4. Outputs produced by LIGPLOT

The output files produced by LIGPLOT are:

ligplot.ps - Colour or black-and-white PostScript showing the plotted LIGPLOT diagram.
This can be viewed using any PostScript viewer, or plotted on any PostScript printer.
ligplot.pdb - Output file, in PDB format, of the final flattened molecules (ligand and interacting protein residues) as shown in the plot.
This file can be loaded into any standard molecular graphics package, and appears as a very flat molecule(!). However, it does allow you to manipulate the different residues that appear in the LIGPLOT diagram, using the facilities provided by the graphics package. You can thus manually adjust the final LIGPLOT diagram to your exact requirements, as described in section 6.
ligplot.hhb - Output file, in LIGPLOT format, of just those hydrogen bonds in the original filename.hhb file that were used by LIGPLOT in producing the final picture (see Appendix B - LIGPLOT file formats).
ligplot.nnb - Output file, in LIGPLOT format, of just those hydrophobic contacts in the original filename.nnb file that were used by LIGPLOT in producing the final picture (see Appendix B - LIGPLOT file formats).
ligplot.bonds - Output file listing of bonds and bond-types in the final LIGPLOT picture.
ligplot.frm - Output file, in PDB format, of the molecules shown in the plot, prior to flattening (ie coordinates as in the original filename.pdb file). You can view this file using any molecular graphics program (eg Rasmol) to see only those residues that interact with the ligand.
For example, the residues surrounding the benzamidine inhibitor of the salmon trypsin structure, 2tsb.
ligplot.rcm - Output file listing all the residues on the plot, together with the x-y coordinates of their centres of mass (see Appendix B - LIGPLOT file formats). The file provides a useful starting point if positional restraints on the residues of the plot are required (see 6. Improving the plots - Same protein different ligands).
ligplot.drw - File for input to the Java-based LIGPLOT editor, LigEd.