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.
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, and all types of hidden items shown with the show command.) If exactly two atoms are selected, the selection context menu will include a Distance option to add a distance monitor between them. If the selection contains part of a single amino acid, the context menu will include a choice to Mutate Residue with the Rotamers tool. See also: context menus, Distances
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.