LIGPLOT v.4.0 - Operating manual
last modified
19-11-2009 14:25
LIGPLOT v.4.0
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
Appendix A - Brookhaven 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 23 Nov 1997.
LIGPLOT Home Page (at UCL)