This menu includes a set of commands to select atoms on the basis of properties. After the selection of a set of atoms, different actions can be performed on the selection; most commonly they are displayed or coloured. The Select commands act on an atomic property [mol]_atom_select. If this property does not exist for a given molecule, it is created.
Several commands make use of the selected atoms, for example: Sam_atom_out, Paint_select, Lego_loop & Patt_cross. When used for display purposes, the selection can be used to create an additional filter in determining which atoms are to be displayed. This filter is made with the atomic property [mol]_atom_visible. Bonds will only be drawn when the value of this property for each atom is on. This atomic property is best manipulated with the Select menu, first defining which atoms are to be selected, and then copied to the correct datablock with Select_visible.
Several O commands make use of the visibility filter datablock feature behind the user's back. For example, in Move_fragment, the atoms in the moving fragment are marked to be visible. The visibility datablock is then inverted and the drawing routine called again to create the rest of the object.