Hi Dmitry, 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. open 1080 from emdb volume copy #1 perframe "turn z 1 model #1 coord #1; vol add #2,1 inplace true" frames 359 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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Hi Dmitry, ChimeraX does have a radial density plot capability. In the case you mention of membrane proteins I'm not even sure what you mean by a radial plot as you only have a patch of membrane and the density probably diminishes as you move away from the embedded protein. I guess you might want a 1-D plot of density along a line segment. I'm not sure how you would place that segment and then to sample density along it would require some Python code. Tom

On Sep 4, 2025, at 7:54 AM, Dmitry Semchonok <semchonok@gmail.com> wrote:

Dear Tom, Thank you very much for your clever solution and help — it was exactly what we needed!

May I also ask if it is possible to generate a radial density plot (density versus radius) from the cylindrically averaged? If so, how to do that in ChimeraX?

Many thanks!

Best regards, Dmitry

From: Tom Goddard <goddard@sonic.net> Sent: 03 September 2025 22:47 To: Dmitry Semchonok <semchonok@gmail.com> Cc: Chimerax Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Cylindrical averaging for radial density profiles

Hi Dmitry,

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.

open 1080 from emdb volume copy #1 perframe "turn z 1 model #1 coord #1; vol add #2,1 inplace true" frames 359 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

<emd108_cylinder_average.png><emd1080.png>

...

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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