Thank you - lovely example and tips Vojo Deretic, Ph.D. Distinguished Professor Department Chair, MGM Director, AIM Center University of New Mexico School of Medicine vderetic@salud.unm.edu<mailto:vderetic@salud.unm.edu> Follow AIM, NIH-funded Center of Biomedical Research Excellence: https://www.autophagy.center/ X/Twitter @AIM_autophagy Don’t forget to acknowledge the AIM Center (Autophagy, Inflammation and Metabolism) and the CoBRE grant in publications The AIM Center is supported by NIH grant P20GM121176. For citation options see suggested wording at https://www.autophagy.center/ From: Elaine Meng <meng@cgl.ucsf.edu> Date: Thursday, October 9, 2025 at 10:59 AM To: Vojo P Deretic <VDeretic@salud.unm.edu> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] RMSD after matchmaker [[-- External - this message has been sent from outside the University --]] Hi Vojo, Did you look in the Log? After Matchmaker, the Log will give two RMSD values, one over all pairs of alpha-carbons paired in the alignment, and the other over just the pairs used in the final fit. For example, I fit 2fw0 to 2gbp, and Log says: Chains used in RMSD evaluation for alignment 1: 2fw0 #1/A, 2gbp #2/A Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1 RMSD between 147 pruned atom pairs is 0.425 angstroms; (across all 305 pairs: 7.702) I can then use the "rmsd" command to measure RMSD of backbone atoms or all atoms. If the proteins are different sequences, however, it would be too difficult to specify parts of sidechains that are only the same between the two structures. In my example the structures are exactly the same protein with the same sequence and the same numbering, so it is not that hard. Even so, 2fw0 does not have residue 1 and starts with 2 so there is a small difference. I can't use residue 1 from 2gbp because 2fw0 doesn't have it. For my example, here are commands to calculate backbone RMSD and all-atom RMSD for all residues that are in both structures: rmsd #1/A:2-306@n,ca,c,o to #2/A:2-306@n,ca,c,o rmsd #1/A:2-306 to #2/A:2-306 Or you could use some subset of the residues, but still you have to give exactly the same numbers of atoms from the two structures: rmsd #1/A:2-110@n,ca,c,o to #2/A:2-110@n,ca,c,o rmsd #1/A:2-110 #2/A:2-110 If the two structures are different sequences (different residue types with different numbers of atoms) you would generally need to just use the backbone atoms because it would be too difficult to specify only pairs of sidechain atoms that are the same between the two structures. Rmsd command help <https://urldefense.com/v3/__https://www.cgl.ucsf.edu/home/meng/chimerax/vdoc... > I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 9, 2025, at 8:56 AM, Vojo P Deretic via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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
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