[Chimera-users] Creating new models from existing crystal structures
Moradkhan, Tiglath A
tmoradkhan at csus.edu
Mon Feb 8 13:53:03 PST 2021
I've been using the biological assembly of 3R2P and I'm thinking that the reason why it's not working is because both chains are labeled A. I'm just following a paper where they're building a monomeric structure using the residue fragments but in their case the biological assembly of 3R2P is labeled as chain A and chain B.
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Monday, February 8, 2021 1:01 PM
To: Moradkhan, Tiglath A <tmoradkhan at csus.edu>
Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Creating new models from existing crystal structures
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:
> 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.
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