From: Peter Freddolino (
Date: Fri Mar 13 2009 - 20:26:06 CDT

Hi Peter,
yes, you're going to need to create a volumetric data file in order to
show a real isosurface. The dx format is not difficult to understand;
you should just be able to run through your pdb and write the needed
values. See the documentation at


Peter Varnai wrote:
> Hello VMD users,
> I obtained with a small script of mine density values on a grid and I
> store those above a certain threshold as a pdb file where the density
> value is in the beta field. Is there an easy way to represent clusters
> of adjacent grid points in VMD 1.8.5 as a solid continuous surface
> colored by beta? I looked at displaying it as beta-colored 'beads' or
> 'dotted' surface which is not optimal. I realise that I would need to
> create a pot.dx volume file from my pdb but some guidance or
> alternative solution would be appreciated.
> Thanks,
> Peter