[chimerax-users] using atomic coordinates to measure volume

[Elaine Meng]

Hi Dan,
I don't understand what you mean by "maximum" volume.  You can calculate a molecular surface that encloses the atoms (solvent-excluded surface based on their VDW radii) and then measure the volume enclosed by that surface.

"surface" command and solvent-excluded surface diagram
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html>

For example, if the set of atoms is selected, command

surface sel enclose sel
measure volume #1

...assuming the structure and surface are opened as model #1.  If some other model number, substitute.  There is also a graphical interface to "measure volume," menu: Tools... Volume Data... Measure Volume and Area. For atomic models in angstrom coordinates, the reported volume will be angstroms cubed.

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#volume>
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/measurevolume.html>

ChimeraX only measures volume inside an enclosed surface.  It does not measure the volume of a pocket that is open to the exterior.

For pocket volumes, especially if open to exterior, you could try CASTp server, or 3Vee server to give a map that you could open in ChimeraX, show as isosurface, and then measure volume as described above.
<http://sts.bioe.uic.edu/castp/calculation.html>
<http://3vee.molmovdb.org/>

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 18, 2022, at 6:02 PM, Harrison, Daniel P via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hello: 
>  
> I would like to calculate the maximum volume made by selection of atoms in a given structure. Can you provide guidance on how to go about this process? It seems like there should be a simple procedure in ChimeraX but I have failed to locate it. 
>  
> My specific problem: I would like to calculate the volume of the void created by ice under various conditions so that my physical chemistry students can quantify and visually understand partial molal volume non-ideality.
>  
> I would greatly appreciate any assistance you can provide. 
>  
> Dan