VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Nov 30 2009 - 09:54:00 CST

Hi guys,
  I've been thinking about how to handle this modification and some
of the others (e.g. secondary color selectors, etc) that are on my
TODO list off and on for some time now. It'll be a while yet before
I have time to implement, but I think I have a handle on how I want
to do this. I'll let you know when I start doing tests on this feature
and seek your feedback.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Nov 30, 2009 at 06:10:54AM -0500, Axel Kohlmeyer wrote:
> On Mon, Nov 30, 2009 at 5:01 AM, Georg Spiekermann <spiek_at_gfz-potsdam.de> 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.
>
> cheers,
> axel.
> > Kind regards,
> > Georg Spiekermann
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> Institute for Computational Molecular Science
> College of Science and Technology
> 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