[chimerax-users] How to produce a multiple sequence alignment

[Elaine Meng]

Hi Luca,
Sorry, ChimeraX does not yet have the ability to do that step (Match->Align tool in Chimera).  

Since a few people have asked about it, I recently listed it in the missing features section in the ChimeraX download page, "calculating a multiple sequence alignment from a multiple structure superposition."
Best,
Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 17, 2021, at 10:04 AM, Luca Pellegrini <lp212 at cam.ac.uk> wrote:
> 
> Hello,
> 
> I have superposed several similar structures with Matchmaker, and now would like to obtain a structure-based multiple sequence alignment. In Chimera, Matchmaker has a nice button ‘After superposition, compute structure-based multiple sequence alignment’. ChimeraX produces all pairwise alignments with the reference structure, but how do I obtain a single alignment with all my sequences? 
> 
> Best wishes,
> Luca