Hi Charles, It was very recently added, probably your version of ChimeraX is too old. You would need to get a ChimeraX build from the last few weeks, i.e. the candidate relase 1.12 or a recent daily build April 22 or later as per the change log: <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> ChimeraX Match->Align tool <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchalign.html> ... and now there is a command, too! Sounds like you already found the documentation on our website... <https://rbvi.ucsf.edu/chimerax/docs/user/commands/msa3d.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 May 11, 2026, at 8:54 AM, Charles via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I am curious if the Match > align tool has been implemented yet in chimerax? I do not see it in any of the tools and using the command line msa3d nor matchmaker #1 to #2 startMatchAlign seems to be working. I can do it manually by aligning each structure individually by chain or by aligning the chains that i know match each other using the pair ss function with matchmaker. i found an old thread that said it was submitted as ticket #7359 but no other updates besides that.
Thank you, Charles