[Biopython] DSSP and secondary structure

xyz mitlox at op.pl
Sun Sep 6 00:40:48 UTC 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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