VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 18 2013 - 09:54:24 CST

Hi,
  There are a number of cases where Surf doesn't work as well as it
could. Have you tried using MSMS or QuickSurf instead? MSMS should
produce a surface of at least as good quality as that produced by
Surf, but it may likely work in cases where Surf is doing poorly.

If you don't have to see the solvent accessible surface, then QuickSurf
is much faster than both Surf or MSMS, and it handles many cases that
neither Surf or MSMS can handle.

To use MSMS, you will need to download it from Scripps:
  http://mgltools.scripps.edu/downloads

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Feb 18, 2013 at 04:45:38PM +0100, 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.
>
> Thanks for reading and
> Cheers,
>
> Sabine 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078