Contents

• Contents
• List of Figures
• List of Tables
• Introduction
  • For more information on BioCoRE, MDTools, NAMD, and VMD
  • Contacting the authors
  • Credits and Program Reference
  • Copyright and Disclaimer
  • Registering VMD
  • Acknowledgments
• Tutorials
  • Rapid Introduction to VMD
  • Viewing a molecule: Myoglobin
  • Rendering an Image
  • A Quick Animation
  • An Introduction to Atom Selection
  • Comparing Two Structures
  • Some Nice Represenations
  • Saving your work
• Loading A Molecule
  • Babel interface
  • What happens when a file is loaded?
  • Raster3D file format
  • Raster3D Caveats
• User Interface Components
  • Using the Mouse in the Graphics Window
    • Mouse Modes
    • Pick Item Mode
    • Hot Keys
  • Description of each VMD form
    • Main Form
    • Mouse Form
    • Molecules (Mol) Form
    • Canceling a Load of a Coordinate File
    • Files Form
    • Graphics Form
    • Animate Form
    • Edit Animation Form
    • Labels Form
    • Display Form
    • Color Form
    • Material Form
    • Render Form
    • Tracker Form
    • Sim Form
• Molecular Drawing Methods
  • Rendering methods
    • Lines
    • Bonds
    • CPK
    • Points
    • VDW
    • Dotted
    • Solvent
    • Tube
    • Trace
    • Licorice
    • Ribbon
    • Surf
    • Cartoon
    • MSMS
    • HBonds
    • Off
  • Coloring Methods
    • Color categories
    • Coloring Methods
    • Coloring by color categories
    • Color scale
    • Materials
    • VMD Script Commands for Colors
    • Changing the color scale definitions
    • Creating a set of black-and-white color definitions
    • Revert all RGB values to defaults
    • Coloring Trick - Override a Coloring Category
  • Selection Methods
    • Definition of Keywords and Functions
    • Boolean Keywords
    • Short Circuiting
    • Quoting with Single Quotes
    • Double Quotes and Regular Expressions
    • Comparison selections
    • Comparison Operators
    • Other selections
• Rendering to Raster Image Files
  • Screen Capture Using Snapshot
  • Higher Quality Rendering
  • Known Problems
  • One Step Printing
  • Making a Movie
• Viewing Modes
  • Perspective/Orthographic views
  • Monoscopic Modes
  • Stereoscopic Modes
    • Side-By-Side and Cross-Eyed Stereo
    • Anaglyph Stereo
    • CrystalEyes Stereo
    • Problems with stereo on some SGI machines
    • Stereo Parameters
  • Making Stereo Raster Images
• Text User Interface
  • Using text commands
  • Tcl/Tk
  • Core Text Commands
    • animate
    • axes
    • color
    • colorinfo
    • debug
    • display
    • echo
    • exit
    • help
    • imd
    • label
    • light
    • logfile
    • material
    • menu
    • mol
    • molecule
    • mouse
    • play
    • quit
    • render
    • rock
    • rotate
    • scale
    • stage
    • tool
    • translate
    • user
    • vmdinfo
    • wait
    • sleep
  • Tcl callbacks
• Python Text Interface
  • Using the Python interpreter within VMD
  • Atom selections in Python
    • An atom selection example
    • Changing the selection and the frame
    • Combining atom selections
  • Python callbacks
    • Using Tkinter menus in VMD
  • Controlling VMD from Python
    • animate
    • axes
    • color
    • display
    • graphics
    • imd
    • label
    • material
    • molecule
    • molrep
    • render
    • trans
• Vectors and Matrices
  • Vectors
  • Matrix routines
  • Multiplying vectors and matrices
  • Misc. functions and values
• User-Defined Graphics
  • Introduction
  • Tutorials and Examples
    • Drawing a graph
    • Triangles
    • Draw a surface plot
    • Drawing a box around a molecule
    • Adding a label
    • Interface to picking
    • Animation
  • Graphics
  • Draw and Drawing Extensions
• Molecular information: molinfo and atomselect
  • molinfo
    • Using molinfo to access the molecule list
    • Using molinfo to access information about a molecule
  • Atom information
  • Analysis scripts
• Interactive Molecular Dynamics
  • How the Connection Works
• RMS Fit and Alignment
  • Fit and Alignment Menus
    • RMSD Calculator
    • RMS Alignment
  • RMS and scripting
    • RMSD Computation
    • Computing the Alignment
    • A simulation example script
• Customizing VMD Sessions
  • VMD Windows Command-Line Options
  • VMD Unix Command-Line Options
  • Environment Variables
  • Startup Files
    • Core Script Files
    • User Script Files
    • .vmdrc File
  • Using VMD as a WWW Client (for chemical/* documents)
    • MIME types
    • Setting up your .mailcap
    • Example sites
• Future Plans
• Index
• About this document ...