Thank you so much, Elaine and Eric. The "sequence header rmsd setting atoms backbone" command worked perfectly! ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Monday, May 2, 2022 5:53 PM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>; Rundlet, Emily <Emily.Rundlet@STJUDE.ORG> Subject: Re: [chimerax-users] Color by RMSD for nucleic acid [You don't often get email from pett@cgl.ucsf.edu. Learn why this is important at http://aka.ms/LearnAboutSenderIdentification.] Caution: External Sender. Do not open unless you know the content is safe. Hi Emily, As Elaine says, that is a bug. Looking at the code, I can see there is a workaround you can use until the bug is fixed. Use the command "sequence header rmsd setting atoms backbone" which will switch from using carbon alphas to the backbone atoms appropriate for the polymer type of the chain. You should then see actual histogram values in the RMSD header on the sequence and the "color byattribute seq_rmsd" command should work. --Eric Eric Pettersen UCSF Computer Graphics Lab

On May 1, 2022, at 9:02 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Emily, That is a bug -- the problem is that currently, ChimeraX assumes the alignment is protein and tries to calculate the alpha-carbon RMSD rather than using nucleic-acid atoms. I will create a bug ticket with you as the reporter so that you will be notified of any fixes.

Thanks for reporting it! Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Apr 30, 2022, at 10:59 AM, Rundlet, Emily via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi ChimeraX developers,

Is there a way to color nucleic acids by seq_rmsd?

When I use the following, no atoms are colored.

mm #1 to #2 matrix Nucleic showAlignment true color byattribute seq_rmsd #2

Thank you in advance for your help!

-Emily

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