Contents

• Acknowledgements
• Conventions
• TNT Refinement Package
  • The Programs of TNT
    • Geometry
    • Rfactor
    • NCS
    • Shift
    • Convert
    • Fourier
  • How do I ... ?
• Theory of TNT Refinement
  • What Direction to Shift?
  • How Far to Shift?
    • Least Squares Refinement
  • The Refinement Script
    • Refinement Script Details
  • Adding your Own Module
• Shared I/O Properties
  • Properties of a Statement
  • File Properties
  • Standard TNT Data Statements
  • Standard TNT Command Statements
• The Stereochemical Module
  • GEOMETRY
    • Required Input
    • Options
    • Unique Input Statements
    • Command Statements
• The Noncrystallographic Symmetry Module
  • NCS
    • Unique Input Statements
    • Command Statements
    • Program Operation
• The X-ray Crystallographic Module
  • RFACTOR
    • The Scaling Function
      • Using the SET Statement
    • Options
    • Unique Input Statements
    • Command Statements
    • Program Operation
• Other Modules for TNT
  • Experimental Phase Refinement Module
    • Problems
    • Example Script
  • Real Space Refinement Module
    • Problems
    • Example Script
  • Rotation Function Refinement Module
    • Command File Example
• Creating Your Own Module
  • Passing Information to TNT
  • Using TNT to Calculate Derivatives
• Refinement Control Program (Shift)
  • Options
  • Unique Input Statements
  • Parameter Editing Statements
  • Program Operation
• Refinement Package Utilities
  • CONVERT
    • Conversion Limitations
      • Residue Names
      • Atom Types
      • Multiple Chains
      • Chain Breaks and Extra Links
      • DNA Connectivity
    • Keywords for Inferring the Sequence
    • Unique Keywords for Specifying Data
    • Command Statements
    • Program Operation
  • DSCREEN
    • Command Statements
  • FOURIER
    • Options
    • Unique Input Statements
    • Command Statements
      • Picking Peaks from a Map
  • GATHER_MAP
    • Options
    • Unique Input Statements
    • Command Statements
    • Program Operation
  • OVERLAY
    • Unique Input Statements
    • Command Statements
    • Program Operation
      • Superimposing ncs Related Chains
      • Superimposing Residues within a Model
      • Symmetry Expansion
      • Applying Arbitrary Transformations
  • SOLVENT
    • Options
    • Unique Input Statements
    • Command Statements
    • Program Operation
• File Formats
  • ATOMx Format Coordinate Files
  • DSN2 (Frodo) Format Coordinate Files
  • HKL Format Structure Factor Files
  • PACKED Format Structure Factor Files
  • Ten Eyck MAP Format Files
  • Alwyn Jones' DSN6 Map Format Files
• Generating REFI Geometry Files from TNT Files
  • The Basic Problem
  • Planes and Chiral Centers
  • Most of This Belongs Somewhere Else...
  • The Messages
• Reciprocal Space Asymmetric Units
• Real Space Asymmetric Units
• Index
• About this document ...

• Acknowledgements
• Conventions