[Chimera-users] Multiple sequence alignment

[Elaine Meng]

Dear Avner,
You can create a multiple sequence alignment from a multiple  
structure alignment using "Match -> Align" (under Tools... Structure  
Comparison).

In the production release of Chimera (Dec 2008, version 1.3) it  
simply uses the current structure alignment:
<http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/ 
matchalign/matchalign.html>

In newer versions (if you get a recent daily build of Chimera), it  
can also iterate to improve the result by creating a sequence  
alignment, refitting, creating a new sequence alignment (etc.):
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/ 
matchalign.html>

It sounds like you superimposed the structures using MatchMaker,  
which makes a separate sequence alignment for each pair.  If the  
structures are now superimposed the way you want, you can Quit from  
each of those pairwise sequence alignments to delete them, then use  
Match -> Align to create a new multiple sequence alignment.  That  
alignment (like the pairwise ones) will be shown automatically in  
Multalign Viewer.  You can save it to a file using "File... Save As"  
in the Multalign Viewer menu.

The "superpositions and alignments" tutorial includes using  
MatchMaker and Match -> Align:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
alignments.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                       http://www.cgl.ucsf.edu/home/meng/index.html

On May 8, 2009, at 12:33 PM, Avner Schlessinger wrote:

> Dear Chimera experts,
>
> Once I create multiple structure alignment i was wondering how I can
> view the corresponding multiple sequence alignment. when I try to view
> it through the MultiAlignViewer it shows all
> possible pairwise alignments with the sequence of the first structure
> rather than all
> the sequences together.
>
> Thanks!
> Avner