[phenixbb] RuntimeError

Young-Jin Cho yjcho at brandeis.edu
Tue Sep 8 13:42:33 PDT 2009


Hi everyone,
while I was running phenix, I got the following error message. Could some one give me any tips to deal with such this problem?
Thanks in advace,

YoungJin


Traceback (most recent call last):
  File "/home/yjcho2/Phenix/phenix-1.4-95/phenix/phenix/command_line/refine.py", line 19, in <module>
    command_line.run(command_name="phenix.refine", args=sys.argv[1:])
  File "/home/yjcho2/Phenix/phenix-1.4-95/phenix/phenix/refinement/command_line.py", line 68, in run
    log=log)
  File "/home/yjcho2/Phenix/phenix-1.4-95/phenix/phenix/refinement/command_line.py", line 227, in __init__
    self.pdb_file_names)
  File "/home/yjcho2/Phenix/phenix-1.4-95/cctbx_project/mmtbx/utils.py", line 876, in process_pdb_files
    raw_records    = raw_records)
  File "/home/yjcho2/Phenix/phenix-1.4-95/cctbx_project/mmtbx/utils.py", line 907, in _process_pdb_file
    log                      = self.log)
  File "/home/yjcho2/Phenix/phenix-1.4-95/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2912, in __init__
    log=log)
  File "/home/yjcho2/Phenix/phenix-1.4-95/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 1962, in __init__
    self.site_symmetry_table().special_position_indices()
  File "/home/yjcho2/Phenix/phenix-1.4-95/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2217, in site_symmetry_table
    sites_cart=self.sites_cart)
  File "/home/yjcho2/Phenix/phenix-1.4-95/cctbx_project/cctbx/crystal/__init__.py", line 394, in site_symmetry_table
    assert_min_distance_sym_equiv=self.assert_min_distance_sym_equiv())
RuntimeError: cctbx Error: site_symmetry: min_distance_sym_equiv too large.

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