From: Emmanuel Levy (emmanuel.levy_at_gmail.com)
Date: Mon Mar 10 2008 - 15:03:40 CDT

Dear John,

Thank you for your help. I will have a look at the code, but my
enquiry was more in case something exists already. Since I am not
familiar with tcl, vmd functions, and geometry in space, I guess for
now it'd be more simple for me to crop, plus resize the pictures.

Best wishes,

Emmanuel

On 10/03/2008, John Stone <johns_at_ks.uiuc.edu> wrote:
> 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
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>