FLYNN

• Front Matter
• Introduction
  • Overview
• Theory
  • Fragment Fitting
• Installation and Platform Notes
  • Licenses
  • Installation
    • General Installation
    • Linux/Unix
    • Windows
    • Mac OS X
  • Uninstallation
    • Linux/Unix
    • Windows
    • Mac OS X
• FLYNN Usage
  • Types of input ligands
  • Stereochemistry Enumeration
  • Refinement Dictionaries
  • Note about REFMAC5 refinement dictionaries
    • Looking up known residues
  • Note on the MMFF94 versus MMFF94s forcefields
  • Note on FLYNN and writing CIF Files
  • Command Line Interface
    • Required Parameters
    • Optional Parameters
  • MTZ File Parameters
  • Advanced Parameters
  • Fragment Fitting Parameters
  • 3D Construction Parameters and Torsion Driving Parameters
  • Example Commands
    • Basic Usage
    • Generating Reports
    • Choosing box regions of density
    • Choosing density close to residues
    • Choosing MTZ columns
    • Fragment usage
  • Results on The Gold Test Set
• WRITEDICT Usage
  • Command Line Interface
    • Required Parameters
  • Example Commands
• ALIGNGRID Usage
  • Command Line Interface
    • Required Parameters
    • Advanced Options
  • MTZ File Parameters
  • Example Commands
• Integration with Coot
  • Using FLYNN
  • FLYNN Advanced Options
    • Box option
    • Check option
    • MMFF94s option
  • Using WriteDict
    • WRITEDICT Advanced Options
    • planarAniline option
    • Installing Coot Interface
    • Installing WinCoot Interface
• Release Notes
  • AFITT-CL 2.1.0
    • WRITEDICT
    • FLYNN
  • AFITT-CL 2.0.1
    • WRITEDICT
    • FLYNN
  • FLYNN 2.0.0
• Bibliography