Coordinates

The coordinates panel shows the coordinates corresponding to the molecule visible in the molecule display. You may edit the coordinate values here as well. Besides the values you can also change the order of the atoms, using the 'Move Atoms' buttons.

You may select to use Cartesian, Internal or Delocalized coordinates.

For internal coordinates you can currently only edit the values for bond lengths and angles, not the connection information. You can, however, change the order of the atoms. The Internal coordinates matrix will be recalculated each time the order is changed. The connection matrix will make as much use as possible of the actual bond information. If possible, vicinal dihedrals will be shown and groups such as methyls will be fully rotatable using one dihedral. If there are separate molecules present, the first atom on the second fragment will be connected to the first on the first fragment. This can be a useful trick to quickly define a certain distance.

The ordering of atoms in Cartesian, Internal and Delocalized coordinates is identical. Obviously the order is only important if you are going to use Internal coordinates.

If you will optimize the geometry (with ADF), the program will perform this optimization in the coordinate type you have selected here. Thus, the Cartesian, Internal or Delocalized pull-down menu is not only for display purposes, but determines the optimization method used.

By checking the checkboxes next to the coordinates you can freeze those coordinates during a geometry optimization.

You can select atoms using the coordinates panel as well as in the molecule pane. The coordinate lines for atoms that are selected will be highlighted in yellow.