[Chimera-users] Backbone RMSD

[Zhang, Bixia]

Hi Elaine,
I was trying to figure out the backbone RMSD yesterday and I just realized that, as you said, by matchmaker I already got RMSD for ca. So now I am wondering if there’s any way to get RMSD for the full protein (including side chain). I am investigating the solution affect on structure, so the change is very tiny, if I can see the RMSD for full protein and backbone I might get some ideas on where it changes. Thank you!
Best,
Bixia

________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Wednesday, September 16, 2020 12:24
To: Zhang, Bixia
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Backbone RMSD

Hi Bixia,
Matchmaker always uses only one atom per residue, CA for amino acid residues.
<https://urldefense.com/v3/__http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html__;!!JmPEgBY0HMszNaDT!5O_WiKmxcIblQ26zQKLIYV7Eg7QfEMgarJp3JpDss8ggtnmYbFSbMFNmzLk6Mw2g-s0$ >
<https://urldefense.com/v3/__http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html__;!!JmPEgBY0HMszNaDT!5O_WiKmxcIblQ26zQKLIYV7Eg7QfEMgarJp3JpDss8ggtnmYbFSbMFNmzLk6o96l658$ >

However, you can do fitting with the "match" command on specific atoms, or "rmsd" command just to measure the current RMSD of those specific atoms without fitting.   The harder part is in that case you have to specify all the atoms in the command and there must be equal numbers of atoms from the two structures, which will be paired in order.  This can be difficult if the structures have different numbers of residues and/or different residue numbering.
<https://urldefense.com/v3/__http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html__;!!JmPEgBY0HMszNaDT!5O_WiKmxcIblQ26zQKLIYV7Eg7QfEMgarJp3JpDss8ggtnmYbFSbMFNmzLk6YjD9ZH8$ >
<https://urldefense.com/v3/__http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html__;!!JmPEgBY0HMszNaDT!5O_WiKmxcIblQ26zQKLIYV7Eg7QfEMgarJp3JpDss8ggtnmYbFSbMFNmzLk63QOas4I$ >

There are examples in the links above and also in tutorials, e.g.
<https://urldefense.com/v3/__http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/images.html*matching__;Iw!!JmPEgBY0HMszNaDT!5O_WiKmxcIblQ26zQKLIYV7Eg7QfEMgarJp3JpDss8ggtnmYbFSbMFNmzLk6nOITpWA$ >

If your two structures were #0 and #1 and they had same numbering, for example, you could match using backbone atoms of residues 10-300 from each with:

match #0:10-300 at n,ca,c,o #1:10-300 at n,ca,c,o

It will be harder if they have different numbering, and/or you wish to omit loop areas that are not well superimposed.

Matchmaker vs. match is discussed here:
<https://urldefense.com/v3/__http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html__;!!JmPEgBY0HMszNaDT!5O_WiKmxcIblQ26zQKLIYV7Eg7QfEMgarJp3JpDss8ggtnmYbFSbMFNmzLk6Mw2g-s0$ >

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

> On Sep 16, 2020, at 12:06 PM, Zhang, Bixia <bixia.zhang at wsu.edu> wrote:
>
> Hi,
> I am trying to get the backbone RMSD between two structures. However I tried selecting backbone and use matchmaker, it gives me same value with the whole protein. So there must be something wrong. Could you please teach me a command that can do this? Thank you so much for helping!
> Best,
> Bixia
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