[Chimera-users] Creating new models from existing crystal structures

Elaine Meng meng at cgl.ucsf.edu
Mon Feb 8 13:01:36 PST 2021

Hi Tiglath,
If you just opened 3r2p one time, you only have one model.  Join works on bonding two separate models.  Also it contains only chain A (there is no chain B in this structure) and residue 130 in chain A is already bonded to residue 131 in chain A.  So I do not understand what you already did to modify the structure(s) before joining, or what you are trying to do now, sorry.

You could send a session file if you want.
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 8, 2021, at 12:35 PM, Moradkhan, Tiglath A <tmoradkhan at csus.edu> wrote:
> Hi
> I'm trying to join two models together using the Build Structure tool but I'm having problems. Here is my process.
> 	• Using the 3R2P crystal structure I select residues 3-130 from chain A and 131-182 from chain B
> 	• Then using the following command in Chimera I select the N atom of residue 130 that will form a bond with the C atom of residue 131: sel #0:130 at N#1:131 at C (#0 is the name of the 3-130 segment and #1 is the name of the 131-182 segment)
> 	• Then using the Build Structure tool I select Form C-N peptide bond, but the Apply button doesn't activate.
> I don't understand what the issue is. Is the command that I've written wrong?
> I would be very glad for your help. I can provide the pdb files of the residue segments if necessary.
>  Thanks
> Tiglath

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