Index

A

active atoms 1, 2

save

specify

Active Atoms palette 1, 2

Type in a Selection

Active Atoms Utilities palette 1, 2

amino acid residue topology file

AMINO.RTF

AMINOH.RTF

Applications menu 1, 2, 3

Builders

generated commands

pull-right selections

atom

clearing IDs

colors

display

label

pick

selected

unselected

atom number

atom specification format

atom specification wildcards

Atom Type File format 1, 2

B

brick map file format 1, 2

Brookhaven Data Bank topology file

Builders menu

button box 1, 2, 3

C

Calculate menu 1, 2

generated commands

pull-right selections

Cambridge Database FDAT file format

carbohydrate residue topology file

CHARMm ASCII file format

CHARMm binary file format

CHARMm binary property file format

CHARMm menu 1, 2

generated commands

pull-right selections

CHARMm/X-PLOR PDB variant file format

ChemNote data file format

chrmpost.typ file

chrmtype.typ file

clip zone

color

assign to structure 1, 2

customize for atoms

default display colors

define for menus 1, 2

define for windows 1, 2

hue 1, 2

intensity 1, 2

saturation 1, 2

Color Atoms palette 1, 2, 3

Proximity Tools

Color Definitions menu

All Definitions 1, 2

Color Dials Set 1, see Dial Emulator Set 5

Color Schemes and Utilities palette 1, 2, 3

Command Line 1, 2

command-driven QUANTA

.cst file 1, 2, 3

Current Session menu

Function Keys

Customize Color Settings dialog box

CPK Drawings

Display Colors 1 to 14

ID/Labels

D

Dial

dial box

Dial Emulator 1, 2, 3, 4

Set 1 Global Transformations

Set 2 Fragment and Set Transform

Set 3 Torsions

Set 4 Atom Translations

Set 5 Atom Colors 1-6, Atom IDs and Labels, H Bond Colors

Set 6 Atom Colors 7-14

Set 7 Menu Colors 1, 2

Set 8 Dynamics

Set A Comparison Flashing

Set U User Defined Dials

Dial Set 5 1, 2

Dial Set 6 1, 2

dialog box 1, 2

E

Edit menu

Active Atoms

generated commands

pull-right selections

external devices

external file formats 1, 2

F

File Librarian 1, 2

import

pull-right selections

Save As

file name

file organization

fractional coordinates (Old Cambridge Database file format)

function keys

function keys, binding commands to

G

Geometry palette

Atom

1, 2

1, 2, 3

1, 2

Delete Distance Monitor 1, 2

1, 2

1, 2, 3

List Neighbors

1, 2

Show Distance Monitors 1, 2

graphics tablet 1, 2

performing fragment and atom transformations

performing global transformations

performing other transformations

performing user-defined transformations

rotating torsions

Gromos atom file format

gromos.ord file

H

hydrogen atom addition template file

hydtpl.dat file

I

ID 1, 2

Information menu 1, 2

Current Session

generated commands

pull-right selections

IONS.RTF

K

keyboard

enter command mode

enter data

exit command mode

keyboard commands 1, 2, 3, 4

Konnert file format

L

label

Label Atoms Components and Utilities palette

Segment Name

Show Labels

Label Atoms menu 1, 2

Residue Name

Selection Tools 1, 2

Label Atoms palette 1, 2, 3

Alpha-Carbon Atoms

Clear

First Atom of Residue

Include

Label Components and Utilities palette 1, 2

Residue ID

Residue Name

Show Labels 1, 2

log file, creating

M

.mbk file 1, 2

menu 1, 2

menu bar 1, 2, 3

menu types

Message Line

metal ions topology file

Modeling palette

.mol file

Molecular Modeling mode

Molecular Modeling Table.

Molecule Management Table

Molecule window 1, 2, 3

mouse 1, 2

mouse cursor

MSF

MSF format 1, 2

N

nucleic acid residue topology file

P

palette 1, 2, 3

using selections 1, 2

PEPTIDE.msf 1, 2, 3

porphyrin topology file

PORPHYRIN.RTF

Preference menu

generated commands

pull-right selections

Preferences menu

Color Definitions 1, 2, 3

customizing the button box

ID Mode and Style

MSF Settings

sticky menu

Protein Data Bank format

proximity dimensions

Proximity Selections palette 1, 2, 3

Clear

proximity tools 1, 2

PSF

.psf file

pull-down menu

pull-right menu 1, 2

Q

QM coordinate file format

.qmc file

.qpt file

QUANTA

exit

restart

set environment 1, 2

start 1, 2

QUANTA functions

QUANTA plot file format

QUANTA script examples

QUANTA windows 1, 2

quanta.tpl file

R

record scripts

Reset View

residue

residue topology file

RNA.RTF

RNAH.RTF

RTF

.rtf file

S

script

adding commands with a text editor

branching and looping

scripting <$startpage

scripts

selection commands 1, 2, 3

spaceball 1, 2

performing transformations

start-up files

sticky menu

enable

structure

customize colors 1, 2

display 1, 2, 3, 4, 5

edit

generate

move 1, 2

rotate 1, 2

scale

translate 1, 2

system commands 1, 2

T

TCL

backslash substitution

basic command syntax

built-in commands

command results

command substitution with brackets

comments

data types

expressions

grouping arguments with braces

grouping arguments with double-quotes

lists

separating commands with semi-colons

Variable substitution with $

variables- scalars and arrays

TCL scripting control

template files format 1, 2

Textport

tmplatall.tlf file

tmplatnoh.tlf file

tmplatpol.tlf.tlf file

Tool Command Language (TCL) <$endpage

Tool Command Language (TCL) <$startpage

U

UNIX operating system

user interface

V

View menu 1, 2

generated commands

pull-right selections