SURFNET v.1.5

Operating manual

A program for visualizing molecular surfaces, cavities and intermolecular interactions.

Roman A Laskowski

December 1997

Contents

1. Introduction
2. How to run SURFNET
3. Editing the surfnet.par file
4. van der Waals surfaces
5. Gaps between molecules
6. Clefts and cavities
7. 3D density distributions
8. Planes, paraboloids and boxes
9. Viewing the SURFNET surfaces
10. Extracting and comparing gap regions

Reference

Appendix A - Program flowchart
Appendix B - PDB file format
Appendix C - Generation of gap regions
Appendix D - van der Waals radii


Acknowledgements

SURFNET Home Page