RAMP HOWTO

Ram Samudrala (ram@compbio.washington.edu)

1. Introduction

2. Installation

• 2.1 System requirements
• 2.2 Setting up the distribution
• 2.3 Using the default setup
• 2.4 Changing the defaults and recompiling
• 2.5 Using RAMBIN
• 2.6 Using a login shell other than tcsh

3. General issues

• 3.1 Command line interface
• 3.2 Terminology
• 3.3 Directory structure
• 3.4 Environment variables
• 3.5 Test sets
• 3.6 Caveats

4. Programs

• 4.1 Scoring functions
• 4.2 Scoring function related programs
• 4.3 Main chain generation related programs
• 4.4 Side chain generation related programs
• 4.5 Graph theory programs
• 4.6 Miscellaneous programs
• 4.7 Music-related programs

5. Troubleshooting

• 5.1 General questions

6. Usage guidelines

7. Acknowledgements

8. Bibliography