VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 29 2004 - 18:04:17 CST

Hi,
  You can draw various user-specified geometry in VMD via the "draw"
and "graphics" commands. There are some examples in the User's Guide here:
  http://www.ks.uiuc.edu/Research/vmd/current/ug/node112.html
  http://www.ks.uiuc.edu/Research/vmd/current/ug/node114.html

In the script library here:
  http://www.ks.uiuc.edu/Research/vmd/script_library/

And in Axel Kohlmeyer's VMD/CPMD tutorial here:
  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/index.html

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Dec 29, 2004 at 08:16:10PM +0000, Jake . wrote:
> I'm relatively new to doing anything more fancy with VMD other than the
> basic molecular representations. I'm trying to find a way to draw several
> cylinders which are in a specific orientation throughout the time course of
> my simulation. Part of the problem is that only one end point exists, the
> other needs to be at a 90 degree angle to one of the chemical bonds, so
> essentially extending out into space.
>
> Here's the basic idea, In my system atoms C and N are bonded, but I want to
> draw a cylinder at 90 degrees to that bond, extending out from the C-atom.
> Is this even possible?
>
> Any suggestions would be great, thanks all.
> Jake
>
>
> C-N
>
> to be re-drawn like this:
>
> |
> C-N
> 

-- 
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