PyMOL runs with its own Python interpreter -- it does not (and cannot) work with external interpreter code unless that interpreter exactly matches the version
Try pointing PYTHONPATH at installed BioPython directly, or try copying BioPython into PyMOL's modules directory.

From: Bradley Hintze []
Sent: Friday, April 24, 2009 9:48 PM
Subject: [PyMOL] importing in scripts

I am trying to import a BioPython module into a pymol script but pymol can' find it. When I import it from the DOS>python command line it imports fine. Obviously pymol isn't looking in the right place for the module. Is there a way to force pymol to look in the right place?

Bradley J. Hintze
Biochemistry Undergraduate
Utah State University