Launching From a Script

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You can also script your launch.

Example 1

Here is an example script that launches PyMol for stereo viewing on a VisBox. It runs PyMol fullscreen stereo, and disables the internal gui. The environment (PYTHON_PATH and PYMOL_PATH) must already be set up for this example to work (see Example 2 below for how to setup within the script).

#!/usr/bin/env python
 
# Tell PyMOL we don't want any GUI features.
import __main__
__main__.pymol_argv = [ 'pymol', '-qei' ]
 
# 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 cmd
cmd.stereo('walleye')
cmd.set('stereo_shift', 0.23)
cmd.set('stereo_angle', 1.0)

Example 2

This script launches PyMOL without any GUI for scripting only. It enables tab-completion on the python command line and does the PyMOL environment setup (you need to adjust the moddir variable!). Hint: You may save this as "pymol-cli" executable.

#!/usr/bin/python2.6 -i
 
import sys, os
 
# autocompletion
import readline
import rlcompleter
readline.parse_and_bind('tab: complete')
 
# pymol environment
moddir='/opt/pymol-svn/modules'
sys.path.insert(0, moddir)
os.environ['PYMOL_PATH'] = os.path.join(moddir, 'pymol/pymol_path')
 
# pymol launching
import pymol
pymol.pymol_argv = ['pymol','-qc'] + sys.argv[1:]
pymol.finish_launching()
cmd = pymol.cmd

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