Question: How to extract calculated RSA values from dssp and its corresponding residue?
0
gravatar for tpm
13 days ago by
tpm10
tpm10 wrote:

Hello. I ran this code below

  from Bio.PDB import *
    parser = PDBParser()
    io = PDBIO()
    structure = parser.get_structure('3F9R', '3F9R.pdb')
    model = structure[0]
    dssp = DSSP(model, '3F9R.pdb')
    residues = list(dssp)
    residues

How do I select columns for calculated RSA and residue from this dictionary?

If I want to see the contents in this for residues, I have an output file that looks in short like this.

[(1,
  'G',
  '-',
  0.7857142857142857,
  360.0,
  -167.6,
  0,
  0.0,
  2,
  -0.1,
  0,
  0.0,
  444,
  -0.1),
 (2,
  'M',
  '-',
  0.14893617021276595,
  -67.2,
  140.1,
  1,
  -0.1,
  36,
  -0.2,
  2,
  -0.0,
  35,
  -0.1),
 (3,
  'K',
  '-',
  0.23902439024390243,
  -78.0,
  -14.6,
  34,
  -2.9,
  35,
  -0.1,
  2,
  -0.2,
  197,
  -0.1),
ADD COMMENTlink modified 13 days ago • written 13 days ago by tpm10

Have you checked the manual? https://biopython.org/docs/1.75/api/Bio.PDB.DSSP.html

ADD REPLYlink written 13 days ago by Fatima860

To be honest Fatima, I did check, I genuinely think that I don't know how I can extract RSA and its corresponding residue. The actual code is what I am kindly asking in case someone may have passed through this phase. Maybe its because I am not a good programmer, and it can be quite confusing especially when I can`t bring it to perspective.

ADD REPLYlink written 13 days ago by tpm10
1

Maybe you can try a simpler database, for example:

https://swift.cmbi.umcn.nl/gv/dssp/DSSP_3.html

If you prefer to use biopython, then try this to get the relative ASA:

dssp = DSSP(model, '3F9R.pdb', dssp='mkdssp')
a_key = list(dssp.keys())[3]
dssp[a_key]

You may need to read more about python dictionaries. Also, I think it's a good idea to take a look at similar questions here. You can see a list of these questions on the right panel.

ADD REPLYlink modified 13 days ago • written 13 days ago by Fatima860

Thank you, so this code computes relative ASA directly. I will read the link you provided through.

ADD REPLYlink modified 12 days ago • written 12 days ago by tpm10
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