From: Luke G. <luk...@gm...> - 2009-05-01 10:57:50
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Hi, I'm trying to set up my machine to be able to run python scripts using the PyMol API, but whenever I try to import the pymol module, I get the following output: > Traceback (most recent call last): > File "/Users/lukegoodsell/Documents/Rotation 2/PDB/potentials.py", > line 9, in <module> > import pymol > File > "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/pymol/pymol/__init__.py", > line 438, in <module> > import _cmd > ImportError: No module named _cmd Does anyone have any idea why this is? A search of Google and this mailing list's archive didn't turn up anything useful. My script contains only the following (as pulled from PyMol wiki, iirc): > #!/usr/bin/env python > > # Tell PyMOL we don't want any GUI features. > import __main__ > __main__.pymol_argv = [ 'pymol', '-Gi' ] > > # Importing the PyMOL module will create the window. > > import pymol > > # Call the function below before using any PyMOL modules. > > pymol.finish_launching() > > from pymol import cm I get the same error when attempting 'import pymol' from the python shell. I am running Mac OS X 10.5.6. I downloaded MacPyMol 1.1r1 from http://delsci.com/macpymol/ (the educational edition, as I am a student). My PYMOL_PATH: /Applications/PyMOLX11Hybrid.app/pymol My PYMOL_EXE: /Applications/PyMOLX11Hybrid.app/Contents/MacOS/MacPyMOL My PYTHONPATH (split for easier reading): /System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python /System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/PyObjC /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-tk /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-darwin /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-mac /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-mac/lib-scriptpackates /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5.zip /System/Library/Frameworks/Python.framework/Versions/2.5/lib/pymol I copied the contents of /Applications/PyMOLX11Hybrid.app/pymol/modules to /System/Library/Frameworks/Python.framework/Versions/2.5/lib/pymol, as per my understanding of the top of __init__.py I am new to Macs, Python and the PyMol API, so the probability of a simple oversight on my part is high. I appreciate any help. |
From: Nathaniel E. <nat...@gm...> - 2009-05-01 16:20:36
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On Fri, May 1, 2009 at 3:57 AM, Luke Goodsell <luk...@gm...>wrote: > I'm trying to set up my machine to be able to run python scripts using > the PyMol API, but whenever I try to import the pymol module, I get the > following output: > . . . > I am running Mac OS X 10.5.6. I downloaded MacPyMol 1.1r1 from > http://delsci.com/macpymol/ (the educational edition, as I am a student). > My PYMOL_PATH: /Applications/PyMOLX11Hybrid.app/pymol > My PYMOL_EXE: /Applications/PyMOLX11Hybrid.app/Contents/MacOS/MacPyMOL > . . . > I copied the contents of /Applications/PyMOLX11Hybrid.app/pymol/modules > to /System/Library/Frameworks/Python.framework/Versions/2.5/lib/pymol, > as per my understanding of the top of __init__.py > It's not entirely clear to me what you're trying to do, but I'm pretty certain it's guaranteed not to work. You can't just take compiled objects from inside app bundles and move them around - especially on Mac. You definitely shouldn't be installing PyMOL modules that way. If you need them available for importing by /usr/bin/python, download the open-source version from SourceForge and install it using python distutils (i.e. "python setup.py build" and so on). I just tried this and it seems to work fine - only takes about 10 minutes. -Nat |