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

Jiang Xu foxjuly at gmail.com
Sat Aug 13 21:56:16 PDT 2022

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,
Lin Chen Lab
University of Southern California

coot manually made link between the C and N terminal
[image: unnamed.jpg]
After refinement
[image: unnamed (1).jpg]
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