[phenixbb] apply_cif_link

[Hansman, Grant (NIH/VRC) [F]]

I am trying to link my sugar molecule (FUC-GAL-NGA-FUC), Lewis y, for phenix.refine, but I keep on getting an error message. I am a beginner at this so I just don't know how to make the links.

For , example, I am using this:

refinement.pdb_interpretation {
  apply_cif_link {
    data_link = BETA1-2
    residue_selection_1 = chain C and resname GAL and resid 224
    residue_selection_2 = chain C and resname FUC and resid 223
  }
  apply_cif_link {
    data_link = BETA1-3
    residue_selection_1 = chain C and resname GAL and resid 224
    residue_selection_2 = chain C and resname NGA and resid 225
  }
  apply_cif_link {
    data_link = BETA1-3
    residue_selection_1 = chain C and resname NGA and resid 225
    residue_selection_2 = chain C and resname FUC and resid 226




     Number of atoms: 46
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 46
          Unusual residues: {'GAL%DEL-HO2%DEL-HO3': 1, 'NGA%DEL-O1%DEL-HO3': 1, 'FUC%DEL-O1': 2}
          Unexpected atoms: {'NGA%DEL-O1%DEL-HO3,O1L': 1, 'NGA%DEL-O1%DEL-HO3,O': 1}
          Classifications: {'undetermined': 4}
          Modifications used: {'DEL-HO2': 1, 'DEL-HO3': 2, 'DEL-O1': 3}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 2
          Unresolved apply_cif_link angles: 1
          Unresolved apply_cif_link chiralities: 1
  Number of atoms with unknown nonbonded energy type symbols: 2
    "HETATM 5649  O   NGA C 225 .*.     O  "
    "HETATM 5655  O1L NGA C 225 .*.     O  "
  Time building chain proxies: 2.31, per 1000 atoms: 0.41

Sorry: Fatal problems interpreting PDB file:
  Number of atoms with unknown nonbonded energy type symbols: 2
  Please edit the PDB file to resolve the problems and/or supply a
  CIF file with matching restraint definitions, along with
  apply_cif_modification and apply_cif_link parameter definitions
  if necessary (see phenix.refine documentation).
  Also note that phenix.elbow is available to create restraint
  definitions for unknown ligands.


Any help and direction would be appreciated.

Grant
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