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