VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 06 2006 - 00:01:55 CDT

Hi,
  I'm glad that MSMS worked for you. Surf and MSMS use slightly different
algorithms for constructing their solvent accessible/excluded surfaces,
so there are various cases where one will succeed and the other will fail
due to the limitations of their respective algorithms and heuristics,
not to mention the occasional bug. The VolMap tool doesn't create a
solvent surface, but can synthesize arbitrarily fine or coarse resolution
volumetric grids from atomic coordinates, which can then be rendered
using the Isosurface representation, much as one would render electron
density maps, or CryoEM maps for example. It's nice to use when rendering
REALLY large structures with millions of atoms, since at that scale you're
often just looking for a more schematic representation in order to reduce
visible geometric detail anyway.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Apr 06, 2006 at 10:24:31AM +0530, M.S.Vijayabaskar wrote:
> Hi,
> Thank you for the suggestion.
> The rendering in MSMS is beautiful.
> The SURF works well for the same protein in a machine with the same
> configuration but with vmd 1.8.4(beta) version. I use vmd 1.8.3 in my
> machine.
> I will try the VolMap tool.
> Do you have any idea why the difference in rendering is ?
> Leaving that issue, the primary objective of rendering is solved.
> Thank you,
> Vijay
> >
> > Hi,
> > I didn't get the attached picture in the email you sent.
> > If you're having trouble with Surf, you might try MSMS instead:
> > http://www.scripps.edu/~sanner/html/msms_home.html
> >
> > There are some structures that neither Surf nor MSMS will be able
> > to process correctly. If you're just looking for a coarse graphical
> > representation (and not an actual solvent accessible surface) for
> > this large 58,000 atom structure, you might prefer to use the
> > Extensions->Analysis->VolMap tool in VMD 1.8.4 to produce a surface
> > representation at a user-selected resolution, rather than using Surf/MSMS.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Wed, Apr 05, 2006 at 03:14:55PM +0530, M.S.Vijayabaskar wrote:
> >> Hi,
> >> The SURF representation is not proper when I render it for the protein
> >> 1AON.pdb
> >> The protein has some 58000 odd atoms and the computer after quite
> >> sometime
> >> gives me a improper picture ..... I have attached a picture for your
> >> reference.
> >>
> >> I work on - Mandriva 10.x Linux with kernel details
> >> -----------------------------------------------
> >> 2.6.12-12mdksmp #1 SMP Fri Sep 9 17:43:23 CEST 2005 i686 Intel(R)
> >> Pentium(R) 4 CPU 3.00GHz unknown GNU/Linux
> >> -----------------------------------------------
> >>
> >> I use a nvidia geforce fx 5200 with 128 memory AGP card.
> >>
> >> Could you please tell me the solution to this problem !
> >>
> >>
> >>
> >> --
> >> Victory goes to the player who makes the next-to-last mistake -
> >> Chessmaster Savielly Grigorievitch Tartakower (1887-1956)
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> >
>
>
> --
> Victory goes to the player who makes the next-to-last mistake -
> Chessmaster Savielly Grigorievitch Tartakower (1887-1956)
> 

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