Hi Victor,
You would choose the option in Matchmaker to show the pairwise sequence alignment in the Sequence Viewer -- then that sequence alignment will show a header that is an RMSD histogram above the sequences, which automatically assigns the RMSD attribute named "seq_rmsd" to the associated structure residues.  (Note that for only 2 structures, it simply boils down to CA-CA distance.)

Then you can use Render by Attribute (or the "worm" = "cartoon byattribute") command to show the seq_rmsd attribute values with worm fatness on one or both structures.   If you don't want to do it on both structures you can just hide (do not close) one of them.

These are described in the manual pages of Matchmaker, Sequence Viewer, and Render by Attribute.
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#headers>
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/render.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#byattribute>

There is also a video for coloring by RMSD that is somewhat similar, but you'd be rendering the values as worms instead of colors.
<https://www.youtube.com/watch?v=XaTpB-UIxnU>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Feb 6, 2026, at 1:00 PM, Victor Ruiz via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Dear ChimeraX community,
>
> I am trying to make a figure to show the loop movement between two conformations of the same protein. For that, I would like to use a worm representation following these steps:
>
> -Trim residues so they all match in length between both models.
> -Matchmaker to align them
> -Calculate RMSD
> -... Next?
>
>> From here, I would like to compute the RMSD value for each residue pair and use it to generate a worm representation; however, I cannot find any information about how to do this in ChimeraX. Is there any manual that I am missing? I appreciate any feedback that you may provide.
>
> Looking for your response.
>
> Best,
> Victor Ruiz