Hi Xavier.

  ChimeraX can measure the enclosed volume of a surface and put caps over holes when measuring the volume (menu Tools /  Volume Data / Measure Volume and Area).  But the trick is how do you get such a surface lining just the tunnel.

  Here's another approach.  Make a density map that is 0 inside atoms of a molecular assembly and is 1 outside the assembly.  So the 1's region includes the tunnel.  But it is connected to the outside region around the molecular assembly via the hole at the end of the tunnel.  If we can erase that connection at the hole then we can make a surface of the density in the tunnel region that can be measured.

  Here's an example using GroES, pdb 2c7c.

open 2c7c

molmap #1 10

volume onesmask #2 invert true

        volume #3 cap false

# Now use volume eraser, menu Tools / Volume Data / Volume Eraser, make the erasing sphere huge just outside

        # the tunnel touching the tunnel hole and erase within the sphere.  Now the tunnel space density is isolated.

        # Use Blob mouse mode to color the tunnel density surface (Right Mouse toolbar, Blobs).

        surface splitbycolor #3

measure volume #5.2

        > Enclosed volume for piece 2 (#5.2) = 2.542e+05

I get 254,000 cubic Angstroms for the cavity of GroES.

Tom

On Nov 20, 2025, at 12:32 AM, F.Xavier Gomis-Rüth via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

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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