From: John Stone (
Date: Thu Aug 28 2014 - 13:22:56 CDT

  In addition to the suggestions others have already provided,
you might also have a look at the Extensions|Analysis|VolMap Tool
and see if you can use the "occupancy" or density map types, and
then plot a zero-density isosurface to see where the pocket/cavity is.

  John Stone

On Wed, Aug 27, 2014 at 06:22:29PM +0000, Ebert Maximilian wrote:
> Hi there,
> I am looking for a possibility to draw in VMD a spherical volume with a giving radius around an atom but only include space not occupied but other molecules. For example I have a protein loaded in VMD and I draw a sphere around an atom I want the sphere volume minus the protein VDW volume. Is this possible?
> I am trying to display a solvent accessible volume so to speak.
> Thank you,
> Max

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349