From: John Stone (
Date: Thu Jun 19 2008 - 00:38:25 CDT

  You can use atom selections when computing maps with volmap, thereby
controlling exactly what atom types are contributing to the occupancy
density values in space. By selecting just your solvent atoms, you
can compute a density map of just that property. You can then render
multiple overlapping isosurfaces of the various properties you're
interested in seeing.

  John Stone

On Fri, Jun 13, 2008 at 03:40:17AM -0700, Ignacio Fernández Galván wrote:
> Hi all,
> I'm analyzing the solvent structure in some dynamics run, and I find the visual information that can be obtained with volume maps very useful. In particular, I'm using the occupancy volmap (without the -points option in the volmap command) and, while I understand how it is calculated, I would like to know whether it is possible to extract any other, more quantitative, information from the generated .dx file. I would be interested, for instance, in obtaining the number of solvent molecules, in average, in a certain region (delimited by an isosurface).
> I guess that I could, for a start, filter the cells in the .dx file with a value larger that the threshold, multiply their value by the cell volume and divide by the volume of the "balls" used to obtain the volmap. Has anyone done anything similar? Any other advice?
> Thanks
> Ignacio
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