## Changing the View

The software provides a number of options that control the display of embeddings in PyMol. These are accessible via checkboxes at the top of the results tree:

1. Show Protein?: if this is checked, the protein structure will be displayed along with each embedding and the reference molecule.
2. Show Neighborhood?: when checked, this causes the surface of the protein around the reference molecule to be displayed. This option is disabled unless `Show Protein?` is checked.
3. Show H Bonds: when checked, this causes likely hydrogen bonds between the aligned embedding and the protein to be drawn.
4. Show Collisions: when checked, this causes close contacts between the embedding and the protein to be drawn.