Hi Andy, In the "matchmaker" command, there is a "reportMatrix true" option you can use to report the transformation matrix, if that is good enough. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#options> Another possibility may require opening an extra (third) copy of one of the models first and placing it in the same position as one of the others (say the first). Then if you use matchmaker to superimpose the first model on the second model, after that you can use "measure rotation" to compare the positions of the extra copy (third model, which is the old position of the first model) and the new position of the first model. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation> 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 8, 2026, at 9:45 AM, Sen, Anindito via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear All,
I have 2 models of a protein positioned in different places in a complex macromolecular assembly. Using Matchmaker I can align the 2 models. How can I get the angles and the axis of rotation/orientation that is calculated to align the 2 models in Matchmaker.
Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu
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