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Index

.vmdrc
Using text commands
.vmdsensors
Supported devices and how
.vmdrc
.vmdrc and vmd.rc Files
vmd.rc
.vmdrc and vmd.rc Files
.mailcap
Setting up your .mailcap
-webhelper
Setting up your .mailcap
.vmdrc
Hot Keys
AMBER
files
Loading A Molecule | Reading Frames
analysis
Sequence Zooming
angles
Label categories
animate
command
Tcl Text Commands | Tcl Text Commands
form
Animate Form
Python module
animate
animation
A Quick Animation
amount
Amount Chooser
appending
Reading Frames
delete
Deleting Frames | animate | animate
edit
Edit Animation Form
goto end
animate
goto start
animate
hot keys
Hot Keys
jump
Jumping to Specific Frames | animate
movie
Making a Movie
play
animate
read
Reading Frames | animate
skip
Animation Speed
speed
Animation Speed | animate
style
animate
loop
Looping Styles
once
Looping Styles
rock
Looping Styles
with user-defined graphics
Animation
write
Writing Frames | animate
animationduplicate frame
animate
antialiasing
Display Form | display
atom
changing properties
Using the atomselect command
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
Graphics Form | Atom Name Lists
picking
Comparing Two Structures
selection
Viewing a molecule: Myoglobin | An Introduction to Atom | Molecular Drawing Methods | Selection Methods | atomselect | Using the atomselect command
changing properties
An atom selection example
comparison
Comparison selections
default
mol
examples
An Introduction to Atom | Selection Methods
keywords
Atom Name Lists | Selection Methods | Definition of Keywords and | Definition of Keywords and
logic
Short Circuiting
math functions
Definition of Keywords and
modes
Selection Methods
Python
Atom selections in Python
quoting
Quoting with Single Quotes
regular expression
Double Quotes and Regular
same
within and same
sequence
sequence
text
Using the atomselect command
update
Finding waters near a
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 Form
command
Tcl Text Commands | atomselect
Python module
axes
Babel
Babel interface
beta values
Root mean square deviation
BioCoRE
For more information on
BMRT
Higher Quality Rendering
bonds
determining
What happens when a
label
Label categories
representation
Rendering methods | Bonds
resolution
Bonds
unusual
What happens when a
button bar
Main Form
callbacks
Python
Python callbacks
Tcl
Tcl callbacks
cartoon representation
Rendering methods | Cartoon
center of mass
Using the atomselect command
CHARMM
files
Loading A Molecule | Reading Frames
chemical2vmd
Setting up your .mailcap
clipping planes
Display Form
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
Image Controls | Coloring Methods
in user-defined graphics
Introduction
index
colorinfo
map
Color Form
material properties
Introduction | Introduction
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
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
CPK
Rendering methods | CPK
debug
command
Tcl Text Commands
depth cue
Display Form | display
depthsort
display
detail
Display Form | display
display
command
Tcl Text Commands | colorinfo
device
VMD Command-Line Options
form
Display Form
Python module
display
update
display | display | Using the molinfo command | Creating a set of | Revert all RGB values
distance between atoms
Comparing Two Structures
dotted van der Waals representation
Rendering methods | Dotted
draw
command
Introduction | Draw and Drawing Extensions
extensions
Draw and Drawing Extensions
drawing
box around molecule
Drawing a box around
method
Viewing a molecule: Myoglobin | Graphics Form
drawn
The Molecule List browser
echo
command
Tcl Text Commands | display
environment variables
Environment Variables
DISPLAY
Environment Variables
MSMSSERVER
MSMS
SURF_BIN
Surf
TCL_LIBRARY
Core Script Files
VMDBABELBIN
Babel interface | Environment Variables
VMDCAVEMEM
Environment Variables
VMDDIR
Environment Variables
VMDFILECHOOSER
Environment Variables
VMDGDISPLAY
Environment Variables
VMDHTMLVIEWER
Environment Variables
VMDIMAGEVIEWER
Environment Variables
VMDSCRDIST
Environment Variables
VMDSCRHEIGHT
Environment Variables
VMDSCRPOS
Environment Variables
VMDSCRSIZE
Environment Variables
VMDTMPDIR
Babel interface | Environment Variables
exit
command
Tcl Text Commands
eye separation
Stereo Parameters | display
file
load
Viewing a molecule: Myoglobin
file types
input
Loading A Molecule | Reading Frames
output
Writing Frames
files
output
Rendering an Image
read
animate
reading
Viewing a molecule: Myoglobin | A Quick Animation | Loading A Molecule | Loading a New Molecule | Files Form | Reading Frames | mol | VMD Command-Line Options
startup
Hot Keys | VMD Command-Line Options | Startup Files | .vmdrc and vmd.rc Files
writing
Babel interface | Writing Frames | animate
fit
RMSD
RMS and scripting | RMSD Computation
flat
Display Form
focal length
Stereo Parameters | display
form
animate
A Quick Animation | Animate Form
color
Comparing Two Structures | Color Form | Coloring Methods | Color categories | Coloring by color categories
display
Mouse Modes | Display Form
edit animation
Edit Animation Form
files
Viewing a molecule: Myoglobin | Files Form
graphics
Viewing a molecule: Myoglobin | An Introduction to Atom | Graphics Form
hot keys
Hot Keys
label
Labels Form
main
Main Form
material
Material Form
molecules
Viewing a molecule: Myoglobin | A Quick Animation | Molecules (Mol) Form
mouse
Mouse Form
RamaPlot
RamaPlot
render
Rendering an Image | Render Form
sequence
Sequence Form
sim
Sim Form
tracker
Tracker Form
forms
menu
frame
delete
Deleting Frames | animate
duplicate
animate
write
animate
frames
The Molecule List browser
full detail
Display Form
geometric center
Using the atomselect command
gopython
command
Using the Python interpreter
graphics
command
Introduction | Graphics
delete
Graphics
form
Graphics Form
loading
Graphics
primitives
Introduction
Python module
graphics
replace
Graphics
user-defined
User-Defined Graphics
Gromacs
files
Loading A Molecule | Reading Frames
gyration, radius of
Radius of gyration
hbonds representation
Rendering methods | HBonds
help
Main Form
command
Tcl Text Commands | exit
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
image
lighting controls
Mouse Modes | Display Form
ray tracing considerations
Caveats
shading and material properties
Material Form
IMD
Interactive Molecular Dynamics
command
Tcl Text Commands | help
Python module
imd
requirements
Interactive Molecular Dynamics
Interactive Molecular Dynamics
Interactive Molecular Dynamics
isosurface
representation
Rendering methods | Isosurface
JMV
For more information on
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 Item Mode
plotting
Plotting a label's value
show
Modifying or deleting a
text
Adding a label
licorice representation
Rendering methods | Licorice
light
command
Tcl Text Commands | label
controlling with mouse
Mouse Modes
toggle
Display Form
line width
Image Controls
lines representation
Rendering methods | Lines
logfile
command
Tcl Text Commands | logfile
logging tcl commands
echo | logfile
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
Python module
material
material properties
Introduction | Introduction
materials
Image Controls
matrix routine
Matrix routines
trans
Matrix routines
transaxis
Matrix routines
transidentity
Matrix routines
transmult
Matrix routines
transoffset
Matrix routines
transtranspose
Matrix routines
transvec
Matrix routines
transvecinv
Matrix routines
MDTools
For more information on
measure
command
Tcl Text Commands | material | Analysis scripts | Coordinate min and max
menu
command
Tcl Text Commands | measure
vs forms
Rapid Introduction to VMD
molecular surface
Rendering methods | Surf | MSMS
molecule
active
The Molecule List browser | Animate Form
analysis
Analysis scripts
best-fit alignment
Computing the Alignment
canceling
Canceling a Load of
command
Tcl Text Commands | menu | mol
data
molinfo
deleting
Deleting a Molecule
drawn
The Molecule List browser
fixed
Comparing Two Structures | The Molecule List browser
graphics
Graphics
id
mol | Graphics
index
mol
info
Molecular Analysis
list
The Molecule List browser
loading
Viewing a molecule: Myoglobin | A Quick Animation | Loading a New Molecule | Graphics | Root mean square deviation
Python module
molecule
status
The Molecule List browser | mol
changing
Changing the Molecule's Status | mol | Using the molinfo command
top
The Molecule List browser | Jumping to Specific Frames | molinfo
translation
Comparing Two Structures
molinfo
command
molecule | Molecular Analysis
keywords
molinfo
molrep
Python module
molrep
mouse
action buttons
Action buttons
command
Tcl Text Commands | molinfo
modes
Viewing a molecule: Myoglobin | Comparing Two Structures | Mouse Modes | Hot Keys | mouse
mouse mode
Mouse mode
move
Object menus
atom
Object menus
fragment
Object menus
highlighted rep
Object menus
molecule
Object menus
residue
Object menus
object menus
Object menus
pick information
Pick information
using
Using the Mouse in
movies
Making a Movie
MSMS
representation
Rendering methods | MSMS
NAMD
For more information on
files
Loading A Molecule | Reading Frames
orthographic view
Display Form | Perspective/Orthographic views
output
format
Rendering an Image
pcre
Copyright and Disclaimer
perspective view
Display Form | Perspective/Orthographic views
picking
angles
Pick Item Mode | Pick Item Mode
atoms
Comparing Two Structures | Pick Item Mode | Pick Item Mode | Pick Item Mode
bonds
Comparing Two Structures | Pick Item Mode | Pick Item Mode
center
Pick Item Mode
dihedrals
Pick Item Mode | Pick Item Mode
distances
Comparing Two Structures
hot keys
Hot Keys
modes
Comparing Two Structures | Pick Item Mode
move atom
Pick Item Mode
move fragment
Pick Item Mode
move highlighted rep
Pick Item Mode
move molecule
Pick Item Mode
move residue
Pick Item Mode
query
Pick Item Mode
text command
mouse
tracing variables
Interface to picking
play
command
Making a Movie | Using text commands | Tcl Text Commands | mouse | VMD Command-Line Options
plot
data with graphics
Drawing a graph
geometry monitors
Plotting a label's value
points
detail
Display Form
representation
Rendering methods | Points
postscript
Higher Quality Rendering | One Step Printing
Pov-Ray
Higher Quality Rendering
Python
Copyright and Disclaimer
interface
Python Text Interface
Tkinter
Using Tkinter menus in
quit
Main Form
command
echo | play
quoting
Quoting with Single Quotes
Radiance
Higher Quality Rendering
radius
of gyration
Radius of gyration
Ramachandran plot
RamaPlot
raster image creation
Rendering to Raster Image
Raster3D
Rendering an Image | Raster3D file format | Rendering | Higher Quality Rendering | One Step Printing | Making a Movie | Making Stereo Raster Images | render
RayShade
Higher Quality Rendering
regular expression
Double Quotes and Regular | Double Quotes and Regular
X-PLOR conversion
Double Quotes and Regular
remote
connection
imd
detaching
Using the Sim form
killing
Using the Sim form
modifiable parameters
Using the Sim form
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 | Rendering | Rendering to Raster Image
caveats
Caveats | Known Problems
exec command
render
in background process
Rendering
method
Higher Quality Rendering | render
stereo
Making Stereo Raster Images
Renderman
Higher Quality Rendering
representation
Graphics Form | Molecular Drawing Methods | mol
add new
Graphics Form
changing
An Introduction to Atom | Graphics Form | Changing Views | mol
deleting
Graphics Form
examples
Some Nice Represenations
off
Off
style
Viewing a molecule: Myoglobin | Graphics Form | Molecular Drawing Methods | Rendering methods | mol
options
Image Controls
reset view
display
resolution
cylinder
Image Controls
level
Display Form | display
sphere
Image Controls
restore
viewpoint
Using the molinfo command
vmd state
Saving your work
ribbon representation
Rendering methods | Ribbon
RMS
Fit
RMS Fit and Alignment
RMS:Alignment
RMS Fit and Alignment
RMSD
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
transformation matrix
Matrix routines | Matrix routines
using mouse
Mouse Modes
save
configuration
Saving your work
viewpoint
Using the molinfo command
vmd state
Saving your work
scale
command
Tcl Text Commands | rotate
scaling
using mouse
Mouse Modes
screen parameters
Display Form | Known Problems
scripts
play
Using text commands
source
Using text commands
selection
Viewing a molecule: Myoglobin | An Introduction to Atom | Graphics Form | Molecular Drawing Methods | atomselect | mol | Using the atomselect command
comparison
Comparison selections
keywords
Atom Name Lists | 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
sensor configuration file
Supported devices and how
sensors
Supported devices and how
sequence
Sequence information
caveats
Caveats
dna
Caveats
form
Sequence Form
zooming
Sequence Zooming
short circuit logic
Short Circuiting | within and same
sleep
command
Tcl Text Commands | wait
solvent accessible surface
Rendering methods | Solvent
solvent representation
Rendering methods | Solvent
source
command
Using text commands
spaceball
driver
Spaceball Driver
unix
Spaceball Driver
windows
Spaceball Driver
modes
Spaceball Driver
using
Using the Spaceball in
stage
Display Form
command
Tcl Text Commands | scale
startup files
Hot Keys | VMD Command-Line Options | Startup Files | .vmdrc and vmd.rc Files
stereo
mode
Stereoscopic Modes
off
Monoscopic Modes
parameters
Display Form | Stereo Parameters | display | display
problems
Problems with stereo on
stride
Copyright and Disclaimer
Structural Biology Software Database
For more information on
surf
Copyright and Disclaimer
representation
Rendering methods | Surf
surface
molecular
Rendering methods | Solvent
solvent accessible
Rendering methods | Solvent
surface plot
Draw a surface plot
Tachyon
Copyright and Disclaimer | Rendering | Higher Quality Rendering | render
Tcl
Tcl/Tk
tcl commands
Tcl Text Commands
text
displayed
Introduction
Tk
Tcl/Tk
tool
command
Tcl Text Commands | stage
tools
Using devices with VMD
topology files
Loading A Molecule
trace
variables
Interface to picking
trace representation
Rendering methods | Trace
tracker
form
Tracker Form
trajectory
files
Loading A Molecule
read
Reading Frames | VMD Command-Line Options
write
Writing Frames
trans
Python module
trans
transformation matrix
Matrix routines
align
Matrix routines
centering
Matrix routines
identity
Matrix routines
offset
Matrix routines | Matrix routines
rotation
Matrix routines | Matrix routines
translate
command
Tcl Text Commands | tool
translation
change atom coordinates
Using the atomselect command
transformation matrix
Matrix routines
using mouse
Mouse Modes
transparency
Image Controls
tube representation
Rendering methods | Tube
universal sensor locator
Supported devices and how
url_get
Copyright and Disclaimer
user
command
Tcl Text Commands | translate
user interfaces
python
Python Text Interface
text
Tcl Text Interface
USL
Supported devices and how
van der Waals representation
Rendering methods | VDW
variables
env
Environment Variables | Core Script Files
M_PI
Misc. functions and values
trace
Tcl callbacks
vmd_pick_atom
Interface to picking
vmd_pick_mol
Interface to picking
vector command
coordtrans
Multiplying vectors and matrices
vecadd
Vectors
veccross
Vectors
vecdist
Vectors
vecdot
Vectors
vecinvert
Vectors
veclength
Vectors
veclength2
Vectors
vecnorm
Vectors
vecscale
Vectors
vecsub
Vectors
vectrans
Multiplying vectors and matrices
veczero
Vectors
vector routines
Vectors and Matrices
view
Graphics Form | Molecular Drawing Methods | mol
adding
Graphics Form
deleting
Graphics Form
viewing modes
changing
Viewing Modes
VMD
For more information on
as MIME helper application
MIME types
command line options
VMD Command-Line Options
compile options
vmdinfo
copyright
Copyright and Disclaimer
customizing
Hot Keys | Customizing VMD Sessions
vmd.rc
Using text commands
vmdinfo
command
Tcl Text Commands | user
volumeslice
representation
Rendering methods | VolumeSlice
volumetric data
Rendering methods | VolumeSlice | Isosurface
VRML
Higher Quality Rendering
wait
command
Tcl Text Commands | vmdinfo
wireframe
Display Form | Lines
XPLOR
files
Loading A Molecule | Reading Frames



vmd@ks.uiuc.edu