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.

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

________________________________________________________________
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

“The greatest value of a picture is when it forces us to notice what we never expected to see.”
John W. Tukey

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