VMD-L Mailing List

From: Olaf Lenz (olenz_at_Physik.Uni-Bielefeld.DE)
Date: Fri Jul 16 2004 - 09:21:03 CDT

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