[phenixbb] NAG-NAG link definition seems to have no effect

Benjamin Stauch bs448c at gmail.com
Wed Jun 11 17:05:11 PDT 2014


Hi Phenix,

apologies for the beginner question, and I do realise that there are some
related threads already but nothing so far has helped me to solve this
problem.

I want to refine a model that has two NAGs linked to an Asn - the sugars
are already part of my initial coordinate file, but upon refinement the
link between the NAGs gets lost. I have defined a cif_link file as follows
that I load (using the GUI),

     apply_cif_link {
       data_link = "NAG-ASN"
       residue_selection_1 = "chain A and resname NAG and resid 401"
       residue_selection_2 = "chain A and resname ASN and resid 74"
     }
     apply_cif_link {
       data_link = "BETA1-4"
       residue_selection_1 = "chain A and resname NAG and resid 401"
       residue_selection_2 = "chain A and resname NAG and resid 402"
     }

when checking the .geo file phenix.refine outputs, I do not see any
restraints between Asn and NAG, nor NAG and NAG.

There might be some clues in the refine.log file:

  Build ligand and use monomer library to name atoms : NAG
  Using monomer library entry NAG as template

which I guess looks good, and then something like this which could be where
things are going wrong:

  Monomer Library directory:
    "c:\phenix-1.8.4-1496\phenix-1.8.4-1496_sources\chem_data\mon_lib"
  Total number of atoms: 11298
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5075
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 319, 4675
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2, 'peptide': 317}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 27, None: 2, 'TRANS': 287, 'PCIS': 2}
            Not linked:
              pdbres="ALA A 317 " segid="A   "
              pdbres="NAG A 401 " segid="A   "
            Not linked:
              pdbres="NAG A 401 " segid="A   "
              pdbres="NAG A 402 " segid="A   "
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2


Refinement doesn't crash or produce errors as far as I can see, however
when checking the MolProbity output after refinement, it complains of
missing atoms O1 in NAG 401 and 402. (Not sure if this is relevant)

Furthermore there's still a HO4 attached to the O4 of NAG ... while the
BETA1-4 should care to delete it .. however the mon_lib reads

BETA1-4  .        DEL-HO4  pyranose .        DEL-O1   pyranose
 glycosidic_bond_beta1-4

which doesn't seem entirely relevant for my case?






Any help would be appreciated

Thanks!

Ben
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