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