deletions | additions       diff --git a/section_Query_Definition_subsection_Inputs__.tex b/section_Query_Definition_subsection_Inputs__.tex  index 8288a4a..14523ef 100644  --- a/section_Query_Definition_subsection_Inputs__.tex  +++ b/section_Query_Definition_subsection_Inputs__.tex 
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The typical starting point for a Pharmit session is a ligand-receptor complex structure, although 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 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 `Enter  Pharmit Search" Search'  on the main page and then choosing "Load receptor" `Load receptor'  and "Load features" `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, if  the histidine protonation state is correct, or if  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.  If a ligand structure is provided Pharmit can also accept initiate queries  without a receptor, Pharmit enables all either in  the pharmacophore features form  of the a  ligand as the initial structure or an externally generated pharmacophore  query to be interactively modified by the user. Alternatively, external software, file, but in this case features that require a receptor,  such as MOE, LigandScout \cite{Wolber_2005}, or PharmaGIST \cite{Schneidman_Duhovny_2008}, may be used to derive a ligand-based pharmacophore and the result may energy minimization, will not  be uploaded to Pharmit. available.  \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.