From: John Stone (
Date: Fri Jul 16 2004 - 10:12:01 CDT

  Yeah, we've been talking about providing a better default mechanism
than the existing C++ code, implemented by scripting so it can be
easily modified by users. In the short-term a simple Tcl script can
be used for this purpose, its just not something we provide by default
yet. We would definitely like to improve this situation soon, it
has been an annoyance for a while...


On Fri, Jul 16, 2004 at 04:21:03PM +0200, Olaf Lenz wrote:
> Hello!
> In the following, I'll write a few messages on issues that I noticed with
> VMD during the last months. Let me state again: I love VMD and it's a great
> piece of work! My messages are thought as suggestions, not as requests for
> features!
> Also, I'm willing to contribute.
> The default VDW-radii and colors are determined by the name of the atom. It
> would be nice if a user could provide default values for different atom
> types.
> As far as the colors are concerned, one can already change the default
> colors of the "known" atom types (i.e. H, O, N, C etc.) via "color Type"
> commands in .vmdrc. If you want to use your own "atom" names (for example
> "HEAD" or "TAIL") or you have a molecule which contains non-standard atoms,
> you can't give default colors.
> As for the default radii, they are hard coded into VMD's C++ code and can
> only be changed via a Tcl script after loading the molecule or when the
> file structure is read.
> It would be nice if the user could provide his own defaults for arbitrary
> atom names.
> Olaf

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:                 Phone: 217-244-3349              
  WWW:      Fax: 217-244-6078