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VMD User's Guide
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VMD User's Guide
 
Index
Contents
Contents
List of Figures
List of Tables
Introduction
For more information on VMD, NAMD, and BioCoRE
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
Mouse Modes
Pick Item Mode
Hot Keys
Using the graphical interface components
Buttons
Sliders
Choosers
Text Entry Areas
Browsers
File Browser
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
Other User 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
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
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
Referencing Tcl data
$references
@references
The differences
Rendering to Raster Image Files
Screen Capture Using Snapshot
Higher Quality Rendering
Known Problems
One Step Printing
Viewing Modes
Perspective/Orthographic views
Monoscopic Modes
Stereoscopic Modes
Side-By-Side and Cross-Eyed Stereo
Crystal Eyes Stereo
Problems with stereo on Indigo2 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
external
help
imd
label
light
logfile
material
menu
mol
molecule
mouse
play
quit
imd
render
rock
rotate
scale
sim
simulation
stage
tool
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 Hot Keys
Customizing the Hot Keys
Automatically loading customization commands
Using VMD as a WWW Client (for chemical/* documents)
MIME types
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
Interactive Molecular Dynamics
How the Connection Works
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
VMD Windows Command-Line Options
VMD Unix Command-Line Options
Environment Variables
Startup Files
Core Script Files
User Script Files
.vmdrc
File
Future Plans
Index
About this document ...
vmd@ks.uiuc.edu