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