Assembling molecular components into low-dimensional structures offers new opportunities for nanoscale device applications. Here we describe the self-assembly of indium atoms into metallic chains on the silicon (001) surface using adsorbed benzonitrile molecules as nucleation and termination sites. Critically, individual benzonitrile adsorbates can be manipulated using scanning tunneling microscopy. This affords control over the position and orientation of the molecular adsorbates, which in turn determine the origin, direction, and length of the self-assembled metallic chains.