Thank you and sorry for the subject line - a very good practice indeed!
So if I understand correctly after command match A to B there will be a single RMSD number representing RMSD of ALL alpha carbons.
And for side chains one would look at the “tricky” one in your second paragraph, correct?

Thank you

From: Elaine Meng <meng@cgl.ucsf.edu>
Date: Thursday, October 9, 2025 at 9:30 AM
To: Vojo P Deretic <VDeretic@salud.unm.edu>
Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Subject: RMSD after matchmaker


[[-- External - this message has been sent from outside the University --]]

I changed the email subject line to describe the current question -- this is helpful for people who search the archives.

Matchmaker itself reports an RMSD in the Log, based on the pairs of alpha-carbons used for the final fit.  If that is sufficient, you can just look in the Log after using it.
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html__;!!KXH1hvEXyw!aCUGSbNn3RD0p-IzQV-hZyZkZ6FCVE-eR9U_IwnbenRPk3PAOHW5ihqRDBPgvFMHnuYnssfjNN5zt_M4jzRv$ >

However, there is also an "rmsd" command to calculate the RMSD based on any atoms that you want (not necessarily just the alpha-carbons) without changing the superposition.  The tricky part will be correctly specifying the atoms in the command.  See
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/rmsd.html__;!!KXH1hvEXyw!aCUGSbNn3RD0p-IzQV-hZyZkZ6FCVE-eR9U_IwnbenRPk3PAOHW5ihqRDBPgvFMHnuYnssfjNN5zt2lE-9Ng$ >
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html__;!!KXH1hvEXyw!aCUGSbNn3RD0p-IzQV-hZyZkZ6FCVE-eR9U_IwnbenRPk3PAOHW5ihqRDBPgvFMHnuYnssfjNN5zt7webM5a$ >

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 Oct 9, 2025, at 5:07 AM, Vojo P Deretic via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Hi
> Is there a function in ChimeraX to calculate RMSD after matchmaking superimposition of structures?
> Thank you