VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Mar 10 2006 - 18:40:17 CST

Vlad,
  I don't have a script, but it would be pretty easy to draw the
octahedron once you can calculate the vertices and edges of
the unit cell. I don't know what basis vectors etc are being used
to specify the unit cell since you didn't say if this is something for
NAMD, Gromacs, etc., so I can't suggest anything specific,
but you may find this helpful:
  http://www.ornl.gov/sci/ortep/topology/lattice.html
  http://www.ac-noumea.nc/maths/amc/polyhedr/polyh_draw_.htm
  http://www.ul.ie/~cahird/polyhedronmode/truncate1.htm

PBCAID presumably contains a lot of routines for dealing with
these unusual PBC unit cell shapes, and presumably for various
different simulation packages. You might take a look at it:
  http://monod.biomath.nyu.edu/index/software.html

  John

On Wed, Mar 08, 2006 at 12:26:06PM +0100, Vlad Cojocaru wrote:
> Hi guys,
>
> Does anyone of you have a tcl script that draws a truncated octahedron
> in vmd (something similar to Axel's script to draw cubic cells)?
>
> Thanks
> vlad
>
> --
> Dr. Vlad Cojocaru
> EML Research gGmbH
> Molecular and Cellular Modeling Group
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg, Germany
> Phone: +49-6221-533266
> Fax: +49-6221-533298
> e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
> http://projects.villa-bosch.de/mcm/people/cojocaru/
> 

-- 
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