[Chimera-users] C-N peptide bond within one peptide

Elaine Meng meng at cgl.ucsf.edu
Mon Oct 8 15:04:37 PDT 2018

Hi Emily,
Sure!  One way is to just use the “bond” command.  E.g., select the two atoms to be bonded (carbonyl C on last residue and N on first residue) and then enter command:

bond sel


Alternatively if you are in the Build Structure tool, the Adjust Bonds section has an option to add bond between selected atoms.  You might have to change from “reasonable” to “all possible” if the bond would be longer than normal.


I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 8, 2018, at 9:15 AM, Emily Xu <emilyxu202 at gmail.com> wrote:
> Hello,
> Is there a way to join two ends of a peptide in Chimera? I am trying the create a peptide bond linking the C and N termini in a singular peptide to form a cyclotide. Is this possible in Chimera?

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