Hello Leonardo,
Matchmaker only creates pairwise alignments.
In Chimera (but not yet in ChimeraX), there is a tool named "Match->Align" to create a multiple sequence alignment from a 3D structure superposition:
<
https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchalign.html>
So for now, you'd have to use Chimera for this task instead. Chimera has basically the same Matchmaker as ChimeraX, so you could start Chimera, use Matchmaker (tool GUI or mmaker command, syntax is somewhat different than in ChimeraX), and then use its Match->Align
tool to get the multiple sequence alignment.
See Chimera help for matchmaker GUI and command:
<
https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html>
<
https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html>
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco
> On Aug 13, 2025, at 7:27 AM, Betancurt, Leonardo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Hello, I would like to display a multiple sequence alignment based on structure after match maker.
> I use the command ”mm #!1-4 to #5 showAlignment true” but ChimeraX shows multiple pairwise alignments, is there a way to create a multiple sequence alignment?
> Thank you,
> Leo Betancurt, Ph.D.
> Post Doctoral Researcher | Zatopek Lab
> New England Biolabs Inc.
> 📞 (978) 380-7290
> 📱 (351) 350-4075<image001[5].jpg>
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