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/