From: Vlad Cojocaru (
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 ...


John Stone wrote:

> 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:
>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:
> 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)?
>>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

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