I have tried to us the GUI Matchmaker interface for this comparison. I loaded the two models into the same window; the reference model was loaded first and the model that was to be matched to that reference was loaded second. I loaded each sequence, and selected the residues to be paired using the mouse. The first (reference) is shaded brown and the second is shaded green. I open the GUI interface and select "also restrict to selection" for both the reference and selection to match. Both the reference and model to match the reference are shaded grey. Then I click apply and receive the follow message:

Hi Phillip,
(1) If you mean you want to specify exactly which residues/atoms to use in fitting (and then get their best-fit RMSD reported in the Log at the end), see the "align" command.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>

(2) Or, if you don't want to move the structures from their current positions, but simply to measure the RMSD between specified residues/atoms in their current locations, see the "rmsd" command.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/rmsd.html>

(3) You *can* use matchmaker on a subset of residues by specifying them in the command, see:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#restrict>

... however, please note:
- matchmaker will only use the alpha-carbon atoms of those residues in calculating the fit and RMSD. If you want to use more atoms than one per residue, you have to use "align" or "rmsd" as mentioned above.
- by default it iterates the fit and prunes some of the residue pairs from the fit, unless you also give the option "cutoffDistance none"
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#options>

The above relate to the "matchmaker" command since you said command. However, if you're actually using the Matchmaker graphical interface (e.g. opened from the Tools menu), the same options are available. To restrict matchmaker to only certain residues using the graphical interface, first select those residues and then check the option "Also restrict to selection"
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html#pairing>

Making selections:
<https://rbvi.ucsf.edu/chimerax/docs/user/selection.html>

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

> On Feb 20, 2023, at 3:27 PM, McClean, Phillip via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Is it possible to use the Chimerax Matchmaker command to obtain the RMSD value between a subset or residues between two different proteins.
> Phil McClean