[phenixbb] CUA Ligand issue
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
$ 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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