[BioPython] Automated ligand extraction from PDB

[Thomas Hamelryck]

On 10/20/06, Tomek Jarzynka <tomee at genesilico.pl> wrote:
> Hi,
>
> I would like to create a script that would take a PDB file as input,
> try and identify the ligand structures and delete them from the PDB
> file.

Take a look at the extract function in Bio.PDB's Dice module.

extract(s, "A", 1 100, "out.pdb")

will write all amino acids between 1 and 100 of chain A in structure s
to file "out.pdb". Hetero residues (ie. ligands) and hydrogens
are not included.

-Thomas