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\subsection{Pharmacophore/Shape Search}  If the primary query is the pharmacophore query, the selected database is  searched for compounds that match the specified pharmacophore using the Pharmer \cite{Koes_2011} search technology. Results are aligned to the pharmacophore to minimize the root mean squared deviation (RMSD) between the query features and the hit compound features. Results are sorted with respect to this pharmacophore RMSD. An example of a pharmacophore-oriented search is shown in Figure~\ref{pharmfig}. If a shape query is also present, then the shape constraints are applied to the pharmacophore aligned pose. Search In this modality, only heavy atom centers are compared to the shape constraints. That is, the pharmacophore-aligned results are filtered to ensure that hits have at least one heavy atom center that falls within the inclusive shape and no heavy atom center that falls within the exclusive shape. With this modality, the exclusive shape is generally the most useful, as it provides a way to eliminate compounds that match the pharmacophore but have significant steric clashes with the receptor.  Due to the importance and increased specificity of the interactions specified by a pharmacophore, pharmacophore search followed by shape filtering is the default and recommend search modality. If desired, the complete result set may be save as a compressed SDF structure file that contains the query-aligned poses.