This is probably more of a installation/debian problem than a pymol
I would say that somehow the freeglut3 package is not installed on your
apt-get install freeglut3 should solve it.
However the Pymol package depends on freeglut3 so there might be more
wrong with your system. try apt-get -f install to search for broken
dependensies. How did you install pymol?
Otherwise install manually from a downloaded .tgz from the pymol
homepage. That way you'll also get the newest version.
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