Question: Biopython module Bio.PDB.DSSP issue with solvent accessible surface area?
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gravatar for westin.kosater
8 months ago by
westin.kosater10 wrote:

Hello

I am working with PDB files in biopython, and I need a quick way to calculate the relative solvent accessibility (RSA) of each residue in a PDB file. Up until now, I have done it this way

from Bio.PDB import *
parser = PDBParser()
io = PDBIO()
structure = parser.get_structure('X', '1fkq.pdb')
model = structure[0]
dssp = DSSP(model, '1fkq.pdb')
residues = list(dssp)

And the residues variable would contain a list of tuples which would contain the RSA. The issue is, according to the documentation https://biopython.org/DIST/docs/api/Bio.PDB.DSSP%27-module.html, the RSA values are by default based off of the Sander values. I want it to compute the RSA based off of the Wilke values. It says in the documentation that any of the values (Wilke, Sander, or Miller) can be used, but I'm not sure how to tell it to use the Wilke values. Does anyone have an idea on how to change this?

dssp biopython python pdb • 360 views
ADD COMMENTlink modified 12 days ago by dmitriy.bobrovnikov10 • written 8 months ago by westin.kosater10
1
gravatar for dmitriy.bobrovnikov
12 days ago by
dmitriy.bobrovnikov10 wrote:

This is definitely a late answer but in case someone else is looking for the answer to this, you can do so by using the argument acc_array when initializing DSSP, like so:

dssp = DSSP(model, '1fkq.pdb', acc_array='Wilke')

The three options are:

  • Wilke
  • Sander
  • Miller
ADD COMMENTlink written 12 days ago by dmitriy.bobrovnikov10
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