VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Feb 17 2004 - 10:32:22 CST

Marcin,
  You could either modify the radius of the atoms in the molecule, or
another way to do this would be to use the graphics commands
"draw sphere { x y z } radius r" to draw the spheres for yourself.
See the VMD User's guide for more info on this:
  http://www.ks.uiuc.edu/Research/vmd/current/ug/node112.html

To modify the atom radii, you'd need to use VMD's 'atomselect' command
similar to this:
  set sel [atomselect top "index 1"]
  $sel set radius 5.0

More atomselect commands are in the User's guide here:
http://www.ks.uiuc.edu/Research/vmd/current/ug/node77.html#table:ug:keywords:cont
http://www.ks.uiuc.edu/Research/vmd/current/ug/node176.html#ug:topic:atomselect

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Feb 17, 2004 at 10:57:21AM +0100, Marcin Krol wrote:
> Dear John and VMD users,
>
> I would like to display a molecule (standard line representation) and add
> balls centred on atoms, the radius of each ball would correspond to value
> of a given property (eg. charge). I would then have ball-coded
> atom-property information. However, I don't know if and how I can do it in
> VMD. Thank you in advance for any clues
>
> marcin
>
>
> Dr Marcin Krol
> Zaklad Bioinformatyki Collegium Medicum UJ
> Kopernika 7E
> 31-501 Krakow
> tel/fax (012) 422-77-64
> e-mail mykrol_at_cyf-kr.edu.pl 

-- 
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