Index

amino acid library

Mutate to

and-based selections

Complex Queries

angles

and calculator: The Command-line Calculator:
between picked atoms: Identify object

annotations

see also labels | (ib to Labels

coloring: Coloring
font selection: Labels
selection: Selection by object or

antialiasing

Image: | Graphics modes | Graphics modes | Saving and exporting images

lines: Graphics modes
scene: Antialias scene

application defaults file

For X-experts:

atom information format

Identify object

atom labels

see labels

atom properties

and calculator: The Command-line Calculator:
setting: Parameters

atom vs. vertex actions

Atom properties

atomic number

see element number

atomic radius property

see also radius files

default: The internal periodic table
defined: Atom Parameters:
setting: Atom Parameters:

atoms

(ib to Atoms

copying: Copy Atoms
listing: Output:
subsets: see subsets

autosave

Prefrerences

auxiliary clipping planes

see clipping

backface

Material Tool | Tie faces

color: Surfaces
culling: Postscript Options: | Graphics modes
material: Material Tool

background color

Coloring | Coloring

batch-mode

Nographics mode

Bessel functions

bonds

(ib to Bonds

creating manually: Structure Editing
deleting: Structure Editing
listing: Output:
recalculating: Control
secondary bond mode: Introduction to spock: movement,
secondary drawing mode: Bond Coloring
style tutorial: Introduction to spock: movement,

bones

Bones

bones files

reading: Bones file:

boolean operators

Complex Queries

button box

Buttons

CA trace

(ib to CA trace

color: Coloring
coloring: CA-trace

calculate

electrostatics

(ib to Electrostatics

hydrogen bonds

errors: PDB File:

calculations

The Command-line Calculator: | (ib to Center of mass

distance: Distance
on density or phimap: Density maps
user-specified: The Command-line Calculator: | Math on One property:

calculator variables

accessing via command line: Calculator Variables:
and the command line: Calculator Variables:
listing: The Command-line Calculator:

cavities

tutorial: Finding internal cavities in

CCP4

see electron density map

center

look command to focus on a spherical region: Viewing Commands
of coordinates, calculating: Center of coordinates
of mass, calculating: Center of mass
on coordinates: Center on coordinates
on selected atoms: Center on selection
on unit cell: Center on cell
recentering display: Center
setting via command line: Viewing Commands

chain name

setting: Atom Parameters:

charge files

saving: Charge File:
writing: Charge File:

charge property

defined: Atom Parameters:

clipping

(ib to Clip Tool

2D contour position using tool: Clip Tool
and 2D contours: 2D Contours | Contours
and backface culling: Graphics modes
and surface cap: Surfaces
and unit cell: Center on cell
and Z-translation: Mouse Bindings
interaction with fog/depth cueing: Material Tool
light position using tool: Light Tool

color

and symmetry replicates: Color by number
as selection property: Selecting on color
background: see background color
default: Coloring
editor: Coloring
fog: Material Tool
names: Coloring
printing default: Coloring
second default for atoms and bonds: Bond Coloring | Coloring
setting: Coloring
tutorial: Introduction to spock: movement,

color map

color names

coloring

by property: see spectra

command line

accessing calculator variables via

Calculator Variables:

spock

Command Line

editing: Command line editing
multiple commands: Command Line
shell escape: Command Line
substitution: Command Line

unix

Running Spock

command line-calculator

see calculations

commands

(ib to Control | looklook | looklook

#set angles

#show angles

#show functions

#show variables

ac

The internal periodic table

actions

defined: Actions

asurf

bc

blist

cac

cc

centering

coloring

connect

contour2d

contour3d

count

Environment Variables

define element

delete

Control | Delete Atoms

draw

endmac

Object Creation

executing on picked atoms

fetch

hbc

hblist

hc

help list

hlist

ic

ilc

ilist

label

lc

list

list formats

listing information

look

Viewing Commands | Viewing Commands | Introduction to spock: movement,

ls

mac

macdef

makeacc

makesurf

mass

menu

mutate

nc

overview

resume

Input: | Input:

printing information

QUIT

Control | Control

read

Input:

read files

Input:

remake

Control | Making movies

renumber

rlist

rotation

rotation, translation and scale

save view

saving and recalling views

sc

selection

defined: Selection

selections

defined: Command Language

set ap1

set ap2

set chain

set charge

set distance

set it

set iv

set list command

set list format

set p

set radius

set sa

set structure

setting atom properties

show helices

show rotation

show sheets

show variables

show version

silent

slist

structure

subdef

swap

syntax

title

tlist

translation

vc

view

vsubdef

wc

xr

Xt

Viewing Commands | Viewing Commands

yr

Yt

Viewing Commands | Viewing Commands

zap

zoom

zr

Constructive Solid Geometry

Zt

Viewing Commands | Viewing Commands

conference mode

Conference

conferencing

Conference to Allow shell commands | Conferencing

and history: Conference mode
setup: Conferencing setup

Constructive Solid Geometry

contours

(ib to Contours

2D: 2D Contours
creating via command line: Object Creation
inside color: Tie faces
position of 2D plane: Clip Tool
tutorial: Electrostatics calculations

control panel

Control Panel

crystal parameters

PDB File:

editing: Edit crystal parameters

CSG

Constructive Solid Geometry

cursor

Mouse Control

customization

Customization

colors: Coloring
default colors: Coloring
dials: Dials | Customize Dial Box
history file path: History / Command Files
paths: For system administrators
preferences file: see .spockrc
radii, charges and atom colors: The internal periodic table
X application defaults file: For X-experts:

degrees

and calculator: The Command-line Calculator:

deleting

see also zap

atoms: Control | Delete Atoms
contours: Contours
electron density maps: Delete map
everything: Control | Delete All
hydrogen bonds: Delete All H-Bonds
interactions: Interactions | Interactions
phimaps: Electrostatics
text: Command line editing

density mask

Make positive/negative mask

interactive drawing: Mask drawing

depth cueing

see fog

dials

Dials and Buttons | Dials

customization: Customize Dial Box
fake: Fake dial box
rotating subsets with: Subsets
sensitivity: Dials | Control Panel

distance

between picked atoms: Identify object
indicating on screen: Interactions

distance calculations

tutorial: Surfaces

distance partner property

and calculator: The Command-line Calculator:

distance partner\\property

defined: Atom Parameters:

distance property

calculating: Distance
defined: Atom Parameters:

DNA spokes

DNA spokes | (ib to DNA spokes

double buffering, swapping buffer

The internal periodic table

drawing on surfaces

see subsets, graphical definition

dssp

Helper applications | Run DSSP

reading files: DSSP File:

edit menu

Edit

electron density map

(ib to Wide lines

reading: XPLOR map file: | CCP4 map file:
solid contours of: Make 3D contour object
tutorial: Cleaning electron density maps
writing: XPLOR map file: | CCP4 map file:

electrostatic contours

see contours

electrostatic potential map

see phimap

element definition

element number

selection on: Selection by object or

environment variables

Environment Variables | Calculator Variables:

help and: Help
listing: Output:
setting and creating: Environment Variables

exernal objects

file format: External objects (.spo) file

exporting images

see image export

external applications

Fractionalize coordinates

external control of spock

Slave to file

external objects

External Objects File:

and raster3d export: Raster3D:
and vrml: VRML 1.0 and VRML

FBRT

Structure Editing | Subsets

fetch a PDB file

tutorial: Introduction to spock: movement,

filename extensions

Input:

files

history, reading: History File:
reading: Open
reading via command line: Input:

FILLED subset

Subsets | Mouse Bindings

fog

Graphics modes | Mouse Bindings | Material Tool

font

and Molscript: Incompatibilities/limitations:
and raster3d: Raster3D:
and vector PostScript: Postscript Options:
for labels and annotations, setting: Labels
interaction label: Interactions
mapping for raster3d and PostScript: Font mapping for Raster3D

fractional coordinates

frodo

Structure Editing

full-screen

Function Keys | Graphics modes

function keys

Function Keys

general atom properties

defined: Atom Parameters:

general vertex (surface) properties

defined: Atom Parameters:

ghostview

For system administrators

GIF

Helper applications | Image: | Graphics modes | Loops LOOP/ENDL

global material

Material Tool

graphical surface selection

see subsets, graphical definition

graphics menu

(ib to Customize Dial Box

grasp

Helper applications | Command Language

helices

(ib to Helices

building: Helices
defining: Helices
distance and angle calculations: Helix/Sheet Information
listing: Output:
picking: Helix/Sheet Information
printing data on: Output:

help

environment variables: External commands/Help:

help menu

(ib to Help

history

(ib to Execution control

multiple spock sessions and: Two concurrent spock sessions:
reading files: History File:
saving: History:
vs command files: History / Command Files
vs. macro files: Macros

history playback

QUIT vs. quit: Control
reading, pausing, resuming, and aborting: Input: | Pause Playback
turning off rendering during: Control

hydrogen bonds

H-Bonds

color: Coloring
creating manually: Structure Editing
deleting: Delete All H-Bonds | Structure Editing
DNA cylinders and: DNA spokes
from PDB CONECT records: PDB File:
listing: Output:
secondary structure and: Calculate Secondary Structure

image export

Image:

Molscript: see Molscript
raster3d: see raster3d
vrml: see vrml

installation

interactions

(ib to Interactions

creating: Interactions
deleting: Interactions
editing: Interactions
file format: Interactions file
files: Interactions File:
from PDB salt bridges: PDB File:
label color: Coloring
listing: Output:
properties: Interactions
selection: Selection by object or
setting type: Atom Parameters:
setting value: Atom Parameters:
writing: Interactions File:

interpolation

Electrostatics

JPEG

Helper applications | Graphics modes

labels

(ib to Labels

and Molscript: Molscript:
and raster3d: Raster3D:
and vector PostScript: Postscript Options:
coloring: Coloring
default colors: Coloring
font selection: Labels
picking: Labels
setting via command line: Object Creation

licensing

License information:

lighting

Graphics modes | (ib to Light Tool

light source position: Mouse Bindings

Linux

performance: Graphics modes | Graphics modes

LIST defined

Selection

lists

.spocklist file: Output:
calculator\\variables: The Command-line Calculator:
controlling destination: Output:
format specification: Output:
generating: Output:
spawning external programs via: Output:

lynx

macros

(ib to Macro packages

defining via command line: Object Creation
mapped to button box: Buttons
running from command line: Object Creation
saving: Macros:
vs history files: History / Command Files

magnification

setting: Mouse Control | Mouse Bindings
setting via command line: Viewing Commands

MARKED subset

Subsets | Mouse Bindings

mass

calculating: Output: | Atom-based mass

materials

see also fog, transparency | (ib to Material Tool

and contour transparency: Contours
and raster3d: Raster3D:
and surface transparency: Surfaces
backface: Surfaces
in external objects: External objects (.spo) file

matrix

applying: Apply 4x4 matrix
entering: Viewing matrices
printing: Output: | Viewing matrices

modeling

(ib to Lock FBRT

and picking menu: Modeling

molecular surface

building: Surfaces
creating via command line: Object Creation

molecules

listing: Output:

molscript

Helper applications | Atom Parameters: | Saving and exporting images

export options: Molscript:
limitations: Incompatibilities/limitations:
saving view to: Molscript:

MORASS files

Helper applications | Interactions File:

motion

dials: Dials and Buttons
mouse: Mouse Control
tutorial: Introduction to spock: movement,

mouse

light position and: Light Tool
motion control with: Mouse Control
picking: Picking
second button functions: Mouse Control | (ib to Mouse Bindings
sensitivity: Mouse Control | Control Panel
tutorial: Introduction to spock: movement,

movies

Helper applications | Image: | Macro packages | Graphics modes | Loops LOOP/ENDL

tutorial: Making movies

MPEG

Helper applications | Image: | Graphics modes | Making movies

mutation

Structure Editing | Mutate to

netscape

The internal periodic table

nographics

Nographics mode

normalization

Math on One property:

objects, external

see external objects

or-based selections

Complex Queries

orientation

setting: Mouse Control
setting via command line: Viewing Commands

pdb files

automatic downloading: Input:
reading: PDB File:
sorting: Sort atoms | Atom order library
writing: PDB File:

performance

Graphics modes

and 2D contours: Contours
and atom mode: Atoms
and auxiliary clip planes: Clip Tool
and backface culling: Graphics modes
and dithering: Graphics modes
and history playback: Control
and lighting: Light Tool
and line antialiasing: Graphics modes
and PB solver: Electrostatics | Electrostatics
and quick motion: Graphics modes
and scene antialiasing: Antialias scene
and transparency: Graphics modes
and worm type: Worms
with PostScript printing: Postscript Options:

periodic table

phimaps

and calculator: The Command-line Calculator:
calculating: Electrostatics
file format: PhiMap file (.phi) files
reading: PhiMap File:
tutorial: Electrostatics calculations
writing: PhiMap File:

picking

Mouse Control | (ib to Identify object

Poisson-Boltzmann equation

Electrostatics

postscript

Helper applications | Image: | Postscript Options: | Print | Saving and exporting images

raster vs bitmap: Postscript Options:
tips: Postscript Options:

potential property

defined: Atom Parameters:

PPM

Image: | Graphics modes

predefined sets

selection with: Atom, Residue, Chain, Altloc,

preferences

Prefrerences

preferences file

see .spockrc

printing

probe radius

Surfaces | Atom-based areas and volumes | Surface-based areas and volumes

projection syntax

Atom properties | Projection | Identify object

property calculations

see calculations

pseudo density

Make pseudo density map

quaternion

Helices | Superimpose

QuickTime

Image: | Making movies

QUIT vs. quit

Control | History / Command Files

radians

and calculator: The Command-line Calculator:

radius files

reading: Radius File:
saving: Radius File:

radius of gyration

Radius of gyration

RANGE defined

Selection

rasmol

Command Language

raster3d

Helper applications | Saving and exporting images

limitations: Incompatibilities/limitations:
reading: External Objects File:
saving view to: Raster3D:

renumbering residues

residues

listing: Output:

RGB

Image:

ribbon

see worms

RMS deviation

calculating: RMS deviation
of helix atoms from axis: Output:

rotamer

Rotamer control | Structure Editing

file format: Rotamer library

rotation

independent õf molecules: Structure Editing
removing: Reset Rotations
setting: Mouse Control
setting via command line: Viewing Commands
subset, independent: Subsets

rotation matrix

see matrix

salt bridges

PDB File:

scale

and clipping box depth: Clip Tool
setting: Mouse Control | Mouse Bindings
setting via command line: Viewing Commands

screen coordinates

Two concurrent spock sessions:

scribing

see subsets, graphical definition

secondary structure

and worms: Worm Coloring | Atom Parameters:
calculating: Calculate Secondary Structure
dssp and: DSSP File:
editor: Secondary structure editor to Secondary structure editor
helix/sheet assignments and: Helices
Molscript and: Molscript:
PDB files and: PDB File:
setting via command line: Atom Parameters:
structure command: Control
worm representation: Worms

secondary structure property

defined: Atom Parameters:

selection

Selection

a=: Atom, Residue, Chain, Altloc,
ac=: Selecting on color
altloc: Atom, Residue, Chain, Altloc, | PDB File:
an=: Atom/Residue Numbering
and calculations: Enter new Selection String:
annotation: Selection by object or
ap1=: Atom properties
ap2=: Atom properties
atom and residue number: Atom/Residue Numbering
atom properties charge, color, etc.: Atom properties
atom vs. vertex actions and: Atom properties
atom, residue, chain, and subset names: Atom, Residue, Chain, Altloc,
bc=: Selecting on color
bcnt=: Atom properties
ch=: Atom, Residue, Chain, Altloc,
combining selections: Complex Queries
d=: Atom properties
dp=: Atom properties
element number: Selection by object or
element=: Selection by object or
hbcnt=: Atom properties
helix and sheet negations: Selection by object or
hn=: Selection by object or
in=: Selection by object or
interaction: Selection by object or | Interactions
ip=: Atom properties
it=: Atom properties
iv=: Atom properties
lc=: Selecting on color
m=: Selection by object or
model=: Selection by object or
molecule number: Selection by object or
nn=: Selection by object or
object number: Selection by object or
on color: Selecting on color
on coordinates: Atom properties
p=: Atom properties
pdban=: Atom/Residue Numbering
predefined sets: Atom, Residue, Chain, Altloc,
q=: Atom properties
r=: Atom, Residue, Chain, Altloc,
radius=: Atom properties
rn=: Atom/Residue Numbering
s=: Selection by object or
sa=: Atom properties
sn=: Selection by object or
sub=: Atom, Residue, Chain, Altloc,
tn=: Selection by object or
tutorial: Introduction to spock: movement,
vc=: Selecting on color
vd=: Atom properties
vn=: Selection by object or
vp1=: Atom properties
vp2=: Atom properties
vp=: Atom properties
vsub=: Atom, Residue, Chain, Altloc,
vX=: Atom properties | Atom properties
vY=: Atom properties | Atom properties
vZ=: Atom properties | Atom properties
wc=: Selecting on color
X=: Atom properties | Atom properties
Y=: Atom properties | Atom properties
Z=: Atom properties | Atom properties

session files

reading: Session File:
writing: Session File:

sheets

(ib to Sheets

distance and angle calculations: Helix/Sheet Information
listing: Output:
picking: Helix/Sheet Information
printing data on: Output:

shininess

Material Tool

size files

see radius files

slab

Dials | Clip Tool | Fake dial box

slave files

Slave to file

spectra

Spectra | (ib to Spectra

control usage: Spectra
tutorial: Electrostatics calculations

spockhist

.spockrc

and atom definitions: The internal periodic table
and color definitions: Coloring
and dial customization: Customize Dial Box
and display options: Display
and macros: Macros
and status line help: Help
and stereo viewing angles: Stereo
as preferences file: Preferences File: | Preferences File:
default macros and: Macros
read on startup: Running Spock | Running Spock

starting over

see delete all

statistics

Statistics: | Math on One property:

status line help

Help

stereo

Stereo

and Molscript: Molscript:
mouse control of: Mouse Bindings
setting parameters via fake dials: Fake dial box

string comparisons

Atom, Residue, Chain, Altloc,

structure property

Worms

subsets

(ib to Subsets

defining via command line

Object Creation

graphical definition

Subsets | (ib to Mouse Bindings

tutorial: Graphical surface selection

scribing

Subsets

superimposition

Helices | RMS deviation | Superimpose

surface

accessible: Surfaces
molecular: Surfaces
MSMS: Surfaces
subsets: see subsets

surface area

see accessible surface area

surface area property

defined: Atom Parameters:

surfaces

(ib to Constructive Solid Geometry

cap color: Coloring
coloring: Coloring
inside color: Tie faces
mapping atom properties to: Map Atom Property to
smoothing: Surfaces
tutorial: Surfaces

symmetry

see also fractional coordinates, crystal parameters

and picking: Picking | Identify object
displaying: Display symmetry
library file: Edit crystal parameters

tie faces

Tie faces

TIFF

Image:

tools menu

Tools

torsion angles

between picked atoms: Identify object
rotating about: Structure Editing | Subsets

transformation matrix

see matrix

translation

setting: Mouse Control
setting via command line: Viewing Commands

transparency

and contours: Contours
and electron density maps: Make 3D contour object
and raster3d: Raster3D:
and surfaces: Surfaces
opacity material property: Material Tool
style of: Graphics modes

turns

listing: Output:

tutorials

Tutorials

typographic conventions

Typographical conventions

undo

Edit

coloring commands: Coloring
FBRT operations: Undo FBRT
mutation: Undo last mutation
subset rotations: Subsets
torsion angle rotations: Undo TOR
viewing orientation change: Undo last orientation change

unit cell

Unit cell | Edit crystal parameters | Display symmetry

centering on: Center on cell

user interface

hiding: Function Keys

Van der Waal

assigning radius: The internal periodic table
radius in density mask calculations: Make positive/negative mask
surface in distance calculations: Distance

variables

calculator: see calculator variables
environment: see environment variables

version

printing: Output:

vertex

subsets: see subsets

vertex distance property

defined: Atom Parameters:

vertex potential\\property

defined: Atom Parameters:

vertex properties

and calculator: The Command-line Calculator:

view

restoring initial: Reset View
saving and recalling: View
saving and recalling, via command line: Viewing Commands

view files

reading: View File:
writing: View File:

VRML

VRML 1.0 and VRML | Saving and exporting images

and external objects: VRML 1.0 and VRML
best worm type: Worms
limitations: Incompatibilities/limitations:

whirlgif

Atom, Residue, Chain, Altloc,

wildcards in string comparisons

worm

inside color: Tie faces

worms

(ib to Worms

negative colors

Worm Coloring | Worm Coloring

secondary structure display

errors: PDB File:

shadow colors

Worm Coloring | Worms

style tutorial

Introduction to spock: movement,

www

and spock help: Help

XPLOR

see electron density map

z-translation

setting: Mouse Bindings

zap