Hi Praveen, The atom specifications in the "select" command that you tried are in the format expected by Chimera (not ChimeraX). In ChimeraX, the chain is indicated by "/" instead of "." See atom specification in ChimeraX: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> So in ChimeraX, you would want something like select #1/A:12@C #2/A:1@N I guess you are using "select" so that you can use the Join Models function in the Build Structure tool: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#join> You can save PDB from the ChimeraX menu (File... Save, choose Files of type: PDB) or with the "save" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Jun 29, 2022, at 9:23 AM, Praveen Ranganath Prabhakar via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi all, I am Praveen, a graduate student at UC Irvine. Hope you are doing well. I am using Chimera X. In my project, I have to join a protein to a peptide sequence via a peptide bond. I have loaded the PDB files of both the protein and the peptide sequence & I have identified where (between which atoms) the peptide bond has to be. After loading the PDBs, I use the following in the command line "select #1:12.A@C#2:1.A@N" (basically identifying the residue/atoms where the peptide bond has to be formed) to join but I get the error "Expected an objects specifier or a keyword" . I am sorry if this is a common error and I have missed something, I am new to Chimera. Also it would be great if someone could tell me if there is a way to save the final pdb after joining them?

Thank you so much for your time, Best, Praveen