From: Axel Kohlmeyer (
Date: Fri Jun 04 2010 - 14:18:40 CDT

On Fri, Jun 4, 2010 at 2:30 PM, Luis Guillermo Cota Preciado
<> wrote:
> Whereas my problem with default installing VMD is still not resolved, I have
> meanwhile installed it locally in my home directory, and this brings me to
> the questions that made me actually join this list. I have only briefly
> perused the manual and I haven't found so far proper answers:

read the manual again. it does have the answers
and also to questions you have not asked yet.

> 1) How can I change the background color?

through the color dialog.

> 2) How can I change an atom's radius

there are different ways and it is difficult to give
a general answer to that. be more specific.

> 3) How can I make a color change for an element permanent?

through adding some code to .vmdinit

> 4) How can I load and correctly display a file containing generic particles
> and their individual radii? The file is in the format x y z radius and I
> look forward to visualizing them with their distinctive radii.

you have to write your own molfile (or tcl plugin) if you want support
for your very own file format. better write your file in one of the supported
formats that contain radius information explicitly, e.g. .pqr

please note that VMD stores radius information only once per trajectory
(from the first frame).


> Thanks in advance for your help.

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.