Hi Nebojša Bogdanović,
In ChimeraX, you would need to show a sequence alignment of the two structures with RMSD displayed on the sequence alignment.  Then you can color the structures by CA RMSD per residue (which is really just the CA-CA distance since you only have two structures).  You don't have to show both structures, but you do have to superimpose them.  You can simply hide one of the structures after that.

If you are using Matchmaker tool or mm command to superimpose the structures, it is easy, you can show the sequence alignment with RMSD displayed in the same step.  Example commands:

open 2gbp
open 2fw0
mm #2 to #1 show true
color byattribute seq_rmsd  #1 palette blue:red:yellow
hide #2 models

Of course you can use whatever coloring palette you like, I just used blue-red-yellow for the example.

Matchmaker
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html>
...or matchmaker (mm) command
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>

sequence viewer headers including RMSD assigned as attribute
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#headers>

coloring by attribute
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute>

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


> On Jan 21, 2022, at 8:51 AM, Nebojsa Bogdanovic via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Hello,
> I am looking to color the atoms (cartoon representation) by RMSD values obtained from the matching of the two structures. Is there such a function? I would like to show which part of the target domain is moving the most in comparison to the previously x-ray solved structure of a know ligand state without showing the actual structures overlaid.
>
> Thank You very much.
>
> Nebojša Bogdanović, Ph.D
> Department of Physiology and Biophysics,
> School of Medicine,
> Case Western Reserve University