[Biopython] DSSP and secondary structure

[km]

use pymol
KM

On Sun, Sep 6, 2009 at 9:40 AM, xyz <mitlox at op.pl> wrote:

> Hello,
> I have a solved structure (1E8W) with a ligand and I would like to know
> which secondary structure are within 16A (cut off) of the ligand. I am no
> interested in coils.
>
> From looking at the PDB file, ligand is last residue in chain A, named QUE.
>
> I wrote a little script (see bellow please) in order to test DSSP and it
> works.
>
> from Bio.PDB import *
>
> pdb_code = "1E8W"
> pdb_filename = "1E8W.pdb"
>
> structure = PDBParser().get_structure(pdb_code, pdb_filename)
> model=structure[0]
> dssp=DSSP(model, pdb_filename, "./dsspcmbi")
>
> for r in dssp:
>   print r
>   print len(dssp)
>
> Unfortunately, I do not know how can I find the secondary structures around
> 16A of the ligand.
>
> Thank you in advance.
>
> Best regards
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>