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 @@
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\ 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 @@
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\ 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 @@
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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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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..642192a6facab10327ee76f0f9bfb7d065229c34
--- /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..21481eee933a42a91bd5ac16975f3ee80215bd5e
--- /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/><post-install type="none"/><requireAuthorization/><installFrom relative="true">DNG.app</installFrom><installTo>/Applications</installTo><flags><followSymbolicLinks/></flags><packageStore type="internal"/><mod>identifier</mod><mod>installFrom.isRelativeType</mod><mod>relocatable</mod><mod>requireAuthorization</mod><mod>parent</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="" isRelocatable="true"><locator-info><token title="pkmk-token-4"><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..96c4158c019fa0700d669659dec7fc756e808cb7
--- /dev/null
+++ b/deployment/macos/OpenStructure.pmdoc/02standalone-contents.xml
@@ -0,0 +1 @@
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diff --git a/deployment/macos/OpenStructure.pmdoc/02standalone.xml b/deployment/macos/OpenStructure.pmdoc/02standalone.xml
new file mode 100644
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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
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p="33188"/><f n="glwin.pyc" o="marco" g="staff" p="33188"/><f n="hud.py" o="marco" g="staff" p="33188"/><f n="hud.pyc" o="marco" g="staff" p="33188"/><f n="images" o="marco" g="staff" p="16877"><f n="openstructure.png" o="marco" g="staff" p="33188"/><f n="rotation.png" o="marco" g="staff" p="33188"/><f n="translation.png" o="marco" g="staff" p="33188"/></f><f n="KEYS" o="marco" g="staff" p="33188"/><f n="level.py" o="marco" g="staff" p="33188"/><f n="level.pyc" o="marco" g="staff" p="33188"/><f n="level_info.py" o="marco" g="staff" p="33188"/><f n="level_info.pyc" o="marco" g="staff" p="33188"/><f n="level_intro.py" o="marco" g="staff" p="33188"/><f n="level_messages.py" o="marco" g="staff" p="33188"/><f n="level_messages.pyc" o="marco" g="staff" p="33188"/><f n="ligand.py" o="marco" g="staff" p="33188"/><f n="ligand.pyc" o="marco" g="staff" p="33188"/><f n="name_enter.py" o="marco" g="staff" p="33188"/><f n="name_enter.pyc" o="marco" g="staff" p="33188"/><f n="protein.py" o="marco" g="staff" p="33188"/><f n="protein.pyc" o="marco" g="staff" p="33188"/><f n="score_updater.py" o="marco" g="staff" p="33188"/><f n="score_updater.pyc" o="marco" g="staff" p="33188"/><f n="spacenav_connect.py" o="marco" g="staff" p="33188"/><f n="spnav_input.py" o="marco" g="staff" p="33188"/><f n="spnav_input.pyc" o="marco" g="staff" p="33188"/><f n="start_dokk.py" o="marco" g="staff" p="33188"/><f n="surface.py" o="marco" g="staff" p="33188"/><f n="surface.pyc" o="marco" g="staff" p="33188"/></f><f n="entity" o="marco" g="staff" p="16877"><f n="bbox.py" o="marco" g="staff" p="33188"/><f n="color_by_property.py" o="marco" g="staff" p="33188"/><f n="fragment.pdb" o="marco" g="staff" p="33188"/><f n="fragment2.pdb" o="marco" g="staff" p="33188"/><f n="gfx_selection.py" o="marco" g="staff" p="33188"/><f n="gfx_symmetry.py" o="marco" g="staff" p="33188"/><f n="gradient.py" o="marco" g="staff" p="33188"/><f n="load_and_display.py" o="marco" g="staff" p="33188"/><f n="pdb1ake.ent" o="marco" g="staff" p="33188"/><f n="pdb4ake.ent" o="marco" g="staff" p="33188"/><f n="primitives.py" o="marco" g="staff" p="33188"/><f n="random_lines.py" o="marco" g="staff" p="33188"/><f n="rendermodes.py" o="marco" g="staff" p="33188"/><f n="sdh.pdb" o="marco" g="staff" p="33188"/><f n="superpose.py" o="marco" g="staff" p="33188"/></f><f n="harmony" o="marco" g="staff" p="16877"><f n="glwin.py" o="marco" g="staff" p="33188"/><f n="glwin.pyc" o="marco" g="staff" p="33188"/><f n="harmony" o="marco" g="staff" p="33261"/><f n="harmony.py" o="marco" g="staff" p="33188"/></f><f n="img" o="marco" g="staff" p="16877"><f n="circle.png" o="marco" g="staff" p="33188"/><f n="create_split_image.py" o="marco" g="staff" p="33188"/><f n="fft_li.py" o="marco" g="staff" p="33188"/><f n="modulate_image.py" o="marco" g="staff" p="33188"/><f n="spoke.png" o="marco" g="staff" p="33188"/><f n="spoke_pattern.py" o="marco" g="staff" p="33188"/><f n="square.png" o="marco" g="staff" p="33188"/><f n="tone1.png" o="marco" g="staff" p="33188"/><f n="tone2.png" o="marco" g="staff" p="33188"/><f n="tone3.png" o="marco" g="staff" p="33188"/><f n="tone4.png" o="marco" g="staff" p="33188"/><f n="tone5.png" o="marco" g="staff" p="33188"/><f n="view_phase_diff.py" o="marco" g="staff" p="33188"/></f><f n="map" o="marco" g="staff" p="16877"><f n="1ppt.map" o="marco" g="staff" p="33188"/><f n="1ppt.pdb" o="marco" g="staff" p="33188"/><f n="gfx_mapiso.py" o="marco" g="staff" p="33188"/><f n="gfx_mapslab.py" o="marco" g="staff" p="33188"/></f><f n="misc" o="marco" g="staff" p="16877"><f n="ambient_occlusion.py" o="marco" g="staff" p="33188"/><f n="bitmap_export.py" o="marco" g="staff" p="33188"/><f n="export_pov.py" o="marco" g="staff" p="33188"/><f n="fragment.face" o="marco" g="staff" p="33188"/><f n="fragment.pdb" o="marco" g="staff" p="33188"/><f n="fragment.vert" o="marco" g="staff" p="33188"/><f n="the_hammer.py" o="marco" g="staff" p="33188"/></f><f n="modelling" o="marco" g="staff" p="16877"><f n="roll_helix.py" o="marco" g="staff" p="33188"/><f n="sdh.pdb" o="marco" g="staff" p="33188"/><f n="strip_sidechains.py" o="marco" g="staff" p="33188"/></f><f n="seq" o="marco" g="staff" p="16877"><f n="seq_viewer.py" o="marco" g="staff" p="33188"/><f n="sh2.aln" o="marco" g="staff" p="33188"/></f><f n="surf" o="marco" g="staff" p="16877"><f n="fragment.pdb" o="marco" g="staff" p="33188"/><f n="sdh.face" o="marco" g="staff" p="33261"/><f n="sdh.pdb" o="marco" g="staff" p="33188"/><f n="sdh.vert" o="marco" g="staff" p="33261"/><f n="test_surf.py" o="marco" g="staff" p="33188"/><f n="test_surf_pov.py" o="marco" g="staff" p="33188"/></f><f n="trj" o="marco" g="staff" p="16877"><f n="fragment.pdb" o="marco" g="staff" p="33188"/><f n="mpor_trj.crd" o="marco" g="staff" p="33261"/><f n="mpor_trj_short.trj" o="marco" g="staff" p="33261"/><f n="sample.dcd" o="marco" g="staff" p="33188"/><f n="sample.pdb" o="marco" g="staff" p="33188"/><f n="test_trj.py" o="marco" g="staff" p="33188"/><f n="test_trj_blur.py" o="marco" g="staff" p="33188"/></f><f n="ui" o="marco" g="staff" p="16877"><f n="board.py" o="marco" g="staff" p="33188"/><f n="color_tool.py" o="marco" g="staff" p="33188"/><f n="mdi_example.py" o="marco" g="staff" p="33188"/><f n="menubar_example.py" o="marco" g="staff" p="33188"/><f n="widget_example.py" o="marco" g="staff" p="33188"/></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..51c204709132729a119f8a71e8ef56455e10aba9
--- /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/><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"/><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
diff --git a/deployment/macos/OpenStructure.pmdoc/index.xml b/deployment/macos/OpenStructure.pmdoc/index.xml
new file mode 100644
index 0000000000000000000000000000000000000000..830dcb05fdbf20e3b8ca3939c6dbb88335645db9
--- /dev/null
+++ b/deployment/macos/OpenStructure.pmdoc/index.xml
@@ -0,0 +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
diff --git a/deployment/macos/bundle.py b/deployment/macos/bundle.py
new file mode 100644
index 0000000000000000000000000000000000000000..5b7e4c113ea2cfca8b3986b91d46ba72e480a346
--- /dev/null
+++ b/deployment/macos/bundle.py
@@ -0,0 +1,73 @@
+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):
+  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):
+  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)
+  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):
+  _CreateBundleSkeleton(bundle_name)
\ No newline at end of file
diff --git a/deployment/macos/deploy.py b/deployment/macos/deploy.py
new file mode 100644
index 0000000000000000000000000000000000000000..396d3c3d8903d6ae1abe7ecb589ad7fd990d747b
--- /dev/null
+++ b/deployment/macos/deploy.py
@@ -0,0 +1,4 @@
+import bundle
+import deps
+bundle.create_bundle('DNG')
+deps.make_standalone('../../stage', 'standalone', True)
diff --git a/deployment/macos/deps.py b/deployment/macos/deps.py
new file mode 100644
index 0000000000000000000000000000000000000000..5b4fcd3af350b4bc92851ce14e45877338ab563a
--- /dev/null
+++ b/deployment/macos/deps.py
@@ -0,0 +1,177 @@
+import os
+import subprocess
+import shutil
+import sys
+def _LibName(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):
+  """
+  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', 
+                                          _LibName(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)
+  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='install_name_tool -id @rpath/%s %s'   
+CHANGE_LOAD_CMD='install_name_tool -change %s @rpath/%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):
+  for binary_name in binary_names:
+    bin_name=os.path.abspath(os.path.join(stage_dir, 'bin', 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)
+    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 update_load_commands(lib):
+  direct_deps=set()
+  _deps_for_lib(lib, direct_deps, recursive=False)
+  for direct_dep in direct_deps:
+    if direct_dep.endswith('.dylib'):
+      new_name=os.path.basename(direct_dep)
+      os.system(CHANGE_LOAD_CMD % (direct_dep, new_name, lib))
+    else:
+      assert direct_dep.find('.framework/')>=0
+      framework_path, rel_path=split_framework_components(direct_dep)
+      framework_name=os.path.basename(framework_path)      
+      dst_name=os.path.join(framework_name, rel_path)
+      new_name=os.path.join(framework_name, rel_path)
+      os.system(CHANGE_LOAD_CMD % (direct_dep, new_name, lib))
+  os.system(ADD_RPATH % ('.', lib))
+
+def copy_deps(dependencies, outdir):
+  for dep in dependencies:
+    if dep.endswith('.dylib'):
+      dst_name=os.path.join(outdir, 'lib', os.path.basename(dep))
+      shutil.copy(dep, dst_name)
+      os.system(CHANGE_ID % (os.path.basename(dep), dst_name))
+      update_load_commands(dst_name)
+    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)
+      os.system(CHANGE_ID % (os.path.join(dst_name, rel_path), 
+                             os.path.join(dst_name, rel_path)))
+      update_load_commands(os.path.join(dst_name, rel_path))
+
+def update_pymod_shared_objects(lib_path, path, files):
+  for f in files:
+    if os.path.splitext(f)[1] == '.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)
+
+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 make_standalone(stage_dir, outdir, no_includes):
+  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)
+  print 'copying dependencies'
+  copy_deps(deps, outdir)
+  print 'copying binaries'
+  copy_binaries(stage_dir, outdir, BINARIES, SCRIPTS)
+  print 'copying pymod'
+  shutil.copytree(os.path.join(stage_dir, 'lib/openstructure'), 
+                  os.path.join(outdir, 'lib/openstructure'))
+  if no_includes:
+    os.system(REMOVE_HEADERS % outdir)
+    os.system(REMOVE_CURRENT % outdir)  
+  site_packages=get_site_package_dir()
+  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', 'openstructure'), 
+               update_pymod_shared_objects, 
+               os.path.join(outdir, 'lib'))