Jeremiah wrote:

However, a problem arises once $PYTHONPATH includes the pymol
directory. To use the pymol api, I add the following to ~/.bashrc:

   PYMOL_PATH=/usr/lib/pymodules/python2.5/pymol
   export PYMOL_PATH
   PYTHONPATH=$PYMOL_PATH
   export PYTHONPATH

Don't change your PYTHONPATH like that. You want to put /usr/lib/pymodules/python2.5 onto your PYTHONPATH and import PyMOL's stuff from the pymol package. I.e., instead of

  import api

Do

  from pymol import api

pymol is a package for precisely this reason.

--
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco

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