AFITT

• Front Matter
• Introduction
  • Welcome To AFITT
  • Differences From Previous Versions
• Installation and Platform Notes
  • Licenses
  • Installation
    • Linux/Unix
    • Windows
    • Mac OS X
• Getting Started
  • AFITT Workflows
  • AFITT Supported Workflows
  • MMFF Settings
  • How to Use AFITT
  • 3D Scene
  • Wizard Operations
  • Basic Ligand Fitting
  • Refinement Dictionaries
    • Fully Compliant Refinement Dictionaries
    • Covalent Bonds
  • Refmac Workflows
  • CNS/X-Plor Workflows
  • Ligand Builder
• Choosing Data: Molecule/Maps Page
  • Selecting Ligands Or Proteins
  • Loading Maps
    • MTZ Maps
  • Looking Up Residues
  • Editing a Ligand
• Find Density: Blobs Page
  • Selecting Analyzed Density
  • Advanced Modes of Operation
    • Locating Density at a Given Contour
    • Merging Density
    • Picking Density
    • Carving Density
    • Making a box that holds density
• Fit Ligand: Fit Page
  • Looking at Results
  • Changing Ligand Residue Information
  • Selecting Ligands For Refinement
  • Covalent Bonds
  • Editing Ligands
• Refine Complex: Refine Page
  • Refinement Dictionary
  • Refinment Parameters
  • REFMAC5 Script
  • Running Refmac
  • Notes about the Refinement Dictionary
• Verify Refinement: Verify Page
  • Selecting a Residue
  • Ramachandran Plot
  • Finishing
• Save CNS/X-plor
• Save Fit - Non Refinement Workflow
• Molecule Manipulation
  • Editing 2D Molecules
  • Editing 3D Molecules
    • Advanced Molecule Operations
    • Alternate Ring Conformations
    • Minimization
    • Monitors
• Release Notes
  • AFITT v2.0.1 (August 2010)
  • AFITT v2.0.0 (February 2010)