Table of Contents

• Preface

• 1. Introduction
  • 1.1 General Remarks
  • 1.2 Coordinate System
  • 1.3 Indexing Method

• 2. Graphical User Interface
  • 2.1 Environment
  • 2.2 Command Line Options
  • 2.3 Main Pages
    • 2.3.1 Text
    • 2.3.2 Setup
      • 2.3.2.1 Setup Directories and Names
      • 2.3.2.2 Setup Crystal Parameters
      • 2.3.2.3 Setup Goniometer Parameters
      • 2.3.2.4 Setup Beam Parameters
      • 2.3.2.5 Setup Detector Parameters
      • 2.3.2.6 Exclude Detector Areas
    • 2.3.3 Display
      • 2.3.3.1 Loading Images
      • 2.3.3.2 Loading Spot Files
      • 2.3.3.3 Using Mouse Buttons
      • 2.3.3.4 Image Colors
      • 2.3.3.5 Image Options
      • 2.3.3.6 Center Tool
      • 2.3.3.7 Editing Spot Lists
      • 2.3.3.8 Saving Graphics
  • 2.4 Plot Pages
    • 2.4.1 Index
    • 2.4.2 Strategy
    • 2.4.3 marPost
    • 2.4.4 marScale
    • 2.4.5 scala
    • 2.4.6 scalepack
  • 2.5 Program Pages
    • 2.5.1 Peak Search
    • 2.5.2 Index
    • 2.5.3 Predict
    • 2.5.4 Strategy
    • 2.5.5 Integrate
      • 2.5.5.1 marProcess
      • 2.5.5.2 mosflm
      • 2.5.5.3 denzo
      • 2.5.5.4 XDS
    • 2.5.6 Join
    • 2.5.7 Scale
    • 2.5.7 Scale
      • 2.5.7.1 marScale
      • 2.5.7.2 scala
      • 2.5.7.3 scalepack
      • 2.5.7.4 XSCALE
    • 2.5.8 Truncate
    • 2.5.9 Convert

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  • 3. Input
    • 3.1 Parameter Files
    • 3.2 Images
    • 3.3 Spot Files
    • 3.4 Others

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  • 4. Output
    • 4.1 Parameter Files
    • 4.2 Command Files
    • 4.3 Log Files
    • 4.4 Other Output Files

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  • 5. How to Integrate and to Scale
    • 5.1 Integration
      • 5.1.1 marProcess
      • 5.1.2 ipmosflm
      • 5.1.3 denzo
      • 5.1.4 XDS
    • 5.2 Scaling
      • 5.2.1 marScale
      • 5.2.2 scala
      • 5.2.3 scalepack
      • 5.2.4 XSCALE

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  • 6. Appendix
    • 6.1 Analogy of Text Fields and Program Keywords
      • 6.1.1 Peak Search
      • 6.1.2 Index
      • 6.1.3 Predict
      • 6.1.4 Strategy
      • 6.1.5 Integrate
        • 6.1.5.1 marProcess
        • 6.1.5.2 ipmosflm
        • 6.1.5.3 denzo
        • 6.1.5.4 XDS
      • 6.1.6 Join&Sort
      • 6.1.7 Scale
        • 6.1.7.1 marScale
        • 6.1.7.2 scala
        • 6.1.7.3 scalepack
        • 6.1.7.4 XSCALE
      • 6.1.8 Truncate
      • 6.1.9 Convert
    • 6.2 Template for cleanup.com

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