(CC-ing chimerax-users@cgl.ucsf.edu since that is the recommended address for ChimeraX questions as long as they do not include private data. Email sent to me directly has more chance of falling through the cracks.) Dear Dr. Sharyn Endow, The Matchmaker algorithm in ChimeraX is the same as in Chimera. So everything I said before about Chimera's Matchmaker is also the case in ChimeraX. If you have the "iteration" option turned on it doesn't use all aligned columns but instead prunes residue pairs for a better fit of the core. If you are showing the sequence alignment, it shows what set of positions were used for the final fit as a light orange colored box. As before, it uses only the CA-CA pairs within those columns, not the side chains. These overall RMSD values are reported in the Log. "pruned" refers only to the fit iteration process, where iteration prunes away some pairs so that they are not used in the final fit. See "Fitting" at the bottom of the "Matchmaker" help: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html#fitting> Or, if you are using the "matchmaker" or "mmaker" command, see the "cutoffDistance" option for the description of iteration and pruning: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#options> If you mean the RMSD header across the top of the sequence alignment, that is a different thing calculated per column (not for the whole structures overall), and you can control in the Sequence Viewer Settings whether this RMSD histogram is calculated CA-only or backbone-only. Neither of them uses the sidechains. If a pairwise alignment, "CA RMSD" boils down to just the CA-CA distance. Simply selecting some range of residues on the sequence alignment doesn't change anything. See help for Sequence Viewer, its header lines, and its Settings: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#headers> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#settings> Finally as mentioned in my previous answer about Chimera, you can use the "rmsd" command to calculate RMSDs over any sets of atoms that you choose (with or without sidechains) without changing the current positions of the structures. The more tricky part is that you have to specify in the command which atoms to pair with which atoms, since it is not calculated automatically like it is in Matchmaker. The syntax is a little different than in Chimera: there is a "to" between the two sets of atomspecs, and in ChimeraX the slash symbol "/" is used to indicate chains. "rmsd" command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rmsd.html> ChimeraX atomspec including many examples: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> 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 Mar 23, 2024, at 8:09 AM, Sharyn Endow, Ph.D. <sharyn.endow@duke.edu> wrote:
Dear Dr Elaine Meng,
We wrote to you a few years ago regarding Chimera RMSD and you were kind enough to send the information below. We now have a few Q's regarding Chimera X Matchmaker, which displays RMSD values, e.g., when all beta-strands are selected in the Sequence Viewer window.
• We would like to know what the RMSD values correspond to after aligning two protein sequences using Matchmaker Iwhich uses only only one point per residue for fitting) and selecting all b-strands in the Sequence Viewer window. Is a single RMSD value calculated for each residue to obtain the average RMSD for the "pruned" or all atom pairs and, if so, is the RMSD value between the single point per residue that was used for fitting?
• Is there some way to obtain the C-alpha RMSD values but not the side chain values, after aligning two protein chains in Matchmaker in Chimera X?
• What does "pruned" atom pairs mean in this context?
T hank you in advance for your help -
Sincerely,
Sharyn A. Endow, PhD Professor of Cell Biology, DUMC DUS, Cell Biology PO Box 3709 / 245/247 Sands Bldg / 303 Research Drive Durham, NC 27710 USA T 919 684-4311 F 919 681-9929
From: Elaine Meng <meng@cgl.ucsf.edu> Date: January 25, 2021 at 4:26:34 PM EST To: "Sharyn Endow, Ph.D." <sharyn.endow@duke.edu> Cc: Chimera <chimera-users@cgl.ucsf.edu> Subject: Chimera RMSD Reply-To: Chimera <chimera-users@cgl.ucsf.edu>
From: "Sharyn Endow, Ph.D." <sharyn.endow@duke.edu> Subject: Chimera RMSD Date: January 23, 2021 at 11:27:17 AM PST
Thank you for your work in developing Chimera. We are trying to use Chimera RMSD to quantitate twisting of a beta-sheet and would like to know what the syntax is to list rmsd values for specified residues corresponding to a beta-strand, not just for single residues. Is it possible to list these values using RMSD? If so, we would greatly appreciate knowing how to get started.
Sincerely, Sharyn
Hi Sharyn, You can specify any sets of atoms/residues that you like in the RMSD command, as long as there are equal numbers of atoms in the two sets that you specify (from two different models). They will be paired in the order specified. We have a command-line "atom specification" syntax for that kind of thing. There is a longish page with lots of examples here: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html >
In your case, you may need to specify residue numbers, chain ID, and possibly atom names if you just want to use alpha-carbons or backbone as opposed to all atoms of the residues. E.g. something like
rmsd #0:12.A,57-63.A #1:14.A,59-65.A
... for all atoms of model 0 residues 12 and 57-63 in chain A vs. all atoms of model 1 residues 14 and 59-65 in chain A. Or to use CA-only or backbone only:
rmsd #0:12.A,57-63.A@ca #1:14.A,59-65.A@ca rmsd #0:12.A,57-63.A@n,ca,c,o #1:14.A,59-65.A@n,ca,c,o
Of course the numbers could be the same in the two models, I just was trying to give a more general example. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
P.S. the chimera-users@cgl.ucsf.edu address CC'd here is recommended for general Chimera how-to or is-it-possible types of questions