We have seen such problems with OpenGL-based applications, including PyMOL, running under ATI Radeon hardware & graphics with older versions of the OpenGL-based Compiz window manager.  
The easiest solution is to reconfigure Linux to disable compositing and/or use a conventional window manager.  It might also be possible to upgrade the Window manager and OpenGL driver to recent versions, which may or may not still exhibit the same problems.

From: John Ladasky []
Sent: Fri 10/23/2009 5:03 AM
Subject: [PyMOL] Upgraded computer, PyMol now unusable :^(

Hi folks,
I was using PyMol with no problems about a year ago.  I believe that my PyMol version was in the 0.9x series.  I was using Ubuntu Linux 6.06 on a Pentium IV machine.
Since then I have upgraded to a new multi-core motherboard, and Ubuntu Linux 8.04.  The Linux repository has a PyMol v1.0 package, so I downloaded that first.  It installed with no apparent errors. 
Running it, though, is another matter.  The command window appears, but the molecule display frame appears for just an instant, and then vanishes.  If I load a PDB file, again the
molecule display frame will appear -- and then disappear again.
I uninstalled PyMol v 1.0 and installed PyMol v 1.1 directly from the PyMol web site.  This made no difference to the program's behavior.
When I run PyMol from the terminal, here's what appears in the terminal window:


...$ pymol
 PyMOL(TM) Evaluation Product - Copyright (C) 2008 DeLano Scientific LLC.
 A current PyMOL Maintenance and/or Support Subscription may be required
 for legal use of this Executable Build beyond a finite evaluation period.
 Please visit for more information and
 contact when you are ready to purchase a Subscription.
 This Executable Build integrates and extends Open-Source PyMOL 1.1eval.
 OpenGL graphics engine:
  GL_VENDOR: ATI Technologies Inc.
  GL_RENDERER: ATI Radeon HD 3200 Graphics
  GL_VERSION: 2.1.7412 Release
 Detected 3 CPU cores.  Enabled multithreaded rendering.

Most of the same text appears in the text frame of the PyMol command window, except for the four lines concerning OpenGL.
As you can see, no errors have been reported.
What could possibly be wrong???  Thanks for any suggestions!