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> 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

 

“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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