LIGPLOT v.4.5.3. - Operating manual

LIGPLOT v.4.5.3

Operating manual

A program to plot schematic diagrams of protein-ligand interactions

Andrew C Wallace & Roman A Laskowski.


 Contents

   1. Introduction
 a. The algorithm
 b. Hydrogen bonds
   2. How to run LIGPLOT
 a. Running LIGPLOT
 b. Running LIGONLY
 c. Showing atom accessibilities
   3. Inputs to LIGPLOT
   4. Outputs produced by LIGPLOT
   5. The ligplot.prm parameter file
   6. Improving the plots
 a. Editing the PostScript file
 b. Editing ligplot.pdb using graphics
 c. Altering minimization parameters
 d. Same protein, different ligands
   7. Missing H-bonds
   8. DIMPLOT - interactions across
 a dimer or domain-domain interface
 a. DIMPLOT for dimers
 b. Domain-domain interface
 c. Defining protein domains
 d. Running DIMONLY

   Reference

   Appendix A - PDB file format
   Appendix B - LIGPLOT file formats
 a. H-bonds file, .hhb
 b. Non-bonded contacts, .nnb
 c. Residue CofM file, .rcm
   Appendix C - The HBADD program
 a. Pre-processor for HBPLUS
 b. The algorithm
 c. Problems

   Sample plots
 a. Sample LIGPLOT outputs
 b. Sample DIMPLOT outputs

Last changed 7 Mar 2003.


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