Each atom you make has the possibility to connect to other atoms. The number of connections depends on the atom type. Some of the 'connectors' may be used by lone pairs and not be available for bonding to other atoms.
For example, carbon has 4 connectors and no lone pairs, oxygen has 4 connectors and 2 lone pairs.
When you use the Add Hydrogen menu command, all unsaturated connectors will be saturated with hydrogen atoms. The number of connectors will determine the geometry (2 linear, 3 flat, 4 tetrahedral). So if you plan to use this command it is essential that the number of connectors and the number of lone pairs is correct.
You can view and change these via the Atoms → Details (Color, Radius, Mass...) menu command. It will activate the Atom Details panel, in which you an change the number of connectors and lone pairs for each atom. Note that only selected atoms will be visible in the Atom Details panel.
You can also see and change other atom properties like the type, screen radius, nuclear charge, mass, color, Amber and Tripos atom types and more.
