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-of-custom-bonds-and-angles

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 : NWMoriarty@LBL.gov
Fax   : 510-486-5909      Web  : CCI.LBL.gov


On Sat, Aug 13, 2022 at 10:00 PM Jiang Xu <foxjuly@gmail.com> 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
unnamed.jpg
After refinement
unnamed (1).jpg
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