VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 02 2010 - 13:48:36 CDT

If you had the radii set appropriately and you made a very high
resolution map, than you could get a rough approximation of this,
but I'm not sure that either the "occupancy" or "density" map types
would give the exact result he's looking for, even picking the isovalue
carefully. It's worth a try though since it would only be something
like a 2 minute calculation...

Cheers,
  John

On Wed, Jun 02, 2010 at 02:46:02PM -0400, Axel Kohlmeyer wrote:
> On Wed, Jun 2, 2010 at 1:57 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> > Hi,
> >  There's no way to do this in VMD itself, but if you exported the
> > scene to POV-Ray and then manually edited the scene file, you could
> > convince POV-Ray to render the intersection of your set of beads
> > using constructive solid geometry (CSG).  That's probably the easiest
> > way to get such an image.  You could also just write a Tcl script that
> > emits the beads to a POV-Ray scene file, that might be even easier than
> > taking the VMD output and then subsequently modifying it again...
>
> hmmmm...
>
> couldn't you do something along those lines with volume maps in VMD?
>
> axel.
>
> >
> > Cheers,
> >  John Stone
> >  vmd_at_ks.uiuc.edu
> >
> > On Wed, Jun 02, 2010 at 01:51:56PM +0200, Bjoern Olausson wrote:
> >> Hi VMD users,
> >>
> >> does anyone know if it is possible to visualize the intersection of
> >> overlapping beads?
> >>
> >> Or more general - calculate and visualize the overlapping parts of multiple
> >> spheres?
> >>
> >> For example:
> >> I have 6 Beads representations of 6 Atoms in my protein. These 6 Beads overlap
> >> and I would like to show only the intersection, not the rest of the beads.
> >>
> >> Since my skill in TCL are not more then the basics I am stuck...
> >>
> >> Thanks for any hints or code snippets I can chew on.
> >>
> >> Cheers
> >> Bjoern
> >>
> >>
> >> --
> >> Bjoern Olausson
> >> Martin-Luther-Universität Halle-Wittenberg
> >> Fachbereich Biochemie/Biotechnologie
> >> Kurt-Mothes-Str. 3
> >> 06120 Halle/Saale
> >>
> >> Phone: +49-345-55-24942
> >
> >
> >
> > --
> > 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
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA. 

-- 
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