Contents

 
• List of Figures
• List of Tables
• Introduction
  • For more information on VMD and MDScope
  • 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
• User Interface Components
  • Using the Mouse in the Graphics Window
    • The Popup Menu
      • Mouse Mode Submenu
      • Pick Item Mode Submenu
      • Display Modes Submenu
      • Fit Submenu
      • Labels Submenu
      • Animate Scene Submenu
      • Spin/Rock Scene Submenu
      • Stop Rotation
      • Reset View
      • Show Form Submenu
      • Hide Form Submenu
      • Help
      • Quit Submenu
      • Play File
      • Save Config
    • Atom/Molecule Specific Popup Menu
      • Center
      • Pick
      • Info
      • Mol Status
      • Atom Selection
      • Rendering Method
      • Coloring Method
    • Delete Representation
    • Hot Keys
  • Using the Forms library
    • Buttons
    • Sliders
    • Choosers
    • Text Entry Areas
    • Browsers
    • File Browser
  • Description of each VMD form
    • Main Form
    • Molecules (Mol) Form
      • Loading a New Molecule
      • The Molecule List browser
      • Changing the Molecule's Status
      • Deleting a Molecule
    • Files Form
    • Graphics Form
      • Image Controls
      • Atom Name Lists
      • Changing Views
    • Animate Form
      • Animation Speed
      • Jumping to Specific Frames
      • Looping Styles
    • Edit Animation Form
      • Reading Frames
      • Writing Frames
      • Deleting Frames
      • Amount Chooser
    • Labels Form
      • Label categories
      • Modifying or deleting a label
      • Plotting a label's value
    • Display Form
    • Color Form
      • Changing the RGB Value of a Color
      • Color Scale
    • Render Form
      • Rendering
      • Caution
    • Tracker Form
      • Trackers
      • Tools
    • Remote Form
      • Establishing a Connection
      • Starting a New Simulation
      • Once a Connection is Made
    • Sim Form
      • Modifiable Parameters
  • Other User Interfaces
    • External Interfaces
• Loading A Molecule
  • Babel interface
  • What happens when a file is loaded?
  • Raster3D file format
  • Raster3D Caveats
• Molecular Drawing Methods
  • Lines
  • Bonds
  • CPK
  • Points
  • VDW
  • Dotted
  • Solvent
  • Tube
  • Trace
  • Licorice
  • Ribbon
  • Surf
  • Cartoon
  • MSMS
  • HBonds
  • Off
• Coloring Molecules and Objects
  • Color categories
  • Coloring Methods
    • Coloring by color categories
    • Color scale
  • Transparency
  • VMD Script Commands for Colors
    • Adjusting the degree of transparency
    • Changing the color scale definitions
    • Creating a set of black-and-white color definitions
    • Revert all RGB values to defaults
    • Setting the transparent colors according to solid
    • Making the molecule to show up slowly
    • Querying VMD for Color Information
• VMD Atom Selection Language
  • Definition of Keywords and Functions
  • Boolean Keywords
  • Short Circuiting
  • Quoting with Single Quotes
  • Double Quotes and Regular Expressions
  • Comparison selections
  • Comparison Operators
  • Other selections
    • sequence
    • within and same
    • annmm
  • Referencing Tcl data
    • $references
    • @references
    • The differences
• Creating Output Raster Images
  • Creating an Output Image File
  • Known Problems
  • One Step Printing
• Viewing Modes
  • Perspective/Orthographic views
  • Monoscopic Modes
  • Stereoscopic Modes
    • Side-By-Side and Cross-Eyed Stereo
    • Crystal Eyes Stereo
      • Stereo in a window (aka new-style stereo):
      • Regular stereo mode:
    • Problems with stereo on Indigo2 machines
    • Stereo Parameters
  • Making Stereo Raster Images
• Interactive Molecular Dynamics Display Using MDComm
  • How the Connection Works
  • Installing VMD Remote Connection Components
  • Installing NAMD Remote Connection Components
  • When Problems Occur
• Text User Interface
  • Using text commands
  • Tcl/Tk
  • Core Text Commands
    • animate
    • axes
    • color
    • colorinfo
    • debug
    • display
    • echo
    • exit
    • external
    • help
    • label
    • light
    • logfile
    • menu
    • mol
    • molecule
    • mouse
    • play
    • quit
    • remote
    • render
    • rock
    • rotate
    • scale
    • sim
    • simulation
    • stage
    • tracker
    • translate
    • user
    • vmdlog
    • vmdinfo
    • wait
    • sleep
• 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
• Tips and Tricks
  • Customizing the Popup Menu and the Hot Keys
    • Customizing the popup menu
    • Customizing the Hot Keys
    • Automatically loading customization commands
  • Using VMD as a WWW Client (for chemical/* documents)
    • MIME types
      • Helper Applications
    • Setting up your .mailcap
    • Example sites
  • Making a Movie
  • Coloring Trick - Override a Coloring Category
  • Some Nice Represenations
  • Finding Contact Residues
  • Tcl Logging
  • Remote Control of VMD
  • Controlling One VMD With Another
• Advanced Script Writing
  • Drawing a distance matrix
  • Analysis of PDB files
  • save/load VMD state information
  • Currently picked molecule/atom
  • Trace on the pick variables
    • Information about the picked atom
    • Making a sphere appear when an atom is picked
    • Drawing a line from the eye to the picked atom
  • Trajectory frames
    • Animating the secondary structure
    • Viewing selections which change during an animation
    • Simulation frames
  • RMSD and best-fit alignments
    • RMSD Computation
    • Computing the Alignment
    • A simulation example script
• Customizing VMD Sessions
  • Command-Line Options
  • Environment Variables
  • Startup Files
    • Core Script Files
    • User Script Files
    • .vmd_init File
    • .vmdrc File
• Future Plans
• Index
• About this document ...