Error in DSSP Module of Biopython

Question

[anasjamshed]

I am trying to get RSA through the DSSP module of PDB by using :

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

But it is giving me following error:

FileNotFoundError                         Traceback (most recent call last)
<ipython-input-62-714e350773f8> in <module>
      4 structure = parser.get_structure('X', '1mot.pdb')
      5 model = structure[0]
----> 6 dssp = DSSP(model, '1mot.pdb',acc_array='Miller')
      7 residues = list(dssp)

Although I have a 1mot pdb file in my directory

plz help me

Answer 1

[Mensur Dlakic]

When I repeat your commands, it works just fine. Here are the first 5 lines of the residues list:

(1, 'A', '-', 1.0, 360.0, 153.9, 0, 0.0, 2, -0.7, 0, 0.0, 3, -0.1)
(2, 'P', '-', 0.5944055944055944, -68.1, 106.5, 0, 0.0, 4, -2.7, 0, 0.0, 5, -0.2)
(3, 'A', 'H', 0.6637168141592921, -61.2, -42.4, -2, -0.7, 4, -3.0, 1, -0.2, 5, -0.2)
(4, 'R', 'H', 0.8381742738589212, -60.6, -44.8, 2, -0.2, 4, -2.7, 1, -0.2, -1, -0.2)
(5, 'V', 'H', 0.5375, -64.9, -48.0, 2, -0.2, 4, -3.2, 1, -0.2, 5, -0.3)

This is exactly how it should be, so you most likely do not have 1mot.pdb in your current directory. Maybe you have 1mot.ent or 1mot.pdb.ent instead?

[anasjamshed]

The pdb file is present in my working directory

[Mensur Dlakic]

In that case you most likely don't have the dssp executable at all, or the system can't find it. In Linux it is simply a matter of putting dssp anywhere in the $PATH and I think it is the same for Windows, but not sure. You may have to compile the program for Windows:

https://github.com/cmbi/dssp

[anasjamshed]

how can I add them to the path?

[Mensur Dlakic]

Google is your friend.

https://www.google.com/search?q=windows+%24path

[anasjamshed]

adding in the path does not remove error

[Mensur Dlakic]

dssp executable for your operating system needs to be placed into a directory (or folder) that is defined in the $PATH variable. I don't have the time to explain all of this one terse statement or question at a time. You should have enough information do solve this on you own by doing some research.

[anasjamshed]

mkdssp is a ddsp executable as mentioned in Github .

i add this link C:\Users\USER\Desktop\dssp-master\doc\mkdssp to my environment path but still it is showing error