Selections can be made by:
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.
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.
The top part of the Select menu allows selection according to:
Atoms (and optionally, bonds with selected atoms at both ends) can also be selected with an Atom Specifier. Select... Sequence... allows contiguous sequence segments to be specified using one-letter amino acid or nucleic acid codes (case is ignored); atoms and bonds within any and all matching sequence segments are selected. 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 removed (deselected) with Clear Selection. Selection Mode controls whether a new selection via the menu 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.
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 sets of pseudobonds 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 up arrow and down arrow keys can be used to broaden and narrow a selection, respectively. Each click of the up arrow key broadens a selection one level and each click of the down arrow key narrows a selection one level. A selection cannot be narrowed more than the original selection, however. The Chimera window must have keyboard focus (it may be necessary to click in the window) for the arrow keys to affect a selection. Selection level cascades are:
In some cases, multiple levels collapse into one level; for example, if a model has only one chain and no submodels, only two clicks of the up arrow key are required to go from an atom to the entire model. The original selection is remembered during broadening so that it can be regenerated by narrowing the selection. Once the top level is reached, clicking the up arrow will not change the selection; similarly, once the original level is reached, clicking the down arrow will not change the selection. 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.