CrystalExplorer allows you to cycle through a number of ways of viewing a disordered structure using,
- Menu option Display → Cycle Disorder Highlighting.
- Ctrl-D Keyboard shortcut (⌘-D on the Mac).
For example, in a system with two disordered components the initial display will show both components. By cycling you will be shown each of the components individually and finally each component given separate colors.
Surface Generation for Disordered Structures
Care has to be taken when generating surfaces of disordered structures since their interpretation is more difficult.
There are two main ways to deal with disorder:
- Include all orientations of the disordered molecule with their partial occupancies. This option lets CrystalExplorer handle the disorder, and results in a Hirshfeld surface based on the smeared electron distribution based on the average structure with electron densities weighted by their partial occupancies.
- Model the structure by choosing a particular disordered component. This requires manually editing the CIF to remove (or comment out) atoms from all disorder components except the one you are interested in, and setting all atoms to be fully occupied.
|Note: In order to handle disorder correctly, the CIF must contain disorder groups as well as appropriate occupancies for all disorder components.|
|Note: When disorder causes a hydrogen atom to be within bonding distance of two different atoms, Tonto cannot determine which is the correct atom, so the bond length to hydrogen cannot be normalised to standard neutron bond lengths, as is usually the case. This hydrogen atom will not be moved.|