In Chimera, selection specifies atoms, bonds, residues, molecule models, and surfaces for subsequent operations with the Actions menu. When selected, these items (as well as pseudobonds) can be inspected and modified with the Selection Inspector. The current selection can also be specified in commands by the word selected, sel, or picked.

Ways to make a selection:

Selecting a ribbon segment selects the atoms/bonds in the corresponding residue(s); selecting a molecular surface selects the atoms/bonds in the corresponding surface category.

Ways to clear a selection:

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

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). Replacement is the default mode. 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).

Picking from the Graphics Window

During selection from the graphics window (picking), the cursor looks like a pointing hand.

The selection mode does not apply to picking.

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-clicking with the assigned button on an atom, bond, or pseudobond may elicit a context-dependent menu for inspecting it, otherwise modifying it, or performing related measurements.

By default, placing the mouse cursor over an object such as an atom, bond, or surface (without clicking any buttons) will show its label information in an atomspec balloon. The atomspec balloon indicates what would be selected by picking at the current position, but more generally, it is useful for identifying objects without displaying their labels. Sometimes one would rather see information for the atoms under a surface than for the surface itself. This can be achieved by making the surface unselectable with the mouse, for example by:

  1. selecting the surface, either picking it with the mouse or using the Model Panel
  2. opening the Selection Inspector, by choosing Actions... Inspect or clicking the button near the lower right corner of the main Chimera window
  3. in that dialog, inspecting Surface and changing selectable with mouse to false
Then, an atomspec balloon will report information for the atom under the cursor position, not necessarily the same as the atom giving rise to the surface patch under the cursor position. The atoms must be displayed for their atomspec balloons to appear, but they do not need to be visible; they could be behind opaque surface. However, the surface can be made transparent (with Actions... Surface... transparency or the command surftransparency) to allow viewing the underlying atoms at the same time.

Selection with Tools

After one or more lines (models) have been chosen in the left side of the Model Panel, any of several functions listed on the right side of the panel may be executed, including select and select chain(s).

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 are mentioned here; many additional tools generate selections.

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.

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 / August 2008