[chimerax-users] Help getting rmsd value per residue of 2 similar structures.

[Binh Nguyen]

Got it. Thank you very much.

B

_____________________________________________
Binh A. Nguyen, Ph.D.
@ Saelices's Lab
Center for Alzheimer’s and Neurodegenerative Diseases

Peter O’Donnell Jr. Brain Institute

UT Southwestern Medical Center


________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Wednesday, February 8, 2023 2:56 PM
To: Binh Nguyen <AnBinh.Nguyen at UTSouthwestern.edu>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: Re: Help getting rmsd value per residue of 2 similar structures.

EXTERNAL MAIL

Hi Binh,
This is almost the same question as asked yesterday on chimerax-users at cgl.ucsf.edu, so I have the same answer:

<https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2023-February/004923.html>

That answer assumes you are using Matchmaker to superimpose these structures first, which has an option to display the pairwise sequence alignment with RMSD values per column, which can then be written out, used for coloring, etc, as detailed in that answer.  Note that this RMSD is only using CA atoms so for two structures, it is simply the distance between the 2 CA atoms.  You can use the Sequence Viewer settings to make it use the 4 backbone atoms per residue instead (N,CA,C,O):
<https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2023-February/004923.html>

Secondarily, remember that Chimera and ChimeraX are two different programs and if you are viewing help/answers for Chimera they may not pertain to ChimeraX.

Finally, for the best chance of getting a good answer to ChimeraX questions in the future, please use chimerax-users at cgl.ucsf.edu unless you are including private data. Thanks!
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Feb 8, 2023, at 12:39 PM, Binh Nguyen <AnBinh.Nguyen at UTSouthwestern.edu> wrote:
>
> Dear Elaine,
>
> Is there a way to generate the rmsd per residue of 2 similar structures using chimeraX? I have searched through but I can only manage to get the overall RMSD.
>
> I have found this too but I have no idea how to get such information.
> https://www.rbvi.ucsf.edu/pipermail/chimera-users/2019-February/015415.html
>
> Please help, thank you.
>
> B

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