Contents

• Introduction
• QuickStart
• Setup and Installation
  • For system administrators
  • For mere mortals (non-root users)
  • License information:
  • Conferencing setup
  • Configuring spock as a WWW browser helper application
  • Customization
  • Helper applications
  • Running Spock
  
  
• The user interface
  • Mouse Control
  • Function Keys
  • Command Line
  • Dials and Buttons
  
  
• Command Language
  • Typographical conventions
  • Actions
  • Selection
  • Complex Queries
  • The Command-line Calculator:
  
  
• Menus
  • File
  • Edit
  • Display
  • Alter
  • View
  • Calculate
  • Modeling
  • Subsets
  • Picking
  • Macros
  • Graphics
  • Tools
  • Help
  
  
• History / Command Files
  • Flow Control in Command Files
  • Nographics mode
  • Conference mode
  
  
• Tutorials
  • Introduction to spock: movement, coloring
  • Surfaces
  • Atom selections
  • Surface area calculations
  • Using distance calculations to find residues in a subunit interface
  • Saving and exporting images
  • Electrostatics calculations
  • Cleaning electron density maps
  • Finding internal cavities in a molecule
  • Graphical surface selection
  • Locating a binding pocket
  • Making movies
  • Conferencing
  • Secondary structure
  • Superimposing structures
  • Subsets
  • Modeling
  
  
• Acknowledgments
• Bibliography
• Pre-defined Sets
• Internal Periodic Table/Default Radii and Default Colors
• Font mapping for Raster3D and Vector PostScript output
• Quick Reference Guide
  • Actions:
  • Selections:
  
  
• Matrix specification
• File Formats
  • Interactions file
  • PhiMap file (.phi) files
  • External objects (.spo) file
  • Rotamer library
  • Atom order library
  
  
• Disclaimer
• Index