[phenixbb] cis peptides

[Ralf W. Grosse-Kunstleve]

Hi Tim,

> Is there an easy way to specify unwanted cis-peptides and
> remove them in refinement or with torsion dynamics or SA?

You can remove dihedral restraints like this:

  refinement.geometry_restraints.remove {
    dihedrals = chain A and ((resid 100 and (name CA or name C)) or (resid 101 
and (name N or name CA)))
  }

Although it will remove all dihedrals that somehow involve the selected
atoms, which may not be what you want.

You can also change

  refinement.pdb_interpretation.peptide_link.cis_threshold=10

(the default is 45 degrees); this will lead to trans restraints.

If this doesn't help, could you describe more what you want to do?

Ralf
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