Hi Rosy, Actually it was added in 2021 and is in every version 1.4+ From Change Log: <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> December 31, 2021: Align sequences with Clustal Omega or MUSCLE - "sequence align" command and Sequence Viewer context menu allow (re)aligning sequences with web services hosted by the RBVI "sequence align" command <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#align> Sequence Viewer tool, context menu: Edit... Realign Sequences... <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#conte...> See above links for details. The Sequence Viewer approach re-aligns the same sequences that are in your current sequence alignment window. If you use the "sequence align" command, however, you can specify sequences by Uniprot IDs or chain IDs of structures that are already open in the graphics window, or sequences that are already open in separate Sequence Viewer windows (e.g. each window could could contain one sequence). 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 Jan 28, 2025, at 9:02 AM, Rosaleen Calvert via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi. Apparently alignment is newly available in Chimerax 1.9. I cannot find how to do this in Tools: sequence or Tools: structure analysis. From Rosy Calvert