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Launching From a Script
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You can also script your launch. Here is an example script that launches PyMol for stereo viewing on a VisBox. It runs PyMol fullscreen stereo, and disables the internal gui.
#!/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 cmd
cmd.stereo('walleye')
cmd.set('stereo_shift', 0.23)
cmd.set('stereo_angle', 1.0)