Atoms can be selected or deselected in a view window with the help of keyboard shortcuts:

• a:     Pressing the 'a' key will select all atoms of the molecule in the active view window.
   
• n:     Pressing the 'n' key will deselect all atoms of the molecule in the active view window.
   
• c:     Mouse-Clicking an atom in the active view window while holding down the 'c' key will select / deselect the atom.
   
• r:     Drawing a rectangular region in the active view window with the mouse while holding down the 'r' key will select all atoms within the rectangle.

Atom selection can also be done in a similar way using corresponding Builder buttons instead of keyboard keys, or more generally by using the "Atom Selection Editor", which is accessible from the "Edit" menu.

If the 'f' key is held down when an atom is selected / deselected by clicking, then all atoms connected directly or indirectly to the clicked atom via bonds will also be selected / deselected.   This provides a quick and easy way to select a molecule in a weakly bound complex or a crystal, for example.

Selected atoms can be used in a variety of ways, such as Cut/Copy/Delete or defining "Atom Groups" such as ONIOM layers and Gaussian Fragments.