Hi Paul, I have been seeing this occasionally with coot 0.8.4 onward (currently using 0.8.7-pre) even with data to 2.5 Å. It usually happens if I use the “auto fit rotamer" on a neighbouring residue. It can be tricky to sort out sometimes taking several goes with “regularise zone” then “real space refine”.
Regards MGM Martin G Montgomery ATP Synthase Group MRC Mitochondrial Biology Unit Wellcome Trust/MRC Building Cambridge Biomedical Campus Hills Road Cambridge Great Britain CB2 0XY www.mrc-mbu.cam.ac.uk > On 13 Oct 2016, at 02:45, Paul Emsley <[email protected]> wrote: > > On 12/10/2016 13:43, Kevin Jude wrote: >> I am frequently getting distortions of proline residues during real space >> refinement - >> specifically, close approaches between C and CD (pictured). It's hard to >> nail down exactly >> what is happening but it seems like planar peptide restraints aren't working >> for Pro >> residues. > > That's weird - I have not seen that before. The C-N-CD angle restraints > should keep these atoms apart. You should tabulate ligand distortions to > investigate. > > Paul.
