From: Axel Kohlmeyer (
Date: Wed Aug 25 2004 - 01:52:26 CDT

>>> "JS" == John Stone <> writes:

JS> Axel,
JS> Thanks for this, I now see the problem you're having. This looks
JS> very similar to Keith's problem, as he just sent me the data and images
JS> to compare with, and I agree that there does seem to be something wrong.

JS> I'll let you know when I've figured out what is going on here.


it seems as if the periodic display shifts the unit cell
only in x-,y-, and z-direction. but to get the desired effect,
you need to shift by the unit cell vectors.

only for orthogonal unit cells this is the same.


JS> There must be a mistake in the code that generates transformations
JS> for the periodic cell images, I'll know for sure after I have a chance
JS> to dig into this a bit.

JS> John Stone

JS> On Tue, Aug 24, 2004 at 06:07:18PM +0200, Axel Kohlmeyer wrote:
>> On Tue, 24 Aug 2004, John Stone wrote:
>> john,
>> please have a look at the attached image.
>> the y-replica row in the top part is obviously
>> off by half a unit cell length in that direction.
>> this is the same with vmd 1.8.2 and the latest cvs version.
>> i'll send you the vmd input and the (large-ish) cube file
>> from which this was created in a separate mail.
>> axel.

JS> --
JS> NIH Resource for Macromolecular Modeling and Bioinformatics
JS> Beckman Institute for Advanced Science and Technology
JS> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
JS> Email: Phone: 217-244-3349
JS> WWW: Fax: 217-244-6078

Axel Kohlmeyer       e-mail:
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum
If you make something idiot-proof, the universe creates a better idiot.