[phenixbb] cis peptide and pdb head
Ralf W. Grosse-Kunstleve
rwgk at cci.lbl.gov
Tue Aug 21 03:40:16 PDT 2007
> 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 "
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.
More information about the phenixbb