VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 25 2004 - 10:18:51 CDT

Axel, Keith,
  The bug was caused by incorrect trigonometry in the code that
generated the offsets for use by the PBC display routine. It was
attempting to do the right thing, and very close, but it interpreted
the relationships of a/b/c/alpha/beta/gamma incorrectly and so the
generated PBC transformation was not correct in many cases. It was
coincidentally correct on the X axis since that offset is independent
of the cell angles, and it was correct for orthogonal cells.

We had a very similar problem with some of the first versions of
the electron density map reader plugins, it could even be that
this code was derived from one of the buggy edm readers way back when.

In any case, I think I have fixed the problem and I should have a new
test version with this fix available soon once I've tested it thoroughly.

  John

On Wed, Aug 25, 2004 at 08:52:26AM +0200, Axel Kohlmeyer wrote:
>
> >>> "JS" == John Stone <johns_at_ks.uiuc.edu> 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.
>
> john,
>
> 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.
>
> axel.
>
> 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> vmd_at_ks.uiuc.edu
>
> 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: johns_at_ks.uiuc.edu Phone: 217-244-3349
> JS> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>
>
>
> --
>
> =======================================================================
> Axel Kohlmeyer e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
> 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 http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot. 

-- 
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