Hi Jim, ChimeraX does not yet have the equivalent to Chimera's Match->Align, so for now you would need to keep using Chimera to do it.

We have a ChimeraX missing features page that mentions it as "calculating a multiple sequence alignment from a multiple structure superposition": https://www.rbvi.ucsf.edu/chimerax/progress.html

(In case you want to find it later, this page is linked to the "see also" links of the ChimeraX download page)

Like Chimera, ChimeraX does have multiple sequence alignment using sequence-based methods (clustal omega or muscle 3.8), but not yet this unique match->align feature. As far as I know we plan to have it in the future, as ChimeraX development continues.

Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Nov 25, 2022, at 6:21 AM, James H Naismith via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

In Chimera I can sort of print out a sequence alignment based on structural superposition.

(Match-align)

I can make a very nice structural superposition of very unrelated proteins with matchmaker, all I want to do is print out the resulting sequence alignment (where residues are with y A of each other)

Any help gratefully received.

With best wishes Jim