Quick Start Guide: Exercise 3


Interacting with the 3D Workspace and Making Selections

With the prepared protein from Task 1 in the Workspace, examine the structures and interact with them using the Selection Toolbar.

Changing pick level

Clicking an atom in the Workspace chooses only that atom by default. Use the Pick Level menu button on the Selection Toolbar to choose a different substructure level:

  • A Atoms
  • R Residues
  • C Chains
  • M Molecules
  • E Entries

Your current pick level is indicated by the letter next to your cursor in the Workspace.

Hovering over an atom highlights all of the atoms that will be selected when you click, based on your current pick level.

Selecting and deselecting objects in the Workspace

Common objects can be selected using the buttons in the Quick Select area of the Selection Toolbar. For instance:

  • Click P to select any protein atoms in the Workspace
  • Clear the selection by clicking the Clear Selection button or by clicking into an empty area of the Workspace

Selecting the ligand and all atoms within 4Å

The Expand menu lets you select atoms related to your current selection, based on various criteria. A common use of this menu is to expand a selection around a ligand by a number of angstroms:

  • Click L in the Quick Select area to select any ligand atoms in the Workspace
  • Click the Expand button and choose "Within 4A Radius" from the menu

Removing ligand atoms from the selection

You can use the [+] and [-] buttons next to the large arrow at the left of the Selection Toolbar to remain in additive and subtractive picking mode, respectively. For example, with your ligand and binding site selected:

  • Click the [-] button to enter subtractive picking mode
  • Click on a ligand atom in the Workspace; the atom is deselected while the rest of the selection is maintained

To exit subtractive picking mode:

  • Click [-] again or click the large arrow button beside it
  • You can also click the REMOVE tag that marks the mode in the Quick Select area

Quickly selecting the binding site

The "..." button in the Quick Select area of the Selection Toolbar opens a menu of common objects and atom sets. The objects include two "Binding Site" options, with or without the associated ligand.

This binding site is equivalent to selecting all protein residues and solvents within 5Å of the ligand.

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