In Chimera, selection is used to specify items (atoms, residues, etc.) for subsequent actions or operations. Items that are selected can be acted upon with the Actions menu, the Selection Inspector, or commands. In commands, selections are indicated with the word selected, sel, or picked as the atom specification. Selections previously named and saved can also be specified, using sel=selection_name or just selection_name.

By default, a selection is outlined in green (controlled in the Background preferences) and its contents are reported on a button in the status line. Clicking the button opens the Selection Inspector.

Ways to make a selection:

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.

Selections can be broadened, narrowed, and inverted. The most recent selection operation can be undone with Select... Undo (or by pressing the left arrow key).

Ways to clear a 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 Certain 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).

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.

The Sequence tool shows the sequences of peptide and nucleotide chains. Selections can be made by dragging with the mouse in the sequence.

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

Broadening, Narrowing, and Inverting 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.

A selection can be inverted to select the currently deselected atoms/bonds and vice versa:

Summary of Arrow Key Shortcuts

When the keyboard focus is in the main Chimera window, arrow key shortcuts adjust the selection:

UCSF Computer Graphics Laboratory / September 2006