T: Sub Index for SYBYL and UNITY Documentation

T chromosome

• Genetic Structure

TABLE

UNITY

• Access Post-processing in SYBYL

use in HQSAR

command

• HQSAR SET

printing

• Printing Spreadsheets

CLOSE

• Close a Spreadsheet or Table

COLUMN_APPEND

• Add a Column in a Spreadsheet or Table

command list

• List of TABLE Commands

CONFORMER

• CONFORMER Column Type

CONSENSUS

• Add a Column in a Spreadsheet or Table

COPY

• Create a Spreadsheet or Table from Existing Data

CREATE

• Create a Spreadsheet or Table from Existing Data

ENDMODE

• List of TABLE Commands

ENTER

• Enter Data in a Table via the Command Line

EVALUATE

• Calculate Cell Values

EXAMINE

• Interact with Graphs

expert's corner

• Expert's Corner

EXPORT

• Export Data from a Spreadsheet or Table to a File

EXTRACT

• Create a Spreadsheet or Table from Existing Data

GRAPH

COLUMN DISTRIBUTION

• Column Distribution Graph

DELETE

• Manage Graphs

DUMP

• Manage Graphs

HISTOGRAM

• Histogram

ISO_CONTOUR

• Isocontour Graph

LIST

• Manage Graphs

MESH

• Mesh Graph

REDRAW

• Customize Graphs

RESIZE

• Manage Graphs

SCATTER

• Scatter Graph

SHOW

• Manage Graphs

SWEEP

• Sweep Graph

TOGGLE

• Manage Graphs

VECTOR

• Vector Graph

IMPORT

• Import Data into a Spreadsheet or Table

LIST

• List Information about a Spreadsheet or Table

MODIFY

• Edit a Spreadsheet or Table

OPEN

• Open a Molecular Spreadsheet or Table

PRINT

• Print a Copy of the Spreadsheet or Table

RECALL

• Open a Molecular Spreadsheet or Table

ROW_APPEND

• Add a Row in a Spreadsheet or Table

SAVE

• Save a Molecular Spreadsheet or Table

SAVE_AS

• Save a Molecular Spreadsheet or Table

SPL_COLUMN_TYPE

• Define and Manage SPL Column Types

DEFINE

• Define an SPL Column Type via the Keyboard

DELETE

• Delete an SPL Column Type

INSTALL

• Install an SPL Column Type via the Keyboard

LIST

• List an SPL Column Type

UNINSTALL

• Uninstall an SPL Column Type

TO_HITLIST

• Save a Molecular Spreadsheet or Table

attributes

• Table Attributes

column and row expressions

• Row and Column Expressions

column types

• MSS Column Types

AMINO_ACID_NUMBER

• AMINO_ACID_NUMBER Column Type

AMPAC

• AMPAC_ANALYSIS Column Type

• AMPAC_COMPUTE Column Type

ANGLE

• ANGLE Column Type

ATOM_PAIR_FP

• ATOM_PAIR_FP Column Type

ATOMIC_COORDINATE

• ATOMIC_COORDINATE Column Type

CLOGP

• CLOGP Column Type

CMR

• CMR Column Type

COMFA

• COMFA Column Type

COMSIA

• COMSIA Column Type

CONFORMATIONAL_ANGLE

• CONFORMATIONAL_ANGLE Column Type

CONFORMER

• CONFORMER Column Type

CONSENSUS

• Add a Column in a Spreadsheet or Table

CPSA

• CPSA Column Type

DEF_ABS

• DEF_ABS Column Type

DICT_ANGLE

• DICT_ANGLE Column Type

DIPOLE_MOMENT

• DIPOLE_MOMENT Column Type

DISTANCE

• DISTANCE Column Type

DOUBLE

• DOUBLE Column Type

DOUBLE_ARRAY

• DOUBLE_ARRAY Column Type

ENERGY

• ENERGY Column Type

EVA

• EVA Column Type

EXPLICIT_DATA

• EXPLICIT_DATA Column Type

FAMILY

• FAMILY Column Type

FINGERPRINT

• FINGERPRINT Column Type

FLOAT

• FLOAT Column Type

FUNCTIONAL_DATA

• FUNCTIONAL_DATA Column Type

GRIDDED_DISTANCE

• GRIDDED_DISTANCE Column Type

HOLOGRAM

• HOLOGRAM Column Type

INT

• INT Column Type

INTER_LOOP_RMS

• INTER_LOOP_RMS Column Type

INTERESTING

• INTERESTING

KINETIC_ENERGY

• KINETIC_ENERGY Column Type

LOCAL_TEMPERATURE

• LOCAL_TEMPERATURE Column Type

MOL_WEIGHT

• MOL_WEIGHT Column Type

MOLPROP_AREA

• MOLPROP_AREA Column Type

MOLPROP_PSA

• MOLPROP_PSA Column Type

MOLPROP_PV

• MOLPROP_PV Column Type

MOLPROP_VOLUME

• MOLPROP_VOLUME Column Type

MOPAC

• MOPAC Column Type

NEIGHBORS

• NEIGHBORS Column Type

NUMBER_OF_HBONDS

• NUMBER_OF_HBONDS Column Type

PLANE_ANGLE

• PLANE_ANGLE Column Type

PLANE_HEIGHT

• PLANE_HEIGHT Column Type

PREDICT

• PREDICT Column Type

RADIUS_OF_GYRATION

• RADIUS_OF_GYRATION Column Type

RANGE

• RANGE Column Type

ROW_NUMBER

• ROW_NUMBER Column Type

SCALE_TO

• SCALE_TO Column Type

SEARCH_COORDINATE_MAP

• SEARCH_COORDINATE_MAP Column Type

SEARCH_DISTANCE_MAP

• SEARCH_DISTANCE_MAP Column Type

SEARCH2D

• SEARCH2D Column Type

SECONDARY_STRUCTURE

• SECONDARY_STRUCTURE Column Type

SEQUENCE_HOMOLOGY

• SEQUENCE_HOMOLOGY Column Type

SEQUENCE_NUMBER

• SEQUENCE_NUMBER Column Type

SIDECHAIN_PROBABILITY

• SIDECHAIN_PROBABILITY Column Type

SIMILARITY

• SIMILARITY Column Type

SIZED_ARRAY

• SIMILARITY Column Type

SLN_PROPERTY

• SLN_PROPERTY Column Type

SOLVATION_FREE_ENERGY

• SOLVATION_FREE_ENERGY Column Type

SPL

• SPL Columns and Column Types

STRAIN

• STRAIN Column Type

STRING

• STRING Column Type

SUBST_CONSTANT

• SUBST_CONSTANT Column Type

SURFACE_AREAS

• SURFACE_AREAS Column Type

TOP_PREDICT

• TOP_PREDICT Column Type

TOPCOMFA

• TOPCOMFA Column Type

TORSION

• TORSION Column Type

TRANSFER_FREE_ENERGY

• TRANSFER_FREE_ENERGY Column Type

TUPLETS_SIMILARITY

• TUPLETS_SIMILARITY Column Type

VDW_CONTACTS

• VDW_CONTACTS Column Type

VECTOR

• VECTOR Column Type

VECTOR_ARRAY

• VECTOR_ARRAY Column Type

VOLSURF

• VOLSURF Column Type

VOLSURF_PRED

• VOLSURF_PRED Column Type

WEIGHTED_SUM

• WEIGHTED_SUM Column Type

XYZ_ABS

• XYZ_ABS Column Type

naming convention

• Create a Spreadsheet or Table from Existing Data

row and column expressions

• Row and Column Expressions

types

BIO_LOOP

• Create a Spreadsheet or Table from Existing Data

DATABASE

• Create a Spreadsheet or Table from Existing Data

DBRANSLATE

• Create a Spreadsheet or Table from Existing Data

DYNAMICS

• Create a Spreadsheet or Table from Existing Data

GENERIC

• Create a Spreadsheet or Table from Existing Data

IMPORT

• Create a Spreadsheet or Table from Existing Data

PROTEIN

• Create a Spreadsheet or Table from Existing Data

UNITY

• Create a Spreadsheet or Table from Existing Data

use in ProTable

• The ProTable Spreadsheet

SEARCH ANALYZE

• Load Search Results into a New Table

use in SiteID

• Create SiteID Table

TAILOR

• TAILOR SET TABLE

DATABASE

• Create/Modify a Table of Data

Tables

COORD_T

• SLN_32727_SET_T Type

counterions (salts)

• SALT_OPS

definitions

• Default Schema Contents

preference table creation

• UDC_CONFIG_CREATE_PRULES

preferences table population

• UDC_CONFIG_UPDATE_PRULES

PRIMARY_SLN

• Default Schema Contents

PRIMARY_SLN_COORD

• Default Schema Contents

property data temporary table

• Non-Structure Data Importing

REG_T

• REG_T Type

REG_TAB

• Default Schema Contents

relationships

• Default Schema Contents

rules table creation

• UDC_CONFIG_CREATE_PRULES

rules table population

• UDC_CONFIG_UPDATE_PRULES

SLN_T

• REG_T Type

structure table creation

• UDC_CREATE_STRDB

Tables and graphs

examining graphs

• Interact with Graphs

family technique

• FAMILY Column Type

graphs

• Graph Properties and Data

managing

• Manage Graphs

row/column expressions

• Row and Column Expressions

dynamic sets

• Row and Column Expressions

examples

• Row and Column Expressions

TABLE_TO_HITLIST

UNITY

• Save/Delete Hitlists

Tailor

UNITY

EXCLUDED_VOLUME_COLOR

• Excluded Volume

RECEPTOR_SITE_COLOR

• Receptor Site

UNITY

CONSTRAINT_COLOR

• Define or Modify Features/Constraints

• Specify a Partial Match Constraint

EXCLUDED_VOLUME_COLOR

• Define or Modify Features/Constraints

FEATURE_COLOR

• Define or Modify Features/Constraints

FEATURE_HILITE_COLOR

• Define or Modify Features/Constraints

RECEPTOR_SITE_COLOR

• Define or Modify Features/Constraints

VDW_RADII_COLOR

• Define or Modify Features/Constraints

LEGION

• TAILOR SET LEGION

2DVIEWER

• TAILOR SET 2DVIEWER

ANNEAL

• TAILOR SET ANNEAL

ANNOTATE

• TAILOR SET ANNOTATE

ATOM_TYPE

• TAILOR SET ATOM_TYPE

AUTO_REGION

• TAILOR SET AUTO_REGION

BIOPOLYMER

• TAILOR SET BIOPOLYMER

CENTROID

• TAILOR SET CENTROID

CHARGE

• TAILOR SET CHARGE

CHIRAL

• TAILOR SET CHIRAL

COLORS

• TAILOR SET COLORS

COMBIFLEXX

• TAILOR SET COMBIFLEXX

COMFA

• TAILOR SET COMFA

COMSIA

• TAILOR SET COMSIA

CONNECT

• TAILOR SET CONNECT

CONSTRUCT_BACKBONE

• TAILOR SET CONSTRUCT_BACKBONE

CONTOUR

• TAILOR SET CONTOUR

CPSA

• TAILOR SET CPSA

CSCORE

• TAILOR SET CSCORE

DATABASE

• TAILOR SET DATABASE

DIALOG

• TAILOR SET DIALOG

dialog

• Tailor Graphical Interface

DISCOTECH

• TAILOR SET DISCOTECH

DOCKING

• TAILOR SET DOCKING

DOTS

• TAILOR SET DOTS

dump

• Save Tailor Variables

DYNAMICS

• TAILOR SET DYNAMICS

EXAMINE

• TAILOR SET EXAMINE

EXPAND

• TAILOR SET EXPAND

FACTOR

• TAILOR SET FACTOR

FIELD_FIT

• TAILOR SET FIELD_FIT

finding a variable

• List and Find Tailor Variables

FORCE_FIELD

• TAILOR SET FORCE_FIELD

FUSE

• TAILOR SET FUSE

GENERAL

• TAILOR SET GENERAL

GENSURF

• TAILOR SET GENSURF

GRAPHICS

• TAILOR SET GRAPHICS

GRAPHS

• TAILOR SET GRAPHS

GRID

• TAILOR SET GRID

GRIDCOMPUTING

• TAILOR SET GRIDCOMPUTING

GRIDSEARCH

• TAILOR SET GRIDSEARCH

HARDCOPY

• TAILOR SET HARDCOPY

HBONDS

• TAILOR SET HBONDS

HELP

• TAILOR SET HELP

HIER

• TAILOR SET HIER

HISTOGRAMS

• TAILOR SET HISTOGRAMS

IMAGE

• TAILOR SET IMAGE

JARVIS

• TAILOR SET JARVIS

JOIN

• TAILOR SET JOIN

LEGION

• TAILOR SET LEGION

listing variables

• List and Find Tailor Variables

MATCH

• TAILOR SET MATCH

MAXIMIN2

• TAILOR SET MAXIMIN2

MERGE

• TAILOR SET MERGE

MOL

• TAILOR SET MOL

MOLCAD

• TAILOR SET MOLCAD

MOLCAD_PLUS

• TAILOR SET MOLCAD_PLUS

MOLPROP

• TAILOR SET MOLPROP

MONITOR

• TAILOR SET MONITOR

MOPAC

• TAILOR SET MOPAC

MO_PLOTS

• TAILOR SET MO_PLOTS

MVOLUME

• TAILOR SET MVOLUME

NORMAL

• TAILOR SET NORMAL

ORCHESTRAR

• TAILOR SET ORCHESTRAR

PDB

• TAILOR SET PDB

PIO

• TAILOR SET PIO

PLANE

• TAILOR SET PLANE

PLS

• TAILOR SET PLS

POTENTIAL

• TAILOR SET POTENTIAL

PROTABLE

• TAILOR SET PROTABLE

PROTEINVIEW

• TAILOR SET PROTEINVIEW

PROTEIN_LOOP

• TAILOR SET PROTEIN_LOOP

PROTEIN_SEARCH

• TAILOR SET PROTEIN_SEARCH

QSAR_ANALYSIS

• TAILOR SET QSAR_ANALYSIS

RAMACHANDRAN

• TAILOR SET RAMACHANDRAN

RANDOMSEARCH

• TAILOR SET RANDOMSEARCH

reading sequence upon startup

• Save Tailor Variables

recall variables

• Load Tailor Variables from a File

REMOVE

• TAILOR SET REMOVE

RENDER

• TAILOR SET RENDER

RIBBON

• TAILOR SET RIBBON

RNN

• TAILOR SET RNN

saving variables

• Save Tailor Variables

SCAN

• TAILOR SET SCAN

SEARCH

• TAILOR SET SEARCH

SELECTOR

• TAILOR SET SELECTOR

sequence viewer

• TAILOR SET BIOPOLYMER

setting variables

• Change Tailor Variables

SIMCA

• TAILOR SET SIMCA

SITEID

• TAILOR SITEID

SKETCH

• TAILOR SET SKETCH

SOLVENT

• TAILOR SET SOLVENT

SUPERIMPOSE

• TAILOR SET SUPERIMPOSE

SURFACE

• TAILOR SET SURFACE

TABLE

• TAILOR SET TABLE

TAILOR command

• Introduction to Tailor

• TAILOR SET VOLUME

TUPLETS

• TAILOR SET TUPLETS

TWEAK

• TAILOR SET TWEAK

UNITY

• TAILOR SET UNITY

VIEW_COMFA

• TAILOR SET VIEW_COMFA

VOLUME

• TAILOR SET VOLUME

PDB

• Read and Write PDB Files

sequence viewer

• Description of the Sequence Viewer

UNITY

EXCLUDED_VOLUME_COLOR

• Excluded Volume

RECEPTOR_SITE_COLOR

• Receptor Site

taipcstartup

• Set Options for Remote Searches of Local Databases

TAKE

SET TAKE_VERIFICATION

• SET

syb3dbserver command

• Record/Play

Command

• TAKE vs. UIMS LOAD

• TAKE

TAKE

• Play Recorded Session

TAKE

• UIMS2 Commands

Tanimoto

Tanimoto

• Similarity Metrics and Database Screening

coefficient in UNITY

• Specify 2D Similarity Search Options via the Menubar

similarity column type

• SIMILARITY Column Type

coefficient in Selector

• Similarity Coefficients

maximum

• Database Dissimilarity (dbdiss)

minimum

• Database Dissimilarity (dbdiss)

Target property

• The QSAR Table

expressing data

• Expressing Target Property Data

extrapolation

• Extrapolation

prediction

• Predictions and Missing Descriptor Values

• Predict Target Property Values

Tautomer

CRC calculation

• SLN_OPS

searching details

• Exact Match Search Operator

TA_3DB_HITS_DAYS

• Note About Hitlist Updates During Search

TA_3DB_HITS_DIR

• Note About Hitlist Updates During Search

TA_3DB_HITS_SEARCHES

• Note About Hitlist Updates During Search

TA_AMIDE_TOLERANCE

• Set and Save Flexible Search Options with Query

• Control Performance of Flexible Searching

• Specify Flexible Search Options via the Menubar

ta_down

• Managing Licenses Outside of SYBYL

TA_MENDYL_TAILVALS

• Save Tailor Variables

ta_remove

• Managing Licenses Outside of SYBYL

ta_reread

• Managing Licenses Outside of SYBYL

TA_ROOT

• Tripos Software Directory Organization

TA_SEARCH_PROPERTY_DATA_DEFAULT

• General Setup of a Search via O/S Utilities

ta_stat

• Managing Licenses Outside of SYBYL

ta_switchr

• Managing Licenses Outside of SYBYL

TA_TPS_DAEMON_PORT

• Set Options for Remote Searches of Local Databases

TA_UNIQ_MINTIMEOUT

• Add Many Records

TA_UNIQ_TIMEOUTINC

• Add Many Records

TA_USER_STRT

• SYBYL Startup Protocol

TCP/IP ports

• TCP/IP Ports in the License File

tdbupdate.sh file

• Upgrade Old UNITY Databases

Tear-off menus

• Menubar

Temperature

in dynamics

• Implementation in SYBYL

• Setup a Dynamics Calculation

column type

• Options for Analyzing Dynamics Results

Temperature factor

column in SiteID

• Create SiteID Table

column type

• Append Structural Columns

display in proteins

• Display Temperature Factors

display in proteins

• Color Biopolymers

Template

creation

• Generate a Customized Report via O/S Utilities

file

• Combine Hitlists

structure

• Specify Details for GASP Run

aligning database

• Align Databases via Command Line

dialog

• Align Databases via the Menubar

molecule

• Ligand Similarity

Template alignment

• Flexibly Align Ligands Individually to a Template

and to other ligands

• Flexibly Align Ligands to Each Other Using a Template

Terminal bell

• SET

Terminal residues

editing

• Edit Termini

Terminal type

• TERMINAL

Terminate SYBYL

• Exit SYBYL

Tetragonal system

• Space Group Tables

Tetrahedral feature

Tetrahedral feature

• Tetrahedral

Tetrahedral feature

• Tetrahedral

Text

alignment

• Text

change color

• Text

change font

• Text

create annotation

• Text

delete

• Text

edit

• Text

move

• Text

symbols

• ANNOTATE

Text screen annotation

• ANNOTATE

Textport

customize size

• Using TA_DISPLAY_CONFIG with SYBYL

show/hide

• Keyboard Function Keys

Textport commands

• Command Mode

Textport window

SYBYL

• Textport Window

Texture mapping of surfaces

• 2D Texture Mapping of Properties

Tick marks graph

dialog

• Customize Graphs

Tighten hits

• Post-process 3D/Flexible Search Hits

Time

per structure

flexible search

• Control Performance of Flexible Searching

tps

• SELECT

specification in Netbatch

• BAL (Batch Application Language) File

performance of command

• Command Mode

Time step in dynamics

• Implementation in SYBYL

TMPDIR environment variable

• Organize Molecules into Groups (Sets and Classes)

tnsnames.ora example file

• Oracle Listener

to template only

• Flexibly Align Ligands Individually to a Template

TodoList file

• ToDoList File

Tolerance

set constraint tolerance

• Set Constraint Tolerances

set constraint tolerance

• Set Constraint Tolerances

specification

• Specify Input Model Criteria

set constraint tolerance

• Set Constraint Tolerances

Toolbar

command

• Menubar Mode

customizing

• Customizing the Toolbar

icons

depth cue

• Depth Cue

display options

• Display Options

graphics attributes

• Graphics Attributes

molecule display options

• Molecule Display Options

mouse focus option

• Mouse Focus

reset

• Reset

Z-clipping

• Z-Clipping

Toolbox icons

overview

• Toolbox Icons

TOPANGLE

• The Computation Behind the Topomer Method

TOPATTACH

• The Computation Behind the Topomer Method

TOPCOMFA column type

• Topomer CoMFA Columns

TOPDIST

• The Computation Behind the Topomer Method

TOPFEAT

• The Computation Behind the Topomer Method

Topography

• List Coordinates, Distances, or Angles (Same Molecule Area)

Topomer

definition

• The Topomer Search Method

Topomer CoMFA

TOP_PREDICT column type

• TOP_PREDICT Column Type

TOPCOMFA column type

• TOPCOMFA Column Type

Topomer CoMFA Contours dialog

• Topomer CoMFA Contours

Topomer CoMFA dialog

• Topomer CoMFA Main Dialog

Topomer CoMFA Prediction from Analysis dialog

• Topomer CoMFA Prediction from Analysis

Topomer Search

2D results browser

• Topomer Search 2D Browser

analyze results

• Analyze Topomer Search Results

caveat

• The Topomer Search Method

computation

• The Computation Behind the Topomer Method

customize 3D browser

• Topomer Search 2D Browser

data fields

• The Computation Behind the Topomer Method

data preparation for re-use

• Topomer Search Input and Output Files

dbtop command

• The dbtop Command

divalent fragment

• The Computation Behind the Topomer Method

feature contribution

• The Computation Behind the Topomer Method

files created

• Files Created by Topomer Search

input and output files

• Topomer Search Input and Output Files

introduction

• Introduction to the Similarity Suite

license requirements

• Introduction to the Similarity Suite

manual preparation of the query

• Topomer Search Input and Output Files

pharmacophoric feature contribution

• The Computation Behind the Topomer Method

query definition

• Access Topomer Search in SYBYL

query display

• Visualization Options

query display

• Visualization Options

references

• The Topomer Search Method

runtime parameters

• Topomer Search Details

setup details

• Topomer Search Details

steric contribution

• The Computation Behind the Topomer Method

SYBYL interface

• Access Topomer Search in SYBYL

theory

• The Topomer Search Method

TOPANGLE

• The Computation Behind the Topomer Method

TOPATTACH

• The Computation Behind the Topomer Method

TOPDIST

• The Computation Behind the Topomer Method

TOPFEAT

• The Computation Behind the Topomer Method

topomer definition

• The Topomer Search Method

topomeric distance

• The Computation Behind the Topomer Method

TOPSTERIC

• The Computation Behind the Topomer Method

tutorial

• Topomer Search Tutorials

TOPSTERIC

• The Computation Behind the Topomer Method

TOP_PREDICT column type

• Topomer CoMFA Columns

Torsion

AMBER4.1 FF95 parameter table

• AMBER4.1_FF95 Force Field

AMBER7_FF99 parameter table

• AMBER7_FF99 Force Field

column type

• TORSION Column Type

define constraint

• Torsion Constraints

Kollman parameter table

• Kollman Force Field

modify constraint

• Torsion Constraints

Tripos parameter table

• Parameters

list angle

• List Coordinates, Distances, or Angles (Same Molecule Area)

measure

• Intra-/Intermolecular Measurements

modify

• Bonds

column type

• Analyze Search Results

Torsion constraint

• Torsion Constraints

data record in mol2 file

• @<TRIPOS>FFCON_TORSION

define

• Torsion Constraints

delete

• Torsion Constraints

energy term, Tripos

• Energy Expression

modify

• Torsion Constraints

Torsion energy

Kollman term

• Kollman Force Field

MMFF94 term

• Energy Expression

Tripos term

• Energy Expression

Torsion manager

• Customize the FlexX RDF File

Torsional bias

• Prepare Structures for GASP

Torsional profile

• Preprocessing of Data for Torsional Bias

Torsmin

parameters

• Torsmin Parameter File

TORSMIN command

• Perform Torsional Minimization via Command Line

Torus constraints

Torus constraints

• Torus

Torus constraints

• Torus

To_atoms built-in set

• Built-in Sets

TPS

close

• TPS Commands

closed connection

• Closed Connections

commands

• TPS Commands

complex_property

• COMPLEX_PROPERTY

credentials

• TPS Security

define

• DEFINE

delete

• DEFINE

encryption

• TPS Security

environment_script

• COMPLEX_PROPERTY

fault tolerance

• Fault Tolerance

regulated access

• Closed Connections

security

• TPS Security

select

• SELECT

time

• SELECT

tpsd command line options

• The TPS daemon:tpsd

user_access

• USER_ACCESS

tpsd

command line options

• The TPS daemon:tpsd

Trace, biopolymer chain

• Biopolymer Chain Trace and Backbone Display

Training set

Training set

• Select the Training Set

prediction

• Predictions and Missing Descriptor Values

Transfer free energy

Transfer free energy

• Append Structural Columns

column type

• TRANSFER_FREE_ENERGY Column Type

Transformation

operations

• Enlarge Atom Set via Transformation Operations

Transformation matrix

• Some Crystallography Basics

Translate

adding 3D coordinates

• A Note on Concord

between formats, SYBYL interface

• Translate Between Connection Table Formats

hits

• Examine Hitlist

images

• STATIC

options

• Specify Translation Options

adding 3D coordinates

• UDCTRANSLATE

API package

• PARSE_OPS

• TRANSLATE_OPS

TRANSLATE_OPS

• TRANSLATE_OPS

Translation

of molecules

• Rotate and Move Molecules

Translucent surface

• SURFACE

Triclinic system

• Space Group Tables

Trigo

commands

add_prod

• add_prod

TaHostType

• add_prod

trigo

• Command Line Syntax

config file syntax

• Configuration File Syntax

configuration

• Trigo Configuration

customizing run names

• Customizing Run Names

definitions

• Trigo Configuration

environment

• Defining Your Environment with Trigo

example config file

• Example Configuration File

installation

• Installation

automatically

• Installation

manually

• Manually Install Trigo

introduction

• Introduction

launching a product

• Using Trigo

launching utility programs

• Launching Utility Programs

listing run names

• Listing Available Run Names

path variable

• Prepending Trigo to the PATH Variable

running products standalone

• Running Products Standalone

running without

• Running SYBYL without Trigo

sanity check

• Customizing Run Names

scripts

• SYBYL Startup Protocol

user config files

• Site and User Configuration Files

Trigonal system

• Space Group Tables

Triple bond

• Bond Specification

Triplet

• Tuplet Definition

Tripos Bookshelf

help

• Get Help

• Get Help

Tripos force field

Tripos force field

• Tripos Force Field

angle bending table

• Parameters

atom

color table

• Parameters

geometry definitions table

• Parameters

geometry vectors

• Parameters

type definitions table

• Parameters

bond

length table

• Parameters

type definitions table

• Parameters

types table

• Parameters

bond stretching table

• Parameters

energy terms

• Energy Expression

optional terms

• Energy Expression

out of plane bending table

• Parameters

parameters

• Parameter Files

references

• Tripos Force Field References

table

• Parameters

torsion angle table

• Parameters

validation

• Validation and Subsequent Modifications

van der Waals table

• Parameters

Tripos Force Field

• Structure Building

Tripos software

directories

• Tripos Software Directory Organization

executable and associated directories

• Executable and Associated Directories

source directories

• Source Directories

utility directories

• Utility Directories

triposlm.sh file

• ToDoList File

• Managing Licenses Outside of SYBYL

tripostbs.sh file

• ToDoList File

Troubleshooting

aromaticity

• Normalize Aromaticity

hardcopy

• HARDCOPY

CombiLibMaker

• CombiLibMaker

Concord

• Concord/StereoPlex

DVS

• DiverseSolutions & DVS Addons

license manager

error codes

• LICENSING MESSAGE: Error Code

StereoPlex

• Concord/StereoPlex

VolSurf

• VolSurf

MOLCAD

• What's New With MOLCAD

TTY

• UIMS2 Commands

TTY command

TTY command

• Play Recorded Session

syb3dbserver command

• Send Input To Server

Tube, color and size in ProTable

• Map Properties onto Surfaces

TUNER

• TUNER

command

example

• TUNER

format

• TUNER

in the ORCHESTRAR project manager

• Add/Analyze Loops

Tuplet

augmented

• Tuplet Definition

configuration

• Advanced Tuplet Configuration

create

• Calculate Tuplets

create/open project

• Create/Open Projects

creation

• Tuplet Creation

definition

• Tuplet Definition

generation parameters

• Tuplet Generation Parameters

prioritize libraries

• Prioritize Combinatorial Libraries

view results

• View Results of Library Prioritization

privileged

• Tuplet Definition

search compounds

• Search Compounds

Tuplet creation

• Tuplet Creation

tupletcmp

• tupletcmp

tupletconvert

• tupletconvert

tupletinfo

• tupletinfo

tupletmanip

• tupletmanip

tupletoptisim

• tupletoptisim

Tuplets

TAILOR

• TAILOR SET TUPLETS

Tuplets similarity

column type

• TUPLETS_SIMILARITY Column Type

tuplets.cfg

• tuplets.cfg

tuplets_parsehitlist.pl

• tuplet_parsehitlist.pl

tuplets_pharm.cfg

• Appendix: Parameter Files

tuplets_sterics.cfg

• Appendix: Parameter Files

Tutorials

CScore

• CScore Tutorials

Tuplets

• Tuplets Tutorial

Distill

• Distill Tutorials

Docking

• Docking Tutorials

FlexE

• Docking with FlexE

FlexX

• Single Molecule Docking with FlexX

• Multiple Molecule Docking with FlexX

FlexX-Pharm

• Docking with FlexX-Pharm Constraints

DiverseSolutions addons

• DiverseSolutions Tutorials

dynamics

• Introduction to Dynamics Tutorial

minimization

• Minimizing Tutorial

minimizing biopolymers

• Annealing Tutorial

FUGUE

• FUGUE Tutorial

GALAHAD

• GALAHAD Tutorials

GASP

• GASP Tutorial

generalized surfaces

• Generalized Surfaces Tutorial

annotations

• Annotation Palette Tutorial

graphics

• Graphics Tutorials

high resolution image

• High Resolution Image Tutorial

volume manipulation

• Volume Manipulation Tutorial

HQSAR

• HQSAR Tutorial

Legion

• Legion Tutorials

MOLCAD

creating a channel surface

• Channel Surfaces Tutorials

creating a cone surface

• Cone and Field Line Surfaces Tutorial

creating a ribbon surface

• Ribbon Surfaces Tutorial

generating surfaces and properties in batch

• MOLCAD Batch Tutorials

getting started

• Getting Started with MOLCAD

property picking

• Comparing Surfaces and Property Picking Tutorial

separating surface

• Separating Surfaces Tutorials

texture mapping

• Multiple Properties and 2D Texture Mapping

MOLCAD Plus

3D volume

• 3D Volume Tutorial

cones

• Interactive Cones Tutorial

create contour files

• Create Contour Files Tutorial

distance surfaces

• Interactive Distance Surface Tutorial

iso surfaces

• Interactive Iso Surfaces Tutorial

separating surfaces

• Separating Surfaces Tutorial

slicing surfaces

• Slicing Surfaces Tutorial

importing and graphing data in a spreadsheet

• MSS Tutorial: Importing and Graphing Data

introduction to the molecular spreadsheet

• MSS Tutorial: Become Familiar with a Molecular Spreadsheet

Molecular Spreadsheet

• MSS Tutorials

MSS QSAR modeling

• MSS Tutorial: QSAR Modeling

ORCHESTRAR

project manager

• ORCHESTRAR Project Manager Tutorial

ProTable

• ProTable Tutorials

Advanced CoMFA

• SAMPLS and Advanced CoMFA Tutorials

clustering methods

• Clustering Methods Tutorial

CoMFA

• CoMFA Tutorial Using Steroids

• CoMFA Tutorial Using Ryanoids

CoMSIA

• CoMSIA Tutorial

conformer columns

• Conformer Columns Tutorial

CPSA

• PLS Analysis of CPSA Descriptors Tutorial

database alignment and field classes

• Database Alignment and Field Classes Tutorial

EVA

• EVA Tutorial

hierarchical analysis

• Hierarchical Analysis Tutorial

hierarchical cluster

• Hierarchical Clustering Tutorial

optimizing QSAR

• Optimizing QSAR Tutorial

Principal Components Analysis

• Principal Components Analysis Tutorial

progressive scrambling

• Progressive Scrambling Tutorial

QSAR

• QSAR Tutorials

region focusing

• Region Focusing Tutorial

SAMPLS

• SAMPLS Tutorial

AMPAC

• Single Molecule AMPAC Calculations Tutorial

AMPAC MSS calculation

• AMPAC Calculation in a Spreadsheet Tutorial

MOPAC

• MOPAC Tutorial

RACHEL

• RACHEL Tutorials

Bridge generation using CHARLIE

• Bridge Generation Using CHARLIE

Create a component database

• Create a RACHEL Component Database

Create a project

• Create a RACHEL Project

Running a combinatorial search

• Run a RACHEL Combinatorial Search

Scaffold replacement using CHARLIE

• Scaffold Replacement Using CHARLIE

Scoring Functions

• RACHEL Scoring Functions

Using chemical templates and descriptors

• Using Chemical Templates and Descriptors

conformational analysis

• Systematic Search Tutorial

conformational comparison

• Conformational Comparison Tutorial

distance map

• Distance Map Tutorial

fitting

• Conformational Comparison Tutorial

grid search

• Grid Search Tutorial

systematic search

• Systematic Search Tutorial

Selector

• Selector Tutorials

FlexS

• FlexS Tutorial

Similarity

• Surflex-Sim

• Topomer Search

• FlexS

Topomer Search

• Topomer Search Tutorials

SiteID

• SiteID Tutorials

atom selection

• Atom Selection Tutorial

bond selection

• Bond Selection Tutorial

building a small molecule

• Small Molecule Sketching Tutorial

file format

• Play Recorded Session

interacting with SYBYL

• Quick Introduction to SYBYL Tutorial

ring fusion

• Ring Fusion Tutorial

sketching a small molecule

• Small Molecule Sketching Tutorial

small molecule sketching

• Small Molecule Sketching Tutorial

substructure selection

• Substructure Selection Tutorial

biopolymer building

• Peptide Building Tutorial

monomer definition

• Monomer Definition Tutorial

peptide building

• Peptide Building Tutorial

peptide display

• Biopolymer Displays Tutorial

prepare protein

• Protein Preparation Tutorial

protein loop search

• Protein Loop Search Tutorial

sets

• Manipulating Sets Tutorial

CombiFlexX

and CScore

• CombiFlexX and CScore Tutorial

FlexXc

• FlexXc Tutorial

OptiDock

• OptiDock Tutorial

CRYSIN

• CRYSIN Tutorial

Tweak conformers

save

• Advanced Tuplet Configuration

TWEAK, tailor variable

• TAILOR SET TWEAK

Twist

• TWIST

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[TOP] [BOTTOM] [Tripos Book Shelf]

Numerics A B C D E F G H I J K L M N O P Q R S Symbols T U V W X Z

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Links to individual Index Files:
• BASICS
• BIO
• CFX
• CONCORD
• CONFORT
• CRYSTAL
• CSCORE
• DISCOTECH
• DISTILL
• DOCKING
• DVS ADDONS
• FORCE FIELD
• FUGUE
• GALAHAD
• GASP
• GENSURF
• GRAPHICS
• HQSAR
• INSTALL_ADMIN
• LEGION
• MOLCAD
• MOLCADPLUS
• MSS
• ORCH
• OVERLAY
• PROTABLE
• QSAR
• QUANTUM
• RACHEL
• SEARCH
• SELECTOR
• SIMILARITY
• SITEID
• SLN
• SLN_AUSPYX
• SPL
• STEREOPLEX
• TAILOR
• TOOLKIT
• TOPCOMFA
• TUPLETS
• UNIFIED_BOOK
• UNITY

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Copyright © 2007, Tripos, Inc. All rights reserverd.