[Biopython] ligand PDB files

[Robert Campbell]

Dear Paul,

On Fri, 2011-10-14 14:00  EDT,  paul at tonair.de wrote:

> Dear all, 
> I'm having trouble to read in the attached PDB file - this
> is my code: 

<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

-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
<robert.campbell at queensu.ca>    http://pldserver1.biochem.queensu.ca/~rlc