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Index

.vmdrc
Hot Keys
.vmdrc
.vmdrc and vmd.rc Files
vmd.rc
.vmdrc and vmd.rc Files
.mailcap
Setting up your .mailcap
.vmdsensors
Configuring input devices
.vmdrc
Using text commands
vmd.rc
Using text commands
ACTC
Copyright and Disclaimer Notices
AMBER
files
Loading A Molecule | Reading Trajectory Frames
analysis
scripting
Using the atomselect command
speed
Using the atomselect command
angles
Label categories
animate
command
Tcl Text Commands | Tcl Text Commands
form
Main Form Animation Controls
Python module
animate
animation
A Quick Animation
appending
Reading Trajectory Frames
delete
Deleting Trajectory Frames | animate | animate
duplicate frame
animate
frames
Reading Trajectory Frames
goto end
animate
goto start
animate
hot keys
Hot Keys
jump
Jumping to Specific Frames | animate
movie
Making a Movie
play
animate
read
Reading Trajectory Frames | animate
smoothing
Trajectory Smoothing. | mol | molrep
speed
Animation Speed | animate
step
Animation Speed
style
animate
loop
Looping Styles
once
Looping Styles
rock
Looping Styles
write
Saving Trajectory Frames | animate
antialiasing
Display Menu | display
atom
changing properties
Using the atomselect command
color
auto-update
mol
coordinates
rotate | scale | translate
changing
Comparing Two Structures | Using the atomselect command
min and max
Coordinate min and max
info
atomselect | Using the atomselect command
name lists
Selections Tab | Selections Tab
picking
Comparing Two Structures
selection
Viewing a molecule: Myoglobin | An Introduction to Atom | Molecular Drawing Methods | Selection Methods | atomselect | Using the atomselect command
auto-update
mol
changing properties
An atom selection example
comparison
Comparison selections
default
mol
examples
An Introduction to Atom | Selection Methods
keywords
Selections Tab | Selection Methods | Definition of Keywords and | Definition of Keywords and
logic
Short Circuiting
macros
Selections Tab | atomselect | The AtomSel class (DEPRECATED)
math functions
Definition of Keywords and
modes
Selection Methods
Python
Atom selections in Python
macros
The AtomSel class (DEPRECATED)
quoting
Quoting with Single Quotes
regular expression
Double Quotes and Regular
same
within and same
sequence
sequence
Tcl
macros
atomselect
text
Using the atomselect command
update
Finding waters near a
volumetric data
Definition of Keywords and
within
within and same
atoms
distance between
Comparing Two Structures
plotting
Plotting a label's value
atomselect
command
Tcl Text Commands | animate | Molecular Analysis | Using the atomselect command
axes
Display Menu
command
Tcl Text Commands | atomselect
Python module
axes
Babel
Babel interface
backface culling
Display Menu
batch mode
VMD Command-Line Options
beta values
Root mean square deviation
BioCoRE
For information on our
bonds
add or remove
Mouse Modes
determining
What happens when a
label
Label categories | Label categories
resolution
Bonds
unusual
What happens when a
cachemode
Display Menu
callbacks
Python
Python callbacks
Tcl
Tcl callbacks | Tcl callbacks
center of mass
Using the atomselect command
CHARMM
files
Loading A Molecule | Reading Trajectory Frames
chemical2vmd
Setting up your .mailcap
clipping planes
Display Menu
user defined
mol
color
access definitions
colorinfo
assignment
Comparing Two Structures
background
Color Form
category
Color Form | Color categories | Color categories | Coloring by color categories | colorinfo | Coloring Trick - Override
command
Coloring Methods | Tcl Text Commands | axes
form
Comparing Two Structures | Color Form | Coloring Methods | Color categories | Coloring by color categories
id
Draw Style Tab | Coloring Methods
in user-defined graphics
graphics
index
colorinfo
map
Color Form
material properties
graphics | graphics
names
Coloring Methods | colorinfo
properties
colorinfo
Python module
color
redefinition
Changing the RGB Value | Creating a set of
revert to default
Revert all RGB values
scale
Color Scale | Color scale | Color scale | color | Changing the color scale
changing
Color Scale
set minmax
mol | molrep
color map
Color categories
colorinfo
command
Tcl Text Commands | colorinfo
coloring
by category
Coloring by color categories
by color scale
Color scale | Color scale
by property
Coloring Trick - Override
methods
Viewing a molecule: Myoglobin | Graphics Form | Molecular Drawing Methods | Coloring Methods | Coloring Methods | Coloring Methods | mol | mol | Coloring Trick - Override
Command line options
VMD Command-Line Options
contact residues
Finding contact residues
copyright
Copyright and Disclaimer Notices
Coulomb potential
volumetric data
volmap
culling
display
debug
command
Tcl Text Commands
density
volumetric data
volmap
depth cue
display
depth cueing
Display Menu
display
command
Tcl Text Commands | colorinfo
device
VMD Command-Line Options
form
Display Menu
Python module
display
update
display | Using the molinfo command | Creating a set of | Revert all RGB values
distance
volumetric data
volmap
distance between atoms
Comparing Two Structures
draw
command
draw
drawing
method
Viewing a molecule: Myoglobin | Graphics Form
drawn
Main Form Molecule List
electrostatics
volumetric data
volmap
environment variables
Environment Variables
DISPLAY
Environment Variables
MSMSSERVER
MSMS
SURF_BIN
Surf
TCL_LIBRARY
Core Script Files
VMD_EXCL_GL_EXTENSIONS
Environment Variables
VMDBABELBIN
Babel interface | Environment Variables
VMDCAVEMEM
Environment Variables
VMDCUSTOMIZESTARTUP
Environment Variables
VMDDIR
Environment Variables
VMDFILECHOOSER
Environment Variables
VMDFORCECONSOLETTY
Environment Variables
VMDFORCECPUCOUNT
Environment Variables
VMDFREEVRMEM
Environment Variables
VMDGDISPLAY
Environment Variables
VMDGLSLVERBOSE
Environment Variables
VMDHTMLVIEWER
Environment Variables
VMDIMAGEVIEWER
Environment Variables
VMDIMMERSADESKFLIP
Environment Variables
VMDMSECDELAYHACK
Environment Variables
VMDMSMSUSEFILE
Environment Variables
VMDPREFERSTEREO
Environment Variables
VMDSCRDIST
Environment Variables
VMDSCRHEIGHT
Environment Variables
VMDSCRPOS
Environment Variables
VMDSCRSIZE
Environment Variables
VMDSHEARSTEREO
Environment Variables
VMDSIMPLEGRAPHICS
Environment Variables
VMDSPACEBALLPORT
Spaceball Driver
VMDTMPDIR
Environment Variables
VMDVMDMACENABLEEEXTENSIONS
Environment Variables
VMDWIREGL
Environment Variables
example scripts
Python
calculation
atom selections
Changing the selection and
changing properties of a selection
An atom selection example
combining atom selections
Combining atom selections
loading molecules
Molecule
RMSD
RMS example
callbacks
Python callbacks
drawing
creating representations
MoleculeRep
Tcl
calculation
center of mass of a selection
Using the atomselect command
geometric center of a selection
Using the atomselect command
mass of a picked atom
Tcl callbacks
matrix transformations
Matrix routines
min and max atom coordinates
Coordinate min and max
move selected atoms
Using the atomselect command
radius of gyration
Radius of gyration
RMSD between two frames
Root mean square deviation
RMSD for all trajectory frames
A simulation example script
total mass of a selection
Total mass of a
customized startup file example
.vmdrc and vmd.rc Files
drawing
arrows
draw
changing color scales
Changing the color scale
coloring by distance
Root mean square deviation
defining grayscale colors
Creating a set of
labels
draw
rendering stereo pairs
Making Stereo Images
reverting colors to defaults
Revert all RGB values
saving and restoring the viewpoint
Using the molinfo command
exit
command
Tcl Text Commands
eye separation
Stereo Parameters | display
file
load
Viewing a molecule: Myoglobin
file types
input
Loading A Molecule | Reading Trajectory Frames
output
Saving Trajectory Frames
files
output
Rendering an Image
read
animate
reading
Viewing a molecule: Myoglobin | A Quick Animation | Loading A Molecule | Molecule File Browser Form | Reading Trajectory Frames | mol
startup
Hot Keys | VMD Command-Line Options | Startup Files | .vmdrc and vmd.rc Files
writing
Saving Trajectory Frames | animate
fit
RMSD
RMS and scripting | RMSD Computation
focal length
Stereo Parameters | display
form
animate
A Quick Animation | Main Form Animation Controls
color
Comparing Two Structures | Color Form | Coloring Methods | Color categories | Coloring by color categories
display
Display Menu
files
Viewing a molecule: Myoglobin
graphics
Viewing a molecule: Myoglobin | An Introduction to Atom | Graphics Form
hot keys
Hot Keys
label
Labels Form
main
Main Form | GUI Shortcuts
material
Material Form
molecule file browser
Molecule File Browser Form
mouse
Mouse Menu
RamaPlot
RamaPlot
render
Rendering an Image | Render Form
sequence
Sequence Form
sim
Simulation Form
tool
Tool Form
forms
menu
frame
delete
Deleting Trajectory Frames | animate
duplicate
animate
write
animate
frames
Main Form Molecule List
frames per second indicator
Display Menu
geometric center
Using the atomselect command
gettimestep
command
Tcl Text Commands | graphics
gopython
command
Using the Python interpreter
graphics
command
graphics
delete
graphics
form
Graphics Form
loading
graphics
primitives
graphics
Python module
graphics
replace
graphics
user-defined
draw
Gromacs
files
Loading A Molecule | Reading Trajectory Frames
gyration, radius of
Radius of gyration
help
Help
command
Tcl Text Commands | gettimestep
topics
help
highlight
Selecting residues from the
hot keys
Hot Keys | user
animation control
Hot Keys
customizing
Hot Keys
menu control
Hot Keys
mouse control
Hot Keys
rotation and scaling
Hot Keys
hydrogen bonds
HBonds | measure
image
lighting controls
Mouse Modes | Display Menu
shading and material properties
Material Form
imd
Interactive Molecular Dynamics
command
Tcl Text Commands | help
Python module
imd
requirements
Simulation Form
implicit ligand sampling
volumetric data
volmap
Interactive Molecular Dynamics
Interactive Molecular Dynamics
joystick
using
Using the Joystick in
label
command
Tcl Text Commands | imd
Python module
label
labels
Comparing Two Structures
categories
Label categories | label
delete
Modifying or deleting a
form
Labels Form
hide
Modifying or deleting a
picking with mouse
Pick Modes
plotting
Plotting a label's value | Tcl callbacks
show
Modifying or deleting a
text
draw
light
command
Tcl Text Commands | label
controlling with mouse
Mouse Modes
toggle
Display Menu
logfile
command
Tcl Text Commands | logfile
logging tcl commands
logfile
mask
volumetric data
volmap
mass
center of
Using the atomselect command
of residue atoms
Tcl callbacks
total
Total mass of a
material
changing
mol
command
Tcl Text Commands | logfile
methods
Graphics Form
Python module
material
material properties
graphics | graphics
matrix routines
alignment
Matrix routines
identity
Matrix routines
inverse alignment
Matrix routines
list of
Matrix routines
multiplication
Matrix routines
rotation
Matrix routines
trans command
Matrix routines
translation
Matrix routines
transpose
Matrix routines
MDTools
For information on our
measure
command
Tcl Text Commands | material | Analysis scripts | Coordinate min and max
menu
command
Tcl Text Commands | measure
molecular surface
Surf | MSMS
molecule
active
Main Form Molecule List | Main Form Animation Controls
analysis
Analysis scripts
best-fit alignment
Computing the Alignment
command
Tcl Text Commands | menu | mol
data
molinfo
deleting
Deleting a Molecule
drawn
Main Form Molecule List
fixed
Comparing Two Structures | Main Form Molecule List
graphics
graphics
id
mol
index
mol
info
Molecular Analysis
list
Main Form Molecule List
loading
Viewing a molecule: Myoglobin | A Quick Animation | graphics | Root mean square deviation
Python module
molecule
status
Main Form Molecule List | mol
changing
Changing the Molecule's Status | mol | Using the molinfo command
top
Main Form Molecule List | Jumping to Specific Frames | molinfo
translation
Comparing Two Structures
molinfo
command
molecule | Molecular Analysis
keywords
molinfo
molrep
Python module
molrep
mouse
add or remove bonds
Mouse Modes
callback
mouse
command
Tcl Text Commands | molinfo
modes
Viewing a molecule: Myoglobin | Comparing Two Structures | Mouse Modes | Hot Keys | mouse
mouse mode
Mouse modes
move
Pick modes
atom
Pick modes
fragment
Pick modes
highlighted rep
Pick modes
molecule
Pick modes
residue
Pick modes
object menus
Pick modes
pick information
Pick information
rocking
mouse
stop rotation
mouse
using
Using the Mouse in
movies
Making a Movie
NAMD
For information on our
files
Loading A Molecule | Reading Trajectory Frames
occupancy
volumetric data
volmap
orthographic view
Display Menu | Perspective/Orthographic views
output
format
Rendering an Image
PCRE
Copyright and Disclaimer Notices
periodic boundary conditions
Periodic Tab
periodic image display
Periodic Tab
perspective view
Display Menu | Perspective/Orthographic views
picking
angles
Pick Modes | Pick Modes
atoms
Comparing Two Structures | Pick Modes | Pick Modes
bonds
Comparing Two Structures | Pick Modes | Pick Modes
center
Pick Modes
dihedrals
Pick Modes | Pick Modes
distances
Comparing Two Structures
hot keys
Hot Keys
modes
Comparing Two Structures | Pick Modes
move atom
Pick Modes
move fragment
Pick Modes
move highlighted rep
Pick Modes
move molecule
Pick Modes
move residue
Pick Modes
query
Pick Modes
text command
mouse
play
command
Using text commands | Tcl Text Commands | mouse | VMD Command-Line Options
plot
geometry monitors
Plotting a label's value
postscript
One Step Printing
potential of mean force
volumetric data
volmap
Python
Copyright and Disclaimer Notices
atomsel
The built-in atomsel type
environment variables
Python modules within VMD
interface
Python Text Interface
libraries
Python modules within VMD
Numeric
Python modules within VMD | vmdnumpy
RMSD
The AtomSel class (DEPRECATED) | The AtomSel class (DEPRECATED) | The AtomSel class (DEPRECATED) | The AtomSel class (DEPRECATED)
startup
VMD Command-Line Options
Tkinter
Python modules within VMD | Using Tkinter menus in
version
Python Text Interface
quit
Main Form
command
draw | play
quoting
Quoting with Single Quotes
radius of gyration
Radius of gyration
Ramachandran plot
RamaPlot
Raster3D
Raster3D file format | One Step Printing | Making Stereo Images
regular expression
Double Quotes and Regular | Double Quotes and Regular
X-PLOR conversion
Double Quotes and Regular
remote
connection
imd
detaching
IMD Using the Sim
killing
IMD Using the Sim
modifiable parameters
IMD Using the Sim
options
imd
simulation control
imd
render
command
Tcl Text Commands | quit
form
Rendering an Image | Render Form
Python module
render
rendering
Rendering an Image | Render Form | Scene Export and Rendering
ART
Higher Quality Rendering
caveats and considerations
Caveats
exec command
render
Gelato
Higher Quality Rendering
in background process
Render Form
list of supported renderers
Higher Quality Rendering
methods
Higher Quality Rendering | render
PostScript
Higher Quality Rendering
POV-Ray
Higher Quality Rendering
Radiance
Higher Quality Rendering
Raster3D
Higher Quality Rendering
Rayshade
Higher Quality Rendering
RenderMan
Higher Quality Rendering
stereo
Making Stereo Images
STL
Higher Quality Rendering
Tachyon
Acknowledgments | Copyright and Disclaimer Notices | Rendering an Image | Higher Quality Rendering | render
TachyonInternal
render
VRML
Higher Quality Rendering
rendering modes
display
rendermode
Display Menu
representation
Molecular Drawing Methods | mol
add new
Adding a rep.
adding
Adding a rep.
auto-update
Selection and Color auto-update.
Beads
Beads
Bonds
Bonds
Cartoon
Cartoon
changing
An Introduction to Atom | Changing a rep. | mol
clipping planes
user defined
mol
CPK
CPK
deleting
Deleting a rep. | Deleting a rep.
dotted van der Waals
Dotted
draw multiple frames
mol
DynamicBonds
DynamicBonds
examples
Some Nice Represenations
HBonds
HBonds
hiding
Hiding a rep.
Isosurface
Isosurface
Licorice
Licorice
Lines
Lines
list of available
Rendering methods
MSMS
MSMS
NewCartoon
NewCartoon
NewRibbons
NewRibbons
Points
Points
Ribbons
Ribbons
show/hide
mol | molrep
solvent representation
Solvent
style
Viewing a molecule: Myoglobin | Graphics Form | Molecular Drawing Methods | mol
Surf
Surf
Trace
Trace
Tube
Tube
van der Waals
VDW
VolumeSlice
VolumeSlice
represention
auto-update
mol
reset view
Display Menu | display
restore
viewpoint
Using the molinfo command
vmd state
Saving your work
RMS
Fit
RMS Fit and Alignment
RMS:Alignment
RMS Fit and Alignment
RMSD
The AtomSel class (DEPRECATED) | The AtomSel class (DEPRECATED) | The AtomSel class (DEPRECATED) | The AtomSel class (DEPRECATED) | RMS example | Root mean square deviation | RMS and scripting | RMSD Computation | A simulation example script
rock
Looping Styles
command
Tcl Text Commands | render
rotate
command
Tcl Text Commands | rock
side chain
Using the atomselect command
rotation
continuous
Mouse Modes
hot keys
Hot Keys
stop
Mouse Modes
using mouse
Mouse Modes
save
configuration
Saving your work
viewpoint
Using the molinfo command
vmd state
Saving your work | Saving and Restoring Molecule
scale
command
Tcl Text Commands | rotate
scaling
using mouse
Mouse Modes
screen parameters
Display Menu
scripts
play
Using text commands
source
Using text commands
secondary structure codes
Sequence information
selection
Viewing a molecule: Myoglobin | An Introduction to Atom | Graphics Form | Molecular Drawing Methods | atomselect | mol | Using the atomselect command
comparison
Comparison selections
keywords
Selections Tab | Selection Methods | Definition of Keywords and
boolean
Boolean Keywords
logic
Short Circuiting
math functions
Definition of Keywords and
modes
Selection Methods
text
Using the atomselect command
volumetric data
Definition of Keywords and
sensor configuration file
Configuring input devices
sensors
Configuring input devices
sequence
Sequence information
caveats
Caveats
dna
Sequence Form
form
Sequence Form
zooming
Sequence Zooming
short circuit logic
Short Circuiting | within and same
sleep
command
Tcl Text Commands | wait
source
command
Using text commands
spaceball
driver
Acknowledgments | Spaceball Driver
MacOS X
Spaceball Driver
Unix
Spaceball Driver
Windows
Spaceball Driver
modes
Using the Spaceball in
using
Using the Spaceball in
stage
Display Menu
command
Tcl Text Commands | scale
startup files
Hot Keys | VMD Command-Line Options | Startup Files | .vmdrc and vmd.rc Files
stereo
mode
Stereoscopic Modes
cross-eyed
Side-By-Side and Cross-Eyed Stereo
CrystalEyes
CrystalEyes Stereo
DTI side-by-side
DTI Side-by-side Stereo
scanline interleaved
Scanline Interleaved Stereo | Anaglyph Stereo
side-by-side
Side-By-Side and Cross-Eyed Stereo
off
Monoscopic Modes
parameters
Display Menu | Stereo Parameters | display | display
stop rotation
Display Menu
stride
Copyright and Disclaimer Notices
surf
Copyright and Disclaimer Notices
surface
molecular
Solvent
solvent accessible
Solvent
Tachyon
Copyright and Disclaimer Notices
Tcl
Tcl/Tk
tcl commands
Tcl Text Commands
text
displayed
graphics
Tk
Tcl/Tk
tool
CAVE
Configuring input devices
command
Tcl Text Commands | stage
form
Tool Form
FreeVR
Configuring input devices
Spaceball
Configuring input devices
VRPN
Configuring input devices
tools
Using Tools
topology files
Loading A Molecule
trajectory
draw multiple frames
Draw Multiple Frames. | mol
files
Loading A Molecule
read
Reading Trajectory Frames
smoothing
Trajectory Smoothing. | mol | molrep
write
Saving Trajectory Frames
trans
Python module
trans
translate
command
Tcl Text Commands | tool
translation
change atom coordinates
Using the atomselect command
using mouse
Mouse Modes
transparency
Draw Style Tab
unit cell information
Periodic Tab
universal sensor locator
Configuring input devices
user
command
Tcl Text Commands | translate
user interfaces
python
Python Text Interface
text
Tcl Text Interface
USL
Configuring input devices
variables
env
Environment Variables | Core Script Files
M_PI
Misc. functions and values
trace
Tcl callbacks
vector command
coordtrans
Multiplying vectors and matrices
vecadd
Vectors
veccross
Vectors
vecdist
Vectors
vecdot
Vectors
vecinvert
Vectors
veclength
Vectors
veclength2
Vectors
vecmean
Vectors
vecnorm
Vectors
vecscale
Vectors
vecstddev
Vectors
vecsub
Vectors
vecsum
Vectors
vectrans
Multiplying vectors and matrices
veczero
Vectors
vector routines
Vectors and Matrices
view
mol
viewing modes
changing
Viewing Modes
VMD
as MIME helper application
MIME types
command line options
VMD Command-Line Options
compile options
vmdinfo
copyright
Copyright and Disclaimer Notices
customizing
Hot Keys | Customizing VMD Sessions
vmdinfo
command
Tcl Text Commands | user
volmap
command
Tcl Text Commands | volmap
volumetric data
VolumeSlice | Isosurface
generating
volmap
wait
command
Tcl Text Commands | volmap
XPLOR
files
Loading A Molecule | Reading Trajectory Frames



vmd@ks.uiuc.edu