Insight II


Contents

December 1998


1. Introduction to Molecular Modeling

Molecular Graphics
Building and Modifying Structures
Molecular Mechanics
Molecular Dynamics
Quantum Mechanics
Finally. . .

2. Introduction to Insight II

What is Insight II?
Starting Insight II
Using Insight II
Commands
Objects
Accessing Objects
By Object Name
By Object Connection
By Atom Selection
Manipulating Objects
Mouse Functions
Dial Box Functions
Slab Thickness Dial
On-Screen Dial Box Icon
Function Keys
Atom Selection
Box and Lasso
Bond Selection
Toggling Selection
Picking vs. Selecting
Deselecting
Selection Levels
Logging and Playback
Using ATOM_SELECTION
Moving
Deleting
Command Hierarchy
Modules
Pulldowns
Commands
Pre-Defined Icons (Icon Palette)
Menu Icons
Atom Selection Icons
Subwindow Icons
Parameter Block Icons
User Definable Icons
Help Icons
Customizing Your Environment
Icon Palette
Nongraphics Mode
Backup, Recover, and Autosave Operations
Command Logging and Restarting
Parameters, Parameter Blocks, and Value-Aids
Parameter Blocks
Value-Aids
Focus
Inactive Parameters
Parameter Defaults and Suggested Values
Command Dispatching: Cancel, Execute, and the Trigger Parameter
Repeat and Activate Modes
Typed Commands
Concurrent Commands
On/Off Parameters
Enumerated Parameters
List Parameters
All Other Parameters
History
Default Objects
Object Types
Molecular Objects
User Objects
Contour Objects
Assembly Objects
Graph Objects
Spectrum Objects
Object Names
Object Name
Monomer/residue Specification
Atom Specification
Pseudoatoms
Periodic Atoms
Using Parentheses
Wildcards
Properties
Predefined Properties
Property name (type)
Use of Color
RGB vs. Color Table Mode
Online Help
Insight II Help Viewer
Using the Insgiht II Help Viewer
Top Menu Bar: Options and Help Menus
Navigational Buttons.
Help Text Viewing Area
Pilot
How Errors are Handled

3. Basic Applications

Pilot Online Tutorials
Choosing a Tutorial

4. Viewer Module

Implementation
Window Layouts
Spreadsheet Introduction
Creating a Spreadsheet
Modifying the Spreadsheet Layout
Manipulating Spreadsheet Data
Displaying Spreadsheet Data
Using the Spreadsheet
Selection
Data Value Editing
Cell References
Command Summary
Module Pulldown (MSI logo icon)
Builder
Biopolymer
Activity_Prediction
DelPhi
Solvation
Discover
Discover_3
Docking
Ligand_Design
Search_Compare
CHARMm
MBOND
Homology
NMR_Refine
XSight
Ampac/Mopac
DMol
Turbomole
Zindo
QuanteMM
Analysis
DeCipher
Licenses
Session Pulldown
Environment
Light_Source
Cmd_Display
Help
Autosave
Backup
Recover
History
Buffer
Alias
Button
Stereo
Env_var
Unix
Change_directory
Sleep
Quit
File Pulldown
Save_Folder
Restore_Folder
Remove_Folder
List_Folder
Import
Export
Export_Plot
Export_Image
Source_File
Export_Molscript
Object Pulldown
Copy Object
Paste Object
Delete Object
Rename Object
Blank Object
Axes_Display Object
Blink Object
DepthCue Object
LineWidth Object
List Object
Molecule Pulldown
Get Molecule
Sybyl Mol2 files and MDL molfiles and SDfiles
Biosym car, arc, and cor files
Brookhaven files
AMPAC and MOPAC files
CSD Fdat
Free Format Files
Put Molecule
Set_Defaults
Color Molecule
Transparency Molecule
Display Molecule
Label Molecule
Bond_Order Molecule
Surface Molecule
Render Molecule
Ribbon Molecule
Color_Ribbon Molecule
SecondaryRender Molecule
List Molecule
Tabulate Molecule
Browse Molecule
Measure Pulldown
Distance
Angle
Dihedral
Monitor_Style
XYZ
Bump
Neighbor
HBond
Energy
Transform Pulldown
Connect
Position
Reset
Store
Axes
Center
Move
Rotate
Scale
Apply
Clip
Rock
Torsion
Overlay
Superimpose
Subset Pulldown
Get Subset
Put Subset
Define Subset
Zone Subset
Interface Subset
Template Subset
Combine Subset
Copy Subset
Delete Subset
Rename Subset
List Subset
Assembly Pulldown
Associate Assembly
Add Assembly
Remove Assembly
Cell Assembly
Cell_display Assembly
Symmetry Assembly
Soak Assembly
List Assembly
User Pulldown
Get User
Color User
Transparency User
Annotate User
Label User
Charsize User
List User
Spectrum Pulldown
Get Spectrum
Put Spectrum
Edit Spectrum
List Spectrum
Custom Pulldown
Add_To_Pulldown
Catalogue
Macro_Delete
Default
Trigger
List_Properties
Window Pulldown
Raise Window
Lower Window
Close Window
Layout_Template Window
Layout Window
Raise_Layout Window
Lower_Layout Window
Close_Layout Window
Help Pulldown
Insight_Help
Traversing Help
Print Window
Pilot_Tutorials
Contour Pulldown (accessed from the Contour icon)
Get Contour
Create_Single Contour
Create_Range Contour
Clip_Display Contour
Color Contour
Transparency Contour
Recalculate Contour
Label Contour
Charsize Contour
List Contour
Spreadsheet Pulldown
New Command
New_Molecule Command
Open Command
Put Command
Spreadsheet Command Summary
New File
Open File
Save File
Save_As File
Duplicate File
Transpose File
Print File
Edit
Cut Edit
Copy Edit
Paste Edit
Clear Edit
Find Edit
Select Edit
Insert Edit
Delete Edit
Fill Edit
Data
Formula Data
Search Data
Sort Data
Summary Data
Highlight Data
Recompute Data
Format
Color Format
Cell_Border Format
Display Format
Style Format
Column_Width Format
Row_Height Format
Protection Format
Preference Format
Graph Plot
Bar Graph
XYZ_Graph Plot
Histogram Plot
Viewer Tutorials

5. Builder Module

Command Summary
Atom Pulldown
Charge Atom
Hybridization Atom
Planar Atom
Potential Atom
Delete Atom
Replace Atom
Rename Atom
List Atom
Fragment Pulldown
Get Fragment
Put Fragment
Remove Fragment
Define Fragment
Repeat Fragment
Delete Fragment
List Fragment
Modify Pulldown
Bond
Fuse_1
Fuse_2
Fuse_3
Fuse_Close
Hydrogens
Merge
Unmerge
Geometry
Ring_Conf
Invert
Reflect
Element
Atom_Position
Forcefield Pulldown
Select
Potentials
Groups
Assign_CFF Forcefield
Tabulate Forcefield
Forcefield Support
Pseudo_Atom Pulldown
Define
Rename
Delete
List
Optimize Pulldown
Optimize
Builder Tutorials

6. Sketcher

Introduction
Tutorial
Application 2: Molecule Building
Building and Manipulating the ACE Inhibitor
Captopril
Background
Introduction
Application
Building Captopril in 3D
Building Captopril in 2D
The Bioactive Conformation of Captopril
The Inactive Stereoisomer
Discussion
Files Created

7. Ampac/Mopac Module

Implementation
Summary of Ampac/Mopac Capabilities
Geometry Optimization--The OPTIMIZE Suite of Algorithms
Introduction
Theory and Implementation
The EF Algorithm and Mode Following
Constrained Optimization
GDIIS
Command and Keyword Correspondance
Command Summary
AM_Setup Pulldown
System
Electronic_State
Calculation
List
Optimize Pulldown
Opt_Parameters
Constraints
AM_Parameters Pulldown
SCF
Optimize
Saddle
Properties
Output
Keywords
List
Background_Job Pulldown
AM_Run Pulldown
Run
AM_Analyze Pulldown
Electron_Density
Molecular_Orbital
Grid Pulldown (accessed from Grid icon)
Get Grid
Put Grid
Display Grid
Color Grid
Histogram Grid
Contour Grid
Slice Grid
Label Grid
CharSize Grid
List Grid
Ampac/Mopac Tutorial

8. Docking Module

Theory
Nonbond Potential in CVFF
Nonbond Potential in CFF9X
Nonbond Potential in AMBER
Implementation
Command Summary
Grid Pulldown
Evaluate Pulldown
Intermolecular
Docking_Grid Pulldown
Create Docking_Grid
Compute Docking_Grid
Display Docking_Grid
Docking Tutorial

9. Analysis Module

Implementation
Average Plane Evaluation
Frequency Filtering
Additional Reading on Frequency Filtering
Clustering of Conformations into Families
Mean Square Displacement Precision
Radial Distribution Functions
Command Summary
Graph Pulldown
Trajectory Pulldown
Get Trajectory
Put Trajectory
Filter Trajectory
Animate Trajectory
Unanimate Trajectory
Conformation Trajectory
Family Trajectory
Repartition_Cluster Trajectory
Construct_Graph Trajectory
Axis_Function Trajectory
Cluster Trajectory
Distance_Def Trajectory
COM_Distance_Def Trajectory
Angle_Def Trajectory
Dihedral_Def Trajectory
PP_Ang_3_Def Trajectory
PP_Ang_n_Def Trajectory
pP_Dist_3_Def Trajectory
pP_Dist_n_Def Trajectory
COM_P_Dist_n_Def Trajectory
Energy_Def Trajectory
Tabulate Trajectory
Pseudo_Atom Pulldown
Background_Job Pulldown
Methodology
Memory Limitations
Analysis Tutorial

10. Graph Pulldown

Implementation
Equation
Correlate
Command Summary
Graph Pulldown
Get
Put
Boolean
Correlate
Equation
Contour
Line_Fit
Interpolation
Integration
Differentiation
FFT_Real
Smoothing
CharSize
Color
Label
Move_Axis
Modify_Display
Scale_Axis
Threshold
Tick_Mark
Info
Tutorial

11. Background_Job Pulldown

Theory
Network Queuing System and Background Jobs
Implementation
Command Summary
Background_Job Pulldown
Setup_Bkgd_Job
Control_Bkgd_Job
Completion_Status
Kill_Bkgd_Job
Methodology
Setting Up a Background Job
Examining Completion Status
Killing a Background Job
Tutorial

12. Biosym Command Language

Introduction
Creating Commands
Creating Pulldown Menus and Modules
BCL vs. Open Interface
How to Use this Guide
Examples
Font Conventions of this Guide
BCL Tutorial
Tutorial 1: hello.bcl
Tutorial 2: myget.bcl
Tutorial 3: Working Example
BCL Overview
BCL Rules
Parameters
Types
Definition
Variables
Types
Definition
Arrays
Pointers
Accessing Parameters and Variables
Coords
Arrays and Pointers
Constants
Operators
Expressions
In Assignment Statements
In Command Statements
Functions
Defining Functions
Accessing Functions
Forward Referencing
Control Statements
Conditionals
If
Switch
Loops
While
ForEach
File I/O and Operating System Access
Reading from a File
By Line
By Token
Writing To a File
Parameter Blocks
Defaults
Setting Defaults
Calculating Defaults
Data Validation
Picking
Appearance
Value-Aids
Conditional Parameters
Accessing Insight II Data
Objects
Properties
System Properties
User-Defined Attribute Properties
User-Defined Function Properties
Property Arrays
Spreadsheet Cells
Debugging
BCL Reference
Reserved Symbols
Operator Precedence
Intrinsic Functions
Insight II Commands that Return a Value
Insight II Parameter Names
BCL Statements
Assy_Fetch_Molecule
BCL_UNIX
Break
Cell_Get_Real, Cell_Get_Int, Cell_Get_String
Cleanup_Command
Close
Command
Condition
Constant
Continue
Define_Macro
Define_Menu
Define_Module
Def_Enum, Def_Enum_Sorted,
Def_Enum_Unique
Def_List, Def_List_Sorted, Def_List_Unique
End_Macro
Fgets
ForEach
FullScreen
Get_Boolean, Get_Integer, Get_Coord,
Get_Real, Get_Sstring, Get_Lstring,
Get_Vlstring, Get_Ident, Get_Enum
Goto
If
Make_File_List
Message_Print_Error
Param_Add_File_List
Param_Comment
Param_New_Column
Param_Pack
Param_Set_Style
Place_Valuator
Preview_Command
Preview_Function
Print
Printf
Prop_Exists
Prop_Get_Arr_Bool, Prop_Get_Arr_Int,
Prop_Get_Arr_Float, Prop_Get_Arr_Str
Prop_Get_Bool, Prop_Get_Int, Prop_Get_Float,
Prop_Get_Str
Prop_Register
Prop_Remove
Prop_Set_Bool, Prop_Set_Int, Prop_Set_Float,
Prop_Set_Str
Read
Input Formats
Remove_Enum
Return
Run_Bkgd_Job
Screen_Update
Setv_Boolean, Setv_Integer, Setv_Coord,
Setv_Real, Setv_Sstring, Setv_Lstring,
Setv_Vlstring, Setv_Ident, Setv_Enum
Setv_Focus
Setv_Precision
Setv_Trigger
Set_Boolean, Set_Integer, Set_Coord, Set_Real,
Set_Sstring, Set_Lstring, Set_Vlstring,
Set_ident, Set_Enum
Set_Param_Pick
Picking Templates
Picking Object
Set_Rand
Set_Random
Set_SideBlock
Set_Slider
Size_List
Switch
System_Fetch_Assy
System_Fetch_Atom
System_Fetch_Mol
System_Fetch_Mono
System_Fetch_Object
System_Fetch_Sketch
Test_Boolean
Test_Enum
Textport
Trigger
While
Write
Output Format
Index of BCL Statements

13. Utilities

Contour 290

Inplot 300


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)

I. 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


List of Figures

Figure 1. Viewer Module 9

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 57

Figure 14. The Forward Button Figure 15. Spreadsheet 62

Figure 16. Molecule Browser
Figure 17. Dial Box for Torsion Navigation Figure 18. Example of the Fuse_1 command 118

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 134

Figure 24. Components of Captopril
Figure 25. 2D Sketch of Captopril
Figure 26. The ACE Pharmacophore Model Figure 27. MOPAC-BIOSYM-Optimizer Cycle 162

Figure 28. Graph/Threshold Examples 215



Last updated December 17, 1998 at 04:25PM PST.
Copyright © 1998, Molecular Simulations Inc. All rights reserved.