write this in pymol command window:

import sys
print sys.path

There you can see where pymol is looking.

Or you can this to your .pymolrc in your home folder:

import sys

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2012/5/15 Boris Kheyfets <kheyfboris@gmail.com>
Is there a way I can add a path to 'run' - so not to type the full
path to the script when I run it:

run /path/to/script.py

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