[Biopython] DSSP and secondary structure
xyz
mitlox at op.pl
Sat Sep 5 20:40:48 EDT 2009
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
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