Contents

• Conventions
• TNT Refinement
• Setting Up a Project
• Importing Your Model
• Coordinate File Editing
• Sequence File Editing
• Control File Editing
• Importing Structure Factor Files
• Selecting a Test Set
• Testing Your Files
• Checking the Scale Factors
• The TNT Control File
• General Data Statements
• Crystallographic Data Statements
• Stereochemistry Data Statements
• Noncrystallographic Symmetry Data Statements
• Refinement Data Statements
• The TNT Sequence File
• Single Residue Molecules
• Single Chain Models
• Links to Other Asymmetric Units
• Multiple Chain Models
• The CHAIN Statement
• Examples of Chain Definitions
• Multichain Model Example
• Nucleic Acid Structure Example
• Standard Geometry Definition
• The Geometry Statement
• Geometry Libraries
• IUPAC Labeling Conventions
• Geometry Definition Example
• Defining Noncrystallographic Symmetry
• Defining Structural Correspondences
• Local Violation of ncs
• Defining ncs Transformations
• Noncrystallographic Constraints
• Noncrystallographic Restraints
• Special Problems in Structure Definition
• Fragmented Structures
• Static Disorder
• Atoms on Special Positions
• Molecular Disorder
• TNT Shell Commands
• Utility Commands
• Command: TNT
• Command: CLEANUP
• Model Evaluation Commands
• Command: GEOMETRY
• Command: NCS
• Command: RFACTOR
• Command: DSCREEN
• Command: DIFFCOR
• Command: DIFFPLOT
• Noncrystallographic Symmetry Commands
• Command: GATHER
• Command: SCATTER
• Communicating with the Graphics Program
• Command: MAKE_MAPS
• Command: PEKPIK
• Command: TO_PDB
• Command: FROM_PDB
• Structure Factor File Commands
• Command: CORRECT
• Command: HKL_SEGREGATE
• Command: REPORT_HKL
• Command: HISTOGRAM
• Running Refinement
• Choosing Weights
• Convergence Criteria
• Examples
• Protein, All Atom Refinement
• Protein, Rigid-Body Refinement
• Protein, Special Geometry
• Nucleic Acid, Noncrystallographic Symmetry
• Protein, Rigid-Body Refinement of Two-Domain Molecules
• Protein, Rigid-Body Refinement of Two Domain Molecules
• Index
• About this document ...

Wed Jul 5 13:21:03 PDT 2000