Jiang I think the issue is that you "made a link" in Coot which is not honoured by Phenix. To "make a link" in Phenix you need to do one of three things. See the documentation here. https://phenix-online.org/documentation/reference/refinement.html#definition... Also, if you send me the model directly, I will take a look at it to see if it can be automated. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464 On Sat, Aug 13, 2022 at 10:00 PM Jiang Xu wrote:

Hello Guys, I have a circular peptide structure solved from Xtal. The peptide is actually a circular peptide that has the N terminal and C terminal joined together by a peptide bond. When refining the structure, I had a problem getting the C-N terminal (between G34 and S2) joined together by the peptide bond. I even made a link between the C terminal carbon atom and N terminal N atom in coot and used this model as the input model to do the refinement using Phenix.refine. It seemed that the program didn't consider the link made in coot as a valid bond and intentionally avoid forming a bond between the C atom and the N atom. So, how can I solve this problem? Thank you, Best regards, Jiang Lin Chen Lab University of Southern California

P.S. coot manually made link between the C and N terminal [image: unnamed.jpg] After refinement [image: unnamed (1).jpg] _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]