C: Sub Index for SYBYL and UNITY Documentation

C-alpha carbon global set

• Global Sets in the Biopolymer macromol Dictionary

C chromosome

• Genetic Structure

C-terminal groups

partial charges

• Partial Charge Derivation

Calculate

similarity score

• Fitness Function

VDW energy

• Fitness Function

volume overlap

• Fitness Function

Calculate fingerprints in parallel

• Parallel Fingerprint Calculation

Callback creation

• Non-Structure Data Importing

Cap atoms

• Edit Termini

adding to terminal residues

• Edit Termini

Cap global set

• Global Sets in the Biopolymer macromol Dictionary

CAPTURE

• Record Output from a Single Command

Carbohydrate

building

• Build Protein, DNA Strand, RNA Strand, Carbohydrate

Cartesian coordinates

• CRYSIN

Cartridge contents

• Appendix B: Dataset Contents from Cartridge

Cavity

building the ligand

FlexX

• The FlexX Method

Surflex-Dock

• The Surflex-Dock Method

creating file

• Define the Active Site

depth parameters

• Define Surface Properties Interactively

placing the base fragment in the model

• The FlexX Method

locating

• Find Pockets

CCR

• Diagnostics

• Structure Building

optimization limit

• Structure Building

relaxation limit

• Structure Building

threshold

• Diagnostics

• Diagnostics

threshold for errors

• Diagnostics

CDF file

creating

• FlexX-Pharm Constraints

Cell

modifying

• Edit Cell Data

selecting via the menubar

• Using the Molecular Spreadsheet

• Cell Selection

Cell-based visualization tools

DiverseSolutions addons

• Cell-based Visualization Tools

Cell contents MSS

DiverseSolutions addons

• Read Cell Coordinates into MSS

Center

• CENTER

Center of mass

Center of mass

• Center of Mass

data record in mol2 file

• @<TRIPOS>CENTER_OF_MASS

VISUALIZE

• VISUALIZE

Centerview

• CENTERVIEW

Centroid

feature

• Centroid

TAILOR

• TAILOR SET CENTROID

Centroid

• Centroid

data record in mol2 file

• @<TRIPOS>CENTROID

feature

• Centroid

CGQ prompt

CGQ prompt

• SET

CGQ prompt

• Textport Window

Chain

of atoms

• Atoms

renaming in biopolymers

• Set Chain Names

trace in biopolymers

• Biopolymer Chain Trace and Backbone Display

Change

background

• Interactive Iso Surfaces Tutorial

cone

• Interactive Cones Tutorial

display styles

• Change Display Style of MOLCAD Plus Molecules

fonts

• Set Display Preferences

iso

• Interactive Iso Surfaces Tutorial

• Interactive Iso Surfaces Tutorial

molecule

• Interactive Iso Surfaces Tutorial

plane

• Slicing Surfaces Tutorial

slicing surface positions

• Slicing Surfaces: Create and Visualize via the Menubar

volume

• 3D Volume Tutorial

molecule name

• Molecule's Center of Rotation, Name, Type, etc.

• Organize Molecules into Groups (Sets and Classes)

substructure name

• Substructures

Channel surfaces

• MOLCAD Channel Surfaces

batch

• Create Channel Surfaces in Batch

creating

• How to Create Channel Surfaces

theory

• Calculating Channel Surfaces

tutorial

• Channel Surfaces Tutorials

Charge

• Atomic Charges

computation in a spreadsheet

• Computations on Spreadsheet Rows

compute

• Handling Charges in SYBYL

derivation for biopolymers

• Partial Charge Derivation

display

• Handling Charges in SYBYL

KOLL_ALLC and KOLL_ALLN

• Biopolymer Charges

parameters

Del Re

• Del Re Charges

Gasteiger and Marsili

• Gasteiger and Marsili Charges

Hückel

• Hückel Charges

remove

• Handling Charges in SYBYL

undisplay

• Handling Charges in SYBYL

use in energy calculation

• Calculate Energy via the Menubar

• Calculate Energy via the Menubar

use in torsional minimization calculation

• Perform Torsional Minimization via Menubar

validate

• Handling Charges in SYBYL

distribution

• Molecular Orbital Theory

use in Selector

• 3D Model Building

TAILOR

• TAILOR SET CHARGE

built-in set

• Built-in Sets

modify

• Atoms

loading in biopolymers

• Load Charges

Charge calculation methods

Del Re

• Del Re Charges

Gasteiger-Marsili

• Gasteiger and Marsili Charges

references

• Gasteiger and Marsili Charges

Gast-Huck

• Gast-Hück Charges

Hückel

• Hückel Charges

references

• Hückel Charges

Pullman

• Pullman Charges

references

• Pullman Charges

Charge derivation for biopolymers

references

• Biopolymer Charge Derivation References

CHARLIE

tutorials

bridge generation

• Bridge Generation Using CHARLIE

scaffold replacement

• Scaffold Replacement Using CHARLIE

ChemScore function

• ChemScore

Child CSLN

adding to UNITY database

• Building Options

definition

• Introduction to Legion

generating

• CSLN Enumeration and Retrieval

naming

• Enumeration Options

• CSLN Enumeration and Retrieval

Child SLN

definition

• Introduction to Legion

generating

• The Legion Menu

• Enumeration Options

CHIRAL

• Chirality

Chiral acyclic atoms

definition

• Priority Rules

Chiral atom count

SLN_OPS method

• SLN_OPS

SLN_T method

• REG_T Type

Chiral atoms

• Diagnostics

Chiral bridgehead atoms

definition

• Priority Rules

Chiral built-in set

• Built-in Sets

Chiral protoinvertible atoms and bonds

definition

• Priority Rules

Chiral ring atoms

definition

• Priority Rules

Chiral ring fusion atoms

definition

• Priority Rules

Chirality

flag

• Fragment Generation

• Model Options

• Add a New Hologram Column

• Create Hologram Column

specify for atoms

• Absolute Stereochemistry

core in Legion

• Legion Builder

Legion variation list

• Variation List Builder

TAILOR

• TAILOR SET CHIRAL

atom attribute

• Chirality

check

• Add a Group

Chirality

• Diagnostics

invert

• Chirality

select by

• Selection How Tos

specify for atoms

• Absolute Stereochemistry

CHORAL

command

• CHORAL

examples

• CHORAL

format

• CHORAL

in the ORCHESTRAR project manager

• Model Conserved Regions

chorus

• chorus

Chromosome definitions

• Genetic Structure

Chromosomes

• Introduction to GASP

• How Does GASP Work?

Class

define in a database

• Organize Molecules into Groups (Sets and Classes)

Cleanup SPL macro

• Cleanup SPL Macro

Clear Model

• HQSAR Menubar

Clear the screen

• Clear and Reset the SYBYL Display

Client

command line

• AUSPYX Command Line Client Usage

Client identification, syb3dbserver

• Get Info From/To Server

Client-side importing

• Client Side Import

Clique detection

• Perform Clique Detection

controlling

• Specify Input Model Criteria

CLOGP

background information

• CLOGP User Guide

column type

• CLOGP Column Type

definition

• Introduction to Selector

error codes

• CLOGP Error Codes

metric in Selector

• Selecting Compounds

Close

hitlist

• Open and Close

hitlist manager

• Open and Close

tps

• TPS Commands

Close Contact Ratio

• Structure Building

Close SYBYL

• Exit SYBYL

Closed Connection

tps

• Closed Connections

Cluster

input molecules

• Access DISCOtech

Tuplets

• Select Compounds by Clustering

definition

• Introduction to Distill

hierarchical

command format

• Hierarchical Clustering via Command Line

dialogs

• Hierarchical Clustering via the Menubar

• Generate Hierarchical Cluster Column(s)

theory

• Theoretical Introduction to Hierarchical Clustering

tutorial

• Hierarchical Clustering Tutorial

• Clustering Methods Tutorial

Jarvis-Patrick

command format

• Jarvis-Patrick Clustering via Command Line

dialog

• Jarvis-Patrick Clustering via the Menubar

theory

• Jarvis-Patrick Clustering

Reciprocal Nearest Neighbor

command format

• Access RNN in SYBYL

theory

• Reciprocal Nearest Neighbors (RNN)

Jarvis-Patrick

setting in Selector

• Cluster Analysis Setup

theory

• Similarity And Dissimilarity Methods

Reciprocal Nearest Neighbor

setting in Selector

• Cluster Analysis Setup

theory

• Similarity And Dissimilarity Methods

selecting central compounds

• Cluster-Based Compound Selection

use in Selector

dialog box

• Cluster Analysis Setup

theory

• Similarity And Dissimilarity Methods

viewing and reselecting

• Reselecting Samples

rows

• Create SiteID Table

Jarvis-Patrick

TAILOR

• TAILOR SET JARVIS

Reciprocal Nearest Neighbor

TAILOR

• TAILOR SET RNN

TAILOR

• TAILOR SET HIER

CMR

background information

• CMR User Guide

column type

• CMR Column Type

definition

• Introduction to Selector

error codes

• CMR Error Codes

metric in Selector

• Selecting Compounds

CODA

• CODA

command

examples

• CODA

format

• CODA

FRAGDB

build and use personal version

• CODA

rebuild the main database

• CODA

FREAD

• CODA

in the ORCHESTRAR project manager

• Search Loops

overview

• CODA

PETRA

• CODA

Coefficient plot

• Graph Analysis Results

Cofactor

adding to biopolymer

• Add Solvent or Cofactor

database

• Databases of Ligands, Cofactors, and Chemical Groups

in the ORCHESTRAR project manager

• Model Conserved Regions

SYBYL atom types

• Fix SYBYL Atom Types in Cofactor

COLLECT

• UIMS2 Commands

Collect commands into a file

Collect commands into a file

• Record Session Commands

syb3dbserver

• Record/Play

Color

• COLOR

background

• Set Display Preferences

dendrogram

• Distill: Color the Dendrogram

ATOM

• COLOR

BOND

• COLOR

By Spectrum

• COLOR

Carbons by Spectrum

• COLOR

Carbons/Hydrogens by Spectrum

• COLOR

color editor

• Graphics Attributes - Color Editor - Colors & Backdrop (OGLX only)

LABEL

• COLOR

SURFACE

• SURFACE

TYPE

• COLOR

coding

• Interpretation of HQSAR Models

MOLCAD problem

• What's New With MOLCAD

MOLCAD surfaces

• Create Surfaces via the Command Line

ramps in MOLCAD

• Property Color Ramps

TAILOR

• TAILOR SET COLORS

dynamic hydrogen bonds

• Manage Dynamic Hydrogen Bonds

static hydrogen bonds

• Manage Static Hydrogen Bonds

protein loop

• Analyze Search Results

Color Editor

• Graphics Attributes - Color Editor - Colors & Backdrop (OGLX only)

Color ramp

electrostatic potential

• Color Ramps

electrostatic potential

• Electrostatic Potential (EP)

• Property Color Ramps

hydrogen bonding

• Hydrogen Bonding Sites (HB)

• Property Color Ramps

lipophilic potential

• Color Ramps

lipophilic potential

• Property Color Ramps

local curvature

• Local Curvature (LC)

Color ranges dialog box

• Sweep Graph

Coloring features

Coloring features

• Special Notes:

Coloring features

• Special Notes:

Column

adding

• Add a Column in a Spreadsheet or Table

copying

• Interact with Columns

deleting

• Interact with Columns

dynamics

• Options for Analyzing Dynamics Results

expressions

• Row and Column Expressions

examples

• Row and Column Expressions

formatting

• Interact with Columns

grid resolution

• Interact with Columns

hiding

• Interact with Columns

modifying

• Interact with Columns

moving

• Interact with Columns

naming

• Interact with Columns

pasting into another spreadsheet

• Interact with Columns

resizing label

• Interact with Columns

resizing width

• Interact with Columns

right-click menu

• Interact with Columns

selecting in table

• Row and Column Expressions

selecting via the menubar

• Using the Molecular Spreadsheet

selection dialog

• Column Selection

types

• MSS Column Types

adding

• Append Structural Columns

ProTable

• Append Structural Columns

AMPAC

• AMPAC Calculation in a Spreadsheet

adding in SiteID

• Create SiteID Table

Column distribution graph

command format

• Column Distribution Graph

dialog box

• Column Distribution Graph

protein loop search

• Analyze Search Results

theory

• Column Distribution Graph

Column type

amino acid number

• AMINO_ACID_NUMBER Column Type

AMPAC

• AMPAC_ANALYSIS Column Type

angle

• ANGLE Column Type

area

• MOLPROP_AREA Column Type

array

• SIMILARITY Column Type

• VECTOR_ARRAY Column Type

atom pair fingerprint

• ATOM_PAIR_FP Column Type

atomic coordinates

• 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

coordinate map

• SEARCH_COORDINATE_MAP Column Type

CPSA

• CPSA Column Type

deformation

• DEF_ABS Column Type

dictionary angle

• DICT_ANGLE Column Type

dipole moment

• DIPOLE_MOMENT Column Type

distance

• DISTANCE Column Type

distance map

• SEARCH_DISTANCE_MAP 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

integer

• 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

molecular weight

• MOL_WEIGHT Column Type

MOPAC

• MOPAC Column Type

neighbors

• NEIGHBORS Column Type

number of hydrogen bonds

• NUMBER_OF_HBONDS Column Type

plane angle

• PLANE_ANGLE Column Type

plane height

• PLANE_HEIGHT Column Type

polar surface area

• MOLPROP_PSA Column Type

polar volume

• MOLPROP_PV Column Type

QSAR prediction

• PREDICT Column Type

radius of gyration

• RADIUS_OF_GYRATION Column Type

range

• RANGE Column Type

RMS movements

• XYZ_ABS Column Type

row number

• ROW_NUMBER Column Type

scale tor

• SCALE_TO Column Type

search 2D

• SEARCH2D Column Type

search coordinate map

• SEARCH_COORDINATE_MAP Column Type

search distance map

• SEARCH_DISTANCE_MAP 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

substituent constant

• SUBST_CONSTANT Column Type

surface area

• SURFACE_AREAS Column Type

TOPCOMFA

• Topomer CoMFA Columns

Topomer CoMFA

• TOPCOMFA Column Type

Topomer CoMFA prediction

• TOP_PREDICT Column Type

torsion

• TORSION Column Type

transfer free energy

• TRANSFER_FREE_ENERGY Column Type

Tuplets similarity

• TUPLETS_SIMILARITY Column Type

van der Waals contact

• VDW_CONTACTS Column Type

vector

• VECTOR Column Type

vector array

• VECTOR_ARRAY Column Type

VolSurf

• VOLSURF Column Type

VolSurf prediction

• VOLSURF_PRED Column Type

volume

• MOLPROP_VOLUME Column Type

weighted sum

• WEIGHTED_SUM Column Type

amino acid number

• Append Structural Columns

conformational angle

• Append Structural Columns

hydrogen bonds

• Append Structural Columns

neighbors

• Append Structural Columns

secondary structure

• Append Structural Columns

sequence number

• Append Structural Columns

solvation free energy

• Append Structural Columns

solvent accessible surface

• Append Structural Columns

surface area

• Append Structural Columns

temperature factor

• Append Structural Columns

transfer free energy

• Append Structural Columns

CoMFA

• Add CoMFA Column

CoMSIA

• Add a New CoMSIA Column

EVA

• Add New EVA Column

Column types

TOP_PREDICT

• Topomer CoMFA Columns

CombiFlexX

CScore

• Run CScore on CombiFlexX Results

TAILOR

• TAILOR SET COMBIFLEXX

analyzing

• Analyze the CombiFlexX Results

analyzing results

• Examine the OptiDock Results

and Legion

• Examine the Combinatorial Library

CScore

• Other CombiFlexX Extraction Formats

• CombiFlexX and CScore Tutorial

• Analyze the CombiFlexX Results

customizing

FlexXc

• Customize the FlexXc Job

graphs

• Customize the CombiFlexX Graphs

OptiDock

• Customize the OptiDock Job

files created

• The CombiFlexX Files

OptiDock glossary

• OptiDock Glossary

OptiSim parameters

• Customize the OptiDock Job

results spreadsheet

• Examine the OptiDock Results

setting up

• Prepare a CombiFlexX Job

example

• Prepare the CombiFlexX Job

theory

• CombiFlexX Theory

tutorials

• CombiFlexX Tutorials

CombiLibMaker

notes & requirements

• CombiLibMaker

troubleshooting

• CombiLibMaker

Combinatorial library

definition

• Introduction to Selector

prioritize using Tuplets

• Prioritize Combinatorial Libraries

view Tuplets results

• View Results of Library Prioritization

docking

• Prepare to Dock a Combinatorial Library

examining

• Examine the Combinatorial Library

Combinatorial library

• Building and Editing Virtual Combinatorial Libraries

building

• Build the Combinatorial Library

definition

• Introduction to Legion

Combinatorial SLN

building

• Build the Combinatorial Library

definition

• Introduction to Legion

Combinatorial structure

example

• Build the Combinatorial Library

Combine

hitlists

• Combine Hitlists

variation sites in Legion

• Combine Sites

search datasets

• Distance Maps

Combined searching

• Combined Searching

CoMFA

column type

• COMFA Column Type

field fit consideration

• Use in QSAR or Minimization

adding column

• Add CoMFA Column

aligning molecules

• Align Molecules for QSAR/CoMFA

alignment rule

• Theoretical Introduction to CoMFA

• Preparing for CoMFA

conformer column

• Specify Usage of Conformer Column

contouring fields

• Examination and Use of CoMFA Results

database align

• Align Databases via Command Line

diagram

• The QSAR Table

dialogs

column definition

• Add CoMFA Column

region

• Define a Region via the Menubar

view CoMFA

• View CoMFA Results

view eva

• Graph EVA Profiles

examination of results

• Examination and Use of CoMFA Results

field

• Theoretical Introduction to CoMFA

• Building Spreadsheet for CoMFA

hints

• Theoretical Introduction to CoMFA

PLS run

• CoMFA PLS Runs

prediction

• Examination and Use of CoMFA Results

preparation

• Preparing for CoMFA

probe atom

• Preparing for CoMFA

QSAR optimize

• Optimize QSAR via the Menubar

region

• Theoretical Introduction to CoMFA

• Preparing for CoMFA

region focusing

command format

• Region Focusing via Command Line

dialog box

• Region Focusing via the Menubar

scatter plot

• Examination and Use of CoMFA Results

table building

• Building Spreadsheet for CoMFA

theory

• Theoretical Introduction to CoMFA

tutorials

• SAMPLS and Advanced CoMFA Tutorials

introduction

• CoMFA Tutorial Using Steroids

• CoMFA Tutorial Using Ryanoids

unique compounds

• CoMFA PLS Runs

use of results

• Examination and Use of CoMFA Results

metric in Selector

• Selecting Compounds

auto_region

TAILOR

• TAILOR SET AUTO_REGION

TAILOR

• TAILOR SET COMFA

• TAILOR SET VIEW_COMFA

Command

descriptions

• Tuplet Commands

descriptions

UNITY

• UNITY Subcommand List

descriptions

CScore

• SYBYL Command: CSCORE

O/S utilities

Distill

• Distill O/S Utilities

descriptions

HQSAR

• HQSAR Commands in SYBYL

O/S utilities

HQSAR

• HQSAR O/S Utilities

descriptions

license management

• Managing Licenses Outside of SYBYL

tps

• TPS Commands

descriptions

MOLCAD Plus

• MOLCAD Plus Commands

descriptions

QSAR

• QSAR Command List

O/S utilities

Selector

• Selector Database Functions

• Associated O/S Utilities

expression generators

define

• UIMS

list

• UIMS

macros

• UIMS

activate command set

• UIMS

deactivate command set

• UIMS

define

• UIMS

delete

• UIMS

list

• UIMS

sets, SPL

• Writing And Saving Macros

• Command Sets

SPL command

definition

• Echoing "Hello World"

descriptions

• SPL Commands

• WHILE ENDWHILE

trigger execution

• UIMS

O/S utilities

protein database

• Create/Update the PRODAT Database

scripts

• Appendix A: Command Scripts

UDCIMPORT

• UDCIMPORT

UDCSEARCH

• UDCSEARCH

Command line

client

• AUSPYX Command Line Client Usage

Command mode

• Command Mode

default values

• Command Mode

special characters

• Command Mode

Commands

basics list

• List of Basic Commands

Confort

• Confort Commands

Common cores

• Distill: Select Common Cores

Common substructure

definition

• Introduction to Distill

Common tasks

• General Instructions for Common Tasks

Common volume overlap

• Fitness Function

Communication file

• ToDoList File

• COMMUNICATION File Format

create

• Create the COMMUNICATION File

Compare SLN_Ts

• REG_T Type

Compare to MOLCAD eps

• Slicing Surfaces Tutorial

Compatibility

cross-platform

• Cross-Platform Compatibility

Compatibility grid, docking functionality

Compatibility grid, docking functionality

• Introduction to the Docking Suite

Compatibility grid, docking functionality

• Introduction to CombiFlexX

COMPLEX_PROPERTY

tps

• COMPLEX_PROPERTY

Components

optimal number

• CoMFA PLS Runs

• Terminology of Multiple Regression and PLS

Composer

Structurally Variable Regions

• ORCHESTRAR Background Reading

using QSAR

• ORCHESTRAR Background Reading

Compound-based visualization tools

DiverseSolutions addons

• Compound-based Visualization Tools

Compound filtering

• Compound Filtering (dbslnfilter)

dbslnfilter

• dbslnfilter O/S Utility

dialog

• Compound Filtering (dbslnfilter)

Compound selection suggestions

• Select Structures to Align

Compress domain index

• Compress Domain Index

Compressed bitmap

• Tuplet Definition

Computing index statistics

• STAT_OPS

CoMSIA

column type

• COMSIA Column Type

field descriptions

• CoMSIA Field Descriptions

theory

• CoMSIA

tutorial

• CoMSIA Tutorial

viewing results

• Display CoMSIA Results

TAILOR

• TAILOR SET COMSIA

Concord

3D coordinate generation

Surflex-Dock

• Surflex-Dock Details

O/S utility

• Compute 3D Coordinates using Concord®

notes & requirements

• Concord/StereoPlex

troubleshooting

• Concord/StereoPlex

computation in a spreadsheet

• Computations on Spreadsheet Rows

3D building in Selector

• 3D Model Building

3D coordinate generation

FlexS

• Access FlexS in SYBYL

Surflex-Sim

• Access Surflex-Sim in SYBYL

• Topomer Search Details

GUI

• Concord Graphical Interface

how to access

• Concord Introduction

input modes

• Input Modes

introduction

• Concord Introduction

licensing

• Concord Introduction

open graphical interface

• XConcord Control Window

output

• Concord Output

size limits

• Size Limitations

• Size Limitations

standalone commands

• Concord Standalone Command List

SYBYL command

• SYBYL's CONCORD Command

concord.pref example file

• UDCTRANSLATE

Cone surfaces

batch

• Working with Cones in Batch

characteristics

• Working with Cones & Field Lines Interactively

coloring

• Working with Cones & Field Lines Interactively

creating

• Working with Cones & Field Lines Interactively

theory

• MOLCAD Cone/Field Line Surfaces

tutorial

• Cone and Field Line Surfaces Tutorial

Cones

changing attributes

• Interactive Cones Tutorial

create and display in MOLCAD Plus

• Interactive Cones: Create and Visualize via the Menubar

in MOLCAD Plus

• Interactive Cones

MOLCAD Plus tutorial

• Interactive Cones Tutorial

Confidence limits

• Concepts Associated With QSAR Analysis

Configuration

files

• A Note About Configuration Files

Tuplets

• Advanced Tuplet Configuration

tuplets.cfg file

• tuplets.cfg

license file

• Configuring the License File

Trigo

• Trigo Configuration

Learned Index

• PKG_LI_TEACH

Oracle

• Oracle Initial Configuration

Confirming predictive power of the model

• Confirm the Predictive Power of the Model

Conformation

generation

• Tuplet Generation Parameters

naming conventions

• Conformational Specifications

SCAN

• Scan Torsions to Remove van der Waals Contacts

valid state names

• Conformational Specifications

changing in biopolymers

• Set Backbone Conformation

• Set Sidechain Conformation

copying in biopolymers

• Copy Conformation

finding in biopolymers

• Find Secondary Structure Conformation

rotamer libraries

• Set Sidechain Conformation

Conformational analysis

background reading

• Conformational Analysis Background Reading

GA conformational search

• GA Conformational Search

grid searching

• Grid Search

multisearch

• Search Multiple Molecules

random searching

• Random Conformational Search

systematic search

• Systematic Conformational Search

Conformational angle

Conformational angle

• Dictionary Files

column type

• Append Structural Columns

Conformational states

• Dictionary Files

Conformer

column type

• CONFORMER Column Type

generation

• Specify 3D Conformers

update in DISCOtech

• Specify 3D Conformers

column

dialog box

• Specify Usage of Conformer Column

tutorial

• Conformer Columns Tutorial

Confort

• Specify 3D Conformers

advanced options

• Specify 3D Conformers

commands

• Confort Command List

diverse conformer subset generation

• Task

exceptions file

• Diagnostics

final optimization and output options

• Task

Generate Conformer Population dialog

• Setup a Calculation

geometry optimization

• Task

input

• File Maintenance

intermediate conformer processing

• Task

introduction

• Introduction to Confort

license requirements

• Introduction to Confort

log file

• Diagnostics

low energy conformer subset generation

• Task

modify output details

• Modify Output Parameters

output

• File Maintenance

search details

• Modify Search Parameters

search limits

• Task

Single entry point energy calculation

• Task

Tripos Force Field

• Introduction to Confort

Confort and FlexS

• Access FlexS in SYBYL

Confort and FlexX

• FlexX Details

Confort command control files

• Options

Confort in SYBYL

• Access Confort in SYBYL

Confort sessions

custom defaults

• Sessions

Confort Sessions Menu

• Sessions

Conjugate gradient method

• Minimization Methods

Connect to server from SYBYL

• Connect/Disconnect Server

CONNECT, tailor variable

• TAILOR SET CONNECT

Connection Bond

• Specify Bonds

Connection flag

• Fragment Generation

• Model Options

• Add a New Hologram Column

• Create Hologram Column

Connection table

Connection table

• SLN Language

Connection table

• SLN Language

Connection tables

• Input Modes

• Input Modes

Connectivity

quick bonds

• Bonds

quick bonds

• Add Single Bonds

search

• Connect Atoms in the Molecule

CONNOLLY

scaling factor

• About Molecular Surfaces

SURFACE

• SURFACE

surface

• About Molecular Surfaces

Consensus

and best consensus

• CScore Subset Extraction Tool

column type

• Add a Column in a Spreadsheet or Table

scoring

definition

• Generating a Consensus

introduction

• Introduction to CScore

selecting the best docked solution

• CScore Subset Extraction Tool

within a spreadsheet

• Use CSCORE in a Spreadsheet or Table

Consistency

chemical structure

• Chemical Structure Consistency

Constraining distances

• Constraining Distances

Constraint

Bond Path

• Overview of Bond Path Constraints

Constraint violations

• List Constraint Violations via Command Line

Constraints

bond path

• Define Bond Path Constraints

normal

• Define Normal Constraints

angle

• Angle

between lines and planes

• 2 Lines/Planes Angle

dihedral angle

• Dihedral

distance

• Distance

partial match

• Define Directives

partial match

• Specify a Partial Match Constraint

spatial

• Define Spatial Constraints

spatial cap

• Spatial Cap

spatial line

• Spatial Line

spatial plane

• Spatial Plane

spatial point

• Spatial Point

torus

• Torus

volume

• Define Volume Constraints

containing

• Containing Volume

exclusion

• Excluded Volume

receptor cavity

• Receptor Cavity

receptor site

• Receptor Site

surface

• Surface

set tolerance

• Set Constraint Tolerances

description file

• FlexX-Pharm Constraints

angle

define

• Angle Constraints

list

• Angle Constraints

modify

• Angle Constraints

remove

• Angle Constraints

dialog description

• General Description of the Constraints Dialog

distance

define

• Distance Constraints

list

• Distance Constraints

modify

• Distance Constraints

remove

• Distance Constraints

multifit

define

• Multifit Constraints

list

• Multifit Constraints

range

define

• Distance Range Constraints

list

• Distance Range Constraints

modify

• Distance Range Constraints

remove

• Distance Range Constraints

torsion

define

• Torsion Constraints

list

• Torsion Constraints

modify

• Torsion Constraints

remove

• Torsion Constraints

viewing

• Manage the Display of Constraints

set tolerance

• Set Constraint Tolerances

add/modify

• Modify Constraints

and flexible rings

• Define Constraints and Flexible Rings

set tolerance

• Set Constraint Tolerances

bond path

• Define Bond Path Constraints

normal

• Define Normal Constraints

angle

• Angle

between lines and planes

• 2 Lines/Planes Angle

dihedral angle

• Dihedral

distance

• Distance

partial match

• Define Directives

spatial

• Define Spatial Constraints

spatial cap

• Spatial Cap

spatial line

• Spatial Line

spatial plane

• Spatial Plane

spatial point

• Spatial Point

torus

• Torus

volume

• Define Volume Constraints

containing

• Containing Volume

exclusion

• Excluded Volume

receptor cavity

• Receptor Cavity

receptor site

• Receptor Site

surface

• Surface

constraints2stream

• constraints2stream

Containing constraints

• Containing Volume

receptor cavity

• Receptor Cavity

receptor cavity

• Receptor Cavity

Continuous Drawing Mode

Cancel point of attachment

• Sketching Techniques

CONTOUR

• CONTOUR

ANALYZE

• CONTOUR

ASCII_CONV

• CONTOUR

DISPLAY

• CONTOUR

header information

• CONTOUR

CoMFA fields

• Examination and Use of CoMFA Results

details

• Control Contour Details

specifications

• Display CoMSIA Results

TAILOR

• TAILOR SET CONTOUR

analyze

TAILOR HISTOGRAM

• TAILOR SET HISTOGRAMS

Contour files

creating

• Create Contour Files Tutorial

creating coulomb ESP

• Create a Coulomb ESP Contour File

creating in batch

• Create a Contour File in Batch

creating poisson-Boltzmann contour

• Create a Poisson Boltzmann ESP Contour File

creating with MOLCAD Plus

MOLCAD Plus

creating contour files

• Create a Contour File via the Menubar

electron density

• Create an Electron Density Contour File

isopotential

• POTENTIAL

MVOLUME

• MVOLUME

MO plot

• MO PLOTS

Contour graph

isocontour

• Isocontour Graph

QSAR

• Graph Field

Contributions

dialog

• Show Contributions

graphs

• HQSAR GRAPH

Convert

files (sln2img)

• Translate SLN or SMILES Files to PNG or GIF

MDL molfile to SLN

• TRANSLATE_OPS

screens

• Rebuild/Convert Screens

SLN to MDL MOL file

• TRANSLATE_OPS

SLN to SMILES

• TRANSLATE_OPS

SLN to SYBYL MOL2 file

• TRANSLATE_OPS

SMILES to SLN

• TRANSLATE_OPS

SYBYL MOL2 file to SLN

• TRANSLATE_OPS

table formats

• Translate Between Formats via O/S Utilities

table formats

• UDCTRANSLATE

Convert old domain index

• Convert Domain Index to AUSPYX 1.7.1 Version

Cooman plot

• Graph Analysis Results

COORDID_SEQUENCE

• Default Schema Contents

Coordinate

attributes

• Appendix B: Hitlist Format

generate 2D

• 2D Coordinate Generation

object type

• SLN_32727_SET_T Type

Coordinate map

• Coordinate Maps

dialog box

• Coordinate Maps

search setup

• Coordinate Maps

Coordinates

duplication check

• Check Nature of Conformations/Structures in Database

generate 2D

• Generate Coordinates

list

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

MODIFY

• Atoms

COORD_T type

• SLN_32727_SET_T Type

Copy

• Copy Between Molecule Areas

molecule area contents

• Copy Between Molecule Areas

Core

definition

• Introduction to Distill

Core File Identifiers

• Advanced Variable Creation

• Core File identifiers

Core placements

definition

• OptiDock Glossary

Core structure, definition

• Introduction to Selector

Core structure, definition

• Introduction to Legion

Cosine

• Similarity Metrics and Database Screening

Cosine coefficient in Selector

• Similarity Coefficients

Cost definition

• Postprocessing

Coulomb

creating contour files

• Create a Coulomb ESP Contour File

Counterion table

• SALT_OPS

counterion.defs

• Remove Salts (Ions)

Coverage Flag Attribute

• Static Attributes

Covering atoms

Covering atoms

• Static Attributes

Covering atoms

• Covering and Non-Covering Atoms

CPK

• CPK

CPSA

columns

• CPSA Column Type

tutorial

• PLS Analysis of CPSA Descriptors Tutorial

TAILOR

• TAILOR SET CPSA

CRC calculation

• SLN_OPS

Create

hypothesis

• Hypothesis Creation

query

• Create Query

Tuplets

• Tuplet Creation

tuplets

• Tuplet Creation

Create fingerprint domain index

• Create Fingerprint Domain Index

Create registrar

• Registrar Creation and Demo Install

Create SLN domain index

• Create SLN Domain Index

from fingerprint set

• Create SLN Domain Index from Fingerprint Set

Create UNITY query

from a ligand

• Create Query by Selecting from Feature Sets and Constraints

create_dataset

• create_dataset

Creating

database

dialog description

• General Description of Dialogs for Creating UNITY Databases

hypothesis

from molecule

• Create a Hypothesis from a Molecule

from UNITY query

• Create a Hypothesis From UNITY Query

Tuplets

• Calculate Tuplets

DISCOtech run

• Access DISCOtech

active site

• Define the Active Site

CDF file

• FlexX-Pharm Constraints

EDF file

• Define the FlexE EDF File

RDF file

• Access FlexX

SFXC file

• Access Surflex-Dock

family

• Create New Family

generalized surfaces

• Create Generalized Surfaces

3D volume

• 3D Volumes: Create and Visualize via the Menubar

contour files

• Create Contour Files Tutorial

density & electrostatic potential contour files

• Create Contour Files Tutorial

density contour file dialog

• Create an Electron Density Contour File

electron density slicing plane

• Slicing Surfaces Tutorial

electrostatic potential contour files

• Create Contour Files Tutorial

• Create Contour Files Tutorial

electrostatic potential iso surfaces

• Interactive Iso Surfaces Tutorial

electrostatic potential slicing plane

• Slicing Surfaces Tutorial

esp contour file dialog

• Create a Coulomb ESP Contour File

• Create a Poisson Boltzmann ESP Contour File

esp surface contour file dialog

• Create a PB ESP Contour File Using a Surface

interactive cones

• Interactive Cones Tutorial

• Interactive Cones Tutorial

interactive iso surfaces

• Interactive Iso Surfaces Tutorial

iso surfaces

• Iso Surfaces: Create and Visualize via the Command Line

separating surface

• Separating Surfaces Tutorial

separating surfaces

• Separating Surfaces Tutorial

slicing plane

• Slicing Surfaces Tutorial

command sets

• UIMS

expression generators

• Writing Expression Generators

• Core File identifiers

definition

• Using Expression Generators

macros

• Writing And Saving Macros

• Core File identifiers

scenes

• %dialog_create_scene()

• SPL Related Tools

variables

associative arrays

• Storing Data In Associative Arrays

• More About Variables

built-in

• More About Variables

core file

• More About Variables

• Advanced Variable Creation

defined arrays

• More About Variables

• Defined Arrays

user defined

• Creating Variables With SETVAR

• More About Variables

small molecules

• Access the Sketcher

biopolymers

• Peptide Building Tutorial

• Build Biopolymer

• Build Protein, DNA Strand, RNA Strand, Carbohydrate

unit cell box

• Generate/Delete Unit Cell Box

Credentials

tps

• TPS Security

Credits

• Concord Introduction

Crippen parameter tables

• Define Surface Properties Interactively

Cross-platform compatibility

• Cross-Platform Compatibility

Crossover

operator

• Apply Genetic Operators

Crossvalidation

diagram

• Crossvalidation

group membership

• Crossvalidation

negative values

• CoMFA PLS Runs

number of groups

• Crossvalidation

prediction

• Crossvalidation

theory

• Crossvalidation

with PLS

• Terminology of Multiple Regression and PLS

CRYSIN

• CRYSIN

data record

• @<TRIPOS>CRYSIN

TAILOR

• TAILOR SET CONNECT

• TAILOR SET EXPAND

transformation matrix

• Some Crystallography Basics

tutorial

• CRYSIN Tutorial

Crystal

add single bonds

• Add Single Bonds

classes

• Some Crystallography Basics

connect atoms

• Connect Atoms in the Molecule

create box

• Generate/Delete Unit Cell Box

delete box

• Generate/Delete Unit Cell Box

expand cells

• Expand Unit Cells to Fill Box

file formats

• CRYSIN File Formats

list molecule information

• List Molecule Information

load coordinates

• Load Fractional Coordinates

modify atom parameters

• Modify Definition of Atom Parameters

remove molecule definition items

• Remove Items from Molecule Definition

save to ASCII file

• Save Entire Definition of Molecule to ASCII File

space group

data files

• Space Group Data Files

tables

• Space Group Tables

specify symmetry

• Specify Symmetry Information for Molecule

specify unit cell parameters

• Designate/Modify Unit Cell Parameters

transformation operations

• Enlarge Atom Set via Transformation Operations

Crystallographic data

• CRYSIN

CScore

best solution

• CScore Subset Extraction Tool

bibliography

• CScore Suggested Reading

ChemScore

• ChemScore

command outside SYBYL

• O/S Command: CScore

command within SYBYL

• SYBYL Command: CSCORE

consensus and best consensus

• CScore Subset Extraction Tool

consensus definition

• Generating a Consensus

D score

• D_Score

details

• Perform CScore Calculations

extraction

• CScore Subset Extraction Tool

F Score

• F_Score

FlexX-Pharm Constraints

• CScore Subset Extraction Tool

G Score

• G_Score

graphical user interface

• Run CScore via the Menubar

introduction

• Introduction to CScore

menu

• Use CSCORE in a Spreadsheet or Table

O/S utility

• O/S Command: CScore

operation mode

• O/S Command: CScore

parameters

• CScore Parameters

PMF score

• PMF_Score

purpose

• Purpose of CScore

requirements

• CScore Input Requirements

running in CombiFlexX

• Run CScore on CombiFlexX Results

running while docking

• Run CScore while Docking

selecting the scoring functions

• Run CScore while Docking

subset extraction

• CScore Subset Extraction Tool

theory

• CScore Theory

tutorials

• CScore Tutorials

using within a spreadsheet

• Use CSCORE in a Spreadsheet or Table

working with metal atoms

• O/S Command: CScore

TAILOR

• TAILOR SET CSCORE

files created

• The CombiFlexX Files

running in CombiFlexX

• Other CombiFlexX Extraction Formats

• CombiFlexX and CScore Tutorial

• Analyze the CombiFlexX Results

CSLN

building

• Build the Combinatorial Library

child

adding to UNITY database

• Building Options

generating

• The Legion Menu

• CSLN Enumeration and Retrieval

naming

• Enumeration Options

definition

• OptiDock Glossary

definition

• Introduction to Legion

enumerating

• Examine the Combinatorial Library

enumerating

• CSLN Enumeration and Retrieval

• Building Options

exploding

• dbexplode

naming

• Enumeration Options

parent

• The Legion Menu

• CSLN Enumeration and Retrieval

retrieval

• CSLN Enumeration and Retrieval

CT

CT

• SLN Language

CT

• SLN Language

Ct Attributes

• Appendix B: Hitlist Format

Cubic system

• Space Group Tables

Current conformation

• Rotatable Bonds and Anchor Atoms

Curvature column

• Create SiteID Table

Customization of

RDF file

• Customize the FlexX RDF File

Customize

start up

• Automatic Command Execution

SYBYL startup

• Choosing the Terminal Type and Interface

texport size

• Using TA_DISPLAY_CONFIG with SYBYL

Customize Concord defaults

• Sessions

• Customization

Customize Confort

sessions

• Sessions

Customize StereoPlex

sessions

• Sessions

Customizing SYBYL

• Customizing SYBYL

during execution

• During SYBYL Execution

environment variables

• Customizing SYBYL

TA_COLORMAP

• Pre-Startup

• SYBYL Defined Variables

TA_COLTYPES

• Pre-Startup

TA_DISPLAY_CONFIG

• Pre-Startup

TA_MENDYL_TAILVALS

• Pre-Startup

TA_SYSTEM_STRT

• Pre-Startup

• SYBYL Defined Variables

TA_USER_STRT

• Pre-Startup

• SYBYL Defined Variables

XUSERFILESEARCHPATH

• Pre-Startup

• SYBYL Defined Variables

example .sybylrc file

• A Sample .sybylrc file

menubar

• Customizing SYBYL

adding new pull-downs

• Customizing the Menubar

adding new pull-downs to spreadsheet

• Customizing the Menubar

adding options to existing pull-downs

• Customizing the Menubar

adding options to existing spreadsheet pull-downs

• Customizing the Menubar

predefined variables

• Customizing SYBYL

OTHER_DIRECTORIES

• During Startup

SYBYL_MENUBAR_ADDONS

• During Startup

TA_MENUBAR_USER_INIT

• During Startup

TA_MSS_USER_INIT

• During Startup

SPL column types

• Customizing SYBYL

• SYBYL Defined Variables

X Resources

• Customizing SYBYL

• SYBYL Defined Variables

.Xdefaults file

• Pre-Startup

Sybyl file location

• Pre-Startup

Cyclic peptide

• Form a Cyclic Peptide

Cylinder options

• Slicing Surfaces: Create and Visualize via the Menubar

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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.