VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Nov 18 2002 - 09:54:24 CST

Hi Marc,
  Generally speaking, VMD doesn't necessarily preserve the original
world coordinate system when it exports geometry to external renderers.
This is because (among other reasons) some renderers use left-hand coordinates
and others use right handed coordinates, some renderers only accept objects
in final world coordinates, others allow a transformation matrices to
be applied to groups of geometry and others don't.

If you want VMD to export a POV scene in a sort of "verbatim" unprocessed
mode, you could modify POV3DisplayDevice.C so that it doesn't call the
transMat.top()).multpoint3d(), transMat.top()).multnorm3d() and similar
functions to transform the geometry during scene export. This should provide
the geometry in its original coordinate system, but you won't get a
scene that renders correctly, so this would only be useful for generating
POV files that you intend to build into your own scene.

If you're trying to accomplish something special by rendering your own
POV-Ray geometry along with what VMD exported, let us know, there might
be an easier way to do it using the VMD "draw" commands or some other
method. At the very least, if you inserted a few special objects into
the scene at the coordinates you want to ultimately place other objects,
you could then find these placeholder objects in the outputted POV-Ray
file and then replace them with the real objects you want to put there.
This way you wouldn't have to worry about having VMD preserve the
original coordinate system for the molecule in its POV-Ray export.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Nov 17, 2002 at 08:52:15PM +0000, Marc Baaden wrote:
>
> Hi,
>
> I was trying to use VMD in order to generate some POV objects/scenes for
> a given protein. I noticed that if you just load a protein and directly
> generate a povray file for one given atom (by restricting the selection to
> it), the coordinates for the location of the povray object (eg a sphere)
> are different from the coordinates of that atom in the PDB file.
>
> Is it possible to maintain the same coordinates ?
>
> My guess is that VMD does some re-orientation/centering at startup ?
> Maybe it is sufficient to suppress that for my purpose .. but I haven't
> yet found out how to do this.
>
> Or is there any other scaling factor/pitfall involved ?
>
> Thanks in advance,
>
> Marc Baaden 

-- 
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