MarvinSpace offers a simple tool to represent pharmacophore models: spheres and arrows can be placed at any position. These can be translated, rotated and resized using controls.
To place a pharmacophore sphere to represents a pharmacophore point follow the steps below:
press the pharmacophore sphere button
click on an arbitrary atom: a sphere appears around the selected atom
Arrows can be placed the same way except that the arrow button has to be pressed to initiate the process.