VMD User's Guide - Draft version

A. Dalke, W. Humphrey, S. Izrailev, J. Ulrich

Version 1.2b2

July 25, 1997

Theoretical Biophysics Group
University of Illinois and Beckman Institute
405 N. Mathews
Urbana, IL 61801
VMD WWW home page: http://www.ks.uiuc.edu/Research/vmd/

Description

The VMD User's Guide - Draft version describes how to run and use the molecular visualization and analysis program VMD . This guide documents the usage of both the graphical user interface and the text console interface for displaying and grapically manipulating molecules, and describes how to customize the appearance and behavior of VMD for each user.

 
• Contents
• List of Figures
• List of Tables
• 1 Introduction
  • 1.1 For more information on VMD and MDScope
  • 1.2 Contacting the authors
  • 1.3 Credits and program reference
  • 1.4 Registering VMD
  • 1.5 Acknowledgments
  • 1.6 Disclaimer
• 2 Tutorials
  • 2.1 Rapid Introduction to VMD
  • 2.2 Viewing a molecule: Myoglobin
  • 2.3 Rendering an Image
  • 2.4 A Quick Animation
  • 2.5 An Introduction to Atom Selection
  • 2.6 Comparing Two Structures
• 3 User Interface Components
  • 3.1 Using the Mouse in the Graphics Window
    • 3.1.1 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
    • 3.1.2 Atom/Molecule Specific Popup Menu
      • Center
      • Pick
      • Info
    • 3.1.3 Mol Status
    • 3.1.4 Atom Selection
    • 3.1.5 Rendering Method
    • 3.1.6 Coloring Method
    • 3.1.7 Delete Rep.
    • 3.1.8 Hot Keys
  • 3.2 Using the Forms library
    • 3.2.1 Buttons
    • 3.2.2 Sliders
    • 3.2.3 Choosers
    • 3.2.4 Text Entry Areas
    • 3.2.5 Browsers
    • 3.2.6 File Browser
  • 3.3 Description of each VMD form
    • 3.3.1 Main Form
    • 3.3.2 Molecules (Mol) Form
      • Loading a New Molecule
      • The Molecule List browser
      • Changing the Molecule's Status
      • Deleting a Molecule
    • 3.3.3 Files Form
    • 3.3.4 Graphics Form
      • Image Controls
      • Atom Name Lists
      • Changing Views
    • 3.3.5 Animate Form
      • Animation Speed
      • Jumping to Specific Frames
      • Looping Styles
    • 3.3.6 Edit Animation Form
      • Reading Frames
      • Writing Frames
      • Deleting Frames
      • Amount Chooser
    • 3.3.7 Labels Form
      • Label categories
      • Modifying or deleting a label
      • Plotting a label's value
    • 3.3.8 Display Form
    • 3.3.9 Color Form
      • Changing the RGB Value of a Color
      • Color Scale
    • 3.3.10 Render Form
      • Rendering
      • Caution
    • 3.3.11 Tracker Form
      • Trackers
      • Tools
    • 3.3.12 Remote Form
      • Establishing a Connection
      • Starting a New Simulation
      • Once a Connection is Made
    • 3.3.13 Sim Form
      • Modifiable Parameters
  • 3.4 Other User Interfaces
    • 3.4.1 3D
    • 3.4.2 External Interfaces
    • 3.4.3 Using the remote commands
    • 3.4.4 Speech
    • 3.4.5 Gesture
    • 3.4.6 Other Uses
• 4 Loading A Molecule
  • 4.1 Babel interface
  • 4.2 What happens when a file is loaded?
  • 4.3 Raster3D file format
  • 4.4 Raster3D Caveats
• 5 Molecular Drawing Methods
  • 5.1 Lines
  • 5.2 Bonds
  • 5.3 CPK
  • 5.4 Points
  • 5.5 VDW
  • 5.6 Dotted
  • 5.7 Solvent
  • 5.8 Tube
  • 5.9 Trace
  • 5.10 Licorice
  • 5.11 Ribbon
  • 5.12 Surf
  • 5.13 Cartoon
  • 5.14 MSMS
  • 5.15 HBonds
  • 5.16 Off
• 6 Coloring Molecules and Objects
  • 6.1 Color categories
  • 6.2 Coloring Methods
    • 6.2.1 Coloring by color categories
    • 6.2.2 Color scale
  • 6.3 Transparency
  • 6.4 VMD Script Commands for Colors
    • 6.4.1 Adjusting the degree of transparency
    • 6.4.2 Changing the color scale definitions
    • 6.4.3 Creating a set of black-and-white color definitions
    • 6.4.4 Revert all RGB values to defaults
    • 6.4.5 Setting the transparent colors according to solid
    • 6.4.6 Making the molecule to show up slowly
    • 6.4.7 Querying VMD for Color Information
• 7 VMD Atom Selection Language
  • 7.1 Definition of Keywords and Functions
  • 7.2 Boolean Keywords
  • 7.3 Short Circuiting
  • 7.4 Quoting with Single Quotes
  • 7.5 Double Quotes and Regular Expressions
  • 7.6 Comparison selections
  • 7.7 Comparison Operators
  • 7.8 Other selections
    • 7.8.1 sequence
    • 7.8.2 within and same
    • 7.8.3 annmm
  • 7.9 Referencing Tcl data
    • 7.9.1 $references
    • 7.9.2 @references
    • 7.9.3 The differences
• 8 Creating Output Raster Images
  • 8.1 Creating an Output Image File
  • 8.2 Known Problems
  • 8.3 One Step Printing
• 9 Viewing Modes
  • 9.1 Perspective/Orthographic views
  • 9.2 Monoscopic Modes
  • 9.3 Stereoscopic Modes
    • 9.3.1 Side-By-Side and Cross-Eyed Stereo
    • 9.3.2 Crystal Eyes Stereo
      • Stereo in a window (aka new-style stereo):
      • Regular stereo mode:
    • 9.3.3 Problems with stereo on Indigo2 machines
    • 9.3.4 Stereo Parameters
  • 9.4 Making Stereo Raster Images
• 10 Interactive Molecular Dynamics Display Using MDComm
  • 10.1 How the Connection Works
  • 10.2 Installing VMD Remote Connection Components
  • 10.3 Installing NAMD Remote Connection Components
  • 10.4 When Problems Occur
• 11 Text User Interface
  • 11.1 Using text commands
  • 11.2 Tcl/Tk
  • 11.3 Core Text Commands
    • 11.3.1 animate
    • 11.3.2 axes
    • 11.3.3 color
    • 11.3.4 colorinfo
    • 11.3.5 debug
    • 11.3.6 display
    • 11.3.7 echo
    • 11.3.8 exit
    • 11.3.9 external
    • 11.3.10 help
    • 11.3.11 label
    • 11.3.12 light
    • 11.3.13 logfile
    • 11.3.14 menu
    • 11.3.15 mol
    • 11.3.16 molecule
    • 11.3.17 mouse
    • 11.3.18 play
    • 11.3.19 quit
    • 11.3.20 remote
    • 11.3.21 render
    • 11.3.22 rock
    • 11.3.23 rotate
    • 11.3.24 scale
    • 11.3.25 sim
    • 11.3.26 simulation
    • 11.3.27 stage
    • 11.3.28 tracker
    • 11.3.29 translate
    • 11.3.30 user
    • 11.3.31 vmdlog
    • 11.3.32 vmdinfo
    • 11.3.33 wait
• 12 Vectors and Matrices
  • 12.1 Vectors
  • 12.2 Matrix routines
  • 12.3 Multiplying vectors and matrices
  • 12.4 Misc. functions and values
    • What's missing
• 13 User-Defined Graphics
  • 13.1 Introduction
  • 13.2 Tutorials and Examples
    • 13.2.1 Drawing a graph
    • 13.2.2 Triangles
    • 13.2.3 Draw a surface plot
    • 13.2.4 Drawing a box around a molecule
    • 13.2.5 Adding a label
    • 13.2.6 Interface to picking
    • 13.2.7 Animation
  • 13.3 Graphics
  • 13.4 Draw and Drawing Extensions
• 14 Molecular information: molinfo and atomselect
  • 14.1 molinfo
    • 14.1.1 Using molinfo to access the molecule list
    • 14.1.2 Using molinfo to access information about a molecule
  • 14.2 Atom information
  • 14.3 Analysis scripts
• 15 Tips and Tricks
  • 15.1 Customizing the Popup Menu and the Hot Keys
    • 15.1.1 Customizing the popup menu
    • 15.1.2 Customizing the Hot Keys
    • 15.1.3 Automatically loading customization commands
  • 15.2 Using VMD as a WWW Client (for chemical/* documents)
    • 15.2.1 MIME types
      • Helper Applications
    • 15.2.2 Setting up your .mailcap
    • 15.2.3 Example sites
  • 15.3 Making a Movie
  • 15.4 Coloring Trick - Override a Coloring Category
  • 15.5 Some Nice Represenations
  • 15.6 Finding Contact Residues
  • 15.7 Tcl Logging
  • 15.8 Remote Control of VMD
  • 15.9 Controlling One VMD With Another
• 16 Advanced Script Writing
  • 16.1 Drawing a distance matrix
  • 16.2 Analysis of PDB files
  • 16.3 save/load VMD state information
  • 16.4 Currently picked molecule/atom
  • 16.5 Trace on the pick variables
    • 16.5.1 Information about the picked atom
    • 16.5.2 Making a sphere appear when an atom is picked
    • 16.5.3 Drawing a line from the eye to the picked atom
  • 16.6 Trajectory frames
    • 16.6.1 Animating the secondary structure
    • 16.6.2 Viewing selections which change during an animation
    • 16.6.3 Simulation frames
  • 16.7 RMSD and best-fit alignments
    • 16.7.1 RMSD Computation
    • 16.7.2 Computing the Alignment
    • 16.7.3 A simulation example script
• 17 Customizing VMD Sessions
  • 17.1 Command-Line Options
  • 17.2 Environment Variables
  • 17.3 Startup Files
    • 17.3.1 Core Script Files
    • 17.3.2 User Script Files
    • 17.3.3 .vmd_init File
    • 17.3.4 .vmdrc File
• 18 Future Plans
• Index
• About this document ...