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@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