From: Axel Kohlmeyer (
Date: Mon Nov 30 2009 - 05:10:54 CST

On Mon, Nov 30, 2009 at 5:01 AM, Georg Spiekermann <> wrote:
> Dear VMD community,

dear georg,

> for visualization of silicate melts and glasses, the Polyhedra option
> has this limitation: One cannot (yet) restrict the polyhedra around one
> type of atom to be drawn just from ONE other neighbour type of atoms,
> like oxygen in most cases.
> Looking for a solution, I found this statement by Axel Kohlmeyer from
> July 16th 2008 on VMD mailing list about the Polyhedra option:
> "the one possible improvement that i am seeing (and i've been suggesting
> something similar for dynamic bonds as well for quite a while now) would
> be to have _two_ selections. one for the center and one for the
> "neigbors". but i would expect that to matter only in very rare
> cases, [...]"
> Maybe someone has already made the small modification that would be
> necessary for these two selections?

unfortunately, this is not exactly a small modification.
it is still on the list, but it is a very long list and it is
not a highest priority item.

> This would be useful for modellers that deal with silicate melts and
> glasses that contain more atom types than just silicon and oxygen.

this is useful for a lot of applications, and for the same reason, it
would be useful for dynamic bonds, too.

> Kind regards,
> Georg Spiekermann

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.