From: Dow Hurst (
Date: Fri Jun 10 2011 - 18:17:50 CDT

I have two ligands known to displace each other experimentally in the GPCR
I'm working on. In the model of the GPCR I have both ligands docked in
their respective, but overlapping binding sites. I would like to create a
surface of the overlapping VdW volume and use that in a picture for a
publication. So far, I have created density volume maps with identical grid
spacing of each ligand separately using the volmap command. Both volume
maps were made from the same min and max coordinates so the maps can be
added, subtracted and so on with the volutil plugin. I've tried several
ways of getting the union of the maps so as to have the overlapping VdW
surface in a volume map to work with, but I must be doing this wrong, since
I'm not getting what I think I should be getting.

What would be the correct method in vmd to accomplish this task? My current
grid spacing is 0.5 Angstroms, and I'm wondering if that isn't fine enough.
I've tried a two step method of subtracting one ligand's map from a combined
map of both and then taking that output and subtracting the other ligand's
map. That map seems to show some semblance of the overlapping volume but
the display of the isosurface is a strangely shaped grouping of small blobs
and doesn't show a continuous surface.

Best wishes,
Dow Hurst