[Biopython] ligand PDB files

[paul at tonair.de]

Dear Rob,

thank you very much for your help, this fixed the error!!


Cheers,
Paul

> <snip>
> Your code is okay.  The problem is in your PDB file:
> 
> 
>>  File
>> "/SW/python/lib/python2.6/site-packages/biopython/Bio/PDB/Atom.py", line
>> 68, in __init__
>>  assert not element or element == element.upper(),
>> element
>> AssertionError: Cl
>> "
>> Does this mean that the PDB parser only
>> recognizes "amino acid-atoms", i.e. a chlorine does not work?
> 
> The chlorine atoms should be "CL" not "Cl" in a proper PDB file.
> 
> Cheers,
> Rob