How to extract calculated RSA values from dssp and its corresponding residue?
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2
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19 months ago
tpm ▴ 30

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),

pdb dssp RSA biopython commandline • 907 views
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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 cant bring it to perspective.

1
Entering edit mode

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.

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