[Chimera-users] rmsd of selected region: multiple chains

Arvind SHARMA arvind.sharma at pasteur.fr
Sat Apr 13 10:04:08 PDT 2019

Thanks a lot Elaine. Its greatly helpful.

Have a lovely weekend
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Saturday, April 13, 2019 6:45:59 PM
To: Arvind SHARMA
Cc: chimera-users at cgl.ucsf.edu BB
Subject: Re: [Chimera-users] rmsd of selected region: multiple chains

Hi Arvind,
The “rmsd” command uses whatever atoms you specify in the command.  If you specify only residues but not atom names, that means all of their atoms.  The following measure RMSD between residues 6-10 chain A of model #0 vs. model #1, based on all atoms, CA only, backbone only (N,CA,C,O), respectively:

rmsd #0:6-10.a #1:6-10.a
rmsd #0:6-10.a at ca #1:6-10.a at ca
rmsd #0:6-10.a at n,ca,c,o #1:6-10.a at n,ca,c,o

The pain is figuring out all the residue numbers you want to list.  If you don’t know exactly which numbers in which chains, but you know how to select them, you could use menu: Actions… Write List to report which residues are selected.  The specifications could include residues from multiple chains, e.g. :26-28.a,45.b at ca


In Multalign Viewer, the values reported in the RMSD column of the Region Browser are CA-only.

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 13, 2019, at 9:22 AM, Arvind SHARMA <arvind.sharma at pasteur.fr> wrote:
> Hi,
> I want to get rmsd of an interface (constituted by 4 chains in heterotetramer protein) in bound and unbound conformations. so far I am trying to do this by using 'rmsd' command, but i am not sure if its the c-alfa or backbone or the full rmsd. I get a different rmsd value when I just open the sequences, perform structure association and then select sequence to get rmsd.
> Is there a command to select residues of different chains (the quaternary interface in my case) and perform either backbone or full rmsd???
> thanks a lot.
> best,
> arvind.

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