There are several ways to make selections, including:

Selections can be broadened and narrowed with the arrow keys or the command select. The status line includes a button that reports what is selected.

Items that are selected can then be acted upon using the Actions menu, the Selection Inspector, or commands. With commands typed into the Command Line, selections are indicated by using the word selected, sel, or picked as the atom specification. Selections previously named and saved with Select... Save Selection... can also be specified, using sel=selection_name.

Whether a new selection is added to, subtracted from, intersected with, or used to replace the existing selection can be set with Select... Selection Mode (current_mode); current_mode shows the current setting. Selection mode does not apply to picking from the graphics window. Regardless of how it was created, the current selection can be deselected with Select... Clear Selection.

Picking from the Graphics Window

During picking from the graphics window, the cursor looks like a pointing hand. By default, an atom or bond is selected by clicking on it with the left mouse button while holding down the Ctrl key. The assignment of buttons to this function can be changed in the Mouse preferences. If the Shift key is held down at the same time, the selection is added to the previous selection rather than replacing it (or if the atom or bond is already selected, it becomes deselected without changing the rest of the selection). Another way to select more than one atom or bond is to hold the mouse button down rather than clicking it; a rectangle shows the area swept out, and all enclosed atoms and bonds will be selected. The selection will be highlighted. The color and type of highlighting are controlled in the Background preferences.

When a plus sign (+) has been typed into the Command Line, it will be replaced by the atom specification string of the next picked atom. Each plus sign must be preceded and followed by a space (or the end of the line).

Double-picking a bond (that is, doubleclicking it with the button assigned to picking) elicits a menu:

Double-picking a pseudobond elicits just the Select Bonded option.

Selection using the Menu

The top part of the Select menu allows selection according to:

Selection by element or atom type only selects atoms; however, selection by functional group, chain, residue, or structure selects both atoms and bonds.

Select... Sequence... selects atoms and bonds within specified sequences. Atoms (and optionally, bonds with selected atoms at both ends) can also be selected with an Atom Specifier. Atoms, residues, and models can be selected By Attribute Value. Finally, atoms and bonds within (or further than) a specified distance from the currently selected atoms can be selected on a per-atom or whole-residue basis with the Select... Zone... option.

There are several other features within the Select menu. The current selection can be deselected with Clear Selection. Selection Mode controls whether a new selection (except those made by picking) will be added to, subtracted from, intersected with, or used to replace the existing selection. Select All may be useful in combination with the subtractive mode. The most recent selection operation can be undone with Undo. The current selection can be named and saved with Save Selection... and later reinvoked with Saved Selections. The saved selection consists of the items actually selected rather than the rules used to select them, and will only apply to the same model(s) that they were defined upon (and the models cannot have been closed and reopened).

Whereas the selected items form a selection, the set of rules used to select them form a selector. Selectors that are boolean combinations of the various selection options can be created with the Selector Construction Panel (Select... Construct Selector...). This is especially helpful if the same complicated set of rules is to be used repeatedly. When saved, a user-defined selector becomes an additional listing under Select.

Selection using the Model Panel and Other Tools

The Model Panel provides an easy route to selecting models, submodels, chains, or sequence segments. Once models and/or submodels have been chosen within the left side of the Model Panel, any of several functions listed on the right side of the panel may be executed. These functions include select (select chosen models/submodels), select all (select chosen models/submodels as well as their constituent atoms, bonds, and residues), select chain(s)... (select chains within the chosen models/submodels), and sequence... (open sequence panel listing chain sequences and allowing sequence segments to be selected).

Analogously, once one or more pseudobond groups have been chosen within the left side of the PseudoBond Panel, the select button in the right side of the panel can be used to select them.

Only the more general approaches to selection are described here; several other tools provide ways to make selections in more specific contexts.

Broadening and Narrowing Selections

A selection can be broadened and narrowed using:

Selection-level cascades are: Although implemented as pseudobonds, chain trace bonds are treated like regular bonds between residues for the purposes of broadening and narrowing selections.

The original selection is remembered during broadening so that it can be regenerated by narrowing the selection. A selection cannot be broadened beyond the top level or narrowed beyond the original level.

In some cases, multiple levels collapse into one level; for example, if a model has only one chain and no submodels, pressing the up arrow key just twice will broaden a selection from one atom to the entire molecule model. If the original selection includes both atom(s) and pseudobond(s), the selection will broaden to pseudobond group in the same step as it broadens to chain, and to all pseudobond groups in the same step as it broadens to all molecule models.

An alternative way of making Actions in the menu apply more broadly than to an initial selection is to broaden the setting of Actions... Target.