Thanks, Elaine! How are you? Long time no see! On 9/25/25, 9:51 AM, "Elaine Meng" <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: [External email - use caution] Hi Shelley! Chimera and ChimeraX are two separate programs, so there are various differences. The email address for ChimeraX questions, chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> is CC'd here. I'll answer for ChimeraX since that's what you're using -- ChimeraX has a Sequence Viewer tool which is basically the logical equivalent of Chimera's Multalign Viewer, see: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html;> See also the detailed tutorial on using ChimeraX to map conservation from a sequence alignment onto structures: <https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-c...> <https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-c...> 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 Sep 25, 2025, at 8:36 AM, Shelley Copley via Chimera-users <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote:

Has Multalign viewer been taken down? I don’t see it in ChimeraX 1.10. Is there a different way to map sequence conservation onto a structure? Thanks! Shelley