Hi Jesse,

There is also a graphical user interface ChimeraX menu Tools / Volume Data / Measure Volume and Area that can measure the volume enclosed in STL surfaces. If the STL surface has holes, for instance at the top or bottom of the tomogram then this tool or the measure volume command will report that it has holes and compute the enclosed volume as if the hole were covered by a flat cap. If the surface has holes that are not flat in shape then it still covers the holes but the shape of the cap is irregular so the "enclosed volume" may be less meaningful.

Tom

On Dec 20, 2023, at 10:54 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Hi Jesse, If the different components are different surface models in ChimeraX, you could use the command "measure volume," e.g. if the surface of the component of interest is model #3:

measure volume #3

...which would give cubic whatever distance units your data are in (angstroms, nanometers, ...)

See help for command options: https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#volume

I hope this helps, Elaine

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Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Dec 20, 2023, at 7:29 AM, Jesse Hansen via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

dear ChimeraX users,

We have a tomogram volume (.mrc) which we have segmented different components (stl files; surfaces). Is there any tool available to estimate the volume within each of the cellular components (within each surface)? Either some approximation of the cubic Angstrom/nanometers, or as a percentage of the total tomogram volume.

thanks in advance! best Jesse Hansen

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Hi Jesse,

The Chimera warning means that the surface triangles do not have a consistent orientation. The order of the 3 vertices of each triangle needs be consistent from one triangle to the next (e.g. all counter-clockwise when viewed from outside the surface). Apparently the segmentation software that generated the STL files did not follow this convention which almost all surface computing software uses -- it allows software to know which side is outside and which side is inside.

The relation between surface area and volume depends on the shape. A 780,000 sq Angstrom surface could have nearly 0 volume if it is a thin pancake or could have a maximum volume of 65,000,000 cubic Angstroms if it is a sphere.

Tom

On Dec 26, 2023, at 12:37 AM, Jesse Hansen via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

hi Tom and Elaine,

thanks for the responses!

I did indeed try this in ChimeraX using the measure volume and area tool, but it only provided the area. The volume was 0, and the area was ~780000 sq A. In older Chimera I tried this and got the same result, but here it also provided the extra output for volume that it was "N/A (non-oriented surface)". I'm not sure, but I think a simple conversion of surface area to volume is not so simple since that depends highly on the shape of the object, am I right? Any input is appreciated (or even an alternative program that could do this calculation)

thanks!

Jesse From: Tom Goddard goddard@sonic.net Sent: December 20, 2023 8:45:07 PM To: Jesse Hansen Cc: ChimeraX Users Help Subject: Re: [chimerax-users] volume amount estimation

Hi Jesse,

There is also a graphical user interface ChimeraX menu Tools / Volume Data / Measure Volume and Area that can measure the volume enclosed in STL surfaces. If the STL surface has holes, for instance at the top or bottom of the tomogram then this tool or the measure volume command will report that it has holes and compute the enclosed volume as if the hole were covered by a flat cap. If the surface has holes that are not flat in shape then it still covers the holes but the shape of the cap is irregular so the "enclosed volume" may be less meaningful.

    Tom

...

On Dec 20, 2023, at 10:54 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Hi Jesse, If the different components are different surface models in ChimeraX, you could use the command "measure volume," e.g. if the surface of the component of interest is model #3:

measure volume #3

...which would give cubic whatever distance units your data are in (angstroms, nanometers, ...)

See help for command options: https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#volume

I hope this helps, Elaine

---

Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Dec 20, 2023, at 7:29 AM, Jesse Hansen via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

dear ChimeraX users,

We have a tomogram volume (.mrc) which we have segmented different components (stl files; surfaces). Is there any tool available to estimate the volume within each of the cellular components (within each surface)? Either some approximation of the cubic Angstrom/nanometers, or as a percentage of the total tomogram volume.

thanks in advance! best Jesse Hansen

---

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