id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6762 matchmaker showAlignment tries to calculate CA RMSD header for nucleic acids Emily.Rundlet@… Eric Pettersen "From: ""Rundlet, Emily via ChimeraX-users"" Subject: [chimerax-users] Color by RMSD for nucleic acid Date: April 30, 2022 at 10:59:22 AM PDT To: ""chimerax-users@cgl.ucsf.edu"" Reply-To: ""Rundlet, Emily"" 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 From: Elaine Meng via ChimeraX-users Subject: Re: [chimerax-users] Color by RMSD for nucleic acid Date: May 1, 2022 at 9:02:55 AM PDT To: ""Rundlet, Emily"" 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. " defect assigned high Sequence all ChimeraX