VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 25 2002 - 11:27:53 CST

Dear Alan,
  From what you describe in your email, it shouldn't be too hard to get
VMD to render what you want. Off the top of my head, there are two obvious
routes to getting this done. The appropriate method will depend on how
your program works, and what data it outputs:
  1) If your program outputs a regularly spaced rectilinear grid of data
     points, with potential values at the grid points, then the best method
     would be to write a simple Tcl script to read in the potential map,
     and apply it as the coloring on an MSMS surface, as is done in the
     potsurf script.

  2) If your program outputs a list of discrete points (not in a grid, just
     list of points which are not on a regular sample interval) then you could
     use a Tcl script to read in the list of points, and draw them with the
     VMD graphics commands. This assumes that your list of points does not
     include any connecttivity information.

  3) Similar to 2), but if you have connectivity information, you can
     draw a solid surface much like MSMS, or Surf. Instead of reading in
     the sample points as points, they are used as vertices in a triangle
     mesh with the face/edge/vertex connectivity information.:w

  4) Similar to 1), but using a feature I'm still developing, which would
     allow any molecular geomtry to be colored by volumetric data, using
     3-D texture mapping.

  5) Similar to 2) but using a feature I'm still developing, which will
     allow VMD to draw big point clouds efficiently. May also implement a
     mode for displaying vector fields...

Let me know which of these options interests you the most, and I'll work with
you to get your program and scripts working with VMD.

Thanks for using VMD!
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Feb 25, 2002 at 01:15:52PM -0500, Alan Wilter Sousa da Silva wrote:
> Hi VMD-list.
>
> Amazing, fantastic VMD!
>
> But I have a problem. Since I don't have Insight/Delphi, I'm
> trying to plot elect. pot. molecular surface with what I have.
> (1) First, loading a pdb file with charges (using beta or
> occupancy column). Then using MSMS and change colour represantation (RWB)
> to beta (or occupancy, whatever I set in the pdb file) results look fine
> but I don't think it's right, I mean, (2) I would like to see a surface
> composed of discretes points and had accounted every atom charge
> interaction (Coulomb, epslon=80) over every point of the grid surface.
> Maybe, it's what potsurf script does, but not what (1) does.
> So, I have a Connolly adapeted program to our situation, which
> calculates a point-surface (Connolly, probe 1.4) with charges values
> attributed as desired in (2) but now I'm looking for a way to show it as
> a graphic surface.
> I'm sorry if I couldn't make myself clear, but I want to find a
> way to make VMD represents my data source in a surface.
> My point-surface data is built by as many as need points to cover
> the molecular Connolly surface with each point having its 3 spatial
> coordnates and its charge value (using pdb format I can see a sketch of
> what I expect).
> I would thank in advance any attention dedicated to my problem.
>
> Sincerely,
>
> -----------------------
> Alan Wilter S. da Silva
> -----------------------
> Laboratório de Física Biológica
> Instituto de Biofísica Carlos Chagas Filho
> Universidade do Brasil/UFRJ
> Rio de Janeiro, Brasil 

-- 
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