old_contents: #!/usr/bin/env ccp4-python
  '''
  Created on 29 Dec 2015
  
  @author: jmht
  '''
  
  import os
  import sys
  
  AMPLE_DIR = os.sep.join(os.path.abspath(os.path.dirname(__file__)).split(os.sep)[ :-2 ])
  sys.path.append(os.path.join(AMPLE_DIR,'python'))
  import test_funcs
  
  test_dict = {}
  
  ###############################################################################
  #
  # Missing Domain
  #
  ###############################################################################
  
  # Specify the arguments to AMPLE to run this test case
  args_missing_domain =  [
                         [ '-fasta', '1k04_.fasta' ],
                         [ '-mtz', '1k04_cad-unique.mtz' ],
                         [ '-domain_all_chains_pdb', 'Known_40.pdb' ],
                         [ '-missing_domain', 'True' ],
                         [ '-frags_3mers', 'aa1k04_03_05.200_v1_3' ],
                         [ '-frags_9mers', 'aa1k04_09_05.200_v1_3' ],
                         [ '-rosetta_dir', '/opt/rosetta-3.5' ]
  ]
  
  class AMPLETest(test_funcs.AMPLEBaseTest):
      def test_missing_domain(self):
          self.assertIn('mrbump_results', self.AMPLE_DICT)
          self.assertGreater(len(self.AMPLE_DICT['mrbump_results']), 0, "No MRBUMP results")
          self.assertTrue(self.AMPLE_DICT['success'])
          self.assertGreater(self.AMPLE_DICT['mrbump_results'][0]['SHELXE_CC'], 25,"SHELXE_CC criteria not met")
          return
  
  # Add everything to the test_dict - the key is used to name the script and run directory
  test_dict['missing_domain'] = { 'args' : args_ideal_helices,
                                 'test' :  AMPLETest,
                                 'directory' : os.path.abspath(os.path.dirname(__file__))
                                  }
  
  ###############################################################################
  #
  # End Test Setup
  #
  ###############################################################################
  
  if __name__ == '__main__':
      test_funcs.parse_args(test_dict)
  
new_contents: #!/usr/bin/env ccp4-python
  '''
  Created on 29 Dec 2015
  
  @author: jmht
  '''
  
  import os
  import sys
  
  AMPLE_DIR = os.sep.join(os.path.abspath(os.path.dirname(__file__)).split(os.sep)[ :-2 ])
  sys.path.append(os.path.join(AMPLE_DIR,'python'))
  import test_funcs
  
  test_dict = {}
  
  ###############################################################################
  #
  # Missing Domain
  #
  ###############################################################################
  
  # Specify the arguments to AMPLE to run this test case
  args_missing_domain =  [
                         [ '-fasta', '1k04_.fasta' ],
                         [ '-mtz', '1k04_cad-unique.mtz' ],
                         [ '-domain_all_chains_pdb', 'Known_40.pdb' ],
                         [ '-missing_domain', 'True' ],
                         [ '-frags_3mers', 'aa1k04_03_05.200_v1_3' ],
                         [ '-frags_9mers', 'aa1k04_09_05.200_v1_3' ],
                         [ '-rosetta_dir', '/opt/rosetta-3.5' ]
  ]
  
  class AMPLETest(test_funcs.AMPLEBaseTest):
      def test_missing_domain(self):
          self.assertIn('mrbump_results', self.AMPLE_DICT)
          self.assertGreater(len(self.AMPLE_DICT['mrbump_results']), 0, "No MRBUMP results")
          self.assertTrue(self.AMPLE_DICT['success'])
          self.assertGreater(self.AMPLE_DICT['mrbump_results'][0]['SHELXE_CC'], 25,"SHELXE_CC criteria not met")
          return
  
  # Add everything to the test_dict - the key is used to name the script and run directory
  test_dict['missing_domain'] = { 'args' : args_missing_domain,
                                 'test' :  AMPLETest,
                                 'directory' : os.path.abspath(os.path.dirname(__file__))
                                  }
  
  ###############################################################################
  #
  # End Test Setup
  #
  ###############################################################################
  
  if __name__ == '__main__':
      test_funcs.parse_args(test_dict)
  
subject: Fix typo