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Up: SPOCK: The Structural Properties Previous: Disclaimer

Index


accessible surface
building : 7.4.5
creating via command line : 6.2.7
accessible surface area
calculating : 7.6.3
calculating via command line : 6.2.7
tutorial : 9.4
alpha blending : 7.11.3.1
amber : 4.7
amino acid library : 7.7.14
and-based selections : 6.4
angles
and calculator : 6.5
between picked atoms : 7.9.1
annotations : see also labels | (ib to 7.4.11
coloring : 6.2.1
font selection : 7.4.11
selection : 6.3.4
antialiasing : 7.1.2.12 | 7.11.3.1 | 7.11.3.1 | 9.6
lines : 7.11.3.1
scene : 7.11.2.1
application defaults file : 5.3.1.1
atom information format : 7.9.1
atom labels : see labels
atom properties
and calculator : 6.5
setting : 6.2.4
atom vs. vertex actions : 6.3.3
atomic number : see element number
atomic radius property : see also radius files
default : 6.2.6
defined : 6.2.4.1
setting : 6.2.4.1
atoms : (ib to 7.4.2
copying : 7.7.5
listing : 6.2.2.3
subsets : see subsets
autosave : 7.1.9
auxiliary clipping planes : see clipping
backface : 7.11.4.2 | 7.11.5
color : 7.4.5
culling : 7.1.2.12.1 | 7.11.3.1
material : 7.11.4.2
background color : 6.2.1 | 7.11.4
batch-mode : 8.2
Bessel functions : 6.5
bonds : (ib to 7.4.1
creating manually : 7.7.13
deleting : 7.7.13
listing : 6.2.2.3
recalculating : 6.2.8
secondary bond mode : 9.1
secondary drawing mode : 6.2.1.1
style tutorial : 9.1
bones : 7.3.20
bones files
reading : 7.1.1.15
boolean operators : 6.4
button box : 5.4.1
CA trace : (ib to 7.4.4
color : 6.2.1
coloring : 7.3.5
calculate
electrostatics : (ib to 7.6.4
hydrogen bonds
errors : 7.1.1.3
calculations : 6.5 | (ib to 7.6.10
distance : 7.6.1
on density or phimap : 7.4.7
user-specified : 6.5 | 7.6.2.1
calculator variables : 6.5
accessing via command line : 6.5.1
and the command line : 6.5.1
listing : 6.5
cavities
tutorial : 9.9
center
look command to focus on a spherical region : 6.2.3
of coordinates, calculating : 7.6.9
of mass, calculating : 7.6.10
on coordinates : 7.11.1.5
on selected atoms : 7.11.1.4
on unit cell : 7.11.1.6
recentering display : 7.11.1.3
setting via command line : 6.2.3
chain name
setting : 6.2.4.1
charge files
saving : 7.1.1.9
writing : 7.1.2.8
charge property
defined : 6.2.4.1
clipping : (ib to 7.11.4.1
2D contour position using tool : 7.11.4.1
and 2D contours : 7.3.8 | 7.4.6
and backface culling : 7.11.3.1
and surface cap : 7.4.5
and unit cell : 7.11.1.6
and Z-translation : 7.11.3.3
interaction with fog/depth cueing : 7.11.4.2
light position using tool : 7.11.4.3
color
and symmetry replicates : 7.7.11.6
as selection property : 6.3.5
background : see background color
default : 6.2.1
editor : 7.11.4
fog : 7.11.4.2
names : 7.11.4
printing default : 7.11.4
second default for atoms and bonds : 6.2.1.1 | 7.11.4
setting : 6.2.1
tutorial : 9.1
color map : 6.2.1
color names : 7.11.4
coloring
by property : see spectra
command line
accessing calculator variables via : 6.5.1
spock : 5.3
editing : 5.3.1
multiple commands : 5.3
shell escape : 5.3
substitution : 5.3
unix : 4.8
command line-calculator : see calculations
commands : (ib to 6.2.8 | looklook | looklook
#set angles : 6.5
#show angles : 6.5
#show functions : 6.5
#show variables : 6.5
ac : 6.2.1
actions
defined : 6.2
asurf : 6.2.7
bc : 6.2.1
blist : 6.2.2.3
cac : 6.2.1
cc : 6.2.1
centering : 6.2.3
coloring : 6.2.1
connect : 6.2.8
contour2d : 6.2.7
contour3d : 6.2.7
count : 6.2.5
define element : 6.2.6
delete : 6.2.8 | 7.7.4
draw : 6.2.8
endmac : 6.2.7
executing on picked atoms : 7.9.1
fetch : 6.2.2.1
hbc : 6.2.1
hblist : 6.2.2.3
hc : 6.2.1
help list : 6.2.2.3
hlist : 6.2.2.3
ic : 6.2.1
ilc : 6.2.1
ilist : 6.2.2.3
label : 6.2.7
lc : 6.2.1
list : 6.2.2.3
list formats : 6.2.2.3
listing information : 6.2.2.3
look : 6.2.3 | 6.2.3 | 9.1
ls : 6.2.2.3
mac : 6.2.7
macdef : 6.2.7
makeacc : 6.2.7
makesurf : 6.2.7
mass : 6.2.2.3
menu : 6.2.8
mutate : 6.2.7
nc : 6.2.1
overview : 6
resume : 6.2.2.1 | 6.2.2.1
printing information : 6.2.2.3
QUIT : 6.2.8 | 6.2.8
read : 6.2.2.1
read files : 6.2.2.1
remake : 6.2.8 | 9.12
renumber : 6.2.8
rlist : 6.2.2.3
rotation : 6.2.3
rotation, translation and scale : 6.2.3
save view : 6.2.3
saving and recalling views : 6.2.3
sc : 6.2.1
selection
defined : 6.3
selections
defined : 6
set ap1 : 6.2.4.1
set ap2 : 6.2.4.1
set chain : 6.2.4.1
set charge : 6.2.4.1
set distance : 6.2.4.1
set it : 6.2.4.1
set iv : 6.2.4.1
set list command : 6.2.2.3
set list format : 6.2.2.3
set p : 6.2.4.1
set radius : 6.2.4.1
set sa : 6.2.4.1
set structure : 6.2.4.1
setting atom properties : 6.2.4
show helices : 6.2.2.3
show rotation : 6.2.2.3
show sheets : 6.2.2.3
show variables : 6.2.2.3
show version : 6.2.2.3
silent : 6.2.2.1
slist : 6.2.2.3
structure : 6.2.8
subdef : 6.2.7
swap : 6.2.8
syntax : 6
title : 6.2.7
tlist : 6.2.2.3
translation : 6.2.3
vc : 6.2.1
view : 6.2.3
vsubdef : 6.2.7
wc : 6.2.1
xr : 6.2.3
Xt : 6.2.3 | 6.2.3
yr : 6.2.3
Yt : 6.2.3 | 6.2.3
zap : 6.2.8
zoom : 6.2.3
zr : 6.2.3
Zt : 6.2.3 | 6.2.3
conference mode : 7.1.7
conferencing : 7.1.7 to 7.1.7.14 | 9.13
and history : 8.3
setup : 4.4
Constructive Solid Geometry : 7.4.5.1
contours : (ib to 7.4.6
2D : 7.3.8
creating via command line : 6.2.7
inside color : 7.11.5
position of 2D plane : 7.11.4.1
tutorial : 9.7
control panel : 7.1.8
crystal parameters : 7.1.1.3
editing : 7.7.11.3
CSG : 7.4.5.1
cursor : 5.1
customization : 4.6
colors : 7.11.4
default colors : 6.2.1
dials : 5.4.2 | 7.11.5.2
history file path : 8
paths : 4.1
preferences file : see .spockrc
radii, charges and atom colors : 6.2.6
X application defaults file : 5.3.1.1
degrees
and calculator : 6.5
deleting : see also zap
atoms : 6.2.8 | 7.7.4
contours : 7.4.6
electron density maps : 7.4.7.5
everything : 6.2.8 | 7.1.3
hydrogen bonds : 7.7.10.1
interactions : 7.4.12 | 7.9.4
phimaps : 7.6.4
text : 5.3.1
density mask : 7.4.7.8
depth cueing : see fog
dials : 5.4 | 5.4.2
customization : 7.11.5.2
fake : 7.11.5.1
rotating subsets with : 7.8
sensitivity : 5.4.2 | 7.1.8
distance
between picked atoms : 7.9.1
indicating on screen : 7.4.12
distance calculations
tutorial : 9.2
distance partner property
and calculator : 6.5
distance partner\\property
defined : 6.2.4.1
distance property
calculating : 7.6.1
defined : 6.2.4.1
DNA spokes : 7.3.14 | (ib to 7.4.10
double buffering, swapping buffer : 6.2.8
drawing on surfaces : see subsets, graphical definition
dssp : 4.7 | 7.7.8
reading files : 7.1.1.7
edit menu : 7.2
electron density map : (ib to 7.4.7.13
reading : 7.1.1.14
solid contours of : 7.4.7.3
tutorial : 9.8
writing : 7.1.2.15
electrostatic contours : see contours
electrostatic potential map : see phimap
element definition : 6.2.6
element number
selection on : 6.3.4
environment variables : 6.2.5 | 6.5.1
help and : 7.12
listing : 6.2.2.3
setting and creating : 6.2.5
exernal objects
file format : 17.3
exporting images : see image export
external applications : 4.7
external control of spock : 7.1.6
external objects : 7.1.1.13
and raster3d export : 7.1.2.11
and vrml : 7.1.2.13
FBRT : 7.7.13 | 7.8
fetch a PDB file
tutorial : 9.1
filename extensions : 6.2.2.1
files
history, reading : 7.1.1.5
reading : 7.1.1
reading via command line : 6.2.2.1
FILLED subset : 7.8 | 7.11.3.3
fog : 7.11.3.1 | 7.11.3.3 | 7.11.4.2
font
and Molscript : 7.1.2.10.1
and raster3d : 7.1.2.11
and vector PostScript : 7.1.2.12.1
for labels and annotations, setting : 7.4.11
interaction label : 7.4.12
mapping for raster3d and PostScript : 14
fractional coordinates : 7.7.11.1
frodo : 7.7.13
full-screen : 5.2 | 7.11.3.1
function keys : 5.2
general atom properties
defined : 6.2.4.1
general vertex (surface) properties
defined : 6.2.4.1
ghostview : 4.7
GIF : 4.7 | 7.1.2.12 | 7.11.3.1 | 8.1.2
global material : 7.11.4.2
graphical surface selection : see subsets, graphical definition
graphics menu : (ib to 7.11.5.2
grasp : 4.7 | 6
helices : (ib to 7.4.8
building : 7.4.8
defining : 7.4.8
distance and angle calculations : 7.9.2
listing : 6.2.2.3
picking : 7.9.2
printing data on : 6.2.2.3
help
environment variables : 4.6.3
help menu : (ib to 7.12
history : (ib to 8.1.5
multiple spock sessions and : 4.8.1
reading files : 7.1.1.5
saving : 7.1.2.6
vs command files : 8
vs. macro files : 7.10
history playback
QUIT vs. quit : 6.2.8
reading, pausing, resuming, and aborting : 6.2.2.1 | 7.1.4
turning off rendering during : 6.2.8
hydrogen bonds : 7.3.2
color : 6.2.1
creating manually : 7.7.13
deleting : 7.7.10.1 | 7.7.13
DNA cylinders and : 7.3.14
from PDB CONECT records : 7.1.1.3
listing : 6.2.2.3
secondary structure and : 7.7.7
image export : 7.1.2.12
Molscript : see Molscript
raster3d : see raster3d
vrml : see vrml
installation : 4.1
interactions : (ib to 7.4.12
creating : 7.9.4
deleting : 7.9.4
editing : 7.9.4
file format : 17.1
files : 7.1.1.11
from PDB salt bridges : 7.1.1.3
label color : 6.2.1
listing : 6.2.2.3
properties : 7.4.12
selection : 6.3.4
setting type : 6.2.4.1
setting value : 6.2.4.1
writing : 7.1.2.14
interpolation : 7.6.4
JPEG : 4.7 | 7.11.3.1
labels : (ib to 7.4.11
and Molscript : 7.1.2.10
and raster3d : 7.1.2.11
and vector PostScript : 7.1.2.12.1
coloring : 6.2.1
default colors : 6.2.1
font selection : 7.4.11
picking : 7.9.3
setting via command line : 6.2.7
licensing : 4.3
lighting : 7.11.3.1 | (ib to 7.11.4.3
light source position : 7.11.3.3
Linux
performance : 7.11.3.1 | 7.11.3.1
LIST defined : 6.3
lists
.spocklist file : 6.2.2.3
calculator\\variables : 6.5
controlling destination : 6.2.2.3
format specification : 6.2.2.3
generating : 6.2.2.3
spawning external programs via : 6.2.2.3
lynx : 4.7
macros : (ib to 7.10.2
defining via command line : 6.2.7
mapped to button box : 5.4.1
running from command line : 6.2.7
saving : 7.1.2.5
vs history files : 8
magnification
setting : 5.1 | 7.11.3.3
setting via command line : 6.2.3
MARKED subset : 7.8 | 7.11.3.3
mass
calculating : 6.2.2.3 | 7.6.5
materials : see also fog, transparency | (ib to 7.11.4.2
and contour transparency : 7.4.6
and raster3d : 7.1.2.11
and surface transparency : 7.4.5
backface : 7.4.5
in external objects : 17.3
matrix
applying : 7.7.11.4
entering : 7.11.3.4
printing : 6.2.2.3 | 7.11.3.4
modeling : (ib to 7.7.19
and picking menu : 7.9.5
molecular surface
building : 7.4.5
creating via command line : 6.2.7
molecules
listing : 6.2.2.3
molscript : 4.7 | 6.2.4.1 | 9.6
export options : 7.1.2.10
limitations : 7.1.2.10.1
saving view to : 7.1.2.10
MORASS files : 4.7 | 7.1.1.12
motion
dials : 5.4
mouse : 5.1
tutorial : 9.1
mouse
light position and : 7.11.4.3
motion control with : 5.1
picking : 7.9
second button functions : 5.1 to 7.11.3.3 | (ib
sensitivity : 5.1 | 7.1.8
tutorial : 9.1
movies : 4.7 | 7.1.2.12 | 7.10.2 | 7.11.3.1 | 8.1.2
tutorial : 9.12
MPEG : 4.7 | 7.1.2.12 | 7.11.3.1 | 9.12
mutation : 7.7.13 | 7.7.14
netscape : 4.7
nographics : 8.2
normalization : 7.6.2.1
objects, external : see external objects
or-based selections : 6.4
orientation
setting : 5.1
setting via command line : 6.2.3
pdb files
automatic downloading : 6.2.2.1
reading : 7.1.1.3
sorting : 7.7.1 | 17.5
writing : 7.1.2.3
performance : 7.11.3.1
and 2D contours : 7.4.6
and atom mode : 7.4.2
and auxiliary clip planes : 7.11.4.1
and backface culling : 7.11.3.1
and dithering : 7.11.3.1
and history playback : 6.2.8
and lighting : 7.11.4.3
and line antialiasing : 7.11.3.1
and PB solver : 7.6.4 | 7.6.4
and quick motion : 7.11.3.1
and scene antialiasing : 7.11.2.1
and transparency : 7.11.3.1
and worm type : 7.4.3
with PostScript printing : 7.1.2.12.1
periodic table : 6.2.6
phimaps
and calculator : 6.5
calculating : 7.6.4
file format : 17.2
tutorial : 9.7
writing : 7.1.2.7
picking : 5.1 | (ib to 7.9.1
Poisson-Boltzmann equation : 7.6.4
postscript : 4.7 | 7.1.2.12 | 7.1.2.12.1 | 7.1.10 | 9.6
raster vs bitmap : 7.1.2.12.1
tips : 7.1.2.12.1
potential property
defined : 6.2.4.1
PPM : 7.1.2.12 | 7.11.3.1
predefined sets
selection with : 6.3.2
preferences : 7.1.9
preferences file : see .spockrc
printing : 7.1.10
probe radius : 7.4.5 | 7.6.3.1 | 7.6.3.2
projection syntax : 6.3.3 | 6.4.1 | 7.9.1
property calculations : see calculations
pseudo density : 7.4.7.11
quaternion : 7.4.8 | 7.7.2
QuickTime : 7.1.2.12 | 9.12
QUIT vs. quit : 6.2.8 | 8
radians
and calculator : 6.5
radius files
reading : 7.1.1.10
saving : 7.1.2.9
radius of gyration : 7.6.7
RANGE defined : 6.3
rasmol : 6
raster3d : 4.7 | 9.6
limitations : 7.1.2.11.3
reading : 7.1.1.13
saving view to : 7.1.2.11
renumbering residues : 6.2.8
residues
listing : 6.2.2.3
RGB : 7.1.2.12
ribbon : see worms
RMS deviation
calculating : 7.6.8
of helix atoms from axis : 6.2.2.3
rotamer : 7.7.12 | 7.7.13
file format : 17.4
rotation
independent õf molecules : 7.7.13
removing : 7.11.1.2
setting : 5.1
setting via command line : 6.2.3
subset, independent : 7.8
rotation matrix : see matrix
salt bridges : 7.1.1.3
scale
and clipping box depth : 7.11.4.1
setting : 5.1 | 7.11.3.3
setting via command line : 6.2.3
screen coordinates : 6.2.3
scribing : see subsets, graphical definition
secondary structure
and worms : 6.2.1.2 | 6.2.4.1
calculating : 7.7.7
dssp and : 7.1.1.7
editor : 7.7.6 to 7.7.6
helix/sheet assignments and : 7.4.8
Molscript and : 7.1.2.10
PDB files and : 7.1.1.3
setting via command line : 6.2.4.1
structure command : 6.2.8
worm representation : 7.4.3
secondary structure property
defined : 6.2.4.1
selection : 6.3
a= : 6.3.2
ac= : 6.3.5
altloc : 6.3.2 | 7.1.1.3
an= : 6.3.1
and calculations : 7.6.2.6
annotation : 6.3.4
ap1= : 6.3.3
ap2= : 6.3.3
atom and residue number : 6.3.1
atom properties charge, color, etc. : 6.3.3
atom vs. vertex actions and : 6.3.3
atom, residue, chain, and subset names : 6.3.2
bc= : 6.3.5
bcnt= : 6.3.3
ch= : 6.3.2
combining selections : 6.4
d= : 6.3.3
dp= : 6.3.3
element number : 6.3.4
element= : 6.3.4
hbcnt= : 6.3.3
helix and sheet negations : 6.3.4
hn= : 6.3.4
in= : 6.3.4
interaction : 6.3.4 | 7.4.12
ip= : 6.3.3
it= : 6.3.3
iv= : 6.3.3
lc= : 6.3.5
m= : 6.3.4
model= : 6.3.4
molecule number : 6.3.4
nn= : 6.3.4
object number : 6.3.4
on color : 6.3.5
on coordinates : 6.3.3
p= : 6.3.3
pdban= : 6.3.1
predefined sets : 6.3.2
q= : 6.3.3
r= : 6.3.2
radius= : 6.3.3
rn= : 6.3.1
s= : 6.3.4
sa= : 6.3.3
sn= : 6.3.4
sub= : 6.3.2
tn= : 6.3.4
tutorial : 9.1
vc= : 6.3.5
vd= : 6.3.3
vn= : 6.3.4
vp1= : 6.3.3
vp2= : 6.3.3
vp= : 6.3.3
vsub= : 6.3.2
vX= : 6.3.3 | 6.3.3
vY= : 6.3.3 | 6.3.3
vZ= : 6.3.3 | 6.3.3
wc= : 6.3.5
X= : 6.3.3 | 6.3.3
Y= : 6.3.3 | 6.3.3
Z= : 6.3.3 | 6.3.3
session files
reading : 7.1.1.1
writing : 7.1.2.1
sheets : (ib to 7.4.9
distance and angle calculations : 7.9.2
listing : 6.2.2.3
picking : 7.9.2
printing data on : 6.2.2.3
shininess : 7.11.4.2
size files : see radius files
slab : 5.4.2 | 7.11.4.1 | 7.11.5.1
slave files : 7.1.6
spectra : 7.3.19 | (ib to 7.4.13
control usage : 7.3.19
tutorial : 9.7
spockhist : 4.8.1
.spockrc
and atom definitions : 6.2.6
and color definitions : 7.11.4
and dial customization : 7.11.5.2
and display options : 7.3
and macros : 7.10
and status line help : 7.12
and stereo viewing angles : 7.11.3.2
as preferences file : 7.1.1.4 | 7.1.2.4
default macros and : 7.10
read on startup : 4.8 | 4.8
starting over : see delete all
statistics : 4.6.4.2 | 7.6.2.1
status line help : 7.12
stereo : 7.11.3.2
and Molscript : 7.1.2.10
mouse control of : 7.11.3.3
setting parameters via fake dials : 7.11.5.1
string comparisons : 6.3.2
structure property : 7.4.3
subsets : (ib to 7.8
defining via command line : 6.2.7
graphical definition : 7.8 | (ib to 7.11.3.3
tutorial : 9.10
scribing : 7.8
superimposition : 7.4.8 | 7.6.8 | 7.7.2
surface
subsets : see subsets
surface area : see accessible surface area
surface area property
defined : 6.2.4.1
surfaces : (ib to 7.4.5.1
cap color : 6.2.1
coloring : 6.2.1
inside color : 7.11.5
mapping atom properties to : 7.6.2.3
smoothing : 7.4.5
tutorial : 9.2
symmetry : see also fractional coordinates, crystal parameters
and picking : 7.9 | 7.9.1
displaying : 7.7.11.5
library file : 7.7.11.3
tie faces : 7.11.5
TIFF : 7.1.2.12
torsion angles
between picked atoms : 7.9.1
rotating about : 7.7.13 | 7.8
transformation matrix : see matrix
translation
setting : 5.1
setting via command line : 6.2.3
transparency
and contours : 7.4.6
and electron density maps : 7.4.7.3
and raster3d : 7.1.2.11
and surfaces : 7.4.5
opacity material property : 7.11.4.2
style of : 7.11.3.1
turns
listing : 6.2.2.3
tutorials : 9
typographic conventions : 6.1
undo : 7.2
coloring commands : 6.2.1
FBRT operations : 7.7.18
mutation : 7.7.15
subset rotations : 7.8
torsion angle rotations : 7.7.16
viewing orientation change : 7.11.1.7
unit cell : 7.3.16 | 7.7.11.3 | 7.7.11.5
centering on : 7.11.1.6
user interface
hiding : 5.2
Van der Waal
assigning radius : 6.2.6
radius in density mask calculations : 7.4.7.8
surface in distance calculations : 7.6.1
variables
calculator : see calculator variables
environment : see environment variables
version
printing : 6.2.2.3
vertex
subsets : see subsets
vertex distance property
defined : 6.2.4.1
vertex potential\\property
defined : 6.2.4.1
vertex properties
and calculator : 6.5
view
restoring initial : 7.11.1.1
saving and recalling : 7.5
saving and recalling, via command line : 6.2.3
view files
reading : 7.1.1.2
writing : 7.1.2.2
VRML : 7.1.2.13 | 9.6
and external objects : 7.1.2.13
best worm type : 7.4.3
limitations : 7.1.2.13.1
whirlgif : 4.7
wildcards in string comparisons : 6.3.2
worm
inside color : 7.11.5
worms : (ib to 7.4.3
negative colors : 6.2.1.2 | 6.2.1.2
secondary structure display
errors : 7.1.1.3
shadow colors : 6.2.1.2 | 7.4.3
style tutorial : 9.1
www : 4.6.3 | 4.7 | 4.7 | 7.1.2.12 | 7.11.3.1 | 8.1.2
and spock help : 7.12
XPLOR : see electron density map
z-translation
setting : 7.11.3.3
zap : 6.2.8
zoom factor
setting : 5.1 | 7.11.3.3
setting via command line : 6.2.3



Jon Christopher
Tue Sep 14 16:44:48 CDT 1999