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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
- 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
- Bibliography
- Index
Subsections
Xplor-NIH 2024-09-13