[chimerax-users] volume threshold-level

[Tom Goddard]

Hi Dmitry,

The volume command has an option to set the surface threshold level to enclose a specified volume.  The average volume occupied by a protein is about 1.2 cubic Angstroms per Dalton (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3055910/ <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3055910/>).  So if I have a 300 KDa complex I could use this command to set the surface threshold level of a cryoEM map

	volume #1 encloseVolume 360000

Here is the documentation for this option

	https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#encloseVolume <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#encloseVolume>

In general this isn't going to always give the best level because of unresolved domains, extra density such as membranes, noise and low resolution.

  Tom


> On May 5, 2022, at 10:53 AM, Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Dmitry,
> As far as I know, there isn't a command to do it directly.  Instead you would need to adjust threshold to reach the target volume as reported by the Measure Volume and Area tool (or perhaps Measure and Color Blobs).  The Measure Volume and Area tool will continuously report the volume as you interactively drag the threshold in the Volume Viewer.
> 
> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/measurevolume.html>
> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/measureblobs.html>
> 
> I also don't know the conversion factor between volume and weight, but others on this list may be able to advise if you don't already know the formula.
> 
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On May 5, 2022, at 12:02 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>> 
>> Dear colleagues,
>> Is there a tool in chimeraX that can set the correct volume threshold level when the Molecular weight of the molecule is known?
>> Thank you!
>> Kind regards,
>> Dmitry
> 
> 
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