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Index

active
animate command
animation , gif
animation
amount
appending
delete
goto end
goto start
jump
loop
loop
loop
once
rock
pause
play , gif
read
skip
speed
step , gif
style
style
Loop
once
Rock
write
antialiasing
axes
axes command
Babel
bonds
determining
unusual
bonds representation
clipping planes
color
background
category
map
scale
color command
ColorID
color map
CPK
debug command
depth cue
display
crosseyes
crystaleyes
left
modes
orthographic
perspective
right
sidebyside
stereo off
display command
dotted van der Waal representation
drawn
echo command
environment variables
VMDBABELBIN
VMDTMPDIR
exit command
external command
eye seperation
files
reading
file types
input
fit
fit
RMSD
calculate
print
two fragments
two molecules
focal length
form
animate
close
color
display
edit animation
files
graphics
label
main
molecules
open
remote
render
sim
tracker
frames
grabber
help
help
specific topic
help command
journal command
keyword
keyword
definitions
label command
labels , gif
labels
categories
delete , gif
delete all
hide , gif
plotting
show , gif
light command
lights
controlling with mouse
toggle
lines representation
log command
MDComm
MDScope
menu command
mol command
molecule
active
changing status
deleting
drawn
fixed
loading
top
molecule command
mouse
modes
mouse command
namd
picking
picking
angle
angles
atom
atoms , gif
bond
bonds
center
dihedral
dihedrals
distances
move atom
move fragment
move residue
query
play command
pointer
points representation
quit
quit command
quoting
Raster3D
regular expression
remote command
remote connection , gif
remote connection
controlling
description
detaching
initializing
installation
killing
modifiable parameters
requirements
starting
troubleshooting
using
render command
rendering
rendering
caveats
representation
representations
reset view
rock , gif
rock command
rotate command
rotation
automatic
automatic
rock
spin
stop , gif
continuous
stop
using mouse
rotation command
rot command
run command
scale command
scaling
short circuit logic
sim command
simulation command
spin
stage
stage command
stereo
parameters , gif
stereo mode
stop command
Tcl
Tcl-DP , gif , gif
TclX
top
tracker command
trans command
translate command
translation
transparent
user command
user interfaces
user interfaces
3D
external
gesture
speech
van der Waal representation
view
view
adding
deleting
viewing modes
changing
views
VMD
vmdinfo command
vmdlog command
wait command



Andrew Dalke
Tue May 14 16:49:45 CDT 1996