VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 27 2008 - 16:51:44 CDT

Hi,
  Both of the previous answers to your question are an excellent starting
point, just relocating the VMD axes to the display origin, but I wanted
to add one note of caution:
  The origin of the display is independent of the origin of the molecule,
and they will only remain concentric if you have reset the view (e.g.
press the '=' key) and you do not translate the molecule subsequent to
this point, and if your molecule was already "centered" within it's
unit cell.

If you want a graphical point of reference that will remain intact even
after you manually reorient the rotation and translation of the molecule,
change the center of rotation, and so on, the best way to achieve this is
to render your own geometry in the molecule's coordinate system.

A trivial example of this is to draw a sphere at the origin:
  draw color red
  draw sphere { 0 0 0 } resolution 16 radius 1.0

This drawn sphere will remain aligned with the origin of the molecule
you add it to unless you actually change the coordinates of the atoms
themselves. You can also draw other geometry such as arrows, lines, etc,
so this would be my recommendation if you want to add graphics to indicate
the origin or other important coordinate references etc.

You might also find the "Ruler" plugin useful in some cases, it's
included in the Extensions->Visualization->Ruler menu item.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 27, 2008 at 05:20:03PM +0100, Utpal Sarkar wrote:
> Dear VMD users,
> I am creating movie with VMD. I am trying to see
> the XYZ-coordinate or Origin (0,0,0) of my sytem in the movie. But the
> origin is VMD shows most probable not the true origin of the system, most
> probably the system traslated (I am not quite sure though). Form the *.XYZ
> file which I use to make the movie, I know that my system is 3.5 Angs. away
> from the XY plane. This origin is the original Origin (0,0,0) with respect
> to the coordinates I feed to VMD through the *.XYZ file. So how can I see
> the Origin or XYZ- axis (with respect to the coordinate of my system) when I
> am creating the movie?
>
> Thanking you in advance
> regards
> utpal 

-- 
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