delete bonds /A:102@C /A:103@N

or the equivalent menu Actions / Atoms and Bonds / delete then you could just recreate it with

bond /A:102@C /A:103@N

I'm not sure why you would do that since there is no need to delete a bond to move the two pieces of the structure. Instead maybe you split the protein into two separate models. In that case you can't simply add a bond between different models, instead you have to combine the models (e.g. command "combine #1,2").

You might get better answers on the ChimeraX mailing list, so I have CC'ed that list.

Tom

On Apr 21, 2025, at 4:06 PM, Singh, Harpreet <harpreet.singh2@ucsf.edu> wrote:

Dear Professor Goddard,

I hope you are doing well.

I am a Postdoctoral scholar from the Robert M. Stroud lab. I recently deleted a peptide bond from our protein structure to adjust the model for cryo-electron microscopy (cryo-EM) mapping. I am now attempting to reconstruct the peptide bond using the Build Structure tool. However, I am encountering an error message indicating that there are no chain-terminal carbons in the atoms.

I would appreciate your assistance in resolving this issue.

Thank you for your time and consideration.

Best regards,
Harpreet Singh
Postdoctoral Fellow, Stroud lab
Department of Biochemistry and Biophysics
UCSF