hi Xavier,
Better to use a new descriptive subject line rather than extending an unrelated conversation.

There is a "Measure Volume and Area" tool  (or "measure volume" command) to report volume enclosed in a surface, which could be an isosurface:

<https://rbvi.ucsf.edu/chimerax/docs/user/tools/measurevolume.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#volume>

However, I don't recall if it handles holes.  You could try it.  If not, maybe you would need to use some method of generating a surface without holes.  As you said, maybe "Segment Map" could do that:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/segment.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 19, 2025, at 8:27 AM, F.Xavier Gomis-Rüth via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Elaine,
I am not sure if this appeared already earlier in the BB, but is there a way to
compute the inner lumen volume of a particle, which has some large openings
(≈40 Å), with ChimeraX? Maybe with some kind of segmentation?
Thanks a lot in advance,
Xavier

--