Hello again,
With some hints from Ubuntu Forums, I tracked down and corrected my problem.
Hopefully this will be of help to someone else.
The fancy new desktop rendering schemes which are part of Ubuntu v.8, but which
were not part of Ubuntu v.6, use 3D graphics to grow, shrink, and move windows
and icons. Apparently, this conflicts with the way that PyMol wants to talk to
OpenGL.
The solution is to tell the desktop to behave simply. From the Ubuntu main
menu, select System > Preferences > Appearance > Visual Effects. Change the
setting from Normal to None.
Then PyMol works as expected!
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