Selecting atoms

Atom selections are needed in several situations: in the  Structure viewer for showing/hiding atoms, for geometry manipulation and in the projected DOS and band structure.

The easiest way to select/unselect atoms is to point to an atom in Structure viewer and press space. This will select/unselect the atom under the mouse arrow.Selected atoms are in the 3d view marked by black spirals around the atom spheres. Each selection can be represented by a selection statement. As you select/unselect atoms in the Sructure viewer, the selection statement is updated and it is shown in the Selection field:

The selection statement uses a simple mini-language for definig groups of atoms.. 

Selection language by example:

  • Ca - shows all calcium atoms. Warning: the case matters, thus ca or CA will not work.
  • 2 - select the second atom in the structure.
  • 2-5 - select the atoms in the range from second to fifth (i.e. 2,3,4,5).
  • 2- -select every atom from the second one (2,3,4,5,6,...).
  • -5 -select every atom up to the fifth (1,2,3,4,5).
  • all - select all atoms.
  • #1 - select all atoms of the 1st specie.
  • Ca:1 - select the first calcium atom (terms like Ca:2-5,Ca:2-,Ca:-5 are also legal).
  • #2:1 - select the first atom of the second specie (terms like #2:2-5, #2:2-, #2:-5 work as well).
  • C:3- Sc  - select all carbon atoms starting from the third, and all scandium atoms. Terms can be joined together (separated by one or more spaces).