VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Feb 20 2007 - 02:04:57 CST

Ivan,
  The current versions of VMD don't presently provide an
2-D isocontour plotting function for volumetric datasets.
I implemented a prototype of such a feature based on 3-D texture mapping
but was dissatisfied with the performance, so that implementation has
not become a standard feature. My most current plan for this is to
implement a 2-D isocontour extraction routine based on marching
squares, for axis aligned slice planes, similar to what you can
do now with the volume slice representation, but with control
over the number of contour lines, spacing, etc. This will likely
be a feature that goes into the version after VMD 1.8.6, as I have
started implementing parts of the code already, but won't have time
to finish for VMD 1.8.6.

Regarding plotting 2-D height fields, you can do this using a variation
of this VMD script:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/3dgraph/

Axel Kohlmeyer implemented something similar which generated 3-D
histograms for Ramachandran plots, which is now built-into the
Ramaplot plugin. You might take a look at what he did here
and adapt it for your purpose:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/mk3drama/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Feb 15, 2007 at 11:04:05PM +0200, Ivan Degtyarenko wrote:
>
> Dear All,
>
> does anyone know how to plot 2D contour map from available 3D grid data
> with VMD? Is it possible at all? I have a Gaussian cube file, with charge
> density distribution, which might be plotted using isosurface
> representation in VMD. But how to get plotted isosurfaces on 2D plane
> at some interval within some range of isovalues? It seems that VolumeSlice
> representation does about what I need, but it does not allow to choose
> isovalues range and interval.
>
> Another one thing. If, say, I have a file with 2D data, having format
> like: on each line x and y coordinates and corresponding charge density "x
> y f(x,y)". Can it be plotted with VMD?
>
> Thanks a lot in advance for you reply,
>
> Ivan Degtyarenko 

-- 
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