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Contents
List of Figures
List of Tables
Introduction
For more information on VMD and MDScope
Contacting the authors
Credits and program reference
Registering VMD
Acknowledgements
Disclaimer
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
General Help
Specific Help Submenu
Quit Submenu
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
3D
External Interfaces
Using the remote commands
Speech
Gesture
Other Uses
Loading A Molecule
Babel interface
What happens when a file is loaded?
Raster3D file format
Raster3D Caveats
Molecular Drawing Methods
Lines
Bonds
Points
VDW
Dotted
CPK
Licorice
Tube
Ribbon
Alpha Shape
Surf
Cartoon
HBonds
None
Coloring Molecules and Objects
Molecular Coloring Methods
Coloring by Coloring Categories
Color Scale
Transparency
VMD Atom Selection Language
Boolean Keywords
Short Circuiting
Definition of Keywords and Functions
Quoting
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
Viewing Modes
Perspective/Orthographic views
Monoscopic Modes
Stereoscopic Modes
Side-By-Side Stereo
Crystal Eyes Stereo
Stereo in a window (aka new-style stereo):
Regular stereo mode:
Problems with stereo in Indigo 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
Core Text Commands
animate
axes
color
debug
display
echo
exit
external
help
journal
label
light
log
menu
mol
molecule
mouse
play
quit
remote
render
rock
rot
rotate
rotation
run
scale
sim
simulation
stage
stop
tracker
trans
translate
user
vmdlog
vmdinfo
wait
Vectors and Matricies
Vectors
Matrix routines
Multiplying vectors and matrices
Misc. functions and values
What's missing
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
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 ...
Andrew Dalke
Tue May 14 16:49:45 CDT 1996