Hi Richard,
I don't understand exactly what you are trying to do.  Are you trying to get an RMSD for only certain parts of the chains instead of over all matched residues?

Matchmaker RMSD is over all of the alpha-carbons of the residue pairs used to align the structures.   If you use the matchmaker option to show the pairwise sequence alignment, then after that, you can draw a box in the sequence alignment to get an RMSD for only the pairs inside the box.  To see that RMSD value you would show the sequence-alignment Regions window by using the Sequence Viewer context menu "Annotations... Regions"

A context menu is shown by right-clicking on the tool (or for Mac it may be Ctrl-clicking instead).

Then in that Region Browser window it will report the alpha-carbon RMSD for your boxed area each time you drag in the sequence alignment window to draw that box.  (There is an RMSD column in the table of regions, where a region is a boxed area on the sequence alignment.)

See Regions:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#regions>

Or if you need to use more atoms than just the alpha-carbons, you can use the "rmsd" command to report RMSD for any sets of atoms such as all backbone without changing the superposition, but you have to give it equal numbers of atoms from the two structures:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/rmsd.html>

RMSD is not necessarily the best way to compare, you might want to just look at that area directly and see if there are other changes that might be important to the structure/function of the protein (binding, catalysis, or whatever it does).

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 Aug 4, 2025, at 9:12 AM, Richard melzack via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Hello
>
> I have started using your excellent Chimera X 1.10.1 visualisation platform and have uploaded a protein and mutated protein onto the matchmaker screen. The RMSD is low so the general appearance is very similar. However, I was wondering (the mutated protein has a 6bp insertion and a nonsynonymous SNP) how to examine the details around the exact points of the mutations (both are on the same exon). I have tried a number of ideas. The command line doesn't like sequence or sequence  #1 #2.
>
> I would be grateful for your assistance.
>
> Thank you
>
> Dr Richard Melzack 
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