Quick Start Guide: Exercise 11

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

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