From: Dow Hurst (
Date: Sat Jun 11 2011 - 11:08:43 CDT

I just got reminded that multiplying the maps should give me the
intersection of the maps. Sorry for the bother!
On Jun 10, 2011 7:17 PM, "Dow Hurst" <> wrote:
> 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
> 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,
> I'm not getting what I think I should be getting.
> What would be the correct method in vmd to accomplish this task? My
> grid spacing is 0.5 Angstroms, and I'm wondering if that isn't fine
> I've tried a two step method of subtracting one ligand's map from a
> 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
> and doesn't show a continuous surface.
> Best wishes,
> Dow Hurst