N U C P L O T - v.1.0

Operating Manual

A program to generate schematic diagrams of protein-nucleic acid interactions

Written by Nicholas M Luscombe & Roman A Laskowski

Contents

		1. Introduction
		2. Installation of programs
		3. How to run NUCPLOT
		a. running nucplot
		b. running nuconly
		4. NUCPLOT outputs
		5. Altering the appearance of the plot
		a. print options
		b. plot parameters
		c. numerical parameters
		d. colour parameters
		e. colour definitions
		f. non-standard bases
		6. Editing the PostScript file
		7. Missing bonds
		a. miscalculation of H-bonds by HBPLUS
		b. expected bond falls outside the criteria
		c. missing water contacts
		d. using the *.bond file
		Reference
		Appendix A - PDB file format
		Appendix B - The *.bond file format
		Appendix C - The HBADD program
		a. pre-processor for HBPLUS
		b. the algorithm
		c. problems