[phenixbb] Inability to connect the N and C terminal of peptide to form a peptid bond of a circular peptide structure

[Nigel Moriarty]

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 at LBL.gov
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 <foxjuly at 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
> [image: unnamed.jpg]
> After refinement
> [image: unnamed (1).jpg]
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