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
    • Paths:
    • License information:
    • External commands/Help:
    • Other variables set by spock:
      • Model information:
      • Statistics:
  • Helper applications
  • Running Spock
    • Two concurrent spock sessions:
• The user interface
  • Mouse Control
  • Function Keys
  • Command Line
    • Command line editing
      • For X-experts:
  • Dials and Buttons
    • Buttons
    • Dials
• Command Language
  • Typographical conventions
  • Actions
    • Coloring
      • Bond Coloring
      • Worm Coloring
      • Examples:
    • Input/Output
      • Input:
      • Examples:
      • Output:
    • Viewing Commands
    • Parameters
      • Atom Parameters:
      • Examples:
    • Environment Variables
    • The internal periodic table
    • Object Creation
    • Control
  • Selection
    • Atom/Residue Numbering
      • Examples:
    • Atom, Residue, Chain, Altloc, Icode and Subset Names:
      • Examples:
    • Atom properties
    • Selection by object or molecule number
      • Examples:
    • Selecting on color
      • Examples:
  • Complex Queries
    • Examples:
    • Projection
  • The Command-line Calculator:
    • Calculator Variables:
• Menus
  • File
    • Open
      • Session File:
      • View File:
      • PDB File:
      • Preferences File:
      • History File:
      • HBPLUS File:
      • DSSP File:
      • PhiMap File:
      • Charge File:
      • Radius File:
      • Interactions File:
      • Interactions File:
      • External Objects File:
      • XPLOR map file:
      • Bones file:
    • Save
      • Session File:
      • View File:
      • PDB File:
      • Preferences File:
      • Macros:
      • History:
      • PhiMap File:
      • Charge File:
      • Radius File:
      • Molscript:
        • Incompatibilities/limitations:
      • Raster3D:
        • Labels and Raster3D
        • Tips on generating good-looking output
        • Incompatibilities/limitations:
      • Image:
        • Postscript Options:
      • VRML 1.0 and VRML 2.0:
        • Incompatibilities/limitations:
      • Interactions File:
      • XPLOR map file:
    • Delete All
    • Pause Playback
    • Resume Playback
    • Slave to file
    • Conference
      • Ignored commands
      • Start server
      • Start client
      • Suspend conference
      • End conference
      • Show conference status
      • Set port number
      • Send session
      • Send view
      • Send macro file
      • Compress redraws/Compression level
      • Conference mouse
      • Print incoming stream
      • Allow shell commands
    • Control Panel
    • Prefrerences
    • Print
    • Quit
  • Edit
  • Display
    • Bonds
    • H-Bonds
    • Atoms
    • Worms
    • CA-trace
    • Surfaces
    • Surface area dots
    • 2D Contours
    • 3D Contours
    • Density maps
    • Axes
    • Helices
    • Sheets
    • DNA spokes
    • Labels and Annotations
    • Unit cell
    • Interactions
    • External objects
    • Spectra
    • Bones
    • None
  • Alter
    • Bonds
    • Atoms
    • Worms
    • CA trace
    • Surfaces
      • Constructive Solid Geometry
    • Contours
    • Density maps
      • Density Contours 1-8
      • Update maps
      • Make 3D contour object
      • Current map
      • Delete map
      • Delete all maps
      • Clone map
      • Make positive/negative mask
      • Make positive binary map
      • Make negative binary map
      • Make pseudo density map
      • Orthogonalize map
      • Wide lines
    • Helices
    • Sheets
    • DNA spokes
    • Labels
    • Interactions
    • Spectra
  • View
  • Calculate
    • Distance
    • Properties
      • Math on One property:
      • Math on Two Properties:
      • Map Atom Property to Surface:
      • Per-residue calculations:
      • Sliding-calculations:
      • Enter new Selection String:
    • Surface Area
      • Atom-based areas and volumes
      • Surface-based areas and volumes
    • Electrostatics
    • Atom-based mass
    • Residue-based mass
    • Radius of gyration
    • RMS deviation
    • Center of coordinates
    • Center of mass
  • Modeling
    • Sort atoms
    • Superimpose
    • Undo superimpose
    • Delete Atoms
    • Copy Atoms
    • Secondary structure editor
    • Calculate Secondary Structure
    • Run DSSP
    • Amber interface
    • Hydrogen bonding
      • Delete All H-Bonds
    • Matrix/symmetry operations
      • Fractionalize coordinates
      • Unfractionalize coordinates
      • Edit crystal parameters
      • Apply 4x4 matrix
      • Display symmetry
      • Color by number
      • Realize symmetry molecules
    • Rotamer control
    • Structure Editing
    • Mutate to
    • Undo last mutation
    • Undo TOR
    • Lock TOR
    • Undo FBRT
    • Lock FBRT
  • Subsets
  • Picking
    • Identify object
    • Helix/Sheet Information
    • Labels
    • Interactions
    • Modeling
  • Macros
    • Default macros
    • Macro packages
  • Graphics
    • Viewpoint
      • Reset View
      • Reset Rotations
      • Center
      • Center on selection
      • Center on coordinates
      • Center on cell
      • Undo last orientation change
    • Scene antialiasing
      • Antialias scene
      • Antialias level
    • Graphics parameters
      • Graphics modes
      • Stereo
      • Mouse Bindings
      • Viewing matrices
    • Coloring
      • Clip Tool
      • Material Tool
      • Light Tool
    • Tie faces
      • Fake dial box
      • Customize Dial Box
  • Help
• History / Command Files
  • Flow Control in Command Files
    • Conditionals -- if..then/else/endif
    • Loops -- LOOP/ENDL
    • Subroutines -- SUB/ENDS/CALL
    • Branches -- TAG/GOTO
    • Execution control -- WAIT/STOP/pause
  • 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
  • Subsets
  • Modeling
  • Secondary structure
  • Superimposing structures
• Acknowledgments
• References
• 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
    • File indirection.
    • Example.
  • Rotamer library
  • Atom order library
• Disclaimer
• Index