Hi Dayna, we need to look at your files (all inputs plus log and eff) to diagnose the issue and hopefully offer a solution. Please reply me directly with files and copy to Nigel Moriarty (cc'ed) and we will investigate. Thanks! Pavel On 3/30/26 23:06, Dayna Louise Holroyd wrote:
Hi all,
I am currently refining a cyclic peptide which I have modelled into my 3A crystal structure. The peptide contains multiple non-natural amino acids, two of which haven't been defined in the PDB before by a three letter code (made cif files with elbow for these). I have been adding custom restraint files each refinement round to connect residues at the ends and maintain cyclisation.
I am encountering various issues during refinement:
1. Certain pairs of non-natural residues drift apart after refinement if I do not include restraints between the two residues. 2. Some backbone dihedral angles are much smaller than expected, while other angles appear unusual or physically implausible, even after defining particular angles in the restraint files.
I suspect that some of these issues may be related to the compact nature of the cyclic peptide and the presence of undefined residues, but I am unsure how to address them effectively.
Has anyone refined similar cyclic peptides with non-natural residues and can offer advice on my problems with restraints, compact backbone angles, non-natural residues, etc? Any guidance or ideas would be greatly appreciated.
Many thanks,
Dayna Holroyd
PhD Candidate Protein Crystallography and Structural Biology Laboratory School of Biological Sciences | College of Science ADELAIDE UNIVERSITY