VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 26 2004 - 14:06:04 CDT

Eckhart,
  That's good to know. If you have any further observations about
this, let me know as it'll save time when we get a chance to write a
built-in routine or plugin for this purpose.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Aug 26, 2004 at 02:14:17PM +0200, Eckhart Guthhrlein wrote:
> On Wed, Aug 25, 2004 at 09:29:13AM -0500, John Stone wrote:
> >
> > Besides the rotation and centering matrices, you'll also need to
> > make molscript and VMD use the same projection matrix, which is probably
> > the trickiest part. If the projection matrix isn't the same, then you'll
> > get different degrees of perspective out of Molscript and VMD. You could
> > probably start out by doing a simple orthographic projection, until you
> > get them lined up with regard to all of the other matrices, then when that
> > works, you could move up to doing the projection matrix. If molscript has
> > an orthographic projection mode, I'd suggest trying that quickly to see
> > how different the views are when that issue is eliminated. Let me know
> > where things stand once you've tried that, and I can help you deal with
> > getting the perspective projections to line up.
>
> Ah! If I use orthographic projection mode in VMD, I can simply use the
> rotate_matrix in molscript like this:
>
> transform atom *
> by centre position atom *
> by rotation
> 0.835655 0.477917 -0.270702
> 0.534086 -0.591997 0.603565
> 0.128199 -0.648951 -0.749955 ;
>
> And the views are perfectly identical! That's already great.
>
> As far as I can see, molscript only has an orthogonal projection mode. I
> browsed through the manual, but there is only a parameter to adjust
> depth-cueing.
>
> Regards,
> Eckhart 

-- 
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