Table of Contents

• Preface

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• 1. Introduction
  • 1.1 The desktop beamline
    • 1.1.1 Overview
    • 1.1.2 Motors
    • 1.1.3 Principles of Operation
    • 1.1.4 Remote Control
      • "S"-Version
      • "M"-Version
      • "XL"-Version
  • 1.2 General Remarks About Program mar345dtb
  • 1.3 General Remarks About Program mar555dtb
  • 1.4 Computer Requirements

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• 2. Graphical User Interface
  • 2.1 Basic Concepts
  • 2.2 Environment
  • 2.3 Command Line Options
  • 2.4 User Interface
    • 2.4.1 "Main" Window
      • 2.4.1.1 Menu Bar
        • 2.4.1.1.1 File Menu
        • 2.4.1.1.2 Edit Menu
        • 2.4.1.1.3 Align Menu
        • 2.4.1.1.4 Image Menu
        • 2.4.1.1.5 Video Menu
        • 2.4.1.1.6 CSC Menu
        • 2.4.1.1.7 Help Menu
      • 2.4.1.2 Pages
        • 2.4.1.2.1 Image
        • 2.4.1.2.2 Edit
        • 2.4.1.2.3 Align
        • 2.4.1.2.4 Motors
        • 2.4.1.2.5 Initialize
        • 2.4.1.2.6 Misc.
          • 2.4.1.2.6.1 Single Scan
          • 2.4.1.2.6.2 Shutter
          • 2.4.1.2.6.3 Remote Control
          • 2.4.1.2.6.4 Settings for mar555 detector
        • 2.4.1.2.7 Log
        • 2.4.1.2.8 Crystal
        • 2.4.1.2.9 CSC
      • 2.4.1.3 Other Windows
        • 2.4.1.3.1 "Progress" Window
        • 2.4.1.3.2 "Image Header Info" Window
        • 2.4.1.3.3 "Administrator" Window
        • 2.4.1.3.4 "Hardware" Window
    • 2.4.2 "Status" Window
      • 2.4.2.1 Menu Bar
        • 2.4.2.1.1 File Menu
        • 2.4.2.1.2 Help Menu
      • 2.4.2.2 Status Buttons

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• 3. Image Display
  • 3.1 Introduction
  • 3.2 Image Menu
  • 3.3 Toolbox
  • 3.4 Image Area
    • 3.4.2 Mouse Button Functions
    • 3.4.3 Information Areas
  • 3.5 "File" Window
  • 3.6 "Colors" Window
  • 3.7 3-D Plot
  • 3.8 "Cross-section" Window

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• 4. Alignment
  • 4.1 Introduction
  • 4.2 Work Areas
    • 4.2.1 Align Menu
      • 4.2.1.1 Load beam data
      • 4.2.1.2 Drive to latest maximum
    • 4.2.2 Status Area
    • 4.2.3 Input Parameter Area
    • 4.2.4 Plot Area
  • 4.3 Alignment Tasks
    • 4.3.1 Find Beam
    • 4.3.2 Optimize Beam
    • 4.3.3 Profile Beam
    • 4.3.4 Shape Beam
    • 4.3.5 Adjust ADC
    • 4.3.6 Manual Operations

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• 5. Edit
  • 5.1 Introduction
  • 5.2 Edit Menu
    • 5.2.1 Description
    • 5.2.2 Load Parameters
    • 5.2.3 Save Parameters
    • 5.2.4 Copy Parameters
  • 5.3 Selecting Data Sets
  • 5.4 Directories, Names and Formats
  • 5.5 Exposure Settings
  • 5.6 Goniometer Settings
  • 5.7 Collimator and Beam Settings
  • 5.8 Options
  • 5.9 Using Shell Commands
  • 5.10 Sample Changer Settings

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• 6. Crystal
  • 6.1 Introduction
  • 6.2 Video Menu
  • 6.3 Video
  • 6.4 Motor Positions
  • 6.5 Crystal Rotation
  • 6.6 Crystal Translation
  • 6.7 Crystal Centering
    • 6.7.1 Find Crystal
    • 6.7.2 Center Crystal (automatic)

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• 7. CSC
  • 7.1 Introduction
    • 7.1.1 Principles of Operation
  • 7.2 CSC Menu
  • 7.3 CSC Operations
    • 7.3.1 Change Sample
    • 7.3.2 Load Sammple
    • 7.3.3 Unload Sample
    • 7.3.4 Give Vial
    • 7.3.5 Take Vial
    • 7.3.6 Move Sample to Stored xyz
    • 7.3.7 Shift Corrections
  • 7.4 Initialize
  • 7.5 Csc Options
  • 7.6 Sample Status

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• 8. marμX
  • 8.1 Introduction
  • 8.2 License
  • 8.3 "Remote Mode" for GeniX Generator
  • 8.4 Network Setup of GeniX Generator
  • 8.5 Operations

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• 9. Input
  • 9.1 Overview
  • 9.2 Configuration File
    • 9.2.1 Keywords
      • 9.2.1.1 General
      • 9.2.1.2 Keywords for dtb
      • 9.2.1.3 Keywords for mar345
    • 9.2.2 Example
  • 9.3 Calibration Files
  • 9.4 Parameter File
    • 9.4.1 Keywords
    • 9.4.2 Example
  • 9.5 Command File
  • 9.6 Shell Script
  • 9.7 Images
  • 9.8 Carousel File

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• 10. Output
  • 10.1 Overview
  • 10.2 Lock File
  • 10.3 Message File
  • 10.4 Log File
  • 10.5 Spy Files
  • 10.6 Statistics File
  • 10.7 Parameter File
  • 10.8 Status File
  • 10.9 Beam History File
  • 10.10 Beam Scan File
  • 10.11 Beam Profile File
  • 10.13 Beamplot File
  • 10.14 mar2thumb: Thumbnail Conversion Script
  • 10.14 Data Images
  • 10.15 ASCII Summary File
  • 10.16 HTML Summary File
  • 10.17 Automar Sync File
  • 10.18 Errors File
  • 10.19 Images used for Crystal Finding
  • 10.20 Carousel File

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• 11. Appendix
  • 11.1 dtb Firmware Update
    • 11.1.1 Firmware Distribution
      • 11.1.1.1 Application Software (APPL)
      • 11.1.1.2 Operating System (RTOS)
    • 11.1.2 Application Software Update
    • 11.1.2.1 Update Procedure for Firmware Versions ≥ 4.0
    • 11.1.2.2 Update Procedure for Firmware Versions ≤ 3.5
    • 11.1.3 Operating System Update
    • 11.1.4 List Firmware Versions
    • 11.1.5 Update of Disks R2, R3 and R5