VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 10 2008 - 14:36:02 CDT

Emmanuel,
  The scaling factor is calculated so that the entire molecule fits into
the view volume. The view volume is defined as a cubic box from eye
coordinates -1,-1,-1 to 1,1,1. In the current VMD CVS, these calculations
are done in:
  DrawMolecule::update_cov_scale()
  DrawMolecule::scale_factor()

Take a look at those and you can see generally how it works.
The reason the view transformations are done for a cubic volume is to
support immersive VR display devices like the CAVE where the scene
is drawn as a "room" rather than as a "window"...

  John

On Mon, Mar 10, 2008 at 07:28:30PM +0000, Emmanuel Levy wrote:
> Dear Axel,
>
> Thanks for your answer - VMD does it to some extent indeed, but there is still
> quite a lot of white space around the molecule.
>
> The question is then how is the amount of white space calculated? If
> it does not depend on the protein, then a scaling factor would be OK.
> However if it does (depend on the protein), that means a particular
> scaling factor might not be suited for all proteins.
>
> Any other suggestion would be very welcome!
>
> Best wishes,
>
> Emmanuel
>
>
>
>
> On 10/03/2008, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu> wrote:
> > On Mon, 10 Mar 2008, Emmanuel Levy wrote:
> >
> > EL> Hello,
> > EL>
> > EL> I was wondering if there is simple function that I could call to zoom
> > EL> on a protein so that it automatically fits the display window.
> >
> > i was under the impression that VMD already does this...
> >
> > if you want to "zoom in" a little closer by default, you could
> > play with the "display height" command or use the 'scale' command
> > after loading a molecule.
> >
> > cheers,
> > axel.
> >
> > EL> So it is a sort of "crop" except that I would like to keep the window
> > EL> size constant.
> >
> >
> >
> > EL>
> > EL> Many thanks for any hint you could give me!
> > EL>
> > EL> Best wishes,
> > EL>
> > EL> Emmanuel
> > EL>
> >
> >
> > --
> > =======================================================================
> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> > Center for Molecular Modeling -- University of Pennsylvania
> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> > =======================================================================
> > If you make something idiot-proof, the universe creates a better idiot.
> > 

-- 
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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