From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Mon Mar 13 2006 - 04:07:17 CST

Hi John,

Thanks ...I will take a look at your suggestions. Also, I could try to
write myself a script for that purpose starting with Axel's script for
drawing a cubic box ... I have truncated octahedron boxes created with
Leap (AMBER) and I thought maybe somebody has already build a script to
draw those boxes ....

I'll see .. at the moment its not a priority for me because its just a
"cosmetic" feature to use in presentations ... but if I'll have time to
come up with something, I'll share it ...

Cheers
vlad

John Stone wrote:

>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/
>>
>>
>>
>
>
>

-- 
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/