Unit cell builder

General Discussion
1

Hello all,

I have a problem with the unit cell builder. I am able to successfully
build a unit cell where a = b = c = 2 and alpha = beta = gamma = 108
with NH3BH3. However, when I go to export the unit cell to NWChem
format, or save as .xyz or .pdb none of the atoms created with the unit
cell builder appear in the input file only the original or starting
molecule coordinates appear. Additionally, the new atom coordinates do
not show up in the Cartesian coordinate editor and labels do not appear
on the constructed crystal lattice molecules in Avogadro. I am using
Avogadro application version 1.0.3, library version 1.0.3, and openbabel
version 2.3.0 on ubuntu 12.04 LTS x64.

-Richard

2

On Wed, Feb 27, 2013 at 2:21 PM, Richard Overstreet <
reoverstreet1@catamount.wcu.edu> wrote:

Hello all,

I have a problem with the unit cell builder. I am able to successfully
build a unit cell where a = b = c = 2 and alpha = beta = gamma = 108
with NH3BH3. However, when I go to export the unit cell to NWChem
format, or save as .xyz or .pdb none of the atoms created with the unit
cell builder appear in the input file only the original or starting
molecule coordinates appear. Additionally, the new atom coordinates do
not show up in the Cartesian coordinate editor and labels do not appear
on the constructed crystal lattice molecules in Avogadro. I am using
Avogadro application version 1.0.3, library version 1.0.3, and openbabel
version 2.3.0 on ubuntu 12.04 LTS x64.

Can you try to reproduce this with Avogadro 1.1.0? There are a lot of new
crystallography features and unit cell creation has been rewritten.

Also, do you have the cell repeat options set? The cell repeat feature only
draws extra unit cells, but does not modify the actual crystal data. Use
the supercell builder if you want to add repeat cells to the crystal data.

Dave