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\subsection{Inputs}  The typical starting point for a Pharmit session is a ligand-receptor complex structure, although ligand-based pharmacophores a ligand-only structure or pharmacophore query file  may be used as well. A Pharmit session can be automatically initialized using any complex in the PDB by inputing the corresponding PDB accession 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. as the basis of the query.  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.