Editing Vina (section)

= Usage =

; Run docking/screening
: The ''target receptor'' and ''box center'' must be selections or objects or extracted objects already loaded into PyMOL. If there are rigid ligands (e.g. a cofactor) or important water molecules, they must be on the ''receptor'' selection/object.
: A ligand input file on a supported format (Molscrub supports .smi, .sdf, .mol) must be supplied alongside a (preferentially) empty folder to place results. Click on ''Run'' to start.

; Analyzing results
: The top ''max load'' conformations ranked up to ''max mode'' are listed on the interface. Click on the molecule name (suffix <code>_m5</code> denotes the fifth model) to render a PLIP visualization of the docked ligand. Click on the ''export table'' to save the loaded molecule's affinity into a XLSX file.
: If the ''Intensive'' computation is enabled, the plugin will compute the PLIP interaction for loaded poses and plot an AuPosSOM-like dendogram tree based on pose similarity. A bar chart counting the number of interactions the residue does for each PLIP interaction type is also plotted.