Contents
Release 97.2, May 1998
Table of Contents
1. Introduction
2. Theory
- Background
- Consensus Theory
- Standard Constraints
- Global Constraints
- Local Constraints
- Distance Geometry Theory
- Describing Molecular Conformation
- Covalent Distance Constraints
- Vicinal Distance Constraints
- Chirality Constraints in DGII
- How to Constrain Torsion Angles
- Steric Distance Constraints
- Conformational Distance Constraints
- Bound Smoothing
- Triangle Bound Smoothing
- Tetrangle Inequality Bound Smoothing
- Embedding Coordinates From Distances
- Metrization
- Embedding
- Majorization
- Optimization of the Coordinates
- The Error Function
- Simulated Annealing Associated With DGII
- Minimization and Analysis
3. Implementation
- Sequence Window
- Sequence Display
- Controls
- Sequence Boxes
- Sequence Gaps
- Manipulating the Sequence Display
- Scrolling Modes
- Seq Mode
- Moving sequences
- Manipulating gaps
- Box Mode
- Initializing boxes
- Moving and resizing boxes
- Freezing and unfreezing boxes
- Deleting boxes
- Distance Geometry
- Invoking DGII
- Database Files
- Step 1 Programs and Files
- Step 2 Programs and Files
- Step 3 Programs and Files
- Support Programs
4. Command Summary
- Sequences Pulldown
- Sequences/Get
- Sequences/Put
- Sequences/Extract
- Sequences/Copy
- Sequences/Delete
- Sequences/AssignCoords
- Sequences/Color
- Boxes Pulldown
- Boxes/Initialize
- Boxes/Delete
- Boxes/Freeze
- Boxes/UnFreeze
- Boxes/Summarize
- Background_Job pulldown
- Background_Job/Setup_Bkgd_Job
- Background_Job/Control_Bkgd_Job
- Background_Job/Completion_Status
- Background_Job/Kill_Bkgd_Job
- Consensus Pulldown
- Consensus/DGII_Setup
- Consensus/DGII_Params
- Consensus/DGII_Run
- Consensus/DGII_Tabulate
5. Methodology
- Consensus Methodology
- DGII Methodology
- Bounds Generation and Smoothing
- Metrization and Embedding
- Optimization
6. Tutorial
A. References
B. File Formats
List of Figures
- 1. Tetrangle Inequality Limits
- 2. Amino Acid Sequences Window
- 3. Sequence Box
- 4. Sequence Gap
- 5. Overview of DGII
- 6. DGII Bounds Generation and Smoothing Data Flow
- 7. DGII Metrization and Embedding Data Flow
- 8. DGII Optimization Data Flow
List of Tables
- 1. Most Distal Corresponding Atoms for Amino Acid Side Chains
- 2. Sequence Box Color Coding
Last updated October 06, 1997 at 06:48PM PDT.
Copyright © 1997, Molecular Simulations, Inc. All rights
reserved.