Unfortunately, this cannot work since MacPyMOL embeds Python directly. Your choices are as follows:
1. run your Python scripts from within MacPyMOL 2. launch PyMOL in command-line mode with your script /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL -qc script.py or 3. compile the open-source code into Fink / X11 / Python via distutils. This will enable 'import pymol' from within external python scripts. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info > -----Original Message----- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of Shatadal Ghosh > Sent: Thursday, February 21, 2008 10:54 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Importing pymol modules into python > > Hi All, > > I am using MacPyMOL 0.99rc6 on Mac OS X leopard (10.5.1). I > wanted to import the pymol modules into python. As suggested > by MacPyMOL.app/pymol/modules/pymol/__init__.py I set the > following environment variables: > > export > PYMOL_PATH=$PYMOL_PATH:/Volumes/Home/shatadal/Programs/MacPyMO > L.app/pymol: > export PYTHONPATH=$PYTHONPATH:$PYMOL_PATH/modules: > > Then when I try to import pymol within python (e.g. as shown in > http://www.rubor.de/bioinf/tips_python.html#pythonscr) I get > the following error: > > $ python > Python 2.5.1 (r251:54863, Oct 5 2007, 21:08:09) [GCC 4.0.1 > (Apple Inc. build 5465)] on darwin Type "help", "copyright", > "credits" or "license" for more information. > >>> import pymol > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > File > "/Volumes/Home/shatadal/Programs/MacPyMOL.app/pymol/modules/py > mol/__init__.py", > line 353, in <module> > import _cmd > ImportError: No module named _cmd > >>> > > When I try to run __init__.py from the bash commandline I get > the same error: > > $ python __init__.py > Traceback (most recent call last): > File "__init__.py", line 109, in <module> > import pymol > File > "/Volumes/Home/shatadal/Programs/MacPyMOL.app/pymol/modules/py > mol/__init__.py", > line 353, in <module> > import _cmd > ImportError: No module named _cmd > > Can anyone help me in getting to import the pymol module in python? > > Thanks, > Shatadal. > > -------------------------------------------------------------- > ----------- > This SF.net email is sponsored by: Microsoft Defy all > challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
