Hi Richard, I don't understand exactly what you are trying to do. Are you trying to get an RMSD for only certain parts of the chains instead of over all matched residues? Matchmaker RMSD is over all of the alpha-carbons of the residue pairs used to align the structures. If you use the matchmaker option to show the pairwise sequence alignment, then after that, you can draw a box in the sequence alignment to get an RMSD for only the pairs inside the box. To see that RMSD value you would show the sequence-alignment Regions window by using the Sequence Viewer context menu "Annotations... Regions" A context menu is shown by right-clicking on the tool (or for Mac it may be Ctrl-clicking instead). Then in that Region Browser window it will report the alpha-carbon RMSD for your boxed area each time you drag in the sequence alignment window to draw that box. (There is an RMSD column in the table of regions, where a region is a boxed area on the sequence alignment.) See Regions: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#regions> Or if you need to use more atoms than just the alpha-carbons, you can use the "rmsd" command to report RMSD for any sets of atoms such as all backbone without changing the superposition, but you have to give it equal numbers of atoms from the two structures: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rmsd.html> RMSD is not necessarily the best way to compare, you might want to just look at that area directly and see if there are other changes that might be important to the structure/function of the protein (binding, catalysis, or whatever it does). 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 Aug 4, 2025, at 9:12 AM, Richard melzack via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello

I have started using your excellent Chimera X 1.10.1 visualisation platform and have uploaded a protein and mutated protein onto the matchmaker screen. The RMSD is low so the general appearance is very similar. However, I was wondering (the mutated protein has a 6bp insertion and a nonsynonymous SNP) how to examine the details around the exact points of the mutations (both are on the same exon). I have tried a number of ideas. The command line doesn't like sequence or sequence #1 #2.

I would be grateful for your assistance.

Thank you

Dr Richard Melzack _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

Hi Richard, Well my previous answers are for if you wanted a more localized RMSD for a specific subset of the sequence. If there is an insertion, however, there aren't atoms in the wild type (or whatever you are calling the one without the insertion) to pair with those in the insertion, so RMSD isn't that helpful. Of course you can display any sidechains and zoom in on any part that you want. You can just move/zoom the structure with the mouse. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> There are several different ways to do any given thing, e.g. commands to label and zoom in on residue 12 of chain A, show atoms of all residues within 5 angstroms of it: label /A:12 view /A:12 show /A:12 :<5 There are help pages for each command (for example display help page for "label" with command "help label") and also for command-line specification of chains, residues, etc. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> You can also do this stuff by selecting using Ctrl-click or by choosing in sequence, then using the Actions menu to do stuff to your selection like show atoms, label, select larger zone around them, etc. You can also examine the structures individually for H-bonds, contacts of specific residues, etc. For example, see the "Protein-Ligand Binding Sites" tutorial: <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html> I hope this helps, Elaine

On Aug 4, 2025, at 10:40 AM, Richard melzack via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Thanks Elaine

Sorry I didn't make it clear. I was wondering if I could "home in" on the mutated residues precisely to see if there are any "misshapes" in comparison to the wild type. The protein I am looking at is a subunit of a 3 protein structure and I want to try to get some indication whether there is any deformation in these specific sites. It might give a clue to its binding ability or lack of to the other two subunits.

Regards

Richard

On Mon, 4 Aug 2025 at 18:12, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Richard, I don't understand exactly what you are trying to do. Are you trying to get an RMSD for only certain parts of the chains instead of over all matched residues?

Matchmaker RMSD is over all of the alpha-carbons of the residue pairs used to align the structures. If you use the matchmaker option to show the pairwise sequence alignment, then after that, you can draw a box in the sequence alignment to get an RMSD for only the pairs inside the box. To see that RMSD value you would show the sequence-alignment Regions window by using the Sequence Viewer context menu "Annotations... Regions"

A context menu is shown by right-clicking on the tool (or for Mac it may be Ctrl-clicking instead).

Then in that Region Browser window it will report the alpha-carbon RMSD for your boxed area each time you drag in the sequence alignment window to draw that box. (There is an RMSD column in the table of regions, where a region is a boxed area on the sequence alignment.)

See Regions: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#regions>

Or if you need to use more atoms than just the alpha-carbons, you can use the "rmsd" command to report RMSD for any sets of atoms such as all backbone without changing the superposition, but you have to give it equal numbers of atoms from the two structures: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rmsd.html>

RMSD is not necessarily the best way to compare, you might want to just look at that area directly and see if there are other changes that might be important to the structure/function of the protein (binding, catalysis, or whatever it does).

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 Aug 4, 2025, at 9:12 AM, Richard melzack via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello

I have started using your excellent Chimera X 1.10.1 visualisation platform and have uploaded a protein and mutated protein onto the matchmaker screen. The RMSD is low so the general appearance is very similar. However, I was wondering (the mutated protein has a 6bp insertion and a nonsynonymous SNP) how to examine the details around the exact points of the mutations (both are on the same exon). I have tried a number of ideas. The command line doesn't like sequence or sequence #1 #2.

I would be grateful for your assistance.

Thank you

Dr Richard Melzack _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/