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
(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
- Contents
- Prologue
- X-PLOR Language
- Words
- Numbers and Strings
- Three-dimensional Vectors
- 3
3 Matrices
- Symbols
- Wildcards
- Filenames
- Control Statements
- Application Statements
- Abbreviations
- On-line HELP and Query
- Input and Output
- Set Statement
- Evaluate Statement
- Atom Selection
- Vector Statement
- Topology, Parameters and Molecular Structure
- Topology Statement
- Parameter Statement
- Writing a Parameter File
- Learning Atom-based Parameters
- Reducing to Type-based Parameters
- 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
- Patching the Molecular Structure
- Deleting Atoms
- Duplicating the Molecular Structure
- Structure Statement
- Writing a Molecular Structure File
- 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
- The Explicit Hydrogen-Bond Term
- Turning Energy Terms On or Off
- Energy Statement
- Energy Calculation between Selected Atoms
- Geometric and Energetic Analysis
- Analysis of Conformational Energy Terms
- Analysis of the Nonbonded Energy Terms
- Deviations from Ideality and Crystal Packing
- Conformation vs. Residue Number
- Ramachandran Plot
- Accessible Surface Area
- Cartesian Coordinates
- Coordinate Statement
- Write Coordinate Statement
- Rms Differences between Coordinates
- Distance Matrix Analysis
- Building Hydrogen Positions
- Coordinate Restraints
- Coordinate Constraints
- Deformable Boundary Forces
- Energy Minimization
- 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
- Internal Coordinate Space
- Cartesian Coordinate Space
- Management of Trajectories
- Trajectory Definitions
- Reading Trajectories
- Writing Trajectories
- Merging Trajectories
- Analysis of Trajectories
- Average Coordinates and Fluctuations
- Density Analysis
- Covariance Analysis
- Time Correlation Analysis
- Radial Distribution Functions
- Angular Distribution Functions
- Power Spectrum Analysis
- Picking Properties for Trajectories
- Crystallographic Diffraction Data
- Crystallographic Target Functions
- Orthogonalization Convention
- Syntax of the Xrefin Statement
- Reflection Files
- Manipulating Reflection Data
- Partial Structure Factors
- Bulk Solvent Mask
- Alternate Conformations
- Anomalous Scattering
- Special Positions
- Luzzati Plot
- Wilson Plot
- Crystallographic
Refinement
- Positional Refinement
- Overall B-Factor Refinement
- Grouped B-Factor and Occupancy Refinement
- Individual B-Factor Refinement
- Analysis of Refined Structures
- Fiber Structure Refinement
- Computational Caveat
- 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
- 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
Value
- Non-crystallographic Symmetry
- Molecular Replacement
- Rotation Search
- Comparing Orientations of Molecules
- Translation Search
- 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
- Choice of Averaging
- Choice of Restraining Functions
- 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
- Scalar J-Coupling Restraints
- Carbon Chemical Shift Restraints
- Proton Chemical Shift Restraints
- Dihedral Angle Database Restraints
- Radius of Gyration Restraints
- Diffusion Anisotropy Restraints
- Residual Dipolar Couplings
- Syntax - SANI
- Syntax - XDIPolar or DIPOlar
- Syntax- VEANngle
- Syntax - TENSOr
- Syntax - ANIS
- Requirements
- Residue-Residue Position/Orientation Database Restraint
- Chemical Shift Anisotropy Restraint
- Pseudo Chemical Shift Anisotropy Restraint
- One-Bond Coupling Restraints
- Angle Database Restraint
- Restraints Associated with Paramagnetic Centers
- Paramagnetic Relaxation Enhancement Restraints
- Distance Calculation from Paramagnetic Relaxation Rate Enhancement Measurements
- Paramagnetic Pseudocontact Shift Restraint
- Paramagnetic Residual Dipolar Coupling Restraint
- Paramagnetic Orientation Restraint
- Paramagnetic Cross-Correlation Rate Restraint
- Hydrogen Bond Geometry Restraint
- Hydrogen Bond Database Restraint
- Distance Geometry
- Metric Matrix Distance Geometry
- Implementation of Distance Geometry
- 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
- 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
- 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 H
O and DO Spectra
- Calculation of Different Values
- Grid Search for Optimal Correlation Time
- Index of Syntactic Definitions
- List of Application Statements
- Bibliography
- Abbreviations
- Index
- About this document ...
Xplor-NIH 2025-03-21