FLYNN
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Front Matter
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FLYNN
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1 Introduction
Contents
1 Introduction
1. Overview
2. Theory
2.1 Input File Preparation
2.2 Types of input ligands
2.2.1 Dangers of PDB format for ligand input
2.3 Stereochemistry Enumeration
2.4 Refinement Dictionaries
2.4.1 Note about REFMAC5 refinement dictionaries
2.4.2 Note on the MMFF94 versus MMFF94s forcefields
2 Applications
3. Using Flynn
3.1 Command Line Interface
3.1.1 Required Parameters
3.1.2 Molecular File Formats
3.1.3 Map File Formats
3.1.4 Basic Parameters
3.1.5 MTZ File parameters
3.1.6 Advanced Parameters
3.1.7 3D Construction Parameters and Torsion Driving Parameters
3.2 Example Executions
3.3 Results on The Gold Test Set
4. Using Writedict
4.1 Command Line Interface
4.1.1 Required Parameters
4.1.2 Output Options
4.2 Example Executions
5. Using Aligngrid
5.1 Command Line Interface
5.1.1 Required Parameters
5.1.2 Advanced Options
5.1.3 MTZ File Parameters
5.2 Example Executions
6. Integration with Coot
6.1 Overview
6.2 Using Flynn
6.2.1 Advanced Options
6.3 Using WriteDict
6.3.1 Advanced Options
6.4 Installing Coot Interface
6.5 Installing WinCoot Interface
6.6 Flynn Takes Forever!
7. Release Notes
7.1 flynn
7.2 flynn - coot interface
7.3 writedict
7.4 writedict - coot interface
7.5 aligngrid
Bibliography
FLYNN
Previous:
Front Matter
Up:
FLYNN
Next:
1 Introduction
Documentation released on July 24, 2008.
