Dear PHENIXBBs,

 

I tried to refine a N-linked glycan using phenix.refine and used the data_link=NAG-ASN for ASN-NAG connection. But I got a RuntimeError of unknown atom_id: HD22. From the mon_lib_list.cif file of Phenix-1.5-2, the atom_id HD22 is already defined. Any suggestions are appreciated.

 

Thanks

 

J.X. QI

 

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Monomer Library directory:
    "/home/jxqi/152Phenix/phenix-1.5-2/chem_data/mon_lib"
  Total number of atoms: 11844
  apply_cif_link:
    data_link: NAG-ASN
      mod_id_1: DEL-O1
      mod_id_2: DEL-HD22
    residue_selection_1: chain A and resname ASN and resid 170
    residue_selection_2: chain A and resname NAG and resid 1
  apply_cif_link:
    data_link: NAG-ASN
      mod_id_1: DEL-O1
      mod_id_2: DEL-HD22
    residue_selection_1: chain C and resname ASN and resid 170
    residue_selection_2: chain C and resname NAG and resid 1
  apply_cif_link:
    data_link: NAG-ASN
      mod_id_1: DEL-O1
      mod_id_2: DEL-HD22
    residue_selection_1: chain E and resname ASN and resid 170
    residue_selection_2: chain E and resname NAG and resid 1
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2559
      Number of conformers: 1
      Conformer: ""
Traceback (most recent call last):
  File "/home/jxqi/152Phenix/phenix-1.5-2/phenix/phenix/command_line/refine.py", line 11, in <module>
    command_line.run(command_name="phenix.refine", args=sys.argv[1:])
  File "/home/jxqi/152Phenix/phenix-1.5-2/phenix/phenix/refinement/command_line.py", line 68, in run
    log=log)
  File "/home/jxqi/152Phenix/phenix-1.5-2/phenix/phenix/refinement/command_line.py", line 227, in __init__
    self.pdb_file_names)
  File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/utils.py", line 907, in process_pdb_files
    stop_if_duplicate_labels = stop_if_duplicate_labels)
  File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/utils.py", line 940, in _process_pdb_file
    log                      = self.log)
  File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2995, in __init__
    log=log)
  File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2105, in __init__
    log=log)
  File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 1575, in __init__
    prev_mm=prev_mm)
  File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 543, in __init__
    mod_mod_id=self.mon_lib_srv.mod_mod_id_dict[apply_data_mod])
  File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 819, in apply_mod
    mod_mon = self.monomer.apply_mod(mod_mod_id)
  File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/cif_types.py", line 359, in apply_mod
    result.delete_atom_in_place(mod_atom.atom_id)
  File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/cif_types.py", line 264, in delete_atom_in_place
    raise RuntimeError("delete_atom_in_place: unknown atom_id: %s" % atom_id)
RuntimeError: delete_atom_in_place: unknown atom_id: HD22
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