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Contents
The SPOCK Program Manual
by Jon A. Christopher
SPOCK: The Structural Properties Observation and Calculation Kit
Jon A. Christopher
SPOCK: The Structural Properties Observation and Calculation Kit
Copyright 2004, Jon A. Chistopher
jchrist@hotpop.com
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:
CCP4 map file:
Bones file:
Save
Session File:
View File:
PDB File:
Preferences File:
Macros:
History:
PhiMap File:
Charge File:
Radius File:
Molscript:
Raster3D:
Image:
VRML 1.0 and VRML 2.0:
Interactions File:
XPLOR map file:
CCP4 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
Map tool
Update maps
Make 3D contour object
Auto-normalize maps
Normalize map
Delete map
Delete all maps
Clone map
Mask drawing
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
Select symmetry replicates
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
Tools
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
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
File indirection.
Example.
Rotamer library
Atom order library
Disclaimer
Index
Jon Christopher
2004-02-19
