Hi Javier, Jim is exactly right (thanks Jim!) ... and here is more information about the attributes that come from the sequence headers, such as the attribute name "seq_rmsd" you would need for saving: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#headers> 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 12, 2025, at 3:03 AM, James Procter (Staff) via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Javier - the RMSDs are reported as attributes, so you could just write them to a file.

take a look at https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes

Hope that helps 🙂 Jim

PS. Jalview uses a similar mechanism to get the attributes imported as features on associated sequences.

From: Javier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: 12 March 2025 08:42 To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Obtain individual RMSD values Hello, I have an issue when applying matchmaker command in ChimeraX. When I execute the command: matchmaker #1 to #2 showAlignment true

I obtain the alignment with the bars in the upper layer showing the individual RMSD of each residue. But the results yields the overall RMSD of the alignment (i.e. RMSD between 108 pruned atoms).

Is there any way to obtain those individual RMSDs of the alignment as a file or have them printed in the log for post-processing?

Thank you in advance