[Chimera-users] matchmaker and MSA

[Elaine Meng]

Hi Zaher,
Yes, but it is a separate step.  After all three structures are superimposed in 3D (using Matchmaker or any other method you like), then you can use the Match->Align tool to create a sequence alignment of all three.  Menu: Tools... Structure Comparison... Match->Align.

<http://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 Sep 18, 2020, at 9:19 AM, arrafzaher at campus.technion.ac.il wrote:
> 
> Hi,
> Suppose I have 3 structures #0 #1 and #2.
> If I impose structure alignment of both #1 and #2 to #0.
> I receive two MSA alignment.
> Is there a way to view one MSA of the 3 structures and not 2 MSA of them.
> Thanks,
> Zaher