Selection

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:

• picking from the graphics window
• using the Select menu
• using the command select
• with tools such as the Model Panel or Sequence

Ways to clear a selection:

• picking in empty space
• choosing Select... Clear Selection from the menu
• using the command ~select
• pressing Shift-left arrow

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).

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

• by default, Ctrl-button 1 (left mouse button) is assigned to picking; button assignments can be changed in the Mouse preferences
• clicking the assigned button over a selectable item selects it, whereas clicking in empty space clears the selection
• holding down the assigned button and dragging a rectangular outline selects all enclosed items
• additionally pressing the Shift key adds to a selection (or toggles its selection status) without deselecting anything else

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).

Doubleclicking while picking an atom, bond, or pseudobond elicits a context menu for inspecting the item or performing related tasks (for example, distance measurement or bond rotation).

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

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.

A selection can be broadened and narrowed using:

• the up arrow and down arrow keys, respectively
• Broaden and Narrow in the Select menu
• the command select with the keywords up and down, respectively

• atom/bond ↔ residue ↔ connected set of atoms ↔ atoms with the same chain ID ↔ submodel ↔ molecule model ↔ all molecule models
• pseudobond (except in a chain trace) ↔ pseudobond group ↔ all pseudobond groups
• surface piece ↔ surface model

The original selection can be broadened to successively higher levels until the top level is reached, or narrowed in one step to nothing. The original selection is remembered and can be regenerated by the reverse process.

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:

• within models containing selections, by:
  • pressing the right arrow key
  • using Select... Invert (selected models)
  • using the command select invert sel
• within all models, by:
  • pressing Shift-right arrow
  • using Select... Invert (all models)
  • using the command select invert

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

• up arrow - broaden the selection
• down arrow - narrow the selection
• right arrow - invert the selection within selected models
• Shift-right arrow - invert the selection within all models
• left arrow - undo the most recent selection operation
• Shift-left arrow - clear the selection