[chimerax-users] Displaying multiple sequences during alignment

[Y. Mutum]

Thank you.

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________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Monday, March 8, 2021 3:31:34 PM
To: Y. Mutum <ym337 at cam.ac.uk>
Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Displaying multiple sequences during alignment

Hi Yaikhomba,
Yes, Matchmaker only makes pairwise alignments.  Chimera (but not yet ChimeraX) has a Match -> Align tool that, after you have multiple structures superimposed in 3D, then you can calculate the multiple sequence alignment from the spatial information.  So currently you would need to use Chimera: first matchmaker to superimpose all three, then Chimera Match->Align (in Chimera menu under: Tools... Structure Comparison) to create the multiple sequence alignment. You could then save the multiple sequence alignment to a file (from the sequence window File menu), then open it in ChimeraX.

Chimera Match->Align
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchalign.html>

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

> On Mar 8, 2021, at 7:19 AM, Y. Mutum <ym337 at cam.ac.uk> wrote:
>
> Hi
> I have a very quick query.
> I opened up 3 models - 3cx5, 2qjp and 1zrt in ChimeraX. I was thinking of aligning on one of the chains and looking at the global-sequence-alignment.
>
> >>> match #3/C #2/A to #1/C showAlignment true
>
> The sequence alignment opens up as pairwise sequence alignement, in 2 separate windows for each of the 2 pairs.
> Picture attached.
>
> Rather, is there a way to get all 3 sequences aligned together, not separately?
> I tried looking up at other options, but I think I am missing out something somewhere.
> Thanks
> Yaikhomba

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