From: Axel Kohlmeyer (
Date: Thu Feb 22 2007 - 09:07:28 CST

On Wed, 21 Feb 2007, Yaser Khan wrote:

YK> Hi all,
YK> I am using VMD to visualize gaussian cube files. When opening the file VMD
YK> warns "coordinates will be rotated to comply with VMD's conventions for
YK> periodic graphics". This is not a problem when I am visualizing a single
YK> cubefile or when I visualize multiple cubefiles all with the same 'grid
YK> orientation'. However, when I attempt to visualize cubefiles with grids that
YK> are rotated with respect to each other the relative positions of the
YK> molecules displayed gets completely messed up.
YK> Is there some way to supress this reorientation?

yes. you have to download the source code and build your own version
of the plugin where you disable this rotation, which is essential
for cases where you look at periodic systems, due to the way periodicity
is computed within VMD. please note, that you have to step up the minor
revision number in the struct at the end, so VMD will override the
built-in plugin with your version.


YK> *i am using VMD version 1.8.5 on Microsoft Windows XP Media Center Edition
YK> (with SP2 installed). The cubefiles have been generated from Gaussian'03 and
YK> their formatting is compliant with the VMD plugin.
YK> thank you,
YK> Yaser.

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.