The VMD User's Guide describes how to run and use the molecular visualization and analysis program VMD. This guide documents the user interfaces displaying and grapically manipulating molecules, and describes how to use the scripting interfaces for analysis and to customize the behavior of VMD.

• Contents
• List of Figures
• List of Tables
• Introduction
  • For information on our other software
  • Contacting the authors
  • Registering VMD
  • Citation Reference
  • Acknowledgments
  • Copyright and Disclaimer Notices
• 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
  • Notes on common molecular file formats
  • What happens when a file is loaded?
  • Babel interface
  • Raster3D file format
• User Interface Components
  • Using the Mouse in the Graphics Window
    • Mouse Modes
    • Pick Modes
    • Hot Keys
  • Using the Spaceball in the Graphics Window
    • Spaceball Driver
  • Using the Joystick in the Graphics Window
  • Description of each VMD form
    • Main Form
      • Help
    • Main Form Molecule List browser
      • Changing the Molecule's Status
      • Saving Trajectory Frames
      • Deleting Trajectory Frames
      • Deleting a Molecule
      • GUI Shortcuts
    • Main Form Animation Controls
      • Animation Speed
      • Jumping to Specific Frames
      • Looping Styles
    • Molecule File Browser Form
      • Reading Trajectory Frames
    • Mouse Menu
      • Mouse modes
      • Pick modes
    • Display Menu
    • Graphics Form
      • Draw Style Tab
      • Selections Tab
      • Trajectory Tab
      • Periodic Tab
    • Labels Form
      • Label categories
      • Modifying or deleting a label
      • Pick information
      • Plotting a label's value
    • Color Form
      • Changing the RGB Value of a Color
      • Color Scale
    • Material Form
    • Render Form
    • Tool Form
      • Configuring input devices
      • Using Tools
    • Simulation Form
      • Interactive Molecular Dynamics
      • IMD Using the Sim form
    • Sequence Form
      • Sequence information
      • Selecting residues from the Sequence form listing
      • Selecting residues by clicking on the 3-D structure
      • Sequence Zooming
      • Turn off highlighting / Change highlight style
      • Caveats
    • RamaPlot
      • Using RamaPlot
• Molecular Drawing Methods
  • Rendering methods
    • Lines
    • Bonds
    • DynamicBonds
    • HBonds
    • Points
    • VDW
    • CPK
    • Licorice
    • Tube
    • Trace
    • Ribbons
    • NewRibbons
    • Cartoon
    • Surf
    • MSMS
    • VolumeSlice
    • Isosurface
    • Dotted
    • Solvent
  • Coloring Methods
    • Color categories
    • Coloring Methods
    • Coloring by color categories
    • Color scale
    • Materials
  • 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
      • sequence
      • within and same
      • Finding contact residues
• Viewing Modes
  • Perspective/Orthographic views
  • Monoscopic Modes
  • Stereoscopic Modes
    • Side-By-Side and Cross-Eyed Stereo
    • DTI Side-by-side Stereo
    • Scanline Interleaved Stereo
    • Anaglyph Stereo
    • CrystalEyes Stereo
    • Stereo Parameters
• Scene Export and Rendering
  • Screen Capture Using Snapshot
  • Higher Quality Rendering
  • Caveats
  • One Step Printing
  • Making Stereo Images
  • Making a Movie
• Tcl Text Interface
  • Using text commands
  • Tcl/Tk
  • Tcl Text Commands
    • animate
    • atomselect
    • axes
    • color
    • colorinfo
    • display
    • draw
    • exit
    • graphics
    • help
    • imd
    • label
    • light
    • logfile
    • material
    • measure
    • menu
    • mol
    • molecule
    • molinfo
    • 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
  • Python modules 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
    • vmdnumpy
  • High-level Python Interface
    • Molecule
    • MoleculeRep
    • Draw Style Methods
    • Saving and Restoring Molecule State
• Vectors and Matrices
  • Vectors
  • Matrix routines
  • Multiplying vectors and matrices
  • Misc. functions and values
• Molecular Analysis
  • Using the molinfo command
  • Using the atomselect command
  • Analysis scripts
  • RMS Fit and Alignment
    • RMS Fit and Alignment Extension
      • RMSD calculation
      • RMS Alignment
    • RMS and scripting
      • RMSD Computation
      • Computing the Alignment
      • A simulation example script
  • 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
• Customizing VMD Sessions
  • VMD Command-Line Options
  • Environment Variables
  • Startup Files
    • Core Script Files
    • User Script Files
    • .vmdrc and vmd.rc Files
  • Using VMD as a WWW Client (for chemical/* documents)
    • MIME types
      • Helper Applications
    • Setting up your .mailcap
    • Example sites
• Index
• About this document ...