VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 19 2008 - 00:54:31 CDT

Hi,
  If you want to draw a set of axes matching a particular scale
for your molecule, rather than using the built-in scale-independent
axes in VMD, you'll instead want to draw your own using the VMD
graphics/draw commands. By drawing your own, the scale of the axes
will always match the scale of your atomic structure preserving
whatever relationship you're aiming to create, and the orientation
of the axes will track the orientation of the molecule precisely.

To learn how to draw your own geometry like this, please have a
look at the nice tutorial section by Axel Kohlmeyer that
provides some excellent examples:
  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part7.html#chap9_sect1

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 13, 2008 at 03:21:06PM -0400, Nazanin Samadi wrote:
> Dear friends,
>
> I have two problems that I hope you will give me the solutions.
>
> 1. I want to set the XYZ axes, coordinates to {0 0 0}
> 2. I want my molecule and the simulation box to be mesured from one unit
> XYZ axes. I need to see the exact position of the molecule in the box.
>
> I hope my question is clear enough!
>
> Thanks in advance.
>
> Nazanin 

-- 
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
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