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Biopython module Bio.PDB.DSSP issue with solvent accessible surface area?

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?

python biopython pdb dssp
• 4,383 views • link
updated by dmitriy.bobrovnikov • dmitriy.bobrovnikov • written by westin.kosater • westin.kosater

1 answer

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
• 0 views • link
written by dmitriy.bobrovnikov • dmitriy.bobrovnikov

How can one make a dataframe for RSA calculated and its corresponding residue. If there are codes to follow up this question above, I would gladly appreciate it very much as I am still in my infancy with regards to coding. Thank you in advance.

• 0 views • link
written by tpm • tpm

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