From: Axel Kohlmeyer (
Date: Mon Feb 18 2013 - 10:37:26 CST

On Mon, Feb 18, 2013 at 4:45 PM, Sabine Reisser <> wrote:
> Hi everyone,
> I parametrized and geometry-optimized a single benzol C6H6 Ring, saved it in
> a pdb-file and tried to visualize its surface within VMD (Drawing method ->
> Surf). In all of my tries, the surface never completely closed. I noticed
> that the amount of closing depends on the coordinates. In the beginning, I
> had all z coordinates on 0 since the molecule is planar. For this, I good
> the worst results, the surface contained many individual patches which
> didn't fuse. Translating and rotating the coordinates enhanced the result.
> It also seemed that negative coordinates are deprecated by the SURF module.
> I also tried pqr structures with different radii, which changed the surface
> volume as expected but didn't enhance closing.
> I suppose that there is a bug or at least some incompleteness in the SURF
> code. If somebody could provide a fix or a workaround, I would be very glad.

have you tried the "QuickSurf" representation?


> Thanks for reading and
> Cheers,
> Sabine

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.