Are you trying to measure the diameter of a spherical virus particle? If not, what do you mean by diameter? Also what do you mean by height? A flexible approach to measuring distances in maps is to use atoms of fit atomic models or place markers and measure the distance between the atoms or markers. But you have to figure you where you want to place the markers or which atoms to use and that depends on what you mean by "diameter" or "height".

On Dec 2, 2025, at 12:39 AM, 张楠 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX Developers,
I have an EM density map and need to measure its diameter and height. I used the "measure and color blob" tool, which displays the length, width, and height of the entire EM density when clicked. However, the values are measured around the entire density map, making them slightly larger than the actual diameter. Therefore, I tried using the "tape" tool to measure, but it is difficult to select two perfectly horizontal points for an accurate measurement. I would like to ask how to measure the correlation length of a map in ChimeraX.
Looking forward to your answer, thank you!
Best regards,
Nan

Nan Zhang

zhangnan@nankai.edu.cn

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