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\subsection{Inputs}  The typical starting point for a Pharmit session is a ligand-receptor complex structure. structure, although ligand-based pharmacophores may be used as well.  A Pharmit session can be automatically initialized using any complex in the PDB by inputing the corresponding PDB ascension code on the Pharmit main page and selecting how active site water molecules should be treated (ignored, as part of the receptor, or as part of the ligand). The dropdown menu next to the box where a PDB code may be entered allows the user to select which ligand found in the PDB file should be used to generate a pharmacophore. Alternatively, a user can upload their own complex, in which case the receptor and ligand structures must be in separate files; these are uploaded by clicking "Enter Pharmit Search" on the main page and then choosing "Load receptor" and "Load features" on the resulting page. Any file format supported by OpenBabel \cite{O_Boyle_2011} may be used. Note that the query ligand must be pre-positioned within the binding site of the receptor - Pharmit does not perform docking.  Pharmit prepares the receptor by protonating it with OpenBabel, but no other modifications are made. Thus the user must decide whether there are missing residues that should be included, the histidine protonation state is correct, or any other structural changes to the receptor are necessary. Note that a partial charge calculation is irrelevant as it is not used by the AutoDock Vina scoring function. The user may choose to provide the If a  ligand structure as the file utilized when loading features, in which case Pharmit will automatically generate a set of relevant features from which is provided without  a receptor, Pharmit enables all the  pharmacophore may features of the ligand as the initial query to  be produced, or interactively modified by the user. Alternatively,  external software (e.g. MOE software, such as MOE, LigandScout \cite{Wolber_2005},  or PharmaGIST) PharmaGIST \cite{Schneidman_Duhovny_2008},  may be used to derive a ligand-based pharmacophore and the result may be uploaded to Pharmit.Note that the query ligand must be pre-positioned within the binding site of the receptor - Pharmit does not perform docking. It uses the pharmacophore and shape features of a known ligand to screen for novel compounds.  \subsection{Pharmacophore Queries}  A pharmacophore \cite{Koes_2015rev,Yang_2010,Leach_2010} defines the essential features of an interaction. Importantly, a pharmacophore includes the spatial arrangement of these features.