VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue May 23 2006 - 15:34:04 CDT

On Tue, 23 May 2006, Berit Hinnemann wrote:

BH> Hi Axel,
BH>
BH> Thanks for your help. I did not understand completely this part
BH>
BH> >>non-orthogonal cells work. however on loading the cell and its
BH> >>embedded coordinates have to be rotated to accomodate the
BH> >>PBC conventions currently employed by VMD. see the cubeplugin docs.
BH>
BH> Does this mean that only a cube file where the first lattice vector along
BH> the x-axis and the second one in the xy-plane will be read and displayed
BH> correctly? The rotation, does VMD do this automatically when loading a cube
BH> file or is this something I have to do?

no, the rotation is done by the cube plugin. the pbc display will be
ok, but the coordinates will not match with those from an external .xyz
or .pdb file. if you embed your coordinates properly into the cube file
they will be rotated correspondingly (at least in theory and for my
test cases).

axel.

BH> Can I then choose to display several unit cells at once (which would be
BH> great as some interesting things happen at the unit cell border)?
BH>
BH> Thanks a lot, Berit
BH>
BH>
BH> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   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.