From: John Stone (
Date: Tue May 26 2009 - 17:03:39 CDT

  I thought I'd answer a couple of the questions you had about
customizing the behavior of VMD, though Axel already addressed
some aspects of your questions previously:

On Wed, May 20, 2009 at 02:11:35PM +0200, MyLinkka wrote:
> 1. The default colors. In my very personal opinion, the default colors
> for atoms are 'unusual'.

You can customize this as you see fit. There are two approaches
for doing this:

1) edit the $install_dir/vmd/scripts/vmd/colordefs.dat to modify the
   default behavior of the program system-wide, e.g. editing the top
   portion of the colordefs.dat file:

# VMD default color assignments
# color category name, category item name, color name
Name H white
Name O red
Name N blue
Name C cyan
Name S yellow
Name P tan
Name Z silver

2) modify the colors in your own .vmdrc file, by adding new lines.
   Copy $install_dir/vmd/.vmdrc to .vmdrc (on unix) or vmd.rc (on windows)
   as a starting point, and then add lines like this one:
color Name C gray

> 2. Python support on windows.

At present, this can't be supported in the precisely same way we can for
the other platforms, due to the architecture of Python itself, as
described in the Python documentation here:

That said, I am looking to work around this problem by changing the VMD
distribution to accomodate Python's linkage requirements, but it's
not going to be easy and it won't be done for VMD 1.8.7.

> 3. Window layout. I know there is some tradition for L(u)nix software
> that many separated
> and modeless windows belong to one program. Normally on windows, in this
> case
> a program will create some child windows. (if you check what gimpshop
> project (and gimp)
> does, probably you will understand this. ) Vmd works in the unix way.
> But one annoying
> thing is, each time when I start vmd, all windows (console, gl and main
> window) are overlapped
> (at the upper-left corner of my screen). I have to manually move and
> rearrange them in
> order to see all of them. (maybe this could be controlled in the startup
> file?)

You can manipulate the location of any of the built-in menus in VMD with the
"menu" commands, e.g.:

# position and turn on menus
menu main move 5 225
menu display move 395 30
menu graphics move 395 500
menu color move 125 225
menu files move 125 325
menu labels move 125 525
menu render move 125 525

menu main on
menu display off
menu graphics on
menu color off
menu labels off
menu render off
menu files off

Please try out these suggestions and let me know if you have
further questions.

  John Stone

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