X-PLOR

(Version 3.1)
A System for X-ray Crystallography and NMR

Axel T. Brünger
Copyright, 1992 The Howard Hughes Medical Institute and
Department of Molecular Biophysics and Biochemistry,
Yale University,
260 Whitney Avenue, P.O. Box 6666,
New Haven, CT 06511

Manual, copyright 1987 by the President and Fellows of Harvard University; copyright 1988, 1990, 1991, 1992 by Yale University. X-PLOR software, copyright 1987 by the President and Fellows of Harvard University; copyright 1988, 1990, 1991, 1992 by Yale University.

• Back to the Main Page

• Contents
  • Acknowledgments
  • Bug Reports
  • Distribution
• Prologue
  • Electronic Location of Example Files
  • Mathematica Interface
  • Notation
    • Example
  • Dimensions and Units
• X-PLOR Language
  • Words
    • Example
  • Numbers and Strings
  • Three-dimensional Vectors
  • 33 Matrices
  • Symbols
    • Example
  • Wildcards
    • Example
  • Filenames
    • Example
  • 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)
      • Van der Waals radii
      • Convention for Hydrogen Names
    • 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
• Energy Minimization
  • Conjugate Gradient Minimization
    • Syntax
    • Requirements
    • Example
  • Rigid-Body Minimization
    • Syntax
      • Requirements
    • Example
• Molecular Dynamics
  • Cartesian Coordinate Space
    • Simple Langevin Dynamics
    • Velocity Assignment
    • Temperature Control
      • Velocity Rescaling
      • Langevin Dynamics
      • Temperature Coupling
    • 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
• 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 Cutoff
    • Example: Generate a Full 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
• Electron Density Maps
  • Syntax
  • Requirements
  • Electron Density Map File
  • Example: Computation of a 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
  • Choice of Restraining Functions
    • Biharmonic 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
• 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 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 HO and DO Spectra
  • Calculation of Different R Values
  • Grid Search for Optimal Correlation Time
• Installation
  • Precompilation
  • Dimensioning
  • Machine-dependent Routines
  • Fast Fourier Transformation Routines
  • Test Suite
  • Directory Structure on Distribution Medium
  • VAX/VMS Installation
    • Minimal Directory Structure to Test and Execute X-PLOR
    • Command Files (Located in Directory [xplor.vax])
    • Symbol Definitions
  • Generic UNIX Installation
    • Minimal Directory Structure to Test and Execute X-PLOR
    • Command Files (Located in Directory xplor/convex)
    • Environment Variables & Aliases
    • Notes and Restrictions
  • CRAY Installation
  • SGI Installation
  • NeXT Installation
  • Benchmark Results
• Index of Syntactic Definitions
• List of Application Statements
• Bibliography
• Abbreviations
• Index
• About this document ...