Add a methyl group to the methane

Select the Structures → Alkyl Chains → Methyl structure (the structures menu is the benzene-like logo)

Notice that the button of the structures menu is glowing, which means that the structure-tool is in use.

Double-click on one of the hydrogen atoms

You will see that the hydrogen is replaced by a methyl group.

Note that:

• The methyl is orientated along the newly formed C-C bond and the new hydrogens point
  away from the existing ones.
• The double-clicked hydrogen is replaced by the carbon atom, since this atom is the 'replacing' atom.
  This atom is defined through having xyz-coordinates (0,0,0).
• The background glow moved from the 'Structures' tool to the 'Pointer' tool button; the 'Pointer' tool is active again.