[chimerax-users] Error when joining two pdbs

[Elaine Meng]

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 at C #2/A:1 at 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 at 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 at C#2:1.A at 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