VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 15 2004 - 10:40:55 CDT

Hi,
  It would not be difficult to have VMD draw ellipsoids rather
than spheres, if enough information was available in the input file(s)
to determine the shape and orientation appropriate for each atom.
The existing code doesn't do this of course, but I don't think it
would be very hard to add such a feature. What data files do you have
that provide the information necessary to correctly orient the
ellipsoids? If someone can provide us with example data files for
this type of molecule, along with examples of POV-Ray scripts produced
from those data files, we could probably add an ellipsoidal atom
representation to VMD in a future version. I can't make any promises
about when until I get some other pending work done, but this sounds
like it would an easy thing to add, so if people can send me data files
and examples of renderings done with other software, that would be
helpful.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jul 15, 2004 at 04:56:21PM +0200, Olaf Lenz wrote:
> Hi!
>
> Leonid Paramonov wrote:
> >Is there any simple way to display elliptic molecules in VMD?
>
> If you actually mean atoms, I don't think there is. You could try to put a
> number of atoms close enough to have them look like ellipsoids, but that is
> probably no good choice.
>
> >Lots of people doing modeling of liquid crystals with GB molecules and
> >plotting it in some software.
> >
> >Is it VMD or something else? In case it is not VMD : what is that?
>
> In my working group, these plots are typically done with POVRAY, using a
> stretched sphere. If you are interested in the details, you could write to
>
> cheung_at_Physik.Uni-Bielefeld.DE
>
> - he has done some of these plots.
>
> In general, I think it would be very nice if VMD would provide methods to
> define "atoms" that are not spheres, like cylinders, ellipsoids, or
> combined objects but still have the nice properties of normal atoms (that
> they can be selected, queried and so on). This would make VMD very usable
> for the visualisation of coarse-grained simulations (it is already quite
> useful, but only for some models). However, I suppose this would be a
> rather large change to VMD.
>
> Olaf 

-- 
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