As with atom colours, you can change bond colours in one of two ways:
Globally, according to bond specification.
Locally, for a selected bond.
Bonds are displayed according to their settings in the Bonds Inspector. Some bonds - such as the "Dual-Band" type - are automatically coloured by the atoms at either end. Other bonds, such as the line, stick and cylinder styles can be coloured using the colour buttons in the Bonds Inspector.
Simply select the bond by clicking on it with the Arrow tool, then use the Selection Inspector to change the colour (and any other properties you require).
See Also