Insight II - Contents

Insight II

Contents

Release 2000, March 2000

APPENDICES

A. References

B. File Formats

C. Setting Up the Brookhaven PDB

PDB Organization

: Getting Brookhaven PDB database
: Coping with more than 8000 PDB files
: The Standard Brookhaven Directory Structure
: Using a Representative Selection of PDB Files

Installing the PDB for use with Insight II Software

Installing PDB Files

: Example of PDB setup for use with Biosym/MSI's software

Keep the INSIGHT_PDB Directory Clean

IBM Workstations Warning: Do Not Use Soft Links to distr Subdirectories

Reading a PDB File into Insight II

: Using the Molecule/Get Command
: Using the File/Import Command
: Creating New Index Files for the File/Import Command

Protein Loop Search (Biopolymer and Homology Modules)

: Setting Up and Using the Protein Loop Search Commands

Sequence Database Searching (Homology Module)

: Seq_extract and the Sequence Database File pdb.seq

3D Profiles Database (Profiles-3D Module)

: Create_Profiles and the Database of 3D Profiles

The Shell Script Utility: link_pdb

D. Fragment Definitions

E. Hydrogen Bonds

F. Space Group Names

G. Potential Template Rules

Potential Type Template

: Atom Tests
: Element Test
: Hybridization Test
: Aromaticity Test
: Ring Test

Precedence Tree

Examples of Potential Assignment for a Small Set of Potential Types

: Examples of Potential Assignments Using These Types
: Adding A New Parameter Type

cvff_templates.dat

Out-of-Plane Assignment Rules

H. Amino Template File

: File Format Description
: Example

I. Classic File Formats

Cartesian Coordinate File (.car, .cor)

Molecular Data File (.mdf)

Header Record

: Comment Record
: Atom Record
: End Record
: Torsion Record
: Pseudo Atom Record
: Pseudo Atom Set Record

Cartesian Coordinate Archive File (.arc)

9. Using Compressed Files

Recognized Compression Formats

Compressed Files Now Appear In Value-aids

A Decompression Program Must Be On Your System

Decompression Creates a Temporary File

Fail-Safe Decompression Strategy

Caveats

: Using Soft Links to Compressed Files
: VMS .Z Files Cannot Be Read

Index

Figures

Figure 1. Viewer Module 12

Figure 2. Mouse Functions

Figure 3. Dial Box Functions

Figure 4. Using the Mouse as a Dial Box Control

Figure 5. Commands in the Molecule Pulldown

Figure 6. Color Command in the Molecule Pulldown

Figure 7. Element Command in the Modify Pulldown

Figure 8. Color Molecule Command Parameter Block

Figure 9. Center Command in the Transform Pulldown

Figure 10. Label Command in the Graph Pulldown

Figure 11. Sample Spectrum

Figure 12. Example of Insight II Help Viewer Window Figure 13. The Pilot Button 73

Figure 14. The Forward Button Figure 15. Spreadsheet 82

Figure 16. Molecule Browser

Figure 17. Dial Box for Torsion Navigation Figure 18. Example of the Fuse_1 command 158

Figure 19. Example of 2-pair Intermolecular Fusion

Figure 20. Example of 3-pair Fusion

Figure 21. Example of Close Atom Fusion

Figure 22. Inversion of a Chiral Center Figure 23. Captopril 177

Figure 24. Components of Captopril

Figure 25. 2D Sketch of Captopril

Figure 26. The ACE Pharmacophore Model 207

Figure 27. MOPAC-BIOSYM-Optimizer Cycle 209

225

Figure 28. Graph/Threshold Examples 277

Tables

Table 1. Function Key Descriptions 18

Table 2. Operator Classes and Syntax 269

Table 3. Reserved Symbols 327

Table 4. Operator Precedence 330

Table 5. Intrinsic Functions 332

Table 6. Insight II Commands that Return a Value 334

Table 7. Insight II Parameter Names 335

Table 1. Out-of-Plane Assignment Rules 446

Table 2. Atom Record Definition 456

Table 3. Torsion Record Definition 459

Table 4. Pseudo Atom Definition 461

Table 5. Pseudo Atom Set Definition 463

Last updated March 17, 2000 at 05:00PM Pacific Standard Time.

1. Introduction to Molecular Modeling

2. Introduction to Insight II

3. Basic Applications

4. Viewer Module

5. Builder Module

6. Sketcher

7. Ampac/Mopac Module

8. Docking Module

9. Analysis Module

10. Graph Pulldown

11. Background_Job Pulldown

12. Biosym Command Language

13. Utilities

APPENDICES

A. References

B. File Formats

C. Setting Up the Brookhaven PDB

D. Fragment Definitions

E. Hydrogen Bonds

F. Space Group Names

G. Potential Template Rules

H. Amino Template File

I. Classic File Formats

9. Using Compressed Files

Index

Figures

Tables