[chimerax-users] using atomic coordinates to measure volume

[Harrison, Daniel P]

Thank you, Elaine!

I will take a look through your suggestions and let you know if I have any further questions. 

My "maximum" volume, I was envisioning that a number of plane-faces would need to be generated for the calculations and envisioned that that can be accomplished any number of ways. Maximum was referring to the space inside of the planes made by the largest polyhedron possible from all of these planes, though I admit that I am not an expert in this area. 

Best wishes and thank you again, 
Dan 



-----Original Message-----
From: Elaine Meng <meng at cgl.ucsf.edu> 
Sent: Monday, December 19, 2022 11:42 AM
To: Harrison, Daniel P <harrisondp at vmi.edu>
Cc: chimerax-users at cgl.ucsf.edu
Subject: Re: [chimerax-users] using atomic coordinates to measure volume

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