Hi Guillaume, I don't know whether there is a ticket, and our expert on this topic is away for a couple of days, but one way or another we will try to make this happen. If there is a ticket we will add your name, if there is not, we would either create a ticket or note in the to-do list to notify you (or possibly the whole mailing list). It is definitely a highly requested feature that is listed on our "missing features" list which I try to keep updated: <https://www.rbvi.ucsf.edu/chimerax/progress.html> We are working actively on several of those missing features and hope that more will be available soon. Regards, 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 14, 2025, at 5:36 AM, Guillaume Gaullier <guillaume.gaullier@kemi.uu.se> wrote:
Hi Elaine,
If there is a ticket for the Match->Align feature in ChimeraX, I'd like to receive the notifications for it please. I have needed to do structure-based multiple sequence alignments in the past, and it would indeed be very convenient to have this feature in ChimeraX. Thank you,
Guillaume
From: Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: Wednesday, August 13, 2025 5:20:11 PM To: Betancurt, Leonardo Cc: chimerax-users@cgl.ucsf.edu Subject: [chimerax-users] Re: Multiple sequence alignment display 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/matcha...>
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/matchm...> <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> _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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