I am using Pymol on Jaunty and came across a similar bug. 
The error I see is this:
Match-Error: unable to open matrix file 
'/usr/share/pymol/pymol/matrices/BLOSUM62'.

When I checked, I noticed that /usr/share/pymol directory does not have another 
'pymol' directory. However, /usr/share/pymol has a 'matrices' directory in 
which BLOSUM62 is present. So, I created a 'pymol' directory in 
/usr/share/pymol and made a symlink to matrices folder there. 
That fixed it! But this is something that may need to be fixed so that it works 
out of the box.

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pymol can not find the BLOSUM62 matrix; wrong path
https://bugs.launchpad.net/bugs/71045
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