Thanks a lot, Tom. The issue is that I have a very wide tunnel connecting the inner and outer surfaces that cannot be erased by a low-resolution map. Is there an option to somehow generate a perpendicular plane or clip the map, "closing" this wide pore? On 19/11/25 20:29, Tom Goddard wrote:
Here is an example of one way to compute an interior cavity volume, in this case a virus capsid, when there are holes. It's a bit tricky.
https://rbvi.github.io/chimerax-recipes/virus_volume/virusvol.html
Tom
On Nov 19, 2025, at 10:43 AM, F.Xavier Gomis-Rüth via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thanks a lot, Elaine. I'll have a try and let you know.
On 19/11/25 18:07, Elaine Meng wrote:
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
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