Hi Priyanka, (1) The address for questions is chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> CC'd here. (2) It would be useful to say what you mean by "did not work." Otherwise it is very hard for us to answer. (3) If you only have two structures, "RMSD" per column is really just the CA-CA distance. Also realize that even if you iterate with matchmaker to some value (1 angstrom for example) the final-fit columns might not be the only ones with CA-CA distance <1. There might be other columns with CA-CA <1 even though they weren't used in the final fit. So a clearer and more correct way to select in your case would be to use the RMSD header attribute value. You said you wanted to display residues with RMSD >1, in this case same as residues with CA-CA >1. Example with my own test case: open 2gbp open 2fw0 mm #2 to #1 show true hide atoms show ::seq_rmsd>1.0 See "sequence alignment headers and attribute values": <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#headers> See specifying attribute values in command line: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes> When I tried to morph I see there is a problem in playback being very slow. Maybe that is what you meant by "does not work"?? It seems to be because the sequence alignment is shown at the same time. We will look into this bug. However, you can do all of the above, including showing the alignment and specifying residues by seq_rmsd value but then be sure to close the sequence alignment window (Sequence Viewer) before you morph. If I do the above example commands, then close the Sequence Viewer, then it works fine for me to run your morph command: morph #1,2 wrap true frames 60 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 11, 2025, at 10:37 AM, Priyanka Abeyrathne via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,

I have two cryo-EM models (PDBs) at neutral and acidic pH conditions, both containing 486 amino acids. I would like to compare them by calculating the RMSD per residue, and then generate a morphing animation between the two structures. I used the following commands in ChimeraX: 1. I aligned the two structures using MatchMaker: mm #1 to #2 showAlignment true

2. I clicked on one amino acid in the MatchMaker alignment results to highlight the aligned residues.

3. Then I used the command: select ~sel to select residues with an RMSD greater than 1 Å.

4. To visualize the atoms of the selected residues with high RMSD, I ran: display sel & protein 5. I then cleared the selection using: select clear

6. Finally, I attempted to generate a morphing animation using: morph #1,2 wrap true frames 60

However, this command did not work. Could you please help me troubleshoot this?

Thank you. Kind regards, Priyanka