[BioPython] Automated ligand extraction from PDB

[Tomek Jarzynka]

On Friday 20 October 2006 11:21, Peter wrote:
> You plan sounds fine.
> If you are going to use BioPython to analyse PDB files later, then this
> would be a good exercise to get to grips with it.

I tried some simple code and it works, but I find the 'H_' comparison
pretty inelegant. Is there any better way to look for HET atoms, or
ligand atoms in particular?

> Also, using the BioPython PDB parser in strict mode (non-permissive)
> then it may also flag up some potential problems in the PDB file which
> you may be interested in for you work.

Thanks, I'll take a look at it. Actually, Kristian Rother who's referenced
as one of the PDB code authors is my 'roommate' at the institute :)

BTW. How does PDB in Biopython relate to pymmlib and cctbx?

> A quick and dirty alternative would be to read in the input file line by
> line, and output selected lines:
> * If is not an atom record, just output it.
> * If is is an atom record, look at the atom id to decide.

Yeah, doing this in a shell script would be easy at first but I am
expecting trouble with some non-standard PDB files.

-- 
Tomasz K. Jarzynka  /  +48 601 706 601  /  tomee(a-t)genesilico(d-o-t)pl
Laboratory of Bioinformatics and Protein Engineering | www.genesilico.pl
International Institute of Molecular and Cell Biology | www.iimcb.gov.pl

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