Hi Max,

How about trying the ChimeraX matrixget command to output the positions of all the models to a file?

    https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.html

This gives both the rotation (a 3x3 matrix in the first 3 columns) and a translation (4th column).  The translation is in Angstroms, not in grid index units.

Tom


On Mar 4, 2024, at 4:04 PM, Maximilian Julian Pokutta via Chimera-dev <chimera-dev@cgl.ucsf.edu> wrote:

Dear Chimera Dev Team,
 
I have a chimera session with the ~500 maps overlayed onto a tomogram saved, and I would like to get their coordinates in relation to the tomogram on which they are overlayed. I am unsure how to get started on this and wanted to know if you had any pointers as to where to start.
 
Best,
Max
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