[Chimera-users] matchmaker and MSA

[Elaine Meng]

There is also a choice on the Matchmaker dialog to open Match->Align, "After superposition, compute structure-based multiple sequence alignment."   That just starts the tool, exactly the same as choosing it from the Tools menu.
Elaine

> On Sep 18, 2020, at 9:39 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> 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   
>