LigPlot prepares a schematic description of the environment of a ligand bound to a protein:
Download the software by going to http://www.ebi.ac.uk/thornton-srv/software/LigPlus/download.html and install it.
The documentation is available at the URL http://www.ebi.ac.uk/thornton-srv/software/LigPlus/manual/manual.html
It LigPlus fails to generate the schematics the it is likely that your PDB file is not following the PDB conventions. Use the 'Structure Conversion function of Simulaid to 'Regularize' your PDB file.
Use LigPlot to visualize the environment of a ligand either by downloading form the PDB a ligand-protein complex or by extracting a docked pose from a docking run complexed with the target protein.
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