[phenixbb] CUA Ligand issue

Bradley Hintze bradley.hintze at duke.edu
Thu Apr 7 06:53:54 PDT 2011


I am trying to refine PDB 1YEW using the default phenix settings.

$phenix.refine 1yew.pdb 1yew.mtz

Sorry: Fatal problems interpreting PDB file:
  Number of atoms with unknown nonbonded energy type symbols: 6
    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.

$ phenix.ready_set 1YEW_H.pdb

    Atoms in the input are supposed to be bound

    CU1(CUA) - CU2(CUA) = 2.58

    Fix the input file and retry

I assume this means that the Cu atoms in CUA are at
an inappropriate distance. Is there an easy way to find out what the
appropriate distance is? Can I fix this in coot?

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