VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 12 2004 - 14:18:15 CDT

If I were to guess, their "gaussian" function is an implementation
of the "metaballs" or "blobs" rendering technique invented by
Jim Blinn, with isosurface extraction via marching cubes.
I haven't even looked at their web page yet, but just the word
gaussian implies that this is what they are doing. This is not
an accurate solvent accessible surface if you implement the fastest
forms of the algorithm, but it may be just fine for getting a
generic "surface" representation on large structures like these
virus structures we're discussing. I'd be curious to hear how
well their code handles a 400,000 atom virus structure.
If you want to try one out, I can provide you some PDB/PSF files.
If their technique scales well, then that might be an interesting
option for viewing surfaces of very large structures. Let me know
if you're interested in giving it a serious test.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, May 11, 2004 at 11:10:22PM +0200, Marc Baaden wrote:
>
> Hi,
>
> >>> John Stone said:
> >> If anyone knows of other solvent accessible/excluded surface calculation
> >> tools that work better, I'd be glad to hear about them.
>
> What a coincidence. Just today I tried out the latest version of
> the Yasara visualization and MD software (www.yasara.org) and they
> have just added surface support. They provide analytical surfaces,
> also using MSMS, but also have a faster algorithm which they call
> "Gaussian", and this one is very fast (you can eg visualize the changing
> surface of a protein in real time by visualizing an MD trajectory, with
> coloring changing as a function of electrostatics).
>
> I don't know whether this method is/will be freely available, maybe
> the best would be to post on the yasara user forum or ask the question
> directly to Elmar Krieger (the main person behind Yasara).
>
> Best wishes,
> Marc Baaden
>
> --
> Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris
> mailto:baaden_at_smplinux.de - http://www.marc-baaden.de
> FAX: +49 697912 39550 - Tel: +33 15841 5176 ou +33 609 843217
> 

-- 
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