[chimerax-users] measure volume in ChimeraX

[Elaine Meng]

Hi Andrew,
As explained in the help, "measure volume" and "measure area" are for measuring surfaces:  surface-enclosed volume and surface area. 
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html>

I'm not sure exactly what you are trying to measure for a residue (a set of atoms).   ChimeraX does not have commands to measure the VDW volume of a set of atoms, or its Voronoi volume in the context of a larger structure, for example.

However, you could generate a solvent-excluded surface enclosing just that residue and then use "measure volume" and "measure area" on the surface model.  E.g.

surface #3/A:457 enclose #3/A:457
... and if the surface model created by that command is #3.1 (look in the Model Panel to figure out the model number of the surface):
measure volume #3.1
measure area #3.1

Or if you care only about the exposed surface area not a surrounding surface area, there is "measure sasa" ... however, that measures surface-accessible surface, not solvent-excluded surface.  
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa>

The difference between the two types of surface (and also compared to the VDW surface) is shown in a diagram in the "surface" help page.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#surfdefs>

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

> On Jul 23, 2021, at 10:09 PM, Andrew Blyth via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi, 
> I am having trouble getting the ‘measure volume’ and ‘measure area’ command to work in chimera.
> I have been trying the command:
> measure volume #3/A:457 
> for the structure that I have been using, however, nothing happens when I execute this command.
> Could you please provide me with an example command that will work for measuring the volume or area of a residue?
> Thanks,   
> Andrew Blyth