\section{Visualization}

The visualization scheme of the Pharmit interface is highly customizable.  Both the color and representation style (e.g., sticks, spheres, cartoon, etc.) of the query receptor and ligand and the result compounds can be set individually as demonstrated in Figure~\ref{pharmfig}.  The transparency of the receptor surface, which is shown colored by electrostatic potential, may be adjusted from not present to fully opaque, and the background may be toggled between white and black.  To facilitate inspection of molecular models, the query and results sidebars may be hidden to provide a full-window molecular viewer. Manipulation of the 3D viewer will be familiar to users of PyMol \cite{PyMOL}: left mouse button to rotate, right or scroll wheel to zoom, and middle button to translate.  