Re: [phenixbb] cis peptide

Hi Jianghai,

Does phenix.refine restrain cis peptide?

Yes, controlled via this parameter scope: peptide_link { cis_threshold = 45 discard_psi_phi = True omega_esd_override_value = None }

How do I know if the refined pdb file contain any cis peptide?

In theory you could tell by inspecting the .geo file, but it is difficult to pin-point the cis peptide restraints. Probably, it is better to use e.g. the pdb deposition tools or something similar to get a listing of the cis peptides. I'll add "list cis peptides" to our to-do list. Ralf