Chapter4.Reference Manual

Table of Contents

System
System command lines
Examples of System Commands
Program initiation lines
Program data lines
ABSORB
Application
Crystal Descriptions
Diffractometer Description
Plot Of Crystal Shape
File Assignments
Examples
References
ADDATM
Calculations Performed
Atoms In Special Positions
File Assignments
Example
References
ADDPAT
Description
File assignments
Data Formats
Examples
ADDREF
Overview
Calculations Performed
File Assignments
Examples
References
ATABLE
File Assignments
BAYEST
Introduction
Intensity Measurements And Bayes Theorem
The Wilson Parameter (S)
Input Output
File Assignments
Example
References
BONDAT
Calculations Performed
Calculation Types
General Information
File Assignments
Examples
BONDLA
Atom Connectivity
Printed Output
Line File Output
File Assignments
Examples
BUNYIP
File Assignments
Examples
References
CBAZA
Operation
References
CHARGE
Hirshfeld Partitioning
Density And Potential Profiles
Density, Distances And Errors
File Assignments
Examples
References
CIFIO
Purpose
CIF Input
CIF Output
arcFile Output
arcFile Input
cifreqcustomization
File Assignments
Examples
CIFENT
CONTRS
Introduction
Layer Input
Specification Of Levels
Search For Points On The Contour
Chaining Of The Points
Drawing Of The Curves
Types Of Lines Drawn
Border And Mesh Points
Atoms In The Vicinity Of The Map
Printed Output
Monochrome Graphics Output
Colour Graphics Output
File Assignments
Examples
References
CREDUC
Cell Reduction
Twin-Law Evaluation
File Assignments
Example
References
CRILSQ
Introduction
Calculations Performed
General Structure Parameters
Atom Specific Parameters
Blocking
Invariant Parameters
Dependent Parameters
Riding Atom Model
Twin Refinement
Final notes
CRISP
Solution Method
Control options
Caveats
File Assignments
CRYLSQ
Calculations Performed
General Structure Parameters
Atom Specific Parameters
Solution Of The Normal Equations
Estimated Standard Deviations
Blocking
Invariant Parameters
Dependent Parameters
Rigid Groups And Identical Molecules
Restrained Parameters
Weighting
Partial Shift Factor
Reflection Classification
Scattering Factors
Space Group Symmetry
Fixed Atom Contribution
Initial Refinement
Derivatives
File Assignments
Examples
References
DIFDAT
Overview
Input diffractometer modes
Derived intensity values
Treatment Of Standards
Calculation Of Sigmas
Reflection Codes (Rcodes)
Data Lines
Scale Factors
Output Data
File Assignments
Examples
References
DYNAMO
Process
Calculation Performed
File Assignments
Example
References
EXPAND
Calculation Performed
File Assignments
Example
FC
Calculation Performed
File Assignments
Example
References
FOURR
Shaded And Packed Printed Output
Limits Of The Transform
Summation Order
Coefficients Used In Summations
Explicit Definition Of Fourier Coefficients
Output
Limits Of Resolution
The F(0,0,0) Term
File Assignments
Examples
References
GENEV
Introduction
Treatment Of Weak Data
Application Of Scaling Options
Choice Of Expectation Values
Inflection-point least-squares
Estimation Of |E(hkl)| Errors
BDF Output Of Genev Items
Some Normalization Tips
File Assignments
Examples
References
GENSIN
Introduction
Application Of Group Structure Factors
Origin And Enantiomorph Definition
Notes On GENSIN Parameters
File Assignments
Examples
References
GENTAN
Tangent Formula
Starting the tangent process
Tangent phase extension and refinement
Weighting
Identifying the correct phase set
Rejection Of Phase Sets
Automatic Termination
Application Of Partial Structure Data
File Assignments
Examples
References
GIP
Overview
General functionality
General control button function
Known shortcomings
References
LATCON
Systematic Errors
File Assignments
References
LISTFC
Description
Control Lines
File Assignments
Examples
LSABS
Overview
Methods of Absorption Correction
Analytical method
Gaussian grid integration
The Linear Absorption Coefficient μ
Input and Output Data Specification
File Assignments
Examples
References
LSLS
Calculations Performed
General Parameters
Scale Factor(s)
Crystal Shape Parameters
Extinction
Twinning parameter(s)
Dispersion and Neutron-Scattering-Factor Parameters
Overall Displacement Parameter
Atomic Parameters
Invariant Parameters
Constrained Parameters
Restraints
Weights
Reflection Classification
R-Factors
File Assignments
Examples
References
LSQPL
Calculations Performed
Choice of Method
File Assignments
Example
References
LSRES
Calculations Performed
File Assignments
Examples
MAPLST
Purpose
File Assignments
Example
MAPXCH
Purpose
Using Wien2k data
Using ABINIT data
Using VALRAY data
Using XD data
File Assignments
Examples
MODEL
Clusters And Subclusters
Search Parameters
Selecting The Best Model
Output Information
File Assignments
Examples
MODHKL
Description
Global HKL Options
File Assignments
Examples
NEWCEL
Description
File Assignments
NEWMAN
Introduction
Plot Information
File Assignments
Examples
References
ORTEP
Modes Of Operation
Automatic Mode
Semi-automatic Mode
Manual Mode
Terminology And Definitions
File Assignments
Examples
References
OUTSRC
Purpose
File Assignments
Examples
PARTN
Hirshfeld Partitioning
Density And Potential Profiles
Program Requirements
Contribution Distances
File Assignments
Examples
References
PATSEE
Introduction
Preparation of the Search
ROTATE- Rotation Search
TRANSL- Translation Search
Combined Solutions
Summary
File Assignments
Example
PEKPIK
Algorithm
File Assignments
Examples
PIG
Description
Interactive Controls
Sort modes
File Assignments
Examples
PLOTX
Function
Scaling And Centring
Colour Graphics
Postscript output
XFIG3.2 output
File Assignments
Examples
POWGEN
Overview
File Assignments
Examples
PREABS
Overview
General control functionality
Known shortcomings
File Assignments
References
PREPUB
Description
Examples
PREVUE
Description
File assignments
REFCAL
Overview
Data Input, Requirements and Transformations
Treatment of Reference Reflections
Calculation and application of scale factors
Calculation and application of instability constants
Reflection Status Codes (rcodes)
Derivation of Intensities and "Observed" Structure Factors
Lorentz-Polarization Factors
Atomic Scattering Factor Interpolation
Symmetry Reinforcement Factor \(\epsilon \)
Examples
References
REFM90
Introduction
Description
File Assignments
Examples
REGFE
Introduction
Standard Deviation Calculation
Atom Connectivity
plane, lineand atomLines
File Assignments
Examples
References
REGWT
Introduction
Normal Weighting Schemes
Estimation Of Weighting Modifications
File Assignments
Examples
RFOURR
Purpose
Grid Restrictions
Sort Order Of Map And Data
Symmetry Considerations And Algorithm
Control Of Input & Output Items
File Assignments
Examples
References
RIGBOD
Calculations Performed
File Assignments
Example
References
RMAP
Introduction
Algorithm
Data Required
File Assignments
Example
RSCAN
Program Calculations
File Assignments
References
SCATOM
Overview
Purpose
Implementation
Examples
SHAPE
Overview
Improving the interpretability of the patterson map
Patterson superposition methods
The symmetry minimum function, automatically evaluating harker vectors
The image seeking minimum function, automatically evaluating cross-vectors
Hints
File Assignments
Example
References
SHELIN
Recent Modifications
Shelx Commands And Data
Function
File Assignments
Example
SIMPEL
The Algorithm
Step 1. Convergence Procedure: selecting the starting set
Step 2. Divergence Procedure: test phase propagation
Step 3. Symbolic Addition Process
Step 4. Correlation of Symbol Phases
Step 5. Figure-of-Merit Tests: Identifying the correct phase set
File Assignments
Examples
References
SLANT
Input And Output Requirements
General Plane Specifications
The Slant Plane Coordinate System
Map Orientation
Interpolation Routines
Transformed Positional Parameters
File Assignments
Examples
SORTRF
Method
Sorting Reflection Data
Averaging Reflection Data
Agreement Factors
Treatment Of Friedel Pairs
File Assignments
Examples
References
STARTX
Unit Cell Data
Symmetry Data
File Assignments
Examples
References
SURFIN
Purpose
Functionality
File Assignments
Examples
VUBDF
Output Controls
Output Formats
File Assignments
Examples
XTINCT
Introduction
Application
XTINCTOptions
File Assignments
Examples
References

This section contains the descriptions of programs in the Xtal System. These were prepared by the program authors who are listed at the head of each program. If you experience difficulties with a program, or require further information, you could, as a last resort, attempt to contact the author indicated for this purpose. However, since the source code is available and it is so well documented, that should be your first resource.