VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 30 2004 - 15:18:25 CST

Marc,
  Jim pointed out to me that you might have been thinking of the
"Stage" in VMD, which draws a checkerboard pattern. The number of
divisions in the checkerboard pattern can be controlled with the
"stage panels xxx" command (where xxx is the number of panels on each axis)
One problem with using the stage as a "ruler" is that the stage is not
scaled/zoomed along with the molecule, so it doesn't provide an absolute
coordinate reference like you'd want. If its the stage that you were thinking
of, that would explain what you had thought you'd seen in an old version.
Its still there in the new versions, just not a commonly used feature.

  John

On Tue, Mar 30, 2004 at 11:28:00AM -0600, John Stone wrote:
>
> Marc,
> As far as I know such a feature never existed in VMD, though
> it would not be too difficult to write one. I assume that what
> you're thinking of is a feature that would draw a regularly spaced
> grid on the display, so that when you view a structure in an
> orthographic projection, you could easily visually estimate distances
> by reading the "ruler" while rotating/translating/zooming your
> structure, right? For an orthographic projection, it would be simple
> since the 'ruler' could be placed at any depth as long as it was
> perpendicular to the view direction.
>
> To be usable in a perspective projection it would have to be implemented
> as a plane that could be positioned within the scene, which is somewhat
> unwieldy, but would work. It could also be auto-oriented to be perpendicular
> to the view direction, but the depth would have to be user selectable since
> the perspective distortion would make it unusable for measurements otherwise.
> I assume that the "ruler" would be obscured by molecular geometry when viewed
> in perspective, since you'd only want to compare against geometry at the
> same depth. In orthographic you could force the ruler to be drawn on top
> of all geometry since its equally accurate at all depths.
>
> Would other people find this useful? Other ideas?
>
> You could implement most of this as a simple Tcl script via the
> 'draw' commands, but a robust/efficient/usable implementation
> would probably require writing C code I suspect.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Mar 29, 2004 at 10:44:03PM +0200, Marc Baaden wrote:
> >
> > Hi,
> >
> > I think I do remember - from the very early days of VMD - that
> > there was an option to display a kind of measuring grid with
> > fixed distances (I think 10x10 times 1 A) in order to estimate
> > distances "geometrically".
> >
> > Did this option exist .. and does it still exist ? (I did not
> > find anything in the user guide)
> >
> > Thanks in advance,
> > Marc Baaden
> >
> > --
> > Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris
> > mailto:baaden_at_smplinux.de - http://www.marc-baaden.de
> > FAX: +49 697912 39550 - Tel: +33 15841 5176 ou +33 609 843217
> >
>
> --
> 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 

-- 
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