From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 26 2005 - 14:28:43 CDT

Hi,
  The VMD internals aren't all directly accessible to the scripting
interfaces as there are thousands of fine grained structures and
state changing functions that would have to be exposed and this would
ultimately hamper our flexibility in upgrading VMD to support new
features, so at present we only expose the higher level interfaces
that are likely to stay fixed for years at a time.

That said, you may not need such access anyway. VMD allows you to individually
set the radius of any atom using the '$sel set radius' atomselct subcommands.
With this, you could set the radii to anything you need. You can color
atoms by atomic element in the new version, so as long as you're doing
atomic models and not something unusual like coarse grain modelling,
you should can assign colors as you so choose.
Let us know if you need help setting your radii etc.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Oct 26, 2005 at 11:46:38AM -0700, Craig Maloney wrote:
> Hi all.
>
> I was wondering if there is any documentation about the core API of
> VMD. What I'd like to be able to do is specify things like bond
> colors/thicknesses and atomic colors/radii a la carte (not really
> doing bio-molecules... I'm doing things more like granular materials
> where the particle radii may vary continuously) and it doesn't seem
> like this kind functionality is exposed in the tcl/python API. Can
> these kinds of things be done using VMD? Or is there not very much
> layered on top of the raw openGL stuff?
>
> Barring that, does anyone know of some kind of lower-level "ball and
> stick" type package?
>
> Thanks,
> Craig

-- 
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