Atom Label Display Options

How to display and label atoms

Olex2 offers a large range of properties that can be displayed as labels on atoms. This provides immediate feedback on these properties of the atoms: Work|Toolbox-Work|Labels:

  • Labels On/Off show or hide atom name labels and Q-peak labels (alternatively press F3). This will switch other types of labelling off but selecting it again will display atom name labels.
  • Atom Names F3 shows non-hydrogen atom and Q-peak labels
  • Crystallographic Occupancy displays the occupancy of any atoms. Please note that atoms in special positions will also display a number, but this does not mean that the site is not fully occupied. Unless you really know what you are doing, the Chemical Occupancy choice is probably the one you want.
  • Chemical Occupancy displays the occupancy of any atoms which are not 100% occupied i.e. their occupancy is not 1. As opposed to the crystallographic occupancy, the multiplicity of atoms in special positions will be taken into account. An atom on a center of inversion has a crystallographic occupancy of 0.5, but from a chemical point of view it is fully occupied. So in this mode, if there is a number displayed next to an atom, this means it is a partially occupied site.
  • Parts displays part numbers for atoms that are not in PART 0. By default, all atoms are in PART 0, unless they have explicitly been assigned to another part.
  • Link-Code this is displayed ShelX FVAR style: 21 and -21 etc. This denotes atoms whose occupancy is linked: The occupancies of atoms in 21 and -21 have to add up to unity.
  • H Atom Labels will include the hydrogen atom labels along with the atom name and Q-peak labels.
  • Fixed Parameters if any parameters are fixed, these will be displayed as the atom label: occupancy, xyz, Ueq.
  • Variables displays all variables associated with the atom.
  • AFIX Commands useful to check the AFIX commands that are being applied to the structure.
  • Q-Peak Intensities intensities of the Q-peaks will be displayed.