Grant

You have two atoms in your PDB named differently from the restraints file you are using for NGA.  You need to reconcile the differences. The standard naming does not include O and O1L.  I would recommend editing your PDB to match the restraints file.

Nigel

On 4/23/10 11:53 AM, Hansman, Grant (NIH/VRC) [F] wrote:

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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Nigel W. Moriarty
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