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:
- 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:
-21etc. This denotes atoms whose occupancy is linked: The occupancies of atoms in
-21have 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.