Re: [phenixbb] cis peptide and pdb head

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