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\section{Example}  To demonstrate Pharmit's capabilities, this section presents describes  atimeline of  virtual screening for screen of  Tyrosin-protein kinase C-SRC in complex with AMP-PNP. This compound AMP-PNP (PDB 2SRC). The resulting query  is PDB code 2SRC, and the reader can reproduce the results of this section by visiting available as an interactive example from  the Pharmit examples page and clicking on the 2SRC link, or by following the process described in this section. page.  Beginning on the Pharmit main page, the user should initiate initiates  a search by typing '2SRC' `2SRC'  into the 'start `start  from PDB' box. This will retrieve the ligands ligands, AMP and PNP,  in the PDB file, which and they  are displayed in the dropdown menu next to the PDB code box; the box. The  user may select any ligand in the PDB file to generate a pharmacophore. If it is not currently selected, then selects  theuser should choose  ANP ligand  and chooses to  ignore the binding site waters, then click 'submit.' The waters. After clicking `submit,' the  user willthen  be taken to the graphical workspace where queries are generated, and a main Pharmit interface. A  set of interacting pharmacophore  features will be automatically generated from the protein-ligand complex.  which the user should select a subset to represent a pharmacophore. Choosing more than five features will generally yield few or no results if tolerance spheres are of size 1.0 or smaller, since this produces a very specific query for which there are likely no hits in the database. To generate a useful query to find hits for 2SRC, we target the canonical hinge site, with which ANP strongly interacts, by including a hydrogen donor and acceptor, as well as two aromatics. We anchor the query at the other side of the pocket by including a hydrogen acceptor, for a total of five features. While this query is reasonable given the structure of the kinase, strong interactions with functional groups in the pocket are possible outside of the narrow constraints derived from the small donor/acceptor tolerance spheres; as it is, few hits are returned. Thus the tolerance spheres for donors and acceptors are increased to 1.0. Finally, several features included in the query are likely interacting with a single group in the pocket, making it reasonable to impose a directionality on these features. The hydrogen acceptor interacting at the hinge site is given a $\phi$ of 90 and $\psi$ of 45, and the second aromatic is given a $\phi$ of 10 and $\psi$ of -50. The DUDe 2SRC benchmark set, which consists of small molecules known to bind 2SRC as well as structurally similar compounds that do not bind, is a contributed library available to search within Pharmit, and this is used to validate the pharmacophore. Searching generates 39 hits, with an enrichment factor of 41.1.