Hi Marco, ChimeraX does not yet have the tool to create a multiple sequence alignment (more than 2) from a structural superposition. It is one of the things still mentioned in our "missing features": <https://www.rbvi.ucsf.edu/chimerax/progress.html> For now you would need to use Chimera for that task. Best, 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 Jul 23, 2025, at 2:02 AM, Marco Sette via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear all,
I have few pdb structure and I would like to build a multiple alignment of the sequences based on structural alignment. While in Chimera it was an easy task I'm find some problems with ChimeraX since it returns a series of pairwise alignments (structure A vs. B, A vs. C, A vs. D) rather than a multiple one (A vs. B vs. C. vs. D). Is it possible to do?
Thanks Best Marco