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ROTGEN - Rotation Image Prediction and Analysis

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Rotgen Montage

Version Number: 3.0

(see also Details of Updates)

John W. Campbell, CCLRC Daresbury Laboratory

CONTENTS

CHAPTER 1: OVERVIEW

1.1  INTRODUCTION
1.2  Running the Program
1.3  Introduction to XDL_VIEW
1.4  Screen Layout
1.5  Some Basic Concepts
1.6  Outline of the Main Options
1.7  The Command Window
1.8  References

CHAPTER 2: PARAMETER AND MATRIX FILES 

2.1  INTRODUCTION
2.2  The 'Read Parameters File' Option
2.3  The 'Read Matrix File' Option
2.4  The 'Write Matrix File' Option
2.5  The 'Write Parameters File' Option
2.6  Usaved Parameters Warning on Quit

CHAPTER 3: THE 'ROTATION SIMULATIONS' OPTION 

3.1  INTRODUCTION
3.2  Selection of the image
3.3  Orientation of the Simulations
3.4  The Colour Display
3.5  The Interactive Display

CHAPTER 4: THE 'INPUT MTZ DATA' OPTION 

4.1  INTRODUCTION
4.2  Inputting the Data
4.3  Using the MTZ Data in Analyses
4.4  Resolution for Data Analyses

CHAPTER 5: THE 'ANALYSE DATA' OPTION 

5.1  INTRODUCTION
5.2  Full Analyses
5.3  Quick Analyses
5.4  MTZ Data
5.5  Overlaps
5.6  Requesting the Analysis
5.7  Examining the Results
     5.7.1    Introduction
     5.7.2    Show Reciprocal Lattice
     5.7.3    Show Graphical Plots
     5.7.4    Log Analyses with Overlaps

CHAPTER 6: THE 'STRATEGY' OPTION 

6.1  INTRODUCTION
6.2  Requesting the Strategy Option
     6.2.1    Introduction
     6.2.2    Maximising Unique Data or Acentric Pairs
     6.2.3    Analysing Overlaps
6.3  The Strategy Method for Maximising Data Coverage
6.4  Examining the Results from Strategy Maximisations
     6.4.1    Introduction
     6.4.2    The Strategy Results Window
     6.4.3    Choosing Multiple Segments
     6.4.4    Analysing the Results
     6.4.5    Accepting a Solution
6.5  Logging of the Results of Maximisations

APPENDIX 1: SETTING UP ROTGEN 

1.1  INTRODUCTION
1.2  Symmetry Operators File
1.3  Fonts
1.4  Program Modes
1.5  Compiling and Linking ROTGEN

APPENDIX 2: THE PARAMETERS

2.1  INTRODUCTION
2.2  Handling the Keyworded Parameters
2.3  Summary of Keyworded Parameters
2.4  Detailed Specification of the Parameters
2.5  Standard Set of Output Parameters
2.6  The NUMIMG parameter

APPENDIX 3: THE LOG FILE 

3.1  INTRODUCTION
3.2  Contents of the Log File
3.3  Key to Analysis Tables

APPENDIX 4: COORDINATE SYSTEMS

4.1  INTRODUCTION

APPENDIX 5: ANALYSIS OF OVERLAPS 

5.1  INTRODUCTION
5.2  The Procedure

FIGURES: CHAPTER 1

1.1  Main Screen of ROTGEN

FIGURES: CHAPTER 3

3.1  Example of a Colour Rotation Simulation
3.2  Example of an Interactive Rotation Simulation

FIGURES: CHAPTER 5

5.1  Example of 'Show Unique Coverage' View-object
5.2  Example of a Unique Data Coverage Graph

FIGURES: CHAPTER 6

6.1  Example of a Strategy Results Table

FIGURES: APPENDIX 4

4.1  The Laboratory Axes used by ROTGEN

John W. Campbell
CCLRC Daresbury Laboratory
Last update 24 Oct 1997