Aten has been published in the Journal of Computational Chemistry, and the article can be found online here. The full reference is:

"Aten - An application for the creation, editing, and visualization of coordinates for glasses, liquids, crystals, and molecules"

T. G. A. Youngs, J. Comp. Chem. 31, 639-648 (2010).

It is not a requirement to cite Aten in your work, but if you feel that it has been particularly useful then the credit would be nice.