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/m... > 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/command... > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... > 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