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