Hi PyMOLers,

I managed to figure out what the problem was.  Although I was generating the 
short peptide without any problems using PyMOL, the name that was I saving the 
PDB file to was called "ala2.pymol.pdb" and I guess PyMOL didn't like this name 
(omitting the ".pymol" part fixed the problem).  

Sean
                                          
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