Dear Baldo Oliva, We are planning to have this capability (structure superposition -> multiple sequence alignment based on spatial proximity) in ChimeraX -- it is actively being worked on but is not ready yet, sorry. It is in the "missing features" list of popular capabilities of Chimera that are not yet in ChimeraX: <https://www.rbvi.ucsf.edu/chimerax/progress.html> The programming is in progess, and when this tool is available, we will update the "missing features" as well as the Change Log: <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> Thanks for asking. It is good to know that people will be using this feature since it is some effort to add it to ChimeraX. Regards, 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 Mar 31, 2026, at 1:06 AM, OLIVA MIGUEL, BALDOMERO via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX Team and Community, First, I would like to apologize if my question is redundant. I have only recently joined the community and may have missed previous discussions on this topic. I have been a user of Chimera on macOS, but with the most recent macOS updates, I have encountered compatibility issues that have led me to transition to ChimeraX. I am currently adapting to the new interface and commands, and I appreciate the many improvements it offers. However, I am missing a feature that I frequently used in Chimera: the ability to obtain a multiple sequence alignment after superimposing several structures using MatchMaker. This functionality was very useful in my workflow. I would like to ask whether there is an alternative approach in ChimeraX to achieve this, or if there are plans to include similar functionality in future updates. Thank you very much for your time and assistance. Baldo Oliva -- -- --------------------------- e-mail:baldo.oliva@upf.edu Baldo Oliva Miguel, PhD Structural Bioinformatics Laboratory (GRIB-IMIM) Universitat Pompeu Fabra, Barcelona Research Park of Biomedicine (PRBB) C/ Doctor Aiguader, 80. Barcelona-08003, Catalonia, Spain (EU) Tfn: 34-933160509 Fax: 34-933160550
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