Index

.vmdrc

.mailcap

eye_line

sscache

.vmd_init

.vmdrc

angles

animate

command

form

frames from remote

remote simulation

animation , ,

animation

amount

appending

delete , ,

edit

goto end ,

goto start ,

jump ,

movie

of secondary structure

pause

play , ,

read ,

skip

speed ,

step ,

style ,

style

loop ,

once ,

rock ,

viewing changes

with user-defined graphics

write ,

animationduplicate frame

annmm

antialiasing ,

atom

changing properties

coordinates , ,

coordinates

changing ,

min and max

info ,

name lists ,

picking

selection , , , , ,

selection

comparison

default

examples ,

keywords , ,

logic

modes

quoting

references in ,

regular expression

same

sequence

text

within

atoms

distance between

distance between

plotting

atomselect

command , ,

axes

axes

command

Babel

beta values

bonds

determining

label

representation

resolution

unusual

button bar

cartoon representation

center

center of mass

clipping planes

color

access definitions

assignment

background

category , , , ,

command ,

form , , , ,

id ,

index

in user-defined graphics

map

material properties

names ,

properties ,

redefinition , , ,

revert to default

scale , , ,

scale

changing

transparent , , , , , , ,

colorinfo

command ,

coloring

by category

by color scale

by property

methods , , , , , , , ,

color map

command line options

contact residues

copyright

core commands

CPK

debug

command

delete

representation

depth cue ,

depthsort ,

detail ,

display

command ,

crosseyes

crystaleyes

device

form

left

modes

NAMD patches

orthographic

perspective

right

sidebyside

stereo off

update , , , , ,

distance

matrix

distance between atoms

dotted van der Waals representation

draw

command ,

extensions

drawing

box around molecule

method ,

drawn

echo

command

environment variables

environment variables

DP_LIBRARY

SURF_BIN

SURF_TMPDIR

TCL_LIBRARY

TCLX_LIBRARY

VMDBABELBIN ,

VMDDIR

VMDHTMLVIEWER

VMDTMPDIR ,

external

command , ,

control of VMD

eye separation ,

file

browser

load

files

initialization

output

read

reading , , , , , , ,

startup , , ,

writing , ,

file types

input ,

output

fit

fit

example

RMSD ,

RMSD

calculate

print

two fragments

two molecules

flat

focal length ,

form

animate , ,

close

color , , , ,

display ,

edit animation

files ,

graphics , , , ,

label ,

main ,

molecules , ,

open

remote ,

render ,

sim

tracker

forms

frame

delete ,

duplicate

write

frames

full detail

geometric center

grabber

graphics

command , ,

delete

form ,

loading

primitives

replace

user-defined

gyration, radius of

hbonds representation

help ,

help

command

hot keys ,

hot keys

customizing

hydrogen bonds

info menu

label

command

labels ,

labels

categories ,

delete ,

delete all

form

hide ,

picking with mouse

plotting

show ,

text

licorice representation

light

command

controlling with mouse

toggle

lines representation

line width ,

logfile

command

logging tcl commands , , , ,

mass

center of

of residue atoms

total

material properties

matrix routine

matrix routine

trans

transaxis

transidentity

transmult

transoffset

transtranspose

transvec

transvecinv

MDComm , ,

MDScope ,

measure

command ,

menu

command

popup , , , ,

popup

customizing

vs forms

molecular surface ,

molecule

active , ,

analysis ,

best-fit alignment

command , ,

deleting

drawn ,

fixed , ,

graphics

id , , , ,

index ,

info

list ,

loading , , , ,

remote ,

source

status , ,

status

changing , ,

top , , , ,

translation

molinfo

command

setting values with

mouse

command

modes , , ,

using

movies

MSMS

representation

namd , , ,

namd_consumer

namdd

orthographic view ,

output

format

pdbload

command

perspective view ,

picking ,

picking

angles ,

atoms , , ,

bonds , ,

center

dihedrals ,

distances ,

modes ,

move atom

move fragment

move molecule

move residue

query

text command

tracing variables ,

play

command , , ,

file

plot

data with graphics

geometry monitors

temperature

pointer

points

detail

representation

popup menu , , , , ,

popup menu

atom specific

customizing

postscript

quit ,

quit

command ,

quoting

radius

of gyration

rapp

Raster3D , , , , , ,

raster image creation

regular expression

remote

command

connection ,

connection

controlling

description

detaching

initializing

installation

killing

modifiable parameters

requirements

starting

troubleshooting

using

form

options

simulation control , ,

remote control of VMD

render

command

form ,

rendering , , ,

rendering

caveats ,

exec command

in background process

method ,

stereo

representation , ,

representation

add new

changing , , ,

deleting

examples

info

off

style , , ,

style

options

reset view ,

resolution

cylinder

level ,

sphere

restore

representations

viewpoint ,

vmd state

ribbon representation

RMSD , , ,

rock ,

rock

command

rotate

command

side chain

rotation

automatic

automatic

rock

spin

stop ,

continuous

stop

transformation matrix ,

using mouse

save

colors

configuration ,

representations

viewpoint ,

vmd state ,

scale

command

scaling

using mouse

screen parameters ,

security ,

selection , , , , ,

selection

comparison

keywords ,

keywords

boolean

logic

modes

text

short circuit logic ,

simulation

command

control ,

form

parameters ,

sleep

command

solvent accessible surface

solvent representation

source

command

spin

stage

stage

command

startup files , , ,

stereo

mode

modes

off

parameters , , ,

problems

surf

representation

surface

molecular

solvent accessible

surface plot

Tcl

Tcl-DP , ,

TclX

text

displayed

Tk

top

topology files

trace

variables , ,

trace representation

tracker

command

form

trajectory

files

read ,

write

transformation matrix

transformation matrix

align

centering

identity

offset ,

rotation ,

translate

command

translation

change atom coordinates

transformation matrix

using mouse

transparency , , , , , ,

tube representation

user

command ,

user interfaces

user interfaces

external , , ,

forms

text

van der Waals representation

variables

env ,

M_PI

vmd_frame

vmd_pick_atom ,

vmd_pick_mol ,

vmd_timestep ,

vector command

coordtrans

vecadd

veccross

vecdist

vecdot

vecinvert

veclength

veclength2

vecnorm

vecscale

vecsub

vectrans

veczero

vector routines

view , ,

view

adding

deleting

viewing modes

changing

VMD

VMD

as a server

as helper application

command line options

compile options

control from another VMD

copyright

customizing ,

vmdinfo

command

vmdlog

command

wait

command

wireframe ,