[chimera-dev] BioPython on Mac OS X

[Greg Couch]

It looks like that bug is fixed in Python 2.7.8 and Chimera is currently 
using Python 2.7.6.  So until we update the daily builds, replace 
/Applications/Chimera.app/Contents/Resources/frameworks/Python.framework/Versions/2.7/lib/python2.7/_osx_support.py 
with the one from the Python repository 
http://hg.python.org/cpython/raw-file/ee879c0ffa11/Lib/_osx_support.py.

     HTH,

     Greg

On 08/13/2014 08:21 AM, Mateusz Dobrychłop wrote:
> Dear Chimera Team,
>
> I'm currently trying to install BioPython using Chimera's Python copy 
> on Mac OS X.
>
> Thanks to the Chimera Programming FAQ, I've already managed to install 
> BioPython succesfully on Ubuntu, but on Mac OS X I get the following 
> error:
>
> Error while importing Combine from 
> /Applications/Chimera.app/Contents/Resources/share:
>
> Traceback (most recent call last):
>
>   File 
> "/Applications/Chimera.app/Contents/Resources/share/chimera/extension/base.py", 
> line 349, in _importExtension
>
> __import__(module)
>
>   File 
> "/Applications/Chimera.app/Contents/Resources/share/Combine/ChimeraExtension.py", 
> line 32, in <module>
>
> balloon="Combine molecular models into new model", moleculesOnly=True)
>
>   File 
> "/Applications/Chimera.app/Contents/Resources/share/ModelPanel/base.py", 
> line 40, in addButton
>
>     "Button named '%s' already exists" % name
>
> KeyError: "Button named 'copy/combine...' already exists"
>
>
> Error while importing Ramachandran from 
> /Applications/Chimera.app/Contents/Resources/share:
>
> Traceback (most recent call last):
>
>   File 
> "/Applications/Chimera.app/Contents/Resources/share/chimera/extension/base.py", 
> line 349, in _importExtension
>
> __import__(module)
>
>   File 
> "/Applications/Chimera.app/Contents/Resources/share/Ramachandran/ChimeraExtension.py", 
> line 29, in <module>
>
> ModelPanel.addButton("Ramachandran plot...", emo.modelPanelCB)
>
>   File 
> "/Applications/Chimera.app/Contents/Resources/share/ModelPanel/base.py", 
> line 40, in addButton
>
>     "Button named '%s' already exists" % name
>
> KeyError: "Button named 'Ramachandran plot...' already exists"
>
>
> running install
>
> running build
>
> running build_py
>
> running build_ext
>
> Error while processing 'setup.py install':
>
> TypeError: argument of type 'NoneType' is not iterable
>
>
>   File 
> "/Applications/Chimera.app/Contents/Resources/frameworks/Python.framework/Versions/2.7/lib/python2.7/_osx_support.py", 
> line 185, in _find_appropriate_compiler
>
>     if 'llvm-gcc' in data:
>
>
> See reply log for Python traceback.
>
>
>
> Is there anything I can do to solve this problem?
>
> Best,
> Mateusz
>
>
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