[Chimera-users] Backbone RMSD

Elaine Meng meng at cgl.ucsf.edu
Fri Sep 18 09:48:48 PDT 2020

HI Bixia,
Even when different crystal structures are for exactly the same protein, one or the other might be missing coordinates for some of the residues in flexible loops and/or N or C terminus, or sometimes there are alternate locations of the atoms in one structure (multiple locations for a single atom so seems like multiple atoms), etc.  It usually takes some work to figure it out.

> On Sep 18, 2020, at 9:42 AM, Zhang, Bixia <bixia.zhang at wsu.edu> wrote:
> Hi Elaine,
> Yes I tried but it always gave me error message saying unequal numbers of atoms chosen when I used n,ca,c,o. However they are the same protein so shouldn’t have this problem. Now I tried “all” and it works so I think I will just use this value. Thank you so much!
> Best,
> Bixia
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Friday, September 18, 2020 8:44:22 AM
> To: Zhang, Bixia <bixia.zhang at wsu.edu>
> Cc: Chimera <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Backbone RMSD
> Hi Bixia,
> Did you read my previous reply?  In that previous message, also shown below, I said to use the "match" command instead of matchmaker to specify whatever atoms you want (could be all atoms or all backbone, for example) for fitting/RMSD -- or if you want RMSD without fitting (without moving the structures from their current positions) use the "rmsd" command.  There are links to the command help pages and tutorial examples in that message.  Those commands would give a single overall RMSD value for the atoms that you specified.
> If you don't mean a single RMSD value but instead that you want to see it at each position of a sequence alignment, then use matchmaker option to show the pairwise sequence alignment.  The sequence alignment window shows above the sequences a histogram "RMSD: ca" but you can use the Headers menu of that window to show "RMSD: full" or "RMSD: backbone" or all three if you want, as shown in the example image.  They might not be very different from each other, however, as in my example.
> This header stuff is explained in the help for the sequence viewer (Multalign Viewer):
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#headers>
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> <Screen Shot 2020-09-18 at 8.39.37 AM.png>
>> On Sep 17, 2020, at 9:05 PM, Zhang, Bixia <bixia.zhang at wsu.edu> wrote:
>> 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$ %3E
>> <https://urldefense.com/v3/__http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html__;!!JmPEgBY0HMszNaDT!5O_WiKmxcIblQ26zQKLIYV7Eg7QfEMgarJp3JpDss8ggtnmYbFSbMFNmzLk6o96l658$ %3E
>> 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$ %3E
>> <https://urldefense.com/v3/__http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html__;!!JmPEgBY0HMszNaDT!5O_WiKmxcIblQ26zQKLIYV7Eg7QfEMgarJp3JpDss8ggtnmYbFSbMFNmzLk63QOas4I$ %3E
>> 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$ %3E
>> 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$ %3E
>> 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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