VMD-L Mailing List

From: Olaf Lenz (olenz_at_Physik.Uni-Bielefeld.DE)
Date: Thu Jul 15 2004 - 09:56:21 CDT

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