Hi Marian, You are correct that "match" (= "matchmaker") uses only CA atoms to calculate the RMSD between protein pairs: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> That page says "To use a different set of atoms, including those not in biopolymer chains, see the align command instead." In other words, to calculate the RMSD of all the atoms that you specify in the command, use "align" (for best-fit) or "rmsd" (to use current positions without fitting): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rmsd.html> Merry Christmas and Happy New Year to you too! You can see our group's holiday card here: <https://www.rbvi.ucsf.edu/Outreach/card-gallery/2025-flotillin/flotillin.htm...> 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 Dec 23, 2025, at 12:46 AM, marian.vincenzi via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear Chimera staff,

I am a PostDock from CNR-IBB of Naples (Italy). I am contacting you on the command "match" because I would use it to evaluate rmsd between two structures. I realized (maybe I am wrong) that the value given as output rises from the overlap only on C-alpha, but I used the command "match #1@n,ca,c,o to #2:904-976@n,ca,c,o". My aim was the RMSD evaluated on all backbone atoms and not only c-alpha. Is there anyway to get RMSD value on all backbone atome and overlap the two analysed structures ? Thank you in advance. While waiting, I wish all you team Merry Christmas and Happy New year :-)

Marian