I have had this problem for the past few weeks, and it has been difficult to diagnose the cause.  The problem is that in the X11 version of pymol run on my mactel osx laptop does not interpret my three button mouse click properly.  When I click on a given atom in the UI, it selects something else, often far away from the the intended selection.  This is more of an annoyance, since I can visualize molecule, but the wizards and click menus are basically non-functional.   

If anyone out there has any suggestions I would love to hear them.

Thanks,

-Scott
____________________________________________ 
Scott Shandler 
Ph.D. Candidate Biochemistry & Molecular Biophysics 
Wharton School of Business MBA '06 
University of Pennsylvania 
shandles @ mail.med.upenn.edu