From: Suman Chakrabarty (
Date: Tue May 12 2009 - 07:53:12 CDT


since I did not get any solution to the following problem, let me try
to reframe my question. I have a hydrophobic molecule in water and
would like to show the regions around the molecule where there is no
water. How do I achieve this? Using volmap and volumeslice
representation I can show this as slices, but I could not show all the
regions together for the whole molecule. I have a feeling that the
isosurface representation can probably do this, but I could not figure
out how to show the regions with density range "0 to <some cut-off
value)" around the solute.

Also, with the volmap type "distance", how is it possible to have a
reference group (like solute) and calculate the distance map with the
solvent molecules?

Thanks and regards,

On Sun, May 10, 2009 at 1:16 AM, Suman Chakrabarty
<> wrote:
> Hi,
> I intend to monitor the excluded volume of the solvent due to presence
> of a solute along the trajectory. Using volmap I could generate the
> density distribution graphically (VolumeSlice), but I need to know how
> to use the grid data to compute the total excluded volume (no
> solvent).
> Also, it seems VolumeSlice representation works only along three axes.
> Is it possible to rotate the plane arbitrarily?
> Regards,
> Suman.