Index

Reading Trajectory Frames

.vmdrc

Using text commands

vmd.rc

Using text commands

ACTC

AMBER

files: Loading A Molecule | Reading Trajectory Frames

ambient occlusion lighting

display | render

analysis

scripting: Using the atomselect command
speed: Using the atomselect command

angles

Label categories

animate

command: Tcl Text Commands | Tcl Text Commands
Python module: animate
window controls: Main Window Animation Controls

animation

A Quick Animation

appending

delete

Deleting Trajectory Frames | animate | animate

duplicate frame

Reading Trajectory Frames

frames

goto end

goto start

hot keys

Hot Keys

jump

Jumping to Specific Frames | animate

movie

Making a Movie

play

read

Reading Trajectory Frames | animate

smoothing

Trajectory Smoothing. | mol | molrep

speed

Animation Speed | animate

step

Animation Speed

style

loop: Looping Styles
once: Looping Styles
rock: Looping Styles

write

Saving Trajectory Frames | animate

antialiasing

Display Menu | display | render

atom

changing properties

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

selection

auto-update

An atom selection example

changing properties

comparison

Comparison selections

default

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

Atom selections in Python

modes

Selection Methods

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

update

Finding waters near a

volumetric data

within

within and same

atoms

distance between

plotting: Plotting a label's value

atomselect

command: Tcl Text Commands | animate | Molecular Analysis | Using the atomselect command

axes

command: Tcl Text Commands | atomselect
Python module: axes

Babel

Babel interface

backface culling

Root mean square deviation

batch mode

VMD Command-Line Options

beta values

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

callbacks

Python: Python callbacks
Tcl: Tcl callbacks | Tcl callbacks

center of mass

CHARMM

files: Loading A Molecule | Reading Trajectory Frames

chemical2vmd

Setting up your .mailcap

clipping planes

user defined: mol

color

access definitions

colorinfo

assignment

background

Color Window

category

command

Coloring Methods | Tcl Text Commands | axes

id

Draw Style Tab | Coloring Methods

in user-defined graphics

graphics

index

colorinfo

map

Color Window

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

window

Comparing Two Structures | Color Window | Coloring Methods | Color categories | Coloring by color categories

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 Window | 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

Coulomb potential

volumetric data: volmap

culling

debug

command: Tcl Text Commands

density

volumetric data: volmap

depth cue

depth cueing

display

ambient occlusion: display
antialiasing: display
backgroundgradient: display
command: Tcl Text Commands | colorinfo
device: VMD Command-Line Options
Python module: display
update: display | Using the molinfo command | Creating a set of | Revert all RGB values
window: Display Menu

distance

volumetric data: volmap

distance between atoms

draw

command: draw

drawing

method: Viewing a molecule: Myoglobin | Graphics Window

drawn

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
VMDDISABLESTEREO: 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
VMDNOCUDA: 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

evaltcl

Python module: evaltcl

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 Window | 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

frame

delete: Deleting Trajectory Frames | animate
duplicate: animate
write: animate

frames

frames per second indicator

geometric center

Hardware and Software Requirements

gettimestep

command: Tcl Text Commands | graphics

gopython

command: Using the Python interpreter

graphics

command: graphics
delete: graphics
loading: graphics
primitives: graphics
Python module: graphics
replace: graphics
user-defined: draw
window: Graphics Window

Gromacs

files: Loading A Molecule | Reading Trajectory Frames

gyration, radius of

Radius of gyration

hardware requirements

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 Window

imd

Interactive Molecular Dynamics

command: Tcl Text Commands | help
Python module: imd
requirements: IMD Connect Simulation Window

implicit ligand sampling

volumetric data: volmap

Interactive Molecular Dynamics

Interactive Molecular Dynamics

interpolation

volumetric data: volmap

joystick

using: Using the Joystick in

label

command: Tcl Text Commands | imd
Python module: label

labels

Main Window Molecule List | Main Window Animation Controls

categories: Label categories | label
delete: Modifying or deleting a
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
window: Labels Window

light

command: Tcl Text Commands | label
controlling with mouse: Mouse Modes
toggle: Display Menu

logfile

command: Tcl Text Commands | logfile
disable from GUI: Tracking Script Command Versions
disable from text: logfile
enable from GUI: Tracking Script Command Versions
enable from text: logfile

logging tcl commands

Tracking Script Command Versions | 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 Window
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

menus

molecular surface

QuickSurf | Surf | MSMS

molecule

active

analysis

Analysis scripts

best-fit alignment

Computing the Alignment

command

Tcl Text Commands | menu | mol

data

molinfo

deleting

Deleting a Molecule

drawn

Comparing Two Structures | Main Window Molecule List

fixed

graphics

graphics

id

index

info

Molecular Analysis

list

loading

Viewing a molecule: Myoglobin | A Quick Animation | graphics | Root mean square deviation

Python module

molecule

status

Main Window Molecule List | mol

changing: Changing the Molecule's Status | mol | Using the molinfo command

top

Main Window Molecule List | Jumping to Specific Frames | molinfo

translation

Quoting with Single Quotes

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 information

rocking

stop rotation

using

movies

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

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

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 Window

command: draw | play

quoting

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 Simulation
killing: IMD Using the Simulation
modifiable parameters: IMD Using the Simulation

options

imd

simulation control

imd

render

command: Tcl Text Commands | quit
Python module: render
window: Rendering an Image | Render Window

rendering

Rendering an Image | Render Window | Scene Export and Rendering

ambient occlusion lighting: display | render
antialiasing: render
ART: Higher Quality Rendering
caveats and considerations: Caveats
exec command: render
Gelato: Higher Quality Rendering
in background process: Render Window
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: Higher Quality Rendering | render
VRML-1: Higher Quality Rendering
VRML-2: Higher Quality Rendering
Wavefront: Higher Quality Rendering

rendering modes

rendermode

Selection and Color auto-update.

representation

Molecular Drawing Methods | mol

add new

Adding a rep.

adding

Adding a rep.

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

DynamicBonds

DynamicBonds

examples

Some Nice Represenations

FieldLines

HBonds

hiding

Isosurface

Licorice

Lines

list of available

MSMS

NewCartoon

NewRibbons

Orbital

PaperChain

Points

Polyhedra

QuickSurf

Ribbons

show/hide

mol | molrep

solvent representation

Solvent

style

Viewing a molecule: Myoglobin | Graphics Window | Molecular Drawing Methods | mol

Surf

Trace

Tube

Twister

van der Waals

VDW

VolumeSlice

VolumeSlice

represention

auto-update: mol

reset view

resetview

restore

viewpoint: Using the molinfo command
vmd state: Saving your work

RMS

Fit: RMS Fit and Alignment

RMS:Alignment

RMS Fit and Alignment

RMSD

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
logfile: Tracking Script Command Versions
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

scripts

play: Using text commands
source: Using text commands

secondary structure codes

Sequence information

selection

comparison

Comparison selections

keywords

Selections Tab | Selection Methods | Definition of Keywords and

boolean: Boolean Keywords

logic

Short Circuiting

math functions

modes

Selection Methods

text

volumetric data

sensor configuration file

sensors

sequence

Sequence information

caveats: Caveats
dna: Sequence Window
window: Sequence Window
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

command: Tcl Text Commands | scale

startup files

Hot Keys | VMD Command-Line Options | Startup Files | .vmdrc and vmd.rc Files

stereo

mode

Stereoscopic Modes

checkerboard: Checkerboard Stereo
column interleaved: Column Interleaved Stereo
cross-eyed: Side-By-Side and Cross-Eyed Stereo
CrystalEyes: Quad-buffered Stereo
DTI side-by-side: DTI Side-by-side Stereo
Quad buffered: Quad-buffered Stereo
row interleaved: Row Interleaved Stereo
scanline interleaved: Row 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

stride

surf

surface

molecular: Solvent
solvent accessible: Solvent

Tachyon

Tcl

Tcl/Tk

tcl commands

Tcl Text Commands

text

displayed: graphics

Tk

Tcl/Tk

tool

CAVE: Configuring input devices
command: Tcl Text Commands | stage
FreeVR: Configuring input devices
Spaceball: Configuring input devices
VRPN: Configuring input devices
window: Tool Window

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

user

command: Tcl Text Commands | translate

user interfaces

python: Python Text Interface
text: Tcl Text Interface

USL

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 | 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