Hi Jan, I can't think of a "nice" way to do this. My only idea is to manually (with the mouse) rotate and translate the proteins and their axis en masse relative to the other items in the your scene, namely your other axis and whatever else you had. This would be very tedious, requiring many switches between rotation and translation and changing the view to see whether the two axes are sufficiently aligned for your purposes. This could be done by selecting the proteins and their axis, and then using the mouse mode to rotate/translate only selected models. See: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> Maybe there is some better way to do this exactly in a single command by reporting transformation matrices, doing linear algebra, and then using the calculated relative transformation matrix to reorient the one set of models onto the other, but that is beyond my skill set. Our expert on that kind of thing is at a workshop right now so it is possible you could get a better answer in a day or two. 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 Oct 28, 2025, at 10:15 AM, Hübbers, Jan via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hey support, I have defined x, y, z symmetry axis for a protein complex by forcing axis through centroids of the different subunits. I also created x, y ,z axis that meet at the origin of my scene. Is it possible to align the protein axis to the scene axis? Best, Jan

Dear Tom and Elaine, Thanks for your swift response. Tom, you are right about the symmetry and the centroids. However, I have different complexes consisting of different isoforms. By aligning the overall symmetry of the protein to the origin of the coordinate system, I was hoping to avoid aligning to template structures in my workflow. Best, Jan From: Tom Goddard <goddard@sonic.net> Sent: Wednesday, 29 October 2025 06:04 To: Hübbers, Jan <jan.huebbers@rwth-aachen.de> Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Align x,y,z axis of Proteins Hi Jan, I guess if you have subunits that define orthogonal axes you have icosahedral or octahedral or dihedral symmetry? If so why not align your centroids to the centroids of another structure of the same symmetry that has the axes aligned with x,y,z? You would use the ChimeraX align command and specify the 6 centroids of one model and the 6 centroids of the other. align #3,4,5,6,7,8 to #9,10,11,12,13,14 Documentation https://www.cgl.ucsf.edu/chimerax/docs/user/commands/align.html Tom On Oct 28, 2025, at 10:15 AM, Hübbers, Jan via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hey support, I have defined x, y, z symmetry axis for a protein complex by forcing axis through centroids of the different subunits. I also created x, y ,z axis that meet at the origin of my scene. Is it possible to align the protein axis to the scene axis? Best, Jan ________________________________________________________________ Dr. rer. nat. Jan W. Hübbers Postdoctoral researcher RWTH Aachen University, Institute for Biology I, Unit of Plant Molecular Cell Biology Assistant Features Editor The Plant Cell, American Society of Plant Biologists Worringerweg 1, 52074 Aachen, Germany +49 (0)241 80 28130 http://www.bio1.rwth-aachen.de/PlantMolCellBiology/index.html<https://urldefense.com/v3/__http:/www.bio1.rwth-aachen.de/PlantMolCellBiology/index.html__;!!Mak6IKo!PhjVkEnzuQN9GkxaI6QPz4AugbqGd03aOCZ0kTcN_5ZtJKWY39KzBsgIA5z_G94egVDs_RQ8USp7ymdy1k6PoiTG8vH6DQ$> “The greatest value of a picture is when it forces us to notice what we never expected to see.” John W. Tukey _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/