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@cgl.ucsf.edu Sent: Monday, December 19, 2022 11:42 AM To: Harrison, Daniel P harrisondp@vmi.edu Cc: chimerax-users@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@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