oxford diffraction Xcalibur Series User manual

User Manual
Xcalibur
Single Crystal Diffractometers
February 26, 2004
Version 1.5
Oxford Diffraction Limited
68 Milton Park, Oxford, Oxfordshire.
OX14 4RX. UK
Tel: [phone]
Fax: [phone]
http://www.oxford-diffraction.com

Xcalibur Xcalibur_Manual_v1.5 Version 1.4
USER MANUAL Page ii
Important Information
This user manual applies to the Xcalibur systems manufactured in Poland by Oxford Diffraction.
Product: XCALIBUR2, XCALIBUR 3, XCALIBUR PX and XCALIBUR PX ULTRA
Model Type: CCD
Electrical Ratings: 1/N AC 230 V 50/60 Hz 4200 Watts
Before attempting to operate the system, PLEASE READ THE
INSTRUCTIONS.
This product should only be used by persons legally permitted to do so.
If the equipment is used in a manner not specified in the User Manual, the protection provided by
the equipment may be impaired.
Important Health and Safety Notice
When returning components for service or repair it is essential that the item is shipped together with
a signed declaration that the product has not been exposed to any hazardous contamination or that
appropriate decontamination procedures have been carried out so that the product is safe to
handle.
Care has been taken to ensure the information in this manual is accurate and at an appropriate
level. Please inform Oxford Diffraction if you have any suggestions for corrections or improvements
to this manual.
Xcalibur service and support is available for technical and operational issues as indicated below.
•E-mail: [email protected]
•Phone: [phone] between 8 a.m. and 4.30 p.m. (UK time), Monday to Friday
•Fax: [phone]
This users' manual has been written according to standard 89/392/EEC and further modifications.
Xcalibur is a trademark of Oxford Diffraction Limited in some jurisdictions and a registered
trademark of Oxford Diffraction Limited in other jurisdictions.
Oxford Diffraction acknowledges all trademarks and registrations.
Copyright 2003 Oxford Diffraction Limited. All rights reserved. No part of this document may be
reproduced or distributed in any form, or by any means, or stored in a database or retrieval system,
without prior written permission of Oxford Diffraction.

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Contents
1. Health and Safety Information ........................................................1
1.1 General.................................................................................................................................... 1
1.2 Electrical Safety....................................................................................................................... 2
1.2.1 Potential Electrical Hazards ........................................................................................... 2
1.2.2 Recommended Precautions........................................................................................... 2
1.2.3 First Aid .......................................................................................................................... 3
1.3 Mechanical Handling Safety.................................................................................................... 3
1.4 Safe Mechanical Practice........................................................................................................ 3
1.5 Moving Parts ........................................................................................................................... 3
1.6 X-ray Radiation........................................................................................................................ 4
1.7 Extreme Temperatures............................................................................................................ 5
1.8 Vacuum ................................................................................................................................... 5
1.9 High Pressures........................................................................................................................ 5
1.10 Hazardous or Toxic Materials ...............................................................................................5
1.11 Modifications and Service ..................................................................................................... 6
2. Introduction......................................................................................7
2.1 Scope ...................................................................................................................................... 7
2.2 How To Use This Manual........................................................................................................ 7
2.3 System Overview .................................................................................................................... 7
3. Specifications...................................................................................8
3.1 Environmental Requirements..................................................................................................8
3.2 Services................................................................................................................................... 8
3.2.1 Electrical Supply............................................................................................................. 8
3.2.2 Water Cooling ................................................................................................................ 9
3.2.3 Helium Gas Supply For Enhance Ultra (where applicable) ........................................... 9
3.3 Performance Data ................................................................................................................... 9
3.3.1 X-ray Tube (Typical Operating Conditions).................................................................... 9
3.3.2 Sapphire 2 CCD Detector ............................................................................................ 10
3.3.2.1 Sapphire 2 CCD Detector Theta and Resolution ......................................... 10
3.3.3 Sapphire 3 CCD Detector ............................................................................................ 11
3.3.3.1 Sapphire 3 CCD Detector Theta and Resolution ......................................... 11
3.3.4 Onyx CCD Detector ..................................................................................................... 12
3.3.4.1 Onyx CCD Detector Theta and Resolution .................................................. 12
3.3.5 PC CCD Interface ........................................................................................................ 13
3.3.6 Four-circle Kappa Geometry X-ray Goniometer .......................................................... 13
4.4 Electrical Data ....................................................................................................................... 14
4. Technical Description....................................................................15
4.1 Overview ............................................................................................................................... 15
4.2 CCD Detector Technology .................................................................................................... 17
4.2.1 Beryllium Window......................................................................................................... 18
4.2.2 Phosphor...................................................................................................................... 18
4.2.3 Taper............................................................................................................................ 18
4.2.4 CCD.............................................................................................................................. 18
4.2.5 Readout Speed ............................................................................................................ 18
4.2.6 Binning ......................................................................................................................... 19
4.2.7 Dark Current and MPP Mode....................................................................................... 19

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4.2.8 Radiation Damage ....................................................................................................... 19
4.2.9 Full Well Depth and 18-bit Digitisation ......................................................................... 19
4.2.10 Anti-blooming ............................................................................................................. 19
4.2.11 Vacuum ...................................................................................................................... 20
4.2.12 Fast Shutter................................................................................................................ 20
4.2.13 Zingers and Cosmic Ray Events................................................................................ 20
4.3 Four-Circle Kappa Geometry Goniometer ............................................................................ 20
4.4 X-ray Generator..................................................................................................................... 21
4.5 Software ................................................................................................................................ 22
4.5.1 Directory Structure .......................................................................................................22
4.5.2 Basic Menu Philosophy................................................................................................ 23
4.6 KMW200CCD Chiller............................................................................................................. 23
4.7 KMW3000C Chiller................................................................................................................ 23
4.8 Low Temperature Option....................................................................................................... 23
4.9 Safety Features ..................................................................................................................... 23
5. Handling, Installation, Storage and Transit Information ............24
5.1 Reception and Handling........................................................................................................ 24
5.1.1 Delivery ........................................................................................................................ 24
5.1.2 Unpacking .................................................................................................................... 24
5.1.3 Mechanical Handling.................................................................................................... 25
5.1.3.1 Weights, Dimensions and Lifting Points .......................................................... 25
5.1.3.2 Boxed Weights, Dimensions and Lifting Points on
Delivery ...................................................................................................................... 26
5.2 Installation and Setting to Work ............................................................................................27
5.2.1 Preparation of Site and Services ................................................................................. 27
5.2.1.1 Environmental Requirements .......................................................................... 27
5.2.1.2 System Layout ................................................................................................. 27
5.2.1.3 Electrical Services............................................................................................ 27
5.2.1.4 Water Supply ................................................................................................... 29
5.2.1.5 Low Temperature Option ................................................................................. 29
5.2.1.6 CCD Camera Pumping .................................................................................... 29
5.2.1.7 Helijet Option ................................................................................................... 29
5.2.2 Setting to Work............................................................................................................. 30
5.2.2.1 Equipment Required ........................................................................................ 30
5.2.2.2 Personnel Required for Installation.................................................................. 30
5.2.2.3 Setting up Procedures ..................................................................................... 30
5.3 Storage ........................................................................................................................ 32
6. Operation........................................................................................33
6.1 Controls and Indicators ......................................................................................................... 33
6.2 Initial Switch on Procedure.................................................................................................... 34
6.3 X-ray Tube Warm-up Procedure........................................................................................... 36
6.4 Software ................................................................................................................................ 37
6.4.1 Software Updates......................................................................................................... 37
6.4.2 Software Installation.....................................................................................................38
6.4.2.1 MGC interface software ................................................................................... 38
6.4.2.2 CrysAlis Software............................................................................................. 39
6.4.3 Changing Machine Correction and Set-up Files .......................................................... 39
6.5 Normal Operation.................................................................................................................. 40
6.5.1 General Commands..................................................................................................... 40

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6.5.2 Changing Xcalibur Settings.......................................................................................... 42
6.5.3 Standard Diffraction Experiment .................................................................................. 46
6.5.3.1 Crystal Mounting and Alignment............................................................................... 46
6.5.3.2 Diffraction Photographs to Determine Crystal Quality .............................................. 48
6.5.3.3 Unit Cell Determination ............................................................................................. 49
6.5.3.4 Data Collection.......................................................................................................... 52
6.5.3.5 Data Processing and Reduction ............................................................................... 53
6.5.3.5.1 Orientation Matrix ......................................................................................... 53
6.5.3.5.2 Run List......................................................................................................... 54
6.5.3.5.3 Scan Width.................................................................................................... 55
6.5.3.5.4 Background Evaluation................................................................................. 55
6.5.3.5.5 Special Corrections....................................................................................... 56
6.5.3.5.6 Outlier Rejection ........................................................................................... 57
6.5.3.5.7 Output Format............................................................................................... 58
6.5.3.6 Changing the Output Format from Data Reduction .................................................. 59
6.5.3.7 Absorption Correction ............................................................................................... 60
6.5.3.8 GRAL - Space Group Determination ........................................................................ 68
6.5.3.9 Structure Solution and Refinement........................................................................... 74
6.5.4 Ewald explorer ............................................................................................................. 74
6.5.5 Dc Movie - Replay of Data Collection Movie................................................................ 80
6.5.6 Reconstruction of Precession Photographs................................................................. 81
6.5.7 Dc opti - Optimisation of Data Collection Strategy....................................................... 86
6.5.8 Indexing and Data Reduction of Incommensurate Samples........................................ 92
6.5.9 Indexing and Data Reduction of Twinned Samples..................................................... 93
6.5.10 Extracting Data from Powder Samples...................................................................... 96
6.5.11 Refining of Machine Parameter File........................................................................... 97
6.5.12 Glossary of CrysAlis Commands ............................................................................. 100
6.6 Normal Shutdown................................................................................................................ 107
6.7 Emergency Shutdown ......................................................................................................... 107
6.7.1 Emergency Shutdown Procedure .............................................................................. 107
7. Mechanical Changeover of Detectors and X-ray Sources .......108
7.1 Interchange of CCD Detectors ............................................................................................ 108
7.1.1 Installation of Sapphire 2 and Sapphire 3 CCD detectors ......................................... 108
7.1.2 Removal of Sapphire 2 and Sapphire 3 CCD detectors ............................................ 109
7.1.3 Installation of the Onyx CCD camera......................................................................... 109
7.1.4 Removal of the Onyx CCD camera............................................................................ 112
7.2 Procedure for Interchange of the Molybdenum and Copper Enhance X-ray Source ......... 113
8. Maintenance Schedules ..............................................................117
8.1 Introduction.......................................................................................................................... 117
8.2 Weekly Maintenance Schedule........................................................................................... 117
8.3 Monthly Maintenance Schedule .......................................................................................... 117
8.4 Six Monthly Maintenance Schedule .................................................................................... 118
8.5 Yearly Maintenance Schedule ............................................................................................ 118
8.6 10,000 Hours Maintenance Schedule................................................................................. 119
9. Maintenance Instructions............................................................120
9.1 Special Tools....................................................................................................................... 120
9.2 Refining the Machine Parameter File.................................................................................. 120
9.3 Changing the X-ray Tube of Enhance................................................................................. 121

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9.4 Changing the X-ray Tube of Enhance ULTRA.................................................................... 122
9.5 X-ray Beam Stop Alignment................................................................................................ 124
9.6 Changing the Collimator of Enhance .................................................................................. 125
9.7 Changing the Collimator of Enhance Ultra.......................................................................... 126
9.8 Aligning the X-ray Collimator of Enhance ........................................................................... 126
9.9 Aligning the Enhance X-ray Source .................................................................................... 126
9.10 Aligning the Enhance Ultra X-ray Source.......................................................................... 129
9.10.1 X-ray Beam Alignment of Enhance Ultra ................................................................. 129
9.10.2 Optic Alignment of Enhance Ultra............................................................................ 131
9.10.3 Collimator Alignment of Enhance Ultra.................................................................... 131
9.10.4 Aligning the beam to the centre of the goniometer – Enhance Ultra ....................... 132
9.11 Checking the Door Safety Interlocks................................................................................. 133
9.12 Checking the Emergency stop .......................................................................................... 133
9.13 Checking the X-ray Radiation Levels................................................................................ 134
9.14 CCD Detector – Pumping Out Vacuum............................................................................. 134
9.15 Dismantling Xcalibur.......................................................................................................... 136
10. Trouble Shooting .......................................................................139
11. Spares.........................................................................................142
12. Disposal Instructions ................................................................144
12.1 X-ray Tube and CCD Detector .......................................................................................... 144
12.2 Third Party Equipment....................................................................................................... 144
13. Additional Information...............................................................145
13.1 Third Party Information...................................................................................................... 145
13.2 Drawings ........................................................................................................................... 146
13.2.1 Mechanical Drawings............................................................................................... 146
OD-01-00-15-C Xcalibur Suggested Layout........................................................... 146
OD-01-00-01 System and Component Dimensions............................................... 146
13.2.2 Electrical Drawings................................................................................................... 148
14. CE Conformity notice ................................................................150
Appendices.......................................................................................151
Appendix 1 X-ray Tubes Wave Lengths.................................................................................... 151
Appendix 2 Standard Crystal Parameters................................................................................ 151
Appendix 3 Temperature Scales Conversion............................................................................ 151
Appendix 4 Maintenance Records ............................................................................................ 151
Appendix 5 Example of Local Rules for the Xcalibur System Set Up at Oxford Diffraction...... 156

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Table of Figures
Figure 4.1.1 Components of the Xcalibur system ............................................................................. 15
Figure 4.1.2 View of the diffractometer ............................................................................................. 16
Figure 4.2.1 Schematic of a fibre-optic-coupled CCD detector for x-rays......................................... 17
Figure 4.3.1 Goniometer phi, kappa, omega and theta axes............................................................ 20
Figure 4.4.1 C3K5 X-ray Generator front panel ................................................................................ 21
Figure 4.4.2 DF3 X-ray Generator front panel .................................................................................. 21
Figure 5.2.1 Xcalibur installation procedure..................................................................................... 30
Figure 6.1.1 Location of switches...................................................................................................... 34
Figure 6.5.1 Screenshot of Image selection and Zoom .................................................................... 40
Figure 6.5.2 Screenshot of CCD parameters window....................................................................... 43
Figure 6.5.3 Screenshot of CrysAlis RED showing a diffraction image with beam stop mask ......... 43
Figure 6.5.4 Screenshot of CrysAlis program options – Instrument model I..................................... 44
Figure 6.5.5 Screenshot of CrysAlis program options –beam stop settings ..................................... 44
Figure 6.5.6 Screenshot of CrysAlis program options – PH and PT size ......................................... 45
Figure 6.5.7 Screenshot of CrysAlis profile inspector window .......................................................... 46
Figure 6.5.8 Optical alignment of the crystal..................................................................................... 47
Figure 6.5.9 Rotation photograph...................................................................................................... 48
Figure 6.5.10 Screenshot of axial photograph orientation screen .................................................... 49
Figure 6.5.11 Screenshot of Edit data collection runs....................................................................... 50
Figure 6.5.12 Screenshot of Edit data collection runs....................................................................... 52
Figure 6.5.13 Screenshot of CrysAlis data reduction screen (crystal lattice).................................... 54
Figure 6.5.14 Screenshot of CrysAlis data reduction screen (run list).............................................. 54
Figure 6.5.15 Screenshot of CrysAlis data reduction screen (scan width) ....................................... 55
Figure 6.5.16 Screenshot of CrysAlis data reduction screen (background evaluation) .................... 56
Figure 6.5.17 Screenshot of CrysAlis data reduction screen (special corrections)........................... 56
Figure 6.5.18 Screenshot of CrysAlis data reduction screen (outlier rejection)................................ 58
Figure 6.5.19 Screenshot of CrysAlis data reduction screen (output format) ................................... 58
Figure 6.5.20 Screenshot of data reduction finalisation window....................................................... 59
Figure 6.5.21 Screenshot of ‘ABS – Acquisition of movie screen’ .................................................... 61
Figure 6.5.22 Screenshot of crystal movie screen............................................................................ 62
Figure 6.5.23 Screenshot of crystal movie configuration screen ...................................................... 63
Figure 6.5.24 Screenshot of crystal movie screen............................................................................ 63
Figure 6.5.25 Screenshot of crystal movie screen............................................................................ 64
Figure 6.5.26 Screenshot of crystal movie screen (crystal shape) ................................................... 65
Figure 6.5.27 Screenshot of crystal movie screen............................................................................ 65
Figure 6.5.28 Screenshot of crystal movie screen............................................................................ 67
Figure 6.5.29 Example of absorption correction ............................................................................... 67
Figure 6.5.30 Screenshot of the GRAL plug-in Settings ................................................................... 68
Figure 6.5.31 Screenshot of the GRAL plug-in Load Window on initialisation (no file loaded)......... 69
Figure 6.5.32 Screenshot of the GRAL plug-in Load Window (File loaded from DC_GAIN8.HKL).. 69
Figure 6.5.33 Screenshot of the GRAL plug-in Load Window (Reciprocal space visualiser) ........... 70
Figure 6.5.34 Screenshot of the GRAL plug-in Centring Window..................................................... 70
Figure 6.5.35 Screenshot of the GRAL plug-in Niggli Window ......................................................... 71
Figure 6.5.36 Screenshot of the GRAL plug-in Lattice Window........................................................ 71
Figure 6.5.37 Screenshot of the GRAL plug-in Centring Window (After Niggli Reduction) .............. 72
Figure 6.5.38 Screenshot of the GRAL plug-in <E2-1> Window ...................................................... 72
Figure 6.5.39 Screenshot of the GRAL plug-in Space Group Window ............................................. 73
Figure 6.5.40 Screenshot of the GRAL plug-in INS-File Window ..................................................... 73

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Figure 6.5.41 Screenshot of Ewald explorer screen ......................................................................... 75
Figure 6.5.42 Screenshot of Ewald explorer screen with vector shown ........................................... 75
Figure 6.5.43 Screenshot of dialog box displayed when exiting the Ewald explorer ........................ 76
Figure 6.5.44 Screenshot of Ewald Explorer – Drag Selection of Reflections and Marking Skip..... 76
Figure 6.5.45 Screenshot of Ewald Explorer – Skip reflections invisible .......................................... 77
Figure 6.5.46 Screenshot of Ewald Explorer – Skip Filter Intensity Menu Selected......................... 77
Figure 6.5.47 Screenshot of Ewald Explorer – Skip Filter Intensity Window (Use Intensity Filter)... 78
Figure 6.5.48 Screenshot of Ewald Explorer – Mark Invisible Skip .................................................. 78
Figure 6.5.49 Screenshot of Ewald Explorer – Mark All Invisible Peaks Skip .................................. 79
Figure 6.5.50 Screenshot of Ewald Explorer – Skip Filter Intensity Window .................................... 79
Figure 6.5.51 Screenshot of Data Collection Movie with Unit Cell Predictions Overlayed ............... 80
Figure 6.5.52 Screenshot of Unwarp Wizard – Step 1: Orientation matrix ....................................... 81
Figure 6.5.53 Screenshot of Unwarp Wizard – Step 2: Open Run List............................................. 82
Figure 6.5.54 Screenshot of Unwarp Wizard – Step 2: Run List Loaded ......................................... 82
Figure 6.5.55 Screenshot of Unwarp Wizard – Step 2: Select Output Directory .............................. 83
Figure 6.5.56 Screenshot of Unwarp Wizard – Step 3: Creation of a Layer List .............................. 83
Figure 6.5.57 Screenshot of Unwarp Wizard – Step 3: Add a Reconstruction Layer ....................... 84
Figure 6.5.58 Screenshot of Unwarp Wizard – Step 4: Background Evaluation............................... 84
Figure 6.5.59 Screenshot of Unwarp Wizard – Step 5: Data Corrections......................................... 85
Figure 6.5.60 An Example of a Reconstructed layer......................................................................... 85
Figure 6.5.61 Screenshot of Run List Optimiser ............................................................................... 87
Figure 6.5.62 Screenshot of Run List Optimiser: Crystal Properties ................................................ 88
Figure 6.5.63 Screenshot of Run List Optimiser: Optimisation Parameters ..................................... 88
Figure 6.5.64 Screenshot of Run List Optimiser: Coverage Statistics .............................................. 89
Figure 6.5.65 Screenshot of Data Reduction: Special Corrections................................................... 94
Figure 6.5.66 Screenshot of Data Reduction: Editing of Twin Overlap Fraction .............................. 94
Figure 6.5.67 Screenshot of Powder Rings and Line Profile ............................................................ 96
Figure 6.5.68 Screenshot of Powder Pattern Data Plotted via a Spreadsheet Program .................. 96
Figure 6.5.69 Screenshot of Refine Model Window.......................................................................... 97
Figure 6.5.70 Screenshot of Refine Model (Constraining all Unit Cell Lengths to be Equal) ........... 98
Figure 6.5.71 Screenshot of Refine Model (Constraining all Unit Cell Angles to 90 degrees) ......... 98
Figure 7.1.3.1 Mounting the Onyx CCD - rotated mounting rail with screw positions..................... 110
Figure 7.1.3.2 Mounting the Onyx CCD - Position of the detector as it is mounted onto the rail.... 111
Figure 7.1.3.3 Mounting the Onyx CCD - replacing the front screw ............................................... 111
Figure 7.1.3.4 Mounting the Onyx CCD - replacing the rear screw ................................................ 111
Figure 7.2.1 Location of Enhance retaining and adjustment nuts................................................... 114
Figure 9.1.1 ‘T’ tool.......................................................................................................................... 120
Figure 9.1.2 Special tool ‘1’ ............................................................................................................. 120
Figure 9.3.1 Position of the X-ray source........................................................................................ 122
Figure 9.5.1 Beam stop adjustment screws .................................................................................... 125
Figure 9.9.1 Enhance X-ray Source mounted on Xcalibur 3........................................................... 126
Figure 9.9.2 Enhance X-ray source adjustments (front view) ......................................................... 128
Figure 9.9.3 Enhance X-ray source adjustments (top view) ........................................................... 128
Figure 9.10.1 Adjustment screws of Enhance Ultra ........................................................................ 129
Figure 9.10.2 Schematic showing the rotated beam stop (dashed line shows “up” position and solid
line shows “down” position)....................................................................................................... 130
Figure 9.10.3 Image of direct X-ray Beam ...................................................................................... 130
Figure 9.10.4 Image during optical alignment of Enhance Ultra ..................................................... 131
Figure 9.14.1 View of the access plates and pump out ports of the Sapphire and Onyx CCD
detectors ................................................................................................................................... 135

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Xcalibur Dimensions........................................................................................................................ 147
KMW3000C Dimensions ................................................................................................................. 147
KMW200CCD Dimensions .............................................................................................................. 147

HEALTH AND SAFETY INFORMATION
Version 1.5 Xcalibur_Manual_v1.5 Xcalibur
Page 1 USER MANUAL
1. Health and Safety Information
1.1 General
In normal operation the system is designed to operate safely. All users of Xcalibur should be aware
of potential hazards which exist in and around equipment of this type and the ways of avoiding
possible injury and equipment damage which may result from inappropriate ways of working. A
description of such potential hazards and how to avoid them is given in this section.
This manual adopts the following convention:
WARNING
Indicates a potential hazard which may result in injury or death
CAUTION
Indicates a potential hazard which may result in damage to equipment
Warning symbols on the equipment are:
Protective conductor terminal
Earth (ground) terminal
CAUTION
Risk of electric shock
CAUTION
Refer to accompanying documents
WARNING
Radiation Hazard
See original manufacturers' manuals for further safety data on third party equipment supplied with
the system. A list of these is given in this manual.
WARNING
Do not take risks. You have a responsibility to ensure the safe
condition and safe operation of equipment.
WARNING
Xcalibur should only be operated and maintained by authorised
operators of the system. An authorised operator is a person who has
undergone specialist radiation training and has been trained in the
use of Xcalibur by Oxford Diffraction personnel.