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A selection is a set of items (atoms, bonds, residues, models) chosen by the user that:

Selecting a standard (atom-associated) molecular surface automatically also selects the atoms used to define it. If the whole surface model is selected, all of the atoms used to define that surface are selected, even atoms that are completely buried. Typically all of the atoms in a biopolymer chain are used to define a surface, but other sets of atoms can be specified with the surface command. If a surface patch is selected with the mouse, only the atom(s) directly contributing to that patch are selected. Conversely, selecting an atom selects its surface patch(es).

Nonmolecular surfaces can be selected as a whole. Selectable objects such as atoms and bonds under or behind a volume surface can be selected with the mouse if the surface is transparent (not completely opaque) or shown as mesh. If the mouseclick is on a surface region that does not overlie another selectable object, however, the surface model will be selected.

Selection Context Menus

Doubleclick-selecting an item in the main window (see mousemode) shows a context menu, typically including options to hide or delete the selected atoms, bonds, and/or pseudobonds. (Hidden selected atoms can be reshown using the icon in the Molecule Display Toolbar, and all types of hidden items shown with the show command.) If two atoms are selected, the context menu also includes an option to add a distance monitor between them. See also: context menus, Distances preferences

Selection vs. Direct Specification in Commands

Command-line target specification strings, including logical operations (and/or/not) and zones, can be given directly in commands, bypassing selection. However, target specification may include sel, selAtoms, and selMaps to indicate the current selection, and selections are useful in other contexts, such as defining the scope of action when an icon is clicked.

UCSF Resource for Biocomputing, Visualization, and Informatics / July 2018