Opened 3 years ago

Closed 2 years ago

#6762 closed defect (fixed)

matchmaker showAlignment tries to calculate CA RMSD header for nucleic acids

Reported by: Emily.Rundlet@… Owned by: pett
Priority: high Milestone:
Component: Sequence Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by pett)

From: "Rundlet, Emily via ChimeraX-users" <chimerax-users@…>
Subject: [chimerax-users] Color by RMSD for nucleic acid
Date: April 30, 2022 at 10:59:22 AM PDT
To: "chimerax-users@…" <chimerax-users@…>
Reply-To: "Rundlet, Emily" <Emily.Rundlet@…>

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 <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" <Emily.Rundlet@…>

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.

Change History (2)

comment:1 by pett, 3 years ago

Status: assignedaccepted

comment:2 by pett, 2 years ago

Description: modified (diff)
Resolution: fixed
Status: acceptedclosed

Nucleic alignments now use C4' instead of C-alpha for RMSD header.

Note: See TracTickets for help on using tickets.