text: user12686: 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?
  
  user12424: 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
  
  user15589: 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.
  
  
original_text: 12686: <p>I have the following settings in PyCharm:</p>
  <p><a href="https://i.stack.imgur.com/WbEgo.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/WbEgo.png" alt="enter image description here" /></a></p>
  <p>BioPython is properly installed:</p>
  <p><a href="https://i.stack.imgur.com/LVf7F.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/LVf7F.png" alt="enter image description here" /></a></p>
  <p><strong>dssp_test.py</strong></p>
  <pre><code>from Bio.PDB import PDBParser
  from Bio.PDB.DSSP import DSSP
  p = PDBParser()
  structure = p.get_structure(&quot;16PK&quot;, &quot;16pk.pdb&quot;)
  model = structure[0]
  dssp = DSSP(model, &quot;16pk.pdb&quot;)
  a_key = list(dssp.keys())[2]
  print(dssp[a_key])
  </code></pre>
  <p><strong>Output</strong></p>
  <pre><code>C:\ProgramData\Miniconda3\python.exe C:/Users/pc/source/repos/DSSP_algoritm_test/dssp_test.py
  Traceback (most recent call last):
    File &quot;C:\Users\pc\source\repos\DSSP_algoritm_test\dssp_test.py&quot;, line 6, in &lt;module&gt;
      dssp = DSSP(model, &quot;16pk.pdb&quot;)
    File &quot;C:\ProgramData\Miniconda3\lib\site-packages\Bio\PDB\DSSP.py&quot;, line 437, in __init__
      dssp_dict, dssp_keys = dssp_dict_from_pdb_file(in_file, dssp)
    File &quot;C:\ProgramData\Miniconda3\lib\site-packages\Bio\PDB\DSSP.py&quot;, line 231, in dssp_dict_from_pdb_file
      p = subprocess.Popen(
    File &quot;C:\ProgramData\Miniconda3\lib\subprocess.py&quot;, line 947, in __init__
      self._execute_child(args, executable, preexec_fn, close_fds,
    File &quot;C:\ProgramData\Miniconda3\lib\subprocess.py&quot;, 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
  </code></pre>
  <p>Why am I unable to execute DSSP algorithm from BioPython?</p>
   12424: <p>This looks like a python problem and not a “biopython”problem.</p>
  <p>Check your file structures. Try giving a full path for 16pk.pdb</p>
  <p>These might help. <a href="https://stackoverflow.com/questions/17658856/why-am-i-getting-a-filenotfounderror">https://stackoverflow.com/questions/17658856/why-am-i-getting-a-filenotfounderror</a></p>
  <p><a href="https://stackoverflow.com/questions/18757127/windowserror-error-2-the-system-cannot-find-the-file-specified-is-not-resol">https://stackoverflow.com/questions/18757127/windowserror-error-2-the-system-cannot-find-the-file-specified-is-not-resol</a></p>
   15589: <p>Ok so this might not provide a solution, but here's a couple things someone might find useful;</p>
  <ul>
  <li>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)</li>
  <li>Secondly, DSSP within Biopython, for whatever reason, accepts the path to the file, not the file itself. I see you have that correctly (<code>dssp = DSSP(model, &quot;16pk.pdb&quot;)</code>), but just pointing it ou</li>
  <li>Third, DSSP originally had <code>dssp</code> executable, but the newer version has <code>mkdssp</code> executable, so you might need to do <code>dssp = DSSP(model, &quot;16pk.pdb&quot;, dssp=&quot;mkdssp&quot;)</code>, so it knows what to associate it with. This was the problem I had, because without specifying the <code>dssp</code>, it is not able to launch DSSP.</li>
  </ul>
  