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 ----- 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@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