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:
- Show Protein?: if this is checked, the protein structure
will be displayed along with each embedding and the reference
molecule.
- 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.
- Show H Bonds:
when checked, this causes likely hydrogen bonds between the aligned
embedding and the protein to be drawn.
- Show Collisions:
when checked, this causes close contacts between the
embedding and the protein to be drawn.