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The Gnu Xtal System User's Manual

Edited by

Sydney Hall

Douglas du Boulay

Roeli Olthof-Hazekamp

Copyright © 1983-2001 The Xtal System of Crystallographic Software. The University of Western Australia. All Rights Reserved

Copyright © 2002 The Gnu Xtal System of Crystallographic Software.

Permission is granted to copy or distribute this manual provided that it is not modified and this copyright notice is retained intact.

2002

Revision History

Abstract

This is the user's manual for the Gnu Xtal System of crystallographic software, version 3.7.2.

Program descriptions prepared by contributing authors.

Compiled and collated by the editors.

http://xtal.sourceforge.net

Table of Contents

User Support
Acknowledging Xtal

Xtal Files

File types
Filename syntax
Archive Files
Auxiliary files
Format of line files

System Terminology

compound id
Reflection Code
Atom labels
Structure Factors
Scale Factor
ADPs

Example Inputs

Step 1: Input primary data
Step 2: Input reflection data
Step 3: Solving the structure
Step 4: Refining atom parameters
Step 5: Checking molecular geometry
Step 6: Preparing for publication
General Advice

3. Program controls

PATTERN SPECIFIC CONTROL LINES
PHASE SPECIFIC CONTROL LINES (one set per phase)
PAGE DESCRIPTION CONTROL LINES (one set per graph)
GRAPH SPECIFIC CONTROL LINES (one set per graph)

4. Reference Manual

System command lines
Examples of System Commands
Program initiation lines
Program data lines

Application
Crystal Descriptions
Diffractometer Description
Plot Of Crystal Shape
File Assignments
Examples
References

Calculations Performed
Atoms In Special Positions
File Assignments
Example
References

Description
File assignments
Data Formats
Examples

Overview
Calculations Performed
File Assignments
Examples
References

File Assignments

Introduction
Intensity Measurements And Bayes Theorem
The Wilson Parameter (S)
Input Output
File Assignments
Example
References

Calculations Performed
Calculation Types
General Information
File Assignments
Examples

Atom Connectivity
Printed Output
Line File Output
File Assignments
Examples

File Assignments
Examples
References

Operation
References

Hirshfeld Partitioning
Density And Potential Profiles
Density, Distances And Errors
File Assignments
Examples
References

Purpose
CIF Input
CIF Output
arcFile Output
arcFile Input
cifreqcustomization
File Assignments
Examples

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

Cell Reduction
Twin-Law Evaluation
File Assignments
Example
References

Introduction
Calculations Performed
General Structure Parameters
Atom Specific Parameters
Blocking
Invariant Parameters
Dependent Parameters
Riding Atom Model
Twin Refinement
Final notes

Solution Method
Control options
Caveats
File Assignments

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

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

Process
Calculation Performed
File Assignments
Example
References

Calculation Performed
File Assignments
Example

Calculation Performed
File Assignments
Example
References

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

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

Introduction
Application Of Group Structure Factors
Origin And Enantiomorph Definition
Notes On GENSIN Parameters
File Assignments
Examples
References

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

Overview
General functionality
General control button function
Known shortcomings
References

Systematic Errors
File Assignments
References

Description
Control Lines
File Assignments
Examples

Overview
Methods of Absorption Correction
Analytical method
Gaussian grid integration
The Linear Absorption Coefficient μ
Input and Output Data Specification
File Assignments
Examples
References

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

Calculations Performed
Choice of Method
File Assignments
Example
References

Calculations Performed
File Assignments
Examples

Purpose
File Assignments
Example

Purpose
Using Wien2k data
Using ABINIT data
Using VALRAY data
Using XD data
File Assignments
Examples

Clusters And Subclusters
Search Parameters
Selecting The Best Model
Output Information
File Assignments
Examples

Description
Global HKL Options
File Assignments
Examples

Description
File Assignments

Introduction
Plot Information
File Assignments
Examples
References

Modes Of Operation
Automatic Mode
Semi-automatic Mode
Manual Mode
Terminology And Definitions
File Assignments
Examples
References

Purpose
File Assignments
Examples

Hirshfeld Partitioning
Density And Potential Profiles
Program Requirements
Contribution Distances
File Assignments
Examples
References

Introduction
Preparation of the Search
ROTATE- Rotation Search
TRANSL- Translation Search
Combined Solutions
Summary
File Assignments
Example

Algorithm
File Assignments
Examples

Description
Interactive Controls
Sort modes
File Assignments
Examples

Function
Scaling And Centring
Colour Graphics
Postscript output
XFIG3.2 output
File Assignments
Examples

Overview
File Assignments
Examples

Overview
General control functionality
Known shortcomings
File Assignments
References

Description
Examples

Description
File assignments

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

Introduction
Description
File Assignments
Examples

Introduction
Standard Deviation Calculation
Atom Connectivity
plane, lineand atomLines
File Assignments
Examples
References

Introduction
Normal Weighting Schemes
Estimation Of Weighting Modifications
File Assignments
Examples

Purpose
Grid Restrictions
Sort Order Of Map And Data
Symmetry Considerations And Algorithm
Control Of Input & Output Items
File Assignments
Examples
References

Calculations Performed
File Assignments
Example
References

Introduction
Algorithm
Data Required
File Assignments
Example

Program Calculations
File Assignments
References

Overview
Purpose
Implementation
Examples

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

Recent Modifications
Shelx Commands And Data
Function
File Assignments
Example

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

Input And Output Requirements
General Plane Specifications
The Slant Plane Coordinate System
Map Orientation
Interpolation Routines
Transformed Positional Parameters
File Assignments
Examples

Method
Sorting Reflection Data
Averaging Reflection Data
Agreement Factors
Treatment Of Friedel Pairs
File Assignments
Examples
References

Unit Cell Data
Symmetry Data
File Assignments
Examples
References

Purpose
Functionality
File Assignments
Examples

Output Controls
Output Formats
File Assignments
Examples

Introduction
Application
XTINCTOptions
File Assignments
Examples
References

lrhist:
lrlabl:
lrcell:
lrsymm:
lrsgnm:
ltrwin:
lrscat:
lrsequ:
lrddef:
lrexpl:
lrdset:
lrdict:
lrgraf:
lratom:
lrcons:
lrslav:
lrmole:
lrrefl:
lrthet:
lrsfls:
lrrfac:
lrdens:
lrbond:
lrcont:
lrangl:
lrdihe:
lrrigi:
endrecord:

B. Symmetry

List of Figures

4.1. Screen shot of GIP
4.2. Screen shot of PIG
4.3. Screen shot of POWGEN
4.4. Screen shot of PREABS
4.5. Screen shot of PREVUE
4.6. Screen shot of SURFIN

Overview
News
Example Graphics
History
Documentation
Xtal Users Manual
Preface
Primer
Program controls
Reference Manual
Archive
Symmetry
FAQ
Developer Info
Retired Program Info
Download
Extra Software
Support
Contributors
Citations
Year 2000
Disclaimer

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