[phenixbb] cis peptide and pdb head

[Ralf W. Grosse-Kunstleve]

> After phenix.refine detects the cis peptide, where does this
> information output?

It gives you a count per chain in the indented pdb interpretation
summary. Look for "CIS" and "PCIS" in the output.

The definitve resource to find out more about the restraints is
the .geo file. To pin-point restraints for certain atoms, copy
the atom/residue/chain etc. labels from the PDB file, e.g.

bond simple: (2, 4)
  " C   GLY A   1 "
  " N   ASN A   2 "
  distance_model: 1.33179
  distance_ideal: 1.329
  weight: 5102.04

This is a peptide bond. " C   GLY A   1 " (without the quotes) is
formatted exactly like in the ATOM record in the PDB file.

Pavel's answer is correct in all points.

Ralf