Table of Contents for Volume 2

CONTENTS VOLUME 1

1. GUIDE TO THE CAMBRIDGE STRUCTURAL DATABASE SYSTEM AND DOCUMENTATION
2. DATABASE CONTENTS AND SEARCHING - AN OVERVIEW
3. THE MENU SYSTEM
4. GETTING STARTED
5. 1D SEARCHING OF TEXT, NUMBERS AND SCREENS
6. 2D SEARCHING OF CHEMICAL STRUCTURES
7. 3D SEARCHING OF CRYSTAL STRUCTURES
8. USE OF CONTROL INSTRUCTIONS
9. INITIATING THE SEARCH PROCESS
10. DISPLAY OF HITS IN THE SEARCH PROCESS
11. CONTINUATION OR TERMINATION OF THE SEARCH
12. THE HELP SYSTEM
13. CUSTOMISING YOUR QUEST/QUEST3D IMPLEMENTATION
14. INTRODUCTION TO GSTAT
15. INTRODUCTION TO PLUTO

CHAPTER 1 GUIDE TO THE CAMBRIDGE STRUCTURAL DATABASE SYSTEM AND DOCUMENTATION

• 1.1 Introduction
• 1.2 The Cambridge Structural Database (CSD)
• 1.3 A Statistical Survey of the CSD
• 1.4 The Basic Software System
  • 1.4.1 QUEST
  • 1.4.2 GSTAT
  • 1.4.3 PLUTO
• 1.5 The Graphics Software System
  • 1.5.1 QUEST3D
  • 1.5.2 VISTA
  • 1.5.3 GSTAT
  • 1.5.4 PLUTO
• 1.6 Guide to the Documentation
  • 1.6.1 Volume 1
  • 1.6.2 Volume 2
  • 1.6.3 Volume 3
  • 1.6.4 Volume 4

CHAPTER 2 DATABASE CONTENTS AND SEARCHING - AN OVERVIEW

• 2.1 Coverage
• 2.2 Information Content
  • 2.2.1 1D Textual and Simple Numeric Information
  • 2.2.2 2D Chemical Connection Table
  • 2.2.3 3D Crystallographic Data
  • 2.2.4 Database Use - Introduction
  • 2.2.5 Database Use - Initialisation
  • 2.2.6 Database Use - Information Content
  • 2.2.7 Database Use - Searching the DBUSE file
• 2.3 Fundamental Concepts - Entry, Reference Code, Residue, Asymmetric Unit and Crystal Chemical Unit
  • 2.3.1 Entry
  • 2.3.2 Reference Code
  • 2.3.3 Residue
  • 2.3.4 Asymmetric Unit and Crystal Chemical Unit
• 2.4 Types of Searches
• 2.5 The Instruction Document
• 2.6 Search Fields And Associated Keywords
• 2.7 Search Tests
  • 2.7.1 Numeric Tests
  • 2.7.2 Text Tests
  • 2.7.3 Chemical Formula Tests
  • 2.7.4 2D Chemical Connectivity Tests
  • 2.7.5 3D Geometric Calculations and Tests
• 2.8 Screens
  • 2.8.1 Database Screens
  • 2.8.2 Query Screens
    • 2.8.2.1 Query Screens Assigned by the User
    • 2.8.2.2 Query Screens Automatically Assigned by QUEST and QUEST3D
• 2.9 Control Instructions
  • 2.9.1 BEGIN-AT-REFCODE
  • 2.9.2 HITALL
  • 2.9.3 PRINT
  • 2.9.4 SAVE
  • 2.9.5 STOP-LIMIT
  • 2.9.6 TYPE
• 2.10 The Search Question and the Initiation of the Search
• 2.11 Display of the Results of the Search
• 2.12 Continuation or Termination of the Search
• 2.13 The Journal File

CHAPTER 3 THE MENU SYSTEM

• 3.1 The Input Menus
  • 3.1.1 Menu Map
  • 3.1.2 Menu Layout
  • 3.1.3 BUILD Menu
    • 3.1.3.1 PERIODIC-TABLE Sub-menu
    • 3.1.3.2 GROUPS Sub-menu
    • 3.1.3.3 TEMPLATES Sub-menu
    • 3.1.3.4 2D-CONSTRAIN Sub-menu
    • 3.1.3.5 3D-CONSTRAIN Sub-menu
    • 3.1.3.6 *MASK Sub-menu
  • 3.1.4 EDIT Menu
    • 3.1.4.1 PERIODIC-TABLE Sub-menu
  • 3.1.5 FILES Menu
  • 3.1.6 SEARCH Menu
    • 3.1.6.1 TEXT Sub-menu
    • 3.1.6.2 NUMERIC Sub-menu
    • 3.1.6.3 SCREEN Sub-menu
    • 3.1.6.4 REDUCED-CELLS Sub-menu
    • 3.1.6.5 ELEMENTS Sub-menu
    • 3.1.6.6 PRINT Sub-menu
• 3.2 The Display Menus
  • 3.2.1 Menu Layout
  • 3.2.2 2D/3D Menu
  • 3.2.3 2D Menu
  • 3.2.4 3D Menu
  • 3.2.4a 1D Menu
  • 3.2.5 Remarks
• 3.3 Summary of the Search Process and its Menus
• 3.4 Basic Conventions and Concepts

CHAPTER 4 GETTING STARTED

• 4.1 Starting QUEST - Introduction
• 4.2 Starting QUEST - VAX/VMS, SG and SUN Implementations
  • 4.2.1 VAX/VMS
  • 4.2.2 SG and SUN
  • 4.2.3 For More Information...
• 4.3 Starting the Graphical Interface Software
  • 4.3.1 Specification of the Terminal Type
  • 4.3.2 Specification of the Graphics Input Device
  • 4.3.3 Specification of the Menu Mode
  • 4.3.4 Specification of the Diagram Display Mode
• 4.4 Automating the QUEST Start-up

CHAPTER 5 1D SEARCHING OF TEXT, NUMBERS AND SCREENS

• 5.1 GRAPHICS QUEST3D
  • 5.1.1 Text Searches
  • 5.1.2 Numeric Searches
  • 5.1.3 Screen Searches
  • 5.1.4 Chemical Formula Searches
  • 5.1.5 Unit Cell Matching Searches
  • 5.1.6 Peptide Sequence Searches
• 5.2 BASIC QUEST
  • 5.2.1 Text Searches
  • 5.2.2 Numeric Searches
  • 5.2.3 Screen Searches
  • 5.2.4 Chemical Formula Searches
  • 5.2.5 Unit Cell Matching Searches
  • 5.2.6 Peptide Sequence Searches
• 5.3 Guide to the Location of Search Details in Vol.2

CHAPTER 6 2D SEARCHING OF CHEMICAL STRUCTURES

• 6.1 Types of 2D Connectivity Search
• 6.2 Basic QUEST
  • 6.2.1 Simple Examples
  • 6.2.2 Summary of Connectivity Search Test Instructions
  • 6.2.3 Bond Property Record
  • 6.2.4 DEFB Instruction
  • 6.2.5 Atom Property Record - Element Symbol
  • 6.2.6 ELDEF Instruction
  • 6.2.7 Atom Property Record - mca Value
  • 6.2.8 Atom Property Record - Exact Value of mca
  • 6.2.9 Atom Property Record - nh Value
  • 6.2.10 Atom Property Record - Total Coordination Number
  • 6.2.11 Atom Property Record - nch Value
  • 6.2.12 Atom Property Record - Cyclicity
  • 6.2.13 Atom Property Record - Unspecified Values
  • 6.2.14 ALLBOND Instruction
  • 6.2.15 No Cyclic Routes Instruction
  • 6.2.16 No Direct Links Instruction
  • 6.2.17 Number of Fragments Instruction
  • 6.2.18 Same Residue Instruction
  • 6.2.19 Comment Instruction
  • 6.2.20 Noscreens Instruction
  • 6.2.21 Computational Limits
  • 6.2.22 Implicit And Explicit Hydrogen Atoms
  • 6.2.23 Bond Type Conventions in the Database
• 6.3 Graphics QUEST3D
  • 6.3.1 Examples
  • 6.3.2 Menu And Sub-Menu Summary
    • 6.3.2.1 BUILD Menu
    • 6.3.2.2 PERIODIC-TABLE SUB-MENU
    • 6.3.2.3 2D-CONSTRAIN Sub-Menu
• 6.4 2D Similarity Searching
  • 6.4.1 Basic QUEST
  • 6.4.2 GRAPHICS QUEST3D

CHAPTER 7 3D SEARCHING OF CRYSTAL STRUCTURES

• 7.1 The 3D-CONSTRAIN Sub-menu
• 7.2 The Connectivity Basis of 3D Searching
• 7.3 The Geometric Basis of 3D Searching
• 7.4 Geometric Objects
• 7.5 Composite Geometrical Parameters
• 7.6 Numerical Limits for the 3D Search
• 7.7 Choosing and Naming Geometrical Parameters
• 7.8 Selecting Suitable 3D Search Constraints
• 7.9 3D Geometrical Surveys as Precursors to 3D Searching
• 7.10 Exhaustive Fragment Location
• 7.11 Topological Symmetry and Fragment Location
• 7.12 Atomic Overlap in Multiple Fragment Situations
• 7.13 Handling Structural Inversion
• 7.14 Searching for Non-Bonded Contacts
  • 7.14.1 The CSD Reference Molecule(s) and the Extended Crystal Structure
  • 7.14.2 Searching for Specific Contact Types
  • 7.14.3 Using van der Waals Radii for Distance Testing
  • 7.14.4 Searching with Functional Groups
  • 7.14.5 Searches Involving Multiple Contacts
  • 7.14.6 Display of Hits from Non-Bonded Searches
  • 7.14.7 Geometrical Surveys of Non-Bonded Fragments
  • 7.14.8 Efficiency of Non-Bonded Searches
  • 7.14.9 Further Examples of Non-Bonded Searches
• 7.15 Commands in the 3D-CONSTRAIN Sub-menu
  • 7.15.1 EXHAUSTIVE/OVERLAP Commands
  • 7.15.2 SETUP Commands
  • 7.15.3 DEFINE Commands
  • 7.15.4 TRANSFORM Command
  • 7.15.5 SELECT Commands
  • 7.15.6 ENANTIOMER Commands
  • 7.15.7 NON-BONDED Commands
• 7.16 Bit Screens for 3D Searching
  • 7.16.1 3D Screening in the CSD System
  • 7.16.2 Differences between 2D and 3D screening
  • 7.16.3 Intramolecular Distance Screens
  • 7.16.4 Single Torsion Screens
  • 7.16.5 Adjacent Torsion Screens
  • 7.16.6 Making the Best Use of 3D Screens
  • 7.16.7 Possible Problems with 3D Screens 7-

CHAPTER 8 USE OF CONTROL INSTRUCTIONS

• 8.0 Instruction Keywords
• 8.1 Graphics QUEST3D
  • 8.1.1 BEGIN-AT-REFCODE
  • 8.1.2 COMMENT
  • 8.1.3 EXIT
  • 8.1.4 HITALL
  • 8.1.5 INFORMATION
  • 8.1.6 JOURNAL
  • 8.1.7 LOCASE
  • 8.1.8 NOJOURNAL
  • 8.1.9 NOSCREENS
  • 8.1.10 PRINT
  • 8.1.11 PURGE
  • 8.1.12 RETRIEVE
  • 8.1.13 SAVE
  • 8.1.14 SCREEN
  • 8.1.15 STATISTICS
  • 8.1.16 STOP-LIMIT
  • 8.1.17 TYPE
• 8.2 Basic QUEST
  • 8.2.1 BEGIN-AT-REFCODE
  • 8.2.2 COMMENT
  • 8.2.3 CONCATENATE
  • 8.2.4 EXIT
  • 8.2.5 HITALL
  • 8.2.6 INFORMATION
  • 8.2.7 JOURNAL
  • 8.2.8 LOCASE
  • 8.2.9 NOJOURNAL
  • 8.2.10 NOSCREENS
  • 8.2.11 PRINT
  • 8.2.12 PURGE
  • 8.2.13 RETRIEVE
  • 8.2.14 SAVE
  • 8.2.15 SCREEN
  • 8.2.16 STATISTICS
  • 8.2.17 STOP-LIMIT
  • 8.2.18 TYPE

CHAPTER 9 INITIATING THE SEARCH PROCESS

• 9.1 Graphics QUEST3D
  • 9.1.1 The QUEST Command
  • 9.1.2 The FASTQUEST Command
  • 9.1.3 The START Command
• 9.2 Basic QUEST
  • 9.2.1 The QUESTION Instruction
  • 9.2.2 The START Instruction 9-

CHAPTER 10 DISPLAY OF HITS IN THE SEARCH PROCESS

• 10.1 GRAPHICS QUEST3D
  • 10.1.1 2D/3D Display
  • 10.1.2 2D Display
  • 10.1.3 3D Display
  • 10.1.4 Menu Commands
• 10.2 Basic QUEST
  • 10.2.1 Display Information
  • 10.2.2 Examples
  • 10.2.3 Options

CHAPTER 11 CONTINUATION OR TERMINATION OF THE SEARCH

• 11.1 Graphics QUEST3D
  • 11.1.1 Continuation of the Search
    • 11.1.1.1 CONTROL KEEP
    • 11.1.1.2 CONTROL REJECT
    • 11.1.1.3 FAST NODIAG
    • 11.1.1.4 FAST DIAG
    • 11.1.1.5 FAST REFCOD
    • 11.1.1.6 FAST HIT-STATS
  • 11.1.2 Termination of the Search
    • 11.1.2.1 CONTROL EXIT
    • 11.1.2.2 CONTROL STOP
    • 11.1.2.3 CONTROL QUIT
• 11.2 Basic QUEST
  • 11.2.1 Continuation of the Search
  • 11.2.2 Termination of the Search

CHAPTER 12 THE HELP SYSTEM

• 12.1 Graphics QUEST3D
  • 12.1.1 HELP When the Banner is Displayed in the VAX Implementation
  • 12.1.2 HELP While Getting Started, Before Invoking the Menu System
  • 12.1.3 HELP in the Build or Search Menus, Using COMMAND
  • 12.1.4 HELP in the Input Menus, for Help on Commands in these Menus
  • 12.1.5 HELP When a Hit is Displayed
• 12.2 Basic QUEST
  • 12.2.1 HELP When the Banner is Displayed in the VAX Implementation
  • 12.2.2 HELP When Composing the Instruction Document, Except in *CONN Tests
  • 12.2.3 HELP When Composing a Connectivity or Similarity Test Instruction Packet
  • 12.2.4 HELP When a Hit is Displayed

CHAPTER 13 CUSTOMISING YOUR QUEST/QUEST3D IMPLEMENTATION

• 13.1 QUEST Initialisation Files
  • 13.1.1 VAX Search Order
  • 13.1.2 SG/SUN Search Order
• 13.2 QUEST3D Configuration Files
  • 13.2.1 Editing the Configuration File.
  • 13.2.2 VAX Search Order
  • 13.2.3 SG/SUN Search Order
  • 13.2.4 QUEST Colour Names
  • 13.2.5 Default QUEST Configuration File 13-

CHAPTER 14 INTRODUCTION TO GSTAT

• 14.1 Introduction
• 14.2 Geometry Calculations for Complete CSD Entries (Volume 4 : Chapter 2)
• 14.3 3D Search and Geometry Calculations for Substructural Fragments (Volume 4 : Chapter 3)
• 14.4 Visual, Statistical and Numerical Analysis of Fragment Geometry
• 14.5 Searchable Connectivity Representations in GSTAT
• 14.6 Ordering of GSTAT Instructions (Volume 4 : Chapter 6)
• 14.7 The QUEST3D-GSTAT link (Volume 4 : Chapter 7)
• 14.8 GSTAT Output Files (Volume 4 : Chapter 8)
• 14.9 Glossary of GSTAT Instructions (Volume 4 : Chapter 9)

CHAPTER 15 INTRODUCTION TO PLUTO

• 15.1 Introduction
• 15.2 Styles of Diagrams and Style Defaults
• 15.3 Plotting Instructions
• 15.4 Easy Use of PLUTO
• 15.5 Interactive Versus Batch Use
• 15.6 Free Format Input Data