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@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