Selecting Atoms by Picking in the Workspace

Picking atoms in the Workspace is controlled by the tools on the Selection toolbar.

To start picking, click the Select by picking button (if it is not already active)

then click on atoms in the Workspace. You can select all atoms by double-clicking the button.

When you are picking, you can click on an atom, a bond, or a ribbon. Clicking on a bond selects the two atoms that are bonded. Clicking on a ribbon is the same as clicking on the alpha carbon for the ribbon segment you clicked.

You can also drag a rectangle out over a group of atoms to select them, or draw a loop (lasso) around them. To change the drawing mode, click the Select by picking button, or choose Select → Pick to Select → Lasso or Select → Pick to Select → Rectangle. The Select by picking button updates to reflect the drawing mode.

Picking a single atom in the Workspace can be used to select multiple atoms rather than just a single atom. The Selection toolbar (and many of the panels where you have to pick atoms in the Workspace) allow you to choose what is selected when you click on an atom. You can select just the atom itself, or the residue or repeating unit, the residues that have the same secondary structure, the chain, the molecule, or the entry to which it belongs. This is referred to as choosing the "pick level" or "selection scope" (both terms are used).

You can set the selection scope, or "pick level", by choosing from the Set selection scope button menu, which is set to Atoms by default for Maestro and Materials Science, and Residues for Bioluminate.

For example, to select all atoms in a residue, choose Residues from the Set selection scope button menu, then click on an atom in the residue. You can also change the selection scope with shortcut keys, or by choosing the selection scope from the menu bar with Select → Set Pick Level → scope. The selection scopes you can choose are as follows (with the shortcut keys in parentheses):

• Atoms (A)
• Residues or Repeating Units (R)
• Chains (C)
• Molecules (M)
• Entries (E)
• Secondary Structure (S)

If you want to use the Secondary Structure scope to pick residues that have the same secondary structure, the secondary structure must be defined (e.g. by displaying ribbons or choosing Edit → Assign → Secondary Structure). This selection scope does not allow you to pick ligands, waters, or solvents, for example, as they have no secondary structure. This scope is not available in the Materials Science profile.

When the pointer moves over an atom, the atoms that would be selected if you picked the atom are highlighted (called "predictive highlighting"). The highlighting includes undisplayed atoms if these atoms are in the selection scope. (You can turn this feature off in the Preferences panel.)

Sometimes, atoms are not available for picking. For these atoms, the pointer icon changes to indicate that the atom can't be picked. For example, you can't pick atoms in a locked entry (because actions are not allowed on these entries, except in special modes like measurement). The pointer icon changes to the one below, to indicate that it's in a locked entry and can't be picked:

A banner is displayed when there are locked entries in the Workspace. For other unavailable atoms, the pointer doesn't have the padlock as part of the icon.

If you pick a different atom in the Workspace, the selection is replaced with the result of the new pick. You can also modify the selection by picking—see Adding Atoms to the Selection, Removing Atoms from the Selection, and Inverting the Selection.