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oxford diffraction Xcalibur Series User Manual

Single crystal diffractometers
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User Manual
Xcalibur
Single Crystal Diffractometers
February 26, 2004
Version 1.5
Oxford Diffraction Limited
68 Milton Park, Oxford, Oxfordshire.
OX14 4RX. UK
Tel: +44 (0)1235 443630
Fax: +44 (0)1235 443631
http://www.oxford-diffraction.com

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  • Page 1 User Manual Xcalibur Single Crystal Diffractometers February 26, 2004 Version 1.5 Oxford Diffraction Limited 68 Milton Park, Oxford, Oxfordshire. OX14 4RX. UK Tel: +44 (0)1235 443630 Fax: +44 (0)1235 443631 http://www.oxford-diffraction.com...
  • Page 2 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.

  • Page 3: Table Of Contents

    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........................
  • Page 4 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........................
  • Page 5 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 ..................
  • Page 6 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 Xcalibur Version 1.5 Xcalibur_Manual_v1.5...
  • Page 7 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 ................
  • Page 8 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 –...
  • Page 9 Xcalibur Dimensions........................147 KMW3000C Dimensions ......................... 147 KMW200CCD Dimensions ......................147 Xcalibur Version 1.5 Xcalibur_Manual_v1.5 Page ix USER MANUAL...

  • Page 10: Health And Safety Information

    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. Xcalibur Version 1.5 Xcalibur_Manual_v1.5...

  • Page 11: Electrical Safety

    HEALTH AND SAFETY INFORMATION 1.2 Electrical Safety In normal use the user is protected from the dangers associated with the voltage, current and power levels used by the equipment. Only personnel qualified to work with the voltages and currents used by this equipment should attempt to disconnect, dismantle or modify the equipment.

  • Page 12: First Aid

    In normal use personnel are not required to undertake mechanical work. However, servicing or repair may necessitate access to any part of the system. Only personnel who have been trained by Oxford Diffraction to carry out service work on this equipment should attempt to dismantle, modify or repair the equipment.

  • Page 13: X-Ray Radiation

    HEALTH AND SAFETY INFORMATION 1.6 X-ray Radiation WARNING This equipment contains an X-ray tube. Ensure that safe working practices relating to radiation are employed. Follow any local, national or international rules and guidelines. Intentional or reckless misuse of the X-ray generator or its safety devices including safety interlocks and cabinet shielding can result in serious injury or even death.

  • Page 14: Extreme Temperatures

    HEALTH AND SAFETY INFORMATION 1.7 Extreme Temperatures WARNINGS 1. Systems fitted with the low temperature option use liquid nitrogen and/or liquid helium as a coolant. Liquid nitrogen and liquid helium are cryogenic liquids and can cause cold burns. Wear gloves when handling cryogenic liquids and use eye protection. Refer to the information supplied with the equipment for more information.

  • Page 15: Modifications And Service

    HEALTH AND SAFETY INFORMATION contact the relevant local agency stating that there is an incident involving possible beryllium or beryllium oxide contamination. 1.11 Modifications and Service The manufacturer will not be held responsible for the safety, reliability or performance of the equipment unless assembly operations, extensions, re-adjustments, modifications and repairs are carried out only by persons authorised by the manufacturer.

  • Page 16: Introduction

    This manual is aimed at operators and maintenance personnel of the Xcalibur system. Operators of the system should be computer literate, familiar with X-ray diffraction techniques, have had training in the use of the Xcalibur system by Oxford Diffraction staff, and have had training about radiation safety.

  • Page 17: Specifications

    SPECIFICATIONS 3. Specifications 3.1 Environmental Requirements 18 – 28 °C Ambient temperature during operation ± 1 °C Stability of ambient temperature during operation Storage temperature >10°C <40°C Relative humidity <80 % non – condensing Location Clean, dust free environment >2m from air conditioning or heating units Floor covering Conductive or, if carpeted, covered with electrostatic mats...

  • Page 18: Water Cooling

    SPECIFICATIONS 3.2.2 Water Cooling Min flow rate 1.8 l/min Pressure 0.5 - 5 bar gauge ± 5 °C Temperature stability 10 – 20 °C Temperature range Composition Filtered, without deposits, chemically neutral and optically clear 3.2.3 Helium Gas Supply For Enhance Ultra (where applicable) Purity 99.99% Regulator...

  • Page 19: Sapphire 2 Ccd Detector

    SPECIFICATIONS 3.3.2 Sapphire 2 CCD Detector Active area 90-92 mm diagonal CCD chip 1024 x 1024 pixels, Sapphire 2 (Kodak KAF-1001E, scientific grade {grade 1}) Pixel size on scintillator ~ 60 µm Gadox (absorption > 90% Mo K α) Scintillator material Fibre optic reduction ~ 2.5:1;...

  • Page 20: Sapphire 3 Ccd Detector

    SPECIFICATIONS 3.3.3 Sapphire 3 CCD Detector Active area 90 - 92 mm diagonal CCD chip Kodak KAF4301-E Pixel size on scintillator 31 µm Scintillator material Gadox Fibre optic reduction 1.3:1; low distortion reduction taper Peltier cooling -45ºC (four stage cooler) Temperature stability ±...

  • Page 21: Onyx Ccd Detector

    SPECIFICATIONS 3.3.4 Onyx CCD Detector Active area 165 mm diagonal CCD chip Kodak KAF4301-E Pixel size on scintillator 60 µm Scintillator material Gadox Fibre optic reduction 2.5:1; low distortion reduction taper Peltier cooling -45ºC (four stage cooler) Temperature stability ± 0.05ºC(micro-processor PID) Analogue-to-digital resolution True 17 bit System noise (so-called read noise)

  • Page 22: Pc Ccd Interface

    SPECIFICATIONS 3.3.5 PC CCD Interface Communication 2 mono-directional fibre-optic taxi channels Control processor TI DSP C31 (Sapphire 2) / TMS 320C6205 (Sapphire 3 / Onyx) Memory 32 Mb Drivers WinXP Typical host computer Sapphire 2 Sapphire 3 / Onyx Pentium III class PC Pentium IV class PC >1 GHz >2.4 GHz...

  • Page 23: Electrical Data

    SPECIFICATIONS 4.4 Electrical Data DF3 X-ray 3K5 X-ray Sapphire 2 Sapphire 3 / X-ray Generator Generator Onyx CCD Goniometer Power connection 1/N AC 198 1/N AC 230 V 1/N AC 230 V 1/N AC 230 V 1/N AC 230 V to 242 V ±...

  • Page 24: Technical Description

    (theta axis), which has a universal mount capable of supporting any Oxford Diffraction CCD area detector or scintillation point detector. The CCD area detector and the point detector are used to measure the X-quanta diffracted from the sample.

  • Page 25: Figure 4.1.2 View Of The Diffractometer

    TECHNICAL DESCRIPTION 1. X-ray tube 4. Collimator 2. 4-circle Kappa goniometer 5. Beamstop 3. X-ray Shutter 6. Beryllium Window Figure 4.1.2 View of the diffractometer The X-rays are generated by a sealed tube, which is mounted on the goniometer and powered by the high voltage X-ray generator.

  • Page 26: Ccd Detector Technology

    TECHNICAL DESCRIPTION 4.2 CCD Detector Technology This section introduces the CCD X-ray detector technology as implemented in the Sapphire and Onyx detectors. A fibre-optic-coupled CCD detector for X-rays is schematised in fig 4.2.1. scintillator Taper cooling electronics Figure 4.2.1 Schematic of a fibre-optic-coupled CCD detector for x-rays X-rays enter the vacuum detector enclosure through a Be window.

  • Page 27: Beryllium Window

    TECHNICAL DESCRIPTION 4.2.1 Beryllium Window The 0.5mm Beryllium window is the entrance for the X-ray photons into the detector unit. The detector unit is held under vacuum to provide thermal isolation for the Peltier cooled CCD chip. The Be window absorbs incoming X-ray photons in the following way: Radiation Pure Be Be with 0.1% contamination (Cu)

  • Page 28: Binning

    TECHNICAL DESCRIPTION but the read noise quickly increases to 8-20 electrons. For the X-ray diffraction application low system noise is of utmost importance for the measurement of weak diffraction signals. 4.2.6 Binning Binning is an operation mode of a CCD chip, which allows grouping together several pixels. There is parallel and serial binning.

  • Page 29: Vacuum

    TECHNICAL DESCRIPTION 4.2.11 Vacuum The CCD chip and the fibre optic taper are confined in a vacuum enclosure to isolate them thermally and to prevent condensation on the cold detector parts. Static vacuum degrades with time due to degassing of the components in the vacuum enclosure. The system is designed to maintain a sufficient vacuum level in the enclosure for at least 6 months.

  • Page 30: X-Ray Generator

    TECHNICAL DESCRIPTION built in frame grabber. A fibre optic halogen flood light system provides brilliant, high contrast illumination of the sample at all goniometer positions. 4.4 X-ray Generator Figure 4.4.1 C3K5 X-ray Generator front panel Figure 4.4.2 DF3 X-ray Generator front panel Xcalibur systems can be supplied with either the C3K5 Ital Structures or the DF3 Spellman X-ray generator.

  • Page 31: Software

    TECHNICAL DESCRIPTION 4.5 Software The programs controlling the measurement procedures of the system are WIN32 applications, which run under Windows XP . The data acquisition is done with the program CrysAlis CCD and the data reduction with the program CrysAlis RED. 4.5.1 Directory Structure The CrysAlis program system is installed in the following directory structure.

  • Page 32: Basic Menu Philosophy

    TECHNICAL DESCRIPTION 4.5.2 Basic Menu Philosophy The CrysAlis programs interact with the user in various ways. Basic commands: The basic tasks are stored in the order that they are likely to be carried out. Expert mode commands: A link to all the available commands is available here. NOTE Every command has a short-cut code, for instance “dc s”...

  • Page 33: Handling, Installation, Storage And Transit Information

    4. Always lift packing cases from the bottom using suitable lifting equipment (refer to list of component weights in the following section. 5. Move packing cases into the designated installation site. 6. Contact Oxford Diffraction to notify them that the equipment is awaiting installation by a factory trained service representative. 5.1.2 Unpacking 1.

  • Page 34: Mechanical Handling

    HANDLING, INSTALLATION, STORAGE AND TRANSIT INFORMATION 5.1.3 Mechanical Handling 5.1.3.1 Weights, Dimensions and Lifting Points Description Dimensions Centre of gravity Lifting points Weight (width x height x depth) Kappa 43 x 64 x 47 Offset from centre of At four corners goniometer unit towards side of (DO NOT lift from...

  • Page 35: Boxed Weights, Dimensions And Lifting Points On Delivery

    OPERATION 5.1.3.2 Boxed Weights, Dimensions and Lifting Points on Delivery Item Length Width Height Weight (kgs) (cm) (cm) (cm) (No.) Goniometer Accessories Protection cabinet Electronics rack Helijet KMW3000C Chiller KMW200CCD Chiller & CCD camera 160L LN2 dewar 17” Monitor Cryojet X-ray generator The weights and dimension above are an estimate and should only act as an indication of the lifting requirements when the system is delivered.

  • Page 36: Installation And Setting To Work

    OPERATION 5.2 Installation and Setting to Work 5.2.1 Preparation of Site and Services 5.2.1.1 Environmental Requirements It is the customer’s responsibility to ensure that all local building and safety regulations are met. Ensure that the environmental conditions of the installation site conform to the requirements stated in the SPECIFICATIONS section of this manual.
  • Page 37 OPERATION Description Voltage Frequency Maximum Main Maximum mains fuse power current X-ray generator 1/N AC 230 ±10% 50/60 4200 CCD detector & 1/N AC 230 ±10% 50/60 KMW200CCD cooler Kappa geometry, X-ray 1/N AC 230 ±10% 50/60 goniometer, video monitor, halogen lamp, fibre optics Computer and 100 - 240...

  • Page 38: Water Supply

    OPERATION 5.2.1.4 Water Supply CCD detector Cooling The CCD detector is water cooled by the KMW200CCD Cooler. Ten metre long water pipes are supplied with the system. The minimum distance required between the back and the side of the casing for KMW200CCD and electronics rack is 30 cm.

  • Page 39: Setting To Work

    3 working days, with an additional 1 day for the low temperature option. This followed by 2 days training from an Oxford Diffraction crystallographer. The numbers on Figure 5.2.1 refer to the step numbers in this section. These notes provide installation guidance only.
  • Page 40 OPERATION 1. Install electronics rack. Use 2 persons to lift electronics rack into position on a level floor (see environmental requirements). 2. Mount table top. Remove vented front, back and side panels at the top of the electronics rack. Screw table top into position (from below and at the four corners). Check that the table top is level.

  • Page 41: Storage

    OPERATION 9. Mount CCD detector Slide detector onto graduated mount from right hand side of Xcalibur (from front) and secure at 60 mm. WARNING Do not touch the Beryllium window at the front of the detector. Beryllium is potentially toxic material. 10.

  • Page 42: Operation

    OPERATION 6. Operation Xcalibur is a computer-controlled system. All functions are controlled from the computer terminal except when control is released from the computer terminal to the remote control unit. Power is switched on and off via manual switches located on Xcalibur. The KMW200CCD chiller must be connected to Xcalibur, before operating the system.

  • Page 43: Initial Switch On Procedure

    OPERATION Power Control Type Location Effect Xcalibur Red switch Interface front panel, left; Power on / off to goniometer goniometer Inside front door of electronics interface rack X-ray Generator Turn ‘MAINS’ Generator front panel; Inside Power on / off to X-ray key switch front door of electronics rack generator...
  • Page 44 OPERATION CAUTION Always switch the CCD on / off via the mains switch on the KMW200CCD chiller. The CCD detector could be damaged if the ON/OFF switch on the CCD detector DC power supply is used. 3. Turn on power to KMW200CCD chiller unit using turn key switch on front panels (see relevant chiller manual) The CCD detector and video telescope camera will now start.

  • Page 45: X-Ray Tube Warm-Up Procedure

    OPERATION 9. Set required voltage and current on X-ray generator (see third party manual), observing maximum values quoted for the X-ray tube and also X-ray safety regulations. 6.3 X-ray Tube Warm-up Procedure WARNING When handling and using X-ray tubes particular care should be taken to avoid injury caused by exposure to the X-rays, exposure to high voltages, possible implosion of the vacuum tube and contact with Beryllium and Beryllium oxide.

  • Page 46: Software

    OPERATION 6.4 Software Normal operation of the Xcalibur system requires the use of the CrysAlis software, which contains two main applications named CrysAlis CCD and CrysAlis RED. CrysAlis CCD is used for control of the Xcalibur system during data collection, whereas CrysAlis RED is used for data reduction. The CrysAlis programs can be controlled either through command line input using short-cut commands such as dc s (data collection start) or via mouse driven menus.

  • Page 47: Software Installation

    OPERATION 6.4.2 Software Installation 6.4.2.1 MGC interface software The Xcalibur goniometer interface is mounted in the electronics cabinet of the Xcalibur diffractometer system. The interface contains an programmable EPROM and serves to translate the signals received from the diffractometer control PC and CrysAlis CCD into machine operations. As with any software the firmware loaded on this EPROM has version updates.

  • Page 48: Crysalis Software

    If you already have CrysAlis installed on your machine you will NOT need the CrysAlisBaseOD.exe. These files can be downloaded from the Oxford Diffraction web-site. You will also need the correction files which are specific to your Xcalibur diffractometer. Without these files the CrysAlis software is not fully functional.

  • Page 49: Normal Operation

    OPERATION 6.5 Normal Operation 6.5.1 General Commands 6.5.1.1 Image Area Statistics, Zoom and Histograms Position the Mouse cursor over the diffraction image window. Hold down the left mouse button and drag out a wire box around the area of interest. Click the right mouse button and select from various zoom options, area statistics / histograms, area pixel value replacement.
  • Page 50 OPERATION 6.5.1.3 Sm – Single Image Commands Single image omega, phi and theta scan photos can be recorded using the following commands: sm o startomegaangle scanwidth time omega scan sm p startphiangle scanwidth time phi scan sm t startthetaangle scanwidth time theta scan sm rp 360 degree phi scan in 30 secs...

  • Page 51: Changing Xcalibur Settings

    OPERATION 6.5.1.8 Writing to disk Current machine parameters, images and the contents of peak hunting tables can be written to disk. wd p write disk parameter settings. Saves the current machine parameters to disk wd i write disk image. Saves the current image to disk write disk peak hunting.

  • Page 52: Figure 6.5.2 Screenshot Of Ccd Parameters Window

    OPERATION Figure 6.5.2 Screenshot of CCD parameters window 6.5.2.2 Changing Beam stop Mask During data processing the area of the CCD which is obscured by the shadow of the beamstop is ignored. This is because a ‘’mask’’ has been defined in this area. The user can change the default values of this mask to suit their experimental needs.

  • Page 53: Figure 6.5.4 Screenshot Of Crysalis Program Options - Instrument Model I

    OPERATION Figure 6.5.4 Screenshot of CrysAlis program options – Instrument model I Figure 6.5.5 Screenshot of CrysAlis program options –beam stop settings A number of options are available for editing. The beam stop support orientation would not normally be changed from the default ‘top’ setting. To change the crystal to beam stop distance click on the button marked Edit X-stop.

  • Page 54: Figure 6.5.6 Screenshot Of Crysalis Program Options - Ph And Pt Size

    OPERATION To visualise the new beam stop mask type dc beamstop. To remove the mask type dc beamstop a second time. CAUTION The ‘wd cal’ command will overwrite the current diffractometer set-up file. Calibration of the diffractometer may be lost at this point if an invalid model exists. Once you are happy with the new settings you must save them to disk using the command wd cal.

  • Page 55: Standard Diffraction Experiment

    OPERATION Figure 6.5.7 Screenshot of CrysAlis profile inspector window 6.5.3 Standard Diffraction Experiment A standard crystallography experiment consists of 8 main steps: 1. Crystal mounting and alignment 2. Diffraction photographs to determine crystal quality 3. Unit cell determination 4. Data collection 5.

  • Page 56: Figure 6.5.8 Optical Alignment Of The Crystal

    OPERATION 5. Press Lower and 0 on the remote control. This will drive the goniometer to the correct orientation to allow optical alignment of the crystal. NOTE The settings lower and upper refer to the glass stick position on the video monitor Upper Setting Lower Setting Figure 6.5.8 Optical alignment of the crystal...

  • Page 57: Diffraction Photographs To Determine Crystal Quality

    OPERATION 6.5.3.2 Diffraction Photographs to Determine Crystal Quality 6.5.3.2.1 Single photograph Single diffraction images can be taken of a crystal to determine its quality. These diffraction photographs are taken without goniometer movement. 1. Type sm i time (time = exposure time in secs) NOTE Images are always taken as double exposures, to allow correction for zingers.

  • Page 58: Unit Cell Determination

    OPERATION Figure 6.5.10 Screenshot of axial photograph orientation screen 4. Type wd i to save the image to disk. 6.5.3.3 Unit Cell Determination A short data collection, typically of 5 minutes duration, is collected to enable fast unit cell determination of a crystal. Data collection is carried out in three sets of omega scans. These scans sample reciprocal space so as to independently define the three crystal axes.

  • Page 59: Figure 6.5.11 Screenshot Of Edit Data Collection Runs

    OPERATION Figure 6.5.11 Screenshot of Edit data collection runs 3. Start data collection by typing dc s. Complete experimental data when prompted and leave to collect data. NOTE Data collection may be interrupted at any time using the ‘Ctrl’ key or the ‘Stop’ menu.
  • Page 60 OPERATION NOTE To avoid having to redo peak hunting in the future save the current peak hunting table to disk using the command ‘wd ph’. 6. Find the unit cell parameters by typing um f NOTE In the case of unsuccessful indexation of a unit cell then the constraints applied to the unit cell lengths and angles can be relaxed or tightened.

  • Page 61: Data Collection

    OPERATION 6.5.3.4 Data Collection Now that we have determined the unit cell parameters we can proceed with the full data collection as follows: 1. In the program Crysalis CCD type dc editruns and follow the on-screen instructions, providing a filename for data collection. Figure 6.5.12 Screenshot of Edit data collection runs 2.

  • Page 62: Data Processing And Reduction

    OPERATION 6.5.3.5 Data Processing and Reduction Data processing and reduction is achieved using the CrysAlis RED application. This allows the conversion of raw experimental data into a format that is compatible with today’s crystallographic solution and refinement software. Data reduction cannot proceed until you have determined the unit cell parameters. During data reduction you will have the option to apply extinction laws, special corrections such as local background least squares and theta filters, reject outliers and specify output format and absorption correction.

  • Page 63: Run List

    OPERATION Figure 6.5.13 Screenshot of CrysAlis data reduction screen (crystal lattice) 6.5.3.5.2 Run List In this step the wizard requests the name of the run list and the image type. 1. Click on the button Browse run list, select the relevant data collection file and click on Next.

  • Page 64: Scan Width

    OPERATION 6.5.3.5.3 Scan Width The scan width is linked to the mosaicity of the sample. The default values are selected for a crystal of average quality. This number may need to be increased for a poor quality crystal. Click on Next. NOTE This number is not the frame width used during the run list editing.

  • Page 65: Special Corrections

    OPERATION Figure 6.5.16 Screenshot of CrysAlis data reduction screen (background evaluation) 6.5.3.5.5 Special Corrections When data have been collected using incorrect parameters this step will allow you to override the parameters written into the images. Standard data reductions should skip this step, simply clicking on the Next button. Figure 6.5.17 Screenshot of CrysAlis data reduction screen (special corrections) When the data reduction is for a difficult / poor sample a number of the special corrections may need to be applied / adjusted.

  • Page 66: Outlier Rejection

    OPERATION Limiting the 2 theta range Often when data reduction is unsatisfactory this is due to the fact that the crystal does not diffract to high angle. The default setting for maximum 2 theta threshold is 180 degrees. 1. As a guide examine a number of diffraction images and place the mouse cursor on the diffraction image at the position where diffraction is essentially zero.

  • Page 67: Output Format

    OPERATION Figure 6.5.18 Screenshot of CrysAlis data reduction screen (outlier rejection) 6.5.3.5.7 Output Format Select the required format of the output file and then click on Finish to start data reduction. Figure 6.5.19 Screenshot of CrysAlis data reduction screen (output format) During data reduction text information is output to the computer screen and listing (of selected outlier rejection) file (filename.lst).

  • Page 68: Changing The Output Format From Data Reduction

    OPERATION resolu- average mean mean tion(A) measured kept unique redundancy F2/sig(F2) Rint ------------------------------------------------------------------------- inf-1.66 1570 1559 50724.25 93.48 0.026 1.66-1.29 1834 1831 11.4 17633.54 39.76 0.030 1.29-1.12 1659 1654 10.3 10832.96 23.90 0.035 1.11-1.00 1503 1489 5639.11 13.81 0.043 1.00-0.93 1363 1356 4112.17...

  • Page 69: Absorption Correction

    OPERATION 6.5.3.7 Absorption Correction As X-rays pass through the crystal sample, a percentage of the X-rays will be absorbed by the sample. The degree of absorption is related to the distance travelled through the sample and also the composition of the sample. To minimise absorption a spherical crystal is ideal, however, this is often unobtainable.

  • Page 70: Figure 6.5.21 Screenshot Of 'Abs - Acquisition Of Movie Screen

    OPERATION Figure 6.5.21 Screenshot of ‘ABS – Acquisition of movie screen’ 5. Provide a crystal name and set parameters as required. Usually you would only record a movie in the lower Kappa position. NOTE Reducing the Phi step size to 4 degrees rather than 1 degrees greatly reduces the disk space required to save the movie.

  • Page 71: Figure 6.5.22 Screenshot Of Crystal Movie Screen

    OPERATION 1. Start the application CrysAlis RED and read in the experimental / data collection parameters by typing rd p. 2. Note that this is going to load the UB matrix, which you are using to evaluate the sample shape. Alternatively you may run dc rrp to re-load the parameters used in the data reduction.

  • Page 72: Figure 6.5.23 Screenshot Of Crystal Movie Configuration Screen

    OPERATION Figure 6.5.23 Screenshot of crystal movie configuration screen 7. Using the ‘Page Up’ and ‘Page Down’ buttons rotate the crystal image such that a crystal face is normal to the plane of the screen. This means that you are not looking onto the face, but glaze its surface.

  • Page 73: Figure 6.5.25 Screenshot Of Crystal Movie Screen

    OPERATION 9. The ‘Crystal shape – add face’ window is now displayed. Select the desired hkl values (real, integer or custom. It is up to the crystallographers’ judgement to choose real, integer or custom. On nicely shaped samples one should use custom and find the custom index with the lowest common denominator, e.g.

  • Page 74: Figure 6.5.26 Screenshot Of Crystal Movie Screen (Crystal Shape)

    OPERATION Figure 6.5.26 Screenshot of crystal movie screen (crystal shape) 13. At any time the faces you have added to the model can be observed / edited using the ‘Faces’ menu in the tool window. NOTE The ‘Faces’ menu in the tool window highlights invalid faces by a *. Invalid faces can occur when the user enters a wrong custom hkl or adds a face which invalidates other faces.
  • Page 75 OPERATION 14. Click on ‘Exit’ to leave the model builder. 15. Save the model to disk using the command wd p and supply a filename. NOTE Keep the intermediate results of your model building so that you can go back to a previous result.

  • Page 76: Figure 6.5.28 Screenshot Of Crystal Movie Screen

    OPERATION Figure 6.5.28 Screenshot of crystal movie screen 6.5.3.7.5 Step 5 – Apply Absorption Correction to Full data Once you have determined a satisfactory absorption correction model. Repeat dc rrp, tick the top right hand corner tick box marked ‘Apply absorption correction’ and output the absorption corrected data with a new file name.

  • Page 77: Gral - Space Group Determination

    OPERATION Rint without abs: 0.12472 Rint with abs: 0.04167 after optimisation Mu(mm-1): 18.00000; transmission factors min/max: 0.25061/ 0.44904 Absorption correction has a marked effect, as shown above. Rint has fallen from approximately 12.5% to 4%. 6.5.3.8 GRAL - Space Group Determination NOTE Data reduction must have been completed with a *.hkl and *.p4p file generated prior to space group determination.

  • Page 78: Figure 6.5.31 Screenshot Of The Gral Plug-In Load Window On Initialisation (No File Loaded)

    OPERATION Figure 6.5.31 Screenshot of the GRAL plug-in Load Window on initialisation (no file loaded) Figure 6.5.32 Screenshot of the GRAL plug-in Load Window (File loaded from DC_GAIN8.HKL) 3. Selecting the Show reciprocal space tick box provides a 2D view of reciprocal space and the distribution of data (by sigma) as depicted in Figure 6.5.33.

  • Page 79: Figure 6.5.33 Screenshot Of The Gral Plug-In Load Window (Reciprocal Space Visualiser)

    OPERATION Figure 6.5.33 Screenshot of the GRAL plug-in Load Window (Reciprocal space visualiser) 5. Next the lattice centring is determined. Figure 6.5.34 shows a table of statistics which allows the user to check the plug-in’s selection. If the user wishes to choose an alternative then the relevant ‘’radio box’’...

  • Page 80: Figure 6.5.35 Screenshot Of The Gral Plug-In Niggli Window

    OPERATION Figure 6.5.35 Screenshot of the GRAL plug-in Niggli Window 7. The GRAL plug-in provides a list of possible Bravais lattice and highlights in blue the programs’ preferred choice. Figure 6.5.36 shows the ORTHORHOMBIC P-lattice as the preferred choice. Clicking on ‘’Apply’’ will accept the plug-ins’ choice, however, anyone of the alternatives may be selected by clicking on the option in the text box and then clicking ‘’Apply’’.

  • Page 81: Figure 6.5.37 Screenshot Of The Gral Plug-In Centring Window (After Niggli Reduction)

    OPERATION Figure 6.5.37 Screenshot of the GRAL plug-in Centring Window (After Niggli Reduction) 9. The data are now examined for acentric or centric E statistics. The user can then choose between Centrosymmetric or Non-centrosymmetric settings by clicking on the relevant radio box and clicking on “Apply”.

  • Page 82: Figure 6.5.39 Screenshot Of The Gral Plug-In Space Group Window

    OPERATION Figure 6.5.39 Screenshot of the GRAL plug-in Space Group Window 11. Finally, GRAL prepares a *.ins file for use with structure solution programs. The user can edit the molecular formula and Z number in the relevant boxes shown in figure 6.5.40. Clicking on “Test”...

  • Page 83: Structure Solution And Refinement

    *.p4p These can be read into the following solution and refinement programs. These are free software and have NO connection with Oxford Diffraction. Jana 2000 – free download from http://www-xray.fzu.cz/jana/jana.html ShelX-97 – George Sheldrick’s solution and refinement software. Available free to academics.

  • Page 84: Figure 6.5.41 Screenshot Of Ewald Explorer Screen

    OPERATION Figure 6.5.41 Screenshot of Ewald explorer screen 4. Click on DragIndex. This will allow you to specify three non-collinear vectors to define a UB matrix and thereby a unit cell. 5. Click on the button b*-order radio button and then left mouse click on the lattice and drag out a vector as shown below.

  • Page 85: Figure 6.5.43 Screenshot Of Dialog Box Displayed When Exiting The Ewald Explorer

    OPERATION 7. Click on the button UM S to set the UB matrix based on the DragIndex vectors, and exit the Ewald explorer using the OK button and select Yes if you are happy with your results. Figure 6.5.43 Screenshot of dialog box displayed when exiting the Ewald explorer 8.

  • Page 86: Figure 6.5.45 Screenshot Of Ewald Explorer - Skip Reflections Invisible

    OPERATION Figure 6.5.45 Screenshot of Ewald Explorer – Skip reflections invisible 6.5.4.2 Intensity Selection of Reflections and Marking them as Skipped 1. With the ‘’Select’’ radio box selected, use the mouse to select ‘’Skip filter’’ from the menu bar at the top of the window. Select ‘’Intensity’’ from the drop down menu. Figure 6.5.46 Screenshot of Ewald Explorer –...

  • Page 87: Figure 6.5.47 Screenshot Of Ewald Explorer - Skip Filter Intensity Window (Use Intensity Filter)

    OPERATION Figure 6.5.47 Screenshot of Ewald Explorer – Skip Filter Intensity Window (Use Intensity Filter) 3. From the menu bar select the Flags menu and then Mark invisible skip. A window will appear asking you ‘Do you want to mark all invisible peaks skip?’ Click on OK. The ‘invisible’...

  • Page 88: Figure 6.5.49 Screenshot Of Ewald Explorer - Mark All Invisible Peaks Skip

    OPERATION Figure 6.5.49 Screenshot of Ewald Explorer – Mark All Invisible Peaks Skip 4. Clicking on the Show radio button ‘skip’ will not show these peaks since the intensity filter is still in use. To view these peaks go to the menu bar at the top of the Ewald explorer window and from the Skip filter menu select Intensity.

  • Page 89: Dc Movie - Replay Of Data Collection Movie

    OPERATION 6.5.5 Dc Movie - Replay of Data Collection Movie The CrysAlis software package enables the user to examine the whole of the data collection as a movie. The user can move back and forth through the data frames in single frame steps or play a continuous movie.

  • Page 90: Reconstruction Of Precession Photographs

    OPERATION 6.5.6 Reconstruction of Precession Photographs CrysAlis RED allows the user to reconstruct precession photographs. This is achieved via a wizard that guides you through the process and can utilise either the complete data set or the unique data. 1. The guided wizard is started by typing: dc unwarp 2.

  • Page 91: Figure 6.5.53 Screenshot Of Unwarp Wizard - Step 2: Open Run List

    OPERATION Figure 6.5.53 Screenshot of Unwarp Wizard – Step 2: Open Run List 4. If required adjust the number of runs / frames used in the unwarp reconstruction by clicking on the relevant run in the main text box. The whole line occupied by that run should be highlighted in blue.

  • Page 92: Figure 6.5.55 Screenshot Of Unwarp Wizard - Step 2: Select Output Directory

    OPERATION Figure 6.5.55 Screenshot of Unwarp Wizard – Step 2: Select Output Directory 6. Click on the ‘New layer’ button, define the required layer for reconstruction using the 3 vectors. Select 2d laue symmetry averaging if required. Use 2d laue symmetry averaging when the symmetry of the crystal is KNOWN.

  • Page 93: Figure 6.5.57 Screenshot Of Unwarp Wizard - Step 3: Add A Reconstruction Layer

    OPERATION Figure 6.5.57 Screenshot of Unwarp Wizard – Step 3: Add a Reconstruction Layer If required click on the tick box marked ‘background subtraction’. Click on Next. Figure 6.5.58 Screenshot of Unwarp Wizard – Step 4: Background Evaluation 8. Click on Finish. Xcalibur Version 1.5 Xcalibur_Manual_v1.5...

  • Page 94: Figure 6.5.59 Screenshot Of Unwarp Wizard - Step 5: Data Corrections

    OPERATION Figure 6.5.59 Screenshot of Unwarp Wizard – Step 5: Data Corrections The defined layer will now be reconstructed. An example of a reconstruction layer follows. Figure 6.5.60 An Example of a Reconstructed layer Xcalibur Version 1.5 Xcalibur_Manual_v1.5 Page 85 USER MANUAL...

  • Page 95: Dc Opti - Optimisation Of Data Collection Strategy

    OPERATION 6.5.7 Dc opti - Optimisation of Data Collection Strategy The CrysAlis system contains a powerful module for determining an optimal data collection strategy. This module is accessed through the command dc opti. NOTE An "optimal" data collection is calculated to meet the following user defined constraints: Time - exposure time and complete experiment.

  • Page 96: Figure 6.5.61 Screenshot Of Run List Optimiser

    OPERATION We would like to measure a sample with monoclinic Laue symmetry or higher to full completeness and 1.0 Å resolution. We assume that Friedel pairs are equivalent. We also choose only omega scans as they are the most precise. 1.

  • Page 97: Figure 6.5.62 Screenshot Of Run List Optimiser: Crystal Properties

    OPERATION Figure 6.5.62 Screenshot of Run List Optimiser: Crystal Properties 6. Click on the coverage radio buttion to see the current result. A pitiful 8.5% completeness and 2.5% coverage. 7. Click on the Optimize button. The Optimiser dialog appears. We will first find the optimal theta.

  • Page 98: Figure 6.5.64 Screenshot Of Run List Optimiser: Coverage Statistics

    OPERATION 8. Now we want to optimise kappa. Click on Optimize, and this time select only kappa and enter the values (From -80, To 80, Steps 10): The result is 92.8% (1: o -124.0 - 43.0 at - - 32.0 -30.0 0.0) 9.
  • Page 99 OPERATION plotting frame vs. coverage, completeness, redundancy. It is sometimes astonishing how much time is spend to get 5% more coverage / completeness. 13. Finally, we need to optimise the scan range. In dc editruns we set run two start end omega to 0 1 and in dc opti we optimize phi (From -180, To 180, Steps 10) and the scan range omega (From -170, To 170, Steps 10, range 30, enlarge 10).
  • Page 100 OPERATION Optimisation of 100 % Coverage Using the final run list from above. Try to work through the following example of how to optimise a list 100% coverage (which same with Friedel not equivalent!). 1. Click on Optimise and select theta, kappa and phi. Enter the following values for theta (From -35, Steps...

  • Page 101: Indexing And Data Reduction Of Incommensurate Samples

    OPERATION 6.5.8 Indexing and Data Reduction of Incommensurate Samples The CrysAlis RED program provides the user with the ability to examine and analyse incommensurate crystal structures. Incommensurates with q vectors in up to 3 directions can be handled. Samples that are both incommensurate and twinned can also be dealt with. 1.

  • Page 102: Indexing And Data Reduction Of Twinned Samples

    OPERATION 6.5.9 Indexing and Data Reduction of Twinned Samples When you suspect a twinned sample visualise the reflections using the Ewald explorer using the pt ewald command. 1. Using the Ewald explorer it should be possible to see that a number of unit-cells are present.

  • Page 103: Figure 6.5.65 Screenshot Of Data Reduction: Special Corrections

    OPERATION 6. During data reduction the number of ‘’active’’ buffers with unit cell UM S matrices assigned are automatically recognised by the data reduction module. 7. Follow the procedure for data reduction as described in section 6.5.3.5. On reaching STEP 5: Special corrections, click on the button ‘Special corrections properties’.
  • Page 104 OPERATION Xcalibur Version 1.5 Xcalibur_Manual_v1.5 Page 95 USER MANUAL...

  • Page 105: Extracting Data From Powder Samples

    OPERATION 6.5.10 Extracting Data from Powder Samples The Xcalibur and Sapphire CCD can be used to collect powder ring data (see figure 6.5.67). Simple powder patterns can be extracted from the images using the powder extract command. The data which is extracted from the powder image is output to the history window and also to the clipboard, allowing its transfer to a spreadsheet program for plotting.

  • Page 106: Refining Of Machine Parameter File

    OPERATION 6.5.11 Refining of Machine Parameter File 1. Mount and optically align the orthorhombic ylid test crystal (C S) (See normal operation) 2. In the Crysalis CCD program type dc editruns. 3. Import the run list named Xcalibur calibration.run and adjust the exposure time if required.

  • Page 107: Figure 6.5.70 Screenshot Of Refine Model (Constraining All Unit Cell Lengths To Be Equal)

    OPERATION Figure 6.5.70 Screenshot of Refine Model (Constraining all Unit Cell Lengths to be Equal) Figure 6.5.71 Screenshot of Refine Model (Constraining all Unit Cell Angles to 90 degrees) 9. Click on the tick box marked Goniometer until the box is empty. 10.
  • Page 108 OPERATION Residuals (wR form): 0.009309 0.001827 0.002769 0.006834 0.004917 0.006349 Resid: 0.014452 This gives a Resid(ual) refinement value. This should be close to 0.0000 but will typically be of the order of 1-2% (here 0.014452 or 1.4452%) when the machine model is correct. Check that this number is falling towards zero.

  • Page 109: Glossary Of Crysalis Commands

    OPERATION 6.5.12 Glossary of CrysAlis Commands Command Meaning Example abs display View movie recording and build absorption abs display correction routine abs grab Initiate movie recording routine for absorption abs grab correction af i Applies an attenuation filter af i af o Removes the attenuation filter af o...
  • Page 110 OPERATION speed parameter setting DL v N v [Deg]/[Sec] = phi scanning speed: 0.01 <= v <= 3.0 N = discrimination level: 0 < N <= 10000 End program and park goniometer Gain setting – amplification in the counting GA g chain g = gain for the counting chain.
  • Page 111 OPERATION geo loadcorrectionfile Load geometric correction file geo loadcorrectionfile gon check Stadi4 goniometer zero check gon check gon help help overview of gon commands gon help gon init Xcalibur goniometer initialisation gon init gon sync Stadi4 goniometer synchronization gon sync gon reinit Xcalibur goniometer re-initialisation gon reinit...
  • Page 112 OPERATION instrument model pt clear Clearing of the peak table pt clear pt a Add a peak to the peak table pt a pt ewald Initiate Ewald explorer pt ewald pt e Peak table edit pt e pt expand Peak table expand pt expand n mmin mmax intmin dmax dmin n = number of reflections required mmin = min order of difference -1 for CCD (-3 Point detector)
  • Page 113 OPERATION if rr_num >0 : interval = interval between reference reflections measured: 1 <= interval <= 32000 om_tol = requested omega repeatability: 0.0025 [Deg] <= om_tol <= 10 [Deg] int_tol = allowed intensity fluctuations parameter (number of sigmas by which a fluctuation triggers the recentering): 1 <= int_tol <= 100 h k l = Miller indices of ref.
  • Page 114 OPERATION sm r Measure a single reflection SM R h k l [psistart [psiend psistep]] h k l = reflection index, may be fractional. psistart = optional psi angle. psiend = optional psi start angle for measuring a sequence. psistep = optional psi step angle for measuring a sequence. sm s Single step scan SM S steps time...
  • Page 115 OPERATION [lengthdeviation angledeviation fractionindexed] = The defaults are 0.05, 0.1, 0.7. You can loosen this condition in case of an unsuccessful indexing: typically 0.3 0.3 0.5. um i Index and refine unit cell um i [indexrejectioncriterion] [indexrejectioncriterion] = rejection criterion which determines the maximum allowed deviation for which a reflection is considered indexed.

  • Page 116: Normal Shutdown

    OPERATION 6.6 Normal Shutdown 1. Gradually reduce to zero the voltage and current settings on the X-ray generator. When at zero press button marked ‘XR / OFF’ or ‘High Voltage OFF’ and where present turn key switch marked ‘MAINS’ to OFF position or else press button marked ‘Control Power ON’ 2.

  • Page 117: Mechanical Changeover Of Detectors And X-Ray Sources

    MECHANICAL CHANGEOVER OF DETECTORS AND X-RAY SOURCES 7. Mechanical Changeover of Detectors and X-ray Sources 7.1 Interchange of CCD Detectors The universal theta arm on the Xcalibur diffractometers facilitates rapid interchange between detectors. The following sections describe the installation and removal procedures for the Sapphire 2, Sapphire 3 and Onyx CCD detectors.

  • Page 118: Removal Of Sapphire 2 And Sapphire 3 Ccd Detectors

    MECHANICAL CHANGEOVER OF DETECTORS AND X-RAY SOURCES 9. When a good model has been refined store the new detector offset by typing ZC detector dd (where dd is the expected detector distance e.g. 50.0 mm – this will type a detector distance offset into the parameter file) then save the remaining parameters by typing wd cal.

  • Page 119: Figure 7.1.3.1 Mounting The Onyx Ccd - Rotated Mounting Rail With Screw Positions

    MECHANICAL CHANGEOVER OF DETECTORS AND X-RAY SOURCES 4. Drive the theta arm round to 90 degrees ‘gt t 90. Slide the CCD camera onto the slider on the theta arm. WARNING During the following steps, take care not to allow the camera to slide into the kappa block as the slider has very low friction.

  • Page 120: Figure 7.1.3.2 Mounting The Onyx Ccd - Position Of The Detector As It Is Mounted Onto The Rail

    MECHANICAL CHANGEOVER OF DETECTORS AND X-RAY SOURCES Figure 7.1.3.2 Mounting the Onyx CCD - Position of the detector as it is mounted onto the rail 7. Rotate Onyx to be parallel to the rail and continue pushing forward until the front screw hole is visible.

  • Page 121: Removal Of The Onyx Ccd Camera

    MECHANICAL CHANGEOVER OF DETECTORS AND X-RAY SOURCES 9. Finally slide the Onyx camera forwards until the block on the end of the drive shaft can be rotated upwards. 10. Turn the end fixing plate clockwise by 180 degrees and fix the CCD slider into place using two screws.

  • Page 122: Procedure For Interchange Of The Molybdenum And Copper Enhance X-Ray Source

    MECHANICAL CHANGEOVER OF DETECTORS AND X-RAY SOURCES WARNING During the following steps, take care not to allow the camera to slide into the kappa block as the slider has very low friction. The Onyx is a delicate electronic instrument. If dropped it may be damaged and warranty will be invalidated Due to the construction of the Onyx camera, it cannot be removed in exactly the same way as the Sapphire 2 and 3 cameras.

  • Page 123: Figure 7.2.1 Location Of Enhance Retaining And Adjustment Nuts

    MECHANICAL CHANGEOVER OF DETECTORS AND X-RAY SOURCES 6. Disconnect the top water pipe at the rear of Enhance X-ray tube shield and position a receptacle to catch the water contained within the tube shield 7. Wait until the water has drained out of the Enhance X-ray tube shield and then disconnect the bottom water pipe 8.
  • Page 124 MECHANICAL CHANGEOVER OF DETECTORS AND X-RAY SOURCES 15. Under the front of the Enhance X-ray tube shield unscrew the nut (1) found below the spring (see Figure 7.2.1) 16. Remove the nut (1), the spring and the two washers and put them aside for later 17.
  • Page 125 MECHANICAL CHANGEOVER OF DETECTORS AND X-RAY SOURCES 37. The vertical adjusting screws may need to be readjusted (one large screw under the plate near the front of the tube shield and two on either side of the tube shield near the rear) to optimise the vertical position of the beam on the crystal 38.

  • Page 126: Maintenance Schedules

    The user’s authorised service representative should carry out other tasks. If in any doubt about the performance of the Xcalibur, contact Oxford Diffraction. 8.2 Weekly Maintenance Schedule Tools and Materials:...

  • Page 127: Six Monthly Maintenance Schedule

    MAINTENANCE SCHEDULES 8.4 Six Monthly Maintenance Schedule This maintenance schedule should also be completed after adjustment of beam, collimator, CCD detector position etc. Tools: Ylid test crystal - (C Action Personnel Estimated task Estimated duration elapsed time 1. Refining machine parameter Authorised Operator 4 –...

  • Page 128: Hours Maintenance Schedule

    MAINTENANCE SCHEDULES 8.6 10,000 Hours Maintenance Schedule Tools and Materials: Set of Allen keys Set of flat-headed screwdrivers Water receptacle (e.g. Bucket) Special tools –special tool 1 and special tool 2 (see section 8 for identification) Action Personnel Estimated task Estimated duration elapsed time...

  • Page 129: Maintenance Instructions

    MAINTENANCE INSTRUCTIONS 9. Maintenance Instructions WARNINGS 1. Read and understand the Health and Safety Information section of this manual before performing any maintenance procedures. 2. Follow any local, national or international rules and guidelines that apply to this equipment when performing maintenance tasks. 3.

  • Page 130: Changing The X-Ray Tube Of Enhance

    MAINTENANCE INSTRUCTIONS Tools: Ylid test crystal - (C Procedure: See section 6.5.11 9.3 Changing the X-ray Tube of Enhance Task Time: 30 mis When: Sealed source X-ray tubes have a limited useful lifetime. Operation of a 3 kW tube at typical output of 2 kW will normally provide 10,000 hours of use (actual values may vary, see third party manual).

  • Page 131: Changing The X-Ray Tube Of Enhance Ultra

    MAINTENANCE INSTRUCTIONS WARNING Ensure that the X-ray tube is correctly mounted. Incorrect mounting may result in exposure of personnel to X-ray radiation. Red plastic spacers may need to be removed to ensure perfect fit of X-ray tube. 9. From the front of the Xcalibur insert the X-ray tube into the tube shield and secure. NOTE X-ray tube must be inserted the correct way up.
  • Page 132 MAINTENANCE INSTRUCTIONS Tools: Set of Allen keys Set of flat-headed screwdrivers Water receptacle (e.g. Bucket) Procedure 1. Turn off all power and water to the Xcalibur system, KMW200CCD and KMW3000C chiller units 2. Leave for at least 20 minutes to ensure that the X-ray tube is not hot (test temperature before proceeding).

  • Page 133: X-Ray Beam Stop Alignment

    MAINTENANCE INSTRUCTIONS 12. Xcalibur system, KMW200CCD and KMW3000C chiller units 13. Align X-ray optics as described below. 9.5 X-ray Beam Stop Alignment Task Time: <5 min When: As necessary Tools: Special tool ‘1’ Set of Allen keys Procedure 1. Set the X-ray generator to 20 mA and 10 kV. 2.

  • Page 134: Changing The Collimator Of Enhance

    MAINTENANCE INSTRUCTIONS Vertical adjust screw Horizontal adjust screw Figure 9.5.1 Beam stop adjustment screws 13. Repeat steps 5 and 6 until the X-ray beam is centred on the scintillation detector screen. 14. Check the position using the CCD detector. 15. The X-ray optics should now be aligned and ready for experimental use. NOTE The flexible end of the beam stop may be slid outwards by loosening the screw at the back.

  • Page 135: Changing The Collimator Of Enhance Ultra

    9.8 Aligning the X-ray Collimator of Enhance The X-ray collimator is factory aligned via the collimator housing. This means that re-alignment is not needed when changing between the collimators supplied by Oxford Diffraction. If collimator re-alignment is required please contact Oxford Diffraction for assistance.
  • Page 136 MAINTENANCE INSTRUCTIONS Enhance is available as an upgrade to the Xcalibur system and can be ordered using the part number below: Enhance (Mo) part number: XA-11-00-000-A Enhance (Cu) part number: XA-10-00-000-B Procedure Alignment of the Enhance X-ray source has been greatly simplified from the traditional sealed tube set-up.

  • Page 137: Figure 9.9.2 Enhance X-Ray Source Adjustments (Front View)

    MAINTENANCE INSTRUCTIONS 1. Vertical adjustment (for back of Enhance) 2. Horizontal adjustment screw 3. Locking screw for (4) 4. Vertical adjustment (for front of Enhance) 5. Screw holding the tube shield on the stand Figure 9.9.2 Enhance X-ray source adjustments (front view) 1.

  • Page 138: Aligning The Enhance Ultra X-Ray Source

    MAINTENANCE INSTRUCTIONS 9.10 Aligning the Enhance Ultra X-ray Source Task Time: 1 hour (from complete mis-alignment) When: After installation / movement Tools: Set of Allen keys Alignment Disc with 0.3 mm hole and scintillator front 9.10.1 X-ray Beam Alignment of Enhance Ultra Procedure CAUTION Do not put the CCD detector in the X-ray beam unless the generator settings are as...

  • Page 139: Figure 9.10.2 Schematic Showing The Rotated Beam Stop (Dashed Line Shows "Up" Position And Solid Line Shows "Down" Position)

    MAINTENANCE INSTRUCTIONS Figure 9.10.2 Schematic showing the rotated beam stop (dashed line shows “up” position and solid line shows “down” position). 1. Set X-ray generator settings to 30 kV and 1 mA. 2. Flip the beam stop to the UP position (see Figure 9.10.2) 3.

  • Page 140: Optic Alignment Of Enhance Ultra

    MAINTENANCE INSTRUCTIONS 12. Adjust the height pivot screw 3 (see Figure 9.10.1) and type card raw on 0.5. Repeat points 11 -12 to give a maximum intensity whilst retaining the sharply defined 45 degree square image. 13. Adjust the tilt screws 5(1) and 5(2) (see Figure 9.10.1) and type card raw on 0.5. Place the mouse cursor over the centre of the 45 degree square image.

  • Page 141: Aligning The Beam To The Centre Of The Goniometer - Enhance Ultra

    MAINTENANCE INSTRUCTIONS 2. We now need to align the collimator. Remove the 0.5 mm collimator cap by sliding it off. 3. Type card raw on 0.5. 4. Adjust the collimator x and y adjustment screws 7 and 8 (see Figure 9.10.1). Repeat 3 -4 until the X-ray beam is visible as a single intense circular spot.

  • Page 142: Checking The Door Safety Interlocks

    MAINTENANCE INSTRUCTIONS 9.11 Checking the Door Safety Interlocks Task Time: 2 minutes When: Once a week Tools: None Procedure WARNING Ensure the interlocks are not defeated. Interlock override key is not present or activated. No warning buzzer to be heard. If interlock defeated there is the risk of exposure to X-ray radiation.

  • Page 143: Checking The X-Ray Radiation Levels

    MAINTENANCE INSTRUCTIONS 9.13 Checking the X-ray Radiation Levels Task Time: 20 minutes When: Once a month Tools: Radiation meter Procedure 1. With the X-ray generator on (at normal settings) and the shutter closed, use the radiation meter to sweep the area around the X-ray tube housing, fast shutter and collimator for any radiation leak (inside the enclosure).

  • Page 144: Figure 9.14.1 View Of The Access Plates And Pump Out Ports Of The Sapphire And Onyx Ccd Detectors

    MAINTENANCE INSTRUCTIONS Sapphire 2 Access plate of Sapphire 2 CCD detector removed. Secured by one screw at centre. Pump out port (with ‘T’ tool attached) Sapphire 3 Access plate of Sapphire 3 (false front to head – spring loaded). Secured by 4 grub screws at corners (2 shown).

  • Page 145: Dismantling Xcalibur

    It doesn’t matter which pipe goes on which connection. 9.15 Dismantling Xcalibur Task Time: When: Personnel This procedure is normally performed by specially-trained Oxford Diffraction Personnel. Tools: Engine hoist/portable lifting device with soft slings capable of lifting 100 kg 1 set of Allen keys...
  • Page 146 MAINTENANCE INSTRUCTIONS Procedure WARNING When components have been removed from the system, ensure that they are put in a safe place, to prevent injury to personnel and/or damage to the components. Perform the Normal Shutdown Procedure. 2. Leave the system for 20 minutes to allow X-ray tube to cool down. 3.
  • Page 147 MAINTENANCE INSTRUCTIONS 4 persons are required to perform this step. 21. Remove goniometer. 22. Remove tabletop. 23. The Xcalibur system is now fully dismantled. Xcalibur Version 1.5 Xcalibur_Manual_v1.5 Page 138 USER MANUAL...

  • Page 148: Trouble Shooting

    TROUBLE SHOOTING 10. Trouble Shooting Symptom Fault Solution X-ray shutter will not 1. Protective cabinet doors are not Close doors properly open closed properly 2. X-ray generator signal light Check light connections and defective bulb. Replace bulb 3. Shutter-open and /or shutter Check light connections and closed lights defective bulbs...
  • Page 149 TROUBLE SHOOTING Click ‘enter’ Select ‘Detector’ and ‘drive relative +’. Click on ‘Start’. This will move the detector away from the goniometer axis in 1 mm steps. This should be repeated several times until there is a clear gap between the detector and the goniometer axis.
  • Page 150 TROUBLE SHOOTING operation the “Hsync” flags should read 1. This is located on the text line below the parameter button. Click on ‘OK’ 8. Type “gon reinit” in the command bar and press “enter”. This will reinitialise all drives and leave the goniometer in its home position ready for operation.

  • Page 151: Spares

    SPARES 11. Spares Fuses Device Location Value Package Designators Power distribution Electronics rack (rear 10 A / 250 V fast 5x20 mm panel) 10 A / 250 V fast 5x20 mm Fan panel Electronics rack (rear 315 mA / 250 V fast 5x20 mm panel) Cabinet illumination Electronics rack (rear...
  • Page 152 SPARES Bulbs Device Location Description Fast shutter Front panel MultiLED T5, 5 RED 12 V / 25 mA (Swisstac) Top panel of CCD MultiLED T5, 5 RED 12 V / 25 mA (Swisstac) camera MultiLED T5, 5 GREEN 12 V / 25 mA (Swisstac) Protective enclosure Inside (top) protective...

  • Page 153: Disposal Instructions

    DISPOSAL INSTRUCTIONS 12. Disposal Instructions 12.1 X-ray Tube and CCD Detector The X-ray tube and CCD detectors have beryllium windows. Dispose of Beryllium in accordance with local government regulations. 12.2 Third Party Equipment Refer to third party manuals for information about disposing of third party equipment. Xcalibur Version 1.5 Xcalibur_Manual_v1.5...

  • Page 154: Additional Information

    3K5 X-ray Generator Ital Structures optional DF3 X-ray generator Spellman optional Material Safety Data Sheet M10 Beryllium Brushwellman KMW200CCD chiller manual Oxford Diffraction optional KMW3000C chiller manual Oxford Diffraction optional Cryojet User Manual Oxford Instruments optional Cryostream User Manual Oxford Cryostreams...

  • Page 155: Drawings

    ADDITIONAL INFORMATION 13.2 Drawings 13.2.1 Mechanical Drawings Drawing no Title Number of pages OD-01-00-15-C Xcalibur Suggested Layout OD-01-00-01 System and Component Dimensions OD-01-00-15-C Xcalibur Suggested Layout OD-01-00-01 System and Component Dimensions Xcalibur Version 1.5 Xcalibur_Manual_v1.5 Page 146 USER MANUAL...
  • Page 156 ADDITIONAL INFORMATION Xcalibur Dimensions KMW3000C Dimensions KMW200CCD Dimensions Xcalibur Version 1.5 Xcalibur_Manual_v1.5 Page 147 USER MANUAL...

  • Page 157: Electrical Drawings

    ADDITIONAL INFORMATION 13.2.2 Electrical Drawings Drawing no Title Number of pages XCALIBUR 2 – BLOCK DIAGRAM INTERFACE CONNECTIONS EC-00-00-001-A GONIO68332 INTERFACE CONNECTIONS DIAGRAM EC-24-01-001-A GONIO68332 ENCODERS (RS485) CABLE EC-02-01-001-A GONIO68332 STEPPER MOTORS CABLE EC-04-09-001-A GONIO68332 INTERFACE RS232 CABLE EC-04-02-001-A GONIO68332 CCD POWER SUPPLY TO PC (RS232) EC-02-04-001-A GONIO68332 SHUTTER INDICATOR EC-24-04-001-B...
  • Page 158 ADDITIONAL INFORMATION EC-24-07-001-A GONIO68332 SAFETY CONNECTIONS GONIO68332 SAFETY MODULE CONNECTIONS XCALIBUR GONIOMETER – ELECTRICAL DIAGRAM Xcalibur Version 1.5 Xcalibur_Manual_v1.5 Page 149 USER MANUAL...

  • Page 159: Ce Conformity Notice

    ISO/IEC Guide 22, 1982, “Information on manufacturer’s declaration of conformity with standards or other technical specifications." Oxford Diffraction’s liability under this declaration is limited to that set forth in the current Oxford Diffraction’s Terms and Conditions of Sale. __________________________________________________________________________________...

  • Page 160: Appendices

    Appendices Appendix 1 X-ray Tubes Wave Lengths Κα Κα Κβ Κα /Κα Anode 2.28976(2) 2.293663(6) 2,08492(2) 1.00170 1.78901(1) 1.79290(1) 1.62083(2) 1.00217 1.540598(2) 1.544426(2) 1.39225(1) 1.00248 0.7093187(4) 0.713609(6) 0.632305(9) 1.00605 0.5594214(6) 0.563812(4) 0.497081(4) 1.00785 0.180199(2) 0.185080(2) 0.158986(3) 1.02709 Appendix 2 Standard Crystal Parameters Compound name: Ylid (2-Dimethylsulfuranylidene-1,3-indandione) Compound formula:...
  • Page 161 completed as directed in this manual. Other maintenance records should be kept as required by any local, national or international regulations. Weekly Maintenance Record Sheet Week Date of Name of person Signature Comments maintenance performing test Xcalibur Version 1.5 Xcalibur_Manual_v1.5 Page 152 USER MANUAL...
  • Page 162 Weekly Maintenance Record Sheet Week Date of Name of person Signature Comments maintenance performing test Xcalibur Version 1.5 Xcalibur_Manual_v1.5 Page 153 USER MANUAL...
  • Page 163 Weekly Maintenance Record Sheet Week Date of Name of person Signature Comments maintenance performing test Monthly Maintenance Record Sheet Month Date of Name of Signature Emergency X-ray Comments maintenance person Stop Check radiation performing check OK? test Xcalibur Version 1.5 Xcalibur_Manual_v1.5 Page 154 USER MANUAL...
  • Page 164 Six Monthly Maintenance Record Sheet Date of Name of Signature Comments maintenance person performing test Yearly Maintenance Record Sheet Date of Name of Signature Machine CCD detector Comments maintenance person parameter vacuum performing file refined? pumped? test Xcalibur Version 1.5 Xcalibur_Manual_v1.5 Page 155 USER MANUAL...

  • Page 165: Appendix 5 Example Of Local Rules For The Xcalibur System Set Up At Oxford Diffraction

    Appendix 5 Example of Local Rules for the Xcalibur System Set Up at Oxford Diffraction An example of the Local Rules for the Xcalibur system set up at Oxford Diffraction is provided for information Xcalibur Version 1.5 Xcalibur_Manual_v1.5 Page 156...

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