Visualizing Non-Covalent Interactions

Use the Interactions pane on the Workspace Configuration Toolbar to visualize non-covalent interactions in the Workspace.

Setting up the Workspace

With 1FJS included in the Workspace:

• Click the Presets button on the Selection Toolbar to quickly focus the view on the ligand and binding site (see Task 7 for more information)

Opening the Interactions pane

• Hover over the Interactions toggle on the Workspace Configuration Toolbar until the ... icon appears
• Click the ... to open the Interactions pane

Configuring interactions

• To show hydrogen bonds in the Workspace, turn on the Non-covalent bonds toggle, then check the Hydrogen bonds option
• To show all Pi interactions, turn on the corresponding toggle and check the two options
• To show only Ugly clashes, toggle off the Non-covalent bonds and Pi interactions, then turn on the Contacts/Clashes toggle; uncheck the Good and Bad options, and check Ugly