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User Manual - Agilent Technologies

1. 6 Emergency stop has been pressed Ensure emergency stop has not been pressed generator will also not function If yes twist to release and turn off on the interface Goniometer will not move Goniometer will not move when the cabinet is open Press and hold the two Motion Enable buttons simultaneously to allow the goniometer to move Water Cooler Symptom Fault Solution Xcalibur USER MANUAL Version 2 4 Page 64 TROUBLESHOOTING Unit cannot be turned on from the front panel Mains power is not connected Connect mains power at the rear panel Level error LED lights after switching on module Reservoir water level is too low Fill the Reservoir with coolant pre mixed solution of 9096 distilled water and 1096 of glycol Flow error LED lights after switching on module Some air bubbles remain in the water circuit Turn off and on the device If needed repeat the procedure a few times to get rid of the air in hoses and pipes Flow error LED flashes during operation Liquid cannot flow through the internal circuit through CCD detector Check if the hoses are properly connected and valves are open Check if the filter is not blocked and clean it if necessary Reservoir error LEDs lights Reservoir cable is not connected Turn off the Water Cooler power supply at the front panel Connect Reservoir cable to the unit Turn on the u
2. o0 gt tr Close the filling port 7 Hold the side panel in the middle of the left and right edges and carefully lift it and tip the top edge towards the rack to engage it onto two hooks inside the top edge Lower the side panel to be vertical and check it is hanging symmetrically between the front and rear sides of the rack Lock the panel into place at the top and bottom using the cabinet key 8 If the water chiller of the CCD detector had shut down due to the level error then open the front door of the electronics rack switch off the water chiller using the front panel illuminated switch wait 55 and switch on again 9 The system should then restart automatically Observe that the level error LED is not illuminated on the front of the water chiller 10 Close the front door of the electronics rack Xca l i b u r Version 2 4 USER MANUAL Page 59 9 Trouble Shooting TROUBLESHOOTING Symptom Fault Solution X ray shutter will not 1 Protective cabinet doors or side Close doors and side panels properly open panels are not closed properly 2 X ray generator signal light defective Check light connections and bulb Replace bulb 3 Beamstop is in up position Move beamstop to down position to block x ray beam 5 Shutter open and or shutter closed lights defective Check light connections and bulbs including the one on the beamstop mounting arm Replace bulbs 6 Protective cabinet
3. 10 PAROS l i b u r Version 2 4 USER MANUAL Page 7 TOT EUSeS 66 10 2 Bulbs cine e eate edet iret 66 11 Disposal Instructions 67 11 1 X ray Tube and CCD Detector 67 11 2 Third Party Equiprrient iiie Pelei als 67 12 Additional Information 66 12 1 Third 1 68 12 2 DraWiN S a ERE 69 Table of Figures Figure 1 Components of a typical Xcalibur Gemini system cesses eene nennen nnne 21 Figure 2 Computer and 21 Figure View of a typical diffractometer 111 senes nnne nn nennen nennen 22 Figure 4 Goniometer phi kappa omega and theta axes shown on a typical diffractometer 23 Figure 5 Water distribution panel and reservoir Gemini 24 Figure 6 Satety IO i 25 Figure 7 10 Device Control 25 Figure 8 Location of s
4. Page 62 TROUBLESHOOTING Symptom Fault Solution 2 Emergency stop button pressed Release the emergency stop button by twisting clockwise and follow the instructions on PC screen Power off interface wait b seconds and then power on Wait 15 seconds for interface to initialise Type gon reinit in CrysAlis and press enter This will reinitialise all drives and return the goniometer to the position it was at when the emergency stop button was pressed Goniometer movement error Goniometer stopped after collision or blockage prevents movement Remove the blockage from the goniometer and follow the instruction on the PC screen Power off interface wait b seconds and then power on Type gon reinit in CrysAlis e and press enter This will reinitialise all drives and return the goniometer to the position it was at when the movement error occurred If the error persists then close and reopen the CrysAlisPro software When the software initialises it will test the goniometer slits definitions and if a fault is found it will ask the user to re run the slit definition Follow the instructions on the PC screen Strange artefacts on CCD images lines blocks chequer board 1 Errors occurring on Ethernet communication between detector and PC 1 Reset the CCD detector by switching off the Water Cooler power on the front panel waiting 10s and restarting 2 Clo
5. c ccccccsesescseseceeeaeseaeaeaeaeaeaeaeaeaeaeaeaeaeaeaeaeaeaeaeaeaeaeaeaeaeanaes 46 7 4 Six Monthly Maintenance Schedule c ccscssscsccccseeeeeeeaeeeaeeeaeaeaeaeaeaeaeaeaeaeaeaeaeaeaeaeaeaeaeaeaes 46 7 5 Yeaily Maintenance Schedule erc eee fees citet vec vat aevo nena 46 7 6 10 000 Hours Maintenance Schedule uuueeeeeeeeeeseseeeeeeee eene nennen nnn nnn nnn nera rn nnns 47 8 Maintenance Instructions eee een nennen nnn neos 8 1 Refining the Machine Parameter 9 48 8 2 Aligning the Video 2 44 110 nennen nennen nnns nnne nnns sd sten nnne ennt 49 8 3 Checking the Door Safety 51 8 4 Checking the Emergency stop ccccccceeeeeeneececeeeeeeeeaaeaeceeeeeeeccaaeaeeeeesesesecaaeaeeeeeeeseescnieeeeeeeess 51 8 5 Checking the X ray Radiation enne nennen tenentes nnns 52 8 6 Pumping Out Vacuum of CCD detector ener eren 52 8 7 Aligning Low Temperature Attachment 54 8 8 Cleaning Water 56 8 9 Refilling water FeServol ice tte 59 9 Trouble 5 6 2 E
6. 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 During operation there is an acceptable level of X ray radiation as based on the recommendations on risk published by the International Commission of Radiological Protection ICRP and endorsed by the National Radiological Protection Board NRPB in the UK For use in the UK the lonising Radiations Regulations 1999 should be adhered to For countries outside the UK the appropriate laws apply such as registration and inspection Customers should be aware of their duty of safety to their employees and visitors and should consult national authorities to determine local operational requirements Xcalibur Version 2 4 USER MANUAL Page 12 HEALTH AND SAFETY INFORMATION To prevent injury to personnel and possible damage to the equipment please note the following guidelines 1 Only authorised personnel who have received appropriate instruction and are aware of the laboratory rules that govern the use of this type of system should operate the system 2 Never dismount the beam stop when the system is operational 3 Do not operate the system without the collimator unless performing the beam alignment procedure 4 Use appropriate X ray detection equip
7. remaining circuits of the instrument 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 Agilent Technologies if you have any suggestions for corrections or improvements to this manual Service and support is available for technical and operational issues as indicated below e Web www agilent com chem contactus e E mail XRDSupport agilent com Phone 44 0 1865 291600 between 8 a m and 4 30 p m UK time Monday to Friday Fax 44 0 1865 291601 Agilent Technologies acknowledges all trademarks registrations Copyright 2014 Agilent Technologies 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
8. 24 Water filters and 11000000 en eren enne sese nns 56 Figure 25 Xcalibur Gemini Suggested 0 0 110000 eene nennen nennen nnns 69 Figure 26 Xcalibur Gemini System 70 Xcalibur Version 24 USER MANUAL Page 8 HEALTH AND SAFETY INFORMATION 1 Health and Safety Information 1 1 General In normal operation the system is designed to operate safely All users of Xcalibur Gemini 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 Indicates warning or caution If you see this symbol on a product you must refer to AN the manuals for specific Warning or Caution information to avoid personal injury or damage to the product 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 This instrument produces X rays when energised CANADA WARNING Radiation Hazard This instrument produces X rays when energised CAUTION Risk of finger squeeze
9. as defined in FAR 52 227 19 1 2 June 1987 U S Government users will receive no greater than Limited Rights as defined in FAR 52 227 14 June 1987 252 227 7015 b 2 November 1995 as applicable in any technical data Safety Notices CAUTION A CAUTION notice denotes a hazard It calls attention to an operating procedure practice or the like that if not correctly performed or adhered to could result in damage to the product or loss of important data Do not proceed beyond a CAUTION notice until the indicated conditions are fully understood and met A WARNING notice denotes a hazard It calls attention to an operating procedure practice or the like that if not correctly performed or adhered to could result in personal injury or death Do not proceed beyond a WARNING notice until the indicated conditions are fully understood and met Safety Summary General Safety Precautions The following general safety precautions must be observed during all phases of operation of this instrument Failure to comply with these precautions or with specific warnings elsewhere in this manual violates safety standards of design manufacture and intended use of the instrument Agilent Technologies Inc assumes no liability for the customer s failure to comply with these requirements Before operation review the instrument and manual for safety markings and instructions You must follow these to ensur
10. authorised personnel as often as required by local rules 7 2 Weekly Maintenance Schedule Tools and Materials None Action Personnel Estimated task Estimated elapsed duration time 1 Check door safety interlocks Authorised Operator 2 minutes 2 minutes Xcalibur Version 2 4 USER MANUAL Page 45 MAINTENANCE SCHEDULES 7 3 Monthly Maintenance Schedule Tools and Materials none Action Personnel Estimated task Estimated elapsed duration time 1 Check Emergency Stop Authorised Operator 10 minutes 10 minutes 7 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 10 11502 Set of Allen keys Action Personnel Estimated task Estimated elapsed duration time 1 Refining machine parameter file Authorised Operator 30 mins 4 5 hours 2 Check alignment of video Authorised Operator 30 mins 30 mins microscope 3 Check alignment low temperature Authorised Operator 30 mins 30 mins attachment if fitted 4 Cleaning water filters Authorised Operator 30 mins 30 mins 5 Refilling water reservoir Authorised Operator 30 mins 30 mins 7 5 Yearly Maintenance Schedule Tools and Materials Special T tool carried by Agilent Technologies service engineer Phillips screw driver Rotary vacuum pump capable of obtaining a pressure of 1 10 mbar Vacuum tubing an
11. e eA er 31 5 3 St0fdg8 aito ete b 32 6 6 1 Controls and Indicators Ree deret Idee eri 33 odes fente nex proe C reete E 33 Mum MN M 33 6 1 3 Eist of ebd 35 6 2 X ray SOUICQ gt Re eem tait tuni E 36 6 21 generatii EE 36 0 2 2 Water COOMIMG T 36 6 2 3 eain adidas 37 6 2 4 Safety shutter operation cte dediti ee atre Eo idet 37 6 2 5 Beamstop rotation 37 6 3 System St rt Up intet eon aei 38 6 4 Switching the wavelength Gemini 39 6 5 System Standby and Normal Shutdown 43 6 6 Emergency Shutdown ccccccceeeeeececeeeeeeeeeeaeceeeeeeeseeaaeaeceeeeeeesceaeaeeeeesesesecaeaeeeeeeesesennieeeeeeeess 44 6 6 1 Emergency Shutdown Procedure 44 7 Maintenance Schedules 45 FA eren Tei o e 45 7 2 Weekly Maintenance Schedule uuueeeeeeeeeesesseeeeeee enses ne nnn nnn 45 7 3 Monthly Maintenance Schedule
12. filter sieve and the cap ensuring it is fitted correctly and the o ring is in place 9 For Gemini instruments repeat for the second X ray source filter 10 Turn on the KMW3000 or TF3500 water cooler using the front mounted key switch or button 11 Open the front door of the electronics rack and locate the CCD water cooler at the bottom 12 Only in the case of an error light on the CCD water cooler turn the cooler off using the front panel mounted power switch wait 5 seconds and turn on again After about one minute the CCD detector should restart 13 Check the filter caps are secure and not leaking liquid Repair if necessary 14 Hold the side panel in the middle of the left and right edges and carefully lift it and tip the top edge towards the rack to engage it onto two hooks inside the top edge Lower the side panel to be vertical and check it is hanging symmetrically between the front and rear sides of the rack Lock the panel into place at the top and bottom using the cabinet key 15 Close the front door of the electrical rack 16 Close and re open the CrysAlisPro software to ensure re connection to the CCD detector 17 Ramp up the active X ray source to the required power 8 8 2 KMW3000 water chiller filters Please refer to the separate user manual for KMW3000 for information on the type of water filters and the procedure for replacing them Xca l i b u r Version 2 4 USER MANUAL Page 58 MAINTENANCE INSTRUCTIONS 8 9 Refi
13. generator off Switch off Generator HV power is off HV sensor and cable switching Turning generator on Next Tube water cooling CrysalisPro Figure 11 Software dialog for wavelength change Gemini only 4 Click the switch off button and the software will then automatically ramp down the X ray generator to zero settings and then turn off HV Click first Next button 5 Open the rear door of the electronics rack this will cause the HV generator interlock to open and X rays cannot be generated Xca l i b u r Version 2 4 USER MANUAL Page 39 OPERATION 6 Turn off the HV generator using the switch on the rear panel Source Select plug Parked HV cable Figure 13 HV cable parking position with Source Select plug Gemini only 7 Unscrew the HV cable from the back of the generator 8 Locate the second parked HV cable above the system interface in the rear of the electronics rack 9 Remove the HV cable from its parking position and also remove the indicator plug from the Source Select PS 06 socket see Figure 13 10 Move that HV cable from the parking position down to the HV generator and screw it in 11 Take the unused HV cable to the parking position and screw it in 12 Be sure to attach the indicator plug for that cable into the Source Select PS 06 socket next to the HV cable parking position Click second Next button 13 Turn on the HV generator using the switch on the rear panel
14. heavy and require careful handling Use safe lifting procedures for heavy items to prevent possible strain injury 1 4 Safe Mechanical Practice 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 Agilent Technologies to carry out service work on this equipment are permitted to service the equipment Water connections should be made and tested in accordance with any local and national safety regulations 1 5 Mechanical stress The protection cabinet housing protects personnel from exposure to various risks including electrical mechanical thermal and electro magnetic radiation Care should be taken to avoid mechanical damage of the cabinet housing The metal panels of the housing shield the device against an impact energy of up to 5J whereas the transparent window in the front door is resistant to an impact energy up to 1J 06 rating If damage is found on the enclosure panels or window then stop using the instrument immediately and inform Agilent Technologies 06 Protect the window against mechanical damage Do not use the instrument if the window is broken Xcalibur Version 2 4 USER MANUAL Page 11 HEALTH AND SAFETY INFORMATION 1 6 Moving Parts There are a number of moving parts in the system which are powered by electric motors Injury could result if clo
15. high voltage cannot be applied until cooling water is flowing normally Do not switch off the water supply while the X ray tube is operational since this will cause it to shut down quickly and this will shorten the lifetime of the tube The tube should first be ramped down slowly to zero power before stopping the water flow 6 2 3 Temperature Sensor The X ray source contains a high temperature cut off switch This switch is connected to the HV generator unit interlock circuit If the temperature of the tube exceeds the limit then the HV generator will shut down the high voltage in order to allow the tube to cool down Such overheating may be caused by failure of cooling water supply or by a fault inside the X ray tube Do not turn on the tube again until the fault has been discovered and corrected 6 2 4 Safety shutter operation The safety shutter will only open if the safety interlocks are closed This shutter is automatically controlled and will close if the interlock opens If the beam stop is open then an intermittent alarm will sound The fast shutter also cannot be opened if the interlock is open If the protection cabinet is opened while the two shutters are opened then the interlock circuit is opened and causes the two shutters to close automatically 6 2 5 Beamstop rotation operation The beamstop may be rotated between down and up positions The down position is for normal operation and covers the primary beam or two beams
16. in the case of a dual source SuperNova to prevent them from reaching the CCD detector The up position moves the beamstop 90 degrees towards the rear of the instrument and thus opens access around the crystal position to aid crystal mounting especially when mounting in liquid nitrogen underneath Cryojet cooling is required The beamstop must be moved back to the down position before making an X ray exposure The beamstop contains an interlock switch which will result in a beeping noise sounding when the beamstop is in the up position and will also prevent the X ray shutter from opening The software collision model of the instrument assumes the beamstop is in the down position Therefore do not move the goniometer axes while the beamstop is in the up position since a collision might occur When moving the beamstop between positions take care not to strike the CCD detector beryllium window with the end of the beamstop If this happens then the beamstop may become misaligned and in the worst case the beryllium window may be damaged The beamstop handle is rotated by hand gripping it in the position shown in the figure below Pulling the beamstop handle forwards and downwards will rotate the beamstop from the down to the up position The opposite movement will return it to the down position The beamstop will be felt to click into position at both the up and down positions Xca i b u r Version 2 4 USER MANUAL Page 37 OPERAT
17. workstation The control program stores the data for further data analysis to the hard disk The five goniometer axes are driven by microprocessor controlled stepping motors with 12 800 microsteps per revolution Figure 4 Goniometer phi kappa omega and theta axes shown typical diffractometer The sample is aligned using a CCD video microscope The sample picture is displayed on the control PC A high brightness LED lighting system provides brilliant high contrast illumination of the sample at all goniometer positions 4 2 Mo Cu X ray Source This source unit contains a long fine focus Mo or Cu X ray sealed tube dual shutter pre aligned graphite monochromator exchangeable collimator and X ray beamstop The sources are positioned with manual adjustment screws The sources require water cooling by a water cooler such as the KMW3000C from Agilent Technologies which is described in a separate manual The X ray tube is connected to the HV generator unit The range of voltage is 10 60kV The supplied high voltage cable should be connected between the X ray tube and the HV Generator The X ray source contains both a fast shutter and a safety shutter The safety shutter is for safety purposes only and cannot react fast enough to make time controlled exposures of a CCD detector Fast exposures are created using the fast shutter The source also contains an over temperature safety switch 4 3 X ray Generator T
18. 4 USER MANUAL Page 34 6 1 3 List of indicators OPERATION Indicator Location Meaning Orange light X ray Red light Shutter open Green Light Shutter closed Red light Shutter open Outside top right of the protective enclosure Outside top right of the protective enclosure Outside top right of the protective enclosure Inside on beamstop mounting arm X ray power is on X ray shutter open X ray shutter closed X ray shutter open Orange LEDs Generator front panel right Inside front door of electronics rack High voltage is ON Interlock is closed thus enabling shutter operation Red LEDs Generator front panel right Inside front door of Interlock is open thus disabling electronics rack shutter operation Error status as indicated Green LEDs Water cooler front panel right Inside front door of Water cooler circuit for CCD Orange LEDs electronics rack Water cooler front panel right Inside front door of electronics rack detector is operational Water cooler circuit for CCD detector has closed interlock for CCD operation to be activated Red LEDs Water cooler front panel right Inside front door of Water cooler circuit for CCD electronics rack detector has an error as indicated Xca b u r Version 2 4 USER MANUAL Page 35 OPERATION 6 2 X ray Source Figure 9 Two X ray sources mounted on Gemini diffractometer 6 2 1 X ray generati
19. Click third Next button Xca l i b ur Version 2 4 USER MANUAL Page 40 OPERATION 14 Close the rear door of the electronics rack this will cause the HV generator interlock to close 15 Open the left side panel of the electronics rack by turning the locks at the top and bottom using the same key used to open the protection cabinet doors Hold the side panel in the middle of the left and right edges and carefully lift it forwards it is supported by two hooks inside the top edge and then lower it to the floor Stand the panel in a safe place where it will not fall over The side panel is heavy and should be held in the middle of the left and right edges to avoid the risk of finger trapping underneath the panel Take care to lower the panel gently to the floor without trapping hands or feet underneath 16 Turn the manual valve see Figure 14 Water switching valve on the water system by 90 degrees to the position for the selected wavelength NOTE the selected water valve position and the selected HV cable in the generator must be for the same wavelength Switching valve Figure 14 Water switching valve Gemini only in Mo position Figure 15 Water switching valve Gemini only in Cu position Xcalibur Version 2 4 USER MANUAL Page 41 OPERATION 17 Hold the side panel in the middle of the left and right edges and carefully lift it and tip the top edge towards the rack to engage it onto two hooks inside the t
20. ER MANUAL Page 14 INTRODUCTION 2 Introduction 2 1 Scope This manual applies to the Xcalibur Gemini system designed and manufactured by Agilent Technologies 2 2 How To Use This Manual This manual is aimed at operators and maintenance personnel of the Xcalibur Gemini system Operators of the system should be computer literate familiar with X ray diffraction techniques have had training in the use of the Xcalibur or Gemini system by Agilent Technologies staff and have had training about radiation safety This manual is intended to provide operators with a practical guide to the system and its operation This is intended to familiarise the user with how the system works and provide a better understanding of the system operation All personnel who are likely to operate the system or who are likely to come into contact with any of the system components should read the HEALTH AND SAFETY INFORMATION section of the manual This provides basic information aimed at highlighting the safety hazards associated with the equipment More detailed information and instructions for component parts of the system are given in the third party manuals supplied with the system which are listed in this manual These manuals should also be read and understood before operating the system The purpose of this manual is to e explain how to operate the equipment e explain how to interface to the equipment e list performance characteristics of the eq
21. F12 command from the CrysalisPre software 5 Adjust the Helijet alignment screws until the alignment tip nearly comes in contact with the end of the metal pointer By screwing in all of the alignment screws equally the Helijet will move down towards the pointer and vice versa By screwing in only one of the alignment screws the Helijet will move sideways relative to the pointer 6 Ensure all four of the adjustment screws are touching the support ring and are not loose in space above the ring 7 Ensure all four attachments screws are tight so that the Helijet remains clamped in the aligned position 8 Remove the goniometer head 9 Remove the alignment tip 8 8 Cleaning Water Filters 8 8 1 System water filters The system includes water filters mounted inside the left side of the electronics rack These are visible on Figure 24 The CCD coolant filter is present on all versions of the system Xcalibur instruments which have one X ray source will have one X ray source coolant filter and Gemini instruments will have two filters one for each source Reservoir filling port CCD coolant filter X ray source s coolant filters Figure 24 Water filters and reservoir Xcalibur Version 2 4 USER MANUAL Page 56 MAINTENANCE INSTRUCTIONS In order to clean the CCD coolant filter the CCD detector will need to be turned off for a period of time while the filter is opened This will cause the CCD to warm up and therefore this proce
22. ION Figure 10 Rotating the beamstop position 6 3 System Start Up Safety devices in the diffractometer protect against damage to the system and the operator during start up The following initial switch on procedure should be followed 1 Plug in all mains power cords to their wall mounted sockets system accessories 2 Ensure that the external circuit water valves are turned on 3 Open all water valves on the KMW3000C water cooler if installed 4 Turn on the KMW3000C or TF3500 water cooler using the key switch button on the front 5 Open the front door of the electrical rack and switch on the top red switch Turn on the CCD Water Cooler red switch on front panel 7 During the start up phase all error status LEDs will be illuminated When they are turned off the unit is operating normally 8 Only when start up has completed successfully the CCD detector will be supplied with power 9 Allow 60 minutes for the CCD detector to cool the Peltier and chip to 40 C CAUTION The CCD detector requires 60 minutes cool down time Allow another 6 hours cool down time for all internal parts to equalise in temperature and give optimum detector performance 10 Turn on the interface using the red switch located on the left side of the interface front panel and wait 10 seconds Ensure 2 green LEDs are illuminated on the right of the interface 11 Confirm the PC has powered up automatically If not then manually resta
23. S OUI GB 23 4 3 X rdy GeneratoT crac oe ide etel ite tette tiet ee 23 4 4 Water Cooler for detector nennen nnns 24 A Electronics Rat Kinect un er eese creto a Deve danda tamea ewe oe 24 4 5 1 Water distribution enne nn nnns nsns 24 4 5 2 10 Device for safety interlocks ueeeeeeeeeeeeeeeeeeee eene nn nennen nena nnt 25 45 3 Ethernet swite We rrr tt tea tr etti teta eee ie e Pe rae exe adv 26 ALG SoftWare cc tinet ta sin dca ien ed oec 26 4 7 Low Temperature enne a 26 Version 24 USER MANUAL Page 6 AB Satety Features contes tttm 26 5 Handling Installation Storage and Transit Information 27 5 1 Reception and Handlirig nr Fra te ie Ur te t itta Pre tee rea E ne ore ley duos 27 RM MNT ERI 27 5 1 2 Unpacking Part edu EH Pare E 27 5 1 3 Mechanical 28 5 2 Installation and Setting to 29 5 2 1 Preparation of Site and nnns 29 5 2 2 WOTK s eee ate ete vd EN P EEG vt 31 52 1 Installation Procedures ihe tede tede te
24. SER MANUAL Page 4 APPENDICES Six Monthly Maintenance Record Sheet Date of Name of person Signature Comments maintenance performing test Yearly Maintenance Record Sheet Date of Name of person Signature Machine CCD detector Comments maintenance performing test parameter file vacuum refined pumped Y N Y N Xcalibur USER MANUAL Version 2 4 Page 5 Agilent Technologies Inc Printed in Poland October 2014 E Agilent Technologies
25. T tool carried by Agilent Technologies service engineer 1 set of Allen keys Rotary vacuum pump capable of obtaining a pressure of 1x10 mbar or if available turbo molecular pump Vacuum tubing and adaptor Procedure 1 Switch off the CCD Water Cooler 2 Wait for 12 hours for the detector to warm up 3 Unscrew cover from pump out port see below For the Eos detector this is underneath the collision protection cover which is removed by loosening four screws as shown in below On the S2 detector range the pump out port is accessed from the rear end of the detector by removing a circular cover as shown in Figure 20 below by inserting the appropriate hexagon key and rotating anticlockwise until the cover becomes loose and drops out 4 Screw into place the T tool the S2 detector range requires a longer version of this tool which is inserted into the opening on the rear side 5 Attach vacuum pump to the side arm of T tool using a suitable adaptor and vacuum tubing CAUTION Only use new clean tubing Apply vacuum before removing the CCD detector vacuum seal to prevent oil etc diffusing into the detector and causing damage Xca i b u r Version 2 4 USER MANUAL Page 52 MAINTENANCE INSTRUCTIONS 6 Switch on vacuum pump and leave for 5 minutes 7 Depress T tool plunger and screw into place This screws into the o ring sealed metal stopper that secures the detector vacuum 8 Withdraw plunger to
26. TALLATION ETC left hand side of the system to allow the side panel to be removed to carry out the wavelength change procedure Unpacked the largest subassembly will fit through a door aperture of 85 cm Check the door aperture to ensure the system can be assembled in its designated area 5 2 1 3 Electrical Services One single phase 32 A outlet for X ray generator and two single phase 16 A outlets are required Additionally four single phase outlets are required for optional accessory items Use only the power cables supplied Do not connect the electrical power supply circuit to any other devices Limit the electrical noise in the system by attaching the earth cable exclusively to an external earth terminal The instrument is equipped with a terminal to attach an external protective grounding cable which should have a cross section of not less than 4mm The resistance between the ground connection and the instrument terminal should be not greater than 0 1 ohm This grounding connection should be made in a secure manner to avoid accidental disconnection Fit a line voltage regulator if the power supply voltage fluctuates more than 10 Locate the mains outlet on the wall behind the system The mains outlet should be of the circuit breaker type Outlet and connecting plugs are not supplied The mains plug should be readily accessible by the operator when the equipment has been installed In areas where the mains power supply is unre
27. UAL Page 57 MAINTENANCE INSTRUCTIONS Procedure to clean the X ray source coolant filter s is as follows 1 UseCrysAlisPro software to turn off the X ray source power Wait for the active source power to ramp down to zero 2 Wait for 20 minutes for the X ray source to cool down 3 Turn off the KMW3000 or TF3500 water cooler using the front mounted key switch or button the CCD water cooler will now start to warm up and result in an error after about 1 minute 4 Open the left side panel of the electronics rack by turning the locks at the top and bottom using the same key used to open the protection cabinet doors Hold the side panel in the middle of the left and right edges and carefully lift it forwards it is supported by two hooks inside the top edge and then lower it to the floor Stand the panel in a safe place where it will not fall over The side panel is heavy and should be held in the middle of the left and right edges to avoid the risk of finger trapping underneath the panel Take care to lower the panel gently to the floor without trapping hands or feet underneath 5 Locate the X ray source coolant filter s towards the top of the panel which will be visible inside 6 Using a cloth or container to catch any spilled liquid unscrew the filter s cap it is pointing diagonally down towards the user 7 Remove the metal filter sieve and clean it under running water and use a brush if necessary 8 Replace the
28. USER MANUAL Page 67 ADDITIONAL INFORMATION 12 Additional Information 12 1 Third Party Information Information marked optional is only supplied when that option is fitted to the system Title Supplier Material Safety Data Sheet M10 Beryllium Brushwellman Cryojet User Manual Oxford Instruments optional Cryostream User Manual Oxford Cryosystems optional Helijet User Manual Agilent Technologies optional Xcalibur Version 24 USER MANUAL Page 68 ADDITIONAL INFORMATION 12 2 Drawings Electrical supply Water Supply AS GOOD GU GP GP GP AG GP GP GP 2 16A single phase 32Asinglephase _ 16A single phase 44cm 16A single phase 16A single phase 42 Water Outlet Water Inlet 105cm 90cm 64cm 61cm 150 100 100 Min Ceiling height 2 2M Figure 25 Xcalibur Gemini Suggested Layout Note the figure above shows the suggested location for the computer monitor and keyboard based upon the cable lengths supplied and the need to access the left side panel of the instrument to change the wavelength in the Gemini configuration The customer should provide a suitable table or pedestal for the User to work in f
29. Xcalibur Gemini Instrument version from September 2013 onwards X ray Diffractometer Systems User Manual Version 2 4 October 2014 Agilent Technologies XRD Products 10 Mead Road Yarnton Oxfordshire 0 5 1QU UK Tel 44 0 1865 291600 Fax 44 0 1865 291601 http www agilent com chem EE Agilent Technologies Notices Agilent Technologies Inc 2014 No part of this manual may be reproduced in any form or by any means including electronic storage and retrieval or translation into a foreign language without prior agreement and written consent from Agilent Technologies Inc as governed by United States and international copyright laws For Assistance and Support http www agilent com find assist Limitation of Warranty The foregoing warranty shall not apply to defects resulting from improper or inadequate maintenance by Buyer Buyer supplied software or interfacing unauthorized modification or misuse operation outside of the environmental specifications for the product or improper site preparation or maintenance No other warranty is expressed or implied Agilent Technologies specifically disclaims the implied warranties of Merchantability and Fitness for a Particular Purpose Warranty The material contained in this document is provided as is and is subject to being changed without notice in future editions Further to the maximum extent permitted by applicable law Agilent discl
30. aims all warranties either express or implied with regard to this manual and any information contained herein including but not limited to the implied warranties of merchantability and fitness for a particular purpose Agilent shall not be liable for errors or for incidental or consequential damages in connection with the furnishing use or performance of this document or of any information contained herein Should Agilent and the user have a separate written agreement with warranty terms covering the material in this document that conflict with these terms the warranty terms in the separate agreement shall control Technology Licenses The hardware and or software described in this document are furnished under a license and may be used or copied only in accordance with the terms of such license Restricted Rights Legend If software is for use in the performance of a U S Government prime contract or subcontract Software is delivered and licensed as Commercial computer software as defined in DFAR 252 227 7014 June 1995 or as a commercial item as defined in FAR 2 101 a or as Restricted computer software as defined in FAR 52 227 19 June 1987 or any equivalent agency regulation or contract clause Use duplication or disclosure of Software is subject to Agilent Technologies standard commercial license terms and non DOD Departments and Agencies of the U S Government will receive no greater than Restricted Rights
31. andling 5 1 3 1 Weights Dimensions and Lifting Points HANDLING INSTALLATION ETC Description NET Dimensions Centre of gravity Lifting points Weight width x height x depth kg cm Kappa 106 43x 64 x 47 Offset from centre of At four corners goniometer unit towards side of X DO NOT lift from ray tube mount below 40 48 x 22x 69 Centre of unit From the sides and X ray generator below Protection 120 100 x 72x 84 Centre of unit By hand from bottom cabinet four corners Electronics rack 140 80 x 104 x 80 Centre of unit By hand from top or bottom four corners CCD water 20 48 x 13 x 48 Centre of unit At the four corners cooler and from below OPTIONAL ITEMS KMW3000C 56 38 54 96 Centre of unit At the four corners and from below Helijet 10 30 x 25 x 10 head only Centre of component From below with parts transfer tube removed Cryojetb 15 15 x 35 x 15 head only Centre of component From below or using parts handles whilst supporting transfer tube MercurylTC 5 44 x 10 x 30 Centre of unit By hand from below GFC1 12 45 x 26 x 38 Centre of unit Front panel handles Xca i b u r Version 2 4 USER MANUAL Page 28 HANDLING INSTALLATION ETC 5 1 3 2 Boxed Weights and Dimensions Weight Length Width Height Box No Item 1 Goniometer 160 95 60 90 2 Electronics rack 185 90 90 134 3 Protection cabinet 220 115 100 100 4 Chiller Accessories 195 122 80 95 5 X
32. at have a 10mm inside diameter the case of KMW3000 water to water cooling the distance between the water supply and the chiller is not limited but the supply must deliver 3 5 bar gauge pressure with a minimum 1 8 litres min flow if the water supply temperature is 12 degC The water supply should have a wall mounted shut off valve Care should be taken on closed loop water supplies that the return line pressure is not so high that water flow is blocked The difference between supply and return line pressures must be 1 2 bar 5 2 1 5 Low Temperature Option A suitable high vacuum pump ideally 70 Litres sec turbo is required to periodically evacuate the low temperature device To demonstrate the operation of the device e g Cryojet 100 litres of liquid nitrogen are required The customer should supply a suitable rack for the device controller 5 2 1 6 CCD Camera Pumping A suitable high vacuum pump ideally 70 Litres sec turbo molecular pump is required to periodically evacuate the CCD camera 5 2 1 7 Helijet Option The customer should provide a minimum of 50 litres of liquid helium and a minimum of 1 full helium gas cylinder of at least 99 99 grade helium gas in order for the operation of the Helijet to be demonstrated 5 2 2 Setting to Work 5 2 2 1 Equipment Required Table shelving for low temperature device controller and a table pedestal stand for the computer monitor keyboard and mouse 5 2 2 2 Personne
33. ature stability Temperature range 1 8 l min at 12 C 3 5 bar gauge 1 2 bar less than supply line pressure Take care to check this on closed loop water systems 5 C 5 20 C 3 3 Performance Data 3 3 1 X ray Tube Maximum radiation dose due to scattering or leakage at 10cm distance from any outside surface lt 1uSv hr Typical Operating Conditions Tube Voltage kV setting Current mA setting Resulting power W Mo 40 2200 Cu 40 2000 Xcalibur Version 2 4 USER MANUAL Page 17 Maximum Operating Conditions SPECIFICATIONS Tube Voltage kV setting Mo 55 Cu 50 Current mA setting Resulting power W 54 3000 44 2200 3 3 2 CCD Detector 3 3 2 1 General CCD chip Scintillator material Peltier cooling Temperature stability Analogue to digital resolution System noise so called read noise Dark current Communication Readout time EosS2 552 TitanS2 Readout time Eos Atlas Titan Truesense Imaging KAF4320 E Gadox 40 C three stage cooler 0 05 C micro processor PID True 18 bit lt 12 e RMS lt 0 05 e pix s Gigabit Ethernet 0 22s 4 x 4 binning 0 38s 2 x 2 binning 0 75s 1 x 1 binning 0 28s 4 x 4 binning 0 46s 2 x 2 binning 1 59s 1 x 1 binning 3 3 2 2 Eos EosS2 detectors Active area Weight Pixel size on scintillator Fibre optic reduction 95mm diagonal 10kg 31pm 1 3 low distort
34. between moving parts gt 8 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 Do not take risks You have a responsibility to ensure the safe condition and safe operation of equipment Xca l i b u r Version 2 4 USER MANUAL Page 9 HEALTH AND SAFETY INFORMATION The equipment 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 Gemini by Agilent Technologies personnel 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 1 2 1 Potential Electrical Hazards The following list is not intended as a complete guide to all the electrical hazards on the system but serves to illustrate the range of potential hazards that exist e electric shock electric burn fire of electrical origin e electric arcing 1 2 2 Recommended Precautions All of the electrical equipment supplied as part of the system should be provided with a protective ground Do not remove protective grounds as this may give rise to an electrical safety hazard It is vitally important that the system is properly grounded at all times Follow local and national electrical regulations a
35. cted of steel and lead equivalent glass Xcalibur Gemini has magnetic switches mounted on the front door and rear left and right side panels of the protective enclosure During operation the X ray shutters will not open unless the doors are closed If the doors are then opened whilst the X ray shutters are open the X ray shutters are both immediately caused to close Access to the interior of the cabinet via the front door is required when changing samples When the door is opened during sample change and alignment the X ray generator remains on for optimum performance but the safety shutter is automatically closed Whilst the cabinet is open only the phi axis of the goniometer may be rotated by software The other axes may be commanded to move by the software but motion will only physically happen if the two Motion Enable button in the cabinet are simultaneously pressed Indicator lights mounted on the outside of the enclosure show when the X ray generator power is on orange light and whether the X ray shutter is open red light or closed green If these lights are defective then the X ray generator will not operate in the case of the orange light and the X ray shutters will not open in the case of the red and green shutter lights The door of the cabinet should remain locked when the system is unattended to prevent unauthorised access to the system Xca i b u r Version 2 4 USER MANUAL Page 26 HANDLING INSTALLATION ETC 5 Handl
36. d adaptor Action Personnel Estimated task Estimated elapsed duration time 1 CCD detector pump out vacuum Agilent Engineer 1 hour 16 hours Xca i b u r Version 2 4 USER MANUAL Page 46 MAINTENANCE SCHEDULES 7 6 10 000 Hours Maintenance Schedule Please contact Agilent Technologies to perform these maintenance tasks Action Personnel Estimated task Estimated elapsed duration time 1 Changing the X ray tube Agilent Engineer 1 2 hours 1 2 hours 2 Alignment of X ray optics Agilent Engineer 2 3 hours 2 3 hours Xca i b u r Version 2 4 USER MANUAL Page 47 MAINTENANCE INSTRUCTIONS 8 Maintenance Instructions D WARNING 1 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 Maintenance tasks must only be performed by authorised operators of the diffactometer 8 1 Refining the Machine Parameter File Task Elapsed 4 5 hours Time When After adjustment of beam collimator CCD detector position etc Otherwise twice a year Tools Ylid test crystal 10 11502 Procedure See operating sections Refining of Machine Parameter File and Service Calibration Experiments in software manual Please note that the test crystal must be precisely centred on the goniometer b
37. doors were opened whilst the shutter was open and safety circuit was activated In CrysAlis e re start experiment Intermittent beeping 1 Beamstop is in up position sound from the system Move beamstop to down position to block x ray beam Generator will not 1 Interlock is open generate X rays 1 Check rear door of electronics rack is closed 2 Confirm that cooling water is supplied 3 Confirm that there is no temperature error caused by overheating the X ray tube 4 Confirm that Emergency stop has not been pressed 2 No power to generator Switch on at rear panel 3 Emergency stop has been pressed and not released 1 Twist emergency stop button clockwise to release 2 Reset generator using switch on rear panel Xcalibur USER MANUAL Version 2 4 Page 60 TROUBLESHOOTING Symptom Fault Solution 4 No cooling water through X ray source 1 Turn on the KMW3000C or TF3500 Water Cooler 2 Confirm all water hoses are connected properly and valves are open 3 Confirm no error states on Water Cooler front panel 5 Cabinet X ray warning lamp is disconnected or not functioning Confirm cable is connected to warning lamp inside protection cabinet on top frame of front right door then contact Agilent Technologies support Problem reading kV and mA from generator Cable s not connected properly Check cables connected to rear of gen
38. dure should not be carried out frequently but only on a regular preventive maintenance visit or in the case of a coolant flow error on the CCD detector circuit Procedure to clean the CCD coolant filter is as follows 1 Open the front door of the electronics rack 2 Locate the CCD water cooler bottom module in the rack and turn it off using the front panel mounted power switch 3 The CCD detector will be turned off automatically by the previous step 4 Open the left side panel of the electronics rack by turning the locks at the top and bottom using the same key used to open the protection cabinet doors Hold the side panel in the middle of the left and right edges and carefully lift it forwards it is supported by two hooks inside the top edge and then lower it to the floor Stand the panel in a safe place where it will not fall over The side panel is heavy and should be held in the middle of the left and right edges to avoid the risk of finger trapping underneath the panel Take care to lower the panel gently to the floor without trapping hands or feet underneath 5 Locate the CCD coolant filter towards the top left of the panel which will be visible inside 6 Using a cloth or container to catch any spilled liquid unscrew the filter s cap it is pointing horizontally towards the user 7 Remove the metal filter sieve and clean it under running water and use a brush if necessary 8 Replace the filter sieve and the cap ensu
39. e gas cylinders and follow it High pressure cylinders are often used to store gases typically at pressures up to 200 bar Most countries have laws about using them e Chain cylinders to a fixed object or keep them in specially designed trolleys e Only use approved and tested high pressure fittings 1 11 Hazardous or Toxic Materials Beryllium and beryllium oxide are toxic materials Follow appropriate handling shipping use storage and disposal procedures and regulations Refer to BrushWellman Material Safety Data Sheet No M10 for further information Beryllium is contained in the front panel of the CCD detector and in the X ray tubes Care should be taken not to touch the beryllium panels windows on the detector and tubes NG A If Beryllium is exposed to fire it may oxidise to highly toxic beryllium oxide powder Do not attempt to clear up the remains of any fire but contact the relevant local agency stating that there is an incident involving possible beryllium or beryllium oxide contamination 1 12 Maintenance 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 Interchangeable parts which are subject to deterioration during operation must be serviced or interchanged during the intervals given Xcalibur Version 2 4 US
40. e safe operation and to maintain the instrument in safe condition General This product is a Safety Class 1 instrument provided with a protective earth terminal The protective features of this product may be impaired if it is used in a manner not specified in the operation instructions Environment Conditions This instrument is intended for indoor use in an installation category II pollution degree 2 environment Refer to the specifications tables for the ac mains voltage requirements and ambient operating temperature range Before Applying Power Verify that all safety precautions are taken The power cable inlet of the instrument serves as a device to disconnect from the mains in case of hazard The instrument must be positioned so that the operator can easily access the power cable inlet When the instrument is rack mounted the rack must be provided with an easily accessible mains switch Environmental Information Xcalibur USER MANUAL Page 3 Ground the Instrument To minimize shock hazard the instrument chassis and cover must be connected to an electrical protective earth ground The instrument must be connected to the ac power mains through a grounded power cable with the ground wire firmly connected to an electrical ground safety ground at the power outlet Any interruption of the protective grounding conductor or disconnection of the protective earth terminal will cause a potential shock hazard t
41. efore starting this refinement calibration task Xca l i b u r Version 2 4 USER MANUAL Page 48 MAINTENANCE INSTRUCTIONS 8 2 Aligning the Video Microscope Including Sample Centring and Sphere of Confusion Check Task Time 30 minutes When When it becomes impossible to centre a sample correctly on the video microscope screen although this can also indicate the much more serious and unlikely problem of the Goniometer being out of alignment Tools Pre mounted 0 3 mm steel ball adjustment key for goniometer head Equivalent to Height Adj Figure 16 Goniometer Head Adjustments Figure 17 Video Microscope Adjustments When first assembled the Goniometer sample centre and the video microscope focal point should be close to each other however the field of view is approximately 1 2mm x 0 8mm and its depth of field is similarly limited Adjustments need to be made so that the sample centre and microscope focal point coincide exactly Both the Goniometer head and the video microscope have adjustments to move their centres in three planes To aid this procedure a pre mounted 0 3mm steel ball is supplied in the accessories box The three adjustments for the microscope can be seen in the picture above The first is to adjust the focal length of the unit the next has the equivalent adjustment to the height of the sample on the Goniometer when sample is in Lower or Upper position Finally there is the left right adjust
42. er cooled dissipates 6000 BTU hr heat not including any optional cryogenic devices Xcalibur Gemini with TF3500 i e air cooled dissipates 16000 BTU hr heat not including any optional cryogenic devices Air temperature in the room during operation 18 25 C Stability of ambient temperature during 1 C operation Storage temperature gt 10 C lt 40 C Relative humidity 20 80 non condensing Location Clean dust free environment gt 2m from air conditioning or heating units Floor strength Able to bear system weight of 500 kg on a footprint 80x80cm Xcalibur Version 2 4 USER MANUAL Page 16 3 2 Services 3 2 1 Electrical Supply SPECIFICATIONS Total power requirements Number of outlets required Voltage fluctuation Location of outlets Protection 200 240V Max 15A 33A peak X Ray Generator Max 5A remaining circuits of the instrument 4 single phase outlets 16A 200 240V 32A 100 120V for diffractometer system comprising goniometer interface detector etc computer monitor and external water chiller such as KMW3000C 1 single phase outlet 33A 200 240V for HV Generator 4 single phase outlets for temperature attachments 10 with line voltage regulator fitted if necessary On wall behind system Circuit breakers to be fitted to all outlets 3 2 2 External Water Cooling when used with KMW3000 Min flow rate Pressure Return line pressure Temper
43. erator and serial cable connected to PC Xcalibur USER MANUAL Version 2 4 Page 61 TROUBLESHOOTING Symptom Fault Solution Goniometer lost angles positions from memory Xcalibur USER MANUAL 1 Power loss to goniometer 1 Restore power to Xcalibur Gemini restart the PC and CrysAlis re program 2 Switch off the system interface wait 5 seconds and then switch on Wait 15 seconds for interface to initialise 3 CrysAlisP open command prompt and type KM4 MGCUTIL and press enter 4 Click on parameters and the two Edit deg buttons Set both to 1 0000 and click on slow Click enter 5 Select offending angle from the radio boxes Click on Set angles and Start Input actual position of each axis as read from the mechanical goniometer Pay special attention to F or 6 Select Rsync all and click Start Note that at the end of the Rsnync operation the Rsync flags should read 1 This is located on the text line below the parameter button 7 Select Hsync all and click Start Note that at the end of the Hsnync 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 Version 2 4
44. g to be attached to the support arm which is universal for all attachments The support rings for low temperature attachments from most major producers can be purchased from Agilent Technologies For low temperature attachments such as Oxford Instrument s Cryojet and Oxford Cryosystem s Cryostream the compatible support ring also allows the attachment to be translated up and down towards or away from the crystal and held in place with a side mounted locking screw Before proceeding with the alignment procedure ensure that the attachment has been translated to the bottom position closest to the crystal Xca i b u r Version 2 4 USER MANUAL Page 54 MAINTENANCE INSTRUCTIONS Figure 21 Helijet adapter plate screws 1 Retract the adjustment screws the support arm so that the support ring is clamped against the underside of the support arm The attachment screws might require tightening to provide sufficient clamping force through the springs Clamp this ring up against the plate Figure 22 Starting position for Helijet alignment Figure 23 Helijet alignment tip Xca l i b ur Version 2 4 USER MANUAL Page 55 MAINTENANCE INSTRUCTIONS 2 Place the alignment tip in the end of the Helijet nozzle 3 Fita metal pointer to the XYZ head as shown in the photo above and place on the goniometer 4 Align optically the end of the metal pointer using the XYZ screws on goniometer head with the centre of the goniometer using the
45. goniometer omega kappa phi and theta axis for sample orientation with a detector arm which has a universal mount capable of supporting any Agilent Technologies CCD area detector The CCD area detector is used to measure the X quanta diffracted from the sample Key 1 X ray tube 4 Video microscope 2 4 circle Kappa goniometer 5 Beamstop 3 X ray Shutter 6 Beryllium Window Figure 3 View of a typical diffractometer The X rays are generated by a long fine focus sealed tube which is mounted on the goniometer and powered by the high voltage generator The X ray optics consist of a high speed shutter located next to the tube shield graphite monochromator and a collimator for refining the X ray beam The sample can be viewed with the video microscope which is attached to the stand doming the instrument The image is displayed on the computer monitor The CCD area detector works according to the following principle The X rays enter the detector through a Beryllium window to the vacuum sealed detector unit A scintillation screen transforms the X ray photons to light which is conducted via a fibre optic reduction taper towards the scientific grade CCD chip The CCD signal Xca i b ur Version 2 4 USER MANUAL Page 22 TECHNICAL DESCRIPTION is digitised to 18 bit resolution by a correlated double sampling circuit with analog to digital converter located in the detector head The data transfer is via a gigabit Ethernet link to the PC
46. h rag 15 2 3 System OAA EA AEAEE E t atate tp e oae te prede lee ni eg 15 2 Specification S 3 1 Environmental nennen nennen nnn 16 SUASIT 17 3 21 Electrical ends al 17 3 2 2 External Water Cooling when used with 3000 2 1 2 1 17 3 3 17 3 3 1 D Oa n 17 22 DIEI ETE 18 3 9 9 PC COD Iritetface c e eet 19 3 3 4 Four circle Kappa Geometry 19 34 Electrical RE e ea M 20 KMW3000 Water 20 4 Technical 2202 4 1 Overview 2 Do foa cade sor 21 12 Mo 7 Cu Xray
47. hat could result in personal injury Do Not Operate in an Explosive Atmosphere Do not operate the instrument in the presence of flammable gases or fumes Do Not Remove the Instrument Cover Operating personnel must not remove instrument covers except for the particular cases described in this manual Component replacement and internal adjustments must be made only by qualified personnel Instruments that appear damaged or defective should be made inoperative and secured against unintended operation until they can be repaired by qualified service personnel Version 2 4 Xcalibur USER MANUAL This product complies with the WEEE Directive 2002 96 EC marketing requirements The affixed label indicates that you must not discard this electrical electronic product in domestic household waste Do not dispose in domestic household waste To return unwanted products contact your local Agilent office or see www agilent com environment product for more information Page 4 Version 2 4 Important Information This user manual applies to the Xcalibur and Gemini systems manufactured in Poland by Agilent Technologies Singapore International ATSI from September 2013 onwards for previous models please refer to the appropriate other user manual Product Xcalibur single X ray source or Gemini dual X ray source Electrical Ratings 1 N AC 200 240V 50 60Hz 4000W Max 15A 33A peak X Ray Generator Max 5A
48. hat should be completed for Xcalibur or Gemini These records are to show only that maintenance has been completed as Version2 4 Page 1 Xcalibur USER MANUAL APPENDICES 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 performing Signature Comments No maintenance test 20 21 22 Xca l i b u r Version 2 4 USER MANUAL Page 2 APPENDICES Weekly Maintenance Record Sheet Week No Date of maintenance Name of person performing test Signature Comments 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 Xcalibur USER MANUAL Version 2 4 Page 3 APPENDICES Weekly Maintenance Record Sheet Week Date of Name of person performing Signature Comments No maintenance test 47 48 49 50 51 52 Monthly Maintenance Record Sheet Month Date of Name of person Signature Emergency X ray radiation Comments maintenance performing test Stop Check check OK OK Y N Y N Xca l i b u r Version 2 4 U
49. he X ray generator is located in the electronics rack in the instrument cabinet The generator power trips out if the interlock circuit opens which happens if X ray tube overheats the cooling water flow is insufficient the cabinet warning lamp fails or the emergency stop button is pressed Warning lights on the front panel indicate the operational status of the generator PC controls and communicates with the X ray Generator using RS232 COM port connection Xca i b u r Version 2 4 USER MANUAL Page 23 TECHNICAL DESCRIPTION 4 4 Water Cooler for CCD detector The Water Cooler model name SBC 70 is located in the electronics rack in the instrument cabinet It is used for cooling only the CCD detector The chiller operates only in water to water mode with a water reservoir see Figure 5 on the left hand side of the electronic rack This reservoir is used to fill the internal circuit for the CCD detector To fill the reservoir in the rack use 1 10 solution of ethylene glycol in distilled water pre mixed to prevent the liquid and circuits from algae growth 3L of liquid should be used to fill the reservoir and an additional 3L of liquid should be needed to fill the pipes The filling port is on the top of the reservoir in the rack The left hand side panel of the electronics rack at the bottom of the system will need to be removed in order to access the reservoir This is done by using the same key as used on the protection cabine
50. ing Installation Storage and Transit Information 5 1 Reception and Handling 5 1 1 Delivery Carry out the following steps on delivery of the Xcalibur Gemini system 1 When the system arrives check that there is no visible damage with the delivery driver present If damage has occurred contact the carrier and Agilent Technologies immediately The packing crates are heavy and could cause serious injury and damage to the equipment if not handled correctly Use suitable lifting equipment and procedures Only lift the packing cases from the bottom Do not remove the equipment from the packing crates until they have been moved to their designated installation site The equipment has been carefully packed to protect the equipment from damage in transit Removal of the packing equipment could make the equipment vulnerable to damage during transit 2 Always lift packing cases from the bottom using suitable lifting equipment refer to list of component weights in the following section 3 Move packing cases into the designated installation site 4 Contact Agilent Technologies to notify them that the equipment is awaiting installation by an Agilent authorised service provider 5 1 2 Unpacking 1 Retain all packing material until installation of the system is completed 2 Ensure that special tools are stored safely for use during maintenance periods Xca l i b u r Version 2 4 USER MANUAL Page 27 5 1 3 Mechanical H
51. ion cabinet in Pushing and holding both push buttons front of the goniometer buttons simultaneously enables goniometer movement while the protection cabinet is open Cabinet Illumination Small black Front of protection cabinet Illuminate inside of enclosure button Sample illumination Small black Front of protection cabinet Illuminate crystal sample button 6 1 2 Power Control Type Location Effect Electrical Rack Red switch Top panel of rack Inside front door Master power on off to whole of electronics rack rack except X ray generator Diffractometer Red switch Interface front panel left Inside Power on off to goniometer goniometer front door of electronics rack interface X ray Generator Black switch Rear panel inside rear door of Power on off to X ray electronics rack generator Water cooler Red switch Water cooler front panel left Power on off to water cooler Inside front door of electronics rack DC power supply Switch Inside rear door of electronics Power on off to CCD detector rack underneath power supply Xcalibur USER MANUAL Version 2 4 Page 33 OPERATION Cabinet Illumination switch Sample Illumination switch Emergency stop button Main power switch to whole rack System interface power switch Water cooler for CCD detector power switch Figure 8 Location of switches Xcalibur Version 2
52. ion reduction taper Xcalibur USER MANUAL Version 2 4 Page 18 3 3 2 3 Atlas AtlasS2 detectors SPECIFICATIONS Active area Weight Pixel size on scintillator Fibre optic reduction 135mm diameter 16kg 48 2 0 1 low distortion reduction taper 3 3 2 4 Titan TitanS2 detectors Active area Weight Pixel size on scintillator Fibre optic reduction 165 mm diameter 20kg 60 um 2 5 1 low distortion reduction taper 3 3 3 PC CCD Interface Communication Drivers Typical host computer Gigabit Ethernet Win 7 Pentium IV class PC 22 8 GHz 21 0 Gb RAM 20 colour display 3 3 4 Four circle Kappa Geometry Goniometer Type Sphere of omega kappa phi coincidence Maximum load Phi axis Resolution Scanning speed range CCD detector angular range CCD detector to sample distance Xcalibur USER MANUAL Four circle Kappa geometry X ray goniometer 10 um 2 kg 0 00125 deg for Omega and Theta 0 0025 deg for Kappa 0 005 deg for Phi 0 005 to 3 0 deg sec 115 to 157 deg depending on the instrument configuration 40 to 150 mm depending on the detector Version 2 4 Page 19 SPECIFICATIONS Shutter response time 3 ms 3 4 Electrical Data Power connection X ray Generator 1 N AC 230 V 10 Goniometer Interface 1 N AC 200 240V CCD Detector 1 N AC 200 240V 50 60 Hz 50 60 Hz 50 60 Hz Maxi
53. l Required for Installation 5 persons for lifting of heavy components 5 2 1 Installation Procedures Agilent Technologies personnel perform the installation The duration of the installation is typically 3 working days with an additional 1 day for the low temperature option This is followed by 2 days training from an Agilent Technologies applications engineer Xca i b u r Version 2 4 USER MANUAL Page 31 HANDLING INSTALLATION ETC 5 3 Storage Before installation commences or when the system is not being used for extended periods store the diffractometer in accordance with the environmental conditions for temperature and humidity stated in the SPECIFICATIONS section of this manual Always store the Xcalibur or Gemini instrument in a secure room Xca i b u r Version 2 4 USER MANUAL Page 32 6 Operation Xcalibur Gemini is a computer controlled system All functions are controlled from the computer terminal OPERATION Power is switched on and off via manual switches located on the Xcalibur or Gemini Local rules and regulations may apply to the use of the diffractometer If these exist refer to these local rules before operating the system 6 1 Controls and Indicators 6 1 1 List of controls Control Type Location Effect Emergency Stop Red button Top right corner of front door of Shutdown X ray generator power electronics rack and stop goniometer Motion Enable Two metallic Inside the protect
54. lack switch on the rear panel Turn off the diffractometer interface red illuminated switch located on the left side of the front face Do NOT turn off the KMW3000C or TF3500 water chiller since this provides cooled water to the CCD cooler and it is advisable to keep this running 6 5 3 Shutdown Procedure Diffractometer not expected to be used for more than 3 weeks 1 Follow the Shutdown Procedure diffractometer not expected to be used for 1 3 weeks 2 Turn off the CCD Water Cooler which in turn shuts down the CCD detector It is advisable to leave this item running unless absolutely necessary Cooling the CCD detector from room temperature will be the time limiting factor when re starting the diffractometer 3 Turn off the KMW3000C or TF3500 water chiller using the key switch button on the front panel 4 Turn off system power using red switch on top panel inside front door of electronics rack 5 Turn off mains water supply 6 Unplug system power cords if required Xcalibur Version 24 USER MANUAL Page 43 OPERATION 6 6 Emergency Shutdown The emergency shutdown procedure should be used e If there is a fire or any other emergency requiring the evacuation of personnel from the area 6 6 1 Emergency Shutdown Procedure N GN The emergency stop button will only shut down HV from the X ray generator Other equipment on the Xcalibur Gemini system will still be powered on e Press red emergency stop bu
55. le buttons will need to be simultaneously pressed 9 Use the height adjustments on both the Head and the microscope equally to re centre the ball send back to Lower and repeat until there is no movement of the ball as the Goniometer moves between the two positions 10 Confirm that the left right position is ok for Upper as well as Lower 11 Adjust the focus on the microscope to bring the ball into sharp focus Once this process is complete the microscope should not need adjusting again unless it is knocked or extra weight is added to or removed from the support arm for example a low temperature environment is added or removed All sample centring should involve only the adjustments on the Head Ey us An indication that the microscope is not properly centred is if the sample cannot be centred to the middle of the video screen then small adjustments of the microscope may be needed during the sample centring process The focus may also need adjusting occasionally if the Crystal size varies widely from one experiment to another For a correctly centred sample and video microscope the variation in position of the sample Sphere of Confusion as it rotates to any of the positions on the remote control except home should one small division on the display 10pm In the unlikely event that correct centring cannot be achieved contact Agilent Technologies for advice When fully centred in the Upper and Lowe
56. liable an uninterruptible power supply UPS is recommended The UPS should have specifications of 10 kVA with 3 phase input and single phase output For example the following unit from APC will run Xcalibur Gemini from a 400V 3 phase input for about 100 minutes APC Smart UPS VT 10kVA 400V w 3 Batt Mod Exp to 4 Start Up 5X8 Int Maint Bypass Parallel Capable 1 SYBT4 Battery Unit Description Voltage Frequency Maximum nominal V Hz mains current A X ray generator 230 10 50 60 19 Water cooler 100 240 50 60 2 5 CCD detector 90 130 180 260 50 60 2 5 Goniometer Interface video 90 130 180 260 50 60 2 5 monitor cabinet lamps sample illumination Computer and peripherals 100 240 50 60 2 5 Cryojet controller option 100 240 50 60 2 KMW3000C water cooler 230 10 50 60 1 5 4A at startup Xca i b u r Version 2 4 USER MANUAL Page 30 HANDLING INSTALLATION ETC 5 2 1 4 Water Supply A cooling system is required to dissipate the heat produced by the X ray tube A closed circuit cooling system is supplied to minimise the effects of particles low pressure and water temperature fluctuation on the performance of the system from local tap water supply This cooling system could be the Agilent Technologies 3000 water to water chiller or a third party water to air chiller for example TF3500 These chillers are closed circuit cooling systems suitable for this purpose The system is supplied with hoses th
57. lling water reservoir The system includes a small water reservoir mounted inside the left side of the electronics rack This is visible on Figure 24 The software may report to the user a water level warning and if no action is taken later a water level error which will shut down the water cooler for the CCD detector The front panel of the water chiller in the electrical rack will also show this warning with a flashing LED In case of this warning or error the user is required to refill the reservoir The procedure is as follows 1 Open the left side panel of the electronics rack by turning the locks at the top and bottom using the same key used to open the protection cabinet doors Hold the side panel in the middle of the left and right edges and carefully lift it forwards it is supported by two hooks inside the top edge and then lower it to the floor Stand the panel in a safe place where it will not fall over The side panel is heavy and should be held in the middle of the left and right edges to avoid the risk of finger trapping underneath the panel Take care to lower the panel gently to the floor without trapping hands or feet underneath Locate the reservoir tank which is towards the front side of the rack Open the filling port on the top of the reservoir Pre mix a solution of 1096 ethylene glycol 90 distilled water Pour the solution into the filling port until the level is visible just under the filling port edge
58. ment To centre both the video screen and check the Sphere of confusion use the following procedure Procedure 1 Press F12 on the computer keyboard to start the alignment procedure a new window opens Xca l i b u r Version 2 4 USER MANUAL Page 49 MAINTENANCE INSTRUCTIONS 2 Mount the 0 3mm steel ball onto the Goniometer 3 Press the Lower then 0 buttons and wait for the Goniometer to stop moving note that if the cabinet is open the Motion Enable buttons will need to be simultaneously pressed 4 Find the steel ball on the video screen using the Goniometer Head adjustments 5 Press 1180 and watch the steel ball as it is rotated it will probably move off screen Use the adjustments on both the Head and Microscope equally to move the ball back to the centre press 0 The ball should end up close to the centre of the screen adjust again to make it central repeat as necessary until the movement of the ball is minimised 6 Press 90 and move the ball to the centre using the Head only 7 Press 270 and watch the ball as it rotates If the microscope is correctly centred left to right it will be possible to centre the ball using only the Head adjustments if not small adjustments of the microscope may be required repeat until the ball appears to spin on the spot for all four angle positions 8 Press 0 then Upper watching the ball as it moves note that if the cabinet is open the Motion Enab
59. ment to perform regular radiation checks as per any laboratory rules 5 Useonly genuine firmware X ray tubes X ray generators goniometer heads and collimators as recommended by Agilent Technologies Use of other products may compromise the performance of the shielding and safety system and may invalidate your warranty 1 8 Extreme Temperatures N 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 1 9 Vacuum A When handling and using X ray tubes and the CCD detector particular care should be taken to avoid injury caused by possible implosion of the vacuum tube Wear eye protection The CCD detector front panel is made from beryllium and can be easily damaged by a strong force by hand or a gentle force by a sharp instrument Such damage can result in vacuum implosion of the CCD detector There is danger of exposure to potentially toxic beryllium material case of such an event take action to close the protection cabinet doors and panels and obtain specialist assistance to clean up the beryllium Xcalibur Version 2 4 USER MANUAL Page 13 HEALTH AND SAFETY INFORMATION 1 10 High Pressures Know the law about high pressur
60. mum power consumption 3000W 250 W 125 W Maximum mains current 19A 12A 12A Main fuse 32A 6 3 A 3 15 A Ground terminal None 2 5 mm Cu 2 5 mm Cu CCD Water chiller KMW3000 Water chiller Power connection Maximum power consumption Maximum mains current Main fuse Ground terminal 1 N AC 200 240V 50 60 Hz 300W 1 5A 230V T 2 5A 230V 2 5 mm Cu 1 N AC 200 240V 50 60 Hz 900W 4A 230V T 6 3A 230V 2 5 mm Cu Xcalibur USER MANUAL Version 2 4 Page 20 TECHNICAL DESCRIPTION 4 Technical Description 4 1 Overview of Xcalibur Gemini The Xcalibur Gemini system consists of 1 Akappa geometry 4 circle diffractometer 2 ACCD area detector 3 Aninstrument cabinet with electronics rack 4 System software installed on PC workstation Note The numbers on this 1 diagram refer to the numbered list above Figure 1 Components of a typical Xcalibur Gemini system Figure 2 Computer and monitor Xcalibur Version 2 4 USER MANUAL Page 21 TECHNICAL DESCRIPTION The diffractometer and CCD area detector are mounted inside a cabinet The cabinet experiment area is mounted on top of the electronics rack The water cooler for the CCD detector is positioned in the electronics rack The water cooler for the X ray source is positioned on the floor adjacent to the rack The system is supplied with a control PC monitor keyboard and mouse The diffractometer consists of one or two X ray tubes a 4 axis Kappa
61. nd procedures Do not defeat interlocks remove connectors disconnect equipment open safety covers dismantle or modify equipment unless you are qualified and authorised to do so and you are fully conversant with its operation and potential hazards or have total assurance through your local electrical permit to work system that the equipment has been made safe Ensure that the mains supply is fused at an appropriate rating or fitted with a circuit breaker and that it can be isolated locally via a clearly labelled clearly visible and easily accessible isolating switch Isolate the supply before carrying out any maintenance work Do not touch any unshielded wires or connectors while mains power is supplied to the system Do not allow water or any other foreign objects to come into contact with the equipment s electrical components Xcalibur Version 2 4 USER MANUAL Page 10 HEALTH AND SAFETY INFORMATION Mains voltages are present in the system High voltages are used by the X ray A tube and power supply Only personnel qualified to work with high voltages and currents are permited to perform service or maintenance work on such equipment 1 3 Mechanical Handling Safety Lifting points are provided for safe handling of components and safe handling practice must be observed to comply with local regulations Check that lifting points are used only for the job intended The system itself and some components are
62. nit Int Ext Temp Error LED lights Liquid in the circuit is too hot Check that the KMW3000C or TF3500 is operating without error Check water valves are open and that water can flow in series through the X ray tube and the SBC Water Cooler in the electronics rack Reduce the temperature of water in the external circuit by changing the thermostat setting on the KMW3000C or TF3500 Xcalibur USER MANUAL Version 2 4 Page 65 SPARES 10 Spares 10 1 Fuses A CMM GEM PN Power distribution Electronics rack right 10 A 250 V fast side Chiller Back of the chiller 3 15 A 250 V fast Fi 10 2 Bulbs Device Location Description Protection cabinet X ray On cabinet front door M LIGHT LED modules yellow green red and shutter indicators Shutter open indicator On beamstop base MultiLED T5 5 RED 12 V 25 mA Swisstac Protection cabinet Inside top protection MEGA X1R WHITE LED illumination cabinet Sample illumination On beamstop arm LED WHITE 10MM 6DEG Xca i b u r Version 2 4 USER MANUAL Page 66 DISPOSAL INSTRUCTIONS 11 Disposal Instructions 11 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 11 2 Third Party Equipment Refer to third party manuals for information about disposing of third party equipment Xca i b u r Version 2 4
63. of Agilent Technologies Original instructions in English language Xca i b u r Version 2 4 USER MANUAL Page 5 Contents 1 Health and Safety Information 9 IMNCIDIBE tec a Ses dave eee eae eee dave eee eds MO ee eae a 9 1 2 Electrical Safety ete et Rente c t e ES 10 1 2 1 Potential Electrical Hazards 2442 00 eene enne nennen nennen nennen nenne 10 12 2 Recommended Precautions c e ree I ene 10 1 3 Mechanical Handling Safety sss eene nnn nennen sten nnne 11 1 4 5 11 1 9 5 a eve Ce ade 11 1 6 Mowing Parts dete eas idoneis eta i ea ptu d Ore 12 1 EX ray Radiationi o e teet erii 12 1 8 Extreme 13 argue ccc 13 1 10 High Pr ssSur8s 5 t ee Pere tec ferie tede iere ae awe aes 14 1 11 Hazardous or Toxic Materials leise 14 T2 Maintenance 5 ee tee e tur ie bees i eate etui iere 14 VA DRUSI NNI TENERETUR rs Lo VARICES 15 2 2 How To t i Pp it e p ee e
64. on This unit generates a focussed beam of X rays during normal operation The long fine focus X ray tube generates X rays when supplied with high voltage and filament current from the HV generator unit The dual shutter blocks X ray emission from the source when either one of the two shutters is closed The shutters are positioned between the X ray tube and the monochromator X rays shine onto the monochromator only when both shutters are opened AN The X ray tube is contained within a shielded housing The shielding should NEVER be removed whilst the high voltage generator is active as this would cause human exposure to damaging X rays The tube shield housing should only be removed by Agilent authorised service provider The long fine focus X ray tube is a consumable item which in time will need to be replaced This should only be carried out by a fully trained operative and the procedure is described later in this manual 6 2 2 Water cooling Generation of X rays causes the production of heat and thus the X ray source requires water cooling On the underside of the source unit there are two quick connectors for the input and output of cooling water The direction of water flow is important and is indicated with labels The water cooler unit should be used to supply Xca l i b u r Version 2 4 USER MANUAL Page 36 OPERATION cooling water to the X ray source The HV generator unit is interlocked to the cooling unit and thus
65. op edge Lower the side panel to be vertical and check it is hanging symmetrically between the front and rear sides of the rack Lock the panel into place at the top and bottom using the cabinet key 18 Click fourth Next button 19 Click the Restart button to restart the software 20 The system can then be used in normal operation through the CrysAlisPre software Xca i b u r Version 2 4 USER MANUAL Page 42 OPERATION 6 5 System Standby and Normal Shutdown Procedure Depending on the period of diffractometer inactivity follow one of the 3 procedures below 6 5 1 Shutdown Procedure Diffractometer not expected to be used for 2 3 days Ramp down the X ray generator to zero settings and then turn off HV using CrysalisP software improves lifetime of the x ray tube Park the goniometer in its home position simply by exiting the CrysAlisPre program Turn off the cabinet amp sample illumination using the front panel mounted switches Warm up turn off sample cooling device following manufacturers guidelines where applicable Turn off computer Monitor Do NOT turn off the KMW3000C or TF3500 water chiller since this provides cooled water to the CCD cooler and it is advisable to keep this running 6 5 2 Shutdown Procedure Diffractometer not expected to be used for 1 3 weeks 1 2 3 4 Follow the Shutdown Procedure Diffractometer not expected to be used for 2 3 days Turn off x ray generator by using the b
66. r positions the Goniometer should be sent back to Home once this is complete the ball or Crystal will appear to be displaced towards the left of the video screen This is an optical illusion caused by the angle of the microscope with respect to the Crystal at Home and can be ignored Xca i b u r Version 2 4 USER MANUAL Page 50 MAINTENANCE INSTRUCTIONS 8 3 Checking the Door Safety Interlocks Task Time 2 minutes When Once a week Tools None Procedure Ensure the interlocks are not defeated If interlock defeated there is the risk of exposure to X ray radiation e With the diffractometer in normal operation and at normal X ray generator settings with the shutter open open the front door of enclosure cabinet The X ray shutter should immediately close e Close the enclosure door From the software open the shutter again e Open the left side panel of the cabinet The X ray shutter should immediately close e Close the side panel From the software open the shutter again e Open the right side panel of the cabinet The X ray shutter should immediately close e Close the side panel From the software open the shutter again e Open the back panel of the cabinet X ray shutter should immediately close e Close the back panel e Record the date persons testing and sign off the outcome 8 4 Checking the Emergency stop Task Time 10 minutes When Once a month Tools None Procedure 1 With the diffractomete
67. r running at minimum settings for example 10 kV 0 05 mA press red Emergency Stop button 2 generator should switch off immediately release the emergency stop button restart the x ray generator Return to required settings 3 Crysalis software will indicate that the emergency stop was activated switch off the interface restart the interface and then type command gon reinit in order to restart the system 4 Record details of the test in the local radiation log stipulating the date person testing outcome and signature Xca l i b u r Version 2 4 USER MANUAL Page 51 MAINTENANCE INSTRUCTIONS 8 5 Checking the X ray Radiation Levels Task Time 20 minutes When As required by local rules 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 Close the protective enclosure doors and open the X ray shutter command sh o in CrysAlisPro Sweep the outside of the enclosure using the radiation meter paying particular attention to the plane of the X ray tube and the door seals Record details of the test in the local radiation log stipulating the date person testing outcome and signature 8 6 Pumping Out Vacuum of CCD detector Task Elapsed 16 hours Time When Once a year Tools Special
68. ray source s Generator 195 122 80 95 6 CCD detector 145 120 95 117 7 LN2 Dewar 120 70 70 155 8 Cryojet 145 70 80 190 9 Helijet 90 60 95 55 10 3000 Chiller 105 47 79 100 The weights dimension above an estimate and should only act as an indication of the lifting requirements when the system is delivered All boxes are fitted with the facility to use forks to unload There is 15 cm clearance from floor to the base of each box It is recommended that a fork lift truck is available to unload the delivery vehicle with a pallet truck to move the packing cases into the systems final location 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 5 2 1 2 System Layout Adequate space is required around the system for servicing The minimum clearance from the walls and a suggested system layout are shown in Figure 25 When the low temperature option is fitted an extra 100 cm space on the left hand side of the system is required When the system is in the Gemini configuration two sources then this 100cm space is also required on the Xca i b u r Version 2 4 USER MANUAL Page 29 HANDLING INS
69. remove stopper Secure plunger in place 9 Leave under vacuum for 16 hours 10 Depress T tool plunger to replace stopper and unscrew plunger AN CAUTION Do not turn off the vacuum pump until the CCD detector has been sealed using the relevant stopper 11 Switch off vacuum pump and disconnect pipes 12 Unscrew tool and replace cover on pump out port or collision cover in the case of Eos leaving 1mm gap to allow the cover to move On the S2 detector range replace the circular cover on the rear side and lock it into place by inserting the appropriate hexagon key and rotating clockwise until tight 13 Switch on the CCD Water Cooler Set screws Figure 19 View of the pump out port of the Eos CCD detector Xca l i b u r Version 2 4 USER MANUAL Page 53 MAINTENANCE INSTRUCTIONS Figure 20 View of the pump out port cover on the AtlasS2 detector 8 7 Aligning Low Temperature Attachment Task Time 30 mins When When the low temperature device s cold stream is observed to be misaligned from the crystal sample which is mounted and centred on the goniometer Tools 1 set of Allen keys Helijet alignment tip goniometer head with metal pointer Procedure The following instructions show how to align Helijet on the Xcalibur or SuperNova diffractometers similar procedure will be used for aligning other low temperature attachments Each of them will require a different compatible support rin
70. ring it is fitted correctly and the o ring is in place 9 Turnon the CCD water cooler using the front panel mounted power switch 10 Wait for the water cooler to start and after about one minute the CCD detector should re start automatically 11 Check the filter cap is secure and not leaking liquid Repair if necessary 12 Hold the side panel in the middle of the left and right edges and carefully lift it and tip the top edge towards the rack to engage it onto two hooks inside the top edge Lower the side panel to be vertical and check it is hanging symmetrically between the front and rear sides of the rack Lock the panel into place at the top and bottom using the cabinet key 13 Close the front door of the electrical rack 14 Close and re open the CrysAlisPro software to ensure re connection to the CCD detector In order to clean the X ray source coolant filter the KMW3000 or TF3500 water cooler will need to be turned off which will remove cooling water from the external side of the CCD water cooler After a short period of time this will result in a temperature error and the CCD water cooler will shut down and hence also turn off the CCD detector Thus the same statement applies as above this will cause the CCD to warm up and therefore this procedure should not be carried out frequently but only on a regular preventive maintenance visit or in the case of a coolant flow error on the X ray source circuit Xca l i b u r Version 2 4 USER MAN
71. ront of the monitor Xca l i b ur Version 2 4 USER MANUAL Page 69 ADDITIONAL INFORMATION 1018 4 1772 Dimensions in mm Figure 26 Xcalibur Gemini System Dimensions Xca l i b u r Version 2 4 USER MANUAL Page 70 APPENDICES Appendices Appendix 1 X ray Tubes Wavelengths Anode Kai Koz Cr 2 28976 2 2 293663 6 2 08492 2 1 00170 Co 1 78901 1 1 79290 1 1 62083 2 1 00217 Cu 1 540598 2 1 544426 2 1 39225 1 1 00248 Mo 0 7093187 4 0 713609 6 0 632305 9 1 00605 Ag 0 5594214 6 0 563812 4 0 497081 4 1 00785 W 0 180199 2 0 185080 2 0 158986 3 1 02709 Appendix 2 Standard Crystal Parameters Compound name Compound formula Cell constants Appendix 3 Ylid 2 Dimethylsulfuranylidene 1 3 indandione C10H1002S a 5 947 b 9 026 18 399 a y 90 Temperature Scales Conversion To convert Fahrenheit to Celsius To convert Celsius to Fahrenheit To convert Celsius to Kelvin To convert Fahrenheit to Kelvin Appendix 4 Maintenance Records subtract 32 from F then multiply by 5 9 multiply by 9 5 then add 32 add 273 15 first convert F to C then add 273 15 C 5 9 F 32 F 9 5C 32 K C 273 15 The attached record sheets are provided as examples of the type of records of maintenance checks t
72. rt it using the front panel button 12 Turn on computer monitor 13 Turn on the X ray HV generator black switch on rear panel 14 Launch the CrysAlisP e program The goniometer should auto initialise providing a system ready dialogue the CrysAlis history window if command prompt window is opened Xca l i b u r Version 2 4 USER MANUAL Page 38 OPERATION 6 4 Switching the wavelength Gemini only AN The wavelength switching procedure is a manual process which involves the exchange of the high voltage cables In order to minimise wear and tear on the high voltage cables it is advised that this process should be performed not more frequently than monthly The Gemini system contains two X ray sources one Molybdenum and the other Copper wavelength The procedure below describes how the User should switch the operating wavelength The User should be appropriately trained to carry out this procedure 1 CrysAlis o software must be running and in normal operation 2 the CrysAlis software click on the button to switch wavelength Mo Cu 3 The software will then open the window shown in the figure below which guides the User through the following steps Completing each step successfully will activate the next step Switching the wavelength dialog Se Status Generator HV sensor Water cooler 0 0kV 0 0 mA Interlock dosed Cable parked Cu Cooler ok Turning generator off Press Switch off button to turn
73. se and restart CrysalisP and open command prompt to confirm that communication has been re established with the CCD Xcalibur USER MANUAL Version 2 4 Page 63 TROUBLESHOOTING Symptom Fault Solution Blank images due to X ray shutter not opening 1 Protection cabinet doors are not closed properly Ensure all doors panels are closed and secured If the safety circuit is closed then CrysAlis will show this on the 10 device window click IO icon to display this 2 Shutter open closed lamps are defective To check if LED arrays are working turn off the interface wait 5 seconds and turn back on the interface For a short period all shutter indicators should be illuminated e g open closed on the exterior of the cabinet and the Shutter Open red lamp inside the cabinet on the beamstop mounting If the LED arrays do not function as indicated contact Agilent Technologies XRD sevice 3 X ray generator is not turned on or is not generating X rays 1 Ensure generator is turned on and that the software indicates that X ray power settings are normal 2 Ensure that the orange X ray LED array is illuminated see section above for fault finding the X ray generator system 4 Shutter signal cable Ensure that the shutter cable Fischer connection is secured to the optics shutter housing 5 Beamstop Ensure beamstop is rotated into data collection position i e vertical
74. t doors to rotate a lock at the top and bottom of the panel The Cooler needs an external water supply tap water integrated building water circuit or additional water chiller to cool the device The heat from the internal circuit is delivered to the external water circuit The external circuit is connected in series with the X ray tube water cooling circuit and the external water supply is connected to supply and return fittings at the rear of the system 4 5 Electronics Rack 4 5 1 Water distribution panel Coolant filters HE Reservoir Figure 5 Water distribution panel and reservoir Gemini version The water distribution panel is mounted in the left side of the rack This panel contains in line water filters for the internal water circuits through CCD detector and X ray sources A reservoir is mounted on this panel which fills the internal circuit separated from external cooling water Xca l i b ur Version 2 4 USER MANUAL Page 24 TECHNICAL DESCRIPTION 4 5 2 I0 Device for safety interlocks Figure 6 Safety IO Device Safety interlock wiring is organised through a PCB named IO Device in the system electrical enclosure After an error state the IO Device has to be reset to clear the error This must be done in order to close the interlock circuit to allow the X ray generator to operate The IO Device window shown in the figure below is opened by clicking on the IO icon near the top right of the CrysalisP sof
75. thing or body parts become caught in moving mechanisms Keep clothing hands and body parts away from moving mechanisms Between the moving parts of the goniometer there are a number of places at which a potential finger squeeze or shearing hazard exists The warning triangle shown to the left is visible on the goniometer close to these places Keep hands away from the goniometer when parts are moving When the protection cabinet is open the goniometer moving parts are disabled The Xcalibur Gemini system contains two MOTION ENABLE switches in front of the goniometer inside the protection cabinet During some operations such as mounting a sample the goniometer must be moved between defined positions while the protection cabinet is open In order to do this BOTH Motion Enable switches must be pressed and held simultaneously and this ensures that both hands of the operator are kept away from the potential finger squeeze or shear locations In the event that the goniometer moving parts become blocked by an obstruction the movement will be automatically stopped and a small reverse movement made so that the blockage can be safely released The control software will report a movement error and will wait for user intervention The procedure to follow to restart the instrument is shown in the troubleshooting section of this user manual 1 7 X ray Radiation This equipment contains an X ray tube Ensure that safe working practices
76. tton located on the front right of the Xcalibur Gemini e Switch off all power at the mains electrical supply including separately connected water chillers e Turn off mains water supply Version 2 4 Xcalibur USER MANUAL Page 44 MAINTENANCE SCHEDULES 7 Maintenance Schedules 7 1 Introduction Various maintenance tasks must be performed to ensure that the diffractometer system continues to operate safely and reliably These tasks are detailed in the maintenance schedules given below 1 Maintenance tasks must only be carried out by authorised operators who have undergone specialist radiation training Refer to local rules for further details 2 Failure to perform scheduled maintenance tasks properly and at the correct intervals can affect the safety and performance of this system 3 Before performing any maintenance task ensure that you have read and understood the HEALTH AND SAFETY INFORMATION at the beginning of this manual and any local rules governing the use of the diffractometer system Planned maintenance that can be performed by the user is limited to replacing consumable items alignment procedures pump down procedures and checking radiation levels and safety features The user s authorised service representative should carry out other tasks If in any doubt about the performance of the diffractometer contact Agilent Technologies NOTE X ray radiation leakage check should be performed by trained
77. tware main window The user must click on the Reset button to clear the error The cabinet lights can also be remotely controlled from this window IO Device Control 10 r Warnings and Errors Emergency stop Off Cooler error Detected Beam stop In Place Cabinet door Front door is open r Lights Firmware version Cabinetlight Sample light 233 123Final Rev517 2 2 logic 5 Status Device connected Figure 7 10 Device Control window Xca l i b ur Version 2 4 USER MANUAL Page 25 TECHNICAL DESCRIPTION 4 5 3 Ethernet switch The Ethernet switch inside the DC8 system Interface is used for connections between the system PC and Ethernet enabled devices such as the CCD water cooler and the IO Box This allows the PC to remotely control and communicate with devices via Ethernet even when isolated from an external network 4 6 Software The programs controlling the measurement procedures of the system are WIN32 applications which run under Windows XP or Windows 7 The data acquisition and reduction are run concurrently with the program CrysAlisPro 4 7 Low Temperature Option If a cryogenic cooler is fitted to the diffractometer system then the correct adapter must be used to mount the cooler on the stand for optional equipment Further details can be obtained from Agilent Technologies 4 8 Safety Features X rays are generated and projected in a totally enclosed cabinet constru
78. uipment e describe how the equipment operates e assist with simple fault finding and maintenance 2 3 System Overview Xcalibur systems are single crystal diffractometers that use the property of X ray diffraction to determine the crystal structure of materials They are intended for use with single crystals of chemical substances inorganic organic or organo metallic mineralogical and biological samples Xcalibur systems may also be used in the analysis of powder samples Intended samples should have a maximum unit cell dimension of 500 Angstrom for macromolecular PX systems Xcalibur systems may be used with crystal conditioning devices Specifically low and high temperature attachments and high pressure cells Some minor modifications may be required by Agilent Technologies to enable use of these devices When the Xcalibur system is equipped with two X ray sources it is named Gemini Xcalibur Version 2 4 USER MANUAL Page 15 SPECIFICATIONS J Specifications 3 1 Environmental Requirements It is essential that the climate of the laboratory is controlled to ensure that the CCD detector is not damaged Typically air conditioning should be installed to maintain the temperature and humidity within the ranges listed below The Relative Humidity is particularly important as the CCD and its cooling pipes can reach 17 C condensation should not be allowed to collect on the CCD at any time Xcalibur Gemini with KMW3000 i e external wat
79. witches 34 Figure 9 Two X ray sources mounted on Gemini diffractometer 36 Figure 10 Rotating the beamstop position 1 01 eene nnne 38 Figure 11 Software dialog for wavelength change Gemini 39 Figure 12 Rear of electronics rack showing HV cables 12000 40 Figure 13 HV cable parking position with Source Select plug Gemini 222 112 40 Figure 14 Water switching valve Gemini only Mo position 41 Figure 15 Water switching valve Gemini only in Cu position 41 Figure 16 Goniometer Head Adjustments 1 49 Figure 17 Video Microscope Adjustments eee teeta 49 Figure 18 View of the pump out port of the Titan CCD detector sees 53 Figure 19 View of the pump out port of the Eos CCD detector sees 53 Figure 20 View of the pump out port cover on the AtlasS2 detector eese 54 Figure 21 Helijet adapter plate screws 55 Figure 22 Starting position for Helijet alignment seen 55 Figure 23 Helijet alignment tip cececeeceeceeeeeeeeeeeeeaeeeeeeeeeeeeaaeaeeeeeeeseceaaaeaeeeseeesescaaeeeeeeeedeesennaeeeeeseess 55 Figure

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