VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 23 2006 - 13:14:29 CDT

Hi,
  The cube plugin rotates the unit cell automatically, but you
should be aware of the issues this raises when loading multiple
files, as Axel mentions in the cube plugin documentation:
  http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/cubeplugin.html

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, May 23, 2006 at 12:00:36PM -0400, Berit Hinnemann wrote:
> Hi Axel,
>
> Thanks for your help. I did not understand completely this part
>
> >>non-orthogonal cells work. however on loading the cell and its
> >>embedded coordinates have to be rotated to accomodate the
> >>PBC conventions currently employed by VMD. see the cubeplugin docs.
>
> Does this mean that only a cube file where the first lattice vector along
> the x-axis and the second one in the xy-plane will be read and displayed
> correctly? The rotation, does VMD do this automatically when loading a cube
> file or is this something I have to do?
>
> Can I then choose to display several unit cells at once (which would be
> great as some interesting things happen at the unit cell border)?
>
> Thanks a lot, Berit
>
> 

-- 
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