[chimerax-users] Color by RMSD for nucleic acid

[Elaine Meng]

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
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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 at 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
>