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X-PLOR On-line Manual
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X-PLOR On-line Manual
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 ...
Acknowledgments
Bug Reports
Distribution
Web Manager
Sat Mar 11 09:37:37 PST 1995
