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.vmdrc
.mailcap
eye_line
sscache
.vmd_init
.vmdrc
angles
animate
command
form
frames from remote
remote simulation
animation , gif , gif
animation
amount
appending
delete , gif , gif
edit
goto end , gif
goto start , gif
jump , gif
movie
of secondary structure
pause
play , gif , gif
read , gif
skip
speed , gif
step , gif
style , gif
style
loop , gif
once , gif
rock , gif
viewing changes
with user-defined graphics
write , gif
animationduplicate frame
annmm
antialiasing , gif
atom
changing properties
coordinates , gif , gif
coordinates
changing , gif
min and max
info , gif
name lists , gif
picking
selection , gif , gif , gif , gif , gif
selection
comparison
default
examples , gif
keywords , gif , gif
logic
modes
quoting
references in , gif
regular expression
same
sequence
text
within
atoms
distance between
distance between
plotting
atomselect
command , gif , gif
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 , gif , gif , gif , gif
command , gif
form , gif , gif , gif , gif
id , gif
index
in user-defined graphics
map
material properties
names , gif
properties , gif
redefinition , gif , gif , gif
revert to default
scale , gif , gif , gif
scale
changing
transparent , gif , gif , gif , gif , gif , gif , gif
colorinfo
command , gif
coloring
by category
by color scale
by property
methods , gif , gif , gif , gif , gif , gif , gif , gif
color map
command line options
contact residues
copyright
core commands
CPK
debug
command
delete
representation
depth cue , gif
depthsort , gif
detail , gif
display
command , gif
crosseyes
crystaleyes
device
form
left
modes
NAMD patches
orthographic
perspective
right
sidebyside
stereo off
update , gif , gif , gif , gif , gif
distance
matrix
distance between atoms
dotted van der Waals representation
draw
command , gif
extensions
drawing
box around molecule
method , gif
drawn
echo
command
environment variables
environment variables
DP_LIBRARY
SURF_BIN
SURF_TMPDIR
TCL_LIBRARY
TCLX_LIBRARY
VMDBABELBIN , gif
VMDDIR
VMDHTMLVIEWER
VMDTMPDIR , gif
external
command , gif , gif
control of VMD
eye separation , gif
file
browser
load
files
initialization
output
read
reading , gif , gif , gif , gif , gif , gif , gif
startup , gif , gif , gif
writing , gif , gif
file types
input , gif
output
fit
fit
example
RMSD , gif
RMSD
calculate
print
two fragments
two molecules
flat
focal length , gif
form
animate , gif , gif
close
color , gif , gif , gif , gif
display , gif
edit animation
files , gif
graphics , gif , gif , gif , gif
label , gif
main , gif
molecules , gif , gif
open
remote , gif
render , gif
sim
tracker
forms
frame
delete , gif
duplicate
write
frames
full detail
geometric center
grabber
graphics
command , gif , gif
delete
form , gif
loading
primitives
replace
user-defined
gyration, radius of
hbonds representation
help , gif
help
command
hot keys , gif
hot keys
customizing
hydrogen bonds
info menu
label
command
labels , gif
labels
categories , gif
delete , gif
delete all
form
hide , gif
picking with mouse
plotting
show , gif
text
licorice representation
light
command
controlling with mouse
toggle
lines representation
line width , gif
logfile
command
logging tcl commands , gif , gif , gif , gif
mass
center of
of residue atoms
total
material properties
matrix routine
matrix routine
trans
transaxis
transidentity
transmult
transoffset
transtranspose
transvec
transvecinv
MDComm , gif , gif
MDScope , gif
measure
command , gif
menu
command
popup , gif , gif , gif , gif
popup
customizing
vs forms
molecular surface , gif
molecule
active , gif , gif
analysis , gif
best-fit alignment
command , gif , gif
deleting
drawn , gif
fixed , gif , gif
graphics
id , gif , gif , gif , gif
index , gif
info
list , gif
loading , gif , gif , gif , gif
remote , gif
source
status , gif , gif
status
changing , gif , gif
top , gif , gif , gif , gif
translation
molinfo
command
setting values with
mouse
command
modes , gif , gif , gif
using
movies
MSMS
representation
namd , gif , gif , gif
namd_consumer
namdd
orthographic view , gif
output
format
pdbload
command
perspective view , gif
picking , gif
picking
angles , gif
atoms , gif , gif , gif
bonds , gif , gif
center
dihedrals , gif
distances , gif
modes , gif
move atom
move fragment
move molecule
move residue
query
text command
tracing variables , gif
play
command , gif , gif , gif
file
plot
data with graphics
geometry monitors
temperature
pointer
points
detail
representation
popup menu , gif , gif , gif , gif , gif
popup menu
atom specific
customizing
postscript
quit , gif
quit
command , gif
quoting
radius
of gyration
rapp
Raster3D , gif , gif , gif , gif , gif , gif
raster image creation
regular expression
remote
command
connection , gif
connection
controlling
description
detaching
initializing
installation
killing
modifiable parameters
requirements
starting
troubleshooting
using
form
options
simulation control , gif , gif
remote control of VMD
render
command
form , gif
rendering , gif , gif , gif
rendering
caveats , gif
exec command
in background process
method , gif
stereo
representation , gif , gif
representation
add new
changing , gif , gif , gif
deleting
examples
info
off
style , gif , gif , gif
style
options
reset view , gif
resolution
cylinder
level , gif
sphere
restore
representations
viewpoint , gif
vmd state
ribbon representation
RMSD , gif , gif , gif
rock , gif
rock
command
rotate
command
side chain
rotation
automatic
automatic
rock
spin
stop , gif
continuous
stop
transformation matrix , gif
using mouse
save
colors
configuration , gif
representations
viewpoint , gif
vmd state , gif
scale
command
scaling
using mouse
screen parameters , gif
security , gif
selection , gif , gif , gif , gif , gif
selection
comparison
keywords , gif
keywords
boolean
logic
modes
text
short circuit logic , gif
simulation
command
control , gif
form
parameters , gif
sleep
command
solvent accessible surface
solvent representation
source
command
spin
stage
stage
command
startup files , gif , gif , gif
stereo
mode
modes
off
parameters , gif , gif , gif
problems
surf
representation
surface
molecular
solvent accessible
surface plot
Tcl
Tcl-DP , gif , gif
TclX
text
displayed
Tk
top
topology files
trace
variables , gif , gif
trace representation
tracker
command
form
trajectory
files
read , gif
write
transformation matrix
transformation matrix
align
centering
identity
offset , gif
rotation , gif
translate
command
translation
change atom coordinates
transformation matrix
using mouse
transparency , gif , gif , gif , gif , gif , gif
tube representation
user
command , gif
user interfaces
user interfaces
external , gif , gif , gif
forms
text
van der Waals representation
variables
env , gif
M_PI
vmd_frame
vmd_pick_atom , gif
vmd_pick_mol , gif
vmd_timestep , gif
vector command
coordtrans
vecadd
veccross
vecdist
vecdot
vecinvert
veclength
veclength2
vecnorm
vecscale
vecsub
vectrans
veczero
vector routines
view , gif , gif
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 , gif
vmdinfo
command
vmdlog
command
wait
command
wireframe , gif


Justin Gullingsrud
Tue Apr 6 09:22:39 CDT 1999