Unable to execute DSSP algorithm from BioPython

Question

I have the following settings in PyCharm:

BioPython is properly installed:

dssp_test.py

from Bio.PDB import PDBParser
from Bio.PDB.DSSP import DSSP
p = PDBParser()
structure = p.get_structure("16PK", "16pk.pdb")
model = structure[0]
dssp = DSSP(model, "16pk.pdb")
a_key = list(dssp.keys())[2]
print(dssp[a_key])

Output

C:\ProgramData\Miniconda3\python.exe C:/Users/pc/source/repos/DSSP_algoritm_test/dssp_test.py
Traceback (most recent call last):
  File "C:\Users\pc\source\repos\DSSP_algoritm_test\dssp_test.py", line 6, in <module>
    dssp = DSSP(model, "16pk.pdb")
  File "C:\ProgramData\Miniconda3\lib\site-packages\Bio\PDB\DSSP.py", line 437, in __init__
    dssp_dict, dssp_keys = dssp_dict_from_pdb_file(in_file, dssp)
  File "C:\ProgramData\Miniconda3\lib\site-packages\Bio\PDB\DSSP.py", line 231, in dssp_dict_from_pdb_file
    p = subprocess.Popen(
  File "C:\ProgramData\Miniconda3\lib\subprocess.py", line 947, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "C:\ProgramData\Miniconda3\lib\subprocess.py", line 1416, in _execute_child
    hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
FileNotFoundError: [WinError 2] The system cannot find the file specified

Process finished with exit code 1

Why am I unable to execute DSSP algorithm from BioPython?

Answer 1

This looks like a python problem and not a “biopython”problem.

Check your file structures. Try giving a full path for 16pk.pdb

These might help. https://stackoverflow.com/questions/17658856/why-am-i-getting-a-filenotfounderror

https://stackoverflow.com/questions/18757127/windowserror-error-2-the-system-cannot-find-the-file-specified-is-not-resol

Answer 2

Ok so this might not provide a solution, but here's a couple things someone might find useful;

• First, Biopython does not automatically contain DSSP, which you have to download as mentioned in the comments below (from here swift.cmbi.umcn.nl/gv/dssp)
• Secondly, DSSP within Biopython, for whatever reason, accepts the path to the file, not the file itself. I see you have that correctly (dssp = DSSP(model, "16pk.pdb")), but just pointing it ou
• Third, DSSP originally had dssp executable, but the newer version has mkdssp executable, so you might need to do dssp = DSSP(model, "16pk.pdb", dssp="mkdssp"), so it knows what to associate it with. This was the problem I had, because without specifying the dssp, it is not able to launch DSSP.