title: WindowsError:[Error 2] The system cannot find the file specified
body: <p>I am facing problem with this error, on the very first place I created the file <code>compcode1</code> and on the second step I am trying to read the same file which is <code>compcode1</code> from the path <code>path_compcode1</code> and it gives me the following error </p>
  
  <blockquote>
    <p>WindowsError: [Error 2] The system cannot find the file specified.</p>
  </blockquote>
  
  <pre><code># Extract Secondary Secondary Structure Elements (SSEs)    
  
  def Secondary_Structure(self, code, flag):
  
      curr_dir = os.path.dirname(os.path.abspath(__file__))     # cuurent directory
      dest_dir = os.path.join(curr_dir, 'Output')
  
      if flag == 1:
          compcode1 = '1Complete_' + code + '.pdb'  
          path_compcode1 = os.path.join(dest_dir, compcode1)
          print path_compcode1
      else:
          compcode2 = '2Complete_' + code + '.pdb'
          path_compcode2 = os.path.join(dest_dir, compcode2)
          print path_compcode2
  
  
  
      self.SSE = []
      p = PDBParser()
      if flag == 1:
          s = p.get_structure('pdb1', path_compcode1)
      else:
          s = p.get_structure('pdb2', path_compcode2)
  
  
      model = s[0]
      if flag == 1:                              #### Flag 1: 1st pdb file
          d = DSSP(model, path_compcode1)
      elif flag == 2:                            #### Flag 2: 2nd pdb file                            
          d = DSSP(model, path_compcode2)
      else:
          print "Oops: Error"    
  
          print "dssp: Secondary Structure"
  </code></pre>
  
  <p>Traceback:</p>
  
  <pre><code>C:\Users\..\Output\1Complete_1cwa.pdb 
  Traceback (most recent call last):
    File "Main_Program.py", line 3353, in &lt;module&gt; 
      main()
    File "Main_Program.py", line 156, in main
      EM_obj1.Secondary_Structure(code, flag)     #### This will extract dssp
    File "C:\Users\..\Output\Module_ContMat.py", line 369, in Secondary_Structure
       d = DSSP(model, compcode1)
    File "c:\Python27\lib\site-packages\Bio\PDB\DSSP.py", line 303, in __init__
       dssp_dict, dssp_keys = dssp_dict_from_pdb_file(in_file, dssp)
    File "c:\Python27\lib\site-packages\Bio\PDB\DSSP.py", line 133, in dssp_dict_from_pdb_file
       stdout=subprocess.PIPE, stderr=subprocess.PIPE)
    File "c:\Python27\lib\subprocess.py", line 711, in __init__
       errread, errwrite)
    File "c:\Python27\lib\subprocess.py", line 959, in _execute_child
       startupinfo) 
  WindowsError: [Error 2] The system cannot find the file specified
  </code></pre>