diff --git a/deployment/macos/OpenStructure.pmdoc/01dng-contents.xml b/deployment/macos/OpenStructure.pmdoc/01dng-contents.xml
index 642192a6facab10327ee76f0f9bfb7d065229c34..07ba5eb54bb1bc79de429156dc817df23e274fb8 100644
--- a/deployment/macos/OpenStructure.pmdoc/01dng-contents.xml
+++ b/deployment/macos/OpenStructure.pmdoc/01dng-contents.xml
@@ -1 +1 @@
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\ No newline at end of file
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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
index 993fe238aef1380ffeb46e91220ffe529aa33d85..08783eb2be2b5b349a3690e009ed429d67353a0d 100644
--- a/deployment/macos/OpenStructure.pmdoc/01dng.xml
+++ b/deployment/macos/OpenStructure.pmdoc/01dng.xml
@@ -1 +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>installFrom.isRelativeType</mod><mod>parent</mod><mod>includeRoot</mod><mod>relocatable</mod><mod>identifier</mod><mod>requireAuthorization</mod></config><contents><file-list>01dng-contents.xml</file-list><component id="org.openstructure.OpenStructure" path="/Users/marco/proj/ost/deployment/macos/DNG.app" version=""><mod>isRelocatable</mod></component><filter>/CVS$</filter><filter>/\.svn$</filter><filter>/\.cvsignore$</filter><filter>/\.cvspass$</filter><filter>/\.DS_Store$</filter></contents></pkgref>
\ No newline at end of file
+<pkgref spec="1.12" uuid="2FD6FA09-D2A6-4765-A83C-B0F8E372E8FD"><config><identifier>org.openstructure.DNG.pkg</identifier><version>1.0</version><description></description><post-install type="none"/><requireAuthorization/><installFrom relative="true" includeRoot="true">DNG.app</installFrom><installTo>/Applications</installTo><flags><followSymbolicLinks/></flags><packageStore type="internal"></packageStore><mod>parent</mod><mod>requireAuthorization</mod><mod>relocatable</mod><mod>installFrom.isRelativeType</mod><mod>includeRoot</mod><mod>identifier</mod></config><contents><file-list>01dng-contents.xml</file-list><component id="org.openstructure.OpenStructure" path="/Users/marco/Projects/prod_ost/deployment/macos/DNG.app" version="" isRelocatable="true"><locator-info><token title="pkmk-token-18"><search-rule><combo identifier="org.openstructure.OpenStructure" default-path="/Applications/DNG.app"/></search-rule></token></locator-info></component><filter>/CVS$</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
index 96c4158c019fa0700d669659dec7fc756e808cb7..017395170b0b9af69db19dd8ec696b7bd3ebe17a 100644
--- a/deployment/macos/OpenStructure.pmdoc/02standalone-contents.xml
+++ b/deployment/macos/OpenStructure.pmdoc/02standalone-contents.xml
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/deployment/macos/OpenStructure.pmdoc/02standalone.xml b/deployment/macos/OpenStructure.pmdoc/02standalone.xml
index b2a5edadc3a412904fde339a505d45e7b9981dc0..7a54f677ae14a43721dfa5a7e3a665ac77f7f68e 100644
--- a/deployment/macos/OpenStructure.pmdoc/02standalone.xml
+++ b/deployment/macos/OpenStructure.pmdoc/02standalone.xml
@@ -1 +1 @@
-<pkgref spec="1.12" uuid="7458E2CA-C8AE-40AC-B086-775A710CD49E"><config><identifier>org.openstructure.OpenStructure.pkg</identifier><version>1.0</version><description></description><post-install type="none"/><requireAuthorization/><installFrom relative="true">standalone</installFrom><installTo mod="true">/Library/OpenStructure</installTo><flags><followSymbolicLinks/></flags><packageStore type="internal"></packageStore><mod>installTo</mod><mod>relocatable</mod><mod>requireAuthorization</mod><mod>parent</mod><mod>identifier</mod><mod>installTo.path</mod><mod>installFrom.isRelativeType</mod></config><contents><file-list>02standalone-contents.xml</file-list><filter>/CVS$</filter><filter>/\.svn$</filter><filter>/\.cvsignore$</filter><filter>/\.cvspass$</filter><filter>/\.DS_Store$</filter></contents></pkgref>
\ No newline at end of file
+<pkgref spec="1.12" uuid="7458E2CA-C8AE-40AC-B086-775A710CD49E"><config><identifier>org.openstructure.OpenStructure.pkg</identifier><version>1.0</version><description></description><post-install type="none"/><requireAuthorization/><installFrom relative="true">standalone</installFrom><installTo mod="true">/Library/OpenStructure</installTo><flags><followSymbolicLinks/></flags><packageStore type="internal"></packageStore><mod>parent</mod><mod>requireAuthorization</mod><mod>relocatable</mod><mod>installFrom.isRelativeType</mod><mod>installTo.path</mod><mod>installTo</mod><mod>identifier</mod></config><contents><file-list>02standalone-contents.xml</file-list><filter>/CVS$</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/03examples-contents.xml b/deployment/macos/OpenStructure.pmdoc/03examples-contents.xml
index 344005f19fb779c9bb00e0a8ea1d0d1c7168cd1f..f18a985612230d440ca95a85e4f7440be08ac5e1 100644
--- a/deployment/macos/OpenStructure.pmdoc/03examples-contents.xml
+++ b/deployment/macos/OpenStructure.pmdoc/03examples-contents.xml
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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
index a9a757dde7bcd13722b5afe7cf68bd36c14e349f..ff0317996f21014d462583eae994b0775529ce4b 100644
--- a/deployment/macos/OpenStructure.pmdoc/03examples.xml
+++ b/deployment/macos/OpenStructure.pmdoc/03examples.xml
@@ -1 +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>installTo.path</mod><mod>installFrom.isRelativeType</mod><mod>installFrom.path</mod><mod>parent</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$</filter></contents></pkgref>
\ No newline at end of file
+<pkgref spec="1.12" uuid="C2FAE439-87F5-415C-91EE-0436CC2E4D66"><config><identifier>org.openstructure.Examples.pkg</identifier><version>1.0</version><description></description><post-install type="none"/><requireAuthorization/><installFrom relative="true" mod="true">../../examples</installFrom><installTo mod="true">/Library/OpenStructure/examples</installTo><flags><followSymbolicLinks/></flags><packageStore type="internal"></packageStore><mod>parent</mod><mod>installFrom.isRelativeType</mod><mod>installTo.path</mod><mod>installFrom.path</mod><mod>installTo</mod><mod>identifier</mod></config><contents><file-list>03examples-contents.xml</file-list><filter>/CVS$</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
index 830dcb05fdbf20e3b8ca3939c6dbb88335645db9..58623dbf2cb0cf54e05205cd5611105624528a24 100644
--- a/deployment/macos/OpenStructure.pmdoc/index.xml
+++ b/deployment/macos/OpenStructure.pmdoc/index.xml
@@ -1 +1 @@
-<pkmkdoc spec="1.12"><properties><title>OpenStructure</title><build>/Users/marco/Documents/OpenStructure.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" starts_selected="true" starts_enabled="true" starts_hidden="false"><pkgref id="org.openstructure.DNG.pkg"/></choice><choice title="OpenStructure" id="choice7" starts_selected="true" starts_enabled="true" starts_hidden="false"><pkgref id="org.openstructure.OpenStructure.pkg"/></choice><choice title="examples" id="choice8" 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><requirements><requirement id="sosv" operator="ge" value="'10.6.0'"><message-title>Snow Leopard Required</message-title><message>OpenStructure requires Snow Leopard in order to run</message></requirement></requirements><flags/><item type="file">01dng.xml</item><item type="file">02standalone.xml</item><item type="file">03examples.xml</item><mod>properties.title</mod><mod>properties.customizeOption</mod><mod>properties.userDomain</mod><mod>properties.anywhereDomain</mod><mod>properties.systemDomain</mod></pkmkdoc>
\ No newline at end of file
+<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/deps.py b/deployment/macos/deps.py
index 1bcb4ab08ee2b25c96025f269ada95380bde21de..aaf1b14b0d6faeff833adbe3cf0d3afc540a1487 100644
--- a/deployment/macos/deps.py
+++ b/deployment/macos/deps.py
@@ -2,6 +2,7 @@ import os
 import subprocess
 import shutil
 import sys
+import glob
 def _lib_name(component):
   return 'libost_%s.dylib' % component
 
@@ -168,26 +169,26 @@ def update_pymod_shared_objects(args, path, files):
       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=='.py':
-      pyc_path=os.path.join(path, '%s.pyc' % base)
-      if os.path.exists(pyc_path):
-        os.unlink(pyc_path)      
-      pyo_path=os.path.join(path, '%s.pyo' % base)
-      if os.path.exists(pyo_path):
-        os.unlink(f)
-
+    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/'
+    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.
@@ -207,6 +208,7 @@ def make_standalone(stage_dir, outdir, no_includes, force_no_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)
@@ -224,6 +226,27 @@ def make_standalone(stage_dir, outdir, no_includes, force_no_rpath=False):
   print 'copying pymod'
   shutil.copytree(os.path.join(stage_dir, 'lib/openstructure'), 
                   os.path.join(outdir, 'lib/openstructure'))
+  assert not os.path.exists(os.path.join(outdir, 'lib', 'Python.framework'))
+  if len(glob.glob(os.path.join(outdir, 'lib', 'libpython*')))>0:
+    print 'looks like we are using a non-standard python.'
+    python_home=get_python_home()
+    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)
+    shutil.rmtree(os.path.join(modules_dst, 'site-packages'))
+    copy_binaries(os.path.join(python_home, '../..'), outdir, 
+                  ['python'], [], use_rpath)
+    # replace the python executable
+    ost_script=os.path.join(outdir, 'bin', 'ost')
+    os.chmod(ost_script, 0666)
+    script=''.join(open(ost_script, 'r').readlines())
+    python_bin=os.path.abspath(os.path.join(python_home, '../../bin/python'))
+    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)  
@@ -236,6 +259,6 @@ def make_standalone(stage_dir, outdir, no_includes, force_no_rpath=False):
     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', 'openstructure'), 
+  os.path.walk(os.path.join(outdir, 'lib'), 
                update_pymod_shared_objects, 
                (os.path.join(outdir, 'lib'), use_rpath))