Contents

• Prologue
  • Electronic Location of Example Files
  • Mathematica Interface
  • Notation
    • Example
  • Dimensions and Units
  
  
• X-PLOR Language
  • Words
    • Example
  • Numbers and Strings
  • Three-dimensional Vectors
  • 3$\times$3 Matrices
  • Symbols
    • Example
  • Wildcards
    • Example
  • Filenames
    • Example
    • Commonly used UNIX variables for directories
  • Control Statements
    • Example: A Conditional Test
    • Example: A Simple Loop
    • Example: A Double Loop with Exit Condition
    • Example: Switch Control to Another File
    • Example: Switch Control to Another File within Loops
  • Application Statements
  • Abbreviations
  • On-line HELP and Query
  • Input and Output
  • Set Statement
  • Evaluate Statement
    • Syntax
    • Example
  • Atom Selection
    • Syntax
    • Examples
  • Vector Statement
    • Syntax
    • Requirements
    • Examples
  
  
• Topology, Parameters and Molecular Structure
  • Topology Statement
    • Syntax
    • Example: Topology of a Leucine Amino Acid
  • Parameter Statement
    • Syntax
    • Requirements
  • Writing a Parameter File
    • Syntax
    • Example of Type-based Parameters
    • How the Type-based Parameter Retrieval Works
    • Examples of Atom-based Modifications of the Parameters
  • Learning Atom-based Parameters
    • Requirements
    • Example: Learning Unknown Equilibrium Parameters from Coordinates
    • Example: Learning Atom-based Parameters from an Ensemble of Structures
  • Reducing to Type-based Parameters
    • Syntax
    • Example: Reducing Parameters Learned Previously
  • Topology and Parameter Files
    • CHARMM ``top_all22*" and ``par_all22*" All Hydrogen Force Field
    • CHARMM ``toph19.pro" and ``param19.pro" Files for Proteins (Explicit Polar Hydrogens)
    • CHARMM ``toph11.dna" and ``param11.dna" Files for Nucleic Acids (Explicit Polar Hydrogens)
    • Files ``topnah1e.dna" and ``parnah1e.dna" for Nucleic Acids (Explicit All Hydrogens)
    • AMBER/OPLS ``tophopls.pro", ``parhopls.pro" Files (Explicit Polar Hydrogens)
    • Files ``toph19.sol" and ``param19.sol" for Water (TIP3p Model)
    • Files ``toph3.cho" and ``param3.cho" for Carbohydrates
    • Files ``toph19.chromo" and ``param19.chromo" for Chromophores
    • Files ``parhcsdx.pro" and ``tophcsdx.pro" for Crystallographic Refinement (Polar Hydrogens)
    • Files ``parallhdg.pro" and ``topallhdg.pro" for NMR Structure Determination of Proteins (All Hydrogens)
    • Files ``parallhdg.dna" and ``topallhdg.dna" for NMR Structure Determination of Nucleic Acids (All Hydrogens)
  • Generating the Molecular Structure
    • Syntax
    • Requirements
    • Example: A Polypeptide Chain
    • Example: A Polypeptide Chain with an Unknown Section
    • Example: Water Molecules
    • Example: Solvation of a Solute
  • Patching the Molecular Structure
    • Syntax
    • Requirements
    • Example: Incorporation of Disulfide Bridges
    • Example: Modification of the Protonation Degree of Histidines
  • Deleting Atoms
    • Syntax
    • Requirements
    • Example: Delete One Atom
  • Duplicating the Molecular Structure
    • Syntax
    • Requirements
    • Example: Duplication of Side-Chain Atoms
  • Structure Statement
    • Syntax
    • Requirements
    • Example: How to Read a Molecular Structure File
    • Example: Append Two Molecular Structure Files
  • Writing a Molecular Structure File
    • Syntax
  • Examples for Molecular Structure Generation
    • What to Do about Unknown Atoms
    • A Standard Protein Structure
    • How to Set Up Unusual Geometries
    • A Protein Structure with Water or Ligands
    • A Protein Structure with a Cofactor or Substrate
    • A Protein Structure with a Metal Cluster
    • A Nucleic Acid Structure
    • Virus Structures or Structures with Many Identical Units
  
  
• Energy Function
  • Empirical Energy Functions
  • Conformational Energy Terms
  • Nonbonded Energy Terms
    • Van der Waals Function
    • Electrostatic Function
    • Intramolecular Interactions
    • Crystallographic Symmetry Interactions
    • Non-crystallographic Symmetry Interactions
  • The Explicit Hydrogen-Bond Term
  • Turning Energy Terms On or Off
    • Syntax
    • Requirements
    • Example: Turn On Energy Terms for X-ray Refinement
  • Energy Statement
    • Syntax
    • Requirements
    • Examples
  • Energy Calculation between Selected Atoms
    • Syntax
    • Requirements
    • Example: Interchain Interaction Energy
  
  
• Geometric and Energetic Analysis
  • Analysis of Conformational Energy Terms
    • Syntax of the Print Statement
    • Syntax of the Pick Statement
    • Requirements
    • Example: Print Bond Length and Bond Angle Deviations
    • Example: Print All Bonds of a Selected Set of Atoms
    • Example: Pick Bond Geometry
    • Example: Pick Distance between Two Atoms
    • Example: Pick Bond Angle among Three Atoms
  • Analysis of the Nonbonded Energy Terms
    • Syntax
    • Requirements
    • Example: Distances between Selected Residues
  • Deviations from Ideality and Crystal Packing
  • Conformation vs. Residue Number
  • Ramachandran Plot
  • Accessible Surface Area
    • Syntax
    • Requirements
    • Example
  
  
• Cartesian Coordinates
  • Coordinate Statement
    • Syntax
    • Requirements
    • Examples
  • Write Coordinate Statement
    • Syntax
    • Requirements
    • Example
  • Rms Differences between Coordinates
  • Distance Matrix Analysis
  • Building Hydrogen Positions
    • Syntax
    • Requirements
    • Example
  
  
• Coordinate Restraints
  • Harmonic Coordinate Restraints
    • Point Restraints
    • Plane Restraints
    • Syntax
    • Requirements
    • Example: Point Restraints
    • Example: Plane and Point Restraints
  • Dihedral Angle Restraints
    • Syntax
    • Requirements
    • Example
  • Planarity Restraints
    • Syntax
    • Requirements
    • Example
  
  
• Coordinate Constraints
  • Fixing Atomic Positions
    • Syntax
    • Requirements
    • Example
  • Fixing Distances
    • Syntax
    • Requirements
    • Example
  
  
• Deformable Boundary Forces
  • The Solvent Boundary Method
  • Syntax
  
  
• Energy Minimization
  • Conjugate Gradient Minimization
    • Syntax
    • Requirements
    • Example
  • Rigid-Body Minimization
    • Syntax
    • Example
  
  
• Molecular Dynamics
  • Cartesian Coordinate Space
    • Simple Langevin Dynamics
    • Velocity Assignment
    • Temperature Control
    • Finite Difference Approximation
    • Dynamics Restarts
    • Syntax of the Dynamics Verlet Statement
    • Requirements
    • Example: Run a Standard Molecular Dynamics Simulation
    • Example: Run a Molecular Dynamics Simulation with Temperature Coupling
    • Example: Run a Slow-cooling Molecular Dynamics Simulation
    • Example: Run Langevin Dynamics
  • Rigid-Body Coordinate Space
    • Initialization
    • Iteration
    • Syntax of the Dynamics Rigid Statement
    • Requirements
    • Example: Run a Rigid-Body Dynamics Simulation
  • Internal Coordinate Space
    • Syntax of the Dynamics Internal Statement
  
  
• Management of Trajectories
  • Trajectory Definitions
    • ASCII Trajectory Files
    • Binary Trajectory Files
    • Trajectory Statement
    • Diagnostic Error Messages
  • Reading Trajectories
    • Syntax
    • Example
  • Writing Trajectories
    • Syntax
    • Requirements
    • Example
  • Merging Trajectories
    • Syntax
    • Requirements
    • Examples
  • Analysis of Trajectories
  • Average Coordinates and Fluctuations
    • Syntax
    • Example
  • Density Analysis
    • Syntax
  • Covariance Analysis
    • Syntax
    • Example
  • Time Correlation Analysis
    • Syntax
  • Radial Distribution Functions
    • Syntax
  • Angular Distribution Functions
    • Syntax
  • Power Spectrum Analysis
    • Syntax
  • Picking Properties for Trajectories
    • Syntax
  
  
• Crystallographic Diffraction Data
  • Crystallographic Target Functions
  • Orthogonalization Convention
  • Syntax of the Xrefin Statement
    • Requirements
  • Reflection Files
    • Syntax
    • Example: A Crystallographic Reflection File
    • Example: Merging Crystallographic Reflection Files
  • Manipulating Reflection Data
    • Syntax
    • Requirements
    • Example: Scaling
    • Example: Definition of a Weighting Scheme
    • Example: Application of a $2\sigma$ Cutoff
    • Example: Generate a Full $F_{calc}$ Data Set
    • Example: Expand a Data Set
  • Partial Structure Factors
  • Bulk Solvent Mask
    • Syntax
    • Requirements
    • Example: Use of a Solvent Mask for Bulk Solvent Correction
  • Alternate Conformations
  • Anomalous Scattering
  • Special Positions
  • Luzzati Plot
  • Wilson Plot
  
  
• Crystallographic Refinement
  • Positional Refinement
    • Check of Data and Initial Structure and Determination of Weights
    • Conventional Positional Refinement
    • Crystallographic Refinement by Simulated Annealing
    • Rigid-Body Refinement
  • Overall B-Factor Refinement
    • Syntax
    • Requirements
    • Example: Refinement of Overall Anisotropic B-Factors
  • Grouped B-Factor and Occupancy Refinement
    • Syntax
    • Requirements
    • Example
  • Individual B-Factor Refinement
    • Syntax
    • Requirements
    • Example
  • Analysis of Refined Structures
  
  
• Fiber Structure Refinement
  • Setting up Fiber Structure Parameters and Diffraction Information: The Fiber_refin Statement
  • Example: setting up structure parameters and fiber diffraction data of a helical virus structure
  • Example of fiber diffraction file
  • Computation of Electron Density Maps of a helical structure
  • Symmetric Linkage
    • Syntax
    • Requirements
    • Example: a viral RNA helix
  
  
• Electron Density Maps
  • Syntax
  • Requirements
  • Electron Density Map File
  • Example: Computation of a $2F_{obs}-F_{calc}$ Map
  • Example: Computation of an Omit Map
  • Example: Computation of an Annealed Omit Map
  • Example: Heavy Atom Derivative Difference Map
  
  
• Cross-validation: The Free $R$ Value
• Non-crystallographic Symmetry
  • NCS Restraints
    • Syntax
    • Requirements
    • Example
  • Strict NCS
    • Syntax
    • Requirements
    • Example
  
  
• Molecular Replacement
  • Rotation Search
    • Syntax
    • Requirements
    • The Rotation Function Listing
    • The Rotation Function Output File
  • Comparing Orientations of Molecules
    • Syntax
    • Requirements
  • Translation Search
    • Syntax
    • Requirements
    • The Translation Function Listing
    • The Translation Function Output File
  • A Mathematica Script File
  • Generalized Molecular Replacement
    • Self-rotation Function
    • Modification of the Elbow Angle of a Known Fab Structure
    • Cross-Rotation Function with the Modified Fab Structure
    • PC-Refinement of the Highest Peaks of the Cross-Rotation Function
    • Analysis of the PC-refinement
    • Translation Function for Molecule A Using the PC-refined Model
    • Translation Function for Molecule B
    • Combined Translation Function to Determine the Relative Position between A and B
    • Rigid-Body Refinement
  • A Packing Function
  • A ``Direct" Rotation Function
  • Generation of All Symmetry Mates
  
  
• Distance Restraints
  • Syntax
    • Requirements
  • Choice of Averaging
    • Expressing ambiguous restraints using the optional OR statement
  • Choice of Restraining Functions
    • Biharmonic Function
    • Log Normal Function
    • Square-Well Function
    • Soft-Square Function
    • Symmetry Function
    • 3D NOE-NOE Function
    • High dimensional Function
  • Setup of Distance Restraints
  • Pseudoatoms
  • Incorporation of Other Distance Information
  • Dihedral Angle Restraints
  • Distance Symmetry Restraints
  • 3D NOE-NOE Example
  • Example for a High Dimensional Restraining Function
  • Refinement Using Time-Averaged Distance Restraints
  
  
• Antidistance Restraints
  • Syntax
  • Requirements
  
  
• Scalar J-Coupling Restraints
  • Syntax
  • Requirements
  
  
• Carbon Chemical Shift Restraints
  • Syntax
  • Requirements
  
  
• Proton Chemical Shift Restraints
  • Syntax
  • Requirements
  
  
• Dihedral Angle Database Restraints
  • Syntax
  • Requirements
  
  
• Radius of Gyration Restraints
  • Syntax
  
  
• Diffusion Anisotropy Restraints
  • Syntax
  • Requirements
  
  
• Residual Dipolar Couplings
  • Syntax - SANI
  • Syntax - XDIPolar or DIPOlar
  • Syntax- VEANngle
  • Syntax - TENSOr
  • Syntax - ANIS
  • Requirements
  
  
• Residue-Residue Position/Orientation Database Restraint
  • Syntax
  
  
• Chemical Shift Anisotropy Restraint
  • Syntax
  • Requirements
  
  
• Pseudo Chemical Shift Anisotropy Restraint
  • Syntax
  • Requirements
  
  
• One-Bond Coupling Restraints
  • Syntax
  
  
• Angle Database Restraint
  • Syntax
  
  
• Restraints Associated with Paramagnetic Centers
  • Paramagnetic Relaxation Enhancement Restraints
    • Syntax
  • Distance Calculation from Paramagnetic Relaxation Rate Enhancement Measurements
    • Syntax
  • Paramagnetic Pseudocontact Shift Restraint
    • Syntax
    • Requirements
  • Paramagnetic Residual Dipolar Coupling Restraint
    • Syntax
    • Requirements
  • Paramagnetic Orientation Restraint
    • Syntax
  • Paramagnetic Cross-Correlation Rate Restraint
    • Syntax
  
  
• Hydrogen Bond Geometry Restraint
  • Syntax
  
  
• Hydrogen Bond Database Restraint
  • Syntax
  
  
• Distance Geometry
  • Metric Matrix Distance Geometry
    • Syntax
    • Requirements
    • Output
  • Implementation of Distance Geometry
    • Input Distances
    • Pseudoatoms
    • Bound Smoothing
    • Embedding
    • Scaling
    • Metrization
  • Test for the Correct Enantiomer
  • Regularization
  • CPU and Memory Requirements
  
  
• NMR Structure Determination
  • Template Structure
  • Options: Distance Geometry, Ab Initio SA, or Random SA
  • Distance Geometry
    • Test for the Correct Enantiomer
    • Options: Full-Structure Embedding or SA
    • SA-Regularization of DG-Structures
    • Full-Structure Distance Geometry
  • Ab Initio SA Starting from the Template
  • Random Simulated Annealing
  • Simulated Annealing Refinement
  • Acceptance of Refined NMR Structures
  • Average Structure and Rmsds
  • Pairwise Rmsds
  • Time-Average Refinement
  • CPU Time Requirements
  
  
• NMR Back-calculation Refinement
  • Setup of the Relaxation Refinement
    • Syntax
    • Requirements
    • Output
  • The Relaxation Matrix
  • Analytical Expression for the Gradient
  • The $E_{relaxation}$ Energy Term
  • Cutoffs
  • Assessing the Quality of the Final Structure
  • Input of the Experimental Data
  • Prediction of a NOESY Spectrum
  • Refinement against NOESY Intensities
  • Simultaneous Refinement with H$_2$O and D$_2$O Spectra
  • Calculation of Different $R$ Values
  • Grid Search for Optimal Correlation Time
  
  
• Bibliography
• Index