Hi there,

I use both pymol via Fink (on MBP 10.6.2) all in 64 bits and MacPymol.

Both work fine but I tried http://pymolwiki.org/index.php/Launching_From_a_Script


1) export PYTHONPATH=/Applications/MacPyMOL.app/pymol/modules

2) export PYTHONPATH=/sw/lib/pymol-py26/modules

and running 'launch_pymol.sh' script that contains:

#!/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.
from pymol import cmd
cmd.set('stereo_shift', 0.23)
cmd.set('stereo_angle', 1.0)

and I got for:

1) amadeus[2027]:~/TMP% ./pymol.sh
Traceback (most recent call last):
  File "./pymol.sh", line 9, in <module>
    import pymol
  File "/Applications/MacPyMOL.app/pymol/modules/pymol/__init__.py", line 472, in <module>
    import _cmd
ImportError: No module named _cmd

2) amadeus[2029]:~/TMP% ./pymol.sh
Xlib:  extension "XFree86-VidModeExtension" missing on display "/tmp/launch-35V4Bz/:0".
freeglut (pymol): XF86VidModeGetViewPort failed
Xlib:  extension "XFree86-VidModeExtension" missing on display "/tmp/launch-35V4Bz/:0".
freeglut (pymol): XF86VidModeGetModeLine failed
freeglut (pymol): failed to change screen settings
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[1]    25649 segmentation fault  ./pymol.sh

Would someone know what else I can try to do?

Many thanks in advance,

Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.pims-lims.org/
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)