ChimeraX doesn't have any map cylindrical averaging capability. But you could do it by adding together say 360 copies of the map each copy rotated by 1 degree about the cylinder axis relative to the previous copy. Here's an example.

save cylinder_average.mrc model #2

Here the cylinder axis is the z axis and I use the perframe command to rotate and add 359 copies separated by 1 degree steps to the original map.

Tom

On Sep 3, 2025, at 11:06 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear Colleagues,

I need to perform cylindrical averaging of membrane protein density maps (MRC files) to generate radial density profiles for membrane thickness analysis.

Does ChimeraX have built-in functionality for this, or are there existing scripts/plugins available?

If not, could you provide guidance on the best approach to implement this?

Thank you!

Kind regards,
Dmitry

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