[chimerax-users] Questions about MultiAlign Viewer

[Elaine Meng]

Hi Beate,
Chimera and ChimeraX are two different programs.  Chimera is our older program, and the link you are looking at is for Chimera.  ChimeraX is our newer program under active development, and although it also has a Sequence Viewer (not named Multalign Viewer), details of how to use it are different than in Chimera. So you should not assume that instructions for one will work for the other.

Things that are the same in both programs (Chimera and ChimeraX):

(1) matchmaker will report the overall RMSD between the two structures in the log, so you don't need to view the sequence if you just wanted the overall CA RMSD

(2) but if you mean you want the "RMSD" at each position (which for only two structures, is simply the CA-CA distance at that position in the alignment), you can show the RMSD header above the pairwise sequence alignment.  If you are using the matchmaker command simply include option "showAlignment true"

ChimeraX "matchmaker" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#options>

If you are using the Matchmaker graphical interface, just turn on the option "Show pairwise sequence alignment(s)"

ChimeraX Matchmaker tool: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html#alignment>

Then using matchmaker will automatically show the pairwise sequence alignment with RMSD header displayed.  

Here are more details about how to use the Sequence Viewer in ChimeraX:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html>

...and its RMSD header, which is assigned as an attribute:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#headers>

...and how to save attributes to a file:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 6, 2023, at 6:09 AM, Beate Aftret via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi, 
> I have some issues accessing the Multiaglin Viewer in ChimeraX. I’ve tried to look at this response: https://www.rbvi.ucsf.edu/pipermail/chimera-users/2019-February/015415.html . However, I’m unable to access it. I’m trying to access the multialign viewer so I can get individual RMSD values on structures compared using Matchmaker. 
> Thank you in advance. Let me know if I need to give more detail. 
> Kind regards, 
> Beate Aftret
>