, args("visitor"))
     .def(self==self)
     .def(self!=self)
     .add_property("handle", &AtomView::GetHandle)
     .def("RemoveBonds", &AtomView::RemoveBonds)
     .def("GetHandle", &AtomView::GetHandle)
     .def("GetBondCount", &AtomView::GetBondCount)
+    .add_property("valid", &AtomView::IsValid)    
     .def("GetBondList", &AtomView::GetBondList)
     .def("GetHashCode", &AtomView::GetHashCode)
     .def("__hash__", &AtomView::GetHashCode)
@@ -50,6 +47,7 @@ void export_AtomView()
   ;
   class_<AtomViewList>("AtomViewList", init<>())
     .def(vector_indexing_suite<AtomViewList>())
+    .def(ost::VectorAdditions<AtomViewList>())
   ;
 }
 
diff --git a/modules/mol/base/pymod/export_bond.cc b/modules/mol/base/pymod/export_bond.cc
index ddfde472156fe0bdaaed309d93182cf42ff9963d..e409f0a86d6412447cff85ceb83612124398c73a 100644
--- a/modules/mol/base/pymod/export_bond.cc
+++ b/modules/mol/base/pymod/export_bond.cc
@@ -30,9 +30,6 @@ using namespace ost::mol;
 
 void export_Bond()
 {
-  void (BondHandle::* apply1)(EntityVisitor&) = &BondHandle::Apply;
-  void (BondHandle::* apply2)(EntityViewVisitor&) = &BondHandle::Apply;
-
   class_<BondHandle> bond_handle("BondHandle", init<>());
   bond_handle
     .def("GetPos", &BondHandle::GetPos)
@@ -55,8 +52,6 @@ void export_Bond()
     .def("GetBondOrder",&BondHandle::GetBondOrder)
     .def("SetBondOrder",&BondHandle::SetBondOrder)
     .def("IsValid", &BondHandle::IsValid)       
-    .def("Apply",apply1)
-    .def("Apply",apply2)
     .def(self == self)
     .def(self != self)
     .def(self_ns::str(self))
diff --git a/modules/mol/base/pymod/export_chain.cc b/modules/mol/base/pymod/export_chain.cc
index 57e717ebac7e5a63c108eb0568c9815d09a7994e..ad473535b85d64e00e3a37bb32e08acaada3443c 100644
--- a/modules/mol/base/pymod/export_chain.cc
+++ b/modules/mol/base/pymod/export_chain.cc
@@ -21,10 +21,11 @@
 using namespace boost::python;
 
 #include <ost/mol/mol.hh>
-
+#include <ost/export_helper/vector.hh>
 using namespace ost;
 using namespace ost::mol;
 #include <ost/export_helper/generic_property_def.hh>
+#include "bounds.hh"
 
 namespace {
   typedef void (ChainHandle::*RnumMethod)(const ResNum&);
@@ -65,7 +66,6 @@ void export_Chain()
     //.def("AppendResidue", append_one_arg, args("residue_key"))
     //.def("AppendResidue", append_two_arg, args("residue_key", 
     //                                            "residue_number"))
-    .def("Apply", &ChainHandle::Apply, args("visitor"))
     .def("GetNext", &ChainHandle::GetNext)
     .def("GetPrev", &ChainHandle::GetPrev)
     //.def("InsertResidueBefore", &ChainHandle::InsertResidueBefore, 
@@ -84,13 +84,23 @@ void export_Chain()
     .def("GetMass", &ChainHandle::GetMass)
     .def("GetCenterOfMass", &ChainHandle::GetCenterOfMass)
     .def("GetCenterOfAtoms", &ChainHandle::GetCenterOfAtoms)
-    .def("GetGeometricCenter", &ChainHandle::GetGeometricCenter)
-    .add_property("geometric_center", &ChainHandle::GetGeometricCenter)
-    .def("GetGeometricStart", &ChainHandle::GetGeometricStart)
-    .def("GetGeometricEnd", &ChainHandle::GetGeometricEnd)
+    .def("GetGeometricCenter", geom_center<ChainHandle>)
+    .add_property("geometric_center", geom_center<ChainHandle>)
+    .add_property("mass", &ChainHandle::GetMass)
+    .add_property("center_of_mass", &ChainHandle::GetCenterOfMass)
+    .add_property("center_of_atoms", &ChainHandle::GetCenterOfAtoms)  
+    .add_property("in_sequence", &ChainHandle::InSequence)  
+    .add_property("valid", &ChainHandle::IsValid)    
+    .def("GetBounds", &ChainHandle::GetBounds)
+    .add_property("bounds", &ChainHandle::GetBounds)
+    .def("GetGeometricStart", geom_start<ChainHandle>)
+    .def("GetGeometricEnd", geom_end<ChainHandle>)
+    .def(self==self)
+    .def(self!=self)
   ;
   
   class_<ChainHandleList>("ChainHandleList", no_init)
     .def(vector_indexing_suite<ChainHandleList>())
+    .def(ost::VectorAdditions<ChainHandleList>())    
   ;
 }
diff --git a/modules/mol/base/pymod/export_chain_view.cc b/modules/mol/base/pymod/export_chain_view.cc
index 8de0f77d7a3220db2fd8abe95fdab72340108285..117e4ce837fba5e8111d1ff0ebf473559b1340f9 100644
--- a/modules/mol/base/pymod/export_chain_view.cc
+++ b/modules/mol/base/pymod/export_chain_view.cc
@@ -24,9 +24,10 @@ using namespace boost::python;
 #include <ost/mol/query.hh>
 #include <ost/mol/chain_handle.hh>
 #include <ost/mol/entity_visitor.hh>
-
+#include <ost/export_helper/vector.hh>
 using namespace ost;
 using namespace ost::mol;
+#include "bounds.hh"
 
 namespace {
 typedef ResidueView (ChainView::*RnumMethod)(const ResNum&) const;
@@ -58,11 +59,9 @@ void export_ChainView()
 {
   class_<ChainViewList>("ChainViewList", no_init)
     .def(vector_indexing_suite<ChainViewList>())
+    .def(ost::VectorAdditions<ChainViewList>())    
   ;
 
-  void (ChainView::* apply1)(EntityVisitor&) = &ChainView::Apply;
-  void (ChainView::* apply2)(EntityViewVisitor&) = &ChainView::Apply;
-
   class_<ChainView, bases<ChainBase> >("ChainView", init<>())
     .def("GetResidueList", &ChainView::GetResidueList,
          return_value_policy<copy_const_reference>())
@@ -80,8 +79,6 @@ void export_ChainView()
          X_add_residue_overloads(args("residue_handle", "view_add_flags")))
     .def("AddResidue", vm, 
          X_add_residue_overloads(args("residue_view", "view_add_flags")))         
-    .def("Apply", apply1, args("visitor"))
-    .def("Apply", apply2, args("visitor"))
     .def("RemoveResidue", &ChainView::RemoveResidue)
     .def("RemoveResidues", &ChainView::RemoveResidues)
     .def("InSequence", &ChainView::InSequence)
@@ -96,10 +93,19 @@ void export_ChainView()
     .def("GetMass", &ChainView::GetMass)
     .def("GetCenterOfMass", &ChainView::GetCenterOfMass)
     .def("GetCenterOfAtoms", &ChainView::GetCenterOfAtoms)
-    .def("GetGeometricCenter", &ChainView::GetGeometricCenter)
-    .add_property("geometric_center", &ChainView::GetGeometricCenter)
-    .def("GetGeometricStart", &ChainView::GetGeometricStart)
-    .def("GetGeometricEnd", &ChainView::GetGeometricEnd)
+    .def("GetGeometricCenter", geom_center<ChainView>)
+    .add_property("geometric_center", geom_center<ChainView>)
+    .add_property("mass", &ChainView::GetMass)
+    .add_property("center_of_mass", &ChainView::GetCenterOfMass)
+    .add_property("center_of_atoms", &ChainView::GetCenterOfAtoms)
+    .add_property("valid", &ChainView::IsValid)      
+    .add_property("in_sequence", &ChainView::InSequence)    
+    .def("GetGeometricStart", geom_start<ChainView>)
+    .def("GetGeometricEnd", geom_end<ChainView>)
+    .def("GetBounds", &ChainView::GetBounds)
+    .add_property("bounds", &ChainView::GetBounds)
+    .def(self==self)
+    .def(self!=self)
   ;
 
 
diff --git a/modules/mol/base/pymod/export_entity.cc b/modules/mol/base/pymod/export_entity.cc
index 733c867d66e3e3231bda88d8ce9a542596ab2aae..b0df16c0c9065f8084127b48a1055cd29090d849 100644
--- a/modules/mol/base/pymod/export_entity.cc
+++ b/modules/mol/base/pymod/export_entity.cc
@@ -23,7 +23,7 @@ using namespace boost::python;
 #include <ost/mol/entity_view.hh>
 #include <ost/mol/query.hh>
 #include <ost/mol/mol.hh>
-
+#include "bounds.hh"
 
 using namespace ost;
 using namespace ost::mol;
@@ -55,6 +55,7 @@ BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(X_xcs_editor_overloads,
 BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(X_ics_editor_overloads, 
                                       EntityHandle::RequestICSEditor, 0, 1)                                      
 
+
 }
 
 void export_Entity()
@@ -81,11 +82,13 @@ void export_Entity()
     .def("GetMass", &EntityHandle::GetMass)
     .def("GetCenterOfMass", &EntityHandle::GetCenterOfMass)
     .def("GetCenterOfAtoms", &EntityHandle::GetCenterOfAtoms)
-    .def("GetGeometricCenter", &EntityHandle::GetGeometricCenter)
-    .add_property("geometric_center", &EntityHandle::GetGeometricCenter)
-    .def("GetGeometricStart", &EntityHandle::GetGeometricStart)
-    .def("GetGeometricEnd", &EntityHandle::GetGeometricEnd)
-    .def("GetBoundarySize", &EntityHandle::GetBoundarySize)
+    .def("GetGeometricCenter", geom_center<EntityHandle>)
+    .add_property("geometric_center", geom_center<EntityHandle>)
+    .add_property("geometric_end", geom_end<EntityHandle>)
+    .add_property("geometric_start", geom_start<EntityHandle>)
+    .def("GetGeometricStart", geom_start<EntityHandle>)
+    .def("GetGeometricEnd", geom_end<EntityHandle>)
+    .def("GetBoundarySize", geom_size<EntityHandle>)
     .def("GetResidueCount", &EntityHandle::GetResidueCount)
     .def("GetAtomCount", &EntityHandle::GetAtomCount)
     .def("GetBondCount", &EntityHandle::GetBondCount)
@@ -95,11 +98,13 @@ void export_Entity()
     .add_property("chain_count", &EntityHandle::GetChainCount)
     .add_property("residue_count", &EntityHandle::GetResidueCount)
     .add_property("atom_count", &EntityHandle::GetAtomCount)
+    .add_property("mass", &EntityHandle::GetMass)
+    .add_property("center_of_mass", &EntityHandle::GetCenterOfMass)
+    .add_property("center_of_atoms", &EntityHandle::GetCenterOfAtoms)
     .def("FindWithin", &EntityHandle::FindWithin)
     .def("GetAngle", get_angle1)
     .def("GetAngle", get_angle2)
     .def("FindTorsion", &EntityHandle::FindTorsion)
-    .def("Apply", &EntityHandle::Apply)
     .def("Copy", &EntityHandle::Copy)
     .def("GetBondList", &EntityHandle::GetBondList)
     .def("GetAtomList", &EntityHandle::GetAtomList)
@@ -108,6 +113,9 @@ void export_Entity()
     .add_property("atoms", &EntityHandle::GetAtomList)
     .add_property("chains", &EntityHandle::GetChainList)
     .add_property("bonds", &EntityHandle::GetBondList)
+    .add_property("valid", &EntityHandle::IsValid)
+    .def("GetBounds", &EntityHandle::GetBounds)
+    .add_property("bounds", &EntityHandle::GetBounds)
     .def("GetTransformationMatrix", &EntityHandle::GetTransformationMatrix,
          return_value_policy<copy_const_reference>())
     .add_property("transform", 
diff --git a/modules/mol/base/pymod/export_entity_property_mapper.cc b/modules/mol/base/pymod/export_entity_property_mapper.cc
new file mode 100644
index 0000000000000000000000000000000000000000..fa271bed83a04df8773f8110e773b94e5a7676e1
--- /dev/null
+++ b/modules/mol/base/pymod/export_entity_property_mapper.cc
@@ -0,0 +1,68 @@
+#include <boost/python.hpp>
+
+#include <ost/mol/entity_property_mapper.hh>
+
+using namespace ost;
+using namespace ost::mol;
+using namespace boost::python;
+
+namespace {
+
+
+Real (EntityPropertyMapper::*get_ah_a)(const AtomHandle&) const=&EntityPropertyMapper::Get;
+Real (EntityPropertyMapper::*get_av_a)(const AtomView&) const=&EntityPropertyMapper::Get;
+Real (EntityPropertyMapper::*get_rh_a)(const ResidueHandle&) const=&EntityPropertyMapper::Get;
+Real (EntityPropertyMapper::*get_rv_a)(const ResidueView&) const=&EntityPropertyMapper::Get;
+Real (EntityPropertyMapper::*get_ch_a)(const ChainHandle&) const=&EntityPropertyMapper::Get;
+Real (EntityPropertyMapper::*get_cv_a)(const ChainView&) const=&EntityPropertyMapper::Get;
+
+
+Real (EntityPropertyMapper::*get_ah_b)(const AtomHandle&, Real) const=&EntityPropertyMapper::Get;
+Real (EntityPropertyMapper::*get_av_b)(const AtomView&, Real) const=&EntityPropertyMapper::Get;
+Real (EntityPropertyMapper::*get_rh_b)(const ResidueHandle&, Real) const=&EntityPropertyMapper::Get;
+Real (EntityPropertyMapper::*get_rv_b)(const ResidueView&, Real) const=&EntityPropertyMapper::Get;
+Real (EntityPropertyMapper::*get_ch_b)(const ChainHandle&, Real) const=&EntityPropertyMapper::Get;
+Real (EntityPropertyMapper::*get_cv_b)(const ChainView&, Real) const=&EntityPropertyMapper::Get;
+
+EntityPropertyMapper create_epm(const String& prop_name, char level)
+{
+  switch(level) {
+    case 'A':
+    case 'a':
+      return EntityPropertyMapper(prop_name, Prop::ATOM);
+    case 'R':
+    case 'r':
+      return EntityPropertyMapper(prop_name, Prop::RESIDUE);
+    case 'C':
+    case 'c':
+      return EntityPropertyMapper(prop_name, Prop::CHAIN);
+    case 'U':
+    case 'u':
+      return EntityPropertyMapper(prop_name, Prop::UNSPECIFIED);
+    default:
+      throw std::runtime_error(String("unknown property level '")+level+"'");
+  }
+}
+
+}
+
+void export_EntityPropertyMapper()
+{
+  class_<EntityPropertyMapper>("EntityPropertyMapper", 
+                               init<const String&, 
+                                    Prop::Level>(arg("level")=Prop::UNSPECIFIED))
+    .def("__init__", &create_epm)
+    .def("Get", get_ah_a)
+    .def("Get", get_av_a)
+    .def("Get", get_rh_a)
+    .def("Get", get_rv_a)
+    .def("Get", get_ch_a)
+    .def("Get", get_cv_a)
+    .def("Get", get_ah_b)
+    .def("Get", get_av_b)
+    .def("Get", get_rh_b)
+    .def("Get", get_rv_b)
+    .def("Get", get_ch_b)
+    .def("Get", get_cv_b)
+  ;  
+}
diff --git a/modules/mol/base/pymod/export_entity_view.cc b/modules/mol/base/pymod/export_entity_view.cc
index 293401f1c16c211c1155b6f6008f714865a5e42b..4eadd54cdcb121c0507ffd2a4f0bdfb06f43f6d3 100644
--- a/modules/mol/base/pymod/export_entity_view.cc
+++ b/modules/mol/base/pymod/export_entity_view.cc
@@ -26,6 +26,7 @@ using namespace boost::python;
 #include <ost/mol/view_op.hh>
 using namespace ost;
 using namespace ost::mol;
+#include "bounds.hh"
 
 namespace {
 
@@ -80,25 +81,22 @@ void export_EntityView()
     .export_values()
   ;
 
-  void (EntityView::* apply1)(EntityVisitor&) = &EntityView::Apply;
-  void (EntityView::* apply2)(EntityViewVisitor&) = &EntityView::Apply;
-
   Real (EntityView::*get_angle1)(const AtomHandle&, const AtomHandle&, const AtomHandle&) const = &EntityView::GetAngle;
   Real (EntityView::*get_angle2)(const AtomView&, const AtomView&, const AtomView&) const = &EntityView::GetAngle;
 
   class_<EntityView, bases<EntityBase> >("EntityView", init<>())
-    .def("Apply",apply1)
-    .def("Apply",apply2)
     .def("Copy", &EntityView::Copy)
+    .def("ExtendViewToResidues", &EntityView::ExtendViewToResidues)
+    .def("ExtendViewToSurrounding", &EntityView::ExtendViewToSurrounding)
     .def("FindChain", find_chain_str)
     .def("FindResidue", &EntityView::FindResidue)
     .def("FindAtom", find_atom_a)
     .def("FindAtom", find_atom_b)    
     .def("GetAtomCount", &EntityView::GetAtomCount)
-    .def("GetGeometricStart", &EntityView::GetGeometricStart)
-    .def("GetGeometricEnd", &EntityView::GetGeometricEnd)
-    .def("GetGeometricCenter", &EntityView::GetGeometricCenter)
-    .add_property("geometric_center", &EntityView::GetGeometricCenter)
+    .def("GetGeometricStart", geom_start<EntityView>)
+    .def("GetGeometricEnd", geom_end<EntityView>)
+    .def("GetGeometricCenter", geom_center<EntityView>)
+    .add_property("geometric_center", geom_center<EntityView>)
     .def("GetCenterOfMass", &EntityView::GetCenterOfMass)
     .def("GetCenterOfAtoms", &EntityView::GetCenterOfAtoms)
     .def("GetMass", &EntityView::GetMass)
@@ -119,6 +117,10 @@ void export_EntityView()
     .add_property("residue_count", &EntityView::GetResidueCount)
     .add_property("atom_count", &EntityView::GetAtomCount)
     .add_property("bond_count", &EntityView::GetBondCount)
+    .add_property("mass", &EntityView::GetMass)
+    .add_property("center_of_mass", &EntityView::GetCenterOfMass)
+    .add_property("center_of_atoms", &EntityView::GetCenterOfAtoms)
+    .add_property("valid", &EntityView::IsValid)    
     .def("GetResidueList", &EntityView::GetResidueList)
     .def("GetAtomList", &EntityView::GetAtomList)
     .add_property("atoms", &EntityView::GetAtomList)
@@ -154,6 +156,8 @@ void export_EntityView()
     .def(self==self)
     .def(self!=self)
     .def("Dump", &EntityView::Dump)
+    .def("GetBounds", &EntityView::GetBounds)
+    .add_property("bounds", &EntityView::GetBounds)    
   ;
   def("Union", &Union);
   def("Difference", &Difference);
diff --git a/modules/mol/base/pymod/export_query.cc b/modules/mol/base/pymod/export_query.cc
index 2a301e0b3407b7f7a20f1a61bdf28954267ba864..4b54cb1865981f4ee125fe01a833a54db745daa6 100644
--- a/modules/mol/base/pymod/export_query.cc
+++ b/modules/mol/base/pymod/export_query.cc
@@ -29,6 +29,12 @@ void translate_QueryError(const QueryError& e) {
   PyErr_SetString(PyExc_RuntimeError, e.GetFormattedMessage().c_str());
 }
 
+String error_msg(Query& q)
+{
+  return QueryError(q.GetQueryString(), 
+                    q.GetErrorDescription()).GetFormattedMessage();
+}
+
 void export_Query()
 {
   
@@ -36,6 +42,7 @@ void export_Query()
   
   class_<QueryErrorDesc>("QueryErrorDesc", no_init)
     .def_readonly("msg", &QueryErrorDesc::msg)
+    .def_readonly("range", &QueryErrorDesc::range)
   ;
   
   enum_<QueryFlag::Flag>("QueryFlag")
@@ -52,7 +59,9 @@ void export_Query()
     .def("IsAtomSelected", &Query::IsAtomSelected)    
     .def("IsResidueSelected", &Query::IsResidueSelected)
     .def("IsChainSelected", &Query::IsChainSelected)    
-    .add_property("String",  
+    .add_property("valid", &Query::IsValid)
+    .add_property("error", &error_msg)
+    .add_property("string",  
                   make_function(&Query::GetQueryString,
                                 return_value_policy<copy_const_reference>()))
     .def("GetErrorDescription", &Query::GetErrorDescription, 
diff --git a/modules/mol/base/pymod/export_query_view_wrapper.cc b/modules/mol/base/pymod/export_query_view_wrapper.cc
index 9c7c58a4b483826cd7f164c2897bc574c939c7cb..9bc933069cca864eb3e5c0d7837e3b2becb7f2ef 100644
--- a/modules/mol/base/pymod/export_query_view_wrapper.cc
+++ b/modules/mol/base/pymod/export_query_view_wrapper.cc
@@ -32,16 +32,18 @@ void export_QueryViewWrapper()
   class_<QueryViewWrapper>("QueryViewWrapper", init<>())
     .def(init<const EntityHandle&>())
     .def(init<const EntityView&>())
-    .def(init<const Query&, const EntityHandle&, optional<QueryFlags> >())
-    .def(init<const Query&, const EntityView&, optional<QueryFlags> >())
+    .def(init<const Query&, const EntityHandle&>())
+    .def(init<const Query&, optional<const EntityView&> >())
+    .def(init<const Query&, QueryFlags, const EntityHandle&>())
+    .def(init<const Query&, QueryFlags, optional<const EntityView&> >())
     .def("GetEntityView",&QueryViewWrapper::GetEntityView)
     .def("DependsOnQuery",&QueryViewWrapper::DependsOnQuery)
     .def("IsDataValid", &QueryViewWrapper::IsDataValid)
     .def("SetQuery", &QueryViewWrapper::SetQuery)
     .def("GetQuery", &QueryViewWrapper::GetQuery
         ,return_value_policy<copy_const_reference>())
-    .def("SetQueryFlags", &QueryViewWrapper::SetQueryFlags)
-    .def("GetQueryFlags", &QueryViewWrapper::GetQueryFlags)
+    .def("GetFlags", &QueryViewWrapper::GetFlags)
+    .def("SetFlags", &QueryViewWrapper::SetFlags)
     .add_property("entity_view", &QueryViewWrapper::GetEntityView)
     .add_property("query", make_function(&QueryViewWrapper::GetQuery
         ,return_value_policy<copy_const_reference>()))
diff --git a/modules/mol/base/pymod/export_residue.cc b/modules/mol/base/pymod/export_residue.cc
index 27575f800ff1b37971cde43d484557ebe3ed855d..ef844831cb222c399cf5a4405803be9224c2c48e 100644
--- a/modules/mol/base/pymod/export_residue.cc
+++ b/modules/mol/base/pymod/export_residue.cc
@@ -22,12 +22,12 @@
 using namespace boost::python;
 
 #include <ost/mol/mol.hh>
-
+#include <ost/export_helper/vector.hh>
 using namespace ost;
 using namespace ost::mol;
 
 #include <ost/export_helper/generic_property_def.hh>
-
+#include "bounds.hh"
 namespace {
   
   
@@ -109,6 +109,8 @@ void export_Residue()
                  &ResidueBase::SetOneLetterCode)  
     .def("GetQualifedName", &ResidueBase::GetQualifiedName)
     .def("IsPeptideLinking", &ResidueBase::IsPeptideLinking)
+    .add_property("peptide_linking", &ResidueBase::IsPeptideLinking)
+    
     .def("GetKey", &ResidueBase::GetKey,
          return_value_policy<copy_const_reference>())
      .def("GetName", &ResidueBase::GetName,
@@ -154,7 +156,6 @@ void export_Residue()
     .add_property("atoms", &ResidueHandle::GetAtomList)
     .def("FindAtom", &ResidueHandle::FindAtom, args("atom_name"))
     .def("FindTorsion", &ResidueHandle::FindTorsion)
-    .def("Apply", &ResidueHandle::Apply, args("visitor"))
     .def("GetAtomCount", &ResidueHandle::GetAtomCount)
     .def("GetBondCount", &ResidueHandle::GetBondCount)
     .add_property("atom_count", &ResidueHandle::GetAtomCount)
@@ -164,16 +165,26 @@ void export_Residue()
     .def("GetMass", &ResidueHandle::GetMass)
     .def("GetCenterOfMass", &ResidueHandle::GetCenterOfMass)
     .def("GetCenterOfAtoms", &ResidueHandle::GetCenterOfAtoms)
-    .def("GetGeometricCenter", &ResidueHandle::GetGeometricCenter)
-    .add_property("geometric_center", &ResidueHandle::GetGeometricCenter)
-    .def("GetGeometricStart", &ResidueHandle::GetGeometricStart)
-    .def("GetGeometricEnd", &ResidueHandle::GetGeometricEnd)
+    .def("GetGeometricCenter", geom_center<ResidueHandle>)
+    .add_property("mass", &ResidueHandle::GetMass)
+    .add_property("center_of_mass", &ResidueHandle::GetCenterOfMass)
+    .add_property("center_of_atoms", &ResidueHandle::GetCenterOfAtoms)  
+    .add_property("geometric_center", geom_center<ResidueHandle>)
+    .add_property("phi_torsion", &ResidueHandle::GetPhiTorsion)
+    .add_property("psi_torsion", &ResidueHandle::GetPsiTorsion)
+    .add_property("omega_torsion", &ResidueHandle::GetOmegaTorsion)
+    .add_property("valid", &ResidueHandle::IsValid) 
+    .def("GetGeometricStart", geom_start<ResidueHandle>)
+    .def("GetGeometricEnd", geom_end<ResidueHandle>)
     .def(self==self)
     .def(self!=self)
     .def("__hash__", &ResidueHandle::GetHashCode)
+    .def("GetBounds", &ResidueHandle::GetBounds)
+    .add_property("bounds", &ResidueHandle::GetBounds)    
   ;
 
   class_<ResidueHandleList>("ResidueHandleList", no_init)
     .def(vector_indexing_suite<ResidueHandleList>())
+    .def(ost::VectorAdditions<ResidueHandleList>())    
   ;
 }
diff --git a/modules/mol/base/pymod/export_residue_view.cc b/modules/mol/base/pymod/export_residue_view.cc
index 29943f54a99392eb06afce6d84d91ffe9e0d4da6..f8dbd089628879641e24731629afe92a108e4403 100644
--- a/modules/mol/base/pymod/export_residue_view.cc
+++ b/modules/mol/base/pymod/export_residue_view.cc
@@ -22,9 +22,10 @@
 using namespace boost::python;
 
 #include <ost/mol/mol.hh>
-
+#include <ost/export_helper/vector.hh>
 using namespace ost;
 using namespace ost::mol;
+#include "bounds.hh"
 
 namespace {
 typedef AtomView (ResidueView::*StringMethod)(const String&) const;
@@ -48,11 +49,9 @@ void export_ResidueView()
 {
   class_<ResidueViewList>("ResidueViewList", no_init)
     .def(vector_indexing_suite<ResidueViewList>())
+    .def(ost::VectorAdditions<ResidueViewList>()) 
   ;
 
-  void (ResidueView::* apply1)(EntityVisitor&) = &ResidueView::Apply;
-  void (ResidueView::* apply2)(EntityViewVisitor&) = &ResidueView::Apply;
-
   class_<ResidueView, bases<ResidueBase> >("ResidueView", init<>())
     .def("GetChain",&ResidueView::GetChain)
     .def("GetAtomList", &ResidueView::GetAtomList,
@@ -66,9 +65,7 @@ void export_ResidueView()
     .def("AddAtom", add_atom_view, X_add_atom_overloads(args("atom_view", "flags")))
     .def("FindAtom", handle_find_atom, args("atom_handle"))
     .def("IsAtomIncluded", &ResidueView::IsAtomIncluded, args("atom_handle"))
-    .def("Apply", apply1, args("visitor"))
-    .def("Apply", apply2, args("visitor"))
-    .def("GetIndex", &ResidueView::GetIndex)
+    .def("GetIndex", &ResidueView::GetIndex)  
     .add_property("chain", &ResidueView::GetChain)
     .add_property("entity", &ResidueView::GetEntity)
     .add_property("index", &ResidueView::GetIndex)
@@ -83,10 +80,16 @@ void export_ResidueView()
     .def("GetMass", &ResidueView::GetMass)
     .def("GetCenterOfMass", &ResidueView::GetCenterOfMass)
     .def("GetCenterOfAtoms", &ResidueView::GetCenterOfAtoms)
-    .def("GetGeometricCenter", &ResidueView::GetGeometricCenter)
-    .add_property("geometric_center", &ResidueView::GetGeometricCenter)
-    .def("GetGeometricStart", &ResidueView::GetGeometricStart)
-    .def("GetGeometricEnd", &ResidueView::GetGeometricEnd) 
+    .def("GetGeometricCenter", geom_center<ResidueView>)
+    .add_property("mass", &ResidueView::GetMass)
+    .add_property("center_of_mass", &ResidueView::GetCenterOfMass)
+    .add_property("center_of_atoms", &ResidueView::GetCenterOfAtoms)    
+    .add_property("geometric_center", geom_center<ResidueView>)
+    .add_property("valid", &ResidueView::IsValid)    
+    .def("GetGeometricStart", geom_start<ResidueView>)
+    .def("GetGeometricEnd", geom_end<ResidueView>) 
+    .def("GetBounds", &ResidueView::GetBounds)
+    .add_property("bounds", &ResidueView::GetBounds)    
   ;
 
 
diff --git a/modules/mol/base/pymod/wrap_mol.cc b/modules/mol/base/pymod/wrap_mol.cc
index 202636aff4ae7cf9b0716ca437407a6e46a746d7..6885a79020eb5a667a498766a7ae6c07df7c54e8 100644
--- a/modules/mol/base/pymod/wrap_mol.cc
+++ b/modules/mol/base/pymod/wrap_mol.cc
@@ -41,6 +41,7 @@ void export_CoordGroup();
 void export_PropertyID();
 void export_BoundingBox();
 void export_QueryViewWrapper();
+void export_EntityPropertyMapper();
 BOOST_PYTHON_MODULE(_mol)
 {
   export_Entity();
@@ -61,7 +62,7 @@ BOOST_PYTHON_MODULE(_mol)
   export_PropertyID();  
   export_BoundingBox();
   export_QueryViewWrapper();
-
+  export_EntityPropertyMapper();
   class_<Transform>("Transform", init<>())
     .def(init<const Transform&>()) // shouldn't this be there automatically ?
     .def("GetMatrix",&Transform::GetMatrix)
diff --git a/modules/mol/base/src/bounding_box.cc b/modules/mol/base/src/bounding_box.cc
index 8fd6a49d80e043d7a82618b54a6ec58603dddbf0..15473b5def7f392e90962d048e1a2bde18e35a74 100644
--- a/modules/mol/base/src/bounding_box.cc
+++ b/modules/mol/base/src/bounding_box.cc
@@ -36,7 +36,7 @@ public:
   PrincipalAxisCalc(const EntityHandle& ent): 
     natoms_(ent.GetAtomCount())
   {
-    mean_=ent.GetGeometricCenter();
+    mean_=ent.GetBounds().GetCenter();
     cov_.setZero();
   }
   PrincipalAxisCalc(const AtomHandleList& atoms):
@@ -55,7 +55,7 @@ public:
   PrincipalAxisCalc(const EntityView& ent): 
     natoms_(ent.GetAtomCount())
   {
-    mean_=ent.GetGeometricCenter();
+    mean_=ent.GetBounds().GetCenter();
     cov_.setZero();
   }  
   virtual bool VisitAtom(const AtomHandle& atom)
diff --git a/modules/mol/base/src/chain_handle.cc b/modules/mol/base/src/chain_handle.cc
index 4581eb7806890f1a12da761cfd6ac18ba906857e..1f0e8094c10c8f95f5e6e71d48fb675f9ee63091 100644
--- a/modules/mol/base/src/chain_handle.cc
+++ b/modules/mol/base/src/chain_handle.cc
@@ -125,23 +125,26 @@ bool ChainHandle::operator!=(const ChainHandle& ref) const
 ResidueHandleIter ChainHandle::ResiduesBegin() const {
   this->CheckValidity();
   impl::ChainImplPtr c=Impl();
-  impl::ChainImplList::iterator cc=c->GetEntity()->GetChain(this->GetName());
-  return ResidueHandleIter(cc, c->GetResidueList().begin(), 
-                           c->GetEntity());
+  return ResidueHandleIter(c->GetEntity()->GetChainIter(this->GetName()), 
+                           impl::begin(c->GetResidueList()), 
+                           c->GetEntity(), true);
 }
 
 ResidueHandleIter ChainHandle::ResiduesEnd() const {
   this->CheckValidity();
   impl::ChainImplPtr c=Impl();
-  impl::ChainImplList::iterator cc=c->GetEntity()->GetChain(this->GetName());
-  impl::ChainImplList::iterator nc=cc; ++nc;
-  if (nc!=c->GetEntity()->GetChainList().end()) {
+  impl::pointer_it<impl::ChainImplPtr> cc=c->GetEntity()->GetChainIter(this->GetName());
+  /*impl::pointer_it<impl::ChainImplPtr> nc=cc; ++nc;
+  
+  if (nc!=impl::end(c->GetEntity()->GetChainList())) {
     return ResidueHandleIter(nc, (*nc)->GetResidueList().begin(), 
-                             c->GetEntity());    
+                             c->GetEntity(), true);    
   } else {
     return ResidueHandleIter(cc, c->GetResidueList().end(), 
-                             c->GetEntity());    
-  }
+                             c->GetEntity(), true);    
+  }*/
+  return ResidueHandleIter(cc, impl::end(c->GetResidueList()), 
+                           c->GetEntity(), true);
 }
 
 AtomHandleIter ChainHandle::AtomsBegin() const 
@@ -152,9 +155,9 @@ AtomHandleIter ChainHandle::AtomsBegin() const
 
     return AtomHandleIter();
   }  
-  impl::ChainImplList::iterator cc=c->GetEntity()->GetChain(this->GetName()); 
-  return AtomHandleIter(cc, c->GetResidueList().begin(),
-                        c->GetResidueList().front()->GetAtomList().begin(),
+  impl::pointer_it<impl::ChainImplPtr> cc=c->GetEntity()->GetChainIter(this->GetName()); 
+  return AtomHandleIter(cc, impl::begin(c->GetResidueList()),
+                        impl::begin(c->GetResidueList().front()->GetAtomList()),
                         c->GetEntity(), true);    
 
 }
@@ -165,15 +168,16 @@ AtomHandleIter ChainHandle::AtomsEnd() const {
   if (c->GetResidueList().empty()) {
     return AtomHandleIter();
   }  
-  impl::ChainImplList::iterator cc=c->GetEntity()->GetChain(this->GetName());
-  impl::ChainImplList::iterator nc=cc; ++nc;
+  impl::pointer_it<impl::ChainImplPtr> cc=c->GetEntity()->GetChainIter(this->GetName());
+  impl::pointer_it<impl::ChainImplPtr> nc=cc; ++nc;
   impl::ResidueImplList& rc=(*nc)->GetResidueList();
-  if (nc!=c->GetEntity()->GetChainList().end()) {  
-    return AtomHandleIter(nc, rc.begin(), rc.front()->GetAtomList().begin(),
+  if (nc!=impl::end(c->GetEntity()->GetChainList())) {  
+    return AtomHandleIter(nc, impl::begin(rc), 
+                          impl::begin(rc.front()->GetAtomList()),
                           c->GetEntity(), false);
   } else {
-    return AtomHandleIter(cc, c->GetResidueList().end(),
-                          c->GetResidueList().back()->GetAtomList().end(),
+    return AtomHandleIter(cc, impl::end(c->GetResidueList()),
+                          impl::end(c->GetResidueList().back()->GetAtomList()),
                           c->GetEntity(), false);
   }  
 }
@@ -193,22 +197,10 @@ void ChainHandle::AssignSecondaryStructure(SecStructure ss,
   Impl()->AssignSecondaryStructure(ss, start, end);
 }
 
-geom::Vec3 ChainHandle::GetGeometricCenter() const
-{
-  this->CheckValidity();
-  return Impl()->GetGeometricCenter();
-}
-
-geom::Vec3 ChainHandle::GetGeometricStart() const
-{
-  this->CheckValidity();
-  return Impl()->GetGeometricStart();
-}
-
-geom::Vec3 ChainHandle::GetGeometricEnd() const
+geom::AlignedCuboid ChainHandle::GetBounds() const
 {
   this->CheckValidity();
-  return Impl()->GetGeometricEnd();
+  return Impl()->GetBounds();
 }
 
 geom::Vec3 ChainHandle::GetCenterOfMass() const
diff --git a/modules/mol/base/src/chain_handle.hh b/modules/mol/base/src/chain_handle.hh
index 0faa7ee8fc2f691b3acc86d539300b93ca211843..6337818deeebc8356c1a08421173edc39da076ee 100644
--- a/modules/mol/base/src/chain_handle.hh
+++ b/modules/mol/base/src/chain_handle.hh
@@ -166,18 +166,7 @@ public:
   /// similar to GetCenterOfMass(), but the atoms are not mass weighted
   geom::Vec3 GetCenterOfAtoms() const;
   
-  /// \brief Get entity's geometric center
-  ///
-  /// Returns the geometric center of the entity's bounding box
-  /// by calculating (GetGeometricStart()+GetGeometricEnd())/2
-  geom::Vec3 GetGeometricCenter() const;
-  
-  /// \brief Get entity's minimum cartesian coordinates
-  geom::Vec3 GetGeometricStart() const;
-  
-  /// \brief Get entity's maximum cartesian coordinates
-  geom::Vec3 GetGeometricEnd() const;
-  
+  geom::AlignedCuboid GetBounds() const;  
   /// \brief assign secondary structure to the inclusive residue range 
   ///        start, end
   void AssignSecondaryStructure(SecStructure ss, 
diff --git a/modules/mol/base/src/chain_view.cc b/modules/mol/base/src/chain_view.cc
index fac143b8527ef1c880c615f9fc5ff47808516fb9..1c5ba252e6c3d526ac711bb99f8031d860bda5e5 100644
--- a/modules/mol/base/src/chain_view.cc
+++ b/modules/mol/base/src/chain_view.cc
@@ -327,44 +327,29 @@ Real ChainView::GetMass() const {
   return mass;
 }
 
-geom::Vec3 ChainView::GetGeometricStart() const
+geom::AlignedCuboid ChainView::GetBounds() const
 {
   this->CheckValidity();
-  geom::Vec3 minimum(std::numeric_limits<Real>::max(),
-                     std::numeric_limits<Real>::max(),
-                     std::numeric_limits<Real>::max());
-  ResidueViewList::const_iterator i;
-  for (i=data_->residues.begin(); i!=data_->residues.end(); ++i) {
-    ResidueView r=*i;
-    for (AtomViewList::const_iterator j=r.GetAtomList().begin(),
-         e2=r.GetAtomList().end(); j!=e2; ++j) {
-      minimum=geom::Min(minimum, j->GetPos());
-    }
-  }
-  return minimum;
-}
+  geom::Vec3 mmin( std::numeric_limits<Real>::max());
+  geom::Vec3 mmax(-std::numeric_limits<Real>::max());
 
-geom::Vec3 ChainView::GetGeometricEnd() const
-{
-  this->CheckValidity();
-  geom::Vec3 maximum(-std::numeric_limits<Real>::max(),
-                     -std::numeric_limits<Real>::max(),
-                     -std::numeric_limits<Real>::max());
-  ResidueViewList::const_iterator i;
-  for (i=data_->residues.begin(); i!=data_->residues.end(); ++i) {
+  
+  bool atoms=false;
+  for (ResidueViewList::const_iterator
+       i=data_->residues.begin(); i!=data_->residues.end(); ++i) {
     ResidueView r=*i;
     for (AtomViewList::const_iterator j=r.GetAtomList().begin(),
          e2=r.GetAtomList().end(); j!=e2; ++j) {
-      maximum=geom::Max(maximum, j->GetPos());
+      mmin=geom::Min(mmin, j->GetPos());
+      mmax=geom::Max(mmax, j->GetPos());
+      atoms=true;
     }
   }
-  return maximum;
-}
-
-geom::Vec3 ChainView::GetGeometricCenter() const
-{
-  this->CheckValidity();
-  return (this->GetGeometricStart() + this->GetGeometricEnd())/2;
+  if (atoms) {
+    return geom::AlignedCuboid(mmin, mmax);
+  } else {
+    return geom::AlignedCuboid(geom::Vec3(), geom::Vec3());
+  }
 }
 
 geom::Vec3 ChainView::GetCenterOfAtoms() const
diff --git a/modules/mol/base/src/chain_view.hh b/modules/mol/base/src/chain_view.hh
index 3be942a5648cbb4f51a5a909e577a1e255c1d4e4..800d1fc82434898e2cd1bd436e8df4dfb1f5be8b 100644
--- a/modules/mol/base/src/chain_view.hh
+++ b/modules/mol/base/src/chain_view.hh
@@ -143,14 +143,8 @@ public:
   /// similar to GetCenterOfMass(), but the atoms are not mass weighted
   geom::Vec3 GetCenterOfAtoms() const;
   
-  /// \brief Get entity's geometric center
-  ///
-  /// Returns the geometric center of the entity's bounding box
-  /// by calculating (GetGeometricStart()+GetGeometricEnd())/2
-  geom::Vec3 GetGeometricCenter() const;
-  
-  geom::Vec3 GetGeometricStart() const;
-  geom::Vec3 GetGeometricEnd() const;
+  /// \brief Get entity's axis aligned bounding box
+  geom::AlignedCuboid GetBounds() const;
   
   /// /// \brief remove all residues from the view
   void RemoveResidues();
diff --git a/modules/mol/base/src/chem_class.hh b/modules/mol/base/src/chem_class.hh
index b7740a94257ef64f7ec8feb365a7fd8ab25b3fe9..f9c0f8279666df6fee4f2370b2ed40ba29432203 100644
--- a/modules/mol/base/src/chem_class.hh
+++ b/modules/mol/base/src/chem_class.hh
@@ -37,6 +37,7 @@ struct ChemClass {
   const static char LSaccharide     ='X';
   const static char DSaccharide     ='Y';    
   const static char Saccharide      ='Z';
+  const static char Water           ='W';
   const static char Unknown         ='U';
   explicit ChemClass(char chem_class)
     : chem_class_(chem_class) {
@@ -62,6 +63,8 @@ struct ChemClass {
     return (chem_class_==ChemClass::DNALinking || 
             chem_class_==ChemClass::RNALinking);
   }
+  
+  bool IsWater() const { return chem_class_==ChemClass::Water; }
   operator char() const {
     return chem_class_;
   }
diff --git a/modules/mol/base/src/coord_source.cc b/modules/mol/base/src/coord_source.cc
index 0afa3597dacfba19e28d790f0a606d7311256877..37d1fbd91cf9ce4dba16bb3614909cf77f064111 100644
--- a/modules/mol/base/src/coord_source.cc
+++ b/modules/mol/base/src/coord_source.cc
@@ -54,12 +54,12 @@ CoordSource::~CoordSource()
 void CoordSource::CopyFrame(uint frame_id)
 {
   if (atoms_.empty()) {
-    LOGN_DEBUG("atom list empty, ignored");
+    LOG_DEBUG("atom list empty, ignored");
     return;
   }  
   CoordFramePtr frame=this->GetFrame(frame_id);
   if (!frame) {
-    LOGN_DEBUG("invalid frame given, ignored");
+    LOG_DEBUG("invalid frame given, ignored");
     return;
   }
   assert(frame->size()==atoms_.size());
diff --git a/modules/mol/base/src/editor_base.cc b/modules/mol/base/src/editor_base.cc
index 5cddb05bfbcb8ef0f28d5087baca457f31823982..02f7d1744240d5b05fdf1d1a8240d67eb503ad7a 100644
--- a/modules/mol/base/src/editor_base.cc
+++ b/modules/mol/base/src/editor_base.cc
@@ -22,7 +22,7 @@
 #include "impl/entity_impl.hh"
 #include "impl/chain_impl.hh"
 #include "impl/residue_impl.hh"
-
+#include "impl/atom_impl.hh"
 #include "mol.hh"
 
 /*
@@ -135,6 +135,12 @@ void EditorBase::ReorderAllResidues()
   ent_.Impl()->ReorderAllResidues();
 }
 
+void EditorBase::RenameAtom(AtomHandle atom, const String& new_name)
+{
+  CheckHandleValidity(atom);
+  atom.Impl()->SetName(new_name);
+}
+
 BondHandle EditorBase::Connect(const AtomHandle& first,
                                  const AtomHandle& second) {
   CheckHandleValidity(first);
diff --git a/modules/mol/base/src/editor_base.hh b/modules/mol/base/src/editor_base.hh
index 53246e7a204522d78617c956b3e046e7378e45ae..4354c82954f995340078c5bf7fafc289b43cd53c 100644
--- a/modules/mol/base/src/editor_base.hh
+++ b/modules/mol/base/src/editor_base.hh
@@ -193,6 +193,9 @@ public:
     
   /// \brief Get edit mode of editor
   EditMode GetMode() const;
+  
+  /// \brief change the name of the atom to the new name  
+  void RenameAtom(AtomHandle atom, const String& new_name);
 protected:
   EditorBase(const EntityHandle& ent, EditMode mode);
   void UpdateTrace();
diff --git a/modules/mol/base/src/entity_handle.cc b/modules/mol/base/src/entity_handle.cc
index 8686df88c286c726648bad9abec259514414a9c2..17c47cd81112c92ef308c598cf7c03202a1c6648 100644
--- a/modules/mol/base/src/entity_handle.cc
+++ b/modules/mol/base/src/entity_handle.cc
@@ -55,25 +55,12 @@ geom::Vec3 EntityHandle::GetCenterOfAtoms() const {
   return Impl()->GetCenterOfAtoms();
 }
 
-geom::Vec3 EntityHandle::GetGeometricCenter() const {
-  this->CheckValidity();
-  return Impl()->GetGeometricCenter();
-}
-
-geom::Vec3 EntityHandle::GetGeometricStart() const {
-  this->CheckValidity();
-  return Impl()->GetGeometricStart();
-}
-
-geom::Vec3 EntityHandle::GetGeometricEnd() const {
+geom::AlignedCuboid EntityHandle::GetBounds() const 
+{
   this->CheckValidity();
-  return Impl()->GetGeometricEnd();
+  return Impl()->GetBounds();
 }
 
-geom::Vec3 EntityHandle::GetBoundarySize() const {
-  this->CheckValidity();
-  return Impl()->GetBoundarySize();
-}
 
 EntityHandle::EntityHandle(const impl::EntityImplPtr& e)
   : EntityBase(e)
@@ -262,8 +249,8 @@ ResidueHandleIter EntityHandle::ResiduesBegin() const {
   }
   impl::EntityImplPtr i=Impl();
   impl::ChainImplPtr chain=i->GetChainList().front();
-  return ResidueHandleIter(i->GetChainList().begin(),
-                           chain->GetResidueList().begin(), i);
+  return ResidueHandleIter(impl::begin(i->GetChainList()),
+                           impl::begin(chain->GetResidueList()), i, true);
 }
 
 ResidueHandleIter EntityHandle::ResiduesEnd() const {
@@ -273,8 +260,8 @@ ResidueHandleIter EntityHandle::ResiduesEnd() const {
   }
   impl::EntityImplPtr i=Impl();
   impl::ChainImplPtr chain=i->GetChainList().back();
-  return ResidueHandleIter(i->GetChainList().end(),
-                           chain->GetResidueList().end(), i);
+  return ResidueHandleIter(impl::end(i->GetChainList()),
+                           impl::end(chain->GetResidueList()), i, false);
 }
 
 ChainHandleIter EntityHandle::ChainsBegin() const {
@@ -298,8 +285,8 @@ AtomHandleIter EntityHandle::AtomsBegin() const {
   if (r.empty()) {
     return AtomHandleIter();
   }
-  return AtomHandleIter(ent->GetChainList().begin(), r.begin(),
-                        r.front()->GetAtomList().begin(), ent, true);
+  return AtomHandleIter(impl::begin(ent->GetChainList()), impl::begin(r),
+                        impl::begin(r.front()->GetAtomList()), ent, true);
 }
 
 AtomHandleIter EntityHandle::AtomsEnd() const 
@@ -313,8 +300,8 @@ AtomHandleIter EntityHandle::AtomsEnd() const
   if (r.empty()) {
     return AtomHandleIter();
   }
-  return AtomHandleIter(ent->GetChainList().end(), r.end(),
-                        r.back()->GetAtomList().end(), ent, false);
+  return AtomHandleIter(impl::end(ent->GetChainList()), impl::end(r),
+                        impl::end(r.back()->GetAtomList()), ent, false);
 }
 
 XCSEditor EntityHandle::RequestXCSEditor(EditMode mode) const
diff --git a/modules/mol/base/src/entity_handle.hh b/modules/mol/base/src/entity_handle.hh
index 9bb291d8ea21cd21907ee65ec4d20b09ed1d99e7..540425c70219e49396c29ce19ef54850712edd70 100644
--- a/modules/mol/base/src/entity_handle.hh
+++ b/modules/mol/base/src/entity_handle.hh
@@ -84,20 +84,8 @@ public:
   
   /// \brief Get entity's center of mass (mass weighted)
   geom::Vec3 GetCenterOfMass() const;  
-  /// \brief Get entity's geometric center
-  ///
-  /// Returns the geometric center of the entity's bounding box
-  /// by calculating (GetGeometricStart()+GetGeometricEnd())/2
-  geom::Vec3 GetGeometricCenter() const;
-
-  /// \brief Get entity's minimum cartesian coordinates
-  geom::Vec3 GetGeometricStart() const;
-
-  /// \brief Get entity's maximum cartesian coordinates
-  geom::Vec3 GetGeometricEnd() const;
 
-  /// \brief Get size of the entity
-  geom::Vec3 GetBoundarySize() const;
+  geom::AlignedCuboid GetBounds() const;
   //@}
   
   /// \brief
diff --git a/modules/mol/base/src/entity_view.cc b/modules/mol/base/src/entity_view.cc
index a3819e1020d4c8dd975f9b2e799d4bf248092a34..945230d2f2779b172c02bc4ffc341fb2d3c96a73 100644
--- a/modules/mol/base/src/entity_view.cc
+++ b/modules/mol/base/src/entity_view.cc
@@ -171,13 +171,6 @@ geom::Vec3 EntityView::GetCenterOfAtoms() const
   return center;
 }
 
-geom::Vec3 EntityView::GetGeometricCenter() const 
-{
-  geom::Vec3 center;
-  center = (this->GetGeometricEnd() + this->GetGeometricStart())/2;
-  return center;
-}
-
 geom::Vec3 EntityView::GetCenterOfMass() const 
 {
   geom::Vec3 center;
@@ -472,8 +465,9 @@ AtomViewIter EntityView::AtomsBegin() const
   if (rvl.empty()) {
     return AtomViewIter();
   }
-  return AtomViewIter(data_->chains.begin(), rvl.begin(),
-                      rvl.front().GetAtomList().begin(), *this, true);
+  return AtomViewIter(impl::begin(data_->chains), impl::begin(rvl),
+                      impl::begin(rvl.front().GetAtomList()), 
+                      *this, true);
 }
 
 AtomViewIter EntityView::AtomsEnd() const {
@@ -485,26 +479,30 @@ AtomViewIter EntityView::AtomsEnd() const {
   if (rvl.empty()) {
     return AtomViewIter();
   }
-  return AtomViewIter(data_->chains.end(), rvl.end(),
-                      rvl.back().GetAtomList().end(), *this, false);
+  return AtomViewIter(impl::end(data_->chains), impl::end(rvl),
+                      impl::end(rvl.back().GetAtomList()), *this, false);
 }
 
-ResidueViewIter EntityView::ResiduesBegin() const {
+ResidueViewIter EntityView::ResiduesBegin() const 
+{
   this->CheckValidity();
   if (data_->chains.empty()) {
     return ResidueViewIter();
   }
   const ResidueViewList& rvl=data_->chains.front().GetResidueList();
-  return ResidueViewIter(data_->chains.begin(), rvl.begin(), *this);
+  return ResidueViewIter(impl::begin(data_->chains), 
+                         impl::begin(rvl), *this, true);
 }
 
-ResidueViewIter EntityView::ResiduesEnd() const {
+ResidueViewIter EntityView::ResiduesEnd() const 
+{
     this->CheckValidity();
     if (data_->chains.empty()) {
       return ResidueViewIter();
     }
     const ResidueViewList& rvl=data_->chains.back().GetResidueList();
-    return ResidueViewIter(data_->chains.end(), rvl.end(), *this);
+    return ResidueViewIter(impl::end(data_->chains), 
+                           impl::end(rvl), *this, false);
 }
 
 
@@ -690,9 +688,14 @@ std::pair<Real,Real> EntityView::GetMinMax(const String& prop,
   Real min_v=std::numeric_limits<Real>::max();
   Real max_v=-std::numeric_limits<Real>::max();  
   for(AtomViewIter it=AtomsBegin(); it!=this->AtomsEnd(); ++it) {
-    Real v=epm.Get(*it);
-    max_v=std::max(v, max_v);
-    min_v=std::min(v, min_v);
+    try {
+      Real v=epm.Get(*it);
+      max_v=std::max(v, max_v);
+      min_v=std::min(v, min_v);      
+    } catch(...) {
+      // do nothing in case of missing property
+      continue;
+    }
   }
   return std::make_pair(min_v,max_v);
 }
@@ -721,17 +724,6 @@ AtomView EntityView::FindXAtom(const AtomHandle& ah)
 }
 #endif
 
-geom::Vec3 EntityView::GetGeometricStart() const
-{
-  this->CheckValidity();
-  geom::Vec3 m(std::numeric_limits<Real>::max(),
-               std::numeric_limits<Real>::max(),
-               std::numeric_limits<Real>::max());
-  for(AtomViewIter it=AtomsBegin(); it!=this->AtomsEnd(); ++it) {
-    m=geom::Min(m, (*it).GetPos());
-  }
-  return m;
-}
 
 AtomView EntityView::FindAtom(const String& chain_name, 
                               const ResNum& num,
@@ -744,16 +736,20 @@ AtomView EntityView::FindAtom(const String& chain_name,
   }
   return AtomView();
 }
-geom::Vec3 EntityView::GetGeometricEnd() const
+geom::AlignedCuboid EntityView::GetBounds() const
 {
   this->CheckValidity();
-  geom::Vec3 m(-std::numeric_limits<Real>::max(),
-               -std::numeric_limits<Real>::max(),
-               -std::numeric_limits<Real>::max());
-  for(AtomViewIter it=AtomsBegin(); it!=this->AtomsEnd(); ++it) {
-    m=geom::Max(m, (*it).GetPos());
+  geom::Vec3 mmin( std::numeric_limits<Real>::max());
+  geom::Vec3 mmax(-std::numeric_limits<Real>::max());
+  if (this->GetAtomCount()) {
+    for(AtomViewIter it=AtomsBegin(); it!=this->AtomsEnd(); ++it) {
+      mmax=geom::Max(mmax, (*it).GetPos());
+      mmin=geom::Min(mmin, (*it).GetPos());
+    }    
+    return geom::AlignedCuboid(mmin, mmax);
+  } else {
+    return geom::AlignedCuboid(geom::Vec3(), geom::Vec3());
   }
-  return m;
 }
 
 
@@ -777,6 +773,42 @@ void EntityView::RemoveAtomInternal(const AtomView& av)
   data_->handle_to_view.erase(av.GetHandle().GetHashCode());
 }
 
+EntityView EntityView::ExtendViewToResidues() const
+{
+  this->CheckValidity();
+  EntityView view=this->CreateEmptyView();
+  ResidueViewList residues=this->GetResidueList();
+  ResidueViewList::const_iterator res_it;
+  for (res_it=residues.begin(); res_it!=residues.end(); ++res_it) {
+    view.AddResidue((*res_it).GetHandle(),
+                    mol::ViewAddFlag::INCLUDE_ALL|mol::ViewAddFlag::CHECK_DUPLICATES);
+  }
+  view.AddAllInclusiveBonds();
+  return view;
+}
+
+EntityView EntityView::ExtendViewToSurrounding(Real gap) const
+{
+  this->CheckValidity();
+  EntityView view=this->CreateEmptyView();
+  AtomViewList atoms=this->GetAtomList();
+  AtomViewList::const_iterator atm_it;
+  Real max_dist=5+gap;
+  for (atm_it=atoms.begin(); atm_it!=atoms.end(); ++atm_it) {
+    view.AddAtom((*atm_it),mol::ViewAddFlag::INCLUDE_ALL|mol::ViewAddFlag::CHECK_DUPLICATES);
+    AtomHandleList prot_atoms=this->GetHandle().FindWithin((*atm_it).GetPos(),max_dist);
+    AtomHandleList::const_iterator protatm_it;
+    for (protatm_it=prot_atoms.begin(); protatm_it!=prot_atoms.end(); ++protatm_it){
+      Real dist=geom::Distance((*atm_it).GetPos(), (*protatm_it).GetPos());
+      if (dist <= (*atm_it).GetRadius() + (*protatm_it).GetRadius() + gap) {
+        view.AddAtom((*protatm_it),mol::ViewAddFlag::INCLUDE_ALL|mol::ViewAddFlag::CHECK_DUPLICATES);
+      }
+    }
+  }
+  view.AddAllInclusiveBonds();
+  return view;
+}
+
 namespace {
 
 class EntityViewDumper : public EntityVisitor {
diff --git a/modules/mol/base/src/entity_view.hh b/modules/mol/base/src/entity_view.hh
index e55894da5fa97e37911942c0151abd01f8ce2eab..e9566a1c2f3c756fbf003031ad4a0d6f01df05b2 100644
--- a/modules/mol/base/src/entity_view.hh
+++ b/modules/mol/base/src/entity_view.hh
@@ -108,14 +108,8 @@ public:
   /// similar to GetCenterOfMass(), but the atoms are not mass weighted
   geom::Vec3 GetCenterOfAtoms() const;
   
-  /// \brief Get entity's geometric center
-  ///
-  /// Returns the geometric center of the entity's bounding box
-  /// by calculating (GetGeometricStart()+GetGeometricEnd())/2
-  geom::Vec3 GetGeometricCenter() const;
-             
-  geom::Vec3 GetGeometricStart() const;
-  geom::Vec3 GetGeometricEnd() const;
+  geom::AlignedCuboid GetBounds() const;
+  
 public:
   /// \name Internal
   //@{
@@ -292,6 +286,16 @@ public:
   Real GetAngle(const AtomView& a1, const AtomView& a2,
                 const AtomView& a3) const;
 
+  /// \brief  Extend current view to include all atoms of each residue where
+  ///         at least one atom is selected currently
+  EntityView ExtendViewToResidues() const;
+
+  /// \brief  Extend current view to include all atoms that are within the sum
+  ///         of their vdw radii + gap
+  ///
+  /// Include all atoms within: at1.GetRadius() + at2.GetRadius() + gap
+  EntityView ExtendViewToSurrounding(Real gap) const;
+
   /// \brief returns a string containing a human-readable summary of the
   ///     entity view
   String Dump() const;
diff --git a/modules/mol/base/src/impl/CMakeLists.txt b/modules/mol/base/src/impl/CMakeLists.txt
index 3de4864e7a11e9dd29904fd60f997bab8cec2e51..41ddeb0b5672a5081a97b63ec1a6a5c3cdc497d5 100644
--- a/modules/mol/base/src/impl/CMakeLists.txt
+++ b/modules/mol/base/src/impl/CMakeLists.txt
@@ -14,6 +14,7 @@ PARENT_SCOPE
 )
 
 set(OST_MOL_IMPL_HEADERS
+pointer_iterator.hh
 atom_group.hh
 atom_impl.hh
 atom_impl_fw.hh
diff --git a/modules/mol/base/src/impl/atom_impl.cc b/modules/mol/base/src/impl/atom_impl.cc
index cb3ecf87a290166e78a14329655b9ff7a733698c..698bc863f2083117655a67901aa8bb7d2fa5bfe0 100644
--- a/modules/mol/base/src/impl/atom_impl.cc
+++ b/modules/mol/base/src/impl/atom_impl.cc
@@ -65,7 +65,7 @@ void AtomImpl::AddSecondaryConnector(const ConnectorImplP& bp)
 
 void AtomImpl::Apply(EntityVisitor& v)
 {
-  LOG_TRACE("visitor @" << &v << " visiting atom impl @" << this << std::endl);
+  LOG_TRACE("visitor @" << &v << " visiting atom impl @" << this);
   v.VisitAtom(AtomHandle(shared_from_this()));
 }
 
@@ -88,11 +88,11 @@ void AtomImpl::TraceDirectionality(FragmentImplP frag, ConnectorImplP conn,
   if (conn) {
 #if !defined(NDEBUG)    
     if (conn->GetFirst()==shared_from_this()) {
-      LOGN_DUMP("dir:" << String(n,' ') << " atom " << res_.lock()->GetNumber()
+      LOG_TRACE("dir:" << String(n,' ') << " atom " << res_.lock()->GetNumber()
                 << "." << GetName() << "  [" << conn->GetSecond()->GetQualifiedName()
                 << " ]");      
     } else {
-      LOGN_DUMP("dir:" << String(n,' ') << " atom " << res_.lock()->GetNumber()
+      LOG_TRACE("dir:" << String(n,' ') << " atom " << res_.lock()->GetNumber()
                 << "." << GetName() << "  [" << conn->GetFirst()->GetQualifiedName()
                 << " ]");
     }
@@ -100,7 +100,7 @@ void AtomImpl::TraceDirectionality(FragmentImplP frag, ConnectorImplP conn,
 
 #endif              
   } else {
-    LOGN_DUMP("dir:" << String(n,' ') << " atom " << res_.lock()->GetNumber()
+    LOG_TRACE("dir:" << String(n,' ') << " atom " << res_.lock()->GetNumber()
               << "." << GetName() << "  [ ]");
   }
   
diff --git a/modules/mol/base/src/impl/chain_impl.cc b/modules/mol/base/src/impl/chain_impl.cc
index d2171b1d85deac02615c4edba7924a8f0c81e5b7..0395a810791cf1201663e5c9e7dacd8591c3f875 100644
--- a/modules/mol/base/src/impl/chain_impl.cc
+++ b/modules/mol/base/src/impl/chain_impl.cc
@@ -184,7 +184,7 @@ ResidueImplPtr ChainImpl::AppendResidue(const ResidueKey& key,
       in_sequence_=false;
     }
     if (in_sequence_) {
-      LOGN_DUMP("appending residue " << num);    
+      LOG_DEBUG("appending residue " << num);    
       // update is only needed if we introduce a new gap.
       if (residue_list_.back()->GetNumber().GetNum()+1<num.GetNum()) {
         Shift s;
@@ -269,7 +269,7 @@ const ResidueImplList& ChainImpl::GetResidueList() const
 
 void ChainImpl::Apply(EntityVisitor& v)
 {
-  LOGN_TRACE("visitor @" << &v << " visiting chain impl @" << this);
+  LOG_TRACE("visitor @" << &v << " visiting chain impl @" << this);
   if (v.VisitChain(ChainHandle(shared_from_this()))) {
     for (ResidueImplList::iterator it=residue_list_.begin();
          it!=residue_list_.end();++it) {
@@ -341,11 +341,23 @@ void ChainImpl::AssignSecondaryStructure(SecStructure ss,
                                          const ResNum& start, 
                                          const ResNum& end)
 {
-  int i=this->GetIndex(start);
-  int j=this->GetIndex(end);
-  if (i>=0 && j>=0 && i<=j && j<static_cast<int>(residue_list_.size())) {
-    std::for_each(residue_list_.begin()+i, residue_list_.begin()+j+1,
-                  bind(&ResidueImpl::SetSecStructure, _1, ss));
+  int start_index=this->GetIndex(start);
+  int i=start_index;
+  bool found_end=false;
+  if (i>=0) {
+    while (i<static_cast<int>(residue_list_.size())) {
+      if (residue_list_[i]->GetNumber()==end) {
+        found_end=true;
+        break;
+      }
+      ++i;
+    }
+  }
+  if (!found_end) {
+    return;
+  }
+  for (int end=i, i=start_index; i<=end; ++i) {
+    residue_list_[i]->SetSecStructure(ss);
   }
 }
 
@@ -363,41 +375,27 @@ Real ChainImpl::GetMass() const
   return mass;
 }
 
-geom::Vec3 ChainImpl::GetGeometricStart() const 
+geom::AlignedCuboid ChainImpl::GetBounds() const 
 {
-  geom::Vec3 minimum(std::numeric_limits<Real>::infinity(),
-                     std::numeric_limits<Real>::infinity(),
-                     std::numeric_limits<Real>::infinity());
+  geom::Vec3 mmin( std::numeric_limits<Real>::infinity());
+  geom::Vec3 mmax(-std::numeric_limits<Real>::infinity());
+  bool atoms=false;
   for (ResidueImplList::const_iterator i=residue_list_.begin(); 
         i!=residue_list_.end(); ++i) {
     ResidueImplPtr r=*i;
     for (AtomImplList::iterator j=r->GetAtomList().begin(); 
           j!=r->GetAtomList().end(); ++j) {
-      minimum=geom::Min(minimum,(*j)->GetPos());
+      mmin=geom::Min(mmin, (*j)->GetPos());
+      mmax=geom::Max(mmax, (*j)->GetPos());
+      atoms=true;
     }
   }
-  return minimum;
-}
-
-geom::Vec3 ChainImpl::GetGeometricEnd() const {
-  geom::Vec3 maximum(-std::numeric_limits<Real>::infinity(),
-                     -std::numeric_limits<Real>::infinity(),
-                     -std::numeric_limits<Real>::infinity());
-  for (ResidueImplList::const_iterator i=residue_list_.begin(); 
-        i!=residue_list_.end(); ++i) {
-    ResidueImplPtr r=*i;
-    for (AtomImplList::iterator j=r->GetAtomList().begin(); 
-          j!=r->GetAtomList().end(); ++j) {
-      maximum=geom::Max(maximum,(*j)->GetPos());
-    }
+  if (!atoms) {
+    return geom::AlignedCuboid(geom::Vec3(), geom::Vec3());
   }
-  return maximum;
+  return geom::AlignedCuboid(mmin, mmax);
 }
 
-geom::Vec3 ChainImpl::GetGeometricCenter() const
-{
-  return (this->GetGeometricStart() + this->GetGeometricEnd()) / 2;
-}
 
 geom::Vec3 ChainImpl::GetCenterOfAtoms() const
 {
diff --git a/modules/mol/base/src/impl/chain_impl.hh b/modules/mol/base/src/impl/chain_impl.hh
index c25d23b88cf7653e57fa9bd4940af12e8d5b6474..23b12119b1569b487510df6cb13932906e86d3f5 100644
--- a/modules/mol/base/src/impl/chain_impl.hh
+++ b/modules/mol/base/src/impl/chain_impl.hh
@@ -81,9 +81,10 @@ public:
   Real GetMass() const;
   geom::Vec3 GetCenterOfMass() const;
   geom::Vec3 GetCenterOfAtoms() const;
-  geom::Vec3 GetGeometricCenter() const;
-  geom::Vec3 GetGeometricStart() const;
-  geom::Vec3 GetGeometricEnd() const;
+  
+  /// \brief returns the axis-aligned bounding box of the entity
+  geom::AlignedCuboid GetBounds() const;
+  
   
   ///\brief  Get residue by number. Returns a invalid pointer if the chain
   ///        does not have any residue with this number.
diff --git a/modules/mol/base/src/impl/connector_impl.cc b/modules/mol/base/src/impl/connector_impl.cc
index 977eb888e220cc1ebde9e734e9e90a723ed71125..31d22f1e432c73e80c8fb0e46cf9cedf8f84d278 100644
--- a/modules/mol/base/src/impl/connector_impl.cc
+++ b/modules/mol/base/src/impl/connector_impl.cc
@@ -38,7 +38,7 @@ ConnectorImpl::ConnectorImpl(const EntityImplPtr& e, const AtomImplPtr& first,
 
 void ConnectorImpl::Apply(EntityVisitor& v)
 {
-  LOGN_TRACE("visitor @" << &v << " visiting bond impl @" << this);
+  LOG_TRACE("visitor @" << &v << " visiting bond impl @" << this);
   v.VisitBond(BondHandle(shared_from_this()));
 }
 
@@ -53,7 +53,7 @@ namespace {
 geom::Mat3 find_rotation(const geom::Vec3& d) {
   // assume the vectors are already normalized
   if (std::abs(Real(1.0-Length(d)))>0.00001) {
-    LOGN_DEBUG("connector find_rotation() has faulty length: " << Length(d));
+    LOG_DEBUG("connector find_rotation() has faulty length: " << Length(d));
     assert(0 && "error is big");
   }
   Real dot=d[2];
diff --git a/modules/mol/base/src/impl/dihedral.cc b/modules/mol/base/src/impl/dihedral.cc
index b984834e3986e0746fd91d8bca989909c69f12e4..ff484d4e694d70256e60525d5000897dfd75dcba 100644
--- a/modules/mol/base/src/impl/dihedral.cc
+++ b/modules/mol/base/src/impl/dihedral.cc
@@ -119,7 +119,7 @@ void Dihedral::SetAngleICS(Real angle, bool update_other) {
   }
   // we operate under the assumption that conn2_->First and atom_1 are
   // connected and not conn2_->Second and atom1_.
-  LOGN_DEBUG("SetAngleICS: " << a1->GetQualifiedName() << " " 
+  LOG_DEBUG("SetAngleICS: " << a1->GetQualifiedName() << " " 
              << a2->GetQualifiedName() << " " << a3->GetQualifiedName() << " " 
              << a4->GetQualifiedName());
   assert(ConnectorExists(a1, conn2->GetFirst()));
diff --git a/modules/mol/base/src/impl/entity_impl.cc b/modules/mol/base/src/impl/entity_impl.cc
index 17937305c55c7a8508fdd2934518b60da60b5113..120c60e475534c1ce4a1080b9fb8364f17705fa2 100644
--- a/modules/mol/base/src/impl/entity_impl.cc
+++ b/modules/mol/base/src/impl/entity_impl.cc
@@ -262,60 +262,29 @@ EntityImpl::~EntityImpl()
     it->second->OnDestroy();
   }
 }
-
-geom::Vec3 EntityImpl::GetGeometricStart() const 
+geom::AlignedCuboid EntityImpl::GetBounds() const
 {
-  geom::Vec3 minimum(std::numeric_limits<Real>::infinity(),
-                     std::numeric_limits<Real>::infinity(),
-                     std::numeric_limits<Real>::infinity());
-  if (this->GetAtomCount()>0) {
-    for(AtomImplMap::const_iterator it = atom_map_.begin();it!=atom_map_.end();++it) {
-      minimum=geom::Min(minimum,it->second->GetPos());
-    }
-  }
-  return minimum;
-}
 
-geom::Vec3 EntityImpl::GetGeometricEnd() const {
-  geom::Vec3 maximum(-std::numeric_limits<Real>::infinity(),
-                     -std::numeric_limits<Real>::infinity(),
-                     -std::numeric_limits<Real>::infinity());
   if (this->GetAtomCount()>0) {
-    for(AtomImplMap::const_iterator it = atom_map_.begin();it!=atom_map_.end();++it) {
-      maximum=geom::Max(maximum,it->second->GetPos());
-    }
-  }
-  return maximum;
-}
-
-geom::Vec3 EntityImpl::GetBoundarySize() const {
-  geom::Vec3 size;
-  geom::Vec3 minimum(std::numeric_limits<Real>::infinity(),
-                     std::numeric_limits<Real>::infinity(),
-                     std::numeric_limits<Real>::infinity());
-  geom::Vec3 maximum(-std::numeric_limits<Real>::infinity(),
-                     -std::numeric_limits<Real>::infinity(),
-                     -std::numeric_limits<Real>::infinity());
-  if (this->GetAtomCount()>0) {
-    for(AtomImplMap::const_iterator it = atom_map_.begin();it!=atom_map_.end();++it) {
-      minimum=geom::Min(minimum,it->second->GetPos());
-      maximum=geom::Max(maximum,it->second->GetPos());
+    geom::Vec3 mmin, mmax;    
+    AtomImplMap::const_iterator it=atom_map_.begin();
+    mmin=mmax=it->second->GetPos();
+    for (++it; it!=atom_map_.end();++it) {
+      mmin=geom::Min(mmin,it->second->GetPos());
+      mmax=geom::Max(mmax,it->second->GetPos());
     }
+    return geom::AlignedCuboid(mmin, mmax);    
+  } else {
+    return geom::AlignedCuboid(geom::Vec3(), geom::Vec3());
   }
-  size=maximum-minimum;
-  return size;
-}
 
-geom::Vec3 EntityImpl::GetGeometricCenter() const {
-  geom::Vec3 center;
-  center = (this->GetGeometricEnd() + this->GetGeometricStart())/2;
-  return center;
 }
 
 geom::Vec3 EntityImpl::GetCenterOfAtoms() const {
   geom::Vec3 center;
   if (this->GetAtomCount()>0) {
-    for(AtomImplMap::const_iterator it = atom_map_.begin();it!=atom_map_.end();++it) {
+    for (AtomImplMap::const_iterator it = atom_map_.begin();
+         it!=atom_map_.end();++it) {
       center+=it->second->GetPos();
     }
     center/=static_cast<Real>(atom_map_.size());
@@ -410,24 +379,24 @@ ConnectorImplP EntityImpl::Connect(const AtomImplPtr& first,
   // check for already existing connection
   if(first->GetPrimaryConnector() &&
      first->GetPrimaryConnector()->GetFirst()==second) {
-    LOGN_DUMP("connect: returning existing bond (1)");
+    LOG_DEBUG("connect: returning existing bond (1)");
     return first->GetPrimaryConnector();
   } else if(second->GetPrimaryConnector() &&
             second->GetPrimaryConnector()->GetFirst()==first) {
-    LOGN_DUMP("connect: returning existing bond (2)");
+    LOG_DEBUG("connect: returning existing bond (2)");
     return second->GetPrimaryConnector();
   } else {
     ConnectorImplList clist = first->GetSecondaryConnectors();
     for(ConnectorImplList::const_iterator it=clist.begin();it!=clist.end();++it) {
       if((*it)->GetSecond()==second) {
-        LOGN_DUMP("connect: returning existing bond (3)");
+        LOG_DEBUG("connect: returning existing bond (3)");
         return *it;
       }
     }
     clist = second->GetSecondaryConnectors();
     for(ConnectorImplList::const_iterator it=clist.begin();it!=clist.end();++it) {
       if((*it)->GetSecond()==first) {
-        LOGN_DUMP("connect: returning existing bond (4)");
+        LOG_DEBUG("connect: returning existing bond (4)");
         return *it;
       }
     }
@@ -447,7 +416,7 @@ ConnectorImplP EntityImpl::Connect(const AtomImplPtr& first,
   first->AddSecondaryConnector(bp);
   second->AddSecondaryConnector(bp);
 
-  LOG_DUMP("adding new connector " << bp << std::endl);
+  LOG_DEBUG("adding new connector " << bp);
   connector_map_.insert(ConnectorImplMap::value_type(bp.get(),bp));
   return bp;
 }
@@ -620,7 +589,7 @@ void EntityImpl::TraceDirectionality()
     for(AtomImplMap::iterator it=atom_map_.begin();it!=atom_map_.end();++it) {
       if (!it->second->IsVisited() && !it->second->HasPrevious()) {
         it->second->SetVisited(true);
-        LOGN_DUMP("dir: new fragment");
+        LOG_DEBUG("dir: new fragment");
 #if MAKE_SHARED_AVAILABLE
         FragmentImplP frag=boost::make_shared<FragmentImpl>(it->second);
 #else
@@ -632,7 +601,7 @@ void EntityImpl::TraceDirectionality()
       }
     }
     if(traced_atom_count<atom_map_.size()) {
-      LOGN_DUMP("entering closed loops search, since only " << traced_atom_count 
+      LOG_DEBUG("entering closed loops search, since only " << traced_atom_count 
                  << " from " << atom_map_.size() << " atoms were traced");
       /*
   identify closed loops that prohibit
@@ -659,7 +628,7 @@ void EntityImpl::TraceDirectionality()
           }
         }
       }
-      LOGN_DUMP("found pair [" << aip1 << "] [" << aip2 << "]");
+      LOG_DEBUG("found pair [" << aip1 << "] [" << aip2 << "]");
       // step 2: swap all connectors pointing to aip2
       // thus removing its 'visited' state
       for(ConnectorImplMap::iterator it=connector_map_.begin();
@@ -679,12 +648,12 @@ void EntityImpl::TraceDirectionality()
 
     // infinite loop safeguard
     if(traced_atom_count == traced_atom_count_prev) {
-      LOGN_VERBOSE("Encountered unbreakable locked state during directionality trace");
+      LOG_VERBOSE("Encountered unbreakable locked state during directionality trace");
       break;
     }
     traced_atom_count_prev=traced_atom_count;
   }
-  LOGN_VERBOSE("Directionality trace completed with " << fragment_list_.size()
+  LOG_VERBOSE("Directionality trace completed with " << fragment_list_.size()
                << " fragment(s)");
 }
 
@@ -695,7 +664,7 @@ bool EntityImpl::IsXCSDirty() const
 
 void EntityImpl::UpdateFromICS()
 {
-  LOG_DEBUG("updating external from internal coordinate system" << std::endl);
+  LOG_DEBUG("updating external from internal coordinate system");
   Profile prof_conv("update external from internal coordinate system");    
   // traverse through all atoms
   for(AtomImplMap::iterator it=atom_map_.begin();it!=atom_map_.end();++it) {
@@ -704,7 +673,7 @@ void EntityImpl::UpdateFromICS()
 
   for (FragmentImplList::iterator it=fragment_list_.begin();
        it!=fragment_list_.end();++it) {
-    LOG_DUMP("entering root of tree for ICS update" << std::endl;);
+    LOG_DEBUG("entering root of tree for ICS update");
     assert(*it);
     AtomImplPtr ap=(*it)->GetAtom();
     // recursive update, using position of first atom
@@ -712,10 +681,10 @@ void EntityImpl::UpdateFromICS()
     pmat=tmat*pmat;
     ap->SetICSMat(pmat);*/
     ap->UpdateFromICS();
-    LOG_DUMP("done with tree traversal for ICS update" << std::endl;);
+    LOG_DEBUG("done with tree traversal for ICS update");
   }
 
-  LOG_DEBUG("refreshing all connector positions" << std::endl;);
+  LOG_DEBUG("refreshing all connector positions");
   // refresh all connector positions
   /*
   for (ConnectorImplMap::iterator it=connector_map_.begin();
@@ -728,23 +697,23 @@ void EntityImpl::UpdateFromICS()
 
 void EntityImpl::UpdateFromXCS()
 {
-  LOGN_DEBUG("rebuilding internal from external coordinate system");
+  LOG_DEBUG("rebuilding internal from external coordinate system");
   Profile prof_conv("updating internal from external coordinate system");
   if(fragment_list_.empty()) {
     // this should have been handled by conopology after the
     // initial connectivity assignments - if not, then do it here
     Profile profile_trace("finished directionality trace");    
-    LOGN_DEBUG("warning: no fragment list, re-running directionality trace");
+    LOG_DEBUG("warning: no fragment list, re-running directionality trace");
     TraceDirectionality();
   }
 
-  if(Logger::Instance().GetLogLevel()>=Logger::DUMP) {
-    LOGN_DUMP("dumping directionality");
+  if(Logger::Instance().GetLogLevel()>Logger::DEBUG) {
+    LOG_TRACE("dumping directionality");
     for(AtomImplMap::iterator it=atom_map_.begin();it!=atom_map_.end();++it) {
-      LOGN_DUMP(" " << it->second << ":");
+      LOG_TRACE(" " << it->second << ":");
       ConnectorImplList clist = it->second->GetSecondaryConnectors();
       for(ConnectorImplList::const_iterator cit=clist.begin();cit!=clist.end();++cit) {
-        LOGN_DUMP("  " << (*cit)->GetFirst() << " -> " << (*cit)->GetSecond());
+        LOG_TRACE("  " << (*cit)->GetFirst() << " -> " << (*cit)->GetSecond());
       }
     }
   }
@@ -756,7 +725,7 @@ void EntityImpl::UpdateFromXCS()
 
   for (FragmentImplList::iterator it=fragment_list_.begin();
        it!=fragment_list_.end();++it) {
-    LOGN_DUMP("entering fragment tree traversal for XCS update");
+    LOG_DEBUG("entering fragment tree traversal for XCS update");
     FragmentImplP frag= *it;
     AtomImplPtr atom = frag->GetAtom();
     {
@@ -767,7 +736,7 @@ void EntityImpl::UpdateFromXCS()
 
 void EntityImpl::Apply(EntityVisitor& v)
 {
-  LOG_TRACE("visitor @" << &v << " visiting entity impl @" << this << std::endl);
+  LOG_TRACE("visitor @" << &v << " visiting entity impl @" << this);
   v.OnEntry();
   for(ChainImplList::iterator 
       it = chain_list_.begin();it!=chain_list_.end();++it) {
@@ -879,36 +848,36 @@ EntityView EntityImpl::do_selection(const EntityHandle& eh,
 {
 
   BondTableType bond_table;
-  LOGN_DUMP("entering do selection");
+  LOG_DEBUG("entering do selection");
 
   size_t chain_count = 0, residue_count = 0, atom_count = 0;
   bool c_added, r_added;
-  LOGN_DUMP("creating view");
+  LOG_DEBUG("creating view");
   EntityView view(eh);
-  LOGN_DUMP("creating query state");
+  LOG_DEBUG("creating query state");
   EntityHandle myself(const_cast<impl::EntityImpl*>(this)->shared_from_this());
   QueryState qs(query.CreateQueryState(myself));
-  LOGN_DUMP("entering chain loop");
+  LOG_DEBUG("entering chain loop");
   for (ChainImplList::const_iterator 
        ch_it=chain_list_.begin(); ch_it!=chain_list_.end();++ch_it) {
-    LOGN_DUMP("checking chain " << (*ch_it)->GetName());
+    LOG_DEBUG("checking chain " << (*ch_it)->GetName());
     c_added = false;
     tribool c = always_true ? tribool(true) : qs.EvalChain(*ch_it);
     if (c == true) {
-      LOGN_DUMP("chain is selected");
+      LOG_DEBUG("chain is selected");
       // Include all residues
       const ChainImplPtr& ci=*ch_it;
       ++chain_count;
       ChainView chain=view.AddChain(ci);
       ResidueImplList::const_iterator re_it = ci->GetResidueList().begin();
       for ( ;re_it!=ci->GetResidueList().end();++re_it) {
-        LOGN_DUMP(" adding residue " << (*re_it)->GetNumber());
+        LOG_DEBUG(" adding residue " << (*re_it)->GetNumber());
         ResidueImplPtr& ri = const_cast<ResidueImplPtr&>(*re_it);
         ++residue_count;
         ResidueView res =chain.AddResidue(ri);
         AtomImplList::const_iterator at_it = ri->GetAtomList().begin();
         for (;at_it != ri->GetAtomList().end(); ++at_it) {
-          LOGN_DUMP("  adding atom " << (*at_it)->GetName());
+          LOG_DEBUG("  adding atom " << (*at_it)->GetName());
           ++atom_count;
           if (flags & QueryFlag::NO_BONDS) {
             res.AddAtom(*at_it);
@@ -925,11 +894,11 @@ EntityView EntityImpl::do_selection(const EntityHandle& eh,
       ChainView chain;
       ResidueImplList::const_iterator re_it = ci->GetResidueList().begin();
       for ( ;re_it!=ci->GetResidueList().end();++re_it) {
-        LOGN_DUMP(" checking residue " << (*re_it)->GetNumber());
+        LOG_DEBUG(" checking residue " << (*re_it)->GetNumber());
         tribool r = qs.EvalResidue(*re_it);
         ResidueImplPtr& ri = const_cast<ResidueImplPtr&>(*re_it);
         if (r == true) {
-          LOGN_DUMP(" residue is selected");
+          LOG_DEBUG(" residue is selected");
           // Include all atoms
           ResidueImplPtr& ri = const_cast<ResidueImplPtr&>(*re_it);
           AtomImplList::const_iterator at_it = ri->GetAtomList().begin();
@@ -941,7 +910,7 @@ EntityView EntityImpl::do_selection(const EntityHandle& eh,
           ++residue_count;
           ResidueView res=chain.AddResidue(ri);
           for (;at_it != ri->GetAtomList().end(); ++at_it) {
-            LOGN_DUMP("  adding atom " << (*at_it)->GetName());
+            LOG_DEBUG("  adding atom " << (*at_it)->GetName());
             ++atom_count;
             if (flags & QueryFlag::NO_BONDS) {
               res.AddAtom(*at_it);
@@ -972,7 +941,7 @@ EntityView EntityImpl::do_selection(const EntityHandle& eh,
               if (flags & QueryFlag::MATCH_RESIDUES) {
                 AtomImplList::const_iterator at_it2 = ri->GetAtomList().begin();
                 for (;at_it2 != ri->GetAtomList().end(); ++at_it2) {
-                  LOGN_DUMP("  adding atom " << (*at_it2)->GetQualifiedName());
+                  LOG_DEBUG("  adding atom " << (*at_it2)->GetQualifiedName());
                   ++atom_count;                  
                   if (flags & QueryFlag::NO_BONDS) {
                     res.AddAtom(*at_it2);
@@ -983,7 +952,7 @@ EntityView EntityImpl::do_selection(const EntityHandle& eh,
                 }          
                 break;
               } else {
-                LOGN_DUMP("  adding atom " << (*at_it)->GetName());
+                LOG_DEBUG("  adding atom " << (*at_it)->GetName());
                 ++atom_count;                
                 if (flags & QueryFlag::NO_BONDS) {
                   res.AddAtom(*at_it);
@@ -1004,7 +973,7 @@ EntityView EntityImpl::do_selection(const EntityHandle& eh,
   }
   int bond_count=0;
   if (!(flags & QueryFlag::NO_BONDS)) {
-    LOGN_DUMP("adding bonds");
+    LOG_DEBUG("adding bonds");
     typedef BondTableType::MapType::const_iterator ConstIt;
     for (ConstIt it=bond_table.bonds.begin();it!=bond_table.bonds.end(); ++it) {
       if ((QueryFlag::EXCLUSIVE_BONDS & flags) || it->second.IsComplete()) {
@@ -1014,7 +983,7 @@ EntityView EntityImpl::do_selection(const EntityHandle& eh,
       }
     }    
   }
-  LOGN_VERBOSE("selected " << chain_count << " chain(s), "
+  LOG_VERBOSE("selected " << chain_count << " chain(s), "
                << residue_count << " residue(s), " << atom_count
                << " atom(s)" << " " << bond_count << " bond(s)");
   return view;
@@ -1094,7 +1063,7 @@ void EntityImpl::UpdateXCSIfNeeded()
     dirty_flags_&=~DirtyTrace;
   }
   if (dirty_flags_ & DirtyXCS) {
-    LOGN_VERBOSE("XCS marked dirty. Updating");
+    LOG_VERBOSE("XCS marked dirty. Updating");
     this->UpdateFromICS();
     dirty_flags_&=~DirtyXCS;
   }
@@ -1132,12 +1101,12 @@ void EntityImpl::UpdateICSIfNeeded()
     return;    
   }
   if (dirty_flags_ & DirtyTrace) {
-    LOGN_VERBOSE("rerunning directionality trace");
+    LOG_VERBOSE("rerunning directionality trace");
     this->TraceDirectionality();
     this->UpdateFromXCS();
     dirty_flags_&=~DirtyTrace;
   } else if (dirty_flags_ & DirtyICS) {
-    LOGN_VERBOSE("updating internal from external coordinates");    
+    LOG_VERBOSE("updating internal from external coordinates");    
     this->UpdateFromXCS();    
     dirty_flags_&=~DirtyICS;    
   }
@@ -1156,7 +1125,7 @@ void EntityImpl::DecXCSEditorCount()
 void EntityImpl::UpdateOrganizerIfNeeded()
 {
   if (dirty_flags_ & DirtyOrganizer) {
-    LOGN_DEBUG("atom organizer marked as dirty. updating");
+    LOG_DEBUG("atom organizer marked as dirty. updating");
     this->UpdateOrganizer();
     dirty_flags_&=~DirtyOrganizer;
   }
@@ -1191,6 +1160,18 @@ impl::ChainImplList::iterator EntityImpl::GetChain(const String& name)
   }
   return  cc.end();
 }
+
+pointer_it<ChainImplPtr> EntityImpl::GetChainIter(const String& name)
+{
+  impl::ChainImplList& cc=this->GetChainList();
+  for (size_t i=0; i<cc.size(); ++i) {
+    if (cc[i]->GetName()==name) {
+      return &cc.front()+i;
+    }
+  }
+  return  pointer_it<ChainImplPtr>(NULL);
+}
+
 void EntityImpl::RenameChain(ChainImplPtr chain, const String& new_name)
 {
   ChainImplList::iterator i;
diff --git a/modules/mol/base/src/impl/entity_impl.hh b/modules/mol/base/src/impl/entity_impl.hh
index 89765122f776d7169048bfb9bc3eb074db38369e..c01285ed2323b376e34d0754ed6e6ef21717999b 100644
--- a/modules/mol/base/src/impl/entity_impl.hh
+++ b/modules/mol/base/src/impl/entity_impl.hh
@@ -39,7 +39,7 @@
 #include <ost/mol/impl/connector_impl_fw.hh>
 #include <ost/mol/impl/torsion_impl_fw.hh>
 #include <ost/mol/impl/fragment_impl_fw.hh>
-
+#include <ost/mol/impl/pointer_iterator.hh>
 #include <ost/mol/entity_visitor_fw.hh>
 #include <ost/mol/entity_observer_fw.hh>
 #include <ost/mol/entity_view.hh>
@@ -75,7 +75,7 @@ typedef enum {
   // dirty trace (implies dirty ICS)
   DirtyTrace=DirtyICS+4,
   DirtyOrganizer=8,
-  DisableICS=16,
+  DisableICS=16
 } EntityDirtyFlags;
 
 
@@ -93,10 +93,11 @@ public:
   Real GetMass() const;
   geom::Vec3 GetCenterOfMass() const;
   geom::Vec3 GetCenterOfAtoms() const;
-  geom::Vec3 GetGeometricCenter() const;
-  geom::Vec3 GetGeometricStart() const;
-  geom::Vec3 GetGeometricEnd() const;
-  geom::Vec3 GetBoundarySize() const;
+  
+  /// \brief returns the axis-aligned bounding box of the entity
+  geom::AlignedCuboid GetBounds() const;
+  
+
 
   // default copy ctor and assignment op should work for now
   AtomImplPtr CreateAtom(const ResidueImplPtr& rp, const String& name,
@@ -242,6 +243,7 @@ public:
 
   impl::ChainImplList::iterator GetChain(const String& name);
 
+  pointer_it<ChainImplPtr> GetChainIter(const String& name);
   void SetName(const String& ent_name);
 
   void ReorderAllResidues();
diff --git a/modules/gui/src/plot_viewer/plot_group.hh b/modules/mol/base/src/impl/pointer_iterator.hh
similarity index 52%
rename from modules/gui/src/plot_viewer/plot_group.hh
rename to modules/mol/base/src/impl/pointer_iterator.hh
index c2b030145b7a0ec42e614a162b942933fc480560..63a5676ca6f22381e5edcf9f2325d2a778718c06 100644
--- a/modules/gui/src/plot_viewer/plot_group.hh
+++ b/modules/mol/base/src/impl/pointer_iterator.hh
@@ -16,44 +16,64 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#ifndef PLOT_GROUP_HH_
-#define PLOT_GROUP_HH_
-
-
-/*
-  Author: Andreas Schenk
-*/
+#ifndef OST_MOL_IMPL_POINTER_ITERATOR_HH
+#define OST_MOL_IMPL_POINTER_ITERATOR_HH
 
 #include <vector>
-#include <boost/shared_ptr.hpp>
-#include "plot_types.hh"
-#include "plot_data.hh"
-#include "plot_function.hh"
-
-namespace ost{namespace gui{
 
-class PlotGroup;
-typedef boost::shared_ptr<PlotGroup> PlotGroupPtr;
+namespace ost { namespace mol { namespace impl {
 
-class DLLEXPORT_OST_GUI PlotGroup : public PlotDataBase
-{
+template <typename T>
+class pointer_it :  public std::iterator<std::forward_iterator_tag, T>{
 public:
-  PlotGroup();
-  virtual ~PlotGroup();
-  void Add(PlotDataPtr dataptr);
-  void Add(PlotFunctionPtr functionptr);
-  void Add(PlotGroupPtr groupptr);
-  unsigned int GetSize();
-  PlotDataBasePtr GetChild(unsigned int index);
-  virtual Real GetMinimumX();
-  virtual Real GetMaximumX();
-  virtual Real GetMinimumY();
-  virtual Real GetMaximumY();
+  pointer_it(T* s): s_(s) { }
+  
+  pointer_it<T>& operator++()
+  {
+    ++s_;
+    return *this;
+  }
+  pointer_it<T>& operator+(int rhs)
+  {
+    s_+=rhs;
+    return *this;
+  }
+  
+  bool operator==(const pointer_it<T>& rhs) const
+  {
+    return rhs.s_==s_;
+  }
+  
+  bool operator!=(const pointer_it<T>&rhs) const
+  {
+    return !(*this==rhs);
+  }
+
+  T& operator*()
+  {
+    return *s_;
+  }
+
+  T* operator->()
+  {
+    return s_;
+  }
 private:
-  std::vector<PlotDataBasePtr> ptr_list_;
+  T* s_;
 };
 
+template <typename T>
+inline pointer_it<T> begin(const std::vector<T>& values)
+{
+  return pointer_it<T>(values.empty() ? NULL : const_cast<T*>(&values.front()));
+}
+
+template <typename T>
+inline pointer_it<T> end(const std::vector<T>& values)
+{
+  return pointer_it<T>(values.empty() ? NULL : const_cast<T*>(&values.back()+1));
+}
 
-}}//ns
+}}}
 
-#endif /*PLOT_GROUP_HH_*/
+#endif
diff --git a/modules/mol/base/src/impl/query_impl.cc b/modules/mol/base/src/impl/query_impl.cc
index 312b38d6db7e483d0e419c2991919e1189997e1f..92b00434666358db3197e01463020751976de0c5 100644
--- a/modules/mol/base/src/impl/query_impl.cc
+++ b/modules/mol/base/src/impl/query_impl.cc
@@ -107,19 +107,24 @@ QueryToken QueryLexer::LexQuotedStringLiteral()
 QueryToken QueryLexer::LexNumericToken() {
   Range range(current_, 0);
   static String allowed_chars("_");  
-  bool dot_present=false, is_string=false;
+  bool dot_present=false, is_string=false, last_was_dot=false;
   //TODO Better checking for duplicate -
   while(current_<query_string_.size()){
     if (isdigit(query_string_[current_]) || query_string_[current_]=='-') {
       current_++;
+      last_was_dot=false;
     } else if (query_string_[current_]=='.') {
       if (dot_present) {
         is_string=true;
         break;
       }
       dot_present = true;
+      last_was_dot=true;
       current_++;
     } else {
+      if (last_was_dot) {
+        break;
+      }
       is_string=isalnum(query_string_[current_]) || 
                 allowed_chars.find_first_of(query_string_[current_])!=String::npos;
       break;
@@ -128,6 +133,11 @@ QueryToken QueryLexer::LexNumericToken() {
   range.Length=current_-range.Loc;
   if (!is_string) {
     if (dot_present) {
+      if (last_was_dot) {
+        current_--;
+        return QueryToken(Range(range.Loc, range.Length-1), 
+                          tok::IntegralValue);
+      }
       return QueryToken(range, tok::FloatingValue);      
     } else {
       return QueryToken(range, tok::IntegralValue);      
@@ -145,16 +155,10 @@ bool is_ident_or_str(char c) {
 QueryToken QueryLexer::LexIdentOrStringToken() {
   static IdentTokens ident_tokens;
   size_t start=current_;
-  bool is_string=false;
   while (current_<query_string_.length() && 
          is_ident_or_str(query_string_[current_])) {
-    if (!isalnum(query_string_[current_]))
-      is_string=true;
     current_++;
   }
-  if (is_string) {
-    return QueryToken(Range(start, current_-start), tok::String);
-  }
   String ident=query_string_.substr(start, current_-start);
   if (tok::Type* t=find(ident_tokens, ident.c_str())) {
     return QueryToken(Range(start, current_-start), *t);
@@ -179,7 +183,10 @@ QueryToken QueryLexer::LexToken() {
         return QueryToken(Range(current_-1, 1), tok::Coma);
       case ':':
         current_++;
-        return QueryToken(Range(current_-1, 1), tok::Colon);        
+        return QueryToken(Range(current_-1, 1), tok::Colon);
+      case '.':
+        current_++;
+        return QueryToken(Range(current_-1, 1), tok::Dot);           
       case '{':
         current_++;
         return QueryToken(Range(current_-1, 1), tok::LeftCurlyBrace);
@@ -384,7 +391,6 @@ QueryImpl::QueryImpl(const String& query_string)
     sel_values_.push_back(sel_value);    
     Node* ast_root = this->BuildAST();
     if (ast_root) {
-      // ast_root->Dump();      
       // Get all selection statements
       this->ExtractSelStmts(ast_root);
       this->ASTToSelStack(ast_root,Prop::CHAIN,
@@ -395,6 +401,7 @@ QueryImpl::QueryImpl(const String& query_string)
                           sel_stacks_[(int)Prop::ATOM]);        
       delete ast_root;
       empty_optimize_=false;
+      has_error_=false;
     } else {
       has_error_=true;
     }  
@@ -427,10 +434,12 @@ bool QueryImpl::ParseValue(const Prop& sel, const QueryToken& op,
       if (sel.type==Prop::INT) {
         // todo. Add check to test that the comparison operator is only one of
         // = and !=. The others don't make too much sense.
-        if (value_string=="true") {
+        if (value_string=="true" || value_string=="True" || 
+            value_string=="TRUE") {
           value=ParamType(int(1));
           break;
-        } else if (value_string=="false") {   
+        } else if (value_string=="false" || value_string=="False" || 
+                   value_string=="FALSE") {   
           value=ParamType(int(0));
           break;
         }
@@ -609,6 +618,44 @@ Node* QueryImpl::ParsePropValueExpr(QueryLexer& lexer) {
   String s=query_string_.substr(sname.GetRange().Loc,sname.GetRange().Length);
   Prop property=PropertyFromString(s);
   QueryToken op=lexer.NextToken();
+  
+  // this block deals with the cname.rnum.aname shortcut.
+  if (op.GetType()==tok::Dot) {
+    QueryToken cname=sname;
+    QueryToken rnum=lexer.NextToken();
+    if (!this->Expect(tok::IntegralValue, "residue number", rnum)) {
+      return NULL;
+    }
+    if (!this->Expect(tok::Dot, "'.'", lexer.NextToken())) {
+      return NULL;
+    }
+    QueryToken aname=lexer.NextToken();
+    if (!this->Expect(tok::Identifier, "atom name", aname)) {
+      return NULL;
+    }
+    LogicOP lop=inversion_stack_.back() ? LOP_OR : LOP_AND;
+    CompOP cop=inversion_stack_.back() ? COP_NEQ : COP_EQ;
+    ParamType cname_val(query_string_.substr(cname.GetValueRange().Loc,
+                        cname.GetValueRange().Length).c_str());
+    Prop cname_prop(Prop::CNAME, Prop::STRING, Prop::CHAIN);
+    SelNode* cname_node=new SelNode(cname_prop, cop, cname_val);
+    ParamType aname_val(query_string_.substr(aname.GetValueRange().Loc,
+                        aname.GetValueRange().Length).c_str());
+   Prop aname_prop(Prop::ANAME, Prop::STRING, Prop::ATOM);
+    SelNode* aname_node=new SelNode(aname_prop, cop, aname_val);
+    ParamType rnum_val(atoi(query_string_.substr(rnum.GetValueRange().Loc,
+                            rnum.GetValueRange().Length).c_str()));
+    Prop rnum_prop(Prop::RNUM, Prop::INT, Prop::RESIDUE);                            
+    SelNode* rnum_node=new SelNode(rnum_prop, cop, rnum_val);
+    LogicOPNode* and_one=new LogicOPNode(lop);
+    LogicOPNode* and_two=new LogicOPNode(lop);  
+    and_one->SetLHS(and_two);
+    and_one->SetRHS(cname_node);
+    and_two->SetLHS(rnum_node);
+    and_two->SetRHS(aname_node);
+    lexer.NextToken();
+    return and_one;
+  }
   if (property.id>=Prop::CUSTOM) {
     property.id=(Prop::ID)(Prop::CUSTOM+num_gen_prop_++);
     EntityPropertyMapper epm=EntityPropertyMapper(s.substr(2), property.level);
@@ -777,8 +824,9 @@ Node* QueryImpl::ParseSubExpr(QueryLexer& lexer, bool paren) {
       error_desc_.range=t.GetRange();
       return NULL;
     }
-    if (t.IsEOF())
-      continue;
+    if (t.IsEOF()) {
+      return root_node.release();
+    }
     if (!this->ExpectLogicalOperator(t))
       return NULL;
     switch(t.GetType()) {
@@ -962,19 +1010,35 @@ Node* QueryImpl::ParseWithinExpr(QueryLexer& lexer) {
     return NULL;
   QueryToken ct=lexer.CurrentToken();
   if (ct.GetType()==tok::LeftCurlyBrace) {
-    geom::Vec3 point;
-    if (this->ParsePoint(lexer, point)) {
-      lexer.NextToken();  
-      ParamType pt(WithinParam(point, rv*rv));
-      CompOP comp_op= COP_LE;
-      if (inversion_stack_.back())
-        comp_op=COP_GE;
-      SelNode* within_node=new SelNode(Prop(Prop::WITHIN, Prop::VEC_DIST,
-                                            Prop::ATOM), 
-                                       comp_op, pt);
-      return within_node;
-    } else {
-      return NULL;
+    Node* points=NULL;
+    while (true) {
+      geom::Vec3 point;
+      if (this->ParsePoint(lexer, point)) {
+        ParamType pt(WithinParam(point, rv*rv));
+        CompOP comp_op= COP_LE;
+        if (inversion_stack_.back())
+          comp_op=COP_GE;
+        SelNode* within_node=new SelNode(Prop(Prop::WITHIN, Prop::VEC_DIST,
+                                              Prop::ATOM), 
+                                         comp_op, pt);
+        if (points) {
+          points=this->Concatenate(points, within_node, LOP_OR);
+        } else {
+          points=within_node;
+        }
+        QueryToken nt=lexer.NextToken();
+        if (nt.GetType()==tok::Coma) {
+          nt=lexer.NextToken();
+          if (!this->Expect(tok::LeftCurlyBrace, "'{'", nt)) {
+            delete points;
+            return NULL;
+          }
+          continue;
+        }
+        return points;
+      } else {
+        return NULL;
+      }
     }
   } else if (ct.GetType()==tok::LeftBracket) {
     // push false onto inversion stack to make sure we have a proper start for
diff --git a/modules/mol/base/src/impl/query_impl.hh b/modules/mol/base/src/impl/query_impl.hh
index 2a025bf4ab1795441bec919a2d52d5a4abd6997a..02915d391cd210055d28fa6cced7c3df3c267b6c 100644
--- a/modules/mol/base/src/impl/query_impl.hh
+++ b/modules/mol/base/src/impl/query_impl.hh
@@ -45,7 +45,8 @@ namespace tok {
     IntegralValue,
     FloatingValue,
     Colon,
-    Coma, 
+    Coma,
+    Dot, 
     And,
     Or, 
     Not,
@@ -66,7 +67,7 @@ namespace tok {
     None,
     UnknownChar,
     UnterminatedQuote,
-    String,
+    String
   }
   Type;
 }
diff --git a/modules/mol/base/src/impl/residue_impl.cc b/modules/mol/base/src/impl/residue_impl.cc
index bfee304770bcb5ec53443cda276127dc1458b074..b997ced3f5ee1e88fb833cec5236d7d0c0702e57 100644
--- a/modules/mol/base/src/impl/residue_impl.cc
+++ b/modules/mol/base/src/impl/residue_impl.cc
@@ -123,7 +123,7 @@ AtomImplPtr ResidueImpl::InsertAltAtom(const String& name,
 
 void ResidueImpl::Apply(EntityVisitor& v)
 {
-  LOGN_TRACE("visitor @" << &v << " visiting residue ; @" << this);
+  LOG_TRACE("visitor @" << &v << " visiting residue ; @" << this);
   if(v.VisitResidue(ResidueHandle(shared_from_this()))) {
     for (AtomImplList::iterator it=atom_list_.begin();
          it!=atom_list_.end();++it) {
@@ -208,7 +208,7 @@ geom::Vec3 ResidueImpl::GetCentralNormal() const
       geom::Vec3 v0=GetCentralAtom()->GetPos();
       nrvo=geom::Cross(geom::Normalize(v0),
                        geom::Normalize(geom::Vec3(-v0[2],v0[0],v0[1])));
-      LOGN_VERBOSE("warning: could not find atoms for proper central normal calculation");
+      LOG_VERBOSE("warning: could not find atoms for proper central normal calculation");
     }
     return nrvo;    
   } else if (chem_class_.IsNucleotideLinking()) {
@@ -222,7 +222,7 @@ geom::Vec3 ResidueImpl::GetCentralNormal() const
       geom::Vec3 v0=GetCentralAtom()->GetPos();
       nrvo=geom::Cross(geom::Normalize(v0),
                        geom::Normalize(geom::Vec3(-v0[2],v0[0],v0[1])));
-      LOGN_VERBOSE("warning: could not find atoms for proper central normal calculation");
+      LOG_VERBOSE("warning: could not find atoms for proper central normal calculation");
     }
     return nrvo;
   }
@@ -263,7 +263,7 @@ TorsionImplP ResidueImpl::GetPsiTorsion() const {
       return t;
   }
 
-  LOGN_DUMP("Can't find torsion PSI for " <<
+  LOG_DEBUG("Can't find torsion PSI for " <<
            this->GetKey() << this->GetNumber());
   return TorsionImplP();
 
@@ -303,7 +303,7 @@ TorsionImplP ResidueImpl::GetOmegaTorsion() const {
       return t;
   }
 
-  LOGN_DUMP("Can't find torsion Omega for " <<
+  LOG_DEBUG("Can't find torsion Omega for " <<
            this->GetKey() << this->GetNumber());
   return TorsionImplP();
 }
@@ -327,7 +327,7 @@ TorsionImplP ResidueImpl::GetPhiTorsion() const {
       return t;
   }
 
-  LOGN_DUMP("Can't find torsion PHI for " <<
+  LOG_DEBUG("Can't find torsion PHI for " <<
            this->GetKey() << this->GetNumber());
   return TorsionImplP();
 }
@@ -427,31 +427,23 @@ Real ResidueImpl::GetMass() const
   return mass;
 }
 
-geom::Vec3 ResidueImpl::GetGeometricEnd() const {
-  geom::Vec3 maximum(-std::numeric_limits<Real>::infinity(),
-                     -std::numeric_limits<Real>::infinity(),
-                     -std::numeric_limits<Real>::infinity());
-  for (AtomImplList::const_iterator i=atom_list_.begin(); 
-       i!=atom_list_.end(); ++i) {
-    maximum=geom::Max(maximum,(*i)->GetPos());
-  }
-  return maximum;
-}
-
-geom::Vec3 ResidueImpl::GetGeometricStart() const {
-  geom::Vec3 minimum(std::numeric_limits<Real>::infinity(),
-                     std::numeric_limits<Real>::infinity(),
-                     std::numeric_limits<Real>::infinity());
-  for (AtomImplList::const_iterator i=atom_list_.begin(); 
-       i!=atom_list_.end(); ++i) {
-    minimum=geom::Min(minimum,(*i)->GetPos());
-  }
-  return minimum;
-}
-
-geom::Vec3 ResidueImpl::GetGeometricCenter() const
+geom::AlignedCuboid ResidueImpl::GetBounds() const 
 {
-  return (this->GetGeometricStart() + this->GetGeometricEnd())/2;
+  
+  geom::Vec3 mmin( std::numeric_limits<Real>::infinity());
+  geom::Vec3 mmax(-std::numeric_limits<Real>::infinity());  
+
+  if (atom_list_.size()>0) {
+    AtomImplList::const_iterator i=atom_list_.begin();
+    mmin=mmax=(*i)->GetPos();
+    for (++i; i!=atom_list_.end(); ++i) {
+      mmax=geom::Max(mmax,(*i)->GetPos());
+      mmin=geom::Min(mmin,(*i)->GetPos());      
+    }    
+    return geom::AlignedCuboid(mmin, mmax);
+  } else {
+    return geom::AlignedCuboid(geom::Vec3(), geom::Vec3());
+  }
 }
 
 geom::Vec3 ResidueImpl::GetCenterOfAtoms() const
diff --git a/modules/mol/base/src/impl/residue_impl.hh b/modules/mol/base/src/impl/residue_impl.hh
index 22e816b6e851d79f2c4f56dedaddf23ae7cd4fef..183a9ccefe8c5025f2790109b0ab3d26acfc17f8 100644
--- a/modules/mol/base/src/impl/residue_impl.hh
+++ b/modules/mol/base/src/impl/residue_impl.hh
@@ -131,9 +131,9 @@ public:
   Real GetMass() const;
   geom::Vec3 GetCenterOfMass() const;
   geom::Vec3 GetCenterOfAtoms() const;
-  geom::Vec3 GetGeometricCenter() const;
-  geom::Vec3 GetGeometricStart() const;
-  geom::Vec3 GetGeometricEnd() const;
+  
+  geom::AlignedCuboid GetBounds() const;
+  
 
   void DeleteAtom(const AtomImplPtr& atom);
   void DeleteAtoms(const String& atom_name);
@@ -199,6 +199,9 @@ public:
   
   int GetIntProperty(Prop::ID prop_id) const;
   
+  void SetProtein(bool protein) { protein_=protein; }
+  
+  bool IsProtein() const { return protein_; }
 private:
   void AddAltAtom(const String& group, const AtomImplPtr& atom,
                   const geom::Vec3& position);
@@ -207,13 +210,15 @@ private:
   AtomEntryGroups            alt_groups_;
   EntityImplW                ent_;
   ChainImplW                 chain_;
-  ResNum              num_;
+  ResNum                     num_;
   ResidueKey                 key_;
   AtomImplList               atom_list_;
   TorsionImplList            torsion_list_;
   SecStructure               sec_structure_;
   ChemClass                  chem_class_;
   char                       olc_;
+  // whether the residue is part of the protein.
+  bool                       protein_;
 };
 
 }}} // ns
diff --git a/modules/mol/base/src/impl/torsion_impl.cc b/modules/mol/base/src/impl/torsion_impl.cc
index 6239f4990d8b377fcb0ec330fb7406eafd84582a..42e6b1bb4a223dd62ab854a5eca6d9c437183c19 100644
--- a/modules/mol/base/src/impl/torsion_impl.cc
+++ b/modules/mol/base/src/impl/torsion_impl.cc
@@ -51,7 +51,7 @@ void TorsionImpl::SetAngle(Real angle, bool up) {
 }
 
 void TorsionImpl::Apply(EntityVisitor& v) {
-  LOG_TRACE("visitor @" << &v << " visiting torsion impl @" << this << std::endl);
+  LOG_TRACE("visitor @" << &v << " visiting torsion impl @" << this);
   v.VisitTorsion(TorsionHandle(shared_from_this()));
 }
 
diff --git a/modules/mol/base/src/iterator.cc b/modules/mol/base/src/iterator.cc
index 74ff90c6514b1fd86517d68aba1ceddfd604694c..05fc8f59e981cd6f7867e60bbbd76b44374dbdc6 100644
--- a/modules/mol/base/src/iterator.cc
+++ b/modules/mol/base/src/iterator.cc
@@ -25,29 +25,36 @@
 
 namespace ost { namespace mol {
 
-
-ResidueHandleIter& ResidueHandleIter::operator++() {
-  ++cur_res_;
-  if (cur_res_==(*cur_chain_)->GetResidueList().end()) {
+void ResidueHandleIter::SkipEmpty()
+{
+  if (cur_res_==impl::end((*cur_chain_)->GetResidueList())) {
     // we have to skip over empty chains otherwise we end up pointing to an 
     // invalid residue.
     do {
       ++cur_chain_;
-      if (ent_->GetChainList().end()==cur_chain_) {
+      if (impl::end(ent_->GetChainList())==cur_chain_) {
         break;        
       }
-      cur_res_=(*cur_chain_)->GetResidueList().begin();
+      cur_res_=impl::begin((*cur_chain_)->GetResidueList());
     } while ((*cur_chain_)->GetResidueList().empty());
-  }        
+  }
+}
+
+ResidueHandleIter& ResidueHandleIter::operator++() 
+{
+  ++cur_res_;
+  this->SkipEmpty();
   return *this;
 }
 
-ResidueHandleIter::ResidueHandleIter(impl::ChainImplList::iterator chain_it, 
-                                     impl::ResidueImplList::iterator res_it,
-                                     impl::EntityImplPtr ent) 
+ResidueHandleIter::ResidueHandleIter(impl::pointer_it<impl::ChainImplPtr> chain_it, 
+                                     impl::pointer_it<impl::ResidueImplPtr> res_it,
+                                     impl::EntityImplPtr ent, bool skip_empty) 
  : cur_chain_(chain_it), cur_res_(res_it),
    ent_(ent) {
-
+  if (skip_empty) {
+    this->SkipEmpty();
+  }
 }
 
 ResidueHandle ResidueHandleIter::operator*() {
@@ -60,48 +67,39 @@ ResidueView ResidueViewIter::operator*() {
   return ResidueView(*cur_res_);
 }
 
-ResidueViewIter& ResidueViewIter::operator++() {
-  ++cur_res_;
-  if (cur_res_==cur_chain_->GetResidueList().end()) {
+void ResidueViewIter::SkipEmpty()
+{
+  if (cur_res_==impl::end(cur_chain_->GetResidueList())) {
     // we have to skip over empty chains otherwise we end up pointing to an 
     // invalid residue.
     do {
       ++cur_chain_;
-      if (ent_.GetChainList().end()==cur_chain_) {
+      if (impl::end(ent_.GetChainList())==cur_chain_) {
         break;        
       }
-      cur_res_=cur_chain_->GetResidueList().begin();
+      cur_res_=impl::begin(cur_chain_->GetResidueList());
     } while (cur_chain_->GetResidueList().empty());
-  }        
+  }  
+}
+ResidueViewIter& ResidueViewIter::operator++() {
+  ++cur_res_;
+  this->SkipEmpty();
   return *this;
 }
 
-ResidueViewIter::ResidueViewIter() 
-#ifdef _MSC_VER
-    : cur_res_() 
-#else
-    : cur_res_(NULL) 
-#endif
-{}
-
-ResidueViewIter::ResidueViewIter(ChainViewList::const_iterator chain_it,
-                                 ResidueViewList::const_iterator res_it,
-                                 EntityView ent) 
+ResidueViewIter::ResidueViewIter(impl::pointer_it<ChainView>   chain_it,
+                                 impl::pointer_it<ResidueView> res_it,
+                                 EntityView ent, bool skip_empty) 
  : cur_chain_(chain_it), cur_res_(res_it),
    ent_(ent) {
+  if (skip_empty) {
+    this->SkipEmpty();
+  }
 }
 
-AtomHandleIter::AtomHandleIter() 
-#ifdef _MSC_VER
-    : cur_atom_() 
-#else
-    : cur_atom_(NULL) 
-#endif
-{}  
-
-AtomHandleIter::AtomHandleIter(impl::ChainImplList::iterator chain_it,
-                               impl::ResidueImplList::iterator res_it,
-                               impl::AtomImplList::iterator atom_it,
+AtomHandleIter::AtomHandleIter(impl::pointer_it<impl::ChainImplPtr> chain_it,
+                               impl::pointer_it<impl::ResidueImplPtr> res_it,
+                               impl::pointer_it<impl::AtomImplPtr> atom_it,
                                impl::EntityImplPtr ent, bool skip_empty)
  : cur_chain_(chain_it), cur_res_(res_it), cur_atom_(atom_it),
    ent_(ent) 
@@ -117,26 +115,26 @@ AtomHandle AtomHandleIter::operator*() {
 
 void AtomHandleIter::SkipEmpty()
 {
-  if ((*cur_res_)->GetAtomList().end()==cur_atom_) {
+  if (impl::end((*cur_res_)->GetAtomList())==cur_atom_) {
     // we have to skip over empty chains and residues otherwise we end up 
     // pointing to an invalid atom.
     do {
       ++cur_res_;
-      if ((*cur_chain_)->GetResidueList().end()==cur_res_) {
+      if (impl::end((*cur_chain_)->GetResidueList())==cur_res_) {
         do {
           ++cur_chain_;
-          if (ent_->GetChainList().end()==cur_chain_) {
+          if (impl::end(ent_->GetChainList())==cur_chain_) {
             return;
           }
 
-          cur_res_=(*cur_chain_)->GetResidueList().begin();
+          cur_res_=impl::begin((*cur_chain_)->GetResidueList());
           if (!(*cur_chain_)->GetResidueList().empty())          
-            cur_atom_=(*cur_res_)->GetAtomList().begin();
+            cur_atom_=impl::begin((*cur_res_)->GetAtomList());
           else
-            cur_atom_=impl::AtomImplList::iterator();
+            cur_atom_=impl::pointer_it<impl::AtomImplPtr>(NULL);
         } while ((*cur_chain_)->GetResidueList().empty());
       } else {
-        cur_atom_=(*cur_res_)->GetAtomList().begin();
+        cur_atom_=impl::begin((*cur_res_)->GetAtomList());
       }
     } while ((*cur_res_)->GetAtomList().empty());
   }
@@ -149,17 +147,9 @@ AtomHandleIter& AtomHandleIter::operator++()
   return *this;
 }
 
-AtomViewIter::AtomViewIter()
-#ifdef _MSC_VER
-    : cur_atom_() 
-#else
-    : cur_atom_(NULL) 
-#endif
-{}  
-
-AtomViewIter::AtomViewIter(ChainViewList::const_iterator chain_it,
-                           ResidueViewList::const_iterator res_it,
-                           AtomViewList::const_iterator atom_it,
+AtomViewIter::AtomViewIter(impl::pointer_it<ChainView> chain_it,
+                           impl::pointer_it<ResidueView> res_it,
+                           impl::pointer_it<AtomView> atom_it,
                            EntityView ent, bool skip_empty)
   : cur_chain_(chain_it), cur_res_(res_it), cur_atom_(atom_it),
     ent_(ent) {
@@ -170,23 +160,24 @@ AtomViewIter::AtomViewIter(ChainViewList::const_iterator chain_it,
 
 void AtomViewIter::SkipEmpty()
 {
-  if (cur_res_->GetAtomList().end()==cur_atom_) {
+  if (impl::end(cur_res_->GetAtomList())==cur_atom_) {
     do {
       ++cur_res_;      
-      if (cur_chain_->GetResidueList().end()==cur_res_) {
+      if (impl::end(cur_chain_->GetResidueList())==cur_res_) {
         do {
           ++cur_chain_;
-          if (ent_.GetChainList().end()==cur_chain_) {
+          if (impl::end(ent_.GetChainList())==cur_chain_) {
             return;
           }          
-          cur_res_=cur_chain_->GetResidueList().begin();
-          if (!cur_chain_->GetResidueList().empty())          
-            cur_atom_=cur_res_->GetAtomList().begin();
-          else
-            cur_atom_=AtomViewList::const_iterator();
+          cur_res_=impl::begin(cur_chain_->GetResidueList());
+          if (!cur_chain_->GetResidueList().empty()) {
+            cur_atom_=impl::begin(cur_res_->GetAtomList());
+          } else {
+            cur_atom_=impl::pointer_it<AtomView>(NULL);
+          }
         } while (cur_chain_->GetResidueList().empty());
       } else {
-        cur_atom_=cur_res_->GetAtomList().begin();
+        cur_atom_=impl::begin(cur_res_->GetAtomList());
       }
     } while (cur_res_->GetAtomList().empty());
   }
diff --git a/modules/mol/base/src/iterator.hh b/modules/mol/base/src/iterator.hh
index 7bbbe48396591eea4ba1af3f8fc991976b754dec..d127985538c923ff3cfac08e80485989f84da085 100644
--- a/modules/mol/base/src/iterator.hh
+++ b/modules/mol/base/src/iterator.hh
@@ -21,9 +21,7 @@
 
 #include <map>
 
-#include <ost/mol/impl/entity_impl_fw.hh>
-#include <ost/mol/impl/chain_impl_fw.hh>
-#include <ost/mol/impl/residue_impl_fw.hh>
+
 #include <ost/mol/chain_handle.hh>
 #include <ost/mol/chain_view.hh>
 #include <ost/mol/residue_handle.hh>
@@ -32,6 +30,10 @@
 #include <ost/mol/atom_view.hh>
 #include <ost/mol/entity_handle.hh>
 #include <ost/mol/entity_view.hh>
+#include <ost/mol/impl/entity_impl_fw.hh>
+#include <ost/mol/impl/chain_impl_fw.hh>
+#include <ost/mol/impl/residue_impl_fw.hh>
+#include <ost/mol/impl/pointer_iterator.hh>
 
 namespace ost { namespace mol {
 
@@ -78,10 +80,12 @@ private:
   I cur_;
 };
 
+
 namespace impl {
-  // forward declearation of chain impl map.
+  // forward declearation of chain impl list.
   typedef std::vector<ChainImplPtr> ChainImplList;
 }
+
 class DLLEXPORT_OST_MOL ChainHandleIter : public std::iterator<std::forward_iterator_tag, 
                                              ChainHandle> {
 public: // internally used constructors
@@ -112,20 +116,20 @@ private:
 class DLLEXPORT_OST_MOL ResidueHandleIter : public std::iterator<std::forward_iterator_tag,
                                                ResidueHandle> {
 public:
-  ResidueHandleIter() {    
-  }
-  ResidueHandleIter(impl::ChainImplList::iterator chain_it, 
-                    impl::ResidueImplList::iterator res_it,
-                    impl::EntityImplPtr ent);
-  bool operator==(const ResidueHandleIter& rhs) const {
-#if defined(_MSC_VER)    
-    return cur_chain_==rhs.cur_chain_ && cur_res_==rhs.cur_res_;
-#else
+  ResidueHandleIter(): cur_chain_(NULL), cur_res_(NULL) { }
+  ResidueHandleIter(impl::pointer_it<impl::ChainImplPtr> chain_it, 
+                    impl::pointer_it<impl::ResidueImplPtr> res_it,
+                    impl::EntityImplPtr ent, bool skip_empty);
+  
+  bool operator==(const ResidueHandleIter& rhs) const 
+  {
     return cur_res_==rhs.cur_res_;
-#endif
   }
   
-  bool operator!=(const ResidueHandleIter& rhs) const {
+  void SkipEmpty();
+  
+  bool operator!=(const ResidueHandleIter& rhs) const 
+  {
     return !this->operator==(rhs);
   }
   ResidueHandleIter& operator++();
@@ -133,28 +137,24 @@ public:
   ResidueHandle operator*();
   
 private:
-  impl::ChainImplList::iterator cur_chain_;
-  impl::ResidueImplList::iterator cur_res_;
+  impl::pointer_it<impl::ChainImplPtr> cur_chain_;
+  impl::pointer_it<impl::ResidueImplPtr> cur_res_;
   impl::EntityImplPtr  ent_;
 };
 
 class DLLEXPORT_OST_MOL ResidueViewIter : public std::iterator<std::forward_iterator_tag,
                                              ResidueView> {
 public:
-  ResidueViewIter();
+  ResidueViewIter(): cur_chain_(NULL), cur_res_(NULL) { }
 
-  ResidueViewIter(ChainViewList::const_iterator chain_it,
-                  ResidueViewList::const_iterator res_it,
-                  EntityView ent);
+  ResidueViewIter(impl::pointer_it<ChainView> chain_it,
+                  impl::pointer_it<ResidueView> res_it,
+                  EntityView ent, bool skip_empty);
 
   bool operator==(const ResidueViewIter& rhs) const {
-#if defined(_MSC_VER)    
-    return cur_chain_==rhs.cur_chain_ && cur_res_==rhs.cur_res_;
-#else
-    return cur_res_==rhs.cur_res_;
-#endif    
     return cur_res_==rhs.cur_res_;
   }
+  void SkipEmpty();
   
   bool operator!=(const ResidueViewIter& rhs) const {
     return !this->operator==(rhs);
@@ -164,72 +164,70 @@ public:
   ResidueView operator*();
   
 private:
-  ChainViewList::const_iterator    cur_chain_;
-  ResidueViewList::const_iterator  cur_res_;
-  EntityView                       ent_;
+  impl::pointer_it<ChainView>    cur_chain_;
+  impl::pointer_it<ResidueView>  cur_res_;
+  EntityView                     ent_;
 };
 
 class DLLEXPORT_OST_MOL AtomHandleIter : public std::iterator<std::forward_iterator_tag,
                                             AtomHandle> {
 public:
-  AtomHandleIter(); 
+  AtomHandleIter(): cur_chain_(NULL), cur_res_(NULL), cur_atom_(NULL) { }
 
-  AtomHandleIter(impl::ChainImplList::iterator chain_it,
-                 impl::ResidueImplList::iterator res_it,
-                 impl::AtomImplList::iterator atom_it,
+  AtomHandleIter(impl::pointer_it<impl::ChainImplPtr> chain_it,
+                 impl::pointer_it<impl::ResidueImplPtr> res_it,
+                 impl::pointer_it<impl::AtomImplPtr> atom_it,
                  impl::EntityImplPtr ent, bool skip_empty);
                  
-  bool operator==(const AtomHandleIter& rhs) const {
-#if defined(_MSC_VER)    
-    return cur_chain_==rhs.cur_chain_ && cur_res_==rhs.cur_res_ &&
-           cur_atom_==rhs.cur_atom_;
-#else
+  bool operator==(const AtomHandleIter& rhs) const 
+  {
    return cur_atom_==rhs.cur_atom_;
-#endif
   }
-  bool operator!=(const AtomHandleIter& rhs) const {
-  return !this->operator==(rhs);
+  
+  bool operator!=(const AtomHandleIter& rhs) const 
+  {
+    return !this->operator==(rhs);
   }
+  
   AtomHandleIter& operator++();
 
   AtomHandle operator*();
 private:
   void SkipEmpty();
-  impl::ChainImplList::iterator cur_chain_;
-  impl::ResidueImplList::iterator cur_res_;
-  impl::AtomImplList::iterator cur_atom_;
+  impl::pointer_it<impl::ChainImplPtr> cur_chain_;
+  impl::pointer_it<impl::ResidueImplPtr> cur_res_;
+  impl::pointer_it<impl::AtomImplPtr> cur_atom_;
   impl::EntityImplPtr  ent_;
 };
 
 class DLLEXPORT_OST_MOL AtomViewIter : public std::iterator<std::forward_iterator_tag,
                                           AtomView> {
 public:
-  AtomViewIter();
+  AtomViewIter(): cur_chain_(NULL), cur_res_(NULL), cur_atom_(NULL) { }
 
-  AtomViewIter(ChainViewList::const_iterator chain_it,
-               ResidueViewList::const_iterator res_it,
-               AtomViewList::const_iterator atom_it,
+  AtomViewIter(impl::pointer_it<ChainView> chain_it,
+               impl::pointer_it<ResidueView> res_it,
+               impl::pointer_it<AtomView> atom_it,
                EntityView ent, bool skip_empty);
                  
-  bool operator==(const AtomViewIter& rhs) const {
-#if defined(_MSC_VER)    
-    return cur_chain_==rhs.cur_chain_ && cur_res_==rhs.cur_res_ &&
-           cur_atom_==rhs.cur_atom_;
-#else
+  bool operator==(const AtomViewIter& rhs) const 
+  {
    return cur_atom_==rhs.cur_atom_;
-#endif
   }
-  bool operator!=(const AtomViewIter& rhs) const {
+  
+  bool operator!=(const AtomViewIter& rhs) const 
+  {
     return !this->operator==(rhs);
   }
+  
   AtomViewIter& operator++();
 
   AtomView operator*();
 private:
   void SkipEmpty();
-  ChainViewList::const_iterator    cur_chain_;
-  ResidueViewList::const_iterator  cur_res_;
-  AtomViewList::const_iterator     cur_atom_;
+  impl::pointer_it<ChainView>    cur_chain_;
+  impl::pointer_it<ResidueView>  cur_res_;
+  impl::pointer_it<AtomView>     cur_atom_;
   EntityView                       ent_;
 };
 
diff --git a/modules/mol/base/src/property_id.cc b/modules/mol/base/src/property_id.cc
index ed19a4f3e85d5d17955d84fd67241f043fb510d4..a6408b83e97407a26060faac0824dc0659403493 100644
--- a/modules/mol/base/src/property_id.cc
+++ b/modules/mol/base/src/property_id.cc
@@ -49,7 +49,9 @@ struct Properties : public boost::spirit::symbols<Prop> {
       ("abfac", Prop(Prop::ABFAC, Prop::FLOAT, Prop::ATOM))
       ("rbfac", Prop(Prop::RBFAC, Prop::FLOAT, Prop::RESIDUE))
       ("peptide", Prop(Prop::PEPTIDE, Prop::INT, Prop::RESIDUE))
-      ("rindex", Prop(Prop::RINDEX, Prop::INT, Prop::RESIDUE))      
+      ("rindex", Prop(Prop::RINDEX, Prop::INT, Prop::RESIDUE))
+      ("protein", Prop(Prop::PROTEIN, Prop::INT, Prop::RESIDUE))
+      ("water", Prop(Prop::WATER, Prop::INT, Prop::RESIDUE))
       ("acharge", Prop(Prop::ACHARGE, Prop::FLOAT, Prop::ATOM));
   }
 } properties;
@@ -112,6 +114,10 @@ String Prop::GetName() const
       return "acharge";
     case RINDEX:
       return "rindex";
+    case PROTEIN:
+      return "protein";
+    case WATER:
+      return "water";
     default:
       return "";
   }
diff --git a/modules/mol/base/src/property_id.hh b/modules/mol/base/src/property_id.hh
index dfc984bc2b465fa70c502fdd8c6653efd82bba14..4ea4be13fc66c96512edfca18169967602f747da 100644
--- a/modules/mol/base/src/property_id.hh
+++ b/modules/mol/base/src/property_id.hh
@@ -40,7 +40,8 @@ public:
   /// respectively.
   typedef enum {
     RNAME, ANAME, CNAME, ELE, RNUM, ANUM, AX, AY, AZ, OCC, RTYPE, ISHETATM,
-    RBFAC, ABFAC, PEPTIDE, ACHARGE, RINDEX, WITHIN, UNDEF, CUSTOM
+    RBFAC, ABFAC, PEPTIDE, ACHARGE, RINDEX, PROTEIN, WATER, WITHIN, 
+    UNDEF, CUSTOM
   } ID;
   
   typedef enum {
diff --git a/modules/mol/base/src/query_state.cc b/modules/mol/base/src/query_state.cc
index c3e68560b175d21de8ad6591161e273a4b50f149..95dc07e16ef138132fc9b8a43c93c23061e994ee 100644
--- a/modules/mol/base/src/query_state.cc
+++ b/modules/mol/base/src/query_state.cc
@@ -63,7 +63,7 @@ bool QueryState::do_within(const geom::Vec3& pos, const impl::WithinParam& p,
     if (op==COP_LE)
       return geom::Dot(d, d) <= p.GetRadiusSquare();
     else
-      return geom::Dot(d, d) >= p.GetRadiusSquare();    
+      return geom::Dot(d, d) > p.GetRadiusSquare();
   } else {
     const LazilyBoundRef& r=this->GetBoundObject(p.GetRef());
     for (AtomViewIter i=r.view.AtomsBegin(), e=r.view.AtomsEnd(); i!=e; ++i) {
@@ -72,7 +72,7 @@ bool QueryState::do_within(const geom::Vec3& pos, const impl::WithinParam& p,
         if (geom::Dot(d, d) <= p.GetRadiusSquare()) {
           return true;
         }
-      } else if (geom::Dot(d, d) <= p.GetRadiusSquare()) {
+      } else if (geom::Dot(d, d) > p.GetRadiusSquare()) {
         return false;
       }
     }
@@ -198,7 +198,7 @@ boost::logic::tribool QueryState::EvalResidue(const impl::ResidueImplPtr& r) {
         s_[*i]=cmp_num<int>(ss.comp_op,int_value,boost::get<int>(ss.param));        
         break;
       case Prop::PEPTIDE:
-        int_value=r->GetChemClass().IsPeptideLinking() ? 1 : 0;
+        int_value=r->GetChemClass().IsPeptideLinking();
         s_[*i] = cmp_num<int>(ss.comp_op,int_value,boost::get<int>(ss.param));        
         break;        
       case Prop::RBFAC:
@@ -209,6 +209,14 @@ boost::logic::tribool QueryState::EvalResidue(const impl::ResidueImplPtr& r) {
         s_[*i] = cmp_num<Real>(ss.comp_op, float_value,
                                  boost::get<float>(ss.param));        
         break;
+      case Prop::PROTEIN:
+        int_value=r->IsProtein();
+        s_[*i]=cmp_num<int>(ss.comp_op,int_value,boost::get<int>(ss.param));
+        break;
+      case Prop::WATER:
+        int_value=r->GetChemClass().IsWater();
+        s_[*i]=cmp_num<int>(ss.comp_op,int_value,boost::get<int>(ss.param));
+        break;
       case Prop::RTYPE:
         p=boost::get<String>(ss.param);
         if (p.length()>1) {
diff --git a/modules/mol/base/src/query_view_wrapper.cc b/modules/mol/base/src/query_view_wrapper.cc
index ae0aa527ab7d9f80082730a9fec78ac442260728..310bc468b9333a6efa2565dabdb40af133e11ab8 100644
--- a/modules/mol/base/src/query_view_wrapper.cc
+++ b/modules/mol/base/src/query_view_wrapper.cc
@@ -27,24 +27,21 @@ QueryViewWrapper::QueryViewWrapper():
         entity_handle_(),
         entity_view_(),
         query_(),
-        flags_(0)
-{}
+        flags_(0){}
 
 QueryViewWrapper::QueryViewWrapper(const EntityHandle& entity_handle):
     view_set_(false),
     entity_handle_(entity_handle),
     entity_view_(),
     query_(),
-    flags_(0)
-{}
+    flags_(0){}
 
 QueryViewWrapper::QueryViewWrapper(const EntityView& entity_view):
     view_set_(true),
     entity_handle_(),
     entity_view_(entity_view),
     query_(),
-    flags_(0)
-{}
+    flags_(0){}
 
 QueryViewWrapper::QueryViewWrapper(const Query& query, 
                                    const EntityHandle& entity_handle,
@@ -53,8 +50,7 @@ QueryViewWrapper::QueryViewWrapper(const Query& query,
     entity_handle_(entity_handle),
     entity_view_(),
     query_(query),
-    flags_(f)
-{}
+    flags_(0){}
 
 QueryViewWrapper::QueryViewWrapper(const Query& query, 
                                    const EntityView& view,
@@ -63,8 +59,23 @@ QueryViewWrapper::QueryViewWrapper(const Query& query,
     entity_handle_(),
     entity_view_(view),
     query_(query),
-    flags_(f)
-{}
+    flags_(0){}
+
+QueryViewWrapper::QueryViewWrapper(const Query& query, QueryFlags flags,
+                                   const EntityHandle& entity_handle):
+    view_set_(false),
+    entity_handle_(entity_handle),
+    entity_view_(),
+    query_(query),
+    flags_(flags){}
+
+QueryViewWrapper::QueryViewWrapper(const Query& query, QueryFlags flags,
+                                   const EntityView& view):
+    view_set_(true),
+    entity_handle_(),
+    entity_view_(view),
+    query_(query),
+    flags_(flags){}
 
 EntityView QueryViewWrapper::GetEntityView() const
 {
@@ -88,18 +99,14 @@ void QueryViewWrapper::SetQuery(const Query& query)
   query_ = query;
 }
 
-void QueryViewWrapper::SetQueryFlags(QueryFlags f)
-{
-  flags_=f;
+void QueryViewWrapper::SetFlags(QueryFlags flags){
+  flags_ = flags;
 }
-
-QueryFlags QueryViewWrapper::GetQueryFlags() const
-{
+QueryFlags QueryViewWrapper::GetFlags() const{
   return flags_;
 }
 
-bool QueryViewWrapper::IsDataValid() const
-{
+bool QueryViewWrapper::IsDataValid() const{
   if(view_set_){
     return entity_view_.IsValid();
   }
diff --git a/modules/mol/base/src/query_view_wrapper.hh b/modules/mol/base/src/query_view_wrapper.hh
index 483b303c9e6704c596aa0e4ab182de5fa816ecb9..44ec53d3b81ea525e2072a7f2dbf9fa86aecec83 100644
--- a/modules/mol/base/src/query_view_wrapper.hh
+++ b/modules/mol/base/src/query_view_wrapper.hh
@@ -32,8 +32,10 @@ public:
   explicit QueryViewWrapper(const EntityHandle& entity_handle);
   explicit QueryViewWrapper(const EntityView& entity_view);
   QueryViewWrapper();
-  QueryViewWrapper(const Query& query, const EntityHandle& handle, QueryFlags f=0);
-  QueryViewWrapper(const Query& query, const EntityView& view, QueryFlags f=0);  
+  QueryViewWrapper(const Query& query, const EntityHandle& handle);
+  QueryViewWrapper(const Query& query, const EntityView& view = mol::EntityView());
+  QueryViewWrapper(const Query& query, QueryFlags flags, const EntityHandle& handle);
+  QueryViewWrapper(const Query& query, QueryFlags flags, const EntityView& view = mol::EntityView());
   EntityView GetEntityView() const;
   bool DependsOnQuery() const;
   bool IsDataValid() const;
@@ -41,8 +43,8 @@ public:
   void SetQuery(const Query& query);
   const Query& GetQuery() const;
 
-  void SetQueryFlags(QueryFlags f);
-  QueryFlags GetQueryFlags() const;
+  void SetFlags(QueryFlags flags);
+  QueryFlags GetFlags() const;
 
 private:
   bool view_set_;
diff --git a/modules/mol/base/src/residue_base.cc b/modules/mol/base/src/residue_base.cc
index f4ce54ee5aafc307e7f31efff4f05ef6975ed7d7..9ae05d783a17e7885f3f1b2f8896cdcb1a7894be 100644
--- a/modules/mol/base/src/residue_base.cc
+++ b/modules/mol/base/src/residue_base.cc
@@ -181,5 +181,17 @@ int ResidueBase::GetIntProperty(Prop::ID prop_id) const
   return Impl()->GetIntProperty(prop_id);
 }
 
+bool ResidueBase::IsProtein() const
+{
+  this->CheckValidity();
+  return Impl()->IsProtein();
+}
+
+void ResidueBase::SetIsProtein(bool protein)
+{
+  this->CheckValidity();
+  Impl()->SetProtein(protein);
+}
+
 }}
 
diff --git a/modules/mol/base/src/residue_base.hh b/modules/mol/base/src/residue_base.hh
index 69749ed492dbc566ad1d3eb72eabb3ad23999257..1ad7438795fa240422afc912645ab5025c48d50d 100644
--- a/modules/mol/base/src/residue_base.hh
+++ b/modules/mol/base/src/residue_base.hh
@@ -139,7 +139,11 @@ public:
   
   /// \brief Get int property by id
   int GetIntProperty(Prop::ID prop_id) const;
-    
+  
+  /// \brief whether the residue is part of the protein.
+  bool IsProtein() const;
+  
+  void SetIsProtein(bool protein);
 public:
   impl::ResidueImplPtr& Impl();
 
diff --git a/modules/mol/base/src/residue_handle.cc b/modules/mol/base/src/residue_handle.cc
index bfc57c1949c209f753e0592730669f82f179c020..6c9e007d80a2d52ea1f69a981f81e5416adf283c 100644
--- a/modules/mol/base/src/residue_handle.cc
+++ b/modules/mol/base/src/residue_handle.cc
@@ -181,9 +181,9 @@ AtomHandleIter ResidueHandle::AtomsBegin() const
   impl::ResidueImplPtr r=Impl();
   int index=this->GetIndex();
   impl::ChainImplPtr c=r->GetChain();
-  impl::ChainImplList::iterator cc=r->GetEntity()->GetChain(c->GetName());
-  return AtomHandleIter(cc, c->GetResidueList().begin()+index,
-                        r->GetAtomList().begin(), r->GetEntity(), true);
+  impl::pointer_it<impl::ChainImplPtr> cc=r->GetEntity()->GetChainIter(c->GetName());
+  return AtomHandleIter(cc, impl::begin(c->GetResidueList())+index,
+                        impl::begin(r->GetAtomList()), r->GetEntity(), true);
 }
 
 AtomHandleIter ResidueHandle::AtomsEnd() const 
@@ -192,14 +192,15 @@ AtomHandleIter ResidueHandle::AtomsEnd() const
   impl::ResidueImplPtr r=Impl();
   int index=this->GetIndex();
   impl::ChainImplPtr c=r->GetChain();
-  impl::ChainImplList::iterator cc=r->GetEntity()->GetChain(c->GetName());
+  impl::pointer_it<impl::ChainImplPtr> cc=r->GetEntity()->GetChainIter(c->GetName());
   if (c->GetResidueList().begin()+index+1==c->GetResidueList().end()) {
-    return AtomHandleIter(cc, c->GetResidueList().begin()+index,
-                          r->GetAtomList().end(), r->GetEntity(), false);
+    return AtomHandleIter(cc, impl::begin(c->GetResidueList())+index,
+                          impl::begin(r->GetAtomList()), r->GetEntity(), false);
   } else {
-    impl::ResidueImplList::iterator x=(c->GetResidueList().begin()+index+1);
-    return AtomHandleIter(cc, c->GetResidueList().begin()+index+1,
-                          (*x)->GetAtomList().begin(), r->GetEntity(), false);
+    impl::pointer_it<impl::ResidueImplPtr> x=(impl::begin(c->GetResidueList())+index+1);
+    return AtomHandleIter(cc, impl::begin(c->GetResidueList())+index+1,
+                          impl::begin((*x)->GetAtomList()), 
+                          r->GetEntity(), false);
   }
 
 }
@@ -225,22 +226,10 @@ geom::Vec3 ResidueHandle::GetAltAtomPos(const AtomHandle& atom,
   return Impl()->GetAltAtomPos(atom.Impl(), group);
 }
 
-geom::Vec3 ResidueHandle::GetGeometricStart() const
+geom::AlignedCuboid ResidueHandle::GetBounds() const
 {
   this->CheckValidity();
-  return Impl()->GetGeometricStart();
-}
-
-geom::Vec3 ResidueHandle::GetGeometricEnd() const
-{
-  this->CheckValidity();
-  return Impl()->GetGeometricEnd();
-}
-
-geom::Vec3 ResidueHandle::GetGeometricCenter() const
-{
-  this->CheckValidity();
-  return Impl()->GetGeometricCenter();
+  return Impl()->GetBounds();
 }
 
 geom::Vec3 ResidueHandle::GetCenterOfMass() const
diff --git a/modules/mol/base/src/residue_handle.hh b/modules/mol/base/src/residue_handle.hh
index 0d85e6e7fd460be23d463f1c7210da729e74edee..f1eb07850185a9b1ea404eeceaedb589e1feff9b 100644
--- a/modules/mol/base/src/residue_handle.hh
+++ b/modules/mol/base/src/residue_handle.hh
@@ -19,9 +19,11 @@
 #ifndef OST_RESIDUE_HANDLE_HU
 #define OST_RESIDUE_HANDLE_HU
 
+#include <ost/geom/vec3.hh>
+#include <ost/geom/aligned_cuboid.hh>
+
 #include <ost/mol/query.hh>
 #include <ost/mol/module_config.hh>
-#include <ost/geom/vec3.hh>
 #include <ost/mol/residue_base.hh>
 #include <ost/mol/atom_prop.hh>
 #include <ost/mol/entity_visitor_fw.hh>
@@ -77,17 +79,8 @@ public:
   /// similar to GetCenterOfMass(), but the atoms are not mass weighted
   geom::Vec3 GetCenterOfAtoms() const;
   
-  /// \brief Get entity's geometric center
-  ///
-  /// Returns the geometric center of the entity's bounding box
-  /// by calculating (GetGeometricStart()+GetGeometricEnd())/2
-  geom::Vec3 GetGeometricCenter() const;
-  
-  /// \brief Get entity's minimum cartesian coordinates
-  geom::Vec3 GetGeometricStart() const;
-  
-  /// \brief Get entity's maximum cartesian coordinates
-  geom::Vec3 GetGeometricEnd() const;
+  /// \brief get axis-aligned bounding box of residue
+  geom::AlignedCuboid GetBounds() const;
   
   /// \brief The chain this residue is attached to
   ChainHandle GetChain() const;
@@ -204,7 +197,7 @@ public:
   /// \brief return view based on query String.
   /// \sa Query
   EntityView Select(const String& query_string, QueryFlags flags=0) const;
-
+    
   bool operator==(const ResidueHandle& ref) const;
   bool operator!=(const ResidueHandle& ref) const;
   
diff --git a/modules/mol/base/src/residue_prop.hh b/modules/mol/base/src/residue_prop.hh
index fb75e52d63a7fb98d79c663ccd2acffa73132242..2bb92b3da49032829c360f069d0ea9d76bf64296 100644
--- a/modules/mol/base/src/residue_prop.hh
+++ b/modules/mol/base/src/residue_prop.hh
@@ -67,20 +67,6 @@ DLLEXPORT_OST_MOL std::ostream& operator<<(std::ostream& os, const ResNum& n);
 
 typedef String ResidueKey;
 
-/// \brief Residue properties
-/// 
-/// Small data structure to aggregate residue properties.
-struct DLLEXPORT_OST_MOL ResidueProp {
-  ResidueProp(const String& k, char a)
-    : key(k), abbrev(a) {    
-  }
-  ResidueProp()
-    :key(""), abbrev('\0') {   
-  }
-  ResidueKey   key;
-  char         abbrev;
-};
-
 }} // ns
 
 
diff --git a/modules/mol/base/src/residue_view.cc b/modules/mol/base/src/residue_view.cc
index 72c5ff76fbd08034f744229f76c24e975ba4ee1d..53e0a3eaa79126ebbd6095a3c69719196a8d6c09 100644
--- a/modules/mol/base/src/residue_view.cc
+++ b/modules/mol/base/src/residue_view.cc
@@ -205,36 +205,17 @@ double ResidueView::GetMass() const
   return mass;
 }
 
-geom::Vec3 ResidueView::GetGeometricStart() const 
+geom::AlignedCuboid ResidueView::GetBounds() const 
 {
   this->CheckValidity();
-  geom::Vec3 minimum(std::numeric_limits<Real>::max(),
-                     std::numeric_limits<Real>::max(),
-                     std::numeric_limits<Real>::max());
+  geom::Vec3 mmin( std::numeric_limits<Real>::max());
+  geom::Vec3 mmax(-std::numeric_limits<Real>::max());  
   AtomViewList::const_iterator i;
   for (i=data_->atoms.begin(); i!=data_->atoms.end(); ++i) {
-    minimum=geom::Min(minimum, (*i).GetPos());
+    mmin=geom::Min(mmin, (*i).GetPos());
+    mmax=geom::Max(mmax, (*i).GetPos());
   }
-  return minimum;
-}
-
-geom::Vec3 ResidueView::GetGeometricEnd() const 
-{
-  this->CheckValidity();
-  geom::Vec3 maximum(-std::numeric_limits<Real>::max(),
-                     -std::numeric_limits<Real>::max(),
-                     -std::numeric_limits<Real>::max());
-  AtomViewList::const_iterator i;
-  for (i=data_->atoms.begin(); i!=data_->atoms.end(); ++i) {
-    maximum=geom::Max(maximum, (*i).GetPos());
-  }
-  return maximum;
-}
-
-geom::Vec3 ResidueView::GetGeometricCenter() const
-{
-  this->CheckValidity();
-  return (this->GetGeometricStart() + this->GetGeometricEnd())/2;
+  return geom::AlignedCuboid(mmin, mmax);
 }
 
 geom::Vec3 ResidueView::GetCenterOfMass() const 
diff --git a/modules/mol/base/src/residue_view.hh b/modules/mol/base/src/residue_view.hh
index 0cd381e86e08046fa59456b6e7cf48f44bfabd03..d771a95ce09a0ba448eaca0be2a391e53020ecdd 100644
--- a/modules/mol/base/src/residue_view.hh
+++ b/modules/mol/base/src/residue_view.hh
@@ -153,14 +153,9 @@ public:
   /// similar to GetCenterOfMass(), but the atoms are not mass weighted
   geom::Vec3 GetCenterOfAtoms() const;
   
-  /// \brief Get entity's geometric center
-  ///
-  /// Returns the geometric center of the entity's bounding box
-  /// by calculating (GetGeometricStart()+GetGeometricEnd())/2
-  geom::Vec3 GetGeometricCenter() const;
+  /// \brief Get entity's axis-aligned bounding box
+  geom::AlignedCuboid GetBounds() const;
   
-  geom::Vec3 GetGeometricStart() const;
-  geom::Vec3 GetGeometricEnd() const;
 
   /// \brief return view based on a query object
   /// \sa Query
diff --git a/modules/mol/base/src/surface_builder.cc b/modules/mol/base/src/surface_builder.cc
index d85db43a5e6c35706dcb1bee6e6f03e97358c792..3be39406778bade182728da22802672862db3fcf 100644
--- a/modules/mol/base/src/surface_builder.cc
+++ b/modules/mol/base/src/surface_builder.cc
@@ -27,7 +27,7 @@ namespace ost { namespace mol {
 
 SurfaceHandle BuildSurface(const EntityView& ev, Real probe_radius, Real patch_size)
 {
-  LOGN_ERROR("not yet implemented");
+  LOG_ERROR("not yet implemented");
   return SurfaceHandle();
 }
 
diff --git a/modules/mol/base/tests/test_delete.cc b/modules/mol/base/tests/test_delete.cc
index 6366822012674e28accc83d826a6b98612e6c18d..c117f5d9ae50dfd0d26a41c665627b957d3dd751 100644
--- a/modules/mol/base/tests/test_delete.cc
+++ b/modules/mol/base/tests/test_delete.cc
@@ -65,20 +65,16 @@ struct Fixture {
   AtomHandle ad;
   TorsionHandle t;
 };
-void test_atom_delete() {
+
+BOOST_AUTO_TEST_SUITE( mol_base )
+
+BOOST_AUTO_TEST_CASE(atom_delete) 
+{
   Fixture f;
   XCSEditor e=f.e.RequestXCSEditor();
   e.DeleteAtom(f.ab);
   E ev;
   BOOST_CHECK_NO_THROW(f.e.Apply(ev));
-
-}
-
-BOOST_AUTO_TEST_SUITE( mol_base )
-
-BOOST_AUTO_TEST_CASE(test_atom_delete) 
-{
-  test_atom_delete();
 }
 
 BOOST_AUTO_TEST_SUITE_END()
\ No newline at end of file
diff --git a/modules/mol/base/tests/test_query.cc b/modules/mol/base/tests/test_query.cc
index 3dd125e4412447d148d216e7b7686fcb801b4406..d84a3156be0375fedf8db262a0970d29c8a0d952 100644
--- a/modules/mol/base/tests/test_query.cc
+++ b/modules/mol/base/tests/test_query.cc
@@ -33,7 +33,7 @@ EntityHandle make_query_test_entity()
   EntityHandle eh = CreateEntity();
   XCSEditor e=eh.RequestXCSEditor();
   ChainHandle chain = e.InsertChain("A");
-  chain.SetFloatProp("testpropc", 1.0);
+  chain.SetFloatProp("testprop_c", 1.0);
   ResidueHandle res = e.AppendResidue(chain, "MET");
   res.SetFloatProp("testpropr", 1.0);
   AtomProp c_atom;
@@ -229,9 +229,9 @@ BOOST_AUTO_TEST_CASE(test_query_eval)
   ensure_counts(e, "grtestpropr:0=1", 1, 1, 8);
   ensure_counts(e, "grtestpropr:1.0=1", 1, 3, 27);
   ensure_counts(e, "grtestpropr:2.0=2", 1, 2, 19);
-  ensure_counts(e, "gctestpropc:0=1", 1, 3, 27);
-  ensure_counts(e, "gctestpropc:1.0=1", 1, 3, 27);
-  ensure_counts(e, "gctestpropc:2.0=2", 0, 0, 0);
+  ensure_counts(e, "gctestprop_c:0=1", 1, 3, 27);
+  ensure_counts(e, "gctestprop_c:1.0=1", 1, 3, 27);
+  ensure_counts(e, "gctestprop_c:2.0=2", 0, 0, 0);
 }
 
 BOOST_AUTO_TEST_CASE(test_query_eval_on_view) 
@@ -261,9 +261,9 @@ BOOST_AUTO_TEST_CASE(test_query_eval_on_view)
   ensure_counts_v(v, "grtestpropr:0=1", 1, 1, 8);
   ensure_counts_v(v, "grtestpropr:1.0=1", 1, 3, 27);
   ensure_counts_v(v, "grtestpropr:2.0=2", 1, 2, 19);
-  ensure_counts_v(v, "gctestpropc:0=1", 1, 3, 27);
-  ensure_counts_v(v, "gctestpropc:1.0=1", 1, 3, 27);
-  ensure_counts_v(v, "gctestpropc:2.0=2", 0, 0, 0);
+  ensure_counts_v(v, "gctestprop_c:0=1", 1, 3, 27);
+  ensure_counts_v(v, "gctestprop_c:1.0=1", 1, 3, 27);
+  ensure_counts_v(v, "gctestprop_c:2.0=2", 0, 0, 0);
 }
 
 BOOST_AUTO_TEST_CASE(test_query_throw) 
@@ -275,8 +275,8 @@ BOOST_AUTO_TEST_CASE(test_query_throw)
   BOOST_CHECK_NO_THROW(e.Select("grtestpropr:0=1"));
   BOOST_CHECK_NO_THROW(e.Select("grtestpropr:1=1"));
   BOOST_CHECK_THROW(e.Select("grtestpropr=1"), std::exception);
-  BOOST_CHECK_NO_THROW(e.Select("gctestpropc:0=1"));
-  BOOST_CHECK_NO_THROW(e.Select("gctestpropc:1=1"));
+  BOOST_CHECK_NO_THROW(e.Select("gctestprop_c:0=1"));
+  BOOST_CHECK_NO_THROW(e.Select("gctestprop_c:1=1"));
   BOOST_CHECK_THROW(e.Select("ganotsetprop=1"), std::exception);
   BOOST_CHECK_THROW(e.Select("grnotsetprop=1"), std::exception);
   BOOST_CHECK_THROW(e.Select("gcnotsetprop=1"), std::exception);
diff --git a/modules/qa/src/all_atom_potential.cc b/modules/qa/src/all_atom_potential.cc
index b59337914c6148d89945a4351930fff5cb1efadf..348880447a93c9f8530bc1a4b65a146f809e2d72 100644
--- a/modules/qa/src/all_atom_potential.cc
+++ b/modules/qa/src/all_atom_potential.cc
@@ -81,7 +81,8 @@ public:
           if (d<0) d=0.0;
 
           if (d>options_.lower_cutoff) {
-            if (abs(atom_handle.GetResidue().GetIndex()-a.GetResidue().GetIndex())<options_.sequence_sep) {
+            // GetHandle() necessary to retriev original index of the view (as compared to index in the view):
+            if (abs(atom_handle.GetResidue().GetIndex()-a.GetResidue().GetHandle().GetIndex())<options_.sequence_sep) {
               continue;
             }
             energy_+=energies_.Get(type_a, type_b, d);
diff --git a/modules/qa/src/amino_acids.hh b/modules/qa/src/amino_acids.hh
index 809e8066a34403253140a491870c0f4bd00f908d..d2337068c8743f8f80a2827112862b60259d88ca 100644
--- a/modules/qa/src/amino_acids.hh
+++ b/modules/qa/src/amino_acids.hh
@@ -38,7 +38,7 @@ typedef enum  {
 	Met, Trp, Tyr,
 	Thr, Val, Ile,
 	Leu, Gly, Pro,
-	His, Phe, Xxx,
+	His, Phe, Xxx
 	
 } AminoAcid;
 
diff --git a/modules/qa/src/packing_statistics.cc b/modules/qa/src/packing_statistics.cc
index 03390bc396356bf7dbf53fc5dbcf420a5aa885c9..8b6baddea1f3bf439b0161ac59409511e0594456 100644
--- a/modules/qa/src/packing_statistics.cc
+++ b/modules/qa/src/packing_statistics.cc
@@ -36,7 +36,7 @@ PackingStatistics::PackingStatistics(Real cutoff,
    histogram_(IntegralClassifier(Xxx, 0),       // Xxx is the last object in enum and therefore corresponds to the total number of atom types
               IntegralClassifier((max_counts/bucket_size)+1, 0)) {      // since zero counts is possible, we have n+1 bins
    if (max_counts%bucket_size!=0) {
-     LOGN_MESSAGE("initialising packing statistics with max_count="
+     LOG_INFO("initialising packing statistics with max_count="
                   << max_counts << "which is not divisible by bucket_size="
                   << bucket_size << "without remainder. Will continue anyway.");
    }
diff --git a/modules/qa/src/solis_torsion_potential.cc b/modules/qa/src/solis_torsion_potential.cc
index 61a4768dd62f3745480cad1cc0555ccfbb3324ec..1a61d4d25db3c97433cf0f73a29cec3c61ec1b59 100644
--- a/modules/qa/src/solis_torsion_potential.cc
+++ b/modules/qa/src/solis_torsion_potential.cc
@@ -33,9 +33,9 @@ namespace ost { namespace qa {
   
 namespace {
 
-class TorsionEnergyCalc : public mol::EntityVisitor {
+class SolisTorsionEnergyCalc : public mol::EntityVisitor {
 public:
-  TorsionEnergyCalc(TorsionPotentialSolis::TorsionEnergies& energies,
+  SolisTorsionEnergyCalc(TorsionPotentialSolis::TorsionEnergies& energies,
                     TorsionPotentialOptsSolis opts):
     energies_(energies), prev_(Xxx), center_(Xxx), energy_(0.0),
     opts_(opts), num_torsions_(0)
@@ -72,7 +72,7 @@ public:
       num_torsions_++;
     } 
     else {
-      LOGN_MESSAGE("Amino acid not found in alphabets...");
+      LOG_INFO("Amino acid not found in alphabets...");
     }
     prev_=center_;
     center_=c;
@@ -193,7 +193,7 @@ void TorsionPotentialSolis::SaveToFile(const String& path)
 
 Real TorsionPotentialSolis::GetTotalEnergy(mol::EntityHandle entity)
 {
-  TorsionEnergyCalc c(energies_, options_);  
+  SolisTorsionEnergyCalc c(energies_, options_);  
   entity.Apply(c);
   num_torsions_ = c.GetEnergyCounts();
   return c.GetEnergy();
@@ -201,7 +201,7 @@ Real TorsionPotentialSolis::GetTotalEnergy(mol::EntityHandle entity)
 
 Real TorsionPotentialSolis::GetTotalEnergy(mol::EntityView entity)
 {
-  TorsionEnergyCalc c(energies_, options_);
+  SolisTorsionEnergyCalc c(energies_, options_);
   entity.Apply(c);
   num_torsions_ = c.GetEnergyCounts();
   return c.GetEnergy();
diff --git a/modules/qa/src/solis_torsion_statistics.cc b/modules/qa/src/solis_torsion_statistics.cc
index dde884087b5f8d3365529da97c5564e95f8e0a4b..9b48639b899c12c4070dfecd612028683a88bda6 100644
--- a/modules/qa/src/solis_torsion_statistics.cc
+++ b/modules/qa/src/solis_torsion_statistics.cc
@@ -34,9 +34,9 @@ namespace ost { namespace qa {
 
 namespace {
 
-class TorsionStat : public mol::EntityVisitor {
+class TorsionStatSolis : public mol::EntityVisitor {
 public:
-  TorsionStat(TorsionStatisticsSolis::TorsionHistogram& histo):
+  TorsionStatSolis(TorsionStatisticsSolis::TorsionHistogram& histo):
     histo_(histo)
   {}
   
@@ -94,13 +94,13 @@ int TorsionStatisticsSolis::GetTorsionBucketSize() const
 
 void TorsionStatisticsSolis::Extract(mol::EntityView view)
 {
-  TorsionStat stat(histogram_);
+  TorsionStatSolis stat(histogram_);
   view.Apply(stat);
 }
 
 void TorsionStatisticsSolis::Extract(mol::EntityHandle entity)
 {
-  TorsionStat stat(histogram_);
+  TorsionStatSolis stat(histogram_);
   entity.Apply(stat);
 }
 
diff --git a/modules/qa/src/torsion_potential.cc b/modules/qa/src/torsion_potential.cc
index 828c6365b2e811f81bcfde3d6c7226977159dc9e..651718a4f04bc0d53faf6fadf3dd1ab8eb328e0c 100644
--- a/modules/qa/src/torsion_potential.cc
+++ b/modules/qa/src/torsion_potential.cc
@@ -85,7 +85,7 @@ public:
       num_torsions_++;
     } 
     else {
-      LOGN_MESSAGE("Amino acid not found in alphabets...");
+      LOG_INFO("Amino acid not found in alphabets...");
     }
     return false;
   }
diff --git a/modules/seq/alg/pymod/CMakeLists.txt b/modules/seq/alg/pymod/CMakeLists.txt
index 22db6f7e887e1b848458c47a004383ae5767d956..dfe07488ea145a451a10f6bb6a47facbc9b3cf40 100644
--- a/modules/seq/alg/pymod/CMakeLists.txt
+++ b/modules/seq/alg/pymod/CMakeLists.txt
@@ -1,8 +1,7 @@
 set(OST_SEQ_ALG_PYMOD_SOURCES
   wrap_seq_alg.cc
-  export_align.cc
 )
 
 pymod(NAME seq_alg OUTPUT_DIR ost/seq/alg 
       CPP ${OST_SEQ_ALG_PYMOD_SOURCES}
-      PY __init__.py)
+      PY __init__.py mat.py renumber.py)
diff --git a/modules/seq/alg/pymod/__init__.py b/modules/seq/alg/pymod/__init__.py
index 22aa0c8632d507f99b0d8943b0a102a94ecedce2..5d4730f17b92b7eed13cf47fe02d802e3267364b 100644
--- a/modules/seq/alg/pymod/__init__.py
+++ b/modules/seq/alg/pymod/__init__.py
@@ -1 +1,5 @@
-from _seq_alg import *
\ No newline at end of file
+from _seq_alg import *
+from ost.seq.alg.mat import *
+
+    
+  
\ No newline at end of file
diff --git a/modules/seq/alg/pymod/export_align.cc b/modules/seq/alg/pymod/export_align.cc
deleted file mode 100644
index 49a8d1c8bc5dffb55230accdbaf988d8014827bd..0000000000000000000000000000000000000000
--- a/modules/seq/alg/pymod/export_align.cc
+++ /dev/null
@@ -1,59 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#include <boost/python.hpp>
-#include <boost/python/register_ptr_to_python.hpp>
-#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
-using namespace boost::python;
-
-#include <ost/info/info.hh>
-
-#include <ost/mol/mol.hh>
-#include <ost/seq/alg/subst_weight_matrix.hh>
-#include <ost/seq/alg/local_align.hh>
-#include <ost/seq/alg/global_align.hh>
-using namespace ost;
-using namespace ost::seq;
-using namespace ost::seq::alg;
-
-void export_Align()
-{
-  class_<SubstWeightMatrix, SubstWeightMatrixPtr>("SubstWeightMatrix", init<>())
-    .def("GetWeight", &SubstWeightMatrix::GetWeight)
-    .def("SetWeight", &SubstWeightMatrix::SetWeight)
-  ;
-class_<AlignmentOpts>("AlignmentOpts", init<int,int, SubstWeightMatrixPtr>())
-  .def_readwrite("gap_open_penalty", &AlignmentOpts::gap_open_penalty)
-  .def_readwrite("gap_extension_penalty", 
-                 &AlignmentOpts::gap_extension_penalty)    
-  .def_readwrite("subst_weights", &AlignmentOpts::subst_weights)
-;  
-  def("SubstWeightMatrixToInfo", &SubstWeightMatrixToInfo);
-  def("SubstWeightMatrixFromInfo", &SubstWeightMatrixFromInfo);
-  
-  class_<AlignedPatch>("AlignedPatch", no_init)
-    .def_readwrite("alignment", &AlignedPatch::alignment)
-    .def_readwrite("offset_a", &AlignedPatch::offset_a)
-    .def_readwrite("offset_b", &AlignedPatch::offset_b)
-  ;    
-  class_<AlignedPatchList>("AlignedPatchList", init<>())
-    .def(vector_indexing_suite<AlignedPatchList>())
-  ;
-  def("LocalSequenceAlign", &LocalSequenceAlign);
-  def("GlobalSequenceAlign", &GlobalSequenceAlign);
-}
diff --git a/modules/seq/alg/pymod/mat.py b/modules/seq/alg/pymod/mat.py
new file mode 100644
index 0000000000000000000000000000000000000000..65152f045bf70ef2c50568b3abcbcfd526f38294
--- /dev/null
+++ b/modules/seq/alg/pymod/mat.py
@@ -0,0 +1,45 @@
+from ost.seq.alg import SubstWeightMatrix
+
+def _InitMatrix(data):
+  """
+  Initialise a new substitution weight matrix with the weights in data. data
+  must be a 24x24 array of ints.
+  """
+  mat=SubstWeightMatrix()
+  # string of valid amino acid one letter codes
+  chars='ABCDEFGHIKLMNPQRSTVWXYZ'
+  for i, row in enumerate(data):
+    for j, weight in enumerate(row):
+      mat.SetWeight(chars[i], chars[j], weight)
+  return mat
+      
+  
+_RAW_BLOSUM62_DATA=(  
+  (4,-2,0,-2,-1,-2,0,-2,-1,-1,-1,-1,-2,-1,-1,-1,1,0,0,-3,-1,-2),
+  (-2,6,-3,6,2,-3,-1,-1,-3,-1,-4,-3,1,-1,0,-2,0,-1,-3,-4,-1,-3),
+  (0,-3,9,-3,-4,-2,-3,-3,-1,-3,-1,-1,-3,-3,-3,-3,-1,-1,-1,-2,-1,-2),
+  (-2,6,-3,6,2,-3,-1,-1,-3,-1,-4,-3,1,-1,0,-2,0,-1,-3,-4,-1,-3),
+  (-1,2,-4,2,5,-3,-2,0,-3,1,-3,-2,0,-1,2,0,0,-1,-2,-3,-1,-2),
+  (-2,-3,-2,-3,-3,6,-3,-1,0,-3,0,0,-3,-4,-3,-3,-2,-2,-1,1,-1,3),
+  (0,-1,-3,-1,-2,-3,6,-2,-4,-2,-4,-3,0,-2,-2,-2,0,-2,-3,-2,-1,-3),
+  (-2,-1,-3,-1,0,-1,-2,8,-3,-1,-3,-2,1,-2,0,0,-1,-2,-3,-2,-1,2),
+  (-1,-3,-1,-3,-3,0,-4,-3,4,-3,2,1,-3,-3,-3,-3,-2,-1,3,-3,-1,-1),
+  (-1,-1,-3,-1,1,-3,-2,-1,-3,5,-2,-1,0,-1,1,2,0,-1,-2,-3,-1,-2),
+  (-1,-4,-1,-4,-3,0,-4,-3,2,-2,4,2,-3,-3,-2,-2,-2,-1,1,-2,-1,-1),
+  (-1,-3,-1,-3,-2,0,-3,-2,1,-1,2,5,-2,-2,0,-1,-1,-1,1,-1,-1,-1),
+  (-2,1,-3,1,0,-3,0,1,-3,0,-3,-2,6,-2,0,0,1,0,-3,-4,-1,-2),
+  (-1,-1,-3,-1,-1,-4,-2,-2,-3,-1,-3,-2,-2,7,-1,-2,-1,-1,-2,-4,-1,-3),
+  (-1,0,-3,0,2,-3,-2,0,-3,1,-2,0,0,-1,5,1,0,-1,-2,-2,-1,-1),
+  (-1,-2,-3,-2,0,-3,-2,0,-3,2,-2,-1,0,-2,1,5,-1,-1,-3,-3,-1,-2),
+  (1,0,-1,0,0,-2,0,-1,-2,0,-2,-1,1,-1,0,-1,4,1,-2,-3,-1,-2),
+  (0,-1,-1,-1,-1,-2,-2,-2,-1,-1,-1,-1,0,-1,-1,-1,1,5,0,-2,-1,-2),
+  (0,-3,-1,-3,-2,-1,-3,-3,3,-2,1,1,-3,-2,-2,-3,-2,0,4,-3,-1,-1),
+  (-3,-4,-2,-4,-3,1,-2,-2,-3,-3,-2,-1,-4,-4,-2,-3,-3,-2,-3,11,-1,2),
+  (-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1),
+  (-2,-3,-2,-3,-2,3,-3,2,-1,-2,-1,-1,-2,-3,-1,-2,-2,-2,-1,2,-1,7),
+  (-1,2,-4,2,5,-3,-2,0,-3,1,-3,-2,0,-1,2,0,0,-1,-2,-3,-1,-2),
+)
+
+BLOSUM62=_InitMatrix(_RAW_BLOSUM62_DATA)
+
+__all__=['BLOSUM62']
\ No newline at end of file
diff --git a/modules/seq/alg/pymod/renumber.py b/modules/seq/alg/pymod/renumber.py
new file mode 100644
index 0000000000000000000000000000000000000000..39ea9fb489949845fb65681ac1cbb6f000f4e56e
--- /dev/null
+++ b/modules/seq/alg/pymod/renumber.py
@@ -0,0 +1,50 @@
+from ost import io, seq, mol, conop
+import ost
+
+def Renumber(seq_handle):
+  """
+  Function to renumber an entity according to an alignment between the model sequence 
+  and the full-length target sequence. The aligned model sequence with an attached 
+  view needs to be provided. Upon succcess, the renumbered entity is returned.
+
+  .. code-block:: python
+
+    from ost.seq.alg import renumber
+    from ost.bindings.clustalw import *
+    ent=io.LoadPDB("path_to_model")
+    s=io.LoadSequence("path_to_full_length_fasta_seqeunce")
+    pdb_seq=seq.SequenceFromChain("model", ent.chains[0])
+    aln=ClustalW(s,pdb_seq)
+    aln.AttachView(1,ent.chains[0].Select(""))
+    e=Renumber(aln.GetSequence(1))
+    io.SavePDB(e, "renum.pdb")
+   
+  """
+  if seq_handle.HasAttachedView()==False:
+    raise RuntimeError, "Sequence Handle has no attached view"
+  changed_residue_count=0
+  renumberingFlag = False
+  ent_n=mol.CreateEntity()
+  ed=ent_n.RequestXCSEditor()
+  c=ed.InsertChain(" ")
+  for pos in range(len(seq_handle)):
+    if seq_handle[pos]!='-':
+      r=seq_handle.GetResidue(pos)
+      if r.IsValid():
+          #print seq_handle[pos],r.number.num,pos+1
+          if r.number.num!=pos+1:
+            changed_residue_count+=1
+            renumberingFlag = True
+          r_n=ed.AppendResidue(c,r.name, mol.ResNum(pos+1))
+          for atom in r.atoms:
+            ed.InsertAtom(r_n,atom.name,atom.pos,atom.prop)
+      else:
+        err='Error: renumbering failed at position %s' %pos
+        raise RuntimeError, err
+  if renumberingFlag == True:
+    err = 'Warning: %s residues have been renumbered!' %changed_residue_count
+    ost.LogMessage(err)
+  conop.ConnectAll(ent_n)
+  return ent_n
+
+
diff --git a/modules/seq/alg/pymod/wrap_seq_alg.cc b/modules/seq/alg/pymod/wrap_seq_alg.cc
index d4c4462c861fdee993e124db514b39991a49d4db..f632d3d6eb4656a2d546c9542cf28321c5a15c9a 100644
--- a/modules/seq/alg/pymod/wrap_seq_alg.cc
+++ b/modules/seq/alg/pymod/wrap_seq_alg.cc
@@ -22,13 +22,12 @@
 #include <ost/seq/alg/merge_pairwise_alignments.hh>
 #include <ost/seq/alg/sequence_identity.hh>
 #include <ost/seq/alg/ins_del.hh>
-
+#include <ost/seq/alg/conservation.hh>
+#include <ost/seq/alg/subst_weight_matrix.hh>
 using namespace boost::python;
 using namespace ost::seq;
 using namespace ost::seq::alg;
 
-void export_Align();
-
 BOOST_PYTHON_MODULE(_seq_alg)
 {
   enum_<RefMode::Type>("RefMode")
@@ -36,8 +35,8 @@ BOOST_PYTHON_MODULE(_seq_alg)
     .value("LONGER_SEQUENCE", RefMode::LONGER_SEQUENCE)
     .export_values()
   ;
-  def("SequenceIdentity", &SequenceIdentity, arg("seq_a")=0, arg("seq_b")=1);
-  
+  def("SequenceIdentity", &SequenceIdentity, 
+      (arg("ref_mode")=RefMode::ALIGNMENT, arg("seq_a")=0, arg("seq_b")=1));
   class_<AlignedRegionList>("AlignedRegionList", init<>())
     .def(vector_indexing_suite<AlignedRegionList>())
   ;
@@ -46,6 +45,12 @@ BOOST_PYTHON_MODULE(_seq_alg)
     .def("GetDeletions", &InsDel::GetDeletions)
     .def("GetInsertions", &InsDel::GetInsertions)
   ;
+  
+  class_<SubstWeightMatrix, SubstWeightMatrixPtr>("SubstWeightMatrix", init<>())
+    .def("GetWeight", &SubstWeightMatrix::GetWeight)
+    .def("SetWeight", &SubstWeightMatrix::SetWeight)
+  ;
   def("MergePairwiseAlignments", &MergePairwiseAlignments);
-  export_Align();  
+  def("Conservation", &Conservation, (arg("assign")=true, arg("prop_name")="cons"));
+
 }
diff --git a/modules/seq/alg/src/CMakeLists.txt b/modules/seq/alg/src/CMakeLists.txt
index ae43bd38d1d9bea4f7fbacd7d50be2d9eef46775..7b4f86f53e5bb8c08feeba088deb1c8319691d0d 100644
--- a/modules/seq/alg/src/CMakeLists.txt
+++ b/modules/seq/alg/src/CMakeLists.txt
@@ -3,19 +3,17 @@ sequence_identity.hh
 module_config.hh
 ins_del.hh
 subst_weight_matrix.hh
-local_align.hh
 alignment_opts.hh
-global_align.hh
 merge_pairwise_alignments.hh
+conservation.hh
 )
 
 set(OST_SEQ_ALG_SOURCES
 merge_pairwise_alignments.cc
-global_align.cc
 sequence_identity.cc
 ins_del.cc
 subst_weight_matrix.cc
-local_align.cc
+conservation.cc
 )
 
 module(NAME seq_alg HEADER_OUTPUT_DIR ost/seq/alg SOURCES ${OST_SEQ_ALG_SOURCES}
diff --git a/modules/seq/alg/src/conservation.cc b/modules/seq/alg/src/conservation.cc
new file mode 100644
index 0000000000000000000000000000000000000000..46cb5cfd8fb9d648c0d9b0f0e0ab797093e9cfa2
--- /dev/null
+++ b/modules/seq/alg/src/conservation.cc
@@ -0,0 +1,135 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+//------------------------------------------------------------------------------
+
+#include <ost/seq/aligned_column.hh>
+#include <ost/seq/alignment_handle.hh>
+#include <ost/seq/alg/conservation.hh>
+
+namespace ost { namespace seq { namespace alg {
+
+// taken from Armon et al., J. Mol. Biol. (2001) 307, 447-463
+static float CHEM_DISSIM[][24]={
+  {0.00, 1.33, 1.39, 2.22, 1.84, 1.45, 2.48, 3.26, 2.83, 3.48, 2.56, 3.27, 3.06, 
+   0.86, 1.65, 1.63, 1.46, 2.24, 2.38, 3.34, 6.00, 6.00, 2.87, 3.15},
+  {0.00, 0.06, 0.97, 0.56, 0.87, 1.92, 2.48, 1.80, 2.40, 2.15, 2.94, 2.90, 1.79, 
+   2.70, 2.62, 2.36, 3.17, 3.12, 4.17, 6.00, 6.00, 2.20, 2.10,-1.00},
+  {0.00, 0.91, 0.51, 0.90, 1.92, 2.46, 1.78, 2.37, 2.78, 3.54, 3.58, 2.76, 3.67, 
+   3.60, 3.34, 4.14, 4.08, 5.13, 6.00, 6.00, 2.19, 2.08,-1.00,-1.00},
+  {0.00, 0.85, 1.70, 2.48, 2.78, 1.96, 2.37, 2.78, 3.54, 3.58, 2.76, 3.67, 3.60, 
+   3.34, 4.14, 4.08, 5.13, 6.00, 6.00, 2.63, 2.17,-1.00,-1.00,-1.00},
+  {0.00, 0.89, 1.65, 2.06, 1.31, 1.87, 1.94, 2.71, 2.74, 2.15, 3.04, 2.95, 2.67, 
+   3.45, 3.33, 4.38, 6.00, 6.00, 1.85, 1.59,-1.00,-1.00,-1.00,-1.00},
+  {0.00, 1.12, 1.83, 1.40, 2.05, 1.32, 2.10, 3.03, 1.42, 2.25, 2.14, 1.86, 2.60, 
+   2.45, 3.50, 6.00, 6.00, 1.47, 1.73,-1.00,-1.00,-1.00,-1.00,-1.00},
+  {0.00, 0.84, 0.99, 1.47, 0.32, 1.06, 1.30, 2.13, 2.70, 2.57, 2.30, 2.81, 2.48, 
+   3.42, 6.00, 6.00, 0.42, 1.23,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00},
+  {0.00, 0.85, 0.90, 0.96, 1.14, 1.45, 2.97, 3.53, 3.39, 3.13, 3.59, 3.22, 4.08, 
+   6.00, 6.00, 0.42, 0.88,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00},
+  {0.00, 0.65, 1.29, 1.84, 2.04, 2.76, 3.49, 3.37, 3.08, 3.70, 3.42, 4.39, 6.00, 
+   6.00, 0.92, 0.33,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00},
+  {0.00, 1.72, 2.05, 2.34, 3.40, 4.10, 3.98, 3.69, 4.27, 3.95, 4.88, 6.00, 6.00, 
+   1.18, 0.33,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00},
+  {0.00, 0.79, 0.82, 2.11, 2.59, 2.45, 2.19, 2.63, 2.27, 3.16, 6.00, 6.00, 0.64, 
+   1.51,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00},
+  {0.00, 0.40, 2.70, 2.98, 2.84, 2.63, 2.85, 2.42, 3.11, 6.00, 6.00, 1.10, 1.95,
+  -1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00},
+  {0.00, 2.43, 2.62, 2.49, 2.29, 2.47, 2.02, 2.72, 6.00, 6.00, 1.29, 2.19,-1.00,
+  -1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00},
+  {0.00, 0.91, 0.85, 0.62, 1.43, 1.52, 2.51, 6.00, 6.00, 2.55, 3.08,-1.00,-1.00,
+  -1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00},
+  {0.00, 0.14, 0.41, 0.63, 0.94, 1.73, 6.00, 6.00, 3.11, 3.80,-1.00,-1.00,-1.00,
+  -1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00},
+  {0.00, 0.29, 0.61, 0.86, 1.72, 6.00, 6.00, 2.98, 3.68,-1.00,-1.00,-1.00,-1.00,
+  -1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00},
+  {0.00, 0.82, 0.93, 1.89, 6.00, 6.00, 2.71, 3.39,-1.00,-1.00,-1.00,-1.00,-1.00,
+  -1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00},
+  {0.00, 0.48, 0.11, 6.00, 6.00, 3.20, 3.99,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,
+  -1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00},
+  {0.00, 1.06, 6.00, 6.00, 2.85, 3.67,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,
+  -1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00},
+  {0.00, 6.00, 6.00, 3.75, 4.64,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,
+  -1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00},
+  {0.50, 6.00, 6.00, 6.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,
+  -1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00},
+  {0.00, 6.00, 6.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,
+  -1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00},
+  {0.00, 1.05,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,
+  -1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00},
+  {0.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,
+  -1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00,-1.00}
+};
+
+float PhysicoChemicalDissim(char c1, char c2)
+{
+  static int indices[]={2, 23, 0, 9, 7, 17, 3, 10, 15, -1, 
+             11, 14, 16, 8, -1, 1, 6, 12, 4, 5, 
+             -1, 13, 19, 21, 18, 22};
+  int idx_a=(c1=='-' || c1<'A' || c1>'Z') ? 20 : indices[c1-'A'];
+  int idx_b=(c2=='-' || c2<'A' || c2>'Z') ? 20 : indices[c2-'A'];  
+
+  if (idx_a<0) {
+    idx_a=20;
+  }
+  if (idx_b<0) {
+    idx_b=20;
+  }
+  float s=0.0;
+  if (idx_a>idx_b)
+    s=CHEM_DISSIM[idx_b][idx_a-idx_b];
+  else
+    s=CHEM_DISSIM[idx_a][idx_b-idx_a];
+  assert(s>=0.0);
+  return s;
+}
+
+std::vector<Real> Conservation(const AlignmentHandle& aln, bool assign, 
+                               const String& prop)
+{
+  std::vector<Real> cons(aln.GetLength(), 0.0);
+  int comb=(aln.GetCount()*(aln.GetCount()-1))/2;
+  for (int col=0; col<aln.GetLength(); ++col) {
+    float score=0.0;
+    AlignedColumn c=aln[col];
+    for (int i=0; i<aln.GetCount(); ++i) {
+      for (int j=i+1; j<aln.GetCount(); ++j) {
+        score+=PhysicoChemicalDissim(c[i], c[j]);
+      }
+    }
+    score=1.0-score/(6.0*comb);
+    cons[col]=score;
+    if (assign) {
+      for (int i=0; i<aln.GetCount(); ++i) {
+        if (c[i]!='-') {
+          mol::ResidueView r=c.GetResidue(i);
+          if (r.IsValid()) {
+            if (r.GetOneLetterCode()!=c[i]) {
+              std::cout << "WARNING: " << col << " " << c[i] << "!=" 
+                        << r.GetOneLetterCode() << std::endl;
+            }
+            r.SetFloatProp(prop, score);
+          }
+        }
+      }
+    }
+  }
+  return cons;
+}
+
+}}}
+
diff --git a/modules/seq/alg/src/global_align.hh b/modules/seq/alg/src/conservation.hh
similarity index 59%
rename from modules/seq/alg/src/global_align.hh
rename to modules/seq/alg/src/conservation.hh
index 9b477fa9bd2c4c06755b7858b5f1f0d2cea6dcee..b1375c4a26926881421ac0f646384e840771663f 100644
--- a/modules/seq/alg/src/global_align.hh
+++ b/modules/seq/alg/src/conservation.hh
@@ -16,27 +16,28 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#ifndef OST_SEQ_ALG_GLOBAL_ALIGN_HH
-#define OST_SEQ_ALG_GLOBAL_ALIGN_HH
-/*
-   Author: Marco Biasini
- */
+
 #include <ost/seq/alignment_handle.hh>
 #include <ost/seq/alg/module_config.hh>
-#include <ost/seq/alg/alignment_opts.hh>
 
+/*
+  Authors: Marco Biasini
+ */
 namespace ost { namespace seq { namespace alg {
 
-/// \brief globally align two sequences
-///
-/// the optimal global alignment of the two sequences, given the substitution
-/// weights and gap opening penalties is computed by using a classical
-/// Needleman-Wunsch algorithm. The algorithm has O(n*m) complexity in both
-/// space and time.
-AlignmentHandle DLLEXPORT_OST_SEQ_ALG 
-GlobalSequenceAlign(const SequenceHandle& seq_a, const SequenceHandle& seq_b,
-                    const AlignmentOpts& opts);
-
+/// \brief Calculates conservation scores for each column in the alignment. 
+/// 
+/// The conservation score is a value between 0 and 1. The bigger the number 
+/// the more conserved the aligned residues are. 
+/// 
+/// \p assign If true, the conservation scores are assigned to attached 
+///     residues. The name of the property can be changed with the prop_name 
+///     parameter. Useful when coloring entities based on sequence conservation.
+/// \p prop_name The property name for assigning the conservation to 
+///     attached residues. Defaults to 'cons'.
+/// 
+std::vector<Real> DLLEXPORT_OST_SEQ_ALG Conservation(const AlignmentHandle& aln,
+                                             bool assign=true,
+                                             const String& prop_name="cons");
 }}}
 
-#endif
\ No newline at end of file
diff --git a/modules/seq/alg/src/global_align.cc b/modules/seq/alg/src/global_align.cc
deleted file mode 100644
index 6003ab84fe79bfbb754913f906e7b8440abf5b51..0000000000000000000000000000000000000000
--- a/modules/seq/alg/src/global_align.cc
+++ /dev/null
@@ -1,128 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-/*
-  Author: Marco Biasini
- */
-#include <ost/seq/alg/global_align.hh>
-
-namespace ost { namespace seq { namespace alg {
-
-namespace {
-  
-class GlobalAlnMatrix {
-public:
-  GlobalAlnMatrix(int num_cols, int num_rows)
-    : num_rows_(num_rows), num_cols_(num_cols) {    
-      data_.resize(num_cols_*num_rows_,0);
-  }
-  short Get(int x, int y) const {
-    assert(x>=0 && x<num_cols_); 
-    assert(y>=0 && y<num_rows_);       
-    return data_[num_cols_*y+x];
-  }
-  void Set(int x, int y, short value) {
-    data_[num_cols_*y+x]=value;
-  }
-
-  int num_rows_;
-  int num_cols_;
-  std::vector<short>  data_;
-};
-
-}
-
-AlignmentHandle GlobalSequenceAlign(const SequenceHandle& seq_a, 
-                                    const SequenceHandle& seq_b,
-                                    const AlignmentOpts& opts)
-{
-  // using the strings directly is much better for performance reasons
-  String ssa=seq_a.GetString();
-  String ssb=seq_b.GetString();
-  GlobalAlnMatrix mat(ssa.size()+1, ssb.size()+1);
-  
-  // build-up aln mattrix
-  for (size_t i=0; i<ssa.size()+1; ++i) {
-    mat.Set(i, 0, i*opts.gap_open_penalty);
-  }
-  for (size_t i=0; i<ssb.size()+1; ++i) {
-    mat.Set(0, i, i*opts.gap_open_penalty);
-  }
-  for (size_t i=1; i<ssa.size()+1; ++i) {
-    for (size_t j=1; j<ssb.size()+1; ++j) {
-      short mm=opts.subst_weights->GetWeight(ssa[i-1], ssb[j-1]);
-      short m11=mat.Get(i-1, j-1)+mm;
-      short m10=mat.Get(i-1, j)-opts.gap_open_penalty;
-      short m01=mat.Get(i, j-1)-opts.gap_open_penalty;
-      mat.Set(i, j, std::max(m11, std::max(m10, m01)));
-    }
-  }
-  
-  // backtracking
-  size_t i=ssa.size();
-  size_t j=ssb.size();
-  String asa;
-  String asb;
-  asa.reserve(ssa.size());
-  asb.reserve(ssb.size());
-
-  while (i>0 && j>0) { 
-    // find out where we came from
-    short m11=mat.Get(i-1, j-1);
-    short m10=mat.Get(i-1, j);
-    short m01=mat.Get(i, j-1);
-    short m00=mat.Get(i, j);
-    short mm=opts.subst_weights->GetWeight(ssa[i-1], ssb[j-1]);    
-    if (m11+mm==m00) { // match
-      asa.append(1, ssa[i-1]);
-      asb.append(1, ssb[j-1]);      
-      --j;
-      --i;
-    } else if (m10-opts.gap_open_penalty==m00) { // seq b has a gap
-      asa.append(1, ssa[i-1]);
-      asb.append(1, '-');      
-      --i;      
-    } else if (m01-opts.gap_open_penalty==m00) { // seq a has a gap
-      asa.append(1, '-');
-      asb.append(1, ssb[j-1]);      
-      --j;      
-    }
-  }
-  while (i>0) {
-    asa.append(1, ssa[i-1]);
-    asb.append(1, '-');    
-    --i;
-  }
-  while (j>0) {
-    asa.append(1, '-');
-    asb.append(1, ssb[j-1]);        
-    --j;
-  } 
-  // reverse the two strings
-  String rasa, rasb;
-  rasa.reserve(asa.size());
-  rasb.reserve(asb.size());  
-  std::copy(asa.rbegin(), asa.rend(), std::back_inserter(rasa));
-  std::copy(asb.rbegin(), asb.rend(), std::back_inserter(rasb));
-  AlignmentHandle aln=CreateAlignment();
-  aln.AddSequence(CreateSequence(seq_a.GetName(), rasa));
-  aln.AddSequence(CreateSequence(seq_b.GetName(), rasb));  
-  return aln;
-}
-
-}}}
diff --git a/modules/seq/alg/src/local_align.cc b/modules/seq/alg/src/local_align.cc
deleted file mode 100644
index 197a34226b214c09c960be1ab8eb046c1b7ac1cf..0000000000000000000000000000000000000000
--- a/modules/seq/alg/src/local_align.cc
+++ /dev/null
@@ -1,160 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#include "local_align.hh"
-
-namespace ost { namespace seq { namespace alg {
-
-namespace {
-
-class AliMatrix {
-public:
-  AliMatrix(int num_rows, int num_cols)
-    : num_rows_(num_rows), num_cols_(num_cols) {    
-      data_.resize(num_cols_*num_rows_,0);
-  }
-  short Get(int x, int y) const {
-    assert(x>=0 && x<num_rows_);
-    assert(y>=0 && y<num_cols_);    
-    return data_[num_cols_*x+y];
-  }
-  void Set(int x, int y, short value) {
-    data_[num_cols_*x+y]=value;
-  }
-
-  int num_rows_;
-  int num_cols_;
-  std::vector<short>  data_;
-};
-
-std::pair<int, int> FindMax(const AliMatrix& mat, int min_col,
-                           int max_col, int min_row, int max_row) {
-  int max_i=0, max_j=0, max_value=-1;
-  for (int i=min_col; i<max_col; ++i) {
-    for (int j=min_row; j<max_row; ++j) {
-      int x=mat.Get(i, j);
-      if (x>max_value) {
-        max_value=x;
-        max_i=i; max_j=j;
-      }
-    }
-  }
-  return std::make_pair(max_i, max_j);
-}
-
-// divide and conquer the alignment matrix to get all patches.
-void CollectPatches(AlignedPatchList& patches, const String& seq_a, 
-                    const String& seq_b, const AliMatrix& ali_mat, int min_col,
-                    int max_col, int min_row, int max_row) {
-  if (max_col-min_col<2 || max_row-min_row<2)
-    return;
-  String seq_c, seq_d;
-  seq_c.reserve(std::max(seq_a.length(), seq_b.length()));
-  seq_d.reserve(std::max(seq_a.length(), seq_b.length()));
-  std::pair<int, int> best=FindMax(ali_mat, min_col, max_col, min_row, max_row);  
-  std::pair<int, int> max_pair=best;
-
-  typedef std::pair<int, int> XY;
-  std::vector<XY> stack;
-  while(ali_mat.Get(best.first, best.second)>0 && best.first>=min_col && 
-          best.second>=min_row) {
-    stack.push_back(XY(best.first, best.second));
-    int a=ali_mat.Get(best.first-1, best.second-1);
-    int b=ali_mat.Get(best.first-1, best.second);
-    int c=ali_mat.Get(best.first, best.second-1);    
-    if (a>=c) {
-      if (a>=b) {
-        best.first-=1;
-        best.second-=1;
-      } else {
-        best.first-=1;
-      }
-    } else {
-      if (c>b) {
-        best.second-=1;
-      } else {
-        best.first-=1;
-      }
-    }
-  }
-  for (int i=static_cast<int>(stack.size())-2; i>=0; --i) {
-    XY next=stack[i];
-    XY curr=stack[i+1];
-    if (next.first==curr.first+1) {
-      if (next.second==curr.second+1) {
-        seq_c.append(1, seq_a[next.first-1]);
-        seq_d.append(1, seq_b[next.second-1]);
-      } else {
-        seq_c.append(1, seq_a[next.first-1]);
-        seq_d.append(1, '-');        
-      }
-    } else {
-      if (next.second==curr.second+1) {
-        seq_c.append(1, '-');
-        seq_d.append(1, seq_b[next.second-1]);
-      } else {
-        seq_c.append(1, seq_a[next.first-1]);
-        seq_d.append(1, '-');
-      }
-    }
-  }
-  if (seq_c.size()>2 && seq_c.size()>2) {
-    patches.push_back(AlignedPatch());  
-    patches.back().offset_a=best.first;
-    patches.back().offset_b=best.second;            
-    if (seq_c[0]=='-' || seq_d[0]=='-') {
-      seq_c.erase(seq_c.begin());
-      seq_d.erase(seq_d.begin());    
-    }
-    patches.back().alignment=CreateAlignment();
-    patches.back().alignment.AddSequence(CreateSequence("seq1", seq_c));
-    patches.back().alignment.AddSequence(CreateSequence("seq2  ", seq_d));  
-    CollectPatches(patches, seq_a, seq_b, ali_mat, max_pair.first+1, max_col,
-                   max_pair.second+1, max_row);    
-  }
-}
-
-}
-
-AlignedPatchList LocalSequenceAlign(const SequenceHandle& sseq_a, 
-                                    const SequenceHandle& sseq_b, 
-                                    const AlignmentOpts& opts)
-{
-  
-  String seq_a=sseq_a.GetString();
-  String seq_b=sseq_b.GetString();  
-  AliMatrix ali_mat(seq_a.length()+1, seq_b.length()+1);
-  // build alignment matrix.
-  for (size_t i=0; i<seq_a.length(); ++i) {
-    for (size_t j=0; j<seq_b.length(); ++j) {
-      int w=opts.subst_weights->GetWeight(seq_a[i], seq_b[j]);
-      int match_mism=std::max(0, w+int(ali_mat.Get(i, j)));
-      int del=ali_mat.Get(i, j+1)-opts.gap_open_penalty;
-      int ins=ali_mat.Get(i+1, j)-opts.gap_open_penalty;
-      ali_mat.Set(i+1, j+1, std::max(match_mism, std::max(del, ins)));
-    }
-  }
-  AlignedPatchList patches;
-  // backtracking  
-  CollectPatches(patches, seq_a, seq_b, ali_mat, 0, seq_a.length()+1, 
-                 0, seq_b.length()+1);
-  return patches;  
-}
-
-}}}
-
diff --git a/modules/seq/alg/src/local_align.hh b/modules/seq/alg/src/local_align.hh
deleted file mode 100644
index b685851d39994c8106c3368b6127c356898d5428..0000000000000000000000000000000000000000
--- a/modules/seq/alg/src/local_align.hh
+++ /dev/null
@@ -1,70 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-//------------------------------------------------------------------------------
-#ifndef OST_SEQ_LOCAL_ALIGN_HH
-#define OST_SEQ_LOCAL_ALIGN_HH
-
-
-#include <ost/seq/alignment_handle.hh>
-#include <ost/seq/alg/module_config.hh>
-#include <ost/seq/alg/alignment_opts.hh>
-#include <ost/seq/alg/subst_weight_matrix.hh>
-/*
-  Author: Marco Biasini
- */
-
-namespace ost { namespace seq { namespace alg {
-
-/// \brief holds the result of a local sequence alignment
-struct DLLEXPORT_OST_SEQ_ALG AlignedPatch {
-  /// \brief offset of aligned patch relative to the start of the first sequence
-  int offset_a;
-  /// \brief offset of aligned patch relative to the start of the first sequence  
-  int offset_b;
-  /// \brief the aligned patch
-  AlignmentHandle alignment;
-  bool operator==(const AlignedPatch& rhs) const {
-    return offset_a==rhs.offset_a && offset_b==rhs.offset_b &&
-           rhs.alignment==alignment;
-  }
-  bool operator!=(const AlignedPatch& rhs) const {
-    return !this->operator==(rhs);
-  }
-};
-
-typedef std::vector<AlignedPatch> AlignedPatchList;
-
-/// \brief  Align pair of sequences locally with Waterman-Smith algorithm
-/// 
-/// The alignment algorithm will return the set of optimal alignments given the
-/// weights of the substitution matrix and gap opening and extension penalties.
-/// The sequence patches are non-overlapping
-/// 
-/// \param seq_a is the first sequence to be aligned
-/// \param seq_b is the second sequence to be aligned
-/// 
-/// \param opts holds a set of alignment options such as gap opening and 
-///     extension penalties and the substitution matrix
-/// 
-/// \return list of locally aligned sequence patches.
-AlignedPatchList DLLEXPORT_OST_SEQ_ALG 
-LocalSequenceAlign(const SequenceHandle& seq_a, const SequenceHandle& seq_b, 
-                   const AlignmentOpts& opts);
-}}}
-
-#endif
diff --git a/modules/seq/alg/src/merge_pairwise_alignments.cc b/modules/seq/alg/src/merge_pairwise_alignments.cc
index f7a7c000ecebf9cc96711b59dff976a6c9620816..f91cc34390ec9caf3e24aea63474b5fd74730778 100644
--- a/modules/seq/alg/src/merge_pairwise_alignments.cc
+++ b/modules/seq/alg/src/merge_pairwise_alignments.cc
@@ -34,7 +34,7 @@ typedef std::map<int, int> ShiftMap;
 namespace {
 
 void update_shifts(const AlignmentHandle& aln, 
-                   const SequenceHandle& ref_seq,
+                   const ConstSequenceHandle& ref_seq,
                    ShiftMap& shifts)
 {
   ConstSequenceHandle s1=aln.GetSequence(0);  
@@ -50,8 +50,13 @@ void update_shifts(const AlignmentHandle& aln,
       j++;
     }
     if (shift>0) {
-      assert(i>0);
-      int res_index=s1.GetResidueIndex(i-1);
+      int res_index=0;
+      if (i == 0){
+        res_index=-1;
+      }
+      else if (i > 0) {
+        res_index=s1.GetResidueIndex(i-1);
+      }
       ShiftMap::iterator p=shifts.find(res_index);
       if (p!=shifts.end()) {
         p->second=std::max(p->second, shift);
@@ -63,28 +68,33 @@ void update_shifts(const AlignmentHandle& aln,
   }  
 }
 
-SequenceHandle shift_reference(const SequenceHandle& ref_seq, 
-                                    const ShiftMap& shifts)
+SequenceHandle shift_reference(const ConstSequenceHandle& ref_seq, 
+                               const ShiftMap& shifts)
 {
   std::ostringstream new_sequence;
   String ref_str=ref_seq.GetString();
   int last=0;
   for (ShiftMap::const_iterator i=shifts.begin(),e=shifts.end();i!=e; ++i) {
-    new_sequence << ref_str.substr(last, i->first-last+1) 
+    if(i->first == -1){
+      new_sequence << String(i->second,'-');
+    }
+    else{
+      new_sequence << ref_str.substr(last, i->first-last+1)
                  << String(i->second, '-');
-    last=i->first+1;
+      last=i->first+1;
+    }
   }
   new_sequence << ref_str.substr(last);
   SequenceHandle s=CreateSequence(ref_seq.GetName(), 
-                                            new_sequence.str());                                               
+                                  new_sequence.str());
   if (ref_seq.HasAttachedView())
     s.AttachView(ref_seq.GetAttachedView());
-  s.SetSequenceOffset(s.GetSequenceOffset());
+  s.SetOffset(s.GetOffset());
   return s;
 }
 
 SequenceHandle realign_sequence(const AlignmentHandle& aln, 
-                                  const ShiftMap& shifts)
+                                const ShiftMap& shifts)
 {
   std::ostringstream new_sequence;
   ConstSequenceHandle s1=aln.GetSequence(0);  
@@ -96,27 +106,31 @@ SequenceHandle realign_sequence(const AlignmentHandle& aln,
       shift++;
       ++j;
     }
-    if (i>0 && s1.GetOneLetterCode(i-1)!='-') {
-      ShiftMap::const_iterator p=shifts.find(s1.GetResidueIndex(i-1));
-      if (p!=shifts.end()) {
-        int d=p->second-shift;
-        assert(d>=0);
-        new_sequence << String(d, '-');
-      }      
+    ShiftMap::const_iterator p=shifts.end();
+    if (i == 0){
+      p=shifts.find(-1);
+    }
+    else if (i>0 && s1.GetOneLetterCode(i-1)!='-') {
+      p=shifts.find(s1.GetResidueIndex(i-1));
+    }
+    if (p!=shifts.end()) {
+      int d=p->second-shift;
+      assert(d>=0);
+      new_sequence << String(d, '-');
     }
-    new_sequence << s2.GetOneLetterCode(i);    
+    new_sequence << s2.GetOneLetterCode(i);
   }
   SequenceHandle s=CreateSequence(s2.GetName(), new_sequence.str());
   if (s2.HasAttachedView())
     s.AttachView(s2.GetAttachedView());
-  s.SetSequenceOffset(s2.GetSequenceOffset());
+  s.SetOffset(s2.GetOffset());
   return s;
 }  
 
 }
 
 AlignmentHandle MergePairwiseAlignments(const AlignmentList& pairwise_alns,
-                                        const SequenceHandle& ref_seq)
+                                        const ConstSequenceHandle& ref_seq)
 {
 
   ShiftMap shifts;
diff --git a/modules/seq/alg/src/merge_pairwise_alignments.hh b/modules/seq/alg/src/merge_pairwise_alignments.hh
index e021dbe09569a95d3cbb2bd0cfedac66ea29958b..565b3144167470cc02386edca5812afb1c071fc0 100644
--- a/modules/seq/alg/src/merge_pairwise_alignments.hh
+++ b/modules/seq/alg/src/merge_pairwise_alignments.hh
@@ -43,7 +43,7 @@ namespace ost { namespace seq { namespace alg {
 ///      contain any gaps.
 AlignmentHandle DLLEXPORT_OST_SEQ_ALG 
 MergePairwiseAlignments(const AlignmentList& pairwise_alns,
-                        const SequenceHandle& ref_seq);
+                        const ConstSequenceHandle& ref_seq);
 }}}
 
 #endif
diff --git a/modules/seq/alg/src/sequence_identity.cc b/modules/seq/alg/src/sequence_identity.cc
index 855d3ec48efe79ae4e4941c0d94b07f08f25f5dc..5d0a7dc2d2237f3abaf1cfd8b2badfe75385f3ff 100644
--- a/modules/seq/alg/src/sequence_identity.cc
+++ b/modules/seq/alg/src/sequence_identity.cc
@@ -30,28 +30,43 @@ Real SequenceIdentity(const AlignmentHandle& aln, RefMode::Type ref_mode,
 {
   int non_gap_count=0;
   int identical_count=0;
-  for (AlignedColumnIterator i=aln.begin(), e=aln.end(); i!=e; ++i) {
-    AlignedColumn col=*i;
-    if (!(col[seq_a] == '-' && col[seq_b]=='-')) {
+  const String& sa=aln.GetSequence(seq_a).GetString();
+  const String& sb=aln.GetSequence(seq_b).GetString();  
+  for (String::const_iterator 
+       i=sa.begin(), e=sa.end(), j=sb.begin(); i!=e; ++i, ++j) {
+    if (!((*i)== '-' || (*j)=='-')) {
       non_gap_count++;
     }
-    if (col[seq_a]!='-' && col[seq_a]==col[seq_b]) {
+    if ((*i)!='-' && (*i)==(*j)) {
       identical_count++;
     }
   }
   Real seq_id=0.0;
-  // devide by length of longer sequence:
+  // divide by length of longer sequence:
   if (ref_mode==RefMode::LONGER_SEQUENCE) {
     int wo_gaps_a=aln.GetSequence(seq_a).GetGaplessString().length();
     int wo_gaps_b=aln.GetSequence(seq_b).GetGaplessString().length();
     if(wo_gaps_a>=wo_gaps_b) {
-      seq_id=100*static_cast<Real>(identical_count)/wo_gaps_a;
+      if (wo_gaps_a==0) {
+        seq_id=0;
+      } else {
+        seq_id=100*static_cast<Real>(identical_count)/wo_gaps_a;        
+      }
+
     } else {
-      seq_id=100*static_cast<Real>(identical_count)/wo_gaps_b;
+      if (wo_gaps_b==0) {
+        seq_id=0;
+      } else {
+        seq_id=100*static_cast<Real>(identical_count)/wo_gaps_b;        
+      }
     }
   } else {
-    // divide by alignment length:
-    seq_id=100*static_cast<Real>(identical_count)/non_gap_count;
+    if (non_gap_count==0) {
+      seq_id=0;
+    } else {
+      // divide by alignment length:
+      seq_id=100*static_cast<Real>(identical_count)/non_gap_count;      
+    }
   }
   return seq_id;
 }
diff --git a/modules/seq/alg/src/sequence_identity.hh b/modules/seq/alg/src/sequence_identity.hh
index 4b775ef9228f7116d1094067ef1ec49828450e90..af9992795a1e254eef57d1270a2ed27527bf50fb 100644
--- a/modules/seq/alg/src/sequence_identity.hh
+++ b/modules/seq/alg/src/sequence_identity.hh
@@ -16,7 +16,7 @@
 // along with this library; if not, write to the Free Software Foundation, Inc.,
 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //------------------------------------------------------------------------------
-#ifndef OST_SEQ_SEQUQENCE_IDENTIY_HH
+#ifndef OST_SEQ_SEQUENCE_IDENTITY_HH
 #define OST_SEQ_SEQUENCE_IDENTITY_HH
 
 /*  
@@ -30,7 +30,7 @@ namespace ost { namespace seq { namespace alg {
 struct RefMode {
   enum Type {
     ALIGNMENT=0,
-    LONGER_SEQUENCE,
+    LONGER_SEQUENCE
   };
 };
   
diff --git a/modules/seq/alg/tests/CMakeLists.txt b/modules/seq/alg/tests/CMakeLists.txt
index 512de085684ed3392d006a2f3151f2174b1a744c..37969a869b14c0f740f2b8e221509120f1cd1a6e 100644
--- a/modules/seq/alg/tests/CMakeLists.txt
+++ b/modules/seq/alg/tests/CMakeLists.txt
@@ -1,5 +1,6 @@
 set(OST_SEQ_ALG_UNIT_TESTS
   test_merge_pairwise_alignments.cc
+  test_sequence_identity.cc
   tests.cc
 )
 
diff --git a/modules/seq/alg/tests/test_merge_pairwise_alignments.cc b/modules/seq/alg/tests/test_merge_pairwise_alignments.cc
index 37d58e7073eebf2726fd5b8e170bb9096fec78bf..4e0e4d67a7bccc504df611dad5c1bad826c38cab 100644
--- a/modules/seq/alg/tests/test_merge_pairwise_alignments.cc
+++ b/modules/seq/alg/tests/test_merge_pairwise_alignments.cc
@@ -60,8 +60,8 @@ BOOST_AUTO_TEST_CASE(merge_pairwise_alignments_one)
 BOOST_AUTO_TEST_CASE(merge_pairwise_alignments_two) 
 {
   SequenceHandle ref=CreateSequence("REF", "abcdefghijklmn");
-  SequenceHandle s1=CreateSequence("S1", "abcd---efghijklmn");
-  SequenceHandle s2=CreateSequence("S2", "abcdxyzefghijklmn");
+  SequenceHandle s1=CreateSequence("S1",   "abcd---efghijklmn");
+  SequenceHandle s2=CreateSequence("S2",   "abcdxyzefghijklmn");
   AlignmentHandle aln1=CreateAlignment();
   aln1.AddSequence(s1);
   aln1.AddSequence(s2);
@@ -82,4 +82,29 @@ BOOST_AUTO_TEST_CASE(merge_pairwise_alignments_two)
   BOOST_CHECK_EQUAL(seqs[2].GetString(), "abcd--yefghijklmn");
 }
 
+
+BOOST_AUTO_TEST_CASE(merge_pairwise_alignments_three)
+{
+  SequenceHandle ref=CreateSequence("REF", "abcdefghijk");
+  SequenceHandle s1=CreateSequence("S1",   "--abcdefghijk");
+  SequenceHandle s2=CreateSequence("S2",   "xyabcdefghijk");
+  AlignmentHandle aln1=CreateAlignment();
+  aln1.AddSequence(s1);
+  aln1.AddSequence(s2);
+
+  SequenceHandle s3=CreateSequence("S1", "-abcdefghijk");
+  SequenceHandle s4=CreateSequence("S2", "zabcdefghijk");
+
+  AlignmentHandle aln2=CreateAlignment();
+  aln2.AddSequence(s3);
+  aln2.AddSequence(s4);
+  AlignmentList l;
+  l.push_back(aln1);
+  l.push_back(aln2);
+  AlignmentHandle m=alg::MergePairwiseAlignments(l, ref);
+  ConstSequenceList seqs=m.GetSequences();
+  BOOST_CHECK_EQUAL(seqs[0].GetString(), "--abcdefghijk");
+  BOOST_CHECK_EQUAL(seqs[1].GetString(), "xyabcdefghijk");
+  BOOST_CHECK_EQUAL(seqs[2].GetString(), "-zabcdefghijk");
+}
 BOOST_AUTO_TEST_SUITE_END()
diff --git a/modules/seq/alg/tests/test_sequence_identity.cc b/modules/seq/alg/tests/test_sequence_identity.cc
new file mode 100644
index 0000000000000000000000000000000000000000..fa2d58eaface67484bfe5c69ed6486c10c33c02b
--- /dev/null
+++ b/modules/seq/alg/tests/test_sequence_identity.cc
@@ -0,0 +1,132 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+//------------------------------------------------------------------------------
+/*
+ *  Authors: Marco Biasini
+ */
+
+#define BOOST_TEST_DYN_LINK
+#include <boost/test/unit_test.hpp>
+
+#include <ost/seq/alg/sequence_identity.hh>
+
+
+
+using namespace ost;
+using namespace ost::seq;
+
+BOOST_AUTO_TEST_SUITE(ost_seq_alg)
+
+BOOST_AUTO_TEST_CASE(seqid_one) 
+{
+  SequenceHandle s1=CreateSequence("S1", "abcdefgh");
+  SequenceHandle s2=CreateSequence("S2", "abcd----");
+  
+  AlignmentHandle aln=CreateAlignment();
+  aln.AddSequence(s1);
+  aln.AddSequence(s2);
+  
+  Real seqid=alg::SequenceIdentity(aln, alg::RefMode::LONGER_SEQUENCE, 0, 1);
+  BOOST_CHECK_CLOSE(seqid, 50.0, 1e-6);
+
+  // check the default sequence indices
+  seqid=alg::SequenceIdentity(aln, alg::RefMode::LONGER_SEQUENCE);
+  BOOST_CHECK_CLOSE(seqid, 50.0, 1e-6);
+
+  // check the default value for reference mode
+  seqid=alg::SequenceIdentity(aln);
+  BOOST_CHECK_CLOSE(seqid, 50.0, 1e-6);  
+  
+  seqid=alg::SequenceIdentity(aln, alg::RefMode::ALIGNMENT);
+  BOOST_CHECK_CLOSE(seqid, 100.0, 1e-6);  
+}
+
+BOOST_AUTO_TEST_CASE(seqid_two) 
+{
+  SequenceHandle s1=CreateSequence("S1", "abcd");
+  SequenceHandle s2=CreateSequence("S2", "xbcx");
+  
+  AlignmentHandle aln=CreateAlignment();
+  aln.AddSequence(s1);
+  aln.AddSequence(s2);
+  
+  Real seqid=alg::SequenceIdentity(aln, alg::RefMode::LONGER_SEQUENCE, 0, 1);
+  BOOST_CHECK_CLOSE(seqid, 50.0, 1e-6);
+
+  // check the default sequence indices
+  seqid=alg::SequenceIdentity(aln, alg::RefMode::LONGER_SEQUENCE);
+  BOOST_CHECK_CLOSE(seqid, 50.0, 1e-6);
+
+  // check the default value for reference mode
+  seqid=alg::SequenceIdentity(aln);
+  BOOST_CHECK_CLOSE(seqid, 50.0, 1e-6);  
+  
+  seqid=alg::SequenceIdentity(aln, alg::RefMode::ALIGNMENT);
+  BOOST_CHECK_CLOSE(seqid, 50.0, 1e-6);  
+}
+
+BOOST_AUTO_TEST_CASE(seqid_three) 
+{
+  SequenceHandle s1=CreateSequence("S1", "a--d");
+  SequenceHandle s2=CreateSequence("S2", "x--x");
+  
+  AlignmentHandle aln=CreateAlignment();
+  aln.AddSequence(s1);
+  aln.AddSequence(s2);
+  
+  Real seqid=alg::SequenceIdentity(aln, alg::RefMode::LONGER_SEQUENCE, 0, 1);
+  BOOST_CHECK_CLOSE(seqid, 0.0, 1e-6);
+
+  // check the default sequence indices
+  seqid=alg::SequenceIdentity(aln, alg::RefMode::LONGER_SEQUENCE);
+  BOOST_CHECK_CLOSE(seqid, 0.0, 1e-6);
+
+  // check the default value for reference mode
+  seqid=alg::SequenceIdentity(aln);
+  BOOST_CHECK_CLOSE(seqid, 0.0, 1e-6);  
+  
+  seqid=alg::SequenceIdentity(aln, alg::RefMode::ALIGNMENT);
+  BOOST_CHECK_CLOSE(seqid, 0.0, 1e-6);  
+}
+
+BOOST_AUTO_TEST_CASE(seqid_empty) 
+{
+  SequenceHandle s1=CreateSequence("S1", "---");
+  SequenceHandle s2=CreateSequence("S2", "---");
+  
+  AlignmentHandle aln=CreateAlignment();
+  aln.AddSequence(s1);
+  aln.AddSequence(s2);
+  
+  Real seqid=alg::SequenceIdentity(aln, alg::RefMode::LONGER_SEQUENCE, 0, 1);
+  BOOST_CHECK_CLOSE(seqid, 0.0, 1e-6);
+
+  // check the default sequence indices
+  seqid=alg::SequenceIdentity(aln, alg::RefMode::LONGER_SEQUENCE);
+  BOOST_CHECK_CLOSE(seqid, 0.0, 1e-6);
+
+  // check the default value for reference mode
+  seqid=alg::SequenceIdentity(aln);
+  BOOST_CHECK_CLOSE(seqid, 0.0, 1e-6);  
+  
+  seqid=alg::SequenceIdentity(aln, alg::RefMode::ALIGNMENT);
+  BOOST_CHECK_CLOSE(seqid, 0.0, 1e-6);  
+}
+
+
+BOOST_AUTO_TEST_SUITE_END()
diff --git a/modules/seq/base/doc/seq.rst b/modules/seq/base/doc/seq.rst
new file mode 100644
index 0000000000000000000000000000000000000000..243ec0d49108938923169456f4ba9e9cef8a927f
--- /dev/null
+++ b/modules/seq/base/doc/seq.rst
@@ -0,0 +1,358 @@
+:mod:`~ost.seq` -- Sequences and Alignments
+================================================================================
+
+.. module:: ost.seq
+   :synopsis: Contains classes and functions to deal with sequences and 
+              alignments
+
+The :mod:`seq` module helps you working with sequence data of various kinds. It 
+has classes for :class:`single sequences <SequenceHandle>`, :class:`lists of 
+sequences <SequenceList>` and :class:`alignments <AlignmentHandle>` of two or
+more sequences. 
+
+
+.. _attaching-views:
+
+Attaching Structures to Sequences
+--------------------------------------------------------------------------------
+
+
+Being a structural biology framework, it is not surprising that the sequence 
+classes have been designed to work together with structural data. Each sequence 
+can have an attached :class:`~mol.EntityView` allowing for fast mapping between 
+residues in the entity view and position in the sequence. 
+
+.. _sequence-offset:
+
+Sequence Offset
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+When using sequences and structures together, often the start of the structure 
+and the beginning of the sequence do not fall together. In the following case, 
+the alignment of sequences B and C only covers a subpart of structure A::
+
+  A acefghiklmnpqrstuvwy
+  B     ghiklm
+  C     123-45
+  
+We would now like to know which residue in protein A is aligned to which residue 
+in sequence C. This is achieved by setting the sequence offset of sequence C to 
+4. In essence, the sequence offset influences all the mapping operations from 
+position in the sequence to residue index and vice versa. By default, the 
+sequence offset is 0.
+
+Loading and Saving Sequences and Alignments
+--------------------------------------------------------------------------------
+
+The :mod:`io` module supports input and output of common sequence formats. 
+Single  sequences can be loaded from disk with :func:`io.LoadSequence`,
+alignments are loaded with :func:`io.LoadAlignment` and lists of sequences are loaded with :func:`io.LoadSequenceList`. In addition to the file based input 
+methods, sequences can also be loaded from a string:
+
+.. code-block:: python
+
+  seq_string='''>sequence
+  abcdefghiklmnop'''
+  s=io.LoadSequenceFromString(seq_string, 'fasta')
+  print s.name, s # will print "sequence abcdefghiklmnop"
+  
+Note that, in that case specifying the format is mandatory.
+
+The SequenceHandle
+--------------------------------------------------------------------------------
+
+.. function:: CreateSequence(name, sequence)
+
+  Create a new :class:`SequenceHandle` with the given name and sequence. 
+  
+  :param name: name of the sequence
+  :type  name: str
+  :param sequence: String of characters representing the sequence. Only   
+       alphanumerical characters and '-' are allowed.
+  :type sequence: str
+  :raises InvalidSequence: When the sequence string contains forbidden
+       characters, that is anything that is not alphanumeric or a hyphen.
+
+.. class:: SequenceHandle
+
+  Represents a sequence. New instances are created with :func:`CreateSequence`.
+  
+  .. method:: GetPos(residue_index)
+  
+    Get position of residue with index in sequence. This is best illustrated in 
+    the following example:
+    
+    .. code-block:: python
+      
+      s=seq.CreateSequence("A", "abc---def")
+      print s.GetPos(1) # prints 1
+      print s.GetPos(3) # prints 6
+    
+    The reverse mapping, that is from position in the sequence to residue index 
+    can be achieved with :meth:`GetResidueIndex`.
+  
+  .. method:: GetResidueIndex(pos)
+     
+    Get residue index of character at given position. This method is the
+    inverse of :meth:`GetPos`. If the sequence contains a gap at that position,
+    an :exc:`Error` is raised.
+    
+    .. code-block:: python
+      
+      s=seq.CreateSequence("A", "abc--def")
+      print s.GetResidueIndex(1) # prints 1
+      print s.GetResidueIndex(6) # prints 4
+      # the following line raises an exception of type
+      # Error with the message "requested position contains 
+      # a gap"
+      print s.GetResidueIndex(3)
+
+  .. method:: GetResidue(pos)
+     
+    As, :meth:`GetResidueIndex`, but directly returns the residue view. If no
+    view is attached, or if the position is a gap, an invalid residue view
+    is returned.
+    
+    :rtype: :class:`~ost.mol.ResidueView`
+    
+  .. method:: GetLastNonGap()
+     
+    Get position of last non-gap character in sequence. In case of an empty
+    sequence, or, a sequence only consisting of hyphens, -1 is returned
+     
+  .. method:: GetFirstNonGap()
+  
+    Get position of first non-gap character in sequence. In case of an empty
+    sequence, or, a sequence only consisting of hyphens, -1 is returned.
+
+  .. method:: AttachView(view)
+              AttachView(view, [chain_name])
+    
+    Attach an :class:`~mol.EntityView` to sequence. The first signature requires
+    that the view contains one chain. If not, an :exc:`IntegrityError` is
+    raised. The second signature will select the chain with the given name. If 
+    no such chain exists, an :exc:`IntegrityError` is raised.
+    
+  .. method:: HasAttachedView()
+  
+    Returns True when the sequence has a view attached, False if not.
+    
+  .. method:: GetAttachedView()
+  
+    Returns the attached :class:`~mol.EntityView`, or an invalid
+    :class:`~mol.EntityView` if no view has been attached. Also available as 
+    the property :attr:`attached_view`.
+    
+  .. method:: GetName()
+  
+    Returns the name of the sequence. Also available as the property
+    :attr:`name`
+  
+  .. method:: SetOffset()
+  
+    Set the :ref:`sequence offset <sequence-offset>`. By default, the offset is
+    0. Also available as the property :attr:`offset`.
+    
+  .. method:: GetOffset()
+    
+    Returns the :ref:`sequence offset <sequence-offset>`. Also available as
+    :attr:`offset`.
+    
+    
+  .. method:: GetGaplessString()
+     
+    Returns a string version of this sequence with all hyphens removed. Also
+    available as the property :attr:`gapless_string`.
+     
+   
+  .. method:: SetName()
+  
+    Set name of the sequence. Also available as the property :attr:`name`.
+  
+  .. attribute:: gapless_string
+     
+    Shorthand for :meth:`GetGaplessString()`
+     
+  .. attribute:: name
+  
+    Shorthand for :meth:`GetName`/:meth:`SetName`
+  
+  .. attribute:: attached_view
+  
+    Shorthand for :meth:`GetAttachedView`.
+
+  .. attribute:: offset
+  
+    Shorthand for :meth:`GetSequenceOffset`/:meth:`SetSequenceOffset`
+
+  .. method:: __len__()
+    
+    Returns the length of the sequence (including insertions and deletions)
+    
+  .. method:: __str__()
+
+    Returns the sequence as a string.
+
+
+The SequenceList    
+--------------------------------------------------------------------------------
+
+.. class:: SequenceList
+
+  Represents a list of sequences. The class provides a row-based interface. New
+  instances are created with :func:`CreateSequenceList`.
+
+
+The AlignmentHandle   
+--------------------------------------------------------------------------------
+
+The :class:`AlignmentHandle` represents a list of aligned sequences. In
+constrast to :class:`SequenceList`, an alignment requires all sequences to be of 
+the same length. New instances of alignments are created with 
+:func:`CreateAlignment` and :func:`AlignmentFromSequenceList`.
+
+Typically sequence alignments are used column-based, i.e by looking at an  
+aligned columns in the sequence alignment. To get a row-based (sequence) view
+on the sequence list, use :meth:`GetSequenceList()`. 
+
+All functions that operate on an alignment will again produce a valid alignment. 
+This mean that it is not possible to change the length of one sequence, without  
+adjusting the other sequences, too.
+
+The following example shows how to iterate over the columns and sequences of
+an alignment:
+
+.. code-block:: python
+
+  aln=io.LoadAlignment('aln.fasta')
+  # iterate over the columns
+  for col in aln:
+    print col
+
+  # iterate over the sequences
+  for s in aln.sequences:
+    print s
+
+.. function:: CreateAlignment()
+
+  Creates and returns a new :class:`AlignmentHandle` with no sequences.
+  
+.. function:: AlignmentFromSequenceList(sequences)
+  
+  Create a new alignment from the given list of sequences
+  
+  :param sequences: the list of sequences
+  :type sequences: :class:`ConstSequenceList`
+  
+  :raises: :exc:`InvalidAlignment` if the sequences do not have the same length.
+
+.. class:: AlignmentHandle
+  
+  .. note:: 
+  
+    Several of these methods just forward calls to the sequence. For more 
+    detailed information, have a look at the :class:`SequenceHandle`
+    documentation.
+  
+  .. method:: GetSequence(index)
+  
+    Returns the sequence at the given index, raising an IndexError when trying
+    to access an inexistent sequence.
+    
+  .. method:: GetSequenceList()
+  
+    Returns a list of all sequence of the alignment.
+    
+  .. method:: GetLength()
+  
+    Returns the length of the alignment.
+    
+  .. method:: GetCount()
+  
+    Returns the number of sequences in the alignment.
+  
+  
+  .. method:: ToString(width=80)
+  
+    Returns a formatted string version of the alignment. The sequences are 
+    split into smaller parts to fit into the number columns specified. 
+    
+    .. code-block:: python
+    
+      aln=seq.CreateAlignment()
+      aln.AddSequence(seq.CreateSequence("A", "abcdefghik"))
+      aln.AddSequence(seq.CreateSequence("B", "1234567890"))
+      # The following command will print the output given below
+      print aln.ToString(7)
+      # A abcde
+      # B 12345
+      #
+      # A fghik
+      # B 67890
+
+  .. method:: FindSequence(name)
+  
+    Find sequence with given name. If the alignment contains several sequences
+    with the same name, the first sequence is returned.
+    
+  .. method:: SetSequenceName(seq_index, name)
+  
+    Set the name of the sequence at index `seq_index` to name
+    
+  .. method:: SetSequenceOffset(seq_index, offset)
+  
+    Set the sequence offset of sequence at index `seq_index`
+    
+  .. method:: Copy()
+    
+    Create a deep copy of the alignment
+
+  .. method:: GetPos(seq_index, res_index)
+    
+    Get position of residue with index equal to `res_index` in sequence at index
+    `seq_index`.
+    
+  .. method:: GetResidueIndex(seq_index, pos)
+  
+    Get residue index of residue at position `pos` in sequence at index
+    `seq_index`.
+  
+  .. method:: AttachView(seq_index, view)
+              AttachView(seq_index, view, chain_name)
+    
+    Attach the given view to the sequence at index `seq_index`.
+    
+  .. method:: Cut(start, end)
+  
+    Removes the columns in the half-closed interval `start`, `end` from the
+    alignment.
+    
+    .. code-block:: python
+    
+      aln=seq.CreateAlignment()
+      aln.AddSequence(seq.CreateSequence("A", "abcd---hik"))
+      aln.AddSequence(seq.CreateSequence("B", "1234567890"))
+      aln.Cut(4, 7)
+      
+      print aln.ToString(80)
+      # will print
+      # A abcdhik
+      # B 1234890
+   
+  .. method:: Replace(new_region, start, end)
+  
+    Replace the columns in the half-closed interval `start`, `end` with the
+    columns in `new_region`.
+    
+    :param new_region: The region to be inserted
+    :type new_region: :class:`AlignedRegion` or :class:`AlignmentHandle`
+  
+  
+  .. method:: ShiftRegion(start, end, amount, master=-1)
+  
+    Shift columns in the half-closed interval `start`, `end`. If amount is a
+    positive number, the columns are shifted to the right, if negative, the 
+    columns are shifted to the left.
+    
+    If master is set to -1, all sequences in the region are affected, otherwise 
+    only the sequence at index equal to master is shifted.
diff --git a/modules/seq/base/pymod/__init__.py b/modules/seq/base/pymod/__init__.py
index 0bc8f1b300e952bbf5ce5ae9bd52cbf9735c3420..5b595c7afa629d379298d3553f2615b1272eaf80 100644
--- a/modules/seq/base/pymod/__init__.py
+++ b/modules/seq/base/pymod/__init__.py
@@ -16,4 +16,20 @@
 # along with this library; if not, write to the Free Software Foundation, Inc.,
 # 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #------------------------------------------------------------------------------
-from _seq import *
\ No newline at end of file
+from _seq import *
+from ost.seq import alg
+
+_CreateAlignment=CreateAlignment
+def CreateAlignment(*seqs):
+  aln=_CreateAlignment()
+  for s in seqs:
+    aln.AddSequence(s)
+  return aln
+  
+_CreateSequenceList=CreateSequenceList
+def CreateSequenceList(*seqs):
+  sl=_CreateSequenceList()
+  for s in seqs:
+    sl.AddSequence(s)
+  return sl
+
diff --git a/modules/seq/base/pymod/const_seq_list_export_def.hh b/modules/seq/base/pymod/const_seq_list_export_def.hh
index 4c8a2706853882c58b4bce556cf89bbb523e061b..baba8115839726d0ecc8e7f3acc063d35efc1f71 100644
--- a/modules/seq/base/pymod/const_seq_list_export_def.hh
+++ b/modules/seq/base/pymod/const_seq_list_export_def.hh
@@ -23,11 +23,11 @@
   .def("AddSequence", &C::AddSequence)                                         \
   .def("GetMaxLength", &C::GetMaxLength)                                       \
   .def("GetMinLength", &C::GetMinLength)                                       \
+  .def("IsValid", &C::IsValid)                                                 \
   .def("Take", &C::Take)                                                       \
-  .def("Slice", &C::Slice)                                                   \
+  .def("Slice", &C::Slice)                                                     \
   .def("SequencesHaveEqualLength",                                             \
        &C::SequencesHaveEqualLength)                                           \
   .def("__getitem__", &C::operator[])                                          \
-  .def("__iter__", iterator<C>())                                              \
   .def("__len__", &C::GetCount)
 
diff --git a/modules/seq/base/pymod/export_sequence.cc b/modules/seq/base/pymod/export_sequence.cc
index 0eb5ce9f29eae682b494d5ffd2cb73f1b981fded..28543e04d50d5375b102ab67474d96978a912c0e 100644
--- a/modules/seq/base/pymod/export_sequence.cc
+++ b/modules/seq/base/pymod/export_sequence.cc
@@ -134,6 +134,55 @@ private:
   AlignedColumnIterator e_;
 };
 
+struct ConstSeqListIter {
+  ConstSeqListIter(ConstSequenceList& list):
+    l_(list), b_(l_.begin()), e_(l_.end())
+  { }
+
+  ConstSequenceHandle next()
+  {
+    if (b_==e_) {
+      boost::python::objects::stop_iteration_error();
+    }
+    ConstSequenceHandle s=*b_;  
+    ++b_;
+    return s;
+  }
+private:
+  ConstSequenceList           l_;
+  ConstSequenceList::iterator b_;
+  ConstSequenceList::iterator e_;
+};
+
+struct SeqListIter {
+  SeqListIter(SequenceList& list):
+    l_(list), b_(l_.begin()), e_(l_.end())
+  { }
+
+  SequenceHandle next()
+  {
+    if (b_==e_) {
+      boost::python::objects::stop_iteration_error();
+    }
+    SequenceHandle s=*b_;
+    ++b_;
+    return s;
+  }
+private:
+  SequenceList           l_;
+  SequenceList::iterator b_;
+  SequenceList::iterator e_;
+};
+
+ConstSeqListIter iter_cs(ConstSequenceList& sl) 
+{
+  return ConstSeqListIter(sl);
+}
+
+SeqListIter iter_sl(SequenceList& sl) 
+{
+  return SeqListIter(sl);
+}
 
 RegionRangeIter iter_range1(AlignmentHandle& aln)
 {
@@ -160,8 +209,9 @@ void const_seq_handle_def(O& bp_class)
     .def("GetResidue", &C::GetResidue)
     .def("GetOneLetterCode", &C::GetOneLetterCode)
     .def("__getitem__", &C::GetOneLetterCode)
-    .def("GetSequenceOffset", &C::GetSequenceOffset)
+    .def("GetOffset", &C::GetOffset)
     .def("Copy", &C::Copy)
+    .def("IsValid", &C::IsValid)
     .def("GetFirstNonGap", &C::GetFirstNonGap)
     .def("GetLastNonGap", &C::GetLastNonGap)
     .add_property("first_non_gap", &C::GetFirstNonGap)
@@ -179,7 +229,7 @@ void const_seq_handle_def(O& bp_class)
     .add_property("name",
                   make_function(&C::GetName,
                                 return_value_policy<copy_const_reference>()))
-    .add_property("sequence_offset", &C::GetSequenceOffset)
+    .add_property("offset", &C::GetOffset)
     .add_property("gapless_string", &C::GetGaplessString)
     .add_property("string",
                   make_function(&C::GetString,
@@ -200,7 +250,9 @@ void export_sequence()
   const_seq_handle_def<SequenceHandle>(seq_handle);
   generic_prop_def<SequenceHandle>(seq_handle);  
   seq_handle
-    .def("SetSequenceOffset", &SequenceHandle::SetSequenceOffset)
+    .def("__setitem__", &SequenceHandle::SetOneLetterCode)
+    .def("SetOneLetterCode", &SequenceHandle::SetOneLetterCode)  
+    .def("SetOffset", &SequenceHandle::SetOffset)
     .def("AttachView", attach_one)
     .def("AttachView", attach_two)
     .def("SetString", &SequenceHandle::SetString)
@@ -213,8 +265,8 @@ void export_sequence()
                   make_function(&SequenceHandle::GetName,
                                 return_value_policy<copy_const_reference>()),
                   &SequenceHandle::SetName)
-    .add_property("sequence_offset", &SequenceHandle::GetSequenceOffset,
-                  &SequenceHandle::SetSequenceOffset)
+    .add_property("offset", &SequenceHandle::GetOffset,
+                  &SequenceHandle::SetOffset)
   ;
 
   implicitly_convertible<SequenceHandle, ConstSequenceHandle>();
@@ -229,6 +281,12 @@ void export_sequence()
     class_<RevRegionRangeIter>("RevRegionRangeIter", no_init)
     .def("next", &RevRegionRangeIter::next)
   ;
+  class_<ConstSeqListIter>("ConstSeqListIter", no_init)
+    .def("next", &ConstSeqListIter::next)
+  ;
+  class_<SeqListIter>("SeqListIter", no_init)
+    .def("next", &SeqListIter::next)
+  ;
   class_<AlignmentHandle>("AlignmentHandle", init<>())
     .def("GetCount", &AlignmentHandle::GetCount)
     .add_property("sequence_count", &AlignmentHandle::GetCount)
@@ -246,6 +304,7 @@ void export_sequence()
     .def("AttachView", attach_view_b)
     .def("Cut", &AlignmentHandle::Cut)
     .def("MakeRegion", &AlignmentHandle::MakeRegion)
+    .def("RemoveSequence", &AlignmentHandle::RemoveSequence)
     .def("Replace",&AlignmentHandle::Replace)
     .def("__getitem__", &slice_aln)
     .def("__getitem__", &AlignmentHandle::operator[])
@@ -259,6 +318,7 @@ void export_sequence()
     .def("GetIndex", &AlignedColumn::GetIndex)
     .def("__getitem__", &AlignedColumn::operator[])
     .def("GetRowCount", &AlignedColumn::GetRowCount)
+    .def("GetResidue", &AlignedColumn::GetResidue)
     .def(self_ns::str(self))
   ;
   class_<AlignedRegion>("AlignedRegion", no_init)
@@ -277,17 +337,18 @@ void export_sequence()
     .def("__getitem__", &AlignedRegion::operator[])
     .def("__len__", &AlignedRegion::GetLength)
     .def("__iter__", iter_range2)
-    //~ .def("__reversed__", iter_range_rev)
     .add_property("start", &AlignedRegion::GetStart)
     .add_property("end", &AlignedRegion::GetEnd)
   ;
   class_<ConstSequenceList>("ConstSequenceList", init<>())
     CONST_SEQ_LIST_DEF(ConstSequenceList)
     .def("__getitem__", &do_slice_a)
+    .def("__iter__", &iter_cs)    
   ;
   class_<SequenceList>("SequenceList", init<>())
     CONST_SEQ_LIST_DEF(SequenceList)
     .def("__getitem__", &do_slice_b)
+    .def("__iter__", &iter_sl)
   ;
   class_<AlignmentList>("AlignmentList", init<>())
     .def(vector_indexing_suite<AlignmentList>())
diff --git a/modules/seq/base/src/alignment_handle.cc b/modules/seq/base/src/alignment_handle.cc
index d4611b5623a69ec8bcfd653f7dd66fd3e2513981..d2a7ab85d387051d43edbadac9419925b5ac7fee 100644
--- a/modules/seq/base/src/alignment_handle.cc
+++ b/modules/seq/base/src/alignment_handle.cc
@@ -82,6 +82,12 @@ String AlignmentHandle::ToString(int width) const
   return impl_->ToString(width);
 }
 
+void AlignmentHandle::RemoveSequence(int seq_index)
+{
+  this->CheckValidity();
+  impl_->RemoveSequence(seq_index);
+}
+
 int AlignmentHandle::GetLength() const
 {
   this->CheckValidity();
@@ -249,12 +255,12 @@ void AlignmentHandle::SetSequenceName(int seq_index, const String& name)
 void AlignmentHandle::SetSequenceOffset(int seq_index, int offset)
 {
   this->CheckValidity();
-  impl_->GetSequence(seq_index)->SetSequenceOffset(offset);
+  impl_->GetSequence(seq_index)->SetOffset(offset);
 }
 
 int AlignmentHandle::GetSequenceOffset(int seq_index)
 {
   this->CheckValidity();
-  return impl_->GetSequence(seq_index)->GetSequenceOffset();
+  return impl_->GetSequence(seq_index)->GetOffset();
 }
 }}
diff --git a/modules/seq/base/src/alignment_handle.hh b/modules/seq/base/src/alignment_handle.hh
index 998618b520ed6e90fa88b81f45ddadf4f4e5dcaa..bcba027d92f718fb0d874e96361dfc4f0387ffbd 100644
--- a/modules/seq/base/src/alignment_handle.hh
+++ b/modules/seq/base/src/alignment_handle.hh
@@ -80,7 +80,9 @@ public:
   /// \brief     Get sequence with given index.
   /// \return    sequence or invalid handle if the index is out of bounds
   ConstSequenceHandle GetSequence(int seq_id) const;
-
+  
+  /// \brief remove sequence at seq_index from alignment
+  void RemoveSequence(int seq_index);
   /// \brief   Convert multiple sequence alignment to string.
   String ToString(int width=80) const;
 
@@ -155,6 +157,8 @@ public:
   /// \brief Column iterator end-point
   iterator end() const;
 
+  bool IsValid() const { return impl_.get()!=0; }
+  
 private:
   void CheckValidity() const;
   impl::SequenceListImplPtr impl_;
diff --git a/modules/seq/base/src/impl/sequence_impl.cc b/modules/seq/base/src/impl/sequence_impl.cc
index 06edaf5d52067124afb76f6a3335c9844e1f3ed6..a99ea9b6389bcc2655db1bdc459ce6e243253aa7 100644
--- a/modules/seq/base/src/impl/sequence_impl.cc
+++ b/modules/seq/base/src/impl/sequence_impl.cc
@@ -36,7 +36,7 @@ namespace {
 
 bool is_sane_code(char code)
 {
-  return (isalpha(code) || code=='?');
+  return (isalpha(code) || code=='?' || code=='.');
 }
 
 }
@@ -74,7 +74,7 @@ void SequenceImpl::SetString(const String& seq)
 
 SequenceImpl::SequenceImpl(const String& seq_name,
                    const String& seq_string)
-  : seq_name_(seq_name), seq_string_(seq_string), sequence_offset_(0)
+  : seq_name_(seq_name), seq_string_(seq_string), offset_(0)
 {
   this->ShiftsFromSequence();
 }
@@ -82,7 +82,7 @@ SequenceImpl::SequenceImpl(const String& seq_name,
 SequenceImplPtr SequenceImpl::Copy() const
 {
   SequenceImplPtr new_seq(new SequenceImpl(seq_name_, seq_string_));
-  new_seq->sequence_offset_=sequence_offset_;
+  new_seq->offset_=offset_;
   new_seq->shifts_=shifts_;
   new_seq->attached_view_=attached_view_;
   return new_seq;
@@ -105,10 +105,31 @@ void SequenceImpl::ShiftsFromSequence()
   }
 }
 
+void SequenceImpl::SetOneLetterCode(int position, char new_char)
+{
+  if (position<0 || position>=static_cast<int>(seq_string_.length()))
+    throw std::out_of_range("Position is not covered in sequence");
+  if (new_char=='-') {
+    if (seq_string_[position]!='-') {
+      seq_string_[position]=new_char;
+      this->ShiftsFromSequence();
+      return;
+    }
+  } else  {
+    if (seq_string_[position]=='-') {
+      seq_string_[position]=new_char;
+      this->ShiftsFromSequence();
+      return;
+    } else {
+      seq_string_[position]=new_char;
+    }
+  }
+}
+
 int SequenceImpl::GetResidueIndex(int pos) const
 {
   if (pos<0 || pos>=static_cast<int>(seq_string_.length()))
-    throw Error("Position is not covered in sequence");
+    throw std::out_of_range("Position is not covered in sequence");
   if (seq_string_[pos]=='-')
     throw Error("Requested position contains a gap");
   std::list<Shift>::const_iterator i;
@@ -118,7 +139,7 @@ int SequenceImpl::GetResidueIndex(int pos) const
     if (s.start<=pos)
       shift+=s.shift;
   }
-  return pos-shift+sequence_offset_;
+  return pos-shift+offset_;
 }
 
 void SequenceImpl::SetName(const String& seq_name)
@@ -133,7 +154,7 @@ const String& SequenceImpl::GetName() const
 
 int SequenceImpl::GetPos(int index) const
 {
-  int shifted_index=index-sequence_offset_;
+  int shifted_index=index-offset_;
   int pos=this->GetPosNoBounds(shifted_index);
   if (pos<0 || pos>=static_cast<int>(seq_string_.length()))
     throw Error("number not covered in sequence");
@@ -153,15 +174,15 @@ int SequenceImpl::GetPosNoBounds(int index) const
 }
 
 /// \brief  Set offset for sequence alignment.
-void SequenceImpl::SetSequenceOffset(int offset)
+void SequenceImpl::SetOffset(int offset)
 {
-  sequence_offset_=offset;
+  offset_=offset;
 }
 
 /// \brief Get sequence offset
-int SequenceImpl::GetSequenceOffset() const
+int SequenceImpl::GetOffset() const
 {
-  return sequence_offset_;
+  return offset_;
 }
 
 int SequenceImpl::GetLength() const {
@@ -171,7 +192,7 @@ int SequenceImpl::GetLength() const {
 char SequenceImpl::GetOneLetterCode(int position) const
 {
   if (position<0 || position>=static_cast<int>(seq_string_.length()))
-    throw Error("Position is not covered in sequence");
+    throw std::out_of_range("Position is not covered in sequence");
   return seq_string_[position];
 }
 
@@ -238,7 +259,7 @@ void SequenceImplToInfo(const SequenceImplPtr& sequence, info::InfoGroup& group)
   group.SetTextData(sequence->GetString());
   group.SetAttribute("name", sequence->GetName());
   std::ostringstream ss;
-  ss << sequence->GetSequenceOffset();
+  ss << sequence->GetOffset();
   group.SetAttribute("offset", ss.str());
 }
 
@@ -250,7 +271,7 @@ SequenceImplPtr SequenceImplFromInfo(const info::InfoGroup& group)
   ss >> offset;
   SequenceImplPtr sequence=SequenceImpl::FromString(group.GetAttribute("name"), 
                                                     text);
-  sequence->SetSequenceOffset(offset);
+  sequence->SetOffset(offset);
   return sequence;
 }
 
diff --git a/modules/seq/base/src/impl/sequence_impl.hh b/modules/seq/base/src/impl/sequence_impl.hh
index d6159402b7c8505c25078bb0ee7208f6ea03f8a6..f89b3c4bf8f939a7b03b2c20f4ccaf37e34d8edf 100644
--- a/modules/seq/base/src/impl/sequence_impl.hh
+++ b/modules/seq/base/src/impl/sequence_impl.hh
@@ -85,15 +85,15 @@ public:
 
   /// \brief Get sequence offset from N-terminus
   ///
-  /// \sa #SetSequenceOffset
-  int GetSequenceOffset() const;
+  /// \sa #SetOffset
+  int GetOffset() const;
 
   /// \brief Set sequence offset
   ///
   /// By default the sequence offset is zero, i.e. the beginning of the sequence
   /// lies exactly at the N-terminus. Setting the sequence offset to a positive
   /// number will shift the sequence towards the C-terminus.
-  void SetSequenceOffset(int offset);
+  void SetOffset(int offset);
 
   /// \brief Get lenght of sequence, including gaps.
   int GetLength() const;
@@ -106,6 +106,7 @@ public:
   /// \brief get one letter code of residue at position
   char GetOneLetterCode(int position) const;
 
+  void SetOneLetterCode(int position, char new_char);
   /// \brief get residue at position
   ///
   /// will return the residue view at the given sequence position or an invalid
@@ -154,7 +155,7 @@ private:
   String              seq_string_;
   std::list<Shift>    shifts_;
   bool                editing_;
-  int                 sequence_offset_;
+  int                 offset_;
   mol::EntityView          attached_view_;
 };
 
diff --git a/modules/seq/base/src/impl/sequence_list_impl.cc b/modules/seq/base/src/impl/sequence_list_impl.cc
index 01f22c779d1ee95ffed4d2202b91ad1e01763f8a..b955d8b4cf1244e144d9c3bed82b4688b47afbed 100644
--- a/modules/seq/base/src/impl/sequence_list_impl.cc
+++ b/modules/seq/base/src/impl/sequence_list_impl.cc
@@ -68,6 +68,9 @@ String SequenceListImpl::ToString(int width) const
     label_size=std::max(label_size, static_cast<int>((*i)->GetName().size()));
   }
   label_size+=2;
+  if (label_size>width/4) {
+    label_size=width/4;
+  }  
   int offset=0;
   bool done=false;
   int text_len=width-label_size;
@@ -76,7 +79,12 @@ String SequenceListImpl::ToString(int width) const
     for (std::vector<SequenceImplPtr>::const_iterator i=list_.begin(),
          e=list_.end(); i!=e; ++i) {
       SequenceImplPtr s=*i;
-      buffer << s->GetName() << String(label_size-s->GetName().size(), ' ');
+      if (static_cast<int>(s->GetName().size())>label_size-2) {
+        buffer << s->GetName().substr(0, label_size-4) << "... ";
+      } else {
+        buffer << s->GetName() << String(label_size-s->GetName().size(), ' ');
+      }
+
       if (offset<s->GetLength()) {
         int rem=s->GetLength()-offset;
         int actual=text_len>rem ? rem : text_len;
@@ -96,7 +104,13 @@ String SequenceListImpl::ToString(int width) const
   return buffer.str();
 }
 
-
+void SequenceListImpl::RemoveSequence(int index)
+{
+  if (index<0 || index>=static_cast<int>(list_.size())) {
+    return;
+  }
+  list_.erase(list_.begin()+index);
+}
 int SequenceListImpl::GetMinLength() const
 {
   int min_length=std::numeric_limits<int>::max();
diff --git a/modules/seq/base/src/impl/sequence_list_impl.hh b/modules/seq/base/src/impl/sequence_list_impl.hh
index 93bc070353780e6c90ddc24add126b5a10560d12..66bedd61f47c4cb5d40374b92dfc94c2213ecee9 100644
--- a/modules/seq/base/src/impl/sequence_list_impl.hh
+++ b/modules/seq/base/src/impl/sequence_list_impl.hh
@@ -46,7 +46,7 @@ public:
     if (index<list_.size()) {
       return list_[index];
     }
-    throw Error("Index not covered SequenceList");
+    throw std::out_of_range("Index not covered SequenceList");
   }
   
   const SequenceImplPtr& GetSequence(unsigned int i) const {
@@ -54,9 +54,11 @@ public:
     if (index<list_.size()) {
       return list_[index];
     }
-    throw Error("Index not covered SequenceList");
+    throw std::out_of_range("Index not covered SequenceList");
   }
   
+  
+  void RemoveSequence(int index);
   int GetPos(int seq_index, int residue_index) const;
 
   int GetResidueIndex(int seq_index, int pos) const;
diff --git a/modules/seq/base/src/invalid_sequence.hh b/modules/seq/base/src/invalid_sequence.hh
index b112df8f3ed902677c65597f28e338e79bde5023..453916403ca34d3f6fdb2a28c47d4e3f0cff880b 100644
--- a/modules/seq/base/src/invalid_sequence.hh
+++ b/modules/seq/base/src/invalid_sequence.hh
@@ -23,6 +23,7 @@
   Author: Marco Biasini
  */
 #include <ost/seq/module_config.hh>
+#include <ost/message.hh>
 namespace ost { namespace seq {
 
 class DLLEXPORT InvalidSequence : public Error {
diff --git a/modules/seq/base/src/sequence_handle.cc b/modules/seq/base/src/sequence_handle.cc
index a7f5347e1f36521635b28d4ef6076b0c876ef8a0..13063990d6f093947354436e4cc619c546c36639 100644
--- a/modules/seq/base/src/sequence_handle.cc
+++ b/modules/seq/base/src/sequence_handle.cc
@@ -57,6 +57,7 @@ char ConstSequenceHandle::operator[](int index) const
   return this->GetOneLetterCode(index);
 }
 
+
 void ConstSequenceHandle::CheckValidity() const
 {
   if (!impl_) {
@@ -87,10 +88,10 @@ String ConstSequenceHandle::GetGaplessString() const
   return Impl()->GetGaplessString();
 }
 
-int ConstSequenceHandle::GetSequenceOffset() const
+int ConstSequenceHandle::GetOffset() const
 {
   this->CheckValidity();
-  return Impl()->GetSequenceOffset();  
+  return Impl()->GetOffset();  
 }
 
 
@@ -182,10 +183,10 @@ void SequenceHandle::SetString(const String& seq)
   return Impl()->SetString(seq);   
 }
 
-void SequenceHandle::SetSequenceOffset(int offset)
+void SequenceHandle::SetOffset(int offset)
 {
   this->CheckValidity();
-  return Impl()->SetSequenceOffset(offset);   
+  return Impl()->SetOffset(offset);   
 }
 
 
@@ -267,10 +268,10 @@ String SequenceHandle::GetGaplessString() const
   return Impl()->GetGaplessString();
 }
 
-int SequenceHandle::GetSequenceOffset() const
+int SequenceHandle::GetOffset() const
 {
   this->CheckValidity();
-  return Impl()->GetSequenceOffset();  
+  return Impl()->GetOffset();  
 }
 
 SequenceHandle::operator ConstSequenceHandle() const
@@ -291,6 +292,12 @@ char SequenceHandle::GetOneLetterCode(int position) const
   return Impl()->GetOneLetterCode(position);
 }
 
+void SequenceHandle::SetOneLetterCode(int position, char new_char)
+{
+  this->CheckValidity();
+  Impl()->SetOneLetterCode(position, new_char);
+}
+
 mol::ResidueView SequenceHandle::GetResidue(int position) const
 {
   this->CheckValidity();
diff --git a/modules/seq/base/src/sequence_handle.hh b/modules/seq/base/src/sequence_handle.hh
index de03a505be77b43ad87b9c5d97edf2a9a681a01b..923dec13f217105a13205f334aec02ed5d7289ab 100644
--- a/modules/seq/base/src/sequence_handle.hh
+++ b/modules/seq/base/src/sequence_handle.hh
@@ -84,8 +84,8 @@ public:
 
   /// \brief Get sequence offset from N-terminus
   ///
-  /// \sa SequenceHandle::SetSequenceOffset
-  int GetSequenceOffset() const;  
+  /// \sa SequenceHandle::SetOffset
+  int GetOffset() const;  
   
   /// \brief Get lenght of sequence, including gaps.
   int GetLength() const;
@@ -118,6 +118,7 @@ public:
   
   char operator[](int index) const;
   
+  
   /// \brief whether the sequence is valid
   bool IsValid() const;
   /// \internal
@@ -139,7 +140,7 @@ private:
 /// "multiple sequence alignment". The class allows for fast mapping between
 /// residue index and position in the sequence. The GetResidueIndex() method
 /// maps from position in the sequence to residue index, taking the
-/// \ref GetSequenceOffset() "sequence offset" into account. The reverse
+/// \ref GetOffset() "sequence offset" into account. The reverse
 /// mapping is done with GetPos().
 /// 
 /// Optionally, an entity view may be attached to the sequence with
@@ -194,8 +195,8 @@ public:
 
   /// \brief Get sequence offset from N-terminus
   ///
-  /// \sa SequenceHandle::SetSequenceOffset
-  int GetSequenceOffset() const;  
+  /// \sa SequenceHandle::GetOffset
+  int GetOffset() const;  
   
   /// \brief Get lenght of sequence, including gaps.
   int GetLength() const;
@@ -245,13 +246,15 @@ public:
   /// By default the sequence offset is zero, i.e. the beginning of the sequence
   /// lies exactly at the N-terminus. Setting the sequence offset to a positive
   /// number will shift the sequence towards the C-terminus.
-  void SetSequenceOffset(int offset);
+  void SetOffset(int offset);
 
   /// \brief attach entity view to sequence
   ///
   /// \throw IntegrityError when the view contains more than one chain
   void AttachView(const mol::EntityView& view);
-
+  
+  void SetOneLetterCode(int position, char new_char);
+  
   operator ConstSequenceHandle() const;
   /// \brief attach entity view to sequence
   ///
diff --git a/modules/seq/base/src/views_from_sequences.cc b/modules/seq/base/src/views_from_sequences.cc
index 7ab0ff1f6806c1d303baac5e0689f12d06d91f89..dad47106b659bb034f577533333019d2e8653258 100644
--- a/modules/seq/base/src/views_from_sequences.cc
+++ b/modules/seq/base/src/views_from_sequences.cc
@@ -66,9 +66,9 @@ ViewsFromSequences(const ConstSequenceHandle& seq1,
   mol::ResidueViewList res_b=src_b.GetResidueList();  
   int pos=0, index_a=0, index_b=0;
   while (skip_gaps(seq1, seq2, pos, index_a, index_b)) {
-    dst_a.AddResidue(res_a.at(seq1.GetSequenceOffset()+index_a), 
+    dst_a.AddResidue(res_a.at(seq1.GetOffset()+index_a), 
                      mol::ViewAddFlag::INCLUDE_ATOMS);
-    dst_b.AddResidue(res_b.at(seq2.GetSequenceOffset()+index_b), 
+    dst_b.AddResidue(res_b.at(seq2.GetOffset()+index_b), 
                      mol::ViewAddFlag::INCLUDE_ATOMS);
     pos+=1;
     index_a+=1;
diff --git a/modules/seq/base/tests/test_alignment.cc b/modules/seq/base/tests/test_alignment.cc
index 260ea5c235a27b3977731f7dab778c27d915b5ec..0491f7d35c124c846b5ddd48cee8965e77492025 100644
--- a/modules/seq/base/tests/test_alignment.cc
+++ b/modules/seq/base/tests/test_alignment.cc
@@ -102,10 +102,10 @@ BOOST_AUTO_TEST_CASE(alignment_onelettercode)
   BOOST_CHECK_EQUAL(a.GetOneLetterCode(0,3),seq1.GetOneLetterCode(3));
   BOOST_CHECK_EQUAL(a.GetOneLetterCode(1,3),'w');
   BOOST_CHECK_EQUAL(a.GetOneLetterCode(1,3),seq2.GetOneLetterCode(3));
-  BOOST_CHECK_THROW(a.GetOneLetterCode(0,-1),Error);
-  BOOST_CHECK_THROW(a.GetOneLetterCode(1,6),Error);
-  BOOST_CHECK_THROW(a.GetOneLetterCode(2,0),Error);
-  BOOST_CHECK_THROW(a.GetOneLetterCode(-1,0),Error);
+  BOOST_CHECK_THROW(a.GetOneLetterCode(0,-1),std::out_of_range);
+  BOOST_CHECK_THROW(a.GetOneLetterCode(1,6),std::out_of_range);
+  BOOST_CHECK_THROW(a.GetOneLetterCode(2,0),std::out_of_range);
+  BOOST_CHECK_THROW(a.GetOneLetterCode(-1,0), std::out_of_range);
 }
 
 BOOST_AUTO_TEST_CASE(alignment_pos_and_index)
@@ -119,8 +119,8 @@ BOOST_AUTO_TEST_CASE(alignment_pos_and_index)
   BOOST_CHECK_EQUAL(a.GetResidueIndex(1,4), 2);
   BOOST_CHECK_THROW(a.GetPos(0,-1),Error);
   BOOST_CHECK_THROW(a.GetPos(1,4),Error);
-  BOOST_CHECK_THROW(a.GetPos(2,0),Error);
-  BOOST_CHECK_THROW(a.GetPos(-1,0),Error);
+  BOOST_CHECK_THROW(a.GetPos(2,0),std::out_of_range);
+  BOOST_CHECK_THROW(a.GetPos(-1,0),std::out_of_range);
 }
 
 BOOST_AUTO_TEST_CASE(alignment_getseq)
@@ -132,8 +132,8 @@ BOOST_AUTO_TEST_CASE(alignment_getseq)
   a.AddSequence(seq2);
   BOOST_CHECK_EQUAL(a.GetSequence(0), seq1);
   BOOST_CHECK_EQUAL(a.GetSequence(1), seq2);
-  BOOST_CHECK_THROW(a.GetSequence(-1), Error);
-  BOOST_CHECK_THROW(a.GetSequence(2), Error);
+  BOOST_CHECK_THROW(a.GetSequence(-1), std::out_of_range);
+  BOOST_CHECK_THROW(a.GetSequence(2), std::out_of_range);
 }
 
 BOOST_AUTO_TEST_CASE(alignment_attach_view)
@@ -156,7 +156,7 @@ BOOST_AUTO_TEST_CASE(alignment_attach_view)
   BOOST_CHECK_NO_THROW(a.AttachView(0,EntityView()));
   BOOST_CHECK_EQUAL(a.GetResidue(0,1), EntityView());
   BOOST_CHECK_EQUAL(a.GetResidue(0,3), EntityView());
-  BOOST_CHECK_THROW(a.GetResidue(-1,0),Error)
+  BOOST_CHECK_THROW(a.GetResidue(-1,0),std::out_of_range)
 }
 
 BOOST_AUTO_TEST_CASE(alignment_cut)
@@ -170,10 +170,10 @@ BOOST_AUTO_TEST_CASE(alignment_cut)
   BOOST_CHECK_EQUAL(a.GetLength(),2);
   BOOST_CHECK_EQUAL(a.GetOneLetterCode(0,0),'r');
   BOOST_CHECK_EQUAL(a.GetOneLetterCode(0,1),'r');
-  BOOST_CHECK_THROW(a.GetOneLetterCode(0,2),Error);
+  BOOST_CHECK_THROW(a.GetOneLetterCode(0,2),std::out_of_range);
   BOOST_CHECK_EQUAL(a.GetOneLetterCode(1,0),'a');
   BOOST_CHECK_EQUAL(a.GetOneLetterCode(1,1),'-');
-  BOOST_CHECK_THROW(a.GetOneLetterCode(1,2),Error);
+  BOOST_CHECK_THROW(a.GetOneLetterCode(1,2),std::out_of_range);
 }
 
 BOOST_AUTO_TEST_CASE(alignment_shift_region)
@@ -194,8 +194,8 @@ BOOST_AUTO_TEST_CASE(alignment_shift_region)
   BOOST_CHECK_EQUAL(a.GetSequence(0).GetString(),"abefcd");
   BOOST_CHECK_EQUAL(a.GetSequence(1).GetString(),"ghlkij");
 
-  BOOST_CHECK_THROW(a.ShiftRegion(0,2,1,2),Error);
-  BOOST_CHECK_THROW(a.ShiftRegion(0,2,1,-2),Error);
+  BOOST_CHECK_THROW(a.ShiftRegion(0,2,1,2),std::out_of_range);
+  BOOST_CHECK_THROW(a.ShiftRegion(0,2,1,-2),std::out_of_range);
 
   BOOST_CHECK_THROW(a.ShiftRegion(0,2,-1),std::out_of_range);
   BOOST_CHECK_THROW(a.ShiftRegion(0,5,2),std::out_of_range);
diff --git a/modules/seq/base/tests/test_seq.py b/modules/seq/base/tests/test_seq.py
index 4eed73b1132f82109cc0250807561cb0675db3c0..26abba6896e53f32f19ef43cb4d44e5999bb6c2f 100644
--- a/modules/seq/base/tests/test_seq.py
+++ b/modules/seq/base/tests/test_seq.py
@@ -113,9 +113,9 @@ class TestSeq(unittest.TestCase):
   def testViewsFromSequences_09(self):
     seq_a=seq.CreateSequence("A", "B-D-FGH")
     seq_a.AttachView(self.ent.Select('rname=A,B,D,F,G,H'))
-    seq_a.SetSequenceOffset(1)
+    seq_a.offset=1
     seq_b=seq.CreateSequence("B", "B-DEF-H")
-    seq_b.SetSequenceOffset(1)
+    seq_b.offset=1
     seq_b.AttachView(self.ent.Select('rname=A,B,D,E,F,H'))
     a, b=seq.ViewsFromSequences(seq_a, seq_b)
     string_a=''.join([r.one_letter_code for r in a.residues])
diff --git a/modules/seq/base/tests/test_sequence.cc b/modules/seq/base/tests/test_sequence.cc
index 97997f9156c63ed1b31a098f405570c02f5da084..e787aafb7c3de95e8d93c2b55de8b3b9bba7c8f4 100644
--- a/modules/seq/base/tests/test_sequence.cc
+++ b/modules/seq/base/tests/test_sequence.cc
@@ -56,7 +56,7 @@ BOOST_AUTO_TEST_CASE(seq_triv)
 {
   BOOST_CHECK_NO_THROW(CreateSequence("S1", "-afbcdefghijkLMNOPQRSTUV-"));
   BOOST_CHECK_THROW(CreateSequence("S1", "1"), InvalidSequence);
-  BOOST_CHECK_THROW(CreateSequence("S1", "."), InvalidSequence);
+  BOOST_CHECK_THROW(CreateSequence("S1", "*"), InvalidSequence);
   BOOST_CHECK_THROW(CreateSequence("S1", " "), InvalidSequence);
   SequenceHandle s=CreateSequence("S1","-afbcdefghijkLMNOPQRSTUV-");
   BOOST_CHECK_EQUAL(s.GetString(),"-afbcdefghijkLMNOPQRSTUV-");
@@ -94,16 +94,16 @@ BOOST_AUTO_TEST_CASE(seq_onelettercode)
   BOOST_CHECK_EQUAL(s.GetOneLetterCode(0),'a');
   BOOST_CHECK_EQUAL(s.GetOneLetterCode(3),'c');
   BOOST_CHECK_EQUAL(s.GetOneLetterCode(9),'f');
-  BOOST_CHECK_THROW(s.GetOneLetterCode(-1),Error);
-  BOOST_CHECK_THROW(s.GetOneLetterCode(10),Error);
+  BOOST_CHECK_THROW(s.GetOneLetterCode(-1),std::out_of_range);
+  BOOST_CHECK_THROW(s.GetOneLetterCode(10),std::out_of_range);
   s=CreateSequence("S1", "-afc--de-f");
   BOOST_CHECK_EQUAL(s.GetOneLetterCode(0),'-');
   BOOST_CHECK_EQUAL(s.GetOneLetterCode(1),'a');
   BOOST_CHECK_EQUAL(s.GetOneLetterCode(9),'f');
-  BOOST_CHECK_THROW(s.GetOneLetterCode(-1),Error);
-  BOOST_CHECK_THROW(s.GetOneLetterCode(10),Error);
+  BOOST_CHECK_THROW(s.GetOneLetterCode(-1),std::out_of_range);
+  BOOST_CHECK_THROW(s.GetOneLetterCode(10),std::out_of_range);
   s=CreateSequence("S1", "");
-  BOOST_CHECK_THROW(s.GetOneLetterCode(0),Error);
+  BOOST_CHECK_THROW(s.GetOneLetterCode(0), std::out_of_range);
 }
 
 BOOST_AUTO_TEST_CASE(seq_getnum) 
@@ -116,8 +116,8 @@ BOOST_AUTO_TEST_CASE(seq_getnum)
   BOOST_CHECK_EQUAL(s.GetResidueIndex(6),4-1);
   BOOST_CHECK_EQUAL(s.GetResidueIndex(7),5-1);
   BOOST_CHECK_EQUAL(s.GetResidueIndex(9),6-1);
-  BOOST_CHECK_THROW(s.GetResidueIndex(-1), Error);
-  BOOST_CHECK_THROW(s.GetResidueIndex(10), Error);
+  BOOST_CHECK_THROW(s.GetResidueIndex(-1), std::out_of_range);
+  BOOST_CHECK_THROW(s.GetResidueIndex(10), std::out_of_range);
 }
 
 BOOST_AUTO_TEST_CASE(seq_getpos) 
@@ -136,7 +136,7 @@ BOOST_AUTO_TEST_CASE(seq_offset)
 {
   SequenceHandle s=CreateSequence("S1", "-afc--de-f");
   SequenceHandle s2=CreateSequence("S1", "-afc--de-f");
-  s.SetSequenceOffset(2);
+  s.SetOffset(2);
   BOOST_CHECK_THROW(s.GetPos(-1), Error);
   BOOST_CHECK_THROW(s.GetPos(0), Error);
   BOOST_CHECK_THROW(s.GetPos(1), Error);
@@ -152,9 +152,10 @@ BOOST_AUTO_TEST_CASE(seq_offset)
   BOOST_CHECK_EQUAL(s.GetResidueIndex(1),s2.GetResidueIndex(1)+2);
   BOOST_CHECK_EQUAL(s.GetResidueIndex(6), 5);
   BOOST_CHECK_EQUAL(s.GetResidueIndex(6),s2.GetResidueIndex(6)+2);
-  BOOST_CHECK_THROW(s.GetResidueIndex(10), Error);
+  BOOST_CHECK_THROW(s.GetResidueIndex(10), std::out_of_range);
+  BOOST_CHECK_THROW(s.GetResidueIndex(-1), std::out_of_range);
 
-  s.SetSequenceOffset(-1);
+  s.SetOffset(-1);
   BOOST_CHECK_THROW(s.GetPos(-2), Error);
   BOOST_CHECK_EQUAL(s.GetPos(-1), 1);
   BOOST_CHECK_EQUAL(s.GetPos(0), 2);
@@ -169,7 +170,7 @@ BOOST_AUTO_TEST_CASE(seq_offset)
   BOOST_CHECK_EQUAL(s.GetResidueIndex(1),s2.GetResidueIndex(1)-1);
   BOOST_CHECK_EQUAL(s.GetResidueIndex(6), 2);
   BOOST_CHECK_EQUAL(s.GetResidueIndex(6),s2.GetResidueIndex(6)-1);
-  BOOST_CHECK_THROW(s.GetResidueIndex(10), Error);
+  BOOST_CHECK_THROW(s.GetResidueIndex(10), std::out_of_range);
 }
 
 BOOST_AUTO_TEST_CASE(seq_gaps)
diff --git a/scripts/dng.in b/scripts/dng.in
index de5a9cf80a9860a2f8b07444a8f43022eb1005c5..aecd82ed9aa8e7a55d8d3911d05a16e9b3db576b 100755
--- a/scripts/dng.in
+++ b/scripts/dng.in
@@ -21,13 +21,28 @@
 # Author: Marco Biasini
 
 # Self detect important directories
-SCRIPT_NAME=$0
-BIN_DIR=`dirname $SCRIPT_NAME`
-export DNG_ROOT=$BIN_DIR/..
-export PATH=$BIN_DIR:$PATH
-export LD_LIBRARY_PATH=$DNG_ROOT/@LIBDIR@:$LD_LIBRARY_PATH
+if [ -h "$0" ] ; then
+  SCRIPT_NAME=`readlink "$0"`
+else
+  SCRIPT_NAME="$0"
+fi
+BIN_DIR=`dirname "$SCRIPT_NAME"`
+export DNG_ROOT=`cd "$BIN_DIR/..";pwd`
+export PATH="$DNG_ROOT/bin:$PATH"
+export LD_LIBRARY_PATH="$DNG_ROOT/@LIBDIR@:$LD_LIBRARY_PATH"
 # set QT_PLUGIN_PATH and pythonpath for bundle (commented except in linux bundles)
-#export PYTHONPATH=$DING_ROOT/@LIBDIR@/python2.6
-#export QT_PLUGIN_PATH=$BIN_DIR/plugins
+#export PYTHONPATH="$DNG_ROOT/@LIBDIR@/python2.6"
+#export QT_PLUGIN_PATH="$BIN_DIR/plugins"
 
-gosty $DNG_ROOT/@LIBDIR@/openstructure/init.py ost $@
+opts=""
+for argument in "$@";do
+  if [ -n "$opts" ]; then
+    opts=$opts"#""$argument"
+  else
+    opts="$argument"
+  fi
+done
+
+IFS="#"
+gosty $DNG_ROOT/@LIBDIR@/openstructure/init.py ost $opts
+IFS=$' \t\n'
diff --git a/scripts/init.py b/scripts/init.py
index ed53db5d73b64245d37d5d39e35541de2b4b6de9..e175e08446fbcb198294093850999b1f3dade0ea 100644
--- a/scripts/init.py
+++ b/scripts/init.py
@@ -1,165 +1,212 @@
-import __main__
-import sys
-import optparse
-from ost import io, mol, seq, geom, conop, gui
-import ost
-try: 
-  from ost import img
-  import ost.img.alg
-  _img_present=True
-except ImportError:
-  _img_present=False
-  pass
-import httplib
-
-from PyQt4 import QtGui, QtCore
-from ost.gui.scene.init_inspector import _InitInspector
-from ost.gui.init_menubar import _InitMenuBar
-from ost.gui.init_spacenav import _InitSpaceNav
-from ost.gui.init_context_menu import _InitContextMenu
-
-def _InitRuleBasedBuilder():
-  compound_lib_path=os.path.join(ost.GetSharedDataPath(), 'compounds.chemlib')
-  if os.path.exists(compound_lib_path):
-    conop_inst=conop.Conopology.Instance()
-    compound_lib=conop.CompoundLib.Load(compound_lib_path)
-    conop_inst.RegisterBuilder(conop.RuleBasedBuilder(compound_lib), 'RBB')
-    conop_inst.SetDefaultBuilder('RBB')
-
-# switch to rule-based builder for high fidelity if compounds.chemlib is 
-# available
-_InitRuleBasedBuilder()
-def _InitPanels(app):
-  panels = app.perspective.panels
-  panels.AddWidgetToPool('ost.gui.FileBrowser', -1)
-  panels.AddWidgetToPool('ost.gui.PythonShell', 1)
-  panels.AddWidgetToPool('ost.gui.RemoteLoader', -1)
-  panels.AddWidgetToPool('ost.gui.SceneWin', 1)
-  panels.AddWidgetToPool('ost.gui.SequenceViewer', 1)
-  panels.AddWidgetToPool('ost.gui.SequenceViewerV2', 1)
-  if not panels.Restore("ui/perspective/panels"):
-    panels.AddWidget(gui.PanelPosition.LEFT_PANEL, app.scene_win)
-    panels.AddWidgetByName(gui.PanelPosition.LEFT_PANEL, 
-                           'ost.gui.FileBrowser', False)    
-    panels.AddWidgetByName(gui.PanelPosition.LEFT_PANEL, 
-                           'ost.gui.RemoteLoader', False)
-    panels.AddWidget(gui.PanelPosition.BOTTOM_PANEL, app.seq_viewer)
-    panels.AddWidget(gui.PanelPosition.BOTTOM_PANEL, app.py_shell)
-
-def _InitFrontEnd(try_stereo):
-  app=gui.GostyApp.Instance()
-  app.SetAppTitle("DNG")
-  app.TryStereo(try_stereo)
-  main_area=app.perspective.main_area
-  _InitPanels(app)
-  _InitMenuBar(app)
-  _InitSpaceNav(app)
-  _InitContextMenu(app)
-  main_area.AddPersistentWidget("3D Scene", "gl_win" , app.gl_win, int(QtCore.Qt.WindowMaximized))
-  app.perspective.Restore()
-  additional_modules=getattr(__main__, 'ADDITIONAL_GUI_MODULES', [])
-  for module_name in additional_modules:
-    __import__(module_name)
-  app.ProcessEvents()
-  _InitInspector(app)
-
-def _load_files():
-  for pdb_id in options.pdb_ids:
-    pdb_id, sel=_SplitIDSel(pdb_id)
-    selection=_get_selection_query(sel)
-    gui.FileLoader.LoadFrom(pdb_id,"pdb.org",selection)
-    
-  input_files=[_SplitIDSel(arg) for arg in loading_list]
-  for f in input_files:
-    selection=_get_selection_query(f[1])
-    gui.FileLoader.LoadObject(f[0],selection)
-
-def _get_selection_query(sel):
-  if len(options.query)>0:
-    if len(sel)>0:
-      return '(%s) and (%s)' % (options.query, sel)
-    else:
-      return options.query
-  elif len(sel)>0:
-    return sel
-  return ""
-
-def _execute_script():
-  script=script_argv[0]
-  sys_argv_backup=sys.argv
-  sys.argv=script_argv
-  try:
-    execfile(script, __main__.__dict__)
-  finally:
-    sys.argv=sys_argv_backup     
-
-def show_help(option, opt, value, parser):
-  parser.print_help()
-  QtGui.QApplication.instance().exit()
-  sys.exit(-1)
-
-def parse_script_option(option, opt, value, parser):
-  script_argv.append(value)
-  for arg in parser.rargs:
-     script_argv.append(arg)
-  del parser.rargs[0:len(parser.rargs)]
-
-def _SplitIDSel(name):
-  pos=name.find('[')
-  if pos>-1:
-    return name[:pos], name[pos+1:-1]
-  return name, ''  
-
-loading_list=[]
-script_argv=[]
-images=[]
-viewers=[]
-usage = 'usage: dng [options] [files to load]'
-class OstOptionParser(optparse.OptionParser):
-  def __init__(self, **kwargs):
-    optparse.OptionParser.__init__(self, **kwargs)
-  def exit(self, status_code, error_message):
-    print error_message,
-    QtGui.QApplication.instance().exit()
-    sys.exit(-1)
-
-parser=OstOptionParser(usage=usage,conflict_handler="resolve")
-parser.add_option("-h", "--help", action="callback", callback=show_help, help="show this help message and exit")
-parser.add_option("-v", "--verbosity_level", action="store", type="int", dest="vlevel", default=0, help="sets the verbosity level [default: %default]")
-parser.add_option("-s", "--script", action="callback", default=[], dest="script", type="string", callback=parse_script_option, help="executes a script (syntax: -s SCRIPT [options] [args]) Anything that follows this option is passed to the script")
-parser.add_option("-p", "--pdb_id", dest="pdb_ids", default=[],action="append", help="PDB file ID. The file will be retrieved from PDB")
-parser.add_option("-b", "--builder", dest="builder", default="HEURISTIC", help="Type of builder used by the progam (either RULE_BASED or HEURISTIC) [default: %default]")
-parser.add_option("-c", "--compound_library", dest="complib", default="compounds.chemlib", help="Compound library for the RULE_BASED builder (only used if --builder option is set to RULE_BASED, otherwise ignored [default: %default]")
-parser.add_option("-q", "--query", dest="query", default="", help="Selection query to be highlighted automatically upon loading (only used together with -p option or when a PDB file is loaded, otherwise ignored [default: None]")
-parser.add_option("-S","--stereo", dest="try_stereo", default=False, action="store_true",help="try to get a quad-buffer stereo visual")
-parser.disable_interspersed_args()
-(options, args) = parser.parse_args()
-
-if len(parser.rargs)!=0:
-  for rargs_string in parser.rargs:
-    if not rargs_string.endswith('.py'):  
-      loading_list.append(rargs_string)
-    else:
-      print 'Error:  one of the files to load is a Python script, use -s flag to execute it\n'
-      QtGui.QApplication.instance().exit()
-      sys.exit(-1)    
-
-if len(options.script)!=0:
-  script_argv=options.script
-
-if options.builder=="RULE_BASED":
-  from ost import conop
-  compound_lib=conop.CompoundLib.Load(options.complib)
-  rbb=conop.RuleBasedBuilder(compound_lib)
-  conop.Conopology.Instance().RegisterBuilder(rbb,'rbb')
-  conop.Conopology.Instance().SetDefaultBuilder('rbb')
-
-PushVerbosityLevel(options.vlevel)
-_InitFrontEnd(options.try_stereo)
-
-if len(loading_list)!=0 or len(options.pdb_ids)!=0:
-  _load_files()
-  scene.Autoslab()
-if len(script_argv)!=0:
-  _execute_script()
-
+import __main__
+import sys
+import os.path
+import optparse
+from ost import io, mol, seq, geom, conop, gui, settings
+import ost
+try: 
+  from ost import img
+  import ost.img.alg
+  _img_present=True
+except ImportError:
+  _img_present=False
+  pass
+import httplib
+
+from PyQt4 import QtGui, QtCore
+from ost.gui.scene.init_inspector import _InitInspector
+from ost.gui.init_menubar import _InitMenuBar
+from ost.gui.init_spacenav import _InitSpaceNav
+from ost.gui.init_context_menu import _InitContextMenu
+from ost.gui.init_splash import _InitSplash
+from ost.gui.dng import termuse
+
+from PyQt4.QtGui import *
+def _my_exit(code):
+  QtGui.QApplication.instance().quit()
+  gui.GostyApp.Instance().ProcessEvents()
+  sys._exit(code)
+
+sys._exit=sys.exit
+sys.exit=_my_exit
+
+def _InitRuleBasedBuilder():
+  compound_lib_path=os.path.join(ost.GetSharedDataPath(), 'compounds.chemlib')
+  if os.path.exists(compound_lib_path):
+    conop_inst=conop.Conopology.Instance()
+    compound_lib=conop.CompoundLib.Load(compound_lib_path)
+    conop_inst.RegisterBuilder(conop.RuleBasedBuilder(compound_lib), 'RBB')
+    conop_inst.SetDefaultBuilder('RBB')
+
+# switch to rule-based builder for high fidelity if compounds.chemlib is 
+# available
+_InitRuleBasedBuilder()
+
+def _CheckRestore():
+  settings = QtCore.QSettings()
+  restore = settings.value("restore_settings",QtCore.QVariant(False)).toBool()
+  if not restore:
+    settings.clear()
+  settings.setValue("restore_settings",QtCore.QVariant(True))
+
+def _InitPanels(app):
+  panels = app.perspective.panels
+  panels.AddWidgetToPool('ost.gui.FileBrowser', -1)
+  panels.AddWidgetToPool('ost.gui.PythonShell', 1)
+  panels.AddWidgetToPool('ost.gui.RemoteLoader', -1)
+  panels.AddWidgetToPool('ost.gui.SceneWin', 1)
+  panels.AddWidgetToPool('ost.gui.SequenceViewer', 1)
+  panels.AddWidgetToPool('ost.gui.MessageWidget', 1)
+  if not panels.Restore("ui/perspective/panels"):
+    panels.AddWidget(gui.PanelPosition.LEFT_PANEL, app.scene_win)
+    panels.AddWidgetByName(gui.PanelPosition.LEFT_PANEL, 
+                           'ost.gui.FileBrowser', False)    
+    panels.AddWidgetByName(gui.PanelPosition.LEFT_PANEL, 
+                           'ost.gui.RemoteLoader', False)
+    panels.AddWidget(gui.PanelPosition.BOTTOM_PANEL, app.seq_viewer)
+    panels.AddWidget(gui.PanelPosition.BOTTOM_PANEL, app.py_shell)
+    panels.AddWidget(gui.PanelPosition.RIGHT_PANEL, app.message_widget)
+    return False
+  return True
+
+
+def _InitFrontEnd():
+  _CheckRestore()
+  app=gui.GostyApp.Instance()
+  app.SetAppTitle("DNG")
+  main_area=app.perspective.main_area
+  _InitMenuBar(app)
+  _InitSpaceNav(app)
+  _InitContextMenu(app)
+  main_area.AddPersistentWidget("3D Scene", "gl_win" , app.gl_win, int(QtCore.Qt.WindowMaximized))
+  app.perspective.Restore()
+  additional_modules=getattr(__main__, 'ADDITIONAL_GUI_MODULES', [])
+  for module_name in additional_modules:
+    __import__(module_name)
+  app.ProcessEvents()
+
+  _InitInspector(app)
+  
+  if not _InitPanels(app):
+    _InitSplash()
+  
+def _load_files():
+  for pdb_id in options.pdb_ids:
+    pdb_id, sel=_SplitIDSel(pdb_id)
+    selection=_get_selection_query(sel)
+    gui.FileLoader.LoadFrom(pdb_id,"pdb.org",selection)
+    
+  input_files=[_SplitIDSel(arg) for arg in loading_list]
+  for f in input_files:
+    selection=_get_selection_query(f[1])
+    gui.FileLoader.LoadObject(f[0],selection)
+
+def _get_selection_query(sel):
+  if len(options.query)>0:
+    if len(sel)>0:
+      return '(%s) and (%s)' % (options.query, sel)
+    else:
+      return options.query
+  elif len(sel)>0:
+    return sel
+  return ""
+
+def _execute_script():
+  script=script_argv[0]
+  sys_argv_backup=sys.argv
+  sys.argv=script_argv
+  try:
+    execfile(script, __main__.__dict__)
+  finally:
+    sys.argv=sys_argv_backup     
+
+def show_help(option, opt, value, parser):
+  parser.print_help()
+  QtGui.QApplication.instance().exit()
+  sys.exit(-1)
+
+def parse_script_option(option, opt, value, parser):
+  script_argv.append(value)
+  for arg in parser.rargs:
+     script_argv.append(arg)
+  del parser.rargs[0:len(parser.rargs)]
+
+def _SplitIDSel(name):
+  pos=name.find('[')
+  if pos>-1:
+    return name[:pos], name[pos+1:-1]
+  return name, ''  
+
+loading_list=[]
+script_argv=[]
+images=[]
+viewers=[]
+usage = 'usage: dng [options] [files to load]'
+class OstOptionParser(optparse.OptionParser):
+  def __init__(self, **kwargs):
+    optparse.OptionParser.__init__(self, **kwargs)
+  def exit(self, status_code, error_message):
+    print error_message,
+    QtGui.QApplication.instance().exit()
+    sys.exit(-1)
+
+parser=OstOptionParser(usage=usage,conflict_handler="resolve")
+parser.add_option("-h", "--help", action="callback", callback=show_help, help="show this help message and exit")
+parser.add_option("-v", "--verbosity_level", action="store", type="int", dest="vlevel", default=2, 
+                  help="sets the verbosity level [default: %default]")
+parser.add_option("-s", "--script", action="callback", default=[], dest="script", type="string", callback=parse_script_option, help="executes a script (syntax: -s SCRIPT [options] [args]) Anything that follows this option is passed to the script")
+parser.add_option("-p", "--pdb_id", dest="pdb_ids", default=[],action="append", help="PDB file ID. The file will be retrieved from PDB")
+parser.add_option("-b", "--builder", dest="builder", default="HEURISTIC", help="Type of builder used by the progam (either RULE_BASED or HEURISTIC) [default: %default]")
+parser.add_option("-c", "--compound_library", dest="complib", default="compounds.chemlib", help="Compound library for the RULE_BASED builder (only used if --builder option is set to RULE_BASED, otherwise ignored [default: %default]")
+parser.add_option("-q", "--query", dest="query", default="", help="Selection query to be highlighted automatically upon loading (only used together with -p option or when a PDB file is loaded, otherwise ignored [default: None]")
+parser.disable_interspersed_args()
+(options, args) = parser.parse_args()
+
+if len(parser.rargs)!=0:
+  for rargs_string in parser.rargs:
+    if not rargs_string.endswith('.py'):  
+      loading_list.append(rargs_string)
+    else:
+      print 'Error:  one of the files to load is a Python script, use -s flag to execute it\n'
+      QtGui.QApplication.instance().exit()
+      sys.exit(-1)    
+
+if len(options.script)!=0:
+  script_argv=options.script
+
+if options.builder=="RULE_BASED":
+  from ost import conop
+  compound_lib=conop.CompoundLib.Load(options.complib)
+  rbb=conop.RuleBasedBuilder(compound_lib)
+  conop.Conopology.Instance().RegisterBuilder(rbb,'rbb')
+  conop.Conopology.Instance().SetDefaultBuilder('rbb')
+
+home = os.getenv('HOME') or os.getenv('USERPROFILE')
+_ostrc=os.path.join(home, '.ostrc')
+if os.path.exists(_ostrc):
+  try:
+    exec(open(_ostrc))
+  except Exception, e:
+    print e
+else:
+  rcfile=open(_ostrc,"w")
+  print >> rcfile, '# This python file is parsed by ost and dng at startup'
+  print >> rcfile, '# Its content is made available in the global namespace'
+  print >> rcfile, '# It can be used to define custom variables and functions'
+  print >> rcfile, '# For example:'
+  print >> rcfile, '# IMPORTANT_DIR="path/to/important/dir"'
+  rcfile.close()
+
+PushVerbosityLevel(options.vlevel)
+working_dir=settings.GetValue("DNG_WORKING_DIR",None)
+
+if working_dir != None and os.path.isdir(working_dir):
+  os.chdir(working_dir)
+
+_InitFrontEnd()
+
+if len(loading_list)!=0 or len(options.pdb_ids)!=0:
+  _load_files()
+  scene.Autoslab()
+if len(script_argv)!=0:
+  _execute_script()
diff --git a/scripts/init_cl.py b/scripts/init_cl.py
index 5582502d44b37291f69db910be9c72f8cf71f710..971b6ea1eff8ae1277a0e2fd93ddf1ac69d27407 100644
--- a/scripts/init_cl.py
+++ b/scripts/init_cl.py
@@ -22,7 +22,7 @@ class OstOptionParser(optparse.OptionParser):
 parser=OstOptionParser(usage=usage,conflict_handler="resolve")
 parser.add_option("-i", "--interactive", action="callback", callback=interactive_flag, help="start interpreter interactively (must be first parameter, ignored otherwise)")
 parser.add_option("-h", "--help", action="callback", callback=show_help, help="show this help message and exit")
-parser.add_option("-v", "--verbosity_level", action="store", type="int", dest="vlevel", default=0, help="sets the verbosity level [default: %default]")
+parser.add_option("-v", "--verbosity_level", action="store", type="int", dest="vlevel", default=2, help="sets the verbosity level [default: %default]")
 parser.disable_interspersed_args()
 (options, args) = parser.parse_args()
 
@@ -60,6 +60,14 @@ if os.path.exists(_ostrc):
     exec(open(_ostrc))
   except Exception, e:
     print e
+else:
+  rcfile=open(_ostrc,"w")
+  print >> rcfile, '# This python file is parsed by ost and dng at startup'
+  print >> rcfile, '# Its content is be made available in the global namespace'
+  print >> rcfile, '# It can be used to define custom variables and functions'
+  print >> rcfile, '# For example:'
+  print >> rcfile, '# IMPORTANT_DIR="path/to/important/dir"'
+  rcfile.close()
 
 PushVerbosityLevel(options.vlevel)
 
diff --git a/scripts/ost.in b/scripts/ost.in
index 7239f70a89e6a550e2814e56feb640f9333c3bed..17b9ba416ce2dbedad14dd288e48128ae1ec2ea9 100755
--- a/scripts/ost.in
+++ b/scripts/ost.in
@@ -22,17 +22,21 @@
 # convenience wrapper for non-gui openstructure interface 'ost'
 #
 # Self detect important directories
-SCRIPT_NAME=$0
+if [ -h "$0" ] ; then
+  SCRIPT_NAME=`readlink "$0"`
+else
+  SCRIPT_NAME="$0"
+fi
 BIN_DIR=`dirname "$SCRIPT_NAME"`
-export DNG_ROOT="$BIN_DIR/.."
-export PATH=$PATH:"$BIN_DIR"
+export DNG_ROOT=`cd "$BIN_DIR/..";pwd`
+export PATH="$DNG_ROOT/bin:$PATH"
 export DYLD_FRAMEWORK_PATH="$BIN_DIR/../@LIBDIR@:${DYLD_FRAMEWORK_PATH}"
 export DYLD_LIBRARY_PATH="$BIN_DIR/../@LIBDIR@:${DYLD_LIBRARY_PATH}"
 
-export LD_LIBRARY_PATH=$DNG_ROOT/@LIBDIR@:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH="$DNG_ROOT/@LIBDIR@:$LD_LIBRARY_PATH"
 # set QT_PLUGIN_PATH and pythonpath for bundle (commented except in linux bundles)
 #export QT_PLUGIN_PATH="$BIN_DIR/plugins"
-#export PYTHONPATH=$DING_ROOT/@LIBDIR@/python2.6
+#export PYTHONPATH="$DNG_ROOT/@LIBDIR@/python2.6"
 
 # retrieve absolute path to python executable
 pyexec=""
diff --git a/website/BeauSou2Index.py b/website/BeauSou2Index.py
deleted file mode 100644
index 544defd6e9c9e66e8e08901e10761a10b56bf218..0000000000000000000000000000000000000000
--- a/website/BeauSou2Index.py
+++ /dev/null
@@ -1,56 +0,0 @@
-# -*- coding: utf-8 -*-
-#html-juergen greets doxygaehn
-
-from BeautifulSoup import BeautifulSoup
-import re,os
-
-def Links(ifile):
-  doxrelpath=os.path.dirname(os.path.dirname(ifile))
-  if doxrelpath.startswith('html/'):
-    doxrelpath=re.sub(r'html\/','',doxrelpath,re.I)
-  if not doxrelpath.endswith('/'):
-    doxrelpath=doxrelpath+'/'
-  ih=open(ifile,'r')
-  lines=ih.readlines()
-  ih.close()
-  soup=BeautifulSoup(''.join(lines))
-  anchors=soup('a')
-  for anch in anchors:
-    namespace=[]
-    if anch.has_key('href'):
-      yield anch
-
-def CreateClassIndex(ifile, ofile):
-  classlist=[]
-  doxrelpath=os.path.dirname(os.path.dirname(ifile))  
-  if doxrelpath.startswith('html/'):
-    doxrelpath=re.sub(r'html\/','',doxrelpath,re.I)
-  if not doxrelpath.endswith('/'):
-    doxrelpath=doxrelpath+'/'
-  for link in Links(ifile):
-    m=re.search('(.*class(ost|geom).*)',link.get('href'),re.I)
-    if m:
-      m2=re.search(r'class([^_]*)',m.group(0))
-      if m2:
-        namespace=[]        
-        namespace.append(m2.group(1))
-        p=re.compile(r'([^_]+)_1_1')
-        res=p.findall(m.group(0))
-        for item in res:
-          if not re.search(r'class',item):
-            namespace.append(item.replace(' &gt;','>').replace('&lt; ','<'))
-        namespace.append(link.string.replace(' &gt;','>').replace('&lt; ','<'))
-        mylink={}
-        mylink['::'.join(namespace)]=m.group(0)
-        classlist.append(mylink)
-  oh=open(ofile,'w')       
-  for myclass in classlist:
-    for key,value in myclass.iteritems():
-      path_prefix=doxrelpath+'html/'+value+'\n'
-      oh.write(key+','+path_prefix) 
-  
-def CreateExampleIndex(ifile, ofile):
-  oh=open(ofile, 'w')  
-  for link in Links(ifile):
-      if link.get('class')=='el':
-         oh.write(link.string+','+link.get('href')+'\n') 
diff --git a/website/Doxyfile b/website/Doxyfile
deleted file mode 100644
index 00c2438ae5fd73b3bee2b6c1ad738236c2a2281b..0000000000000000000000000000000000000000
--- a/website/Doxyfile
+++ /dev/null
@@ -1,259 +0,0 @@
-# Doxyfile 1.5.7
-
-#---------------------------------------------------------------------------
-# Project related configuration options
-#---------------------------------------------------------------------------
-DOXYFILE_ENCODING      = UTF-8
-PROJECT_NAME           = OpenStructure
-PROJECT_NUMBER         = 
-OUTPUT_DIRECTORY       = html/dox
-CREATE_SUBDIRS         = YES
-OUTPUT_LANGUAGE        = English
-BRIEF_MEMBER_DESC      = NO
-REPEAT_BRIEF           = YES
-ABBREVIATE_BRIEF       = "The $name class" \
-                         "The $name widget" \
-                         "The $name file" \
-                         is \
-                         provides \
-                         specifies \
-                         contains \
-                         represents \
-                         a \
-                         an \
-                         the
-ALWAYS_DETAILED_SEC    = NO
-INLINE_INHERITED_MEMB  = NO
-FULL_PATH_NAMES        = NO
-STRIP_FROM_INC_PATH    = 
-SHORT_NAMES            = NO
-JAVADOC_AUTOBRIEF      = NO
-QT_AUTOBRIEF           = NO
-MULTILINE_CPP_IS_BRIEF = NO
-INHERIT_DOCS           = YES
-SEPARATE_MEMBER_PAGES  = NO
-TAB_SIZE               = 2
-ALIASES                = 
-OPTIMIZE_OUTPUT_FOR_C  = NO
-OPTIMIZE_OUTPUT_JAVA   = YES
-OPTIMIZE_FOR_FORTRAN   = NO
-OPTIMIZE_OUTPUT_VHDL   = NO
-BUILTIN_STL_SUPPORT    = NO
-CPP_CLI_SUPPORT        = NO
-SIP_SUPPORT            = NO
-IDL_PROPERTY_SUPPORT   = YES
-DISTRIBUTE_GROUP_DOC   = NO
-SUBGROUPING            = YES
-TYPEDEF_HIDES_STRUCT   = NO
-SYMBOL_CACHE_SIZE      = 0
-#---------------------------------------------------------------------------
-# Build related configuration options
-#---------------------------------------------------------------------------
-EXTRACT_ALL            = YES 
-EXTRACT_PRIVATE        = NO
-EXTRACT_STATIC         = YES
-EXTRACT_LOCAL_CLASSES  = YES
-EXTRACT_LOCAL_METHODS  = NO
-EXTRACT_ANON_NSPACES   = NO
-HIDE_UNDOC_MEMBERS     = NO
-HIDE_UNDOC_CLASSES     = NO
-HIDE_FRIEND_COMPOUNDS  = NO
-HIDE_IN_BODY_DOCS      = NO
-INTERNAL_DOCS          = NO
-CASE_SENSE_NAMES       = NO
-HIDE_SCOPE_NAMES       = YES
-SHOW_INCLUDE_FILES     = YES
-INLINE_INFO            = YES
-SORT_MEMBER_DOCS       = YES
-SORT_BRIEF_DOCS        = NO
-SORT_GROUP_NAMES       = NO
-SORT_BY_SCOPE_NAME     = NO
-GENERATE_TODOLIST      = NO
-GENERATE_TESTLIST      = NO
-GENERATE_BUGLIST       = NO
-GENERATE_DEPRECATEDLIST= NO
-ENABLED_SECTIONS       = 
-MAX_INITIALIZER_LINES  = 30
-SHOW_USED_FILES        = YES
-SHOW_DIRECTORIES       = NO
-SHOW_FILES             = YES
-SHOW_NAMESPACES        = YES
-FILE_VERSION_FILTER    = 
-LAYOUT_FILE            = 
-#---------------------------------------------------------------------------
-# configuration options related to warning and progress messages
-#---------------------------------------------------------------------------
-QUIET                  = YES
-WARNINGS               = NO
-WARN_IF_UNDOCUMENTED   = NO
-WARN_IF_DOC_ERROR      = YES
-WARN_NO_PARAMDOC       = NO
-WARN_FORMAT            = "$file:$line: $text"
-WARN_LOGFILE           = 
-#---------------------------------------------------------------------------
-# configuration options related to the input files
-#---------------------------------------------------------------------------
-INPUT                  = ../modules ../stage
-INPUT_ENCODING         = UTF-8
-FILE_PATTERNS          = *.hh \
-                         *.dox \
-                         *.py
-RECURSIVE              = YES
-EXCLUDE_SYMLINKS       = NO
-EXCLUDE_PATTERNS       = *CMakeFiles* *src* *pymod* *tests* *impl*
-EXCLUDE_SYMBOLS        = 
-EXAMPLE_PATH           = ../examples
-EXAMPLE_PATTERNS       = *
-EXAMPLE_RECURSIVE      = NO
-IMAGE_PATH             = 
-INPUT_FILTER           = 
-FILTER_SOURCE_FILES    = NO
-#---------------------------------------------------------------------------
-# configuration options related to source browsing
-#---------------------------------------------------------------------------
-SOURCE_BROWSER         = NO
-INLINE_SOURCES         = NO
-STRIP_CODE_COMMENTS    = YES
-REFERENCED_BY_RELATION = NO
-REFERENCES_RELATION    = NO
-REFERENCES_LINK_SOURCE = NO
-USE_HTAGS              = NO
-VERBATIM_HEADERS       = YES
-#---------------------------------------------------------------------------
-# configuration options related to the alphabetical class index
-#---------------------------------------------------------------------------
-ALPHABETICAL_INDEX     = YES
-COLS_IN_ALPHA_INDEX    = 1
-IGNORE_PREFIX          = 
-#---------------------------------------------------------------------------
-# configuration options related to the HTML output
-#---------------------------------------------------------------------------
-GENERATE_HTML          = YES
-HTML_OUTPUT            = html
-HTML_FILE_EXTENSION    = .html
-HTML_HEADER            = ./header.html
-HTML_FOOTER            = ./footer.html
-HTML_STYLESHEET        = ./stylesheet.css
-HTML_ALIGN_MEMBERS     = YES
-HTML_DYNAMIC_SECTIONS  = NO
-GENERATE_DOCSET        = NO
-DOCSET_FEEDNAME        = "Doxygen generated docs"
-DOCSET_BUNDLE_ID       = org.doxygen.Project
-GENERATE_HTMLHELP      = NO
-CHM_FILE               = 
-HHC_LOCATION           = 
-GENERATE_CHI           = NO
-CHM_INDEX_ENCODING     = 
-BINARY_TOC             = NO
-TOC_EXPAND             = NO
-GENERATE_QHP           = NO
-QCH_FILE               = 
-QHP_NAMESPACE          = org.doxygen.Project
-QHP_VIRTUAL_FOLDER     = doc
-QHG_LOCATION           = 
-DISABLE_INDEX          = YES
-ENUM_VALUES_PER_LINE   = 4
-GENERATE_TREEVIEW      = NO
-TREEVIEW_WIDTH         = 250
-FORMULA_FONTSIZE       = 10
-#---------------------------------------------------------------------------
-# configuration options related to the LaTeX output
-#---------------------------------------------------------------------------
-GENERATE_LATEX         = NO
-LATEX_OUTPUT           = latex
-LATEX_CMD_NAME         = latex
-MAKEINDEX_CMD_NAME     = makeindex
-COMPACT_LATEX          = NO
-PAPER_TYPE             = a4wide
-EXTRA_PACKAGES         = 
-LATEX_HEADER           = 
-PDF_HYPERLINKS         = YES
-USE_PDFLATEX           = YES
-LATEX_BATCHMODE        = NO
-LATEX_HIDE_INDICES     = NO
-#---------------------------------------------------------------------------
-# configuration options related to the RTF output
-#---------------------------------------------------------------------------
-GENERATE_RTF           = NO
-RTF_OUTPUT             = rtf
-COMPACT_RTF            = NO
-RTF_HYPERLINKS         = NO
-RTF_STYLESHEET_FILE    = 
-RTF_EXTENSIONS_FILE    = 
-#---------------------------------------------------------------------------
-# configuration options related to the man page output
-#---------------------------------------------------------------------------
-GENERATE_MAN           = NO
-MAN_OUTPUT             = man
-MAN_EXTENSION          = .3
-MAN_LINKS              = NO
-#---------------------------------------------------------------------------
-# configuration options related to the XML output
-#---------------------------------------------------------------------------
-GENERATE_XML           = NO
-XML_OUTPUT             = xml
-XML_SCHEMA             = 
-XML_DTD                = 
-XML_PROGRAMLISTING     = YES
-#---------------------------------------------------------------------------
-# configuration options for the AutoGen Definitions output
-#---------------------------------------------------------------------------
-GENERATE_AUTOGEN_DEF   = NO
-#---------------------------------------------------------------------------
-# configuration options related to the Perl module output
-#---------------------------------------------------------------------------
-GENERATE_PERLMOD       = NO
-PERLMOD_LATEX          = NO
-PERLMOD_PRETTY         = YES
-PERLMOD_MAKEVAR_PREFIX = 
-#---------------------------------------------------------------------------
-# Configuration options related to the preprocessor   
-#---------------------------------------------------------------------------
-ENABLE_PREPROCESSING   = YES
-MACRO_EXPANSION        = YES
-EXPAND_ONLY_PREDEF     = NO
-SEARCH_INCLUDES        = YES
-INCLUDE_PATH           = 
-INCLUDE_FILE_PATTERNS  = *.hh
-PREDEFINED             = 
-EXPAND_AS_DEFINED      = 
-SKIP_FUNCTION_MACROS   = YES
-#---------------------------------------------------------------------------
-# Configuration::additions related to external references   
-#---------------------------------------------------------------------------
-TAGFILES               = 
-GENERATE_TAGFILE       = 
-ALLEXTERNALS           = NO
-EXTERNAL_GROUPS        = YES
-PERL_PATH              = /usr/bin/perl
-#---------------------------------------------------------------------------
-# Configuration options related to the dot tool   
-#---------------------------------------------------------------------------
-CLASS_DIAGRAMS         = YES
-HIDE_UNDOC_RELATIONS   = YES
-HAVE_DOT               = YES
-DOT_FONTNAME           = Verdana
-DOT_FONTPATH           = 
-CLASS_GRAPH            = YES
-COLLABORATION_GRAPH    = YES
-GROUP_GRAPHS           = YES
-UML_LOOK               = NO
-TEMPLATE_RELATIONS     = NO
-INCLUDE_GRAPH          = NO
-INCLUDED_BY_GRAPH      = NO
-CALL_GRAPH             = NO
-CALLER_GRAPH           = NO
-GRAPHICAL_HIERARCHY    = YES
-DIRECTORY_GRAPH        = NO
-DOT_IMAGE_FORMAT       = png
-DOTFILE_DIRS           = 
-DOT_GRAPH_MAX_NODES    = 50
-MAX_DOT_GRAPH_DEPTH    = 2
-DOT_TRANSPARENT        = NO
-DOT_MULTI_TARGETS      = NO
-GENERATE_LEGEND        = YES
-DOT_CLEANUP            = YES
-#---------------------------------------------------------------------------
-# Configuration::additions related to the search engine   
-#---------------------------------------------------------------------------
-SEARCHENGINE           = YES
diff --git a/website/doxypattern.py b/website/doxypattern.py
deleted file mode 100644
index cf1bc09730ff5fc8540327ece4d3794f057ccdf7..0000000000000000000000000000000000000000
--- a/website/doxypattern.py
+++ /dev/null
@@ -1,65 +0,0 @@
-# -*- coding: utf-8 -*-
-# class to extend inlinepatterns class to handle  doxygen references by
-#inserting links(<a>) created from a previuosly compiled list of classnames
-#within ost and their relative location within the source tree
-#
-#Author Juergen Haas
-import markdown
-import re
-
-
-
-doxBRK=r'(dox|ex)\[(.*?)(\|.*?)?\]'
-DOXYREF_RE= doxBRK
-
-class DoxyRefPattern(markdown.inlinepatterns.LinkPattern):
-    """ Match to a stored doxygen reference and return link element. """
-    def __init__ (self, pattern, markdown_instance=None, doxyref={}, example_dict={}):
-        """
-        Create an instant of an inline pattern.
-
-        Keyword arguments:
-
-        * pattern: A regular expression that matches a pattern
-
-        """
-        self.pattern = pattern
-        self.doxyref = doxyref
-        self.example_dict=example_dict
-        self.compiled_re = re.compile("^(.*?)%s(.*?)$" % pattern, re.DOTALL)
-        # Api for Markdown to pass safe_mode into instance
-        self.safe_mode = False
-        if markdown_instance:
-            self.markdown = markdown_instance
-
-    def handleMatch(self, m):
-       if m.group(2)=='dox':
-         text = m.group(3)
-         if m.group(4):
-           if m.group(4).find('\|'):
-             linktext=m.group(4).replace('|','')
-           else:
-             linktext=text
-         else:
-           linktext=text
-         if text in self.doxyref:
-             href = self.doxyref[text]
-         else:
-             print 'doxyref  not found for', text
-             return
-         title= None
-         return self.makeTag(href, title, linktext)
-       else:
-         ref=m.group(3)
-         text=ref
-         if m.group(4):
-           text=m.group(4)[1:]
-         return self.makeTag('dox/html/'+self.example_dict.get(ref, ''), None, text) 
-
-    def makeTag(self, href, title, text):
-        el = markdown.etree.Element('a')
-
-        el.set('href', self.sanitize_url(href))
-
-        el.text = text
-        return el
diff --git a/website/footer.html b/website/footer.html
deleted file mode 100644
index ba5dfc16f084d63e68e2f5cdc4fddd6d67ca7825..0000000000000000000000000000000000000000
--- a/website/footer.html
+++ /dev/null
@@ -1,7 +0,0 @@
-       <div id="footer">
-            Copyright 2008-2010 by the OpenStructure authors
-        </div>            
-    </div>        
-    </div>  
-</body>
-</html>
diff --git a/website/gen_site.py b/website/gen_site.py
deleted file mode 100644
index f0c250794eed1b04fc82085cb8096c471920ba94..0000000000000000000000000000000000000000
--- a/website/gen_site.py
+++ /dev/null
@@ -1,152 +0,0 @@
-# -*- coding: utf-8 -*-
-#Authors Marco Biasini, Juergen Haas
-import markdown
-import os, re
-import codecs,shutil
-import doxypattern
-from xml import etree
-from optparse import OptionParser
-from BeauSou2Index import *
-
-
-#please use this to flag a mkdown document as incomplete:
-#> <div style="height:70px;background-color:#DD0000;border-bottom:1px solid #DDDDDD;border-top:1px solid #DDDDDD;">This document needs love!
-#
-#default path to classes.html
-#please omit the leading ''./''
-doxrelpath='html/dox/'
-CLASSES_PATH=doxrelpath+'html/classes.html'
-
-p=OptionParser()
-p.add_option('--output_dir', '-o', help='output directory', 
-             default='html')
-p.add_option('--input_dir', '-i', help='input directory', default='raw')
-p.add_option('--base_url', '-b', 
-             help='base url to be used for all relative links. if not specified, '+
-                  'will be set to the output directory')
-p.add_option('--doxy_ref_file', '-d', help='file with compiled classnames, '+
-                  'and corresponding doxygen page', default='index.txt')
-p.add_option('--doxy_classfile','-c',help='file, where doxygen store the'+
-             'alphabetical index',default='%s'%(CLASSES_PATH))
-p.add_option('--run_doxygen','-r',help='run doxygen with Doxyfile given as'+
-             'argument')
-opts, args=p.parse_args()
-
-if os.path.exists('../modules/scratch') or \
-   os.path.exists('../modules/dng_scratch'):
-  print '\nERROR ...exiting!\n\nPlease generate webpage from public checkout\n'
-  os._exit(-1)
-if not opts.base_url:
-  opts.base_url='file://%s' % os.path.abspath(opts.output_dir)
-scaffold_file=codecs.open('raw/scaffold.html', mode='r', 
-                           encoding='utf8')
-SCAFFOLD=scaffold_file.read()
-
-def run_doxygen(doxyfile):
-    if os.path.exists(doxyfile):
-      print '\nrunning doxygen now...\n'
-      cmd='doxygen %s' %(doxyfile)
-      output=os.popen(cmd)
-    else:
-      print '\nDoxygen input file not found!\nPlease provide a valid doxygen '\
-            'input file specifying --run_doxygen YOURFILE\n'
-      os._exit(-1)
-    
-def load_doxy_refs():
-  doxy_file=opts.doxy_ref_file
-  if not os.path.isfile(doxy_file):
-    print '\nWarning: Index file with doxygen classname references'\
-          ' not found!\n         Use -d to specify filename'\
-          '(default=index.txt)\n'
-    return
-  doxy_refs=codecs.open(doxy_file, mode="r",
-                              encoding="utf8")
-  lines=doxy_refs.readlines()
-
-  for line in lines:
-    fields=[]
-    if re.search(',',line):
-      fields=line.split(',')
-    if len(fields)==2:
-      doxy_dict[fields[0]]=fields[1]
-  for line in open('examples_index.txt'):
-    key, val=line.split(',')
-    example_dict[key.strip()]=val.strip()
-
-def mkdown_to_html(opts, dirname, names):
-#  base_dir=os.path.relpath(dirname, opts.input_dir)
-  if dirname==opts.input_dir: 
-    base_dir=dirname[len(opts.input_dir):]
-  else:
-    base_dir=dirname[len(opts.input_dir)+1:]
-    
-  out_dir=os.path.join(opts.output_dir, base_dir)
-  if out_dir.find('.svn')!=-1:
-    return
-  print out_dir
-  if not os.path.exists(out_dir):
-    os.mkdir(out_dir)
-  for name in names:
-    if name.endswith('.mkdown'):
-      print '*- converting', name
-      base_out_name=os.path.splitext(name)[0]+'.html'
-      out_name=os.path.join(out_dir, base_out_name)            
-      full_name=os.path.join(dirname, name)
-      input_file=codecs.open(os.path.join(dirname, name), mode="r", 
-                             encoding="utf8")
-      text=input_file.read()
-      md=markdown.Markdown(extensions=['toc2', 'codehilite', 'meta','tables'])
-      md.inlinePatterns["doxylink"] = \
-                      doxypattern.DoxyRefPattern(doxypattern.DOXYREF_RE,
-                                              md,
-                                              doxy_dict, example_dict)
-      md.doc_url=os.path.join(base_dir, base_out_name)
-      html=md.convert(text)
-      meta=md.Meta
-      toc=etree.ElementTree.tostring(md.TOC)
-      title=''
-      if 'title' in meta.keys():
-        title=meta['title'][0]
-
-      out_file=codecs.open(out_name, mode='w', encoding='utf8')
-      out_file.write(SCAFFOLD % { 'CONTENT' : html, 'TITLE' : title, 
-                                  'SITE_NAV' : toc, 'BASE' : opts.base_url})
-
-def copy_images(opts, dirname, names):
-   if dirname==opts.input_dir: 
-     base_dir=dirname[len(opts.input_dir):]
-   else:
-     base_dir=dirname[len(opts.input_dir)+1:]
-   out_dir=os.path.join(opts.output_dir, base_dir)
-   for name in names:
-     if name.endswith('.jpg') or name.endswith('.png'):
-       shutil.copy(os.path.join(dirname,name), os.path.join(out_dir,name))
-
-if not os.path.exists(opts.output_dir):
-  os.mkdir(opts.output_dir)
-if not os.path.exists(os.path.join(opts.output_dir, 'css')):
-  os.mkdir(os.path.join(opts.output_dir, 'css'))
-shutil.copy(os.path.join(opts.input_dir, 'css/ost.css'),
-            os.path.join(opts.output_dir, 'css'))
-if opts.run_doxygen:
-  run_doxygen(opts.run_doxygen)
-  if os.path.exists(opts.doxy_ref_file):
-    os.unlink(opts.doxy_ref_file)
-if not os.path.exists(opts.doxy_classfile):
-  print 'Warning: Could not find the alphabetical index file generated\n'\
-        'by doxygen (classes.html). Please specify with -c'\
-        '(default=''%s'')' %(CLASSES_PATH)
-  os._exit(-2)
-else:
-  print 'Found doxygen class file:',opts.doxy_classfile
-
-doxy_dict={}
-example_dict={}
-#now create the index file listing the classnames and the corresponding
-#doxygen html files for resolving the dox[ost::mol::BondHandle] mkdown tags
-if not os.path.exists(opts.doxy_ref_file):
-  CreateClassIndex(opts.doxy_classfile, opts.doxy_ref_file)
-  CreateExampleIndex('html/dox/html/examples.html', 'examples_index.txt')
-load_doxy_refs()
-os.path.walk(opts.input_dir, mkdown_to_html, opts)
-os.path.walk(opts.input_dir, copy_images, opts)
\ No newline at end of file
diff --git a/website/header.html b/website/header.html
deleted file mode 100644
index 2767659fdacde2c39434c6786a076c8174b5162b..0000000000000000000000000000000000000000
--- a/website/header.html
+++ /dev/null
@@ -1,48 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<html>
-<head>
-    <meta http-equiv="Content-type" content="text/html; charset=utf-8">
-    <title>$title</title>
-    <link rel="stylesheet" href="$relpath$../../css/ost.css" 
-          type="text/css" media="screen" 
-          title="no title" charset="utf-8">
-</head>
-<body>
-    <div id="content-holder">
-        <div id="toc-box">
-        <div id="menu">    
-            <a class="toc-title" >Site Navigation</a>
-	        <div class="toc-sep">
-            <ul>
-                <li><a href="$relpath$../../index.html">Home</a></li>
-                <li><a href="$relpath$../../docs/tut/intro.html">Getting Started</a></li>
-                <li><a href="$relpath$../../features.html">Features</a></li>
-                <li><a href="$relpath$../../download.html">Download</a></li>                
-                <li><a href="$relpath$../../gallery.html">Gallery</a></li>                
-                <li><a href="$relpath$../../docs/index.html">Documentation</a></li>
-                <ul>
-                  <li><a href="$relpath$../../docs/tutorials.html">Tutorials</a></li>
-                  <li><a href="$relpath$../../docs/examples.html">Examples</a></li>
-                  <li><a href="$relpath$../../dox/html/classes.html">Class List</a></li>
-                </ul>
-                <li><a href="$relpath$../../FAQ.html">Frequently Answered Questions</a></li>
-
-                <li>
-                    <a href="$relpath$../../ack.html">Acknowledgements</a>
-                </li>
-                <li>
-                    <a href="$relpath$../../contact.html">Contact</a>
-                </li>
-            </ul>
-            </div>
-            <a class="toc-title" >API Documentation</a> 
-            <div class="toc-sep" >
-              <ul>
-                <li><a href="$relpath$functions.html">Function List</a></li>
-                <li><a href="$relpath$classes.html">Class List</a></li>
-                <li><a href="$relpath$files.html">File List</a></li>
-             </ul>
-            </div> <!--toc-sep-->
-        </div><!--menu-->
-        </div><!--toc-box-->
-        <div id="content" >
diff --git a/website/mdx_toc2.py b/website/mdx_toc2.py
deleted file mode 100644
index e729eba58e42a695e1dbf32323896d6338a7b46e..0000000000000000000000000000000000000000
--- a/website/mdx_toc2.py
+++ /dev/null
@@ -1,139 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Table of Contents Extension for Python-Markdown
-* * *
-
-(c) 2008 [Jack Miller](http://codezen.org)
-
-Dependencies:
-* [Markdown 2.0+](http://www.freewisdom.org/projects/python-markdown/)
-
-"""
-import markdown
-from markdown import etree
-import re
-
-class TocTreeprocessor(markdown.treeprocessors.Treeprocessor):
-    # Iterator wrapper to get parent and child all at once
-    def iterparent(self, root):
-        for parent in root.getiterator():
-            for child in parent:
-                yield parent, child
-    def __init__(self, md):
-      markdown.treeprocessors.Treeprocessor.__init__(self, md)
-      self.md=md
-    def run(self, doc):
-        div = etree.Element("div")
-        self.md.DOC=doc
-        div.attrib["class"] = "toc"
-        last_li = None
-        self.md.TOC=div
-        # Add title to the div
-        if self.config["title"][0]:
-            header = etree.SubElement(div, "span")
-            header.attrib["class"] = "toctitle"
-            header.text = self.config["title"][0]
-
-        level = 0
-        list_stack=[div]
-        header_rgx = re.compile("[Hh][12]")
-
-        # Get a list of id attributes
-        used_ids = []
-        for c in doc.getiterator():
-            if "id" in c.attrib:
-                used_ids.append(c.attrib["id"])
-
-        for (p, c) in self.iterparent(doc):
-            if not c.text:
-                continue
-
-            # To keep the output from screwing up the
-            # validation by putting a <div> inside of a <p>
-            # we actually replace the <p> in its entirety.
-            # We do not allow the marker inside a header as that
-            # would causes an enless loop of placing a new TOC 
-            # inside previously generated TOC.
-
-            if c.text.find(self.config["marker"][0]) > -1 and not header_rgx.match(c.tag):
-                for i in range(len(p)):
-                    if p[i] == c:
-                        p[i] = etree.Element('span')
-                        break
-                    
-            if header_rgx.match(c.tag):
-                tag_level = int(c.tag[-1])
-                
-                while tag_level < level:
-                    list_stack.pop()
-                    level -= 1
-
-                if tag_level > level:
-                    newlist = etree.Element("ul")
-                    if last_li:
-                        last_li.append(newlist)
-                    else:
-                        list_stack[-1].append(newlist)
-                    list_stack.append(newlist)
-                    level += 1
-
-                # Do not override pre-existing ids 
-                if not "id" in c.attrib:
-                    id = self.config["slugify"][0](c.text)
-                    if id in used_ids:
-                        ctr = 1
-                        while "%s_%d" % (id, ctr) in used_ids:
-                            ctr += 1
-                        id = "%s_%d" % (id, ctr)
-                    used_ids.append(id)
-                    c.attrib["id"] = id
-                else:
-                    id = c.attrib["id"]
-
-                # List item link, to be inserted into the toc div
-                last_li = etree.Element("li")
-                link = etree.SubElement(last_li, "a")
-                link.text=c.text
-                link.attrib["href"] = self.md.doc_url+'#' + id
-                if int(self.config["anchorlink"][0]):
-                    anchor = etree.SubElement(c, "a")
-                    anchor.text = c.text
-                    anchor.attrib["href"] = "#" + id
-                    anchor.attrib["class"] = "toclink"
-                    c.text=""
-
-                list_stack[-1].append(last_li)
-
-class Toc2Extension(markdown.Extension):
-    def __init__(self, configs):
-        self.config = { "marker" : ["[TOC]", 
-                            "Text to find and replace with Table of Contents -"
-                            "Defaults to \"[TOC]\""],
-                        "slugify" : [self.slugify,
-                            "Function to generate anchors based on header text-"
-                            "Defaults to a built in slugify function."],
-                        "title" : [None,
-                            "Title to insert into TOC <div> - "
-                            "Defaults to None"],
-                        "anchorlink" : [0,
-                            "1 if header should be a self link"
-                            "Defaults to 0"]}
-
-        for key, value in configs:
-            self.setConfig(key, value)
-
-    # This is exactly the same as Django's slugify
-    def slugify(self, value):
-        """ Slugify a string, to make it URL friendly. """
-        import unicodedata
-        value = unicodedata.normalize('NFKD', value).encode('ascii', 'ignore')
-        value = unicode(re.sub('[^\w\s-]', '', value).strip().lower())
-        return re.sub('[-\s]+','-',value)
-
-    def extendMarkdown(self, md, md_globals):
-        tocext = TocTreeprocessor(md)
-        tocext.config = self.config
-        md.treeprocessors.add("toc2", tocext, "_begin")
-
-def makeExtension(configs={}):
-    return Toc2Extension(configs=configs)
diff --git a/website/raw/100212_BE_Score.png b/website/raw/100212_BE_Score.png
deleted file mode 100644
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diff --git a/website/raw/FAQ.mkdown b/website/raw/FAQ.mkdown
deleted file mode 100644
index 18cdb1afaf32c3da6e0d2d1d5a0053224221cd03..0000000000000000000000000000000000000000
--- a/website/raw/FAQ.mkdown
+++ /dev/null
@@ -1,28 +0,0 @@
-title: FAQ - Frequently Answered Questions
-
-#FAQ - Frequently Answered Questions
-
-**Which licensing does Openstructure come with?**  
-
-Openstructure is released under GNU-LGPL license 
- 
-**Why another molecular Viewer?**  
-
-Openstructure is not aiming to be a Viewer, but more a molecular modelling platform, a toolkit. It features nice graphics, though!  
-
-**How do I load all PDB files in a directory?**
-
-The python glob module can be used to match files in a certain directory against a glob pattern. Then use LoadPDB as you normally would.
-
-    ::::python
-    import glob
-    pdbs=[]
-    for pdb_file in glob.glob(os.path.join(dir_path, '*.pdb')):
-      pdbs.append(io.LoadPDB(os.path.join(dir_path, pdb_file)))
-
-**How do I load a crappy PDB file?**
-
-The easiest way is to use the `fault_tolerant` option of LoadPDB. If you set the value to true, it will load the structure and just skip erroneus records:
-
-    ::::python
-    ent=io.LoadPDB('pdb_with_errors.pdb', fault_tolerant=True)
\ No newline at end of file
diff --git a/website/raw/ack.mkdown b/website/raw/ack.mkdown
deleted file mode 100644
index 8a33b4bbdab8d985ccd66fa9ff3f4c79d9d19669..0000000000000000000000000000000000000000
--- a/website/raw/ack.mkdown
+++ /dev/null
@@ -1,32 +0,0 @@
-title: Acknowledgements
-
-# Acknowledgements
-
-Several people have been involved in the development and design of OpenStructure.
-
-## Core Development Team
-
-In alphabetical order:
-
- * *Marco Biasini      [1]*
- * *Juergen Haas       [1,2]*
- * *Valerio Mariani    [1,2]*
- * *Ansgar Philippsen* 
- * *Andreas Schenk     [3]*
- * *Stefan Scheuber    [1,2]*
-
-## Testing
-
- * *Tobias Schmidt     [1,2]* 
- * *Pascal Benkert     [1,2]*
- 
-
- [1] Swiss Institute of Bioinformatics, Basel, Switzerland  
- [2] Biozentrum University of Basel, Basel, Switzerland  
- [3] Department of Cell Biology, Harvard Medical School, Boston, MA, USA
-
-
-## Financial Support
-
-<a target="extern" href="http://www.isb-sib.ch/"><img alt="Swiss Institute of Bioinformatics" src="http://www.isb-sib.ch/images/stories/SIBlogo/sib_logoq_low.jpg" width="200" height="120"> </img></a>
-<a target="extern" href="http://www.biozentrum.unibas.ch"><img alt="Biozentrum" src="http://www.biozentrum.unibas.ch/logos101007/bio115_257.gif"> </img></a>
diff --git a/website/raw/contact.mkdown b/website/raw/contact.mkdown
deleted file mode 100644
index 9a67822ef330e46a7441d593b91ab9a1b6c01530..0000000000000000000000000000000000000000
--- a/website/raw/contact.mkdown
+++ /dev/null
@@ -1,16 +0,0 @@
-title: Contact
-
-# Contact 
-
-## Community
-
-For general user inquiries and support: [openstructure-users mailing list](https://www.maillist.unibas.ch/mailman/listinfo/openstructure-users)
-
-Where the developers of OpenStructure discuss new features: [openstructure-devel mailing list](https://www.maillist.unibas.ch/mailman/listinfo/openstructure-devel) 
-
-## Address
-Prof. Torsten Schwede  
-SIB Swiss Institute of Bioinformatics  
-Biozentrum University of Basel  
-Klingelbergstrasse 50/70  
-CH-4056 Basel / Switzerland  
\ No newline at end of file
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diff --git a/website/raw/docs/compile.mkdown b/website/raw/docs/compile.mkdown
deleted file mode 100644
index 56fe8da3b9d7d7524e065f67eb1f17120bd568f4..0000000000000000000000000000000000000000
--- a/website/raw/docs/compile.mkdown
+++ /dev/null
@@ -1,90 +0,0 @@
-title: Compiling and Building
-
-[TOC]
-
-# Compiling and Building OpenStructure
-
-## Installing the Dependencies
-
-OpenStructure uses a bunch of OpenSource libraries. If you haven't already installed them, please install them now!
-
- * [CMake][cmake]
- * [Eigen2](http://eigen.tuxfamily.org/)
- * [Boost](http://boost.org)
- * [libpng](http://www.libpng.org/)
- * [Python](http://python.org)
- * [Qt](http://qt.nokia.com/)
-
-When you enable support for image processing, you will need:
-
- * [FFTW3](http://fftw.org). By default, OpenStructure is compiled with single precision and thus also requires FFTW to be compiled with single precision. Most platforms offer this as a second package. If you are compiling manually, use the `--enable-single` option.
-
- * [libtiff](http://www.libtiff.org)
-
-
-
-If you would like to use the graphical user interface, also install:
-
- * [SIP](http://www.riverbankcomputing.co.uk/software/sip/download)
- * [PyQt4](http://www.riverbankcomputing.co.uk/software/pyqt/download)
-
-In case you are compiling under Windows you have to install [Visualstudio
-2008](http://www.microsoft.com/express/Downloads/) to compile the dependecies and
-OpenStructure. We recommend to compile the dependecies manually.
-Enter the directories where the dependencies are located in Tools->Options->Projects and Solutions->VC++
-directories. Choose 'bin' directories to enter program paths to cmake, qmake and python,
-'lib' directories to point to the location(s) of your dependencies.
-
-## Checking out the Source
-
-You can checkout the source from SVN. The repository is located at
-
-   https://ost.biozentrum.unibas.ch/svn/openstructure/trunk
-
-If you are using the commandline client, type in your shell 
-
-   svn co https://ost.biozentrum.unibas.ch/svn/openstructure/trunk
-
-On Windows install svn clients like [tortoisesvn](http://tortoisesvn.tigris.org/) and use the function 'checkout' then enter the above mention URL.
-
-
-## Configuring
-
-OpenStructure uses [CMake][cmake] for compiling and building the project. The next required step is to configure the build environment using cmake. You can do that by invoking `cmake` in the project directory (On Windows choose Tools->visualstudio commandline prompt from within visualstudio) :
-
-    cmake . <options>
-
-There are two kinds of options: Options that let you control the building behaviour, enabling and disabling the compilation of certain modules and options that let you tell CMake where to find the dependencies. All of them are passed to CMake with via `-D<opt>=<value>`.
-
-### Flag to choose build system
-
-On Windows make sure you specify -G"Visual Studio 9 2008"!
-
-### Flags that control the dependencies
-
-By default, [CMake] searches the standard directories for dependencies. However, on some systems, this might not be enough. Here is a short description of how CMake figures out what dependencies to take and how you can influence it.
-
- * Boost is mainly controlled via the `BOOST_ROOT` option. If boost wasn't found, it should be set to the prefix of the boost installation.
-
- * `QT_QMAKE_EXECUTABLE` defines the exact Qt installation to take. It should be set to the full path to ``qmake`.
- 
- * `PYTHON_ROOT` is the Python equivalent of BOOST_ROOT. It should be set to the prefix path containing the python binary, headers and libraries.
-
- * `SYS_ROOT` controls the general prefix for searching libraries and headers. By default, it is set to `/`.
-
-### Flags that control the build
-
- * `ENABLE_UI` controls whether to build the graphical user interface module. By default it is set to true. 
- * `ENABLE_IMG` controls whether to build the image processing module. This will enable support for density maps, and general image processing in 1, 2 an 3 dimensions. By default it is set to true. 
- * `ENABLE_GFX` controls whether to build the graphics module. By default, this is set to true. If set to none, this implies `ENABLE_UI=NO`.
- * Shader support is controlled with `USE_SHADER`. By default, no shaders are used.
- * If `OPTIMIZE` is set to 1, an optimized version of OpenStructure is built.
-
-## Building the project
-
-Type `make`. If you are using a multi-core machine, you can use the `-j` flag to run
-multiple jobs at once.
-
-On Windows run 'Build OpenStructure' from the build menu.
-
-[CMake]: http://cmake.org
diff --git a/website/raw/docs/examples.mkdown b/website/raw/docs/examples.mkdown
deleted file mode 100644
index 71e660b483342780242fff07b40db231d8947f91..0000000000000000000000000000000000000000
--- a/website/raw/docs/examples.mkdown
+++ /dev/null
@@ -1,34 +0,0 @@
-title: Examples
-[TOC]
-# Examples
-
-Below you find a list of examples that should illustrate various aspects of interaction with OpenStructure itself and proteins in particular. Feel free to browse the [alphabetical examples list](dox/html/examples.html).
-
-## Examples by Topic
-
-### Graphics
- * ex[load_and_display.py|Loading And Displaying an Entity]
- * ex[rendermodes.py|Render Modes]
- * ex[primitives.py|Adding Lines and Quads] | ex[random_lines.py|Random Lines]
- * ex[bbox.py|Displaying a Bounding Box]
- * ex[gfx_symmetry.py|Drawing Symmetry Equivalents]
- * ex[gradient.py|Gradients]
- * ex[gfx_selection.py|Graphical Selection]
- * ex[color_by_property.py|Color Entity By Property]
- 
-### GUI
- * ex[menubar_example.py|Adding a Menu]
- * ex[color_tool.py|Write a Tool in Python]
- * ex[widget_example.py|Add a custom Widget]
- * ex[mdi_example.py|Add a Widget to MDI]
- 
-### Molecular Entities
- * ex[roll_helix.py|Modifying Protein Backbone Torsion Angles] 
- * ex[bbox.py|Calculating an Oriented Bounding Box]
-
-### Image Processing
- * ex[create_split_image.py|Creating a Split Image from Several Images]
- * ex[fft_li.py|Load Images and Show Fourier Transforms]
- * ex[modulate_image.py|Load and Modulate Image by a Sine]
- * ex[spoke_pattern.py|Create a Spoke Pattern Image]
- * ex[view_phase_diff.py|Display Phase Difference of Two Images]
\ No newline at end of file
diff --git a/website/raw/docs/index.mkdown b/website/raw/docs/index.mkdown
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-title: Documentation
-[TOC]
-# Documentation
-
-## New to OpenStructure?
-
-Newcomers might want to have a look at our gentle [introduction to the framework](docs/tut/intro.html) and the [features list](features.html). 
-
-For a conceptual overview of the framework, we have prepared a few [tutorials](docs/tutorials.html). You can also find [code examples](docs/examples.html) with a short description.
-
-
-## For Those Who Know
-
-The following links provide direct access to the API documentation.
-
-### Molecular Structures
- * dox[ost::mol::EntityHandle|EntityHandle] | dox[ost::mol::EntityView|EntityView] | [Queries](dox/html/query.html) | [Conop](dox/html/module_conop.html)
-
-### Sequence
-
- * [Overview](dox/html/module_seq.html)
-
-### Reading and writing files
-
- * [io](dox/html/module_io.html)
-
-### Graphics
-
- * dox[ost::gfx::Scene|Scene] | [Graphical Entity](dox/html/gfx_ent.html)
-
-### Image Manipulation
-
-
- * dox[ost::img::ImageHandle|ImageHandle] 
-
-### Global Data Structure Index
- * [Data Structure index](dox/html/classes.html)
-
-
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-title: Using External Programs within OpenStructure
-
-[TOC]
-
-# Using External Programs within OpenStructure
-
-## Introduction
-It is often very useful to use external programs to do a specific task. In principle, this can be done by writing out files from OpenStructure and manually running an external program, however, for convenience, this can also be done directly from within OpenStructure using Python commands. 
-
-This tutorial will give you some hints how to do this for a new external program. The process basically consists of four steps:
-
-  * locate the executable of the external program
-  * prepare all necessary files
-  * execute the external program from python
-  * read in generated output
-  
-All existing bindings to external programs are placed under ost::bindings. 
-
-## Locating the Executable
-There is a helper function available to locate files. It can be found at ost::settings::Locate(). Using this, you can obtain the full path of an executable.
-
-As an example, we would like to obtain the full path of the msms executable (a program to calculate molecular surfaces):
-
-    ::::python
-    from ost import settings
-    exe_path=settings.Locate('msms', search_paths=['/opt/app','/home/app'],
-                env_name='MSMS', search_system_paths=True)
-    print exe_path
-
-The Locate command looks for the program with the name 'msms'. If env_name is set, it first looks if an environment variable with the name 'MSMS' is set. If not, all paths in search_paths are searched. If the executable could still not be found and search_system_paths is set to True, the binary search paths are searched.
-If the executable could not be found, a FileNotFound exception is raised with a detailed description where Locate was searching for the executable.
-    
-## Prepare All Files
-The preparation of the necessary files is very dependent on the external program. Often it is useful to generate a temporary directory or file. For this, the python module tempfile is very handy.
-
-An example how to generate a temporary directory, open a file in this directory and write the position and radius of all atoms into this file is shown here:
-
-    ::::python
-    import tempfile
-    import os
-    
-    # generate a temporary directory
-    tmp_dir_name=tempfile.mkdtemp()
-    print 'temporary directory:',tmp_dir_name
-    
-    # generate and open a file in the temp directory
-    tmp_file_name=os.path.join(tmp_dir_name,"entity")
-    tmp_file_handle=open(tmp_file_name, 'w')
-    print 'temporary file:',tmp_file_handle
-    
-    # write position and radius of all atoms to file
-    for a in entity.GetAtomList():
-      position=a.GetPos()
-      tmp_file_handle.write('%8.3f %8.3f %8.3f %4.2f\n' % (position[0],
-                            position[1], position[2], a.GetProp().radius))
-                            
-    # close the file
-    tmp_file_handle.close()
-
-## Execute the External Program
-The external program can be executed from python using the python module subprocess.
-
-To run the external program msms from the above example, with the temporary file generated before, we can use the following:
-
-    ::::python
-    import subprocess
-    
-    # set the command to execute
-    command="%s -if %s -of %s" % (exe_path,
-              tmp_file_name, tmp_file_name)
-    print 'command:',command
-    
-    # run the executable with the command
-    proc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
-    stdout_value, stderr_value = proc.communicate()
-
-    #check for successful completion of msms
-    if proc.returncode!=0:
-      print "WARNING: msms error\n", stdout_value
-      raise subprocess.CalledProcessError(proc.returncode, command)
-
-    # print everything written to the command line (stdout)
-    print stdout_value
-    
-## Read Generated Output
-The last step includes reading of generated files (like in the case of msms) and/or processing of the generated command line output.
-
-Here we first print the command line output and then load the generated msms surface and print the number of vertex points:
-
-    ::::python
-    # print everything written to the command line (stdout)
-    print stdout_value
-    
-    # read msms surface from file
-    surface=io.LoadSurface(tmp_file_name, "msms")
-    print 'number of vertices:',len(surface.GetVertexIDList())
diff --git a/website/raw/docs/tut/genericprop.mkdown b/website/raw/docs/tut/genericprop.mkdown
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-title: Storing Custom Data in an Entity
-
-[TOC]
-
-# Storing Custom Data in an Entity
-This tutorial will guide you through the use of GenericProperties to store any custom data inside an Entity.
-
-## Introduction
-It is often very convenient to store any arbitrary data inside an Entity. A few examples are: 
-
-  * calculated properties of atoms
-  * sequence conservation of a residue
-  * interaction energy of a substructure with its surrounding
-  * fit of a fragment inside an electron density map
-
-In OpenStructure this is supported by the use of GenericProperties. Most building blocks are a dox[ost::GenericPropertyContainer|GenericPropertyContainer], meaning that arbitrary key-value pairs can be stored in them, namely:
-
-  * EntityHandle and EntityView
-  * ChainHandle and ChainView
-  * ResidueHandle and ResidueView
-  * AtomHandle and AtomView
-  * BondHandle
-
-The view variants will reflect the generic properties of the handle variants.
-
-A generic property key is always a String, and a value can be one of String, Real, int or bool. For each of these data types, methods to retrieve and store values are available both in Python and C++.
-
-## Storing and Accessing Data
-
-All OpenStructure building blocks that are GenericPropertyContainers, have four different methods to store generic data, depending on the data type (i.e. String, Float, Int or Bool).
-
-To store a float value with the key 'myfloatprop' in all atoms of an entity:
-
-    ::::python
-    import math
-    for atom in entity.GetAtomList(): 
-      val=5*math.sin(0.4*atom.GetPos().GetX())
-      atom.SetGenericFloatProperty("myfloatprop", val)
-
-If a GenericProperty at a given level (i.e. atom, bond, residue, chain or entity) already exists, it will be overwritten. To check if it exists, use:
-
-    ::::python
-    exists=atom.HasGenericProperty("myfloatprop")
-    print exists
-    
-To access the value of a GenericProperty, we first check if the property exists and then access it, using the method suitable for the data type of the property. For the previously set property "myfloatprop" of the data type Real, at the atom level:
-
-    ::::python
-    for atom in entity.GetAtomList(): 
-      if atom.HasGenericProperty("myfloatprop"):
-        print atom.GetGenericFloatProperty("myfloatprop")
-        
-When trying to access a property that has not been set, or one that has been set, but at a different level, an error is thrown. The same is true when trying to access a property of a different data type, e.g.:
-
-    ::::python
-    # all of the following lines will throw errors
-    # error because the property does not exist 
-    print atom.GetGenericFloatProperty("unknownprop")
-    
-    # error because the property was set at another level
-    print entity.GetGenericFloatProperty("myfloatprop")
-    
-    # error because the data type of the property is different
-    print atom.GetGenericStringProperty("myfloatprop")
-    
-For more details see dox[ost::GenericPropertyContainer|GenericPropertyContainer].
-
-## Use of GenericProperties in Queries
-
-The [query language](docs/tut/query.html) can also be used for numeric generic properties (i.e. GenericFloatProperty and GenericIntProperty), but the syntax is slightly different. To access any generic properties, it needs to be specified that they are generic and at which level they are defined. Therefore, all generic properties start with a 'g', followed by an 'a', 'r' or 'c' for atom, residue or chain level respectively. For more details [see documentation](dox/html/query.html#gen_prop). 
-
diff --git a/website/raw/docs/tut/gui.mkdown b/website/raw/docs/tut/gui.mkdown
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-title: Graphical User Interface
-
-[TOC]
-
-# Graphical User Interface
-
-The GUI of OpenStructure is designed to be intuitive, flexible and extensible. Most of the widgets are organized in a big main window which is divided into four parts: the main area and three panels containing one or more smaller widgets:
-  
-![Openstructure UI](docs/tut/100208_OpenStructure_UI_Colored.png "Openstructure user interface")
-   
-The panels primarily contains widgets interacting with the 3D window.
-All parts of the GUI are exported to Python and can be expanded with C++ Qt widgets as well as with PyQt widgets.
-
-## SceneWin
-The scene win holds a list of all graphical objects currently registered to the  dox[ost::gfx::Scene|scene].
-  
-![Scene Win](docs/tut/100208_Scene_Win.png "Openstructure Scene Win")
-   
-Every node of the graphical scene tree is shown as a subnode of the scene. It is possible to select one or more objects in the scenewin (ctrl+ left mouse click). The available actions of the context menu are applied to all currently selected objects.
-
-## Inspector Gadget
-With our Inspector Gadget it is straightforward to modify rendering and coloring options of scene objects without using the keyboard:
- 
-![Inspector Gadget](docs/tut/100208_Inspector_Gadget.png "Inspector Gadget")
-   
-The render and coloring options affect only the currently selected objects of the scene win. The Shortcut "Ctrl+I" toggles the visibility of the inspector.
-
-## Tools
-OpenStructure has several dox[ost::gui::Tool|tools] which are all listed in the toolbar close to the 3D window. A tool is activated upon selecting it in the toolbar. Input events are sent to the tool as long as the `Ctrl` key (`Cmd` on Mac) is pressed. For example the rigid body manipulator will rotate and shift the currently selected nodes in the scene win. Upon releasing `Ctrl`, the events are sent to the camera, making it possible to rapidly switch between adjusting the viewing angle of the camera and manipulating the position and orientation of scene objects.
- 
-![Tools](docs/tut/100208_Tools.png "Tools")  
- 
-The example ex[color_tool.py|Write a Tool in Python] demonstrates how to add a simple tool (written in python) to OpenStructure.
-
-## Drag and Drop support
-The user interface of OpenStructure supports drag and drop events. Every file format that is supported by Openstructure can be opened by dragging and dropping it on the main window. When a python script (ending with .py) is being dropped on the UI, the script will be executed. For any other file type (for example PDB files, images and density maps), OpenStructure will try to load the file and either display in the 3D window or in the data viewer for images.
-
-## Python Shell
-OpenStructure has a integrated python shell which allows you interactively enter Python commands. Learn more about it in the [Python Shell tutorial](docs/tut/pythonshell.html).  
-
-## The Side Panels
-
-### View Modes
-Each dox[ost::gui::PanelBar|side panel] can have different dox[ost::gui::PanelWidgetContainer|view modes]. View modes can display the widgets which are held by the Side Panel in a different style. Every panel has the splitter and the tabbed view mode. The view mode can be changed in the Window menu of the Menubar.
-
-### Drag and Drop
-The widgets which are held by a Side Panel can be moved to an other position in the panel or even to another side panel. The widget can be moved by simply clicking on the border of the widget and drag and drop it to the desired position. The drag and drop feature is currently only supported by the splitter view mode.
-
-### Adding a custom Widget
-The Left-, Bottom- and Right-Panel are organized by one dox[ost::gui::Panels|Superclass]. It is only possible to display a widget which is in the dox[ost::gui::WidgetPool|widget pool] of the panels class. Once a widget is in the pool all the methods of the Panels class can be used to display / hide the widget in any position of the panels.
-The Example ex[widget_example.py|Add a custom Widget] describes, how to add a fancy PyQt Widget to the widget pool and finally display it in the right side bar.
-OpenStructure remembers the size and location of a Widget. So, OpenStructure should look the same after restarting it.
-
-## Main Area
-
-### Adding an own Widget
-The dox[ost::gui::MainArea|main area] is a mdi (multi document interface). Therefore it's possible to display multiple widgets in it. The example ex[mdi_example.py|Add a Widget to MDI] demonstrates how to add a  widget to the MDI area.
-
-## Menubar
-### Adding an new Menupoint
-It is really straightforward to add a custom menupoint. Since the menubar is exported to Python it is even easier to create such e menupoint. See the example ex[menubar_example.py|Adding a Menu] which describes how this is done within python and PyQt.
-
-## Nice to know
-As you might have noticed nearly every gui example needs the dox[ost::gui::GostyApp|gosty app] and the dox[ost::gui::Perspective|perspective] within the code. Gosty app is a singleton class which has getter methods to all important gui classes. The perspective class has all the information about the layout of the whole application, it is accessible over the gosty app instance.  
diff --git a/website/raw/docs/tut/imgalg.mkdown b/website/raw/docs/tut/imgalg.mkdown
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-title: Algorithms for Images and Density Maps
-
-[TOC]
-
-# Algorithms for Images and Density Maps
-
-
-## The Basics
-
-To allow various image manipulation routines that are decoupled from the actual
-image implementations, an extensive set of algorithm base classes is provided to facilitate
-the implementation of novel algorithms.
-
-The 'img' module is using the concept of algorithm objects: In order to apply an algorithm
-to an image, an instance of that particular algorithm class must be created, which
-is then passed to one of the various Apply methods of the dox[ost::img::ImageHandle|ImageHandle] 
-interface. This extends the possibilities of algorithms beyond what is possible with simple
-function calls.
-
-## Algorithm Types
-
-Five different types of algorithms can be identified:
-
-### NonMod
-An algorithm that will not modify the values in the image, but rather gather
-some data. Example: a histogram. Implemented as dox[ost::img::NonModAlgorithm|NonModAlgorithm].
-
-### ModIP
-An algorithm that will modify the image values directly in place; in addition,
-it may choose to write to its internal state during application of the algorithm.
-Implemented as dox[ost::img::ModIPAlgorithm|ModIPAlgorithm]. 
-
-### ConstModIP
-Similar to ModIP, this algorithm will modify the values directly in place.
-However, it does not need to store information itself beyond the application of the algorithm
-itself. Example: setting all image values to zero. Implemented as 
-dox[ost::img::ConstModIPAlgorithm|ConstModIPAlgorithm].
-
-### ModOP
-An algorithm that will return a new, modified version of the image, while
-leaving the original untouched. Again, the algorithm can store information to be available
-after it has been applied. Implemented as dox[ost::img::ModOPAlgorithm|ModOPAlgorithm].
-
-### ConstModOP
-Similar to ModOP, except that no information can be stored beyond the
-application of the algorithm itself. Example: rotation around an arbitrary angle. Implemented
-as dox[ost::img::ConstModOPAlgorithm|ConstModOPAlgorithm].
-
-## Implemented algorithms
-
-A list of implemented algorithms can be found [here](docs/tut/imgalglist.html)
-
-## Custom Algorithms (for developers)
-
-Writing custom algorithms for the 'img' module is fairly straightforward, in view of the fact that the final
-algorithm will integrate seamlessly into the build environment, both at the C++ and Python runtime
-levels. Information on how to write custom algorithms can be found at the
-[Algorithm Tutorial page](docs/tut/imgalgdata.html).
-
-There are two fundamental types of algorithms, those that operate on high level
-ImageHandle instances, [Data Algorithms](docs/tut/imgalgdata.html), and those that
-operate on the low level ImageState instances, [ImageState Algorithms](docs/tut/imgalgdistate.html).
diff --git a/website/raw/docs/tut/imgalgdata.mkdown b/website/raw/docs/tut/imgalgdata.mkdown
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index 23b0bb130eb97169f375b7c7a0ba8bd6038cdeec..0000000000000000000000000000000000000000
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-title: Data Algorithms - An Algorithm Tutorial
- 
-[TOC]
-
-# Data Algorithms - An Algorithm Tutorial
-
-This tutorial shows how to create custom high level dox[ost::img::ImageHandle|ImageHandle] algorithms and
-embed them into the OpenStructure build system. As an example, two very simple algorithm will be written:
-The first will count all values in an image or function that are larger than a certain threshold. Since this
-algorithm only needs to read values, it will be implemented by deriving it from ConstAlgorithm. The second algorithm
-will set all values below a certain threshold to the threshold value; this will be implemented
-using ModIPAlgorithm.
-
-Naming is important. We need a name for the collection (or module) of algorithms, as well as
-a name for each individual one within the collection. For this example, the module name is
-'thres', the first algorithm will be called 'ThresCount', and the second one 'ThresSet'.
-
-The new module will be built following the guidelines on [this page](docs/tut/newmodule.html).
-The information on the linked page will not be repeated here, so it advisable to read it before
-continuing with this tutorial 
-
-In the end, this algorithm module will consist of:
-
-* Two header files, which are staged under 'stage/include/ost/thres' to allow other
-components (such as the unit-tests, the python module, or other algorithms) to utilize
-the module.
-* A shared library called 'libost_thres', which is staged in 'stage/lib' and
-required at run-time.
-* A shared Python object named '_thres.so', which is staged under
-'stage/lib/ost/pymod/ost/thres'.
-* A Python initialization file '\_\_init\_\_.py', which is also staged under
-'/lib/ost/pymod/ost/thres' and is required for the directory 'thres' to be recognized as a
- Python module.
-
-
-## Algorithm Test Setup
-
-Surprising or irritating as it may seem, the first thing on the agenda is the unit
-test for this algorithm, located under 'thres/tests';.
-
-Note 
-:   Tests, and in this particular case unit-test, are an essential component of any
-modern software development effort. They not only ascertain the continued correct
-functionality after refactoring cycles or platform porting, they often consist
-in the first step of writing new code: First you write the test, then you
-implement the functionality. Sounds crazy? Really works! You can call that
-developing in expectancy mode.
-
-### Preparing the Testing Framework
-
-The main testing code is put into 'tests.cc', there is nothing particular to discuss here:
-    
-    :::cpp
-    #include <boost/test/unit_test.hpp>
-    using boost::unit_test_framework::test_suite;
-
-    #include "test_thres_count.hh"
-    #include "test_thres_set.hh"
-
-    test_suite*
-    unit_unit_test_suite( int argc, char * argv[] ) {
-      std::auto_ptr<test_suite> test(BOOST_TEST_SUITE( "Module thres Test" ));
-
-      test->add(CreateThresCountTest()); 
-      test->add(CreateThresSetTest()); 
-
-      return test.release(); 
-    }
-
-        
-The factory function declaration for the counting algorithm is put into 'test\_thres\_count.hh':
-
-    :::cpp
-    #ifndef OST_THRES_TEST_COUNT_H
-    #define OST_THRES_TEST_COUNT_H
-
-    #include <boost/test/unit_test.hpp>
-    using boost::unit_test_framework::test_suite;
-
-    test_suite* CreateThresCountTest();
-
-    #endif
-    
-And the one for the threshold setting algorithm is put into 'test\_thres\_set.hh':
-
-    :::cpp
-    #ifndef OST_THRES_TEST_SET_H
-    #define OST_THRES_TEST_SET_H
-
-    #include <boost/test/unit_test.hpp>
-    using boost::unit_test_framework::test_suite;
-
-    test_suite* CreateThresSetTest();
-
-    #endif
-
-
-## Writitng the UnitTests
-
-Now lets fill in the actual algorithm usage code. First, the declaration of the
-algorithm needs to be included from its header. These are the two 'include'
-statements we want to add, along with the 'namespace' code:
-
-    :::cpp
-    #include <ost/img/image.hh>
-    #include <ost/thres/thres_count.hh>
-
-    using namespace ost::img;
-    using namespace ost::thres;
-    
-    
-The first 'include' line and the 'ost::img' 'namespace' directive are needed
-for creating and handling an ImageHandle. They use elements which are part of
-the standard OpensStructure distribution. The others lines are required for our
-particular algorithm class.
-
-Note
-:   Neither the file 'thres\_count.hh' exists yet nor the namespace 'thres'.
-Remember, this is coding in expectency mode, ie we expect the algorithm to be
-used in this way.
-
-Next, the testing routine. As a first thing, an image needs
-to be created, with which the functionality of the algorithm can be tested:
-
-    :::cpp
-    ImageHandle ih = CreateImage(Extent((Size(4,4))));
-
-The factory method CreateImage() from the standard OpenStructure
-distribution takes care of this. The dox[ost::img::ImageHandle|ImageHandle]
-'ih' now referes to a 4x4 real, spatial image, with all values set to zero. To
-populate the image with values, the following code is used:
-
-    :::cpp
-    double v=0.0;
-    for(ExtentIterator(ih.GetExtent()); !it.AtEnd(); ++it) {
-      ih.SetReal(it, v);
-      v+=1.0;
-    }
-
-Now the algorithm object of our ThresCount class is created.
-
-    ThresCount thres_count(5.0);
-
-Note
-:   Again, this is in expectancy mode: We want to have an algorithm that uses a
-threshold, and it makes only sense that this threshold is given upon instantiation;
-we will need to remember this once we implement the constructor.
-As the next step, the algorithm is applied to the image, using the appropriate
-method from dox[ost::img::ImageHandle|ImageHandle]:
-
-    :::cpp 
-    ih.Apply(a);
-
-Finally the test: since the values in the image were consecutively set from 0.0
-to 15.0, what is the expected outcome of the algorithm? In the above description,
-it says "counts all values larger than a given threshold". In this case particular
-test case this means all values above 5.0, so the expected count is 10.
-
-To retrieve the count, the algorithm object requires some sort of getter method,
-which we expect to be called 'GetCount()'. This is combined with the 'boost::test'
-facility macro to see if the algorithm worked:
-
-    :::cpp
-    BOOST_CHECK(a.GetCount()==10);
-
-That's it.
-
-Here is the finished file 'test\_thres\_count.cc'.
-
-    :::cpp
-    #include "test_thres_count.hh"
-
-    #include <ost/img/image.hh>
-    #include <ost/thres_count.hh>
-    using namespace ost::img;
-    using namespace ost::thres;
-
-    namespace test_thres_count {
-
-      void test() 
-      {
-        ImageHandle ih = CreateImage(Extent((Size(4,4))));
-
-        double v=0.0;
-        for(ExtentIterator it(ih.GetExtent()); !it.AtEnd(); ++it) {
-          ih.SetReal(it, v);
-          v+=1.0;
-        }
-      ThresCount thres_count(5.0);
-
-      ih.Apply(thres_count);
-
-      BOOST_CHECK(thres_count.GetCount()==10);
-      }
-
-    }
-
-    test_suite* CreateThresCountTest()
-    {
-      using namespace test_thres_count;
-      test_suite* ts=BOOST_TEST_SUITE("ThresCount Test");
-
-      ts->add(BOOST_TEST_CASE(&test));
-
-      return ts;
-    }
-
-The test for 'ThresSet' algorithm is build in a similar way. A test image is setup, and the
-initialization of the algorithm should also accept the threshold value to be used:
-
-    :::cpp
-    ImageHandle ih = CreateImage(Extent((Size(4,4))));
-
-    double v=0.0;
-    for(ExtentIterator it(ih.GetExtent()); !it.AtEnd(); ++it) {
-      ih.SetReal(it, v);
-      v+=1.0;
-    }
-
-    ThresCount thres_set(5.0);
-
-    ih.ApplyIP(thres_set);
-  
-Note
-:   There are two posibilities to apply this algorithm to the image: in-place
-(used here) and out-of-place. This works even though the ThresSet algorithm itself
-is implemented in-place. What is the expected outcome of applying the algorithm?
-The description above said: "will set all values below a certain threshold to
-the threshold value". Therefore there should not be a value below 5.0 in the image:
-
-    :::cpp
-    for(ExtentIterator it(ih.GetExtent()); !it.AtEnd(); ++it) {
-      BOOST_CHECK(ih.GetReal(it)>=5.0);
-    }
-
-Here is the final test file 'test\_thres\_set'.cc:
-
-    :::cpp
-    #include "test_thres_set.hh"
-
-    #include <ost/img/image.hh>
-    #include <ost/thres/thres_set.hh>
-    using namespace ost::img;
-    using namespace ost::thres;
-
-    namespace test_thres_set {
-
-      void test() 
-      {
-        ImageHandle ih = CreateImage(Extent((Size(4,4))));
-
-        double v=0.0;
-        for(ExtentIterator it(ih.GetExtent()); !it.AtEnd(); ++it) {
-          ih.SetReal(it, v);
-          v+=1.0;
-        }
-
-        ThresSet thres_set(5.0);
-
-        ih.ApplyIP(thres_set);
-
-        for(ExtentIterator it(ih.GetExtent()); !it.AtEnd(); ++it) {
-          BOOST_CHECK(ih.GetReal(it)>=5.0);
-        }
-      }
-    }
-
-    test_suite* CreateThresSetTest()
-    {
-      using namespace test_thres_set;
-      test_suite* ts=BOOST_TEST_SUITE("ThresSet Test");
-
-      ts->add(BOOST_TEST_CASE(&test));
-
-      return ts;
-    }
-
-Obviously, all files need to be added to the 'CMakeLists.txt' file in 'thres/tests.'
-Also, all the module dependencies must be added. In our example the dependencies are
-the 'ost\_img' and 'ost\_img\_alg' module, plus the 'ost\_thres' moudle itself.
-
-## Coding Algorithm
-
-After so much expecting and looking into the future, this is the part where the
-actual algorithm gets implemented. The CMake building script will also be setup to place the
-headers and library files at the right location, so thay they are found by the unit tests.
-
-In the 'thes/src' directory, let's add the header and source files for the two algorithms.
-
-Here is 'thres\_count.hh:
-
-    :::cpp 
-    #ifndef OST_TRES_THRES_COUNT_H
-    #define OST_TRES_THRES_COUNT_H
-
-    #include <ost/img/algorithm.hh>
-  
-    namespace ost { namespace thres {
-
-      class ThresCount: public NonModAlgorithm
-      {
-       public:
-        ThresCount(Real thres);
-
-        // retrieve count
-        int GetCount() const;
-
-        // algorithm interface
-        virtual void Visit(const ConstImageHandle& i);
-        virtual void Visit(const Function& f);
-
-       protected:
-        void VisitData(const Data& d);
-
-       private:
-        Real thres_;
-       int count_;
-      };
-
-    }} // namespaces
-
-    #endif
-
-And here is 'thres\_count.cc':
-
-    :::cpp
-    #include "thres_count.hh"
-
-    using namespace ost::img;
-    using namespace ost::thres;
-
-    ThresCount::ThresCount(Real thres):
-      NonModAlgorithm("ThresCount"),
-      thres_(thres),
-      count_(0)
-    {}
-
-    void ThresCount::Visit(const ConstImageHandle& i)
-    {
-      // reroute to generic method
-      VisitData(i);
-    }
- 
-    void ThresCount::Visit(const Function& f)
-    {
-      // reroute to generic method
-      VisitData(f);
-    }
-
-    void ThresCount::VisitData(const Data& d)
-    {
-      count_=0; // make sure count is reset for each visit
-      for(ExtentIterator it(d.GetExtent()); !it.AtEnd(); ++it) {
-        if(d.GetReal(it)>thres_) {
-          ++count_;
-        }
-      }
-    }
-
-    int ThresCount::GetCount() const
-    {
-      return count_;
-    }
-
-Note
-:   The polymorphic separation into  'dox[ost::img::ConstImageHandle|ConstImageHandle]' and
-'Function' is not utilized in this example, since both 'Visit()' methods just call
-'VisitData()' to perform the actual calculation. The method body of 'VisitData()'
-is the actual algorithm implementation, using the private member variables 'thres\_'
-and 'count\_'.
-
-Here is the 'thres\_set.hh' file:
-
-    :::cpp  
-    #ifndef OST_THRES_THRES_SET_H
-    #define OST_THRES_THRES_SET_H
-
-    #include <ost/img/algorithm.hh>
-
-    namespace ost { namespace thres {
-
-      class ThresSet: public ModIPAlgorithm
-      {
-       public:
-        ThresSet(Real thres);
-
-        // algorithm interface
-        virtual void Visit(ImageHandle& i);
-
-       private:
-        Real thres_;
-      };
-
-    }} // namespaces
-
-    #endif
-
-
-And here is 'thres_set.cc':
-
-    :::cpp
-    #include "thres_set.hh"
-
-    using namespace ost::img;
-    using namespace ost::thres;
-
-    ThresSet::ThresSet(Real thres):
-     ModIPAlgorithm("ThresSet"),
-     thres_(thres)
-    {}
-
-    void ThresSet::Visit(ImageHandle& i)
-    {
-      for(ExtentIterator it(i.GetExtent()); !it.AtEnd(); ++it) {
-        if(i.GetReal(it)<thres_) {
-          i.SetReal(it,thres_);
-        }
-      }
-    }
-
-Once again, all the files must be added to the 'CMakeLists.txt' file, this time in
-'thres/src'. This will make sure that all the headers and the newly created shared libraries
-are staged correctly. The 'DEPENDS ON' directive in the file should include the 'img'
-and 'img_alg' modules, since those are the modules 'thres' depends on.
-
-## Python Wrapper
-
-Finally, let's export both both 'ThresCount' and 'ThresSet' to Python, as part of
-the 'thres' module. Let's put the following 'wrap\_thres.cc' file in the 'src/pymod' directory 
-
-    :::cpp
-    #include <boost/python.hpp>
-    using namespace boost::python;
-
-    #include <ost/thres/thres_count.hh>
-    #include <ost/thres/thres_set.hh>
-
-    using namespace ost::img;
-    using namespace ost::thres;
-
-    BOOST_PYTHON_MODULE(_tres)
-    {
-      class_<ThresCount, bases<NonModAlgorithm> >("ThresCount", init<Real>() )
-        .def("GetCount", &ThresCount::GetCount)
-      ;
-  
-      class_<ThresSet, bases<ModIPAlgorithm> >("ThresSet", init<Real>() )
-      ;
-    }
-
-After adding the 'wrap_thres.cc' file to the 'CMakeLists.txt' file in 'thres/pymod, let's also put the
-following '\_\_init.py\_\_' file in the same directory:
-
-    :::python
-    from _thres import *
- 
-The next time that the OpenStructure project will be compiled, the headers, the shared libraries and
-the python modules from the new 'thres' module wil be staged and the two new Image algorithms will be made available
-in both Python and C++.
-    
-    
-
-
-
-
-
diff --git a/website/raw/docs/tut/imgalgdistate.mkdown b/website/raw/docs/tut/imgalgdistate.mkdown
deleted file mode 100644
index 1b544b8c3ac001c6f98c50a931f0e6e83bf882c9..0000000000000000000000000000000000000000
--- a/website/raw/docs/tut/imgalgdistate.mkdown
+++ /dev/null
@@ -1,51 +0,0 @@
-title: Image State Algorithms
-
-[TOC]
-
-# Image State Algorithms
-
-## Overview
-
-In order to allow fast access to the low level image state implementation, the
-data algorithms are complemented by a similar concept, namely image state algorithms.
-
-Analogous to the image state implementation, each of the different image state
-algorithms is composed of a double template combination, specifying the data type
-(real or complex) and the domain (spatial, frequency or half-frequency). And
-analogous to the data algorithm, there are different algorithms dependent on the
-purpose of the algorithm to be implemented: non-modifying, in-place modifying and
--of-place modifying.
-
-In should be pointed out the the image state algorithms are really a hybrid
-concept, as they may be used as normal data algorithms as well !
-
-A class with a specific structure is required that is later used as a template
-parameter. The exact syntax is dependent on the type of algorithm. The minimal
-interface comprises two methods: a ding VisitState(), and a (possibly static)
-GetAlgorithmName(). Additional methods may be added, in particular a destruct or
-and/or special constructors.
-
-## Example of ImageState algorithm
-
-This is an example of a NonMod algorithm
-
-    :::pp
-    class MyAlgorithmFnc
-    {
-     public:
-      MyAlgorithmFunc();
-  
-      // other ctors
-
-      // entry point for image state visitor
-      template<typename T, class D>
-      void VisitState(const img::image_state::ImageStateImpl<T,D>& isi);
-
-      // entry point for function visitor
-      void VisitFunction(const Funcion& f);
-
-      // name of algorithm
-      static string GetAlgorithmName();
-
-      // other methods may follow here
-     };
diff --git a/website/raw/docs/tut/imgalglist.mkdown b/website/raw/docs/tut/imgalglist.mkdown
deleted file mode 100644
index 6d52a91969f32fb077ecdfb5caf1308b0c3ba538..0000000000000000000000000000000000000000
--- a/website/raw/docs/tut/imgalglist.mkdown
+++ /dev/null
@@ -1,82 +0,0 @@
-title: List of image algorithms
-
-[TOC]
-
-# List of image algorithms
-
-## General Algorithms
-
-* dox[ost::img::alg::Clear|Clear]
-* dox[ost::img::alg::Fill|Fill]
-* dox[ost::img::alg::Stat|Stat]
-* dox[ost::img::alg::StatMinMax|StatMinMax]
-* dox[ost::img::alg::Negate|Negate]
-* dox[ost::img::alg::Polar|Polar]
-* dox[ost::img::alg::Randomize|Randomize]
-* dox[ost::img::alg::AutoCorrelate|AutoCorrelate]
-* dox[ost::img::alg::Conjugate|Conjugate]
-* dox[ost::img::alg::Convolute|Convolute]
-* dox[ost::img::alg::Correlate|Correlate]
-* dox[ost::img::alg::CrossCorrelate|CrossCorrelate]
-* dox[ost::img::alg::HighestPeakSearch3D|HighestPeakSearch3D]
-* dox[ost::img::alg::Histogram|Histogram]
-* dox[ost::img::alg::RsCrosscorr|RsCrosscorr]
-* dox[ost::img::alg::LineAverage|LineAverage]
-* dox[ost::img::alg::LineIterator|LineIterator]
-
-## Fourier Transforms
-
-* dox[ost::img::alg::FFT|FFT]
-* dox[ost::img::alg::DFT|DFT]
-* dox[ost::img::alg::PowerSpectrum|PowerSpectrum]
-
-
-## Transformations
-
-* dox[ost::img::alg::Mirror|Mirror]
-* dox[ost::img::alg::Shift|Shift]
-* dox[ost::img::alg::Transform|Transform]
-* dox[ost::img::alg::FractionalShift|FractionalShift]
-* dox[ost::img::alg::DiscreteShrink|DiscreteShrink]
-
-
-## Masking
-
-* dox[ost::img::alg::MaskImage|MaskImage]
-* dox[ost::img::alg::SmoothMaskImage|SmoothMaskImage]
-
-
-## Normalizer
-
-* dox[ost::img::alg::LinearNormalizer|LinearNormalizer]
-* dox[ost::img::alg::LogNormalizer|LogNormalizer]
-* dox[ost::img::alg::ODNormalizer|ODNormalizer]
-
-
-## Thresholding
-
-* dox[ost::img::alg::ClipMinMax|ClipMinMax]
-* dox[ost::img::alg::DensitySlice|DensitySlice]
-* dox[ost::img::alg::Threshold|Threshold]
-* dox[ost::img::alg::LocalSigmaThreshold|LocalSigmaThreshold]
-
-
-## General filters
-
-* dox[ost::img::alg::Anisotropic|Anisotropic]
-* dox[ost::img::alg::Gaussian|Gaussian]
-* dox[ost::img::alg::GaussianGradientMagnitude|GaussianGradientMagnitude]
-* dox[ost::img::alg::GaussianLaplacian|GaussianLaplacian]
-
-
-## High/low pass filters
-
-* dox[ost::img::alg::LowPassFilter|LowPassFilter]
-* dox[ost::img::alg::HighPassFilter|HighPassFilter]
-* dox[ost::img::alg::GaussianLowPassFilter|GaussianLowPassFilter]
-* dox[ost::img::alg::GaussianHighPassFilter|GaussianHighPassFilter]
-* dox[ost::img::alg::FermiLowPassFilter|FermiLowPassFilter]
-* dox[ost::img::alg::FermiHighPassFilter|FermiHighPassFilter]
-* dox[ost::img::alg::ButterworthLowPassFilter|ButterworthLowPassFilter]
-* dox[ost::img::alg::ButterworthHighPassFilter|ButterworthHighPassFilter]
-
diff --git a/website/raw/docs/tut/imgdataviewer.mkdown b/website/raw/docs/tut/imgdataviewer.mkdown
deleted file mode 100644
index bbf902d9f7cccb1bcb6d96f9c073e748afe67e3d..0000000000000000000000000000000000000000
--- a/website/raw/docs/tut/imgdataviewer.mkdown
+++ /dev/null
@@ -1,120 +0,0 @@
-title: Data Viewer
-
-[TOC]
-
-#Data Viewer
-
-## Introduction
-
-The Data Viewer can display a single real or reciprocal space image with adjustable
-contrast. Phases in reciprocal space images can be visualized using the phase color mode.
-The data viewer can be created and also be controlled via the Python/C++ interface.
-Extension of the data viewer is possible using additional [overlays](docs/tut/imgoverlays.html).
-
-The DataViewer shows several  panels. In each several actions can be performed using
-the keyboard and mouse interface, as described below. A status bar is also present in
-the DataViewer, displaying the zoom level of the image shown in the main panel, and showing
-the coordinates of the last clicked pixel.
-
-## Components
-
-## Main panel
-
-The main panel shows the image either in Real space or Fourier space. The phase
-color display mode can be activated using the pop up menu.
-
-|Mouse Event     | Action                         |
-|:---------------|-------------------------------:|
-|Left Button     | Draw Selection Box             |
-|Middle Button   | Move Selection                 |
-|Right Button    | Move Image, Display Popup Menu |
-|Wheel           | Zoom In And Out                |
-
-|Key             | Action                         |
-|:---------------|-------------------------------:|
-|N               | Renormalize                    |
-|C               | Center                         |
-|I               | Invert                         |
-|P               | Toggle Phasecolor Mode         |
-|V               | Show / Hide Pixel Values       |
-|S               | Toggle Selection Mode          |
-|R               | Show / Hide Ruler              |
-|+,L             | Zoom In                        |
-|-,K             | Zoom Out                       |
-|Z               | Previous Slab                  |
-|X               | Next Slab                      |
-|SHIFT + Mouse   | Update Zoom and Live FFT Panel |
-|CTRL   + Mouse  | Interact with Overlay          |
-
-## Zoom panel
-
-The zoom panel shows a zoomed version of the image centered at the mouse position.
-
-|Mouse Event     | Action                         |
-|:---------------|-------------------------------:|
-|Left Button     | Draw Selection Box             |
-|Middle Button   | Move Selection                 |
-|Right Button    | Move Image, Display Popup Menu |
-|Wheel           | Zoom In And Out                |
-
-|Key             | Action                         |
-|:---------------|-------------------------------:|
-|N               | Renormalize                    |
-|I               | Invert                         |
-|P               | Toggle Phasecolor Mode         |
-|V               | Show / Hide Pixel Values       |
-|S               | Toggle Selection Mode          |
-|+,L             | Zoom In                        |
-|-,K             | Zoom Out                       |
-
-## Live FFT panel
-
-The live FFT panel show a live FFT of the area centered at the current mouse
-position. The size of the Fourier transformed area can be adjusted using the
-popup menu.
-
-|Mouse Event     | Action                         |
-|:---------------|-------------------------------:|
-|Left Button     | Draw Selection Box             |
-|Middle Button   | Move Selection                 |
-|Right Button    | Move Image, Display Popup Menu |
-|Wheel           | Zoom In And Out                |
-
-|Key             | Action                         |
-|:---------------|-------------------------------:|
-|N               | Renormalize                    |
-|C               | Center                         |
-|I               | Invert                         |
-|P               | Toggle Phasecolor Mode         |
-|V               | Show / Hide Pixel Values       |
-|S               | Toggle Selection Mode          |
-|+,L             | Zoom In                        |
-|-,K             | Zoom Out                       |
-
-## Argand panel
-
-The argand panel shows an argand diagram of the selected pixels.
-
-## Info panel
-
-The Info panel shows the x an y coordinates and the value of the last clicked
-pixel and the pixel at the current mouse position. In addition the extent of
-the selection box is displayed.
-
-|Mouse Event     | Action                         |
-|:---------------|-------------------------------:|
-|Right Button    | Display Popup Menu             |
-
-## Python/C++ interface
-
-The data viewer can be created and also be controlled via a Python/C++ interface.
-Following python code loads an image and creates a new viewer for it.
-
-    ::::python
-    im=io.LoadImage("...")
-    v=gui.CreateDataViewer(im)
-
-The viewer instance v provides following methods. See the dox[ost::img::gui::DataViewer|DataViewer]
-class documentation.
-
-
diff --git a/website/raw/docs/tut/imgintro.mkdown b/website/raw/docs/tut/imgintro.mkdown
deleted file mode 100644
index 0c177c565ce87cbc41a7858a0177f1d127239f32..0000000000000000000000000000000000000000
--- a/website/raw/docs/tut/imgintro.mkdown
+++ /dev/null
@@ -1,172 +0,0 @@
-title: Images / Density Maps - An Introduction
-
-[TOC]
-
-# Images / Density Maps - An Introduction
-
-## Introduction : The ImageHandle
-
-OpenStructure offers extensive processing capabilities for planar 2d images and
-3d maps using the img module. Images are manipulated through the use of
-dox[ost::img::ImageHandle|ImageHandles].
-
-ImageHandles provide a clean and efficient interface to interact
-with images and maps. An ImageHandle can store an image in either real
-('SPATIAL') or Fourier ('FREQUENCY') space and always keep track of the currently active domain.
-This means,for example that one can apply a Fourier Transformation to an ImageHandle containing a
-'SPATIAL' image and the ImageHandle will correctly identify the new active domain as 'FREQUENCY'. The
-ImageHandle also understands, for example, that applying a Fourier Transform to a centrosymmetric
-'FREQUENCY' image results in a real 'SPATIAL' image, but applying it to a non-centrosymmetric one results
-in a complex 'SPATIAL' image.
-
-Furthermore, the ImageHandle will make sure that real and
-Fourier space information about the image are always in sync. If, for example, the pixel sampling is
-changed while the current active domain is real space,
-the pixel sampling in Fourier space will be adjusted accordingly, and vice versa.
-
-Moreover, the ImageHandle allows the extraction of both complex and real numeric values
-from images in any active domain. If the domain is complex in nature, but a real numeric value
-is requested, the amplitude of the complex number will be returned. If the numerical nature
-of the domain is real and a complex number is requested, the complex part will be set
-to 0.
-
-## Creating  and visualizing ImageHandles
-
-As a first step, enter the following lines in the OpenStructure python console:
-
-    :::python
-    im=img.CreateImage(img.Size(200,200))
-
-
-This will create an empty, 2D image, with a height and width of 200 pixels, whose
-origin (ie the pixel with the coordinates <0,0>) is in the top-left corner.
-
-    :::python
-    v=gui.CreateDataViewer(im)
-
-A viewer window will pop up (see below), showing a white frame on a black background.
-The inner area of the white frame is the image, which is empty.
-
-## Reading and writing into an image
-
-Data can be read and written from and into an image using the following commands:
-
-    ::python
-    # writes the real value 23.4 into pixel 10,10
-    im.SetReal(img.Point(10,10),23.4)
-    # reads the value in pixel 10,10
-    val=im.GetReal(img.Point(10,10))
-    
-The complex equivalents are also available    
-
-    ::python
-    # writes the complex value value 2+3j into pixel 10,10
-    im.SetComplex(img.Point(10,10),2+3j)
-    # reads the value in pixel 10,10
-    val=im.GetComplex(img.Point(10,10))
-
-The image knows in which domain it is, and will adjust the type of data being written
-accordingly. For example, if one writes a complex value in a 'SPATIAL' image, the value
-will be automatically converted to a real one by taking the amplitude of the complex number
-On the other hand, if one writes a real value in a 'FREQUENCY' image, the value is automatically
-converted to complex by setting the imaginary part to 0.
-
-## Applying algorithms
-
-Let us fill the image with random values.
-
-    :::python
-    rand_alg = img.alg.Randomize() # create algorithm object
-    im.ApplyIP( rand_alg ) # apply algorithm object in-place
-
-As you can see, applying an algorithm is conceptually a two-step process. First,
-an instance of an algorithm class is created, yielding an algorithm object (in this
-case 'rand\_alg'). In a second step, the algorithm object is applied to an image,
-either in-place, modifying the image, or out-of-place, leaving the original image
-untouched, and returning the result as a new image. Note that the in-place/out-of-place
-logic is decoupled from the algorithm object.
-
-Now that we have some (noisy) data present, let us run another algorithm, this time
-a Gaussian filter with a sigma of 4 pixel.
-
-    :::python
-    im.ApplyIP( img.alg.GaussianFilter(4.0) ) # apply temporary algorithm object in-place
-
-As you can see, it is not always necessary to create an independent algorithm instance first,
-in many cases a temporary object will suffice (this applies to the randomization
-algorithm as well, 'im.ApplyIP(alg.Randomize())' would have been fine). However,
-when used this way, the algorithm class will cease to exist as soon as the algorithm
-is applied. This can be important if the algorithm stores some values that need to be
-recovered later. For example:
-
-    :::python
-    stat=img.alg.Stat()
-    im.ApplyIP(stat)
-    mean=stat.GetMean()
-    
-Algorithms are stateful objects and can store values. The 'Stat' algorithm computes
-basic statistics about the image it is applied on (maximum and minimum values, standard
-deviations, etc). The data are stored within the algorithm instance and can be recovered
-using the algorithm's methods. It would obviously make very little sense not to create an
-instance of the 'Stat' algorithm. When the algorithms ceases to exist, all
-information would be lost.
-
-## Applying a Fourier Transform
-
-An image is Fourier-transformed using the 'img.alg.FFT()' algorithm object:
-
-    :::python
-    im=io.LoadImage("imagename.tif") # load the image
-    # create an instance of the fft algorithm object
-    fft=img.alg.FFT() 
-    # do the actual Fourier transformation
-    im_ft=im.Apply(fft) 
-    # back-transform
-    im2 = im_ft.Apply(fft) 
-    # if this is run from within the dng graphical frontend, open viewers to look at the images
-    gui.CreateDataViewer(im)
-    gui.CreateDataViewer(im_ft)
-    gui.CreateDataViewer(im2)
- 
-It is not really necessary to use the 'fft' variable to store the 'im.alg.FFT()' instance, a temporary object can be used, since the 'FFT' algorithm object is stateless. In addition, the algorithm can be applied in-place to avoid the creation of a second image:
-
-    :::python
-    im=io.LoadImage("imagename.tif") # load the image
-    # do the actual Fourier transformation, in-place using temporary object
-    im.ApplyIP(alg.FFT()) 
-    # repeating this command will do the back-transform
-    im.ApplyIP(alg.FFT()) 
-
-As said before, the 'alg.FFT()' algorithm does not require a direction to be given, this is implicitly
-determined by the active domain of the underlying image state: a 'SPATIAL' image will always be
-transformed to the 'FREQUENCY' domain, and vice-versa.
-
-## Extracting and Pasting Images
-
-An image can be extracted and pasted into another image using the 'Extract()' and
-'Paste()' member functions:
-
-    :::python
-    # load the image
-    im=io.LoadImage("imagename.tif")
-    # generate a subimage from the region going from (10,10) to (30,30)
-    im2=im.Extract(img.Extent(img.Point(10,10),img.Point(30,30)))
-    # generate an empty image with the same size as the original image
-    im3=img.CreateImage(im.GetExtent())
-    # paste the subimage into the empty image
-    im3.Paste(im2)
-
-Note that the extent is fully honored for the paste operation, i.e. only the
-region where the pasted-to and the pasted-in image overlap will be affected.
-
-
-
-
-|                                                   |                                                                     |                                                                          |
-|:-------------------------------------------------:|:-------------------------------------------------------------------:|:------------------------------------------------------------------------:|
-|![Empty Image] (docs/tut/dv1.jpg "Empty Image")    | ![After Randomization] (docs/tut/dv2.jpg "After Randomization")     | ![After Gaussian Filtering] (docs/tut/dv3.jpg "After Randomization")  |
-|Empty Image                                        | After Randomization                                                 | After Gaussian Filtering                                                 |
-
-
-
-
diff --git a/website/raw/docs/tut/imgoverlays.mkdown b/website/raw/docs/tut/imgoverlays.mkdown
deleted file mode 100644
index f84b883fb3c05a8183647c369ce1587e515f9bed..0000000000000000000000000000000000000000
--- a/website/raw/docs/tut/imgoverlays.mkdown
+++ /dev/null
@@ -1,59 +0,0 @@
-[TOC]
-
-# Overlays
-
-The DataViewer may be extended by an arbitrary amount overlays. These are
-classes derived from 'ost::img::gui::Overlay', either directly in Python or
-written in C++ and then exported to Python. They are added dynamically to each
-viewer by means of the DataViewer::AddOverlay method.
-
-An overlay can draw on top of an image in the OnDraw method. If it is the
-active Overlay, it also receives mouse and keyboard events via the OnMouseEvent
-and OnKeyEvent methods. A minimalistic overlay that demonstrates this functionality
-is given below, and can also be found in `modules/gui/src/data_viewer/null_overlay.hh'.
-
-    :::cpp
-    #include <ost/gui/data_viewer/overlay_base.hh>
-
-    class NullOverlay: public ost::img::gui::Overlay
-    {
-     public:
-      // the ctor must initialize the Overlay base class with a name
-      NullOverlay(): 
-      Overlay("NullOverlay")
-      {}
-
-      // This must be implemented to allow duplication
-      virtual OverlayPtr Clone() const {
-        return OverlayPtr(new NullOverlay(*this));
-      }
-
-      // This method is called for each redraw of the image viewer, after the image itself
-      // has been rendered in the view widget. The device context as well as the data viewer
-      // panel are passed
-      virtual void OnDraw(wxDC& dc, const img::gui::DataViewerPanel* dvp, bool is_active)
-      {
-      }
-
-      // Called if this is the active overlay, passing the mouse event. Must return flag to 
-      // indicate wether the event was handled (true), or not (false), where the latter allows
-      // the image viewer to handle the event itself
-      virtual bool OnMouseEvent(const wxMouseEvent& e)
-      {
-        return false;
-      }
-
-      // dito for a key event
-      virtual bool OnKeyEvent(const wxKeyEvent& e)
-      {
-        return false;
-      }
-
-      // allows a custom overlay menu to be included, a return of 0 indicates no menu
-      virtual wxMenu* GetMenu()
-      {
-        return 0;
-      }
-    }
-    
-    
\ No newline at end of file
diff --git a/website/raw/docs/tut/intro.mkdown b/website/raw/docs/tut/intro.mkdown
deleted file mode 100644
index caa28d45b49c0b0036e219db3c285122d87a4ec3..0000000000000000000000000000000000000000
--- a/website/raw/docs/tut/intro.mkdown
+++ /dev/null
@@ -1,249 +0,0 @@
-title: Introduction to OpenStructure
-
-[TOC]
-
-# A gentle introduction to OpenStructure
-
-In this tutorial you will be learning by example how to use the OpenStructure framework. 
-
-We assume that you already have a version of OpenStructure installed. If not, please refer to the [installation instructions](download.html).
-
-## What will be covered in this tutorial?
-
-This tutorial is aimed at users that would like to get their hands dirty and execute commands in Python and write scripts rather clicking their way through a shiny user interface. The user interface of OpenStructure is in a very early state anyway that you probably won't go far by clicking you way through...
-
-The first part of the tutorial is a walk-through of the basic functionality you will be using in your everyday work. You will learn how to load structure datasets, inspect, display them in the 3D window and save them. 
-
-
-## Getting ready to rumble
-
-The files we will be using in the tutorial are available in the examples folder that comes with OpenStructure. Depending on your platform, the examples are located at a different location:
-
- * on *MacOS X* the files are in /Applications/OpenStructure/Examples
- * on *Linux* and *Windows* PREFIX/share/openstructure/examples, where PREFIX is the path to the directory containing OpenStructure.
-
-### Starting DNG
-
-The graphical user interface of OpenStructure is called DNG (Dino/DeepView Next Generation). To start it, 
-
- * on *MacOS X* double click DNG.app in /Applications/OpenStructure
- * on *Windows* double click dng.bat inside the PREFIX/bin directory
- * on *Linux* fire up a terminal change into the OpenStructure installation directory and type 'bin/dng'. If you have the binary directory in the PATH, typing dng is sufficient.
-
-### Interactive Python Shell
-Now we will enter commands in the [python shell](docs/tut/pythonshell.html) (in the screenshot above, the python shell is located at the bottom of the main window). If you want to get more information on any object, function or class, the python help command may be useful. For example:
-
-    ::::python
-    # get list of methods of EntityView
-    help(mol.EntityView)
-    # get help for method Select
-    help(mol.EntityView.Select)
-    
-## Loading and inspecting a protein structure
-
-OpenStructure has a module that is dedicated to deal with input and output of data, including sequence alignment formats, protein structures and density data and images.  If you are reading this tutorial you most certainly have dealt with protein structures before and you are most certainly aware that they are usually stored in Brookhaven structure files (aka PDB files). The official name for molecules stored in a PDB file is an entity. You will hear this word throughout this tutorial, but you can replace the word entity with molecule in your head.
-
-Before using the load functionality, you have to import the io module. This is done by typing the following command in the [python shell](docs/tut/pythonshell.html):
-
-     ::::python
-     from ost import io
-To load a PDB file, type
-
-     ::::python
-     fragment=io.LoadPDB('OST_INSTALLATION_PATH/share/openstructure/examples/misc/fragment.pdb')
-This will load the fragment from the specified file 'fragment.pdb' and store the result in fragment. For more information on the LoadPDB function, type
-
-     ::::python
-     help(io.LoadPDB)
-Now let's inspect what we just loaded:
-
-     ::::python
-     print fragment.chain_count
-     print fragment.residue_count
-     print fragment.atom_count
-
-As you can see, our fragment consists of one peptide chain of 12 amino acids and has 81 atoms in total. Now let's examine our fragment even further. Enter the command
-
-     ::::python
-     for residue in fragment.residues:
-       print residue  
-This will print a list of all residues in the fragment. Similarly to get a list of atoms, use:
-
-    ::::python
-    for atom in fragment.atoms:
-      print atom
-
-Of course, we can also get a list of atoms grouped by residues:
-    
-    ::::python
-    for residue in fragment.residues:
-      print residue, 'has', residue.atom_count, 'atom(s).'
-      for atom in residue.atoms:
-        print ' ', atom.name, atom.pos
-
-And, for completeness, we will first group them by chain, then by residues.
-
-    ::::python
-    for chain in fragments.chains:
-      print 'chain', chain.name, 'has', chain.residue_count, 'residue(s)'
-      for residue in chain.residues:
-        print ' ', residue, 'has', residue.atom_count, 'atom(s).'
-        for atom in residue.atoms:
-          print '    ', atom.name, atom.pos
-Aah, wait! A protein fragment would not be complete without bonds: Let's see what bonds we have in there:
-
-    ::::python
-    for bond in fragment.bonds:
-      print bond
-From these short code examples we already see how the entity is structured: On one hand we have a hierarchy of chains, residues and atoms. On the other hand, we have bonds that form a network overlayed on the hierarchy. This is illustrated in the picture on the left. An important feature of entities is that we can always assume that the hierarchy is intact. You will never find an atom without residues, no residue can exist without a parent chain and chains belong always to an entity. 
-
-## Let There Be Shiny Graphics
-
-For visually inspecting the fragment, we now create a graphical representation:
-
-     ::::python
-     go=gfx.Entity("Fragment", fragment)
-     scene.Add(go)
-     scene.CenterOn(go)
-
-Now you will see the fragment in the 3D window (left):
-
-![](docs/tut/sel.png)
-
-Use the mouse to rotate, zoom in an shift the camera. Double clicking on an atom will center the camera on that atom. 
-
-## Introduction to Views
-
-Often during processing and visualisation of data, only parts of a protein structure are of interest. This realisation has had a major impact on the design of OpenStructure and is tied very deeply into the core of the framework. Subparts of structure are modeled as so-called dox[ost::mol::EntityView|EntityViews]. You can think of them as a selection of chains, residues, atoms and bonds of an entity. A views has almost the same interface as the underlying entity, making it very easy to mix entity views with handles in Python due to the dynamic nature of the language. An algorithm that is written for entities will almost always (with some care) also work for dox[ost::mol::EntityHandle|EntityHandles]. This is referred to as [duck-typing](http://en.wikipedia.org/wiki/Duck_typing) (I don' t care if it is a duck as long as it looks like a duck), a concept used all over the place in Python. 
-
-A typical view can be seen in the image on the left. The view consists of one chain, one residue and two atoms. Again the same rule applies: No atom can be part of the view without it's residue. In this example, no bonds are included, since there is at most one atom per bond in the original structure.
-
-To familiarize yourself with the concept of views, we will use the fragment in the 3D window.
-
-We will use several ways to select parts of our fragment:
- * By using a dedicated query language
- * By manually constructing a view
-
-## The Query Language
-
-The first way to select parts of a structure is with a dedicated mini-language, called ["the query language”](docs/tut/query.html). In the Python Shell, type
-
-    ::::python
-    go.selection=fragment.Select('')
-A green halo will be displayed around the selected parts (image in the middle).
-
- As you can see the previous statement created a “full view”, containing all the chains, residues, atoms and bonds. To select lysine residues, type
-
-    ::::python
-    go.selection=fragment.Select('rname=LYS')
-    
-
-As you can see (image in the middle), the  only lysine residue is now highlighted in the 3D window, because it was the only one matching the predicate “residue name must be equal to LYS”. Several such predicates can be combined with boolean operators such as “and” and “or”. To select residues with residue number 1 to 3, the following statement will do the job:
-
-    ::::python
-    go.selection=fragment.Select('rnum>=1 and rnum<=3')
-but this is very cumbersome. That's why there is a shortcut to this statement. You can specify a range of values.
-
-    ::::python
-    go.selection=fragment.Select('rnum=1:3')
-For a complete description of what you can do with the query language, have a look at the [query language introduction](docs/tut/query.html) or at the [reference page](dox/html/query.html).
-
-
-## Constructing Views Manually
-
-Sometimes the query language Is Not Enough (TM). For these cases the construction of manual entities becomes neccessary. This is pretty straight forward:
-
-    ::::python
-    view=fragment.CreateEmptyView()
-    ca=fragment.FindAtom('A', mol.ResNum(1), 'CA')
-    cb=fragment.FindAtom('A', mol.ResNum(1), 'CB')
-    view.AddAtom(ca)
-    view.AddAtom(cb)
-    go.SetSelection(view)
-
-The last step sets our constructed view as the current selection, displaying it in the 3D window. As you can see, C-alpha and C-beta of the first residue are not connected by bonds, even though both atoms are in the view. You have either to add the bond manually with
-
-    ::::python
-    ca_cb=ca.FindBondToAtom(cb)
-    view.AddBond(ca_cb)
-    
-Or as a very convenient shortcut 'view.AddAllInclusiveBonds()' to add all bonds that have both bonding partners in the view.
-
-Don't forget to call update the selection of the graphics object to see what view you have created.
-
-## Saving an Entity
-
-Saving an entity (or a view) is a breeze:
-
-Type
-
-     ::::python
-     io.SavePDB(fragment, 'full.pdb')
-to save the full view. To save only the backbone atoms, we can first select the backbone atoms and then save it:
-
-     ::::python
-     io.SavePDB(fragment.Select('aname=CA,C,N,O'), 'backbone.pdb')
-
-
-## Loading  images and density maps
-
-Openstructure features a img module that is dedicated to the manipulation of images / density maps. The images or density maps can either be one-, two- or three-dimensional. The most common formats used in x-ray and electron crystallography and atomic force microscope are supported in addition to several general purpose image formats. See (feature list)[feature_list.html] for details.
-The img module was originally developed as part of the Image Processing Library & Toolbox IPLT. More documentation and examples can also be found on the [IPLT website](http://www.iplt.org).
-
-Before using the load functionality for an image, you have to import the io module. This is done by typing the following command in the python shell:
-
-     ::::python
-     from ost import io
-
-To load a density map, type
-
-     ::::python
-     map=io.LoadImage('OST_INSTALLATION_PATH/share/openstructure/examples/map/1ppt.map')
-
-This will load the fragment density map from the specified file 'fragment.map' and store the result in fragment_map.
-
-Now let's inspect what we just loaded:
-
-    ::::python
-    print map.GetPixelSampling()
-    
-We can see that the sampling is set to 1.0 Angstroems in all three dimensions.
-
-## Manipulating  images and density maps
-
-The algorithms used for manipulation of an image are found in the img module. Therefore before using an algorithm we first have to import the img module.
-
-    ::::python
-    from ost import img
-
-
-The img module provides a wide range of algorithm to manipulate image data. Here for the example we use a LowPassFilter to restrict the resolution of the density map.
-
-     ::::python
-     map_filtered=map.Apply(img.alg.LowPassFilter(3.0))
-
-The filtered map is stored in a new variable called fragment\_map\_filtered.
-
-
-## Displaying images and density maps
-
-Now that we have a filtered map it's time to have a look at it. There are fundamentally two ways to visualize 3-dimensional density maps.
-One is by drawing isosurfaces. These are conceputally similar to contour lines used in cartography: every point on an isosurface has the same
-density value. Isosurfaces are easy to create in OpenStructure:
-
-     ::::python
-     go=gfx.MapIso("filtered", map_filtered,0.5)
-     scene.Add(go)
-
-The other way to visualize a 3-dimensional map is by showing one 2-dimensional density slice at a time, allowing
-the user to move through the slices. In OpenStructure this is achieved using a DataViewer docs/tut/imgdataviewer.html). A DataViewer showing the
-filtered map is created using the following command:
-
-    ::::python
-    gui.CreateDataViewer(map_filtered)
-
-This command displays a panel showing one slice of the density map lying on a particular (x,y) plane in the coordinate reference system.
-The 'z' and 'x' keys can be used to move to slices lying at a lower or higher coordinate along the 'z' axis, allowing the examination of
-the full 3-dimensional volume.
-
-Are more detailed explanation of the img module can be found in the tutorial section for [images and density maps](docs/tut/imgintro.html).
diff --git a/website/raw/docs/tut/newmodule.mkdown b/website/raw/docs/tut/newmodule.mkdown
deleted file mode 100644
index a8a200ba19991558639d1300ce6bd5342b48b6c1..0000000000000000000000000000000000000000
--- a/website/raw/docs/tut/newmodule.mkdown
+++ /dev/null
@@ -1,274 +0,0 @@
-title: Extending OpenStructure - Creating a New Module
- 
-[TOC]
-
-# Extending OpenStructure - Creating a new module
-
-OpenStructure can be extended by writing additional modules. A module will consist of
-a set of C++ classes and methods, most of which will also be exported to Python.
-
-The build system of OpenStructure is quite simple. The main difference to other projects
-is the use of a so-called stage  directory. The stage directory replicates the normal layout of
-a standard Linux directory structure, with an 'include' directory for the headers, a 'lib' directory
-containing the shared library files, a 'bin' directory  for the executables and a 'share' directory for the
-platform-independent data like icons, images and examples.
-
-OpenStructure uses [CMake](http://www.cmake.org/) to build the project. The rules for the build-system
-are defined in 'CMakeLists.txt' files. When running CMake, the files are  compiled and copied into stage. The
-real installation, if necessary, happens at a later stage. This is referred to as staging of the files.
-
-If a new module is written following the guidelines in this page, it will be
-seamlessly included in the build system and will then be available form both
-the DNG python console and the OpenStructure command line as any other native module.
-
-As a first step, a new directory structure must be created to accommodate the new module.
-
-## Directory structure
-
-For the purpose of this example, let's assume we are creating a new module called
-'mod' (for 'modeling'). Let's create a directory named 'mod' under the 'modules' directory
-in the OpenStructure development tree, and  populate it with the three subdirectories 'src', 'pymod',
-and 'tests'.  Then we add a 'CMakeLists.txt' file in the 'mod' directory, consisting of three lines:
-
-    :::cpp
-    add_subdirectory(src)
-    add_subdirectory(pymod)
-    add_subdirectory(tests)
-
-## The module code
-
-In the 'src' subdirectory we put the code that implements the functionality of the new module,
-plus a 'config.hh' header file.
-
-Here is a skeleton of one of the files in  the directory , 'modeling\_new\_class\.hh':
-
-    :::cpp 
-    #ifndef OST_MOD_NEW_CLASS_H
-    #define OST_MOD_NEW_CLASS_H
-
-    #include <ost/mol/entity.hh>
-
-    // All other necessary includes go here
-  
-    namespace ost { namespace mod {
-
-      class NewClass
-      {
-       public:
-         void NewMethod();
-               
-      // All declarations of NewClass go here 
-      
-      };
-
-    }} // namespaces
-
-    #endif
-
-And here is the skeleton of the corresponding 'modeling\_new\_class.cc' file:
-
-    :::cpp
-    #include "modeling_new_class.hh"
-
-    using namespace ost::mol;
-    using namespace ost::mod;
-
-    // All other necessary includes and namespace directives
-    // go here
-
-    void DLLEXPORT NewClass::NewMethod():
-    {
-      // Implementation     
-    }
-
-    // Implementation code for NewClass goes here
-
-Obviously, the 'src' directory can contain many files, each implementing classes
-and functions that will end up in the module. In order to build and stage
-the module shared library, a 'CMakeLists.txt' file needs to be written for the
-'src' directory:
-
-    :::cpp
-    set(OST_MOD_SOURCES 
-    modeling_new_class.cc
-    // All other source files 
-    )
-
-    set(OST_MOD_HEADERS
-    modeling_new_class.hh
-    // All other header files
-    )
-
-     module(NAME mod SOURCES "${OST_MOD_SOURCES}"
-            HEADERS ${OST_MOD_HEADERS}
-            DEPENDS_ON mol mol_alg)
-
-
-The line containing the 'DEPENDS ON' directive lists all the modules on which
-the new module depends (in this case 'mol' and 'mol.alg').  The 'module' macro
-will take care of staging the headers, in this case into 'ost/mod' and compiling,
-linking and staging of a library with the  name 'libost_mod.so' ('libost_gmod.dylib' on MacOS X).
-
-Note
-:   Due to a limitation in the built-int install command of CMake, for modules
-    that have their headers in several directories, it is required to group the
-    headers by directory, leading to a call of module like:
-
-    :::cpp
-    module(NAME mol SOURCES atom_handle.cc impl/atom_impl.cc
-          HEADERS atom_impl.hh IN_DIR impl
-           atom_handle.hh)   
-   
-The 'config.hh' header is required for each module to setup the environment on
-Windows: Each public class, method and function needs to marked with
-'DLLEXPORT' or 'DLLIMPORT' to teach the linker where to look for the symbol.
-The correct use of either 'DLLIMPORT' and 'DLLEXPORT' is depending on the
-context: While compiling a header file that is part of the same shared
-library, 'DLLEXPORT' must be used. When compiling a header that is part of
-an external shared library, 'DLLIMPORT' must be used. A typical module_config
-header looks like this:
-
-    :::cpp   
-    #ifndef OST_MOD_MODULE_CONFIG_HH
-    #define OST_MOD_MODULE_CONFIG_HH
-
-    #include <ost/base.hh>
-
-    #if defined(OST_MODULE_OST_MOD)
-    #  define DLLEXPORT_OST_MOD DLLEXPORT
-    #else
-    #  define DLLEXPORT_OST_MOD DLLIMPORT
-    #endif
-    #endif
-    
-## The Testing Framework
-
-The 'tests' directory contains code for Unit Tests. The code is compiled and executed when one invokes
-compilation using the 'make check' command.  Tests are run by means of the ['Boost Test Library'](http://www.boost.org/doc/libs/1_37_0/libs/test/doc/html/index.html)
- Framework, which is used throughout OpenStructure. Before coding the test routines, the required skeleton
- needs to be put in place.
-
-The main code is put into 'tests.cc', which will become the test executable:
-    
-    :::cpp
-    #include <boost/test/unit_test.hpp>
-    using boost::unit_test_framework::test_suite;
-
-    #include "test_modeling.hh"
-
-    test_suite*
-    unit_unit_test_suite( int argc, char * argv[] ) {
-      std::auto_ptr<test_suite> test(BOOST_TEST_SUITE( "Module Mod Test" ));
-
-      test->add(CreateModelingTest()); 
-
-      return test.release(); 
-    }
-
-        
-The most relevant line adds the test suite for the new module to the global test list.
-The test suite is created by the factory function CreateModelingTest(), which is declared in
-the 'test_modeling.hh' header file. 
-
-    :::cpp
-    #ifndef OST_MOD_TEST_MODELING_H
-    #define OST_MOD_TEST_MODELING_H
-
-    #include <boost/test/unit_test.hpp>
-    using boost::unit_test_framework::test_suite;
-
-    test_suite* CreateModelingTest();
-
-    #endif
-    
-The definition of the factory function is found in the actual test code,
-which we put in 'test\_modeling.cc'. Here is a skeleton version of that file:
-
-    :::cpp
-    #include "test_modeling.hh"
-
-    // additional include statements will go here
-
-    namespace test_modeling {
-
-      void test() 
-      {
-        // test code will go here
-      }
-
-    }
-
-    test_suite* CreateModelingTest()
-    {
-      using namespace test_modeling;
-      test_suite* ts=BOOST_TEST_SUITE("Modeling Test");
-       ts->add(BOOST_TEST_CASE(&test));
-
-       return ts;
-    }
-
-In this file, all the normal 'Boost Test Library' macros and functions can be used.
-(For example 'BOOST\_CHECK', 'BOOST\_FAIL', etc.)
-
-Here is finally the build script skeleton that needs to be put into 'mod/tests/':
-
-    :::cpp
-    set(OST_MOD_UNIT_TESTS
-    tests.cc
-    test_modeling.cc
-    )
-
-    ost_unittest(mod "${OST_MOD_UNIT_TESTS}")
-    target_link_libraries(ost_mol ost_mol_alg ost_mod)
-
-In the last line the call to the 'target\_link\_libraries'
-function contains the names of the modules on which the 'mod' unit test code depends
-(in this case, the 'mol' and 'mol\_alg' modules) , in addition to the 'mod' module itself.
-
-## The python wrapper
-
-FInally, the module API is exported to Python using the [Boost Python Library](http://www.boost.org/doc/libs/1_37_0/libs/python/doc/index.html).
-In 'mod/pymod', the wrapper code for the classes in the new module is put into a file named 'wrap\_mod.cc':
-
-    :::cpp
-    #include <boost/python.hpp>
-    using namespace boost::python;
-
-    #include <ost/mod/modeling_new_class.hh>
-    
-    using namespace ost::mol;
-    using namespace ost::mod;
-
-    // All other necessary includes and namespace directives
-    // go here
-
-    BOOST_PYTHON_MODULE(_mod)
-    {
-      class_<NewClass>("NewClass", init<>() )
-        .def("NewMethod", &NewClass::NewMethod)
-      ;
-  
-      // All other Boost Python code goes here    
-    }
-
-The 'mod/pymod' directory must obviously contatin a 'CMakeLists.txt' file:
-
-    :::cpp
-    set(OST_MOD_PYMOD_SOURCES
-    wrap_mod.cc
-    )
-
-    pymod(NAME mod OUTPUT_DIR ost/mod 
-          CPP ${OST_MOD_PYMOD_SOURCES} PY __init__.py)
-
-The directory should also contain an '\_\_init.py\_\_' file with the
-following content:
-
-    :::python
-    from _mod import *
-    
-In case one wants to implement Python-only functionality for the new module, any
-number of function definitions can be added to the '\_\_init.py\_\_' file.
-
-That's it!. The next time the OpenStructure project is compiled, the new module will
-be built and made available at both the C++ and the Python level.
diff --git a/website/raw/docs/tut/pythonshell.mkdown b/website/raw/docs/tut/pythonshell.mkdown
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-title: Python Shell
-
-[TOC]
-
-# The Python Shell
-OpenStructure has a powerful Python Shell which has some handy features. It is completely integrated into OpenStructure and allows you enter Python code. 
-
-## Multi line detection
-The Python Shell detects automatically if a code block is complete or not. 
-For example a simple print statement in the command line is a complete code block. Therefore the code will be executed after pressing enter:
- 
-![Single line](docs/tut/100210_single_line.png "Single line")
- 
-When a multiline codeblock (like a for loop or an if instruction) is being entered in the command line, the code is not executed until the code block is complete:
-   
-![Multi line detection](docs/tut/100210_multi_line.png "Multi line detection")
- 
-When a code block is not complete, pressing enter appends an empty line at the end of the code block. To execute such a code block, you simply have to press enter twice. 
-
-## Auto completion
-After pressing tab in the Python Shell, it returns you possible extensions to your entered text. This feature can be used for completing variable names or functions:
-  
-![Auto completion](docs/tut/100210_auto_completion.png "Auto completion")
- 
-It is also possible to complete a file system path string. By pressing tab while editing a string, the shell displays all file or folders of the given directory: 
- 
-![Path completion](docs/tut/100210_path_completion.png "Path completion")
diff --git a/website/raw/docs/tut/query.mkdown b/website/raw/docs/tut/query.mkdown
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-[TOC]
-
-# Queries
-
-
-## The Basics
-
-It is often convenient to highlight or focus certain parts of the structure. 
-OpenStructure includes a powerful query system that allows you to perform custom 
-selections in a convenient way.
-Selections are carried out mainly by calling the Select method made available by EntityHandle and EntityView objects while providing a query string. Queries are written using a dedicated mini-language. For example, to select all arginine residues of a given structure, one would write:
-
-    ::::python
-    arginines=model.Select('rname=ARG')    
-A simple selection query (called a predicate) consists in a property (here, `rname`), a comparison operator (here, `=`) and an argument (here, `ARG`).  The return value of a Select method is always an EntityView. The EntityView always contains a full hierarchy of elements, never standalone separated elements. In the above example, the EntityView called `arginines` will contain all chains from the structure called 'model' that have at least one arginine. In turn these chains will contain all residues that have been identified as arginines. The residues themselves will contain references to all of their atoms. Of course, queries are not limited to selecting residues based on their type, it is also possible to select atom by name:
-
-    ::::python
-    c_betas=model.Select('aname=CB') 
-As before, c`betas is an instance of an EntityView object and contains a full hierarchy. The main difference to the previous example is that the selected residues do not contain a list of all of their atoms but only the C-beta. These examples clarify why the name 'view' was chosen for this result of a Select statement. It represents a reduced, restrained way of looking at the original structure.
-
-Both the selection statements that have been used so far take strings as their arguments. However, selection properties such as `rnum` (residue number), take numeric arguments. With numeric arguments it is possible to use identity operators ( `!=` and `=`). It is also possible to compare them using the `>`, `<`, `>=` and `<=` operators. For example, the 20 N-terminal residues of a protein can be selected with:
-
-    ::::python
-    n_term=model.Select('rnum<=20')
-## Combining predicates
-
-Selection predicates can be combined with boolean operators. For example , you might want to select all C atoms with crystallographic occupancy higher than 50. These atoms must match the predicate `ele=C` in addition to the predicate `occ>50`. In the query language this can be written as:
-
-    ::::python
-    model.Select('ele=C and occ>50')
-Compact forms are available for several selection statements. For example, to select all arginines and aspargines, one could use a statement like:
-
-    ::::python
-    arg_and_asn=model.Select('rname=ARG or rname=ASN')
-
-However, this is rather cumbersome as it requires the word `rname` to be typed  twice. Since the only difference between the two parts of the selection is the argument that follows  the word `rname`, the statement can also be written in an abbreviated form:
-
-    ::::python
-    arg_and_asn=model.Select('rname=ARG,ASN')
-Another example: to select residues with numbers in the range 130 to 200, one could use the following statement
-
-    ::::python
-    center=model.Select('rnum>=130 and rnum<=200')
-or alternatively use the much nicer syntax:
-
-    ::::python
-    center=model.Select('rnum=130:200')
-This last statement is completely equivalent to the previous one. This syntax  can be used when the selection statement requires a range of integer values within a closed interval.
-
-## Distance Queries
-
-
-The query
-
-    ::::python
-    around_center=model.Select('5 <> {0,0,0}')
-selects all chains, residues and atoms that lie with 5 Å to the origin of the reference system ({0,0,0}). The `<>` operator is called the ‘within’ operator. 
-Instead of a point, the within statements can also be used to return a view containing all chains, residues and atoms within a radius of another selection statement applied to the same entity.  Square brackets are used to delimit the inner query statement. 
-
-    ::::python
-    around_hem=model.Select('5 <> [rname=HEM]')
-    model.Select('5 <> [rname=HEM and ele=C] and rname!=HEM')
-
-## Bonds and Queries
-
-When an EntityView is generated by a selection, it includes by default only bonds for which both connected atoms  satisfy the query statement. This can be changed by passing the parameters `EXCLUSIVE_BONDS` or `NO_BONDS` when calling the Select method. `EXCLUSIVE_BONDS` adds bonds to the EntityView when at least one of the two atoms falls within the boundary of the selection. `NO_BONDS` suppresses the bond inclusion step completely. 
-
-## Whole Residue Queries
-
-If the parameter `MATCH_RESIDUES` is passed when the Select method is called, the resulting EntityView will include whole residues for which at least one atom satisfies the query. This means that if at least one atom in the residue  falls within the boundaries of the selection, all atoms of the residue will be included in the View.
-
-## More Query Usage
-
-The high level interface for queries are the Select methods of the 
-EntityHandle and EntityView classes. By passing in a query string, a view
-consisting of a subset of the elements is returned. 
-
-Queries also offer a second interface: `IsAtomSelected()`, 
-`IsResidueSelected()` and `IsChainSelected()` take an atom, residue or 
-chain as their argument and return true or false, depending on whether the 
-element fulfills the predicates.
-
-Read more about queries in the [query language reference](dox/html/query.html)
-
-## Special Topics
-
-### Distance-based selections
-
-Distance-based selections within a given atom position are supported by the ‘within’ operator (`<>`) . To select atoms within 5 Angstrom of the point `{1,2,3}`, one would write:
-5 <> {1,2,3}To select atoms which lie at a distance further than 5 Angstrom one would use the negation operator: 
-
-    not 5 <> {1,2,3}
-
-### Compact forms
-
-Instead of writing:
-`aname=CA or aname=C or aname=O or aname=N` one can write: 
-
-aname=CA,N,C,OFor integer value ranges, one can use the colon syntax. Instead of `rnum>=10 and rnum<=20` one can write `rnum=10:20`.
-
-
-## Constructing views manually
-
-
-Sometimes the query language is not enough. For these cases the construction of manual entities becomes neccessary. This is pretty straight forward. Starting off with an empty view, bonds, atoms, residues and chains can be added at will.
-
-    ::::python
-    view=ent.CreateEmptyView()
-To populate the entity view, use one of the EntityView.AddResidue(), EntityView.AddChain(), EntityView.AddAtom() and EntityView.AddBond() member functions:
-
-    ::::python
-    ca=ent.FindAtom('A', mol.ResNum(1), 'CA')
-    view.AddAtom(ca)
-This call will automatically insert the residue and the chain of the atom into the view, so `GetChainCount()`, `GetResidueCount()` and `GetAtomCount()` will all return 1.
-
-To add a residue, use
-
-    ::::python
-    res=ent.FindResidue('A', mol.ResNum(1))
-    view.AddResidue(res)
-This will not add any atoms. To add the atoms, pass `mol.INCLUDE`ATOMS` to AddResidue:
-
-    ::::python
-    view.AddResidue(res, mol.INCLUDE_ATOMS)
-Due to performance reasons, all of the add method do not check for duplicates by default. To turn duplicate-checking on, pass `mol.CHECK`DUPLICATES` as the second argument.
diff --git a/website/raw/docs/tut/tut02.mkdown b/website/raw/docs/tut/tut02.mkdown
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-[TOC]
-# Exercises
-
-## Queries and Views
-
-First load myo.pdb. This can be done by either loading it in the file browser, or by loading it manually in the python shell. 
-
-## Loading manually
-
-    
-    myo=io.LoadPDB(‘myo.pdb’)
-    myo_go=gfx.Entity(‘Myo’, myo)
-    scene.Add(myo_go)
-    scene.SetCener(myo_go.GetCenter())
-    
-## Loading in the file browser
-
-Double click the file in the file browser. Now we have to get our hands on the myo object from the python shell:
-
-    myo_go=scene[‘myo’]
-    myo=myo_go.view.GetHandle()
-
-To display your views as a halo around the myo object, use
-    
-    myo_go.current_selection=whatever_view
-    # or
-    myo_go.SetCurrentSelection(whatever_view)
-
-
-Now go ahead and try to create the following selections. Not all of them can be solved by using selection statements. 1-4 and 7 can be solved by using selection statements alone, but 5 and 6 require you to create views manually.
-
-* Select all atoms of the HEM residue
-* Select carbon atoms of the HEM residue
-* Select the atoms within 8.0A of the HEM by using a selection statement.
-* Select all atoms of residues for which at least one atom is within 8.0A 
-  of the HEM
-* Select the atoms within 8.0A of the HEM by using EntityHandle.FindWithin().
-  This method takes a position and a radius and returns a list of atoms that are
-  within the given distance of the point. These have then to be assembled into a
-  view by populating an initially empty view as described in “Manually 
-  Constructing Views”.
-* Assemble a view that contains C-beta atoms for residues that have a CB and CA
-  for residues that don't have a CB. To find out, if a certain residue has an
-  atom, call residue.FindAtom(atom_name) and check if the returned atom is
-  valid,i.e

-    
-    ca=residue.FindAtom(‘CA’)
-    if ca.IsValid():
-      print ca
-    else:
-      print residue, ‘does not have a CA’
-    
-* Select sidechains of residues for which at least one atom is within 8.0A of
-  the HEM
-  
-## Writing a Parser for your own file format
-
-
-In this exercise you will learn how to build and entity from the ground up by writing a parser for a custom file format. The skeleton of the parser can be found in 02_conop.py. Your task is to fill-in the missing parts. To do so, you will be first creating an empty entity (mol.CreateEntity()) and then assemble the entity with an XCSEditor.
-
-But first some background on what editors are:
-
-## Editors
-
-The structure, topology and connectivity of entities is edited via editors. This includes operations such as changing atom positions, connecting atoms with bonds as well as adding and removing chains, residues and atoms. To insert a new chain, append a residue or insert an atom, use EditorBase.InsertChain, EditorBase.AppendResidue or EditorBase.InsertAtom, respectively.
-
-You can create an editor by calling
-
-    edi=ent.RequestXCSEditor()
-
-on your entity. Adding chains, residues and atoms is pretty straigh-forward:
-
-    chain=edi.InsertChain(chain_name)
-    gly=edi.AppendResidue(chain, “GLY”)
-    edi.InsertAtom(gly, “N”, geom.Vec3())
-    edi.InsertAtom(gly, “CA”, geom.Vec3())
-    edi.InsertAtom(gly, “C”, geom.Vec3())
-    edi.InsertAtom(gly, “O”, geom.Vec3())
-
-You might have noticed that the above code snippet does not add any bonds, nor does it fill any atom properties such as element, radius and so on. OpenStructure has a module dedicated to only do that: The conop module. After importing it, a single call is sufficient to connect the atoms, fill in residue and atom properties:
-
-    conop.ConnectAll(ent)
-
-### Editor for external coordinate system
-
-The XCSEditor defines the interface for manipulating the external coordinate system. The external coordinate system directly operates on atom positions in euclidian space. A specific atom position can be changed with XCSEditor.SetAtomPos. XCSEditor.ApplyTransform applies a transformation to all atoms.
-
-###Editor for internal coordinate system
-
-The ICSEditor is used to manipulate the internal coordinate system that is defined by bond lengths and angles. By default the internal coordinate system is not calculates. However, upon requesting an ICSEditor for the first time, the internal coordinate system is initialized. This involves the build-up of a directed-graph for the bond network as well as calculating the internal coordinate matrices.
-
-The use XCSEditor and ICSEditor are mutually exlusive. This means that whenever a XCSEditor has pending changes, the results of using an ICSEditor is undefined and vice versa.
-
-
-## Processing of Density Maps
-
-In this exercise you will learn how to do basic processing of density map data. For the exercise you will use real experimental data coming from a single particle reconstruction of the YscC protein from Yersinia entercolitica. 
-
-The first step to the processing of density data in OpenStructure is the loading of the ‘img’ and ‘img.alg’ module.
-Go ahead and load the module in the OpenStructure python shell.
-
-The second step consists in loading the density data into memory. OpenStructure provides a LoadMap function in the ‘io’ module that can be used, not surprisingly, to load a density map.
-map=io.LoadMap(‘YscC.spi')The file is in Spider format( Spider is one of the most celebrated software packages for single particle reconstruction).
-
-The dataset is very big and is stored in a large density map. It will take a few seconds to load. To find out how large the density map is, you can use the interface of the ImageHandle object used to store the image. The interfaces provides functions to get several items of information about the map:
-
-    print map.GetSize()
-    print map.GetAbsoluteOrigin()
-    print map.GetSpatialOrigin()
-    print map.GetSpatialSampling()
-    print map.GetExtent()
-
-This last command returns an Extent object containing additional information about the extent of the map. Its interface can be used to learn even more.
-
-    print map.GetExtent().GetStart()
-    print map.GetExtent().GetEnd()
-    print map.GetExtent().GetCenter()
-
-You will notice that the GetSpatialSampling method shows that the map has a pixel sampling of 1 Angstrom in all directions. This is not correct. The correct pixel sampling information was not saved on disk. Let’s go ahead and set it manually: it is 2 Angstrom in all directions, so:
-
-    map.SetSpatialSampling(2.0*Units.A)
-
-The map is way too large to be manipulated and visualized comfortably. Since the data have low resolution anyway, we will shrink the map using the DiscreteShrink algorithm.
-
-First, go ahead and import the `img.alg` module.
-
-Then let’s create an instance of the DiscreteShrink algorithm. Let’s pass it a size parameter of 4x4x4. The map will be shrunk by a factor of 4 in all directions.
-Let’s now apply the algorithm to the map. We apply it in place, because we want to overwrite the original data
-map.ApplyIP(shrink_alg)Now go ahead and try to recover the information about the spatial sampling from the map. Verify that the pixel sampling has been adjusted to reflect the shrinking.
-shrink_alg=img.alg.DiscreteShrink(img.Size(4,4,4))
-
-Now, let’s use another algorithm to normalize the density values of the map between the 0 and 1
-norm=img.alg.CreateLinearRangeNormalizer(map,0.0,1.0)When you create an instance of this algorithm, you need to pass it information about the map it will be applied to (map) and the lowest and highest value of the normalization range(0.0 and 1.0)
-
-The algorithm can then be applied to the map. Go ahead and apply it in place, overwriting the original data.
-
-In order to visualize the map, we are now going to create an iso-surface graphical object
-map_go=gfx.MapIso(“map”,map,0.5)This will create a an iso-surface graphical object based on the object “map”, drawing the iso-surface at a threshold level of 0.5. The object will appear in the scene menu with the name “map”.
-
-The graphical object needs to be now added to the scene and center the scene on the object
-scene.Add(map_go)
-scene.SetCenter(map_go.GetCenter())Tah-da! There it is on the screen! If you now select the “map” object in the scene menu, and press the “M” button beside the scene view, you can change the iso-surface threshold interactively. You do this by keeping the ‘command’ key on Mac Computers (or the ‘Control’ key on Linux) and moving the mouse to the left or to the right.
-
-You can always get value of the current iso-surface threshold level using the interface of the graphical object:
-print map_go.GetLevel()
-Finally, let’s create a low-pass-filtered version of the map and display it on the screen.
-We use the LowPassFilter algorithm:
-
-filter=img.alg.LowPassFilter(4.0*Units.nm)
-
-We pass to the algorithm the resolution threshold for the filtering. Please notice that we pass it in nanometers, because we have been working with electron tomography in the past, so it comes easier to us to think in terms of nanometers as opposed to Angstrom. OpenStructure does the necessary conversion internally.
-
-Now let’s apply the algorithm, but this time let’s do it out of place to create a new map.
-
-filtered_map=map.Apply(filter)
-
-Please now go ahead and create a graphical object for this map, give it an appropriate threshold, the name “filtered_map” and add it to the scene. Then play with the iso-surface.
-
-Congratulations, you have completed the exercise!
-
diff --git a/website/raw/docs/tut/vecmath.mkdown b/website/raw/docs/tut/vecmath.mkdown
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-title: Vector Math in OpenStructure
-
-[TOC]
-
-# Vector Math in OpenStructure
-
-## Vector Math
-
-OpenStructure has built-in support for vectors in 2,3 and 4 dimension. They are called
-'Vec2', 'Vec3' and 'Vec4' respectively. You can use the vector classes like in a math formula:
-You can add them together, multiply them by scalar values or calculate the inner and outer
-product. This short code snippet gives an idea of how you can use vectors.
-
-    :::python
-    a=geom.Vec2(1,0)
-    b=geom.Vec2(0,1)
-    # print the vectors
-    print a,b
-
-Here is another example:
-
-    :::python
-    # create a new vector by using components of both a and b.
-    # The components of a vector can be accessed by using the 
-    # array subscript notation:
-    c=geom.Vec2(a[0],b[1])
-    # print length of vector a and b
-    print geom.Length(a), geom.Length(b)
-
-    # calculate dot (inner) product
-    print geom.Dot(a,b)
-
-    # do some fancy calculation
-    d = a+2*b
-    print '%s+2*%s is %s' % (a,b,d)
-   
-In the same tokens, you can use 3 and 4-dimensional vectors. If you want to
-calculate the angle between two vectors, you can use the properties of the
-inner product: Calculating the inner product of two unit-length vectors is
-identical to the cosine of the angle between the two vectors. But the 'geom'
-library also offers a function to directly compute the Angle between two vectors.
-Here are examples of both approaches:
-
-    :::python 
-    # the standard python math module defines the pi constant and the acos function
-    import math
-    angle= math.acos(geom.Normalize(c),geom.Normalize(d))*180.0/math.pi
-    # computing the angle using the geom.Angle function
-    angle2=geom.Angle(c,d)
-
-## Linear Transforms
-
-Linear transforms, such as scaling and rotation of vectors, can be achieved easily.
-
-### Rotation
-
-Rotations are usually carried out using quaternions or rotation matrices. There
-are several helper classes in OpenStructure that encapsulate the logic of rotation.The
-'Rotation3' class represents a rotation in 3D space defined by 3 Euler angles. Please
-notice that although the class requires to be initialized with radiants, one can use
-the Units function to express the value using any homogenous unit (for example, degrees)
-and the conversion will be done automatically. The Units function is available in all OpenStructure modules.
-
-    :::python
-    # define rotation around x axis by 180 degrees (PI radians)
-    rot=geom.Rotation3(math.pi,0,0)
-    # define the same rotation explicitly using radiant units
-    # this is equivalent to the line above
-    rot=geom.Rotation3(math.pi*Units.rad,0,0)
-    # define the same rotation using angle units (again equivalent)
-    rot=geom.Rotation3(180.0*Units.deg,0,0)
-    rot=geom.Rotation3(math.pi)
-    # define the same rotation using the Units 
-    v=geom.Vec3(0,1,0)
-    # rotate v by rot
-    print rot.GetRotationMatrix()*v
-
-In two dimensions, the 'Rotate' function can be used to rotate a vector by a certain amount
-
-    :::python
-    #rotate by 90 degrees (PI/2 radians)
-    print geom.Rotate(geom.Vec2(1,0),math.pi/2)
-
-
-### Scaling
-
-Uniform vector scaling can be accomplished by multiplication of the vector by a
-scalar factor. For non-uniform scaling you can use a 3x3 matrix with all but the
-main diagonal elements set to zero.
-
-    :::python
-    scale=geom.Mat3(1.0,0.0,0.0,
-                    0.0,2.0,0.0,
-                    0.0,0.0,4.0)
-
-    print scale*geom.Vec3(1,1,1)
diff --git a/website/raw/docs/tutorials.mkdown b/website/raw/docs/tutorials.mkdown
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-title: Tutorials
-
-# Tutorials
-
-## For Users
-
- * [Introduction](docs/tut/intro.html)
- * [Vector Math in OpenStructure](docs/tut/vecmath.html)
- 
-### User Interface
- * [Graphical User Interface](docs/tut/gui.html)
- * [Python Shell](docs/tut/pythonshell.html)
- 
-### Molecular Datasets
- * [The query language](docs/tut/query.html)
- * [Connecting Atoms - Conopology](dox/html/module_conop.html)
- * [Storing Custom Data in an Entity](docs/tut/genericprop.html)
-
-### Images and Density Maps
- * [Images / Density Maps - An Introduction](docs/tut/imgintro.html)
- * [Algorithms for Images and Density Maps](docs/tut/imgalg.html)
- * [The Data Viewer](docs/tut/imgdataviewer.html) 
-
- 
-## For Developers
- * [Expanding OpenStructure - Creating a New Module](docs/tut/newmodule.html)
- * [Using External Programs within OpenStructure](docs/tut/external.html)
- * [Creating new algorithms for Images and Density Maps](docs/tut/imgalgdata.html)
- * [Creating new image state algorithms](docs/tut/imgalgdistate.html)
diff --git a/website/raw/download.mkdown b/website/raw/download.mkdown
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-title: Download
-
-[TOC]
-
-# Download
-
-Please choose your platform
-
- * [Windows XP](windowsdownload.html)
- * [MacOS X 10.5 and 10.6](macdownload.html)
- * [Linux](linuxdownload.html)
-
-    
\ No newline at end of file
diff --git a/website/raw/features.mkdown b/website/raw/features.mkdown
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-title: Features
-
-# Features
-
-## General Features
-
- * Cleanly designed API available in both <a target="extern" href="http://www.python.org">Python</a> an C++
- * command line interface for batch processing
- * graphical user interface that is completely scriptable from Python.
-
-## License
-  
-  OpenStructure is released under the <a target="extern" href="http://www.gnu.org/licenses/lgpl-3.0-standalone.html">LGPL Version 3</a> license.
- 
-## Supported Platforms
-
- * [Windows XP](windowsdownload.html)
- * [MacOS X 10.5 and 10.6](macdownload.html)
- * [Linux](linuxdownload.html)
-
-## Macromolecules
-
- * Rich understanding of macromolecular structure datasets.  
- * Support for common file formats.
-   
-## 2D Images and Density Maps
-
- * Image processing tools for both 2-dimensional images and 3-dimensional density maps (Masks,
-   real and Fourier space filters, correlation).
- * Support for the most common formats
-   used in the fields of x-ray, electron crystallography, and atomic force microscopy.
-
-## Supported File Formats
-
-### Molecules
-
- * Brookhaven Database <a target="extern" href="http://www.wwpdb.org/docs.html">PDB</a>
- * <a target="extern" href="http://www.poissonboltzmann.org/file-formats/biomolecular-structurw/pqr">PQR</a>
- * Structure Data File <a target="extern" href="http://www.symyx.com/solutions/white_papers/ctfile_formats.jsp">SDF</a>
-
-### Image/Map Formats
-
- * <a target="extern" href="http://www.libtiff.org/">TIFF</a>
- * <a target="extern" href="http://www.libpng.org/">PNG</a>
- * <a target="extern" href="http://ami.scripps.edu/software/mrctools/mrc_specification.php">MRC</a>/<a target="extern" href="http://2dx.org/">2dx</a>[]()
- * <a target="extern" href="http://www.ccp4.ac.uk/">CCP4</a>
- * <a target="extern" href="http://situs.biomachina.org/">Situs</a>
- * <a target="extern" href="http://www.wadsworth.org/spider_doc/spider/docs/spider.html">Spider</a>
- * <a target="extern" href="http://www.jpk.com/index.2.en.html">JPK</a>
- * <a target="extern" href="http://www.gatan.com/imaging/dig_micrograph.php">Digital Micrograph</a>
- * <a target="extern" href="http://www.veeco.com/">Nanoscope</a>
-
- Binary formats can be read and saved in both little and big endianness.
-
-### Sequence/Alignment Formats
-
- * <a target="extern" href="http://mcast.sdsc.edu/doc/clustalw-format.html">ClustalW</a>
- * <a target="extern" href="http://en.wikipedia.org/wiki/FASTA_format">Fasta</a>
- * Promod (Swiss PDB-Viewer)
diff --git a/website/raw/gallery.mkdown b/website/raw/gallery.mkdown
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index 2d475d0fd1ad85baf32c6cf313929310cb2354e5..0000000000000000000000000000000000000000
--- a/website/raw/gallery.mkdown
+++ /dev/null
@@ -1,8 +0,0 @@
-title: Gallery 
-
-# Gallery 
-|   |   |
-| - | - |
-| [![Loop modelling using our fragment library](100212_Loops_Tn.png "Loop Modelling")](100212_Loops.png "Loop Modelling")| [![BE Scroe](100212_BE_Score_Tn.png "BE Score")](100212_BE_Score.png "BE Score") |
-| [![Screenshot Mac OS](100212_Openstructure1.0a1_1622_Mac_Tn.png "Screenshot Mac OS")](100212_Openstructure1.0a1_1622_Mac.png "Screenshot Mac OS") | [![Screenshot Windows](100212_Openstructure1.0a1_1622_Win_Tn.png "Screenshot Windows")](100212_Openstructure1.0a1_1622_Win.png "Screenshot Windows")|
-| [![Screenshot Linux](100212_Openstructure1.0a1_1622_Linux_Tn.png "Screenshot Linux")](100212_Openstructure1.0a1_1622_Linux.png "Screenshot Linux") ||
diff --git a/website/raw/index.mkdown b/website/raw/index.mkdown
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index 41115478ba33aa810d18e6b1a6f098ab02c64e65..0000000000000000000000000000000000000000
--- a/website/raw/index.mkdown
+++ /dev/null
@@ -1,14 +0,0 @@
-title: Welcome to OpenStructure
-
-
-# Welcome to OpenStructure
-
-This project aims to provide an open-source, modular, flexible, molecular modelling and visualization environment. It is targeted at interested users and method developers in the field of structural bioinformatics.
-
-![Modules](modules.png)
-
-Interested? Then have a look at the [features](features.html) list.
-
-## Getting Started
-
-For users new to OpenStructure, we have prepared an [introduction to the framework](docs/tut/intro.html), a bunch of [tutorials](docs/tutorials.html) and [examples](docs/examples.html) that will help you getting started. For people that are already familiar with the basics, the [API documentation](dox/html/classes.html) provides detailed information on different topics in and around OpenStructure.
diff --git a/website/raw/linuxdownload.mkdown b/website/raw/linuxdownload.mkdown
deleted file mode 100644
index 85664b45372b366f98fdf2ab26ab444689c49840..0000000000000000000000000000000000000000
--- a/website/raw/linuxdownload.mkdown
+++ /dev/null
@@ -1,53 +0,0 @@
-title: Download - Linux
-
-[TOC]
-
-# Download - Linux
-
-OpenStructure is released under the  <a target="extern" href="http://www.gnu.org/licenses/lgpl-3.0-standalone.html">LGPL Version 3</a> license.
-
- * [OpenStructure Linux Bundle](downloads/OSTcurrent_linux.tgz)
-
-This archive file contains a stand-alone self-contained version of OpenStructure for the Linux platform. .
-
-To run it, follow this simple instructions:
-
-1. Unpack the archive. If you are using a graphical desktop manager (like Gnome or KDE), this can be done by
-clicking on the file and selecting the appropriate option in the archiving tool application. If you are using
-a command line terminal, type:
-
-        :::bash
-        tar xvfz <archive name>
- 
-2. Open a terminal, move to the package directory and then to the 'bin' subdirectory:
-
-        :::bash
-        cd <directory name>
-        cd bin
-    
-3. Launch the graphical front end 'DNG':
-
-        :::bash
-        ./dng
-    
-    Or the OpenStructure console 'ost'
-    
-        :::bash
-        ./ost
-        
-Note
-:   The package has been created on a 32bit machine (but should work also on 64 bit machines, provided
-that the correct 32-bit compatibility libraries are installed).
-The following Linux distributions are supported:
-
-* Ubuntu 9.10
-* Ubuntu 9.04
-* Ubuntu 8.10
-* Fedora Core 12
-* Fedora Core 11
-* Fedora Core 10
-* OpenSUSE 11.2
-
-The package does not contain drivers for the graphic card on your machine. In order to fully appreciate
-the OpenStructure experience, you have to install the graphic drivers yourself and activate 3D acceleration.
-This procedure in distribution and architecture specific, so it can not be described in details here.
diff --git a/website/raw/logo.png b/website/raw/logo.png
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diff --git a/website/raw/loops.png b/website/raw/loops.png
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diff --git a/website/raw/macdownload.mkdown b/website/raw/macdownload.mkdown
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index 77820634f199a8e688b086e71a171634c252fd72..0000000000000000000000000000000000000000
--- a/website/raw/macdownload.mkdown
+++ /dev/null
@@ -1,14 +0,0 @@
-title: Download MacOS X
-
-[TOC]
-
-# Download - MacOS X
-
-OpenStructure is released under the  <a target="extern" href="http://www.gnu.org/licenses/lgpl-3.0-standalone.html">LGPL Version 3</a> license.
-
-## Install It
- * [Download the package](downloads/OSTcurrent_macos.pkg). It contains a full-fledged version of OpenStructure. *Important*: You need MacOS 10.5 or later to run OpenStructure.
- *  Double click the package to start the installation
-
-## Run It
- * Run DNG in /Applications/OpenStructure. You can find some example scripts in /Applications/OpenStructure/Examples
\ No newline at end of file
diff --git a/website/raw/modules.png b/website/raw/modules.png
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diff --git a/website/raw/scaffold.html b/website/raw/scaffold.html
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--- a/website/raw/scaffold.html
+++ /dev/null
@@ -1,52 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<html>
-<head>
-    <meta http-equiv="Content-type" content="text/html; charset=utf-8">
-    <base href="%(BASE)s/">
-    <title>%(TITLE)s</title>
-    <link rel="stylesheet" type="text/css" href="css/ost.css" media="screen,print" title="Stylesheet" charset="utf-8">
-
-</head>
-<body>
-    <div id="content-holder">
-        <div id="toc-box">
-        <div id="menu">    
-            <a class="toc-title" >Site Navigation</a>
-	        <div class="toc-sep">
-            <ul>
-                <li><a href="index.html">Home</a></li>
-                <li><a href="docs/tut/intro.html">Getting Started</a></li>
-                <li><a href="features.html">Features</a></li>
-                <li><a href="download.html">Download</a></li>                
-                <li><a href="gallery.html">Gallery</a></li>                
-                <li><a href="docs/index.html">Documentation</a></li>
-                <ul>
-                  <li><a href="docs/tutorials.html">Tutorials</a></li>
-                  <li><a href="docs/examples.html">Examples</a></li>
-                  <li><a href="dox/html/classes.html">Class List</a></li>
-                </ul>
-                <li><a href="FAQ.html">Frequently Answered Questions</a></li>
-
-                <li>
-                    <a href="ack.html">Acknowledgements</a>
-                </li>
-                <li>
-                    <a href="contact.html">Contact</a>
-                </li>
-            </ul>
-			</div>
-            <a class="toc-title" >Table of Contents</a> 
-            <div class="toc-sep" >
-                  %(SITE_NAV)s
-            </div> <!--toc-sep-->
-        </div><!--menu-->
-        </div><!--toc-box-->
-        <div id="content" >
-            %(CONTENT)s
-            <div id="footer">
-                Copyright 2008-2010 by the OpenStructure authors
-            </div>            
-        </div>        
-        </div>  
-</body>
-</html>
diff --git a/website/raw/windowsdownload.mkdown b/website/raw/windowsdownload.mkdown
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--- a/website/raw/windowsdownload.mkdown
+++ /dev/null
@@ -1,16 +0,0 @@
-title: Download/Installation Instructions for the Windows platform 
-
-# Download - Windows
- 
-OpenStructure is released under the  <a target="extern" href="http://www.gnu.org/licenses/lgpl-3.0-standalone.html">LGPL Version 3</a> license.
-
-## Installation
- 1. [Download](downloads/OSTcurrent_windows.zip) the complete OpenStructure package for windows. 
- * Extract the zip archive to your desired folder.  
-## Starting DNG - The Graphical User Interface to OpenStructure
- * Simply start DNG by double clicking ***dng.bat*** in the bin directory.
- * Located in the same directory is also ***ost.bat*** a command line interface to the openstructure framework.
-
-## Supported Windows Platforms
-Currently we only truely support Windows XP.
-
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