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Xcalibur II manual

1. gt j 80 ra 96 re 75 TE tk ED 78 75 q ul e ES Version 1 4 Xcalibur Manual v1 4 Page 142 Xcalibur USER MANUAL ADDITIONAL INFORMATION 13 2 2 Electrical Drawings Drawing no Title Number of pages XCALIBUR 2 BLOCK DIAGRAM 1 INTERFACE CONNECTIONS 1 EC 00 00 001 A GONIO68332 INTERFACE CONNECTIONS DIAGRAM 1 EC 24 01 001 A GONIO68332 ENCODERS RS485 CABLE 2 EC 02 01 001 A GONIO68332 STEPPER MOTORS CABLE 2 EC 04 09 001 A GONIO68332 INTERFACE RS232 CABLE 2 EC 04 02 001 A GONIO68332 CCD POWER SUPPLY TO PC RS232 2 EC 02 04 001 A GONIO68332 SHUTTER INDICATOR 2 EC 24 04 001 B GONIO68332 FAST SHUTTER CABLE 2 EC 04 02 003 A GONIO68332 CCD POWER SUPPLY TO INTERFACE RS232 2 EC 24 08 001 A GONIO68332 REMOTE CONTROL CABLE 2 EC 04 02 002 A GONIO68332 FIP31 TO INTERFACE CABLE 2 CCD POWER SUPPLY CONNECTIONS 1 EC 01 02 001 A CCD POWER SUPPLY 230VAC SUPPLY CABLE 2 EC 02 05 001 A LCD MONITOR AND VIDEO MICROSCOPE POWER SUPPLY 2 CABLE EC 05 05 001 A VIDEO MICROSCOPE AND LCD MONITOR CONNECTIONS 1 OD 1 11 01 CABINET ILLUMINATION SCHEME 1 OD 1 14 01 POWER DISTRIBUTION 1 OD 1 14 02 POWER DISTRIBUTION SCHEME 1 OD 1 14 03 POWER DISTRIBUTION CONNECTION VIEW 1 C2K5 X RAY GENERATOR CONNECTIONS 1 EC 04 06 002 A C3K5 X RAY GENERATOR TEMPERATURE SENSOR 1 EC 24 06 001 A KMW3000C FLOW S
2. Acquisition of ABS movie Stop with Cancel button The ABS pulgin allows you to capture a movie of your crystal shape to disk The actual face evaluation of the sample may be done using the movie pictures Itis a good idea to store the face images in a seperate directory Sample name pig r Kappa position Gnlyiower Gry upper Bottlswer and Upper Phi step size ap ye d 5 a fou gius C users Mathias CrysAlisCCD crystal m Movie information Disk space 211 38Mb free 2 65Mb required Number of frames 121 Acquiring image 115 O 57 00 T 30 00 K 134 00 P 177 00 m 5 Ready z 447 Y 13 Int 0 0 602 3 282 1 029 L 0 33 T 10 05 R 2 03 fo o000 T noo K oooo ooo iT Wsten e gt A E B pxcetiburtversion 1 3 B crysis RED c t 1200 5 Provide acrystal name and set parameters as required Usually you would only record a movie in the lower Kappa position E NOTE Reducing the Phi step size to 4 degrees rather than 1 degrees greatly reduces the disk space required to save the movie A 3 or 4 degree Phi step size will usually be sufficient 6 Specify the directory where the movie will be recorded using Browse for dir and then click on Start movie The crystal sample will now be rotated about the Phi axis in the specified steps and record a movie of the sample E NOTE It is a good idea to keep
3. MAINTENANCE INSTRUCTIONS 3 Record details of the test in the local radiation log stipulating the date person testing outcome and signature 9 13 Checking the X ray Radiation Levels Task Time 20 minutes When Once a month Tools Radiation meter Procedure 1 With the X ray generator on at normal settings and the shutter closed use the radiation meter to sweep the area around the X ray tube housing fast shutter and collimator for any radiation leak inside the enclosure 2 Close the protective enclosure doors and open the X ray shutter command sh o in CrysAlis CCD 3 Sweep the outside of the enclosure using the radiation meter paying particular attention to the plane of the X ray tube the area of the secondary beam stop mounted on the enclosure window and the door seals 4 Record details of the test in the local radiation log stipulating the date person testing outcome and signature 9 14 CCD Detector Pumping Out Vacuum Task Time 16 hours When Once a year Tools Special T tool 1 set of Allen keys Rotary vacuum pump capable of obtaining a pressure of 1x10 mbar Vacuum tubing and adaptor Procedure 1 Switch off the cooling water KMW200CCD chiller unit 2 Detach water pipes from top of CCD detector these are self sealing although there may be a few drops of water have something absorbent to hand 3 Unscrew top access plate of CCD detector See figure 9 14 1 for
4. m Niggli cell a 5 96570 b 9 03330 t 1840670 p 30 01 050 P 30 0120 Y 90 03130 m Niggli form aa 25 58958 bb a1 60051 ce 338 8060 be 0 03047 ac 0 02300 ab 0 02944 Original Change Figure 6 5 35 Screenshot of the GRAL plug in Niggli Window 7 The GRAL plug in provides a list of possible Bravais lattice and highlights in blue the programs preferred choice Figure 6 5 36 shows the ORTHORHOMBIC P lattice as the preferred choice Clicking on Apply will accept the plug ins choice however anyone of the alternatives may be selected by clicking on the option in the text box and then clicking Apply six i Settings EY Load Centering f Niggli Jo Lattice m Current cell amp 5 96570 b 9 03330 t 1840670 ot 90 01 050 P 90 0120 Y 90 03130 r Transformation matrix from original cell o000 0 0000 0 0000 0000 1 0000 2 0000 0 0000 2 0000 1 0000 Option 32 err 0 096 ORTHORHOMBIC P lattice R int MONOCLINIC P lattice R int MONOCLINIC P lattice R int MONOCLINIC P lattice R int TRICLINIC P lattice R int Cancel Apply Help Figure 6 5 36 Screenshot of the GRAL plug in Lattice Window 8 Following Niggli reduction the centring of the cell is re examined Click on Apply Version 1 4 Xcalibur_Manual_v1 4 Xcal i b u r Page 68 USER MANUAL OPERATION c ax T Settings E Load fe Centering p Niggli p Lattice
5. resolu average mean mean tion A measured kept unique redundancy F2 F2 sig F2 Rint inf 1 66 570 559 6 9 7 50724 25 93 48 0 026 1 66 1 29 834 831 6 11 4 17633 54 39 76 0 030 12951512 659 654 6 10 3 10832 96 23 90 0 035 1 11 1 00 503 489 6 9 2 5639 11 13 81 0 043 11 00 70 93 363 356 6 8 4 4112 17 10 73 0 052 0 93 0 87 289 282 6 8 0 2199 86 EAS 0 064 0 87 0 82 220 208 6 qub 1922 69 5 67 0 086 0 82 0 78 154 139 6 Fed 1600 45 4 54 0 095 0 78 0 T5 102 082 6 6 7 1268 05 3 69 0 124 0 7550 VL 482 458 6 2 8 853 13 2 63 0 133 inf 0 71 13176 13058 1610 8 1 11698 16 24 52 0 034 6 5 3 6 Changing the Output Format from Data Reduction Data reduction is a time consuming process which mainly consists in extracting profile information This information is stored in a rrp file which can be used for repeating the data reduction finalisation e g with a different rejection Laue group To redo the final stages of data reduction 1 Type dc rrp and select the relevant rrp file 2 A window such as figure 6 5 18 will be opened This window allows the user to do the last stages of data reduction applying Lattice extinction absorption correction 2 theta limits etc The window also allows the user to output data in an alternative format and or with direction cosines r Outlier rejection nique Absorption correction C Don tuse outlier rejection T Apply numeric correction No face information availablel
6. ssssssssseeee nennen nnne nnns 121 9 10 Aligning the Enhance Ultra X ray Source sssssessseee eene mnes 124 9 10 1 X ray Beam Alignment of Enhance Ultra ssesem 124 9 10 2 Optic Alignment of Enhance Ultra em 126 9 10 3 Collimator Alignment of Enhance Ultra sssss m 127 9 10 4 Aligning the beam to the centre of the goniometer Enhance Ultra 127 9 11 Checking the Door Safety Interlocks ssssee eene 128 9 12 Checking the Emergency stop sssssssseeeeee ener nennen nennen 128 9 13 Checking the X ray Radiation Levels eene 129 9 14 CCD Detector Pumping Out Vacuum ssssesee eene meer nnns 129 9 15 Dismantling XcallDUr 2 35 2 eae petant ec iem etia dtes 131 10 Trouble Shooting 1i i Ee ee eret eric 134 TVs SPAl OS MR 137 12 Disposal Instructions iiri cerrrrr eee coo een eee tnnt 139 12 1 X ray T be and CCD Detector ie iden n e T eR RR RH AEn 139 12 2 Third Party Equipment i b e HE RR Ms aA cel lag lameutans 139 13 Additional Information eeeeeeernneneeneee 140 13 1 Third Party Information iiit em ean PER HERR ERR DR ne 140 13 2 Drawings irrita e ei tle dee debe ee tige ie ce ebd e eae 141 13 2 1 Mechanical Drawings eira eena aia AAAA aE RENAA A m nennen menn nennen 141 OD 01 00 15 C Xcalibur Suggested Layout 141 OD 01 00 01 System and
7. MECHANICAL CHANGEOVER OF DETECTORS AND X RAY SOURCES Two positions of the X ray tube mounting plate Mo left and Cu right 7 2 1 Location of Enhance retaining and adjustment nuts Under the front of the Enhance X ray tube shield unscrew the nut 1 found below the spring see Figure 7 2 1 Remove the nut 1 the spring and the two washers and put them aside for later Lift off the Enhance X ray tube shield and carefully place it on its side optic collimator housing face upwards in a safe place Cover the open hole in the optic housing to prevent the entrance of dust Unscrew the four M8 bolts holding the base plate which was under the Enhance X ray tube shield Re position the plate on the second set of four holes and replace the four bolts screwing them into the tower below see Figure 7 2 1 for respective Mo and Cu positions Take the new Enhance X ray tube shield and place it onto this plate so that the threaded mounting rod pass through the plate and the front mounting point rests on the vertical adjusting screw in the plate Onto this rod place the spring with a washer on either side and then the nut 1 see Figure 7 2 1 Tighten the nut 1 until the spring is compressed and the Enhance X ray tube shield is securely mounted and resting on all three vertical adjustment screws two at the rear and one at the front Reconnect the cable to the shutter Reconnect the earth cable to the back of the Enhance X ray tube sh
8. Maximum resolution in d value Mo 0 386 0 373 0 366 Detector opening angle 47 4 35 9 23 5 Version 14 Xcalibur Manual v4 Xcalibur Page 9 USER MANUAL SPECIFICATIONS 3 3 3 Sapphire 3 CCD Detector Active area CCD chip Pixel size on scintillator Scintillator material Fibre optic reduction Peltier cooling Temperature stability Analogue to digital resolution System noise so called read noise Dark current Control processor Communication Correlated double sampling CDS speed Readout time complete duty cycle including chip readout CDS analogue to digital conversion transfer detector PC disk storage 90 92 mm diagonal Kodak KAF4301 E 31 um Gadox 1 3 1 low distortion reduction taper 50 C four stage cooler 0 05 C micro processor PID True 17 bit lt 10 e RMS 0 06 e pix s MC 68322 2 mono directional fibre optic taxi channels 1 5 MHz 2 8 s 4 x 4 binning 4 4 s 2 x 2 binning 3 3 3 1 Sapphire 3 CCD Detector Theta and Resolution Ranges Detector to sample distance 40 mm 60 mm 80 mm Detector position minimum 90 0 105 0 111 0 Detector position maximum 111 0 127 0 134 0 Maximum resolution in 2 theta 135 6 145 8 149 0 Maximum resolution in d value Mo 0 383 A 0 371A 0 368 A Detector opening angle 49 2 37 7 24 9 Version 14 Xcalibur Manual v4 Xcalibur Page 10 USER MANUAL SPECIFICATIONS 3 3 4 Onyx CCD Detector
9. Active area CCD chip Pixel size on scintillator Scintillator material Fibre optic reduction Peltier cooling Temperature stability Analogue to digital resolution System noise so called read noise Dark current Control processor Communication Correlated double sampling CDS speed Readout time complete duty cycle including chip readout CDS analogue to digital conversion transfer detector PC disk storage 165 mm Kodak KAF4301 E 60 um Gadox 2 5 1 low distortion reduction taper 50 C four stage cooler 0 05 C micro processor PID True 17 bit 10 e RMS 0 06 e pix s MC 68322 2 mono directional fibre optic taxi channels 1 5 MHz 2 8 s 4 x 4 binning 4 4 s 2 x 2 binning 3 3 4 1 Onyx CCD Detector Theta and Resolution Ranges Detector to sample distance 60 mm 80 mm 100 mm Detector position minimum 90 0 102 0 111 0 Detector position maximum 112 0 119 0 126 0 Maximum resolution in 2 theta 144 6 146 7 149 7 Maximum resolution in d value Mo 0 373 A 0 371A 0 368 A Detector opening angle 65 3 55 4 41 0 Version 14 Xcalibur Manual v4 Xcalibur Page 11 USER MANUAL 3 3 5 PC CCD Interface SPECIFICATIONS Communication Control processor Memory Drivers Typical host computer 2 mono directional fibre optic taxi channels TI DSP C31 Sapphire TMS 320C6205 Sapphire 3 Onyx 32 Mb WinXP Sapphire 2 Sapphire 3 Onyx Pentium II
10. Hffabatbmp Pain RE 08 51 Figure 6 5 26 Screenshot of crystal movie screen crystal shape 13 At any time the faces you have added to the model can be observed edited using the Faces menu in the tool window NOTE E The Faces menu in the tool window highlights invalid faces by a Invalid faces can occur when the user enters a wrong custom hkl or adds a face which invalidates other faces inbierieci CrysAlis RED CCD camern date reduction un EI Gdi DOT ass Crystal movie H i Fie Faces Log Unites Preferences 100 000011520 40 ooos oo UU0021084 EL 000 Q00016041 no aw 100019000 QUU QUU 1 001730 Status enoe Ms P Hide Messa O 57 00 T 30 00K 13400 P 171 00 3 HKL 000 0 00 1 00 D 0 17330 Reety F Show tool window E Xa50v i58Int 00709 3294 1717 L0 33 T 10 30 FC1 00 jo 0000 0000 K 0000 P 0000 i Stat AWS BE ifcrysatis RED c BA xcaiiburvirsion 13 Sif ebs bmp Paint F 08 42 Figure 6 5 27 Screenshot of crystal movie screen 14 Click on Exit to leave the model builder Version 1 4 Xcalibur_Manual_v1 4 Xcal i b u r Page 62 USER MANUAL 15 OPERATION Save the model to disk using the command wd p and supply a filename E NOTE Keep the intermediate results of your model building so that you can go back to a previous result Make it a habit to choose meaningful filenames like sample
11. Mount the 1mm collimator cap Type card raw on 0 5 Fine adjust the collimator x and y adjustment screws 7 and 8 see Figure 9 10 1 Repeat 6 7 until the X ray beam is visible as a single intense circular spot Finally dismount the 1mm collimator cap and re mount the 0 6 mm cap Type card raw on 1 Adjust the collimator x and y adjustment screws 7 and 8 Repeat 9 10 until the X ray beam is visible as a single intense circular spot The X ray beam and focusing optics are now fully aligned We now need to point the focused X ray beam through the centre of the diffractometer s sphere of confusion The sample position 9 10 4 Aligning the beam to the centre of the goniometer Enhance Ultra 1 Set X ray generator settings to 12 kV and 1mA 2 Flip beamstop to the up position see Figure 9 10 2 3 Mount the alignment disc with a 0 3 mm pinhole on a goniometer head and place on the goniometer 4 Optically align the alignment disc at the centre of the goniometer as with a crystal sample using F12 etc 5 Move the detector to 60 mm using km4 detector 60 6 Type card raw on 0 5 Version 1 4 Xcalibur Manual v1 4 Xcal ibu r Page 127 USER MANUAL MAINTENANCE INSTRUCTIONS 7 We are looking for an image of the X ray beam with no shadowed areas resulting Adjust the screws on the mounting plate of the Enhance Ultra which reorient the whole assembly to point the focused X ray beam in the correct direction Remember that the
12. 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 Version 1 4 Xcalibur_Manual_v1 4 Xcal l b u r Page 148 USER MANUAL Weekly Maintenance Record Sheet Week Date of Name of person Signature Comments No maintenance performing test 51 52 Monthly Maintenance Record Sheet Month Date of Name of Signature Emergency X ray Comments maintenance person Stop Check radiation performing OK check OK test Y N Y N Version 1 4 Xcalibur_Manual_v1 4 Xcal ib u r Page 149 USER MANUAL Six Monthly Maintenance Record Sheet Date of Name of Signature Comments maintenance person performing test Yearly Maintenance Record Sheet Date of Name of Signature Machine CCD detector Comments maintenance person parameter vacuum performing file refined pumped test YIN YIN Xcalibur Version 1 4 Xcalibur Manual v1 4 Page 150 USER MANUAL Appendix 5 Example of Local Rules for the Xcalibur System Set Up at Oxford Diffraction An example of the Local Rules for the Xcalibur system set up at Oxford Diffraction is provided for information Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 151
13. 3 1 6 X ray Radiation pode Le e dee e deed eee dee RE ee A AA 3 1 7 Extreme Temperatures x tainen ER Dee EUN ena as 4 TWOP VACUUM a tsp LU eL ANI ESL E dte 5 1 9 High Pressutes 2 ood t eei boo br iei Pin bob etie beta re Da asbq iieri e ibo then 5 1 10 Hazardous or Toxic Materials ssssssssssssssseseeeeeneeeen enne emere nennen 5 1 11 Modifications and Service ssssssssssssssssssssssesseeneneee nme neer testen nnns 5 2 Introduction ect fi ioo aai hot Hoi 6 Van SCOPC ETE 6 2 2 How To Use This Mantab aae aae riaa eatae eda a keria aea idaraan iiy 6 2 9 SyStem OVOrVieW 35 3 2 tatem eia pietate f tte 6 CERSDIMDeuj tfe 7 3 1 Environmental Requirements sssssssssssssesee eene nennen rre nnne 7 3 2 90 VICOS 15 cc d eii e b Uri i bitte secu Adieu ted inchs A bal Teo above E 7 3 2 1 Electrical Supply dE e de Lr e co tr el aus 7 32 2 Water Coolinig 4 intero aed c e qa Cut as Dux eee ee qae vx eine 7 3 2 3 Helium Gas Supply where applicable sssssssssseeeRR 8 3 9 Performance Data 5 5 tinte mte ERU S PRADESH ETRRI TH RUP AETATIS DTE 8 3 3 1 X ray Tube Typical Operating Conditions 8 3 3 2 Sapphire 2 CCD Detector 2 0 0 2 2 ce cececcecceceeeeeeeeeeneeeceeeeeeesecencaeceeeeeseseccaeaeeeeeeeseseeesncieeeeees 9 3 3 2 1 Sapphire 2 CCD Detector Theta and Resolution Ranges 9 3 3 3 Sapphire 3 CCD Detector aiieieo ea a d a a ea a a e Aeg 10 3 3 3 1 Sapphire 3 CC
14. 5 2 1 2 System Layout mite Rr ro tne i 25 5 2 1 3 Electrical Services ssssssssssssssssesee eene 26 5 2 1 4 Water Supply 5 aede b gi eti Intt aaa 27 5 2 1 5 Low Temperature Option eene 27 5 2 1 6 CCD Camera Pumping ssseseeeenee ener 27 5 2 1 7 Helijet Option dne ree ae eee 27 5 2 2 Setting to WoR areen enee d teu aae e epe dea ene eene nip 28 5 2 2 1 Equipment Required esssssssssssssssese enne nnne 28 5 2 2 2 Personnel Required for Installation cccccecceceeceeeeeeeeneeceeeeeeeseteeesenaeeeeees 28 5 2 2 3 Setting up PrOGCedUres i e p ge eb dt a cem UE tun 28 5 3 SIOr age decet ne en d Lum c dd ne tutte ure fro sette 30 meni cup Me m 31 06 1 Controls and Indicators Rede ree pee e pt ee elated ee ag 31 6 2 Initial Switch on Procedure sssssssssssssseseseee eren ener 32 6 3 X ray Tube Warm up Procedure ssssssssssssseeeee nennen nemen nennen 33 e melo T IR HR 34 6 4 1 Software Updates ssssssssssssssssssssssenee nennen nennen enne rre nnne res 34 6 4 2 Software Installation i22 hat eec t qe nta Heus te iet baie nins ate eda 35 6 4 2 1 MGC interface software sssssssssssssssese eene emen 35 6 4 2 2 CrysAlis Software teet Eee be eed zo bedient Lodi deu aie eed 36 6 4 3 Changing Machine Correction and Set up Files ssssseeeee 36 Version 1 4 Xcalibur Manual v1 4 Xc
15. 7 Angstroms unless a new unit cell has been determined Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 71 USER MANUAL OPERATION Ewald sphere explorer x Exit Show Skip filter Flags Turn90deg Turn 90deg Clear Drag Properties Help Rotation axis fx ey Ciz Slow rotation alej o200 Edit Fast rotation 4j gt 3 000 Edit r Zoom 4 1 100 Edit L Lattice Stereog M Drag Select C Draglndex Show al C used C skip C wrong Gee Intensity skip on Figure 6 5 41 Screenshot of Ewald explorer screen 4 Click on Draglndex This will allow you to specify three non collinear vectors to define a UB matrix and thereby a unit cell 5 Click on the button b order radio button and then mouse click on the lattice and drag out a vector as shown below The corresponding d value is shown below the a order button Count the diffraction orders you covered and enter the value in by clicking on the button order b Exit Show Skip filter Flags Turn 90deg Turn 90deg Clear Drag Properties Help 7 x Rotation axis C x 2 ol yO C z 9 Slow rotation 0 200 Edit Fast rotation gt 3 000 Edit Zoom MA 1 100 Edit F Lattice T Drag C Select Draglndex UMS Dragilndex axis C a order 4 00 order a4 0 104 0 003 0 432 d 6 392 b order 7 00 order b 0 047 0 434 0 008 d 11 367 C c order 1 00 order c eeee Show all C used C skip C wrong
16. 73 54286 Edit r3 I al 48934087 Edit al T be 0 00065 Editbe M o0 0 26653 Edit 00 Iv t0 0 63198 Edit 0 T k0 0 06821 Editk M po mno Edit ao M Detector Help wdi 0 49103 Edit d1 Ww d2 0 19800 Edit d2 F a3 ani Edita Cancel IV x 50474444 Editx IV y0 53110288 Edity Iv dd 5307038 Editdd Fb3 mogan ANG 1209090 E EL d Le 6 5 71 Screenshot of Refine Model Constraining all Unit Cell Angles to 90 degrees Click on the tick box marked Goniometer until the box is empty Click on the tick box marked Detector until the box is empty Click on the tick box marked dd until the box contains a tick Click on Edit dd and input the detector distance which has been read off the scale on the Xcalibur E NOTE You must be within 1mm of the correct dd detector distance or else refinement may fail 12 13 14 15 16 Version 1 4 Click on OK The detector distance dd will now be refined and details are output to the history window You should routinely check this output by scrolling up the history window An immediate indication of the quality of the model is given in the block of text that reads Residuals wR form DA 0 009309 SX 0 001827 SY 0 002769 H 0 006834 K 0 004917 L 0 006349 Resid 0 014452 This gives a Resid ual refinement value This should be close to 0 0000 but will typically be of the order of 1 296 here 0 014452 or 1 445296 when the machine mo
17. completeness and 2 5 coverage 7 Click on the Optimize button The Optimiser dialog appears We will first find the optimal theta Select only theta so that a tick is present in the theta tick box Click on From To Xcalibur_Manual_v1 4 Xcal i b u r Page 84 USER MANUAL Version 1 4 OPERATION and Step Enter the values 40 40 and 2 respectively Select Completeness to 100 from the General Properties drop down menu Click on OK When the computation is complete click on the Coverage radio button This will give the values 8096 complete and 4696 coverage 1 o 135 0 71 0 at 32 0 0 0 0 0 The optimum theta is 32 The scan range has been enlarged to cover the collision free zone Elle Edit Colo es Look H DESEE EE Instrument Run list optimizer Optimization parameters x0 519 3 y0 510 8 dd 52 8 d 117 090 0 681 6 00 0 0 1020 2 k0 0 1 al 50 2 l omega scan 540 5108t 30 0 25 0 260 0 b2 0 0 wave 0 709 L 0050 notused peak l0 THETAAXIS beam stop 15 0 3 0 not used 2 From 0 0 To 00 Step 10 0 Current run 1 0 540 510at 3 KAPPAAXIS Optimize Duplicate Iv From 0 0 To 0 0 Step 10 0 PHI AXIS vs resolution Iv From 0 0 To 0 0 Step 10 0 Conpletenes Res Data Th Scan axis OMEGA AXIS 10 85 1 72 131 1 72 1 36 144 v From 0 0 To 0 0 Step 10 0 1 36 1 20 149 1 20 1 09 152 TH 3 1 599 Ot 142 Min width 30 0 Enlarge 10 0 0 90 0 86 130 General
18. geo applyinverseflood geo buildgrid Grid building from geometric correction image geo buildgrid threshold surrounding8pixelaverage threshold threshold for finding peaks in the grid image surrounding8pixelaverage second threshold to specify an 8 pixel surrounding average geo chessboard Compute chessboard pattern to visualize the geometric corrections geo chessboard geo cleargrid Clear geometric correction grid geo cleargrid geo computeflood Compute geometric flood field correction geo computeflood geo distortion Compute geometric correction for x and y pixel position GEO DISTORTION xinpix yinpix xinpix 7 pixel position in direction x yinpix 7 pixel position in direction y geo editgrid Editing of the geometric correction grid geo editgrid geo help help overview of geo commands geo help geo imagedividebypixelsize Divide currently displayed image by pixel size geo imagedividebypixelsize destination source scalefactor destination destination buffer Source source buffer scalefactor scale factor applied to the result image geo loadcorrectionfile Load geometric correction file geo loadcorrectionfile gon check Stadi4 goniometer zero check gon check gon help help overview of gon commands gon help gon init Xcalibur goniometer initialisation gon init gon sync Stadi4 goniometer synchronization gon sy
19. is insufficient for this task 18bit 262k readout gives the best technically available match 4 2 10 Anti blooming Scientific CCDs use 100 of their surface for image detection If a very bright object is shines onto the CCD the full well of the chip may be exceeded and charges may spill bloom into neighbouring pixels There are optical video CCD designs which sacrifice a small part of the sensitive area to implement an anti blooming gate which takes off overflowing charges For integrative flux measurement it is better to spill the signal the integral stays correct rather than loosing the charges in the anti blooming gate integral lost 4 2 11 Vacuum The CCD chip and the fibre optic taper are confined in a vacuum enclosure to isolate them thermally and to prevent condensation on the cold detector parts Static vacuum degrades with time due to degassing of the components in the vacuum enclosure The system is designed to maintain a sufficient vacuum level in the enclosure for at least 6 months A bad vacuum can be recognized by the fact that the detector cannot be cooled to the set operating temperature of 45 C This can be monitored using the software program ODBench accessible through the plugin menu of CrysAlis Loss of vacuum is also indicated by a blinking green light red light off on the top of the CCD detector Pumping the vacuum enclosure is a regular service task A normal rotary vacuum pump is sufficient for this
20. measurement Collisions the instrument has only a limited angular access due to its construction The user has to find a optimal combination of runs in a multi parameter space scan type omega or phi goniometersettings theta detector setting kappa phi omega detector distance The DC OPTI strategy software finds the optimal combination of runs by a systematic search of the parameter space The software optimizes a chosen run at a time For this it takes the current instrument model and the UB and Laue group and predicts the pattern for a given parameter combination The outcome is merged with the prediction of the constant runs and the coverage completeness is computed If a parameter set is better it replaces the current best parameters NOTE E The prediction computation scales with cell volume Try to scale the cell volume to 200 500 to keep computations to a reasonable size NOTE EI To a first approximation the run list optimization is independent of the current UB matrix provided that the completeness is close to 100 Using the point detector we were used to measuring a particular class of unique reflections e g Pmmm only with hkl positive The area detector will always measure for a given run set the same portion of the Ewald sphere but choosing different classes of hkl The following section describes a worked example of how to optimise a run set for a typical sample Try and work through the pr
21. 050 25 noes it oon 172 00 2590749 C Centrosymmetric Lo Non Centrosymmetric Cancel Apply Help Figure 6 5 38 Screenshot of the GRAL plug in lt E2 1 gt Window 10 GRAL now examines the systematic absence exceptions where applicable and provides a statistical table for user confirmation of its preferred choice of space group Figure 6 5 39 shows the space group P2 1 2 1 2 1 selected The user can accept this choice by clicking on Apply or select from one of the alternative choices when present Version 1 4 Xcalibur_Manual_v1 4 Xcal i b u r Page 69 USER MANUAL OPERATION c E T Settings E Load E Centering p Niggli p Lattice E Centering B lt E2 1 gt J Space Group Systematic absence exceptions 21i b c n 21 a c n 21 a b n N 3 338 337 337 Ge SB pL SE pe 55 5 58 NI gt 3s 0 266 242 244 Oo dst 426 429 oss a2 39 lt I gt One 954 11 85 1257 Od 41974 18 0 dove OD 12 73 14 5 13 0 SI s 1173 25 3 28 8 30 5 40 4 38 2 37 3 22A O6 26 1 30 3 25 5 Space Group No C A Enant OptAct Piezo Pyro CCDC ICSD Riint Nieq P2 1 2 1 2 1 Y Y yo A Y Y Y 0 029 2099 Figure 6 5 39 Screenshot of the GRAL plug in Space Group Window 11 Finally GRAL prepares a ins file for use with structure solution programs The user can edit the molecular formula and Z number in the relevant boxes shown in figure 6 5 40 Clicking on Test allo
22. 0770 mP 0 6236 4 3 35 9 0304 5 9798 18 3358 90 5494 90 4427 90 0770 mP 0 6236 Dp 3 44 5 9798 9 0304 18 3398 90 4427 90 5494 90 0770 aP 0 6236 9 Select a particular reduced cell e g Cell 1 orthorhombic primitive oP type um c 1 NOTE E The command um c followed by a transformation matrix can be used to change the current unit cell settings 10 Save the results of peak hunting and unit cell determination to disk using the wd ph and wd p commands 6 5 3 4 Data Collection Now that we have determined the unit cell parameters we can proceed with the full data collection as follows 1 In the program Crysalis CCD type dc editruns and follow the on screen instructions providing a filename for data collection Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 48 USER MANUAL OPERATION Name ofexperiment est Help Clipboard Data collection directory C My Documents yxtldata Browse Total of frames 0 Disk space required Mbytes 0 00 DC frames Disk space available Mbytes 14084 56 Ref frames Approximate data collection time h min 0 00 run scan pars type start end width time speedratio gonio pars omega detector kappa phi to do done i T Activate reference frames reference runs frequency 1 per 0 dc frames Change ref freq Edit run Delete run Import run list Export run list Clear run list Clear done runs Selection to new Change frame width Change exposure Chan
23. 1 3 2 Slide the rail up to the position shown front end of mounting rail in line with the front surface of the universal theta arm taking care to prevent the camera sliding too far forwards into the kappa block and also supporting the weight of the camera Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 105 USER MANUAL MECHANICAL CHANGEOVER OF DETECTORS AND X RAY SOURCES Figure 7 1 3 2 Mounting the Onyx CCD Position of the detector as it is mounted onto the rail 7 Rotate Onyx to be parallel to the rail and continue pushing forward until the front screw hole is visible Replace the front screw Do not fully tighten Figure 7 1 3 3 Mounting the Onyx CCD replacing the front screw 8 Slide the Onyx camera backwards until the middle screw hole is visible Replace the middle screw Then tighten all three screws on the rail Figure 7 1 3 4 Mounting the Onyx CCD replacing the rear screw Version 1 4 Xcalibur Manual v1 4 Xcal i b u r Page 106 USER MANUAL MECHANICAL CHANGEOVER OF DETECTORS AND X RAY SOURCES 9 Finally slide the Onyx camera forwards until the block on the end of the drive shaft can be rotated upwards 10 Turn the end fixing plate clockwise by 180 degrees and fix the CCD slider into place using two screws Connect the fibre optic cables and water pipes to the back of the camera 11 Turn the CCD camera on by turning the key on the front of the KMW200CCD chiller clockwise The red light
24. 17 Screenshot of CrysAlis data reduction screen special corrections 53 Figure 6 5 18 Screenshot of CrysAlis data reduction screen outlier rejection 55 Figure 6 5 19 Screenshot of CrysAlis data reduction screen output format ssssss 55 Figure 6 5 20 Screenshot of data reduction finalisation window sess 56 Figure 6 5 21 Screenshot of ABS Acquisition of movie screen ssssssssseeeee 58 Figure 6 5 22 Screenshot of crystal movie screen ssssssssssseee eene 59 Figure 6 5 23 Screenshot of crystal movie configuration screen sssssseeeeeee 60 Figure 6 5 24 Screenshot of crystal movie screen ssssssssessseeeeeeene eene 61 Figure 6 5 25 Screenshot of crystal movie screen sssssssssssseee eene 61 Figure 6 5 26 Screenshot of crystal movie screen crystal shape sssssseess 62 Figure 6 5 27 Screenshot of crystal movie screen ssssssssssseeee eene 62 Figure 6 5 28 Screenshot of crystal movie screen ssssssssssseeeeeeene ener 64 Figure 6 5 29 Example of absorption correction ssssssssssssseee eee 65 Figure 6 5 30 Screenshot of the GRAL plug in Settings sse 65 Figure 6 5 31 Screenshot of the GRAL plug in Load Window on initialisation no file loaded 66 Figure 6 5 32 Screens
25. 260 000 GEM Mso 25 NE GE R or uico Soo Pgyomiss QT m 3a 2 1133 Figure 6 5 55 Screenshot of Unwarp Wizard Step 2 Select Output Directory 6 Click on the New layer button define the required layer for reconstruction using the 3 vectors Select 2d laue symmetry averaging if required Use 2d laue symmetry averaging when the symmetry of the crystal is KNOWN This will enable faster and more complete layer reconstruction Only the data required to define the unique part of the layer need be present in the data collection Click on OK rysAlis unwarp assistent unwarp layers gt Step 3 Creation of a layer list Layer reconstructions may create a lot of files Try to organize them into a sub directory of your data directories Output base name perse 8a Output path C My Documents xtldata BaTh Sel 8 de Browse for output dir oh ok ol llh llk digit l2h l2k 121 res n New layer Cancel Figure 6 5 56 Screenshot of Unwarp Wizard Step 3 Creation of a Layer List Version 1 4 Xcalibur_Manual_v1 4 Xcal i b u r Page 80 USER MANUAL OPERATION NWARP Add a reconstruction layer C no 2D Laue averaging 0 00 0 00 0 00 Ger egrenon unites Figure 6 5 57 Screenshot of Unwarp Wizard Step 3 Add a Reconstruction Layer 7 If required click on the tick box marked background subtraction Click on Next TySAlis unwarp assistent background evaluation Figure 6 5 58 Screenshot o
26. 4 Centering Lattice exceptions P a B Cc ar F Obv Rev All N total 0 2520 2522 2524 2513 3783 3362 3353 5042 N int 3sicgma M o H D n H D N e H iD Co Iu H fa tn N N Iu H N tn en ao N tn N w co iD I i o o m o H m o H Oo tn m m H o e H m to H N H H Mean intensity Mean int sigma Wir Negi ei ial UOS es 2576 25o 25 r Lattice type giz CA CB we r1 CIE C Obv C Bev Intensity divided by 1000 Figure 6 5 37 Screenshot of the GRAL plug in Centring Window After Niggli Reduction 9 The data are now examined for acentric or centric E statistics The user can then choose between Centrosymmetric or Non centrosymmetric settings by clicking on the relevant radio box and clicking on Apply dix T Settings E Load e Centering p Niggli p Lattice B Centering By lt E2 1 gt Experimental Acentric Centric Hypercentric for n 2 lt E gt 0 785 0 886 0 798 0 718 E 2 0 817 1 000 1 000 1 000 lt E 3 gt AOL lt 1 329 gt 1 596 1 916 E 4 1 414 2 000 3 000 4 500 E 5 2 169 c3og2d 6 383 12 260 lt E 6 3 597 6 000 15 000 37 500 E E 1 Dd 0 736 0 968 1 145 lt E E 1 2 gt 0 780 lt 1 000 gt 2 000 3 500 lt E E 1 3 gt 1 366 2 415 8 691 26 903 number of asymmetric units in one cell n 2 n 3 n 4 n 5 n 6 n 7 n 8 nau n 10 n 11 n 12 Soe k Deen OVO STS Sato pa ic ete 3317
27. A h k I the machine h k I optional Indices of the reflection to use otherwise the programme will use the current angular setting 6 6 Normal Shutdown 1 Gradually reduce to zero the voltage and current settings on the X ray generator When at zero press button marked XR OFF and turn key switch marked MAINS to off position 2 Switch off Xcalibur goniometer interface using the green power on off switch located on the far left of the unit s front panel 3 Switch off fibre optic light source located inside protective enclosure 4 Switch off KMW200CCD using turn key MAINS switch 5 Turn of mains water supply to chillers 6 7 Emergency Shutdown The emergency shutdown procedure should be used e fthere is a fire or any other emergency requiring the evacuation of personnel from the area AND e The procedure can be performed without endangering any persons safety Version 1 4 Xcalibur Manual v1 4 Xcalibur Page 101 USER MANUAL OPERATION 6 7 1 Emergency Shutdown Procedure 11 Press red emergency stop button located on the front left of the Xcalibur WARNING The emergency stop button will only shut down power to the X ray generator Other equipment on the Xcalibur system will still be powered on 12 Switch off all power at the mains electrical supply 13 Turn of mains water supply Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 102 USER MANUAL M
28. ANC M E eaae Select C Draglndex Show al C used C skip C wrong Intensity skip on Re ady West 5 0 NEED OS O 43280 r 30000 k 25 000 P 260 000 Amm Qu orde munro M xcalibur ig CrysAii Srintensiys Hajom OG v8 a2 0146 Figure 6 5 48 Screenshot of Ewald Explorer Mark Invisible Skip Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 75 USER MANUAL OPERATION x x Rotation axis a x Cyt 30 Slow rotation gt A 0 200 Edit Fast rotation 3 000 Edit 0 700 Edit hd 4 gt F Stereog M Drag B un c 1 UB fit C Dragindex v UB M Show al C used C skip C wrong Ve Wavelength 0 70930 Mo pt ewa e j v ica Intensity skip on Ready O 43280 T 30 000 K 25 000 P 260 000 O WBst 25 e E EI gt 56 y orde munro Fr xcalibur A Bi CrysAri Hf mark invi 1 Bossa al ota k 01 47 Figure 6 5 49 Screenshot of Ewald Explorer Mark All Invisible Peaks Skip EN 4 Clicking on the Show radio button skip will not show these peaks since the intensity filter is still in use To view these peaks go to the menu bar at the top of the Ewald explorer window and from the Skip filter menu select Intensity The Skip filter intensity window will appear Click on the Use intensity filter radio box until the tick disappears and the box is empty 5 Click on OK Select the Show skip button from the bottom left
29. Beryllium is potentially toxic material 2 Ensure that the collimator is correctly fitted as incorrect mounting may result in exposure of X ray radiation Select the required size of collimator and push into position on the Xcalibur such that it is flush to the housing surface 11 Mount video tower Screw into position 12 Mount DC power supply Attach to support arm or back of goniometer table Xcalibur PX 13 Mount fibre optic power supply Attach to support arm 14 Mount video monitor Lift monitor into position and secure from below 15 Mount video telescope camera Slide video camera into video camera support arm 16 Connect halogen cabinet lights Attach fibre optic lights cabinet vents and Xcalibur remote control 17 Using 5 persons lift chiller units into position see layout drawing OD 01 00 15 18 Connect cables Do not connect to mains power and water pipes as per wiring instructions refer to electrical drawings and third party manuals listed in chapter 12 19 Fill chiller water reservoirs see the third party manuals 20 Connect mains power Turn on power as described in initial switch on procedure chapter 6 21 With the X ray generator settings at 0 kV and 0 mA Turn on water to chillers very slowly at first and check for leaks around the X ray tube shield and all water connections including chiller units and the back of X ray generator 5 3 Storage Before installation commences or
30. Beryllium oxide Version 1 4 Xcalibur_Manual_v1 4 Xcal l b u r Page 33 USER MANUAL OPERATION If the X ray tube is stored for a lengthy period the vacuum may become impaired We recommend carrying out the following warm up procedure for new tubes and tubes that have not been used for more than 100 hours Perform the warm up procedure as follows 13 Switch on the tube with settings of 0 kV and OMA 14 Set to 10kV and OmA 15 After waiting for 3 minutes switch to 20kV and 10mA 16 After waiting for 3 minutes switch to 30kV and 20mA 17 After waiting for 3 minutes switch to 40kV and 30mA 18 After waiting for 3 minutes switch to 45kV and 35mA 19 After waiting for 3 minutes switch to 50kV and 40mA 20 Wait at least 5 minutes If after completion of this procedure a flashover occurs in the next 30 minutes repeat the whole procedure If the tube has been used within 100 hours or less then perform the above procedure using half minute steps rather than 3 minute steps 6 4 Software Normal operation of the Xcalibur system requires the use of the CrysAlis software which contains two main applications named CrysAlis CCD and CrysAlis RED CrysAlis CCD is used for control of the Xcalibur system during data collection whereas CrysAlis RED is used for data reduction The CrysAlis programs can be controlled either through command line input using short cut commands such as dc s data collection start or via mouse driven menu
31. Figure 6 5 2 Screenshot of CCD parameters window sseseeeeen eee 40 Figure 6 5 3 Screenshot of CrysAlis RED showing a diffraction image with beam stop mask 40 Figure 6 5 4 Screenshot of CrysAlis program options Instrument model l 41 Figure 6 5 5 Screenshot of CrysAlis program options beam stop settings ssssssss 41 Figure 6 5 6 Screenshot of CrysAlis program options PH and PT size aeee 42 Figure 6 5 7 Screenshot of CrysAlis profile inspector window sse 43 Figure 6 5 8 Optical alignment of the crystal ssssssssssseeeeneene eene 44 Figure 6 5 9 Rotation photograph sssssssesseeeeene nennen nennen nnne nennen ASAA RA 45 Figure 6 5 10 Screenshot of axial photograph orientation screen ssssseeeee 46 Figure 6 5 11 Screenshot of Edit data collection runs ssssseeene enn 47 Figure 6 5 12 Screenshot of Edit data collection runs seseee emen 49 Figure 6 5 13 Screenshot of CrysAlis data reduction screen crystal lattice 51 Figure 6 5 14 Screenshot of CrysAlis data reduction screen run list 51 Figure 6 5 15 Screenshot of CrysAlis data reduction screen scan width ssssssuss 52 Figure 6 5 16 Screenshot of CrysAlis data reduction screen background evaluation 53 Figure 6 5
32. Figure 6 5 60 An Example of a Reconstructed layer ssssssee eene 82 Figure 6 5 61 Screenshot of Run List Optimiser ssssssseeeeneeneeemerenn 84 Figure 6 5 62 Screenshot of Run List Optimiser Crystal Properties sssssssesss 84 Figure 6 5 63 Screenshot of Run List Optimiser Optimisation Parameters sssssss 85 Figure 6 5 64 Screenshot of Run List Optimiser Coverage Statistics sss 86 Figure 6 5 65 Screenshot of Data Reduction Special Corrections ssssssse 90 Figure 6 5 66 Screenshot of Data Reduction Editing of Twin Overlap Fraction 90 Figure 6 5 67 Screenshot of Powder Rings and Line Profile seeeee 91 Figure 6 5 68 Screenshot of Powder Pattern Data Plotted via a Spreadsheet Program 91 Figure 6 5 69 Screenshot of Refine Model Window sssseeeen eee 92 Figure 6 5 70 Screenshot of Refine Model Constraining all Unit Cell Lengths to be Equal 92 Figure 6 5 71 Screenshot of Refine Model Constraining all Unit Cell Angles to 90 degrees 93 Figure 7 1 3 1 Mounting the Onyx CCD rotated mounting rail with screw positions 105 Figure 7 1 3 2 Mounting the Onyx CCD Position of the detector as it is mounted onto the rail 106 Figure 7 1 3 3 Mounting the Onyx CCD replacing the front screw
33. Figure 9 10 4 Image during optical alignment of Enhance Ultra Version 1 4 Xcalibur_Manual_v1 4 Xcal l b u r Page 126 USER MANUAL 9 MAINTENANCE INSTRUCTIONS Adjust the x and y tilt screws and type card raw on 0 5 Repeat point 5 until an image results where the maximum intensity resides on the right hand spot This is typically 5 5 turns of each of the x and y tilt screws from point 1 above screws are 1 4 mm pitch 20 turns range Position the mouse cursor over the right hand spot Right mouse click and select integration at pixel position Record the intensity figure from the history window Fine adjust x tilt screw i e screw 5 1 in Figure 9 10 1 Type card raw on 0 5 Repeat points 6 7 until a maximum intensity figure results Fine adjust y tilt screw i e screw 5 2 in Figure 9 10 1 Type card raw on 0 5 Record intensity of the right hand spot as in point 6 above Repeat point 8 until a maximum intensity figure results The optics are now aligned 9 10 3 Collimator Alignment of Enhance Ultra 1 10 11 Remount the collimator by pushing on and tighten the grub screws 2 see Figure 9 10 1 Note the collimator has a specific orientation We now need to align the collimator Dismount the 0 6 mm collimator cap by sliding it off Type card raw on 0 5 Adjust the collimator x and y adjustment screws 7 and 8 see Figure 9 10 1 Repeat 3 4 until the X ray beam is visible as a single intense circular spot
34. Intensity skip on Figure 6 5 42 Screenshot of Ewald explorer screen with vector shown 6 Repeatthe previous bullet point for a order rotate through 90 degrees and repeat for c order Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 72 USER MANUAL OPERATION 7 Click on the button UM S to set the UB matrix based on the Draglndex vectors and exit the Ewald explorer using the OK button and select Yes if you are happy with your results ATTENTION Potential loss of crystal information e Do you wantto replace the current UB Figure 6 5 43 Screenshot of dialog box displayed when exiting the Ewald explorer 8 Index the reflections by typing um i and repeat if necessary A percentage figure of merit for the cell is displayed 9 Sometimes a negative and non standard cell will result so we apply a lattice reduction by typing um reduce which invokes the Bravais reduction normally automatically invoked by um f The high Niggli reduced cell which indexes the most peaks is chosen automatically 6 5 4 1 Drag Selection of Reflections and Marking them as Skipped 1 Making sure that the Select radio box is selected Depress the left mouse button drag out a wire box around the reflections to be skipped right mouse click and select Mark selection skip These reflections will then turn red in colour indicating they are skipped Ewald sphere explorer Hl jag Exit Show Skipfilter Flags Turn930deg Turn 90deg ClearDrag
35. Properties Help Rotation axis Cx 8 yC Cai Slow rotation 0 200 Edit Fast rotation 3 000 Edit Zoom lt gt 0 900 Edit T Stereog Drag C Dragindex Mark selection used SN al C used C skip C wrong Wavelength 0 70930 Mo EET Intensity skip on X 480 Y 162 Int 1 11 860 4 275 10 763 L 0 83 T 29 42 R 0 72 O 43280 T 30 000 K 25 000 P 260 000 O HA Start um ONE GG Qworddocume m xcalibur manua Bil crysAlis RE poa op ve C 95 k 0137 Figure 6 5 44 Screenshot of Ewald Explorer Drag Selection of Reflections and Marking Skip 2 Click on the used radio box Only those white reflections to be used in unit cell indexation and not the red skipped reflections or wrong ie Unindexed reflections are now shown Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 73 USER MANUAL OPERATION RED C lel x Ewald sphere explorer x Hl jag Exit Show Skipfilter Flags Turn90deg Turn 90deg ClearDrag Properties Help Rotation axis x ey tz Slow rotation ale 020 Edit Fast rotation 3000 Edit Zoom oso Edit T Lattice M Stereog M Drag Select C Draglndex J E y E p Show 4 C all used C skip C wrong Peak t B Peak ti Wavelength 0 70930 Mo pt ewa ors Intensity skip on 490 162Int 1 11 860 4 275 10 763 L0 83 7 29 42 0 72 O 43 280 T 30 000 k 25 000 P 260 000 O CrysAli Wstn ASB
36. Some of the maintenance instructions in this section require the use of special tools that have been supplied with Xcalibur The illustrations below identify these special tools Key 1 Screw onto CCD detector 2 Attach vacuum tubing 3 Plunger Figure 9 1 1 T tool Figure 9 1 2 Special tool 1 9 2 Refining the Machine Parameter File Task Time 4 5 hours When After adjustment of beam collimator CCD detector position etc Otherwise twice a year Version 1 4 Xcalibur Manual v1 4 Xcal ib u r Page 115 USER MANUAL MAINTENANCE INSTRUCTIONS Tools Ylid test crystal C49H44SO Procedure See section 6 5 12 9 3 Changing the X ray Tube of Enhance Task Time 30 mis When Sealed source X ray tubes have a limited useful lifetime Operation of a 3 kW tube at typical output of 2 kW will normally provide 10 000 hours of use actual values may vary see third party manual Note X ray tubes also have a limited shelf life Tools Set of Allen keys Set of flat headed screwdrivers Water receptacle e g Bucket Procedure 1 Turn of all power and water to the Xcalibur and chiller units 2 Leave for at least 20 minutes to ensure that the X ray tube is not hot test temperature before proceeding CAUTION Have a receptacle ready to receive water from the pipes and X ray tube shield 3 Disconnect water pipes from back of X ray tube shield These are attached with quick re
37. Taper cooling electronics Be Figure 4 2 1 Schematic of a fibre optic coupled CCD detector for x rays X rays enter the vacuum detector enclosure through a Be window The photons are intercepted by a scintillation screen which transforms the X rays to visible light The light is conducted towards the CCD detector via a fibre optic taper The CCD chip integrates the light dose received from the taper Its electric signal is then amplified and digitised in a readout circuit The central component of the detector is the CCD chip which is situated in a vacuum enclosure The vacuum enclosure isolates the chip thermically and protects it from condensation in the cooled state The CCD chip requires cooling to reduce its dark current The chip is cooled by a Peltier cooler which dissipates its heat into a Cu heat sink which is water cooled by the CCD water chiller The Peltier is powered with 100W to maintain the CCD chip at an operating temperature of 45 to 50 C A number of security systems ensure that the Peltier will not overheat the detector due to lack of cooling The CCD detector power supply is supplied by the CCD water chiller which checks the water flow rate and temperature In the case of loss of cooling water the chiller shuts down the CCD power supply Additionally there are two heat sensor on the heat sink which shut down the system when the heat sink is gt 40 C The CCD chip has a size of approximately 25 x
38. Version 1 4 Xcalibur_Manual_v1 4 Xcal l b u r Page 19 USER MANUAL TECHNICAL DESCRIPTION 4 4 X ray Generator AMEN goa Cum COMPACT 3K5 x ray generator Figure 4 4 1 C3K5 X ray Generator front panel Figure 4 4 2 DF3 X ray Generator front panel Xcalibur systems can be supplied with either the C3K5 Ital Structures or the DF3 Spellman X ray generator The X ray generator is located in the electronics rack in the instrument cabinet The generator power trips out if the X ray tube overheats Warning lights on the front panel indicate the operational status of the generator Further information about the X ray generator can be found in the third party manual supplied with this equipment Version 1 4 Xcalibur_Manual_v1 4 Xcal i b u r Page 20 USER MANUAL TECHNICAL DESCRIPTION 4 5 Software The programs controlling the measurement procedures of the system are WIN32 applications which run under Windows XP The data acquisition is done with the program CrysAlis CCD and the data reduction with the program CrysAlis RED 4 5 1 Directory Structure The CrysAlis program system is installed in the following directory structure Windows program files directory typically C Program Files Xcalibur root typically C Program Files Xcalibur Corrections directory correction Site directory sitename ffi par ccd and geo correction files These files describe the machine setup Log directory log log This
39. Write parameter file wd p filepath filename filepath filename Optionally you can put the path and filename on the command line Note that you have to use quote for filenames with spaces wd cal Save current parameters into current setup file wd cal wd help help overview of wd commands wd help wd inc Save current image non compressed wd inc filepath filename filepath filename Optionally you can put the path and filename on the command line Note that you have to use quote for filenames with spaces wd ph Save peak hunting table raw profiles wd ph filepath filename filepath filename Optionally you can put the path and filename on the command line Note that you have to use quote for filenames with spaces wdt Save peak table indexed xyzs without wd t filepath filename profiles filepath filename Optionally you can put the path and filename on the command line Note that you have to use quote for filenames with spaces wi window height of the analyser WI wi wim wi wim 7 window level for the counting chain 0 0 2 55 xx S Installation and test command Allows the xx is time n x y xy xz same image to be recorded n times with output of statistics within a defined box time time in secs n number of images xxi Installation and test command Allows the xx i time n same image to be recorded n times time time in secs n number of images zca finds the theta zero and the equator horizon of ZC
40. be input by clicking on the individual boxes and typing in the parameters Version 1 4 Xcalibur Manual v1 4 Xcal i b u r Page 65 USER MANUAL OPERATION 3 x T Settings Load m Cell parameters Ea r Errors of cell parameters z umm EB Bd EN af mnm mmm umm F Read parameters fram file radiation Append Show reciprocal space EN T Settings Load m Cell parameters 5042 DC GAINSG HKL 90 01200 90 03130 r Errors of cell parameters 0 00220 b 00140 c ou fo 01110 p roo 7 x Enzo A Iv Read parameters from file radiation Show reciprocal space 0 71073 Cancel Apply Help Figure 6 5 32 Screenshot of the GRAL plug in Load Window File loaded from DC GAINS HKL 3 Selecting the Show reciprocal space tick box provides a 2D view of reciprocal space and the distribution of data by sigma as depicted in Figure 6 5 33 This reciprocal space view can be adjusted by hkl planes and zoomed in and out 4 Atany point click on Apply to progress to the next window Version 1 4 Xcalibur Manual v1 4 Xcal i b u r Page 66 USER MANUAL OPERATION ET Settings E Load m Cell parameters 9155 26 Q SO 1000 v i PM Take Append lv Read porum from file espe E Iv Show reciprocal space Cancel Apply Help Figure 6 5 33 Screenshot of the GRAL plug in Load Window R
41. beam is only 0 2 0 3 mm diameter Small adjustments are necessary or you may pass the correct position 8 Repeat points 5 7 until the X ray beam is centred on the 0 3 mm hole Enhance ULTRA is now aligned 9 Re mount the Enhance ULTRA front face panel and secure using the screw 1 see Figure 9 10 1 10 Goto alignment of the beam stop 9 11 Checking the Door Safety Interlocks Task Time 2 minutes When Once a week Tools None Procedure WARNING Ensure interlocks not defeated Interlock override key is not present or activated No warning buzzer to be heard If interlock defeated there is the risk of exposure to X ray radiation 1 With Xcalibur in normal operation and at normal X ray generator settings open the front doors of enclosure cabinet The X ray shutter should immediately close 2 Close the enclosure doors 3 Toreset the system type sh c shutter close in CrysAlis CCD and restart data collection if relevant using ctrl r 4 Record the date persons testing and sign off the outcome 9 12 Checking the Emergency stop Task Time 10 minutes When Once a month Tools None Procedure 1 With the Xcalibur running at minimum settings for example 28 kV 2mA for Mo press red Emergency Stop button 2 The X ray generator should switch off immediately Restart X ray generator Return to required settings Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 128 USER MANUAL
42. diffractometer The X rays are generated by a sealed tube which is mounted on the goniometer and powered by the high voltage X ray generator The X ray optics consist of a high speed shutter located next to the tube shield a monochromator for selecting a specified bandwidth from tube spectrum and a collimator for limiting beam divergence The sample can be viewed with the video microscope which is attached to the stand doming the instrument 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 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 via a fibre optic data link to the frame buffer located in the PC workstation The control program reads the data from the frame buffer to the PC workstation and stores it for further data analysis to the hard disk 4 2 CCD Detector Technology This section introduces the CCD X ray detector technology as implemented in the Sapphire and Onyx detectors A fibre optic coupled CCD detector for X rays is schematised in fig 4 2 1 Version 1 4 Xcalibur_Manual_v1 4 Xcal l b u r Page 15 USER MANUAL TECHNICAL DESCRIPTION scintillator
43. enclosure door closed Maximum radiation dose due to scattering 0 18 uSv h with Mo 3 kW tube operating at 2 2 kW door open with shutter closed Version 1 4 Xcalibur_Manual_v1 4 Xcal l b u r Page 8 USER MANUAL SPECIFICATIONS 3 3 2 Sapphire 2 CCD Detector Active area CCD chip Pixel size on scintillator Scintillator material Fibre optic reduction Peltier cooling Temperature stability Analogue to digital resolution System gain for Mo System noise so called read noise Dark current Control processor Communication Correlated double sampling CDS speed Readout time complete duty cycle including chip readout CDS analogue to digital conversion transfer detector PC disk storage 90 92 mm diagonal 1024 x 1024 pixels Sapphire 2 Kodak KAF 1001E scientific grade grade 1 60 um Gadox absorption gt 90 Mo K a 2 5 1 low distortion reduction taper 45 to 50 C four stage cooler 0 05 C micro processorized PID 18 bits in single read 30 e X ray lt 6 e RMS lt 0 2 e pix s TI DSP C50 2 mono directional fibre optic taxi channels 2 x 37 5 kHz 3 1 s 2 x 2 binning 14 s 1 x 1 binning 3 3 2 1 Sapphire 2 CCD Detector Theta and Resolution Ranges Detector to sample distance 40 mm 60 mm 80 mm Detector position minimum 105 0 116 0 116 0 Detector position maximum 110 0 126 0 138 0 Maximum resolution in 2 theta 133 7 144 0 152 3
44. following standard s or other normative document s when installed in conformance with the installation instructions contained in the product documentation EN 55011 Group 1 Class A for radiated emissions EN 55011 Group 1 Class A for mains conducted emissions EN 50082 2 Conducted Immunity ESD and EFT EN 50081 2 Generic emissions standard EN 50082 2 Generic emissions standard Pertinent LVD sections of EN 61010 1 1993 Amendment A2 1995 Safety requirements for electrical equipment for measurement control and laboratory use Part 1 General requirements Technical Information is maintained at Oxford Diffraction Ltd 20 Nuffield Way Abingdon Oxfordshire OX14 1RL United kingdom Last two digits of year of CE Marking low Voltage Directive 00 We the undersigned hereby declare that the product s specified above conforms to the listed directive s and standard s Signature Full Name Position Date Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 145 USER MANUAL Appendices Appendix 1 X ray Tubes Wave Lengths Anode Ka Ka Kp Ka Ko 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 n
45. for Interchange of the Molybednum and Copper Enhance X ray Source 108 8 Maintenance Schedules eeeeeeeeeeeeeeeessss 112 821 MtrODUGHION e D 112 8 2 Weekly Maintenance Schedule sss eene nnne 112 8 3 Monthly Maintenance Schedule sssssssssee eene eene nennen enne 112 8 4 Six Monthly Maintenance Schedule ssssssssseeseeeeee nemen 113 8 5 Yearly Maintenance Schedule sss eene enne nnns 113 8 6 10 000 Hours Maintenance Schedule ssssesessssssee nennen 114 9 Maintenance Instructions eeeeeeeeeeeeeeeeeees 115 91 Special TOONS 3 itr M E d erba e PER redeo bet E re reet ds 115 Version 1 4 Xcalibur Manual v1 4 Xcal i b ur Page v USER MANUAL 9 2 Refining the Machine Parameter File sssseeneene enne 115 9 3 Changing the X ray Tube of Enhance eene 116 9 4 Changing the X ray Tube of Enhance ULTRA ssssssseee eene 117 9 5 X ray Beam Stop Alignment sssssssssssssseeeeneeeene nennen ener enne 119 9 6 Changing the Collimator of Enhance ssssssesseeee eene eene 120 9 7 Changing the Collimator of Enhance Ultra sssen mn 121 9 8 Aligning the X ray Collimator of Enhance sssseee eene 121 9 9 Aligning the Enhance X ray Source
46. images to the disk needs additional disk space default not used Cancel Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 52 USER MANUAL OPERATION Figure 6 5 16 Screenshot of CrysAlis data reduction screen background evaluation 6 5 3 5 5 Special Corrections When data have been collected using incorrect parameters this step will allow you to override the parameters written into the images Standard data reductions should skip this step simply clicking on the Next button Step 5 Special corrections The special corrections can be classified as expert corrections If data were collected with wrongly set parameters this dialog allows you to override the parameters written into the images Standard data reductions should skip this step Special corrections properties Back I Cancel Figure 6 5 17 Screenshot of CrysAlis data reduction screen special corrections When the data reduction is for a difficult poor sample a number of the special corrections may need to be applied adjusted For instance To adjust the peak finding window Start data reduction as normal and observe the size of the black mask placed over the reflections If this mask is too large or small then its size can be adjusted 1 Click on Special Corrections and select the tab marked Peak finding 2 Click on the tick box marked User LL mask then click on the button Edit LL mask This defines the minimum size of the mask used in
47. line If the filename is specified on the command line the open run file dialog is skipped run 7 The number of the run to be repeated frame The number of the frame to be repeated dc opti Initialise run list optimiser dc opti dc ref Reference frames inspection dc ref dc visualizecorrections Visualize data reduction corrections dc visualizecorrections typeofcorrection L P AIWI S scalefactor typeofcorrection L lorentz correction P polarization correction A air path correction W window absorption correction S scintillator correction scalefactor scale factor with respect to the ideal image 1 0 dc editruns Set up data collection strategy dc editruns filepath filename dcs Data collection start dcs dcr Data collection restart dc r filepath filename dc red Data collection reduction initiate guided dc red routine dc rrp Data reduction finalization dc rrp dc unwrap Reciprocal space reconstruction dc unwrap dl speed parameter setting DLvN v Deg Sec phi scanning speed 0 01 lt v lt 3 0 N discrimination level 0 N lt 10000 en End program and park goniometer En ga Gain setting amplification in the counting GA g chain g 7 gain for the counting chain 0 0 150 0 gta goto angles gt a om th ka ph omega theta kappa phi om omega angle th 7 theta angle ka 7 kappa angle ph phi angle gt d Moves
48. lt interval lt 32000 om tol requested omega repeatability 0 0025 Deg lt om tol lt 10 Deg int_tol allowed intensity fluctuations parameter number of sigmas by which a fluctuation triggers the recentering 1 lt int_tol lt 100 hkl Miller indices of ref reflection 126 lt h k lt 126 at attenuation filter use 0 1 0 filter out 1 filter in scale3 scale3abs Initialise absorption correction shape optimisation routine scale3 scale3abs scale3 scale3pack Initialise scale3pack data scaling plug in scale3 scale3pack script start a script A script is an ASCII file with the extension mac and contains a sequence of CrysAlis commands which will be executed one after another script filepath filename filepath filename Optionally you can put the path and filename on the command line Note that you have to use quote for filenames with spaces Script help help overview of script commands Script help scs scan speed PD SC S Vo Vo scan speed 0 004768 Deg Sec lt Vo lt 1 5 Deg Sec sct scan type PD SC T Tx f Tx threshold angle deg 0 0 Deg lt Tx lt 90 0 Deg f multiplier for theta motor 0 0 lt f lt 2 0 sc W scan width SC W Oa Ob C Oa scan width omega 0 0 Deg lt Oa lt 180 0 Deg Ob scan widening parameter 0 0 Deg lt Ob lt 2 0 Deg C scan center shift parameter 1 0 lt C lt
49. on the camera will start to flash as the camera starts its cool down procedure 12 Drive all angles back to zero gt a 0 0 0 0 13 Set the detector distance to 130mm gt d 130 and open the cabinet door Drive theta to 90 degrees gt t 90 and 90 gt t 90 and check that there are no potential collisions with the cabinet 14 Once the camera is fully cooled collect a short data collection Xcalibur calibration run and refine the machine parameter file as described in section 6 5 12 CAUTION The wd cal command will overwrite the current diffractometer set up file Calibration of the diffractometer may be lost at this point if an invalid model exists 15 When a good model has been refined store the new detector offset by typing ZC detector dd where dd is the expected detector distance e g 50 0 mm this will type a detector distance offset into the parameter file then save the remaining parameters by typing wd cal NOTE E Back up files of the parameter file are automatically created of format bup 7 1 4 Removal of the Onyx CCD camera WARNING Two people are needed for this procedure The Onyx camera is heavy The Onyx is a delicate electronic instrument If dropped it may be damaged and warranty will be invalidated 1 Drive the detector distance to 100 mm gt d 100 and the theta arm round to 90 degrees gt t 90 2 Turn the camera off by turning the key on the front of the KMW200CCD chill
50. or death Only personnel qualified to work with high voltages and currents should perform service or maintenance work on such equipment 1 3 Mechanical Handling Safety WARNING 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 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 Oxford Diffraction to carry out service work on this equipment should attempt to dismantle modify or repair the equipment Water connections should be made and tested in accordance with any local and national safety regulations 1 5 Moving Parts There are a number of moving parts in the system which are powered by electric motors N WARNING Injury could result if clothing or body parts become caught in moving mechanisms Keep clothing hands and body parts away from moving mechanisms 1 6 X ray Radiation WARNING This equipment contains an X ray tube Ensure that safe working practices relating to radiation are employed Follow any local national o
51. out TOP 4 4 OIN 4 lWH3d4dl3s 10 11 12 13 14 BOTTOM Mount Seiffert and Philips X ray tubes so that the tube label is upside down as shown above with the cooling water flowing in through the top and out at the bottom Figure 9 3 1 Position of the X ray source Secure temperature sensor to base of X ray tube Reconnect water supply to back of X ray tube shield Align X ray optics as described below BOTTOM Mount older tubes manufactured by AEG as shown in the diagram above Replace the front plate of the Enhance by tightening the two grub screws holding it to the optic housing Switch on water and power to Xcalibur and chiller units 9 4 Changing the X ray Tube of Enhance ULTRA Task Time When 30 mins Sealed source X ray tubes have a limited useful lifetime Operation of a 3 kW tube at typical output of 2 kW will normally provide 10 000 hours of use actual values may vary see third party manual Note X ray tubes also have a limited shelf life Version 1 4 Xcalibur Manual v1 4 Xcalibur USER MANUAL MAINTENANCE INSTRUCTIONS Tools Set of Allen keys Set of flat headed screwdrivers Water receptacle e g Bucket Procedure 1 Turn off all power and water to the Xcalibur system KMW200CCD and KMW3000C chiller units 2 Leave for at least 20 minutes to ensure that the X ray tube is not hot test temperature before proceeding CA
52. properties m2 m Friedel yes 0 83 0 80 125 Global coverage to 100 xl HIE a Global coverage to 100 rd i rd i Finished at Fri Sep 28 11 Cancel dc opt R199 65Int 13 6 746 2 443 5 477 L0 33 T 15 86 R 1 30 o 46 400 T 30 000 k 25 000 P 260 000 N Figure 6 5 63 Screenshot of Run List Optimiser Optimisation Parameters 8 ANOBE SOS mm mic zv Hoc EM A3 o me a RS 33 11 31 Now we want to optimise kappa Click on Optimize and this time select only kappa and enter the values From 80 To 80 Steps 10 The result is 92 8 1 o 124 0 43 0 at 32 0 30 0 0 0 Try and optimise phi From 180 To 180 Steps 20 no improvements NOTE E In optimizing a one run data collection essentially only theta and kappa are relevant E NOTE If you have fully optimised a run set and the completeness or coverage values are not 100 or the values you are aiming for then you will need to add additional runs using dc editruns and optimise 10 Save your work by clicking on Export and providing a file name Exit the run list optimiser 11 Type dc editruns and add a new omega run Start dc opti again We now have two runs and mutual optimization is possible Click on the Coverage radio button this shows that the Version 1 4 new run has almost no influence as it stands Xcalibur Manual v1 4 Page 85 Xcalibur USER MANUAL OPER
53. 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 Always lift packing cases from the bottom using suitable lifting equipment refer to list of component weights in the following section Move packing cases into the designated installation site Contact Oxford Diffraction to notify them that the equipment is awaiting installation by a factory trained service representative 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 Version 1 4 Xcalibur_Manual_v1 4 Xcal l b u r Page 23 USER MANUAL 5 1 3 Mechanical Handling 5 1 3 1 Weights Dimensions and Lifting Points HANDLING INSTALLATION STORAGE AND TRANSIT INFORMATION Description NET Dimensions Centre of gravity Lifting points Weight width x height x depth kg cm Kappa 106 43x 64 x A7 Offset from centre of At four corners goniometer unit towards side of DO NOT lift from X ray tube mount below X ray 40 48 x 22x 69 Centre of unit From the sides and generator below Enclosure 15 115 x 100 x 100 N A N A Electronics 60 80x 85 x 80 Centre of unit By hand from top rack four corners otherwise from
54. 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 Never switch off the CCD detector s power supply when the KMW200CCD is operational To switch off the CCD detector use the KMW200CCD s switch 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 Xcalibur s electrical components 1 2 3 First Aid A course in first aid to include methods of artificial respiration is recommended for those whose work involves equipment that may produce a high voltage Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 2 USER MANUAL HEALTH AND SAFETY INFORMATION WARNING Do not attempt to administer first aid to someone who may have suffered electric shock until the source of the shock has been isolated Mains voltages are present in the system High voltages are used by the X ray tube and power supply These can cause serious injury
55. supply unit to CCD detector and video telescope camera This will not start at this time CAUTION Always switch the CCD on off via the mains switch on the KMW200CCD chiller The CCD detector could be damaged if the ON OFF switch on the CCD detector DC power supply is used 3 Turn on power to KMW200CCD chiller unit using turn key switch on front panels see relevant chiller manual The CCD detector and video telescope camera will now start CAUTION The CCD detector requires between 30 minutes and 1 hour cool down time DO NOT use until GREEN light is ON and RED light is OFF Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 32 USER MANUAL OPERATION On start up the CCD detector will carry out a self test Red and green lights indicate the state of the detector See table Red Light Green Light State of Detector Fast blinking Fast blinking Start up self test Slow blinking Off Hot plate too hot Peltier switched off On Off Set point not reached cooling according to program On Slow blinking Set point not reached cooling slower than expected Off On Cooled Ready for use 4 Switch on X ray tube generator chiller See relevant manual It will not start at this time 5 Switch on X ray generator using turn key switch marked MAINS if present or CONTROL POWER ON button Depress the button marked XR ON or X RAY ON See third party X ray generator manual NOT
56. task 0 04mbar 4 2 12 Fast Shutter The CCD X ray detector is an integrative detector The precision of the intensity measurement critically depends on the dose released by the X ray shutter The normal electro magnetic shutters are too imprecise for this task Specially designed fast and reproducible shutters have to be used Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 18 USER MANUAL TECHNICAL DESCRIPTION 4 2 13 Zingers and Cosmic Ray Events The silicon matrix of the CCD detector may also detect charged particles omni present in our environment These particles may produce sudden random intensity bursts in the CCD matrix due to their ionising nature The charged particles may be muons radioactive decay particles mainly from the taper glass and others Due to their random nature these events can be removed by taking two correlated exposures of the same scene 4 3 Four Circle Kappa Geometry Goniometer The four goniometer axis is driven by microprocessor controlled stepping motors with 12 800 microsteps per revolution O Figure 4 3 1 Goniometer phi kappa omega and theta axes The sample is aligned using a CCD video microscope The sample picture is displayed on a video monitor next to the goniometer and can also be displayed on the control computer by using the built in frame grabber A fibre optic halogen flood light system provides brilliant high contrast illumination of the sample at all goniometer positions
57. the CCD camera to a requested gt d dd distance dd detector distance in mm gte The gt e command has the same meaning as GT E ome the chi phi the gt a command but its parameters are the Euler geometry setting angles omega 2theta ome omega angle in deg chi and phi instead of kappa geometry setting the detector angle in deg angles omega 2theta kappa and phi chi 7 chi angle in deg phi phi angle in deg gto goto omega gt o om om omega angle gtt goto theta angle gt t th th theta angle gtk goto kappa angle gt k ka ka 7 kappa angle gtp goto phi angle gt p ph ph phi angle Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 95 USER MANUAL OPERATION gtr goto reflection gtrhkl h h index k k index index gt chi goto equivalent omega theta kappa phi gt c chi values for chi chi 7 chi angle in degrees gts Positions the goniometer at a specified GT S curset goset symmetric setting curset setting at current pos goset required setting for next move gt help Help overview of gt commands gt help gt orient Initialise guided axial photo routine once unit gt orient cell is known F1 Activation of the CrysAlis online help F1 F12 Activation of the optical alignment menu F12 ffi help help overview of ffi commands ffi help geo applyflood Apply flood field non uniformity correction geo applyflood geo applyinverseflood Apply inverse flood field non uniformity correction
58. the sample movie in a separate directory as a large number of files are generated for the movie 7 When finished click on Exit 8 You can now remove your sample from the diffractometer The remaining steps involve 6 5 3 7 2 Step 2 Build modify a 3 D model of the crystal sample software only The absorption correction contained within the CrysAlis software package allows a 3 D model of the crystal sample to be built using the jpeg movie recorded above This is achieved as follows Version 1 4 Xcalibur Manual v1 4 Page 58 Xcalibur USER MANUAL OPERATION 1 Start the application CrysAlis RED and read in the experimental data collection parameters by typing rd p 2 Note that this is going to load the UB matrix which you are using to evaluate the sample shape Alternatively you may run dc rrp to re load the parameters used in the data reduction 3 Type the command abs display to start the absorption correction module and select the button for show tool window The display should look like the screenshot below _CrysAlis RED CCD camera data reduction userinterface lel x File Edit ColorT pa E LCONEEEYTS File Faces Log Utities Preferences jpr file abs movie summary CAMy Documents tldata Customer Demos york sample 2 movie movie jpr Status 4 Goniom Help abs di Message from O 57 00 T 30 00 K 134 00 P 177 00 l hkl 500 00 500 00 500 00 X 469 Y
59. 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 drawing number OD 01 00 15 Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 25 USER MANUAL OPERATION When the low temperature option is fitted an extra 100 cm space on the left hand side of the system is required 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 A 3 phase 63 A supply with one 32A outlet and two 16A outlets Additionally four single phase outlets are required as described in drawing OD 01 00 015 C 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 with a resistance of less than 0 5 o
60. value Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 47 USER MANUAL OPERATION NOTE E To avoid having to redo peak hunting in the future save the current peak hunting table to disk using the command wd ph 6 Find the unit cell parameters by typing um f NOTE E In the case of unsuccessful indexation of a unit cell then the constraints applied to the unit cell lengths and angles can be relaxed or tightened This is achieved eg um f 0 3 0 3 0 5 This command will allow the length to deviate by 0 3 Angstrom the angles to deviate by 0 3 degrees and the fraction indexed to be 0 5 Alternatively type the command pt e to edit the peak table Remove some of the weaker reflections and retry indexing using um f 7 If this procedure fails to find a sensible unit cell type pt ewald which will initiate the Ewald explorer which allows interactive peak indexing Ewald explorer is mouse driven using drag select techniques to enable indexing of complex lattices see section 6 5 4 8 Once a unit cell has been obtained type um c to produce a table of all possible reduced cells along with a figure of merit last figure on right 62 here reduced form 71 0733 162 0899 668 2548 5 0861 4 1790 0 2886 possible lattices ly 3 32 5 9798 9 0304 18 3358 90 4427 90 5494 90 0770 oP 0 6236 24 34 5 9798 18 3358 9 0304 90 4427 90 0770 90 5494 mP 0 6236 Sy R 33 5 9798 9 0304 18 3358 90 4427 90 5494 90
61. view B8 Key LL mE zm 1 Vertical adjustment ff QL for back of Enhance 2 Horizontal adjustment gt n 7 screw SE 7 7 3 Locking screw for 4 BEEN i 4 Vertical adjustment for 5 mh O front of Enhance E 5 Screw holding the tube shield on the stand 4 Figure 9 9 3 Enhance X ray source adjustments front view Version 1 4 Xcalibur Manual v1 4 Xcal i b u r Page 123 USER MANUAL MAINTENANCE INSTRUCTIONS Key 1 Vertical adjustment for back of Enhance 2 Horizontal adjustment Screws 3 Locking screw for 4 4 Vertical adjustment for front of Enhance 5 Screw holding the tube shield on the stand T t Figure 9 9 4 Enhance X ray source adjustments top view 9 10 Aligning the Enhance Ultra X ray Source Task Time 1 hour from complete mis alignment When After installation movement Tools Set of Allen keys 9 10 1 X ray Beam Alignment of Enhance Ultra Procedure CAUTION Do not put the CCD detector in the X ray beam unless the generator settings are as indicated in step 1 below Otherwise the scintillator may be over excited and give off light even without X ray exposure If over exposure occurs let the scintillator de excite for at least 10 to 20 minutes Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 124 USER MANUAL MAINTENANCE INSTR
62. 1 1 setup correctionfiles CCD correction files setup correctionfiles setup detectortype detector type setup detectortype setup help help overview of setup commands setup help setup options program options setup options Version 1 4 Xcalibur_Manual_v1 4 Page 98 Xcalibur USER MANUAL OPERATION setup setupfile start up file setup file setup setupfile sho X ray shutter open sho shc X ray shutter closed shc sm ao Single measurement omega scan with angles sm ao om th ka ph scanwidth time om omega degrees th 7 theta degrees ka 7 kappa degrees ph phi degrees scanwidth degrees time seconds sm eta step scan moving every reflection vertically in SM ETA starteta step steps time the aperture window starteta starting eta value Actual goniometer position is assumed to be theta 0 0 step scanstep in deg steps number of steps for scan time exposure time in sec per step sm help help overview of sm commands sm help sm i time single image photo static of exposure time sm i time secs time time in secs sm rp 30 secs phi rotation photo sm rp smo omega scan sm o startangle scanwidth time smp phi scan sm p startangle scanwidth time smq records a q scan SM Qh kIst s1 sw1 u1 v1 w1 s2 sw2 u2 v2 w2 filename HKL indices of selected peak for which the Omega and Theta angles w
63. 1 4 Xcalibur_Manual_v1 4 Page 135 Xcalibur USER MANUAL TROUBLE SHOOTING operation the Hsync flags should read 1 This is located on the text line below the parameter button Click on OK 8 Type gon reinit in the command bar and press enter This will reinitialise all drives and leave the goniometer in its home position ready for operation 3 Emergency stop button pressed Release the emergency stop button by twisting clockwise and follow the instructions on PC Screen Power off interface wait 5 seconds and then power on Type gon reinit in CrysAlis CCD 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 Version 1 4 Xcalibur Manual v1 4 Page 136 Xcalibur USER MANUAL SPARES 11 Spares Fuses Power distribution Cabinet illumination Shutter driver KM4 interface COMPACT 3K5 x ray generator Version 1 4 Electronics rack rear 10A 250V fast panel Electronics rack rear 315mA 250V fast 5x20mm F3 panel Electronics rack rear 6 3A 250V fast 5x20mm F4 panel Shutter driver PCB 0 8A 250V fast KM4 interface front 2A 250V 5x20mm F5 panel C3K5 generator rear 1 6A 250V slow panel Inside C3K5 generator 20A 250V fast 10x38mm Inside C3K5 generator 2 5A 250V slow 5x20mm F3 8157 PCB Inside C3K5 generator 2A 250V s
64. 25mm arranged in 1024 x 1024 pixels In order to obtain an X ray sensitive area of 62 x 62mm the chip is coupled to fibre optic taper The taper is characterised by its reduction ratio The reduction ratio of the taper is measured in a factory calibration procedure and is typically 2 45 2 5 1 The large end of the taper is covered with scintillation screen The screen is composed of GdOS z Tb which is the most efficient screen material with respect to stopping power and light output Note that the screen thickness determines the resolution of the detector 4 2 1 Beryllium Window The 0 5mm Beryllium window is the entrance for the X ray photons into the detector unit The detector unit is held under vacuum to provide thermal isolation for the Peltier cooled CCD chip The Be window absorbs incoming X ray photons in the following way Radiation Pure Be Be with 0 1 contamination Cu Absorption coeff Transmission Absorption coeff Transmission mm mm Cu 0 11 94 6 0 14 93 2 Mo 0 02 99 0 06 97 Version 14 Xcalibur Manual v4 Xcalibur Page 16 USER MANUAL TECHNICAL DESCRIPTION 4 2 2 Phosphor The phosphor transforms the X ray photons to light The phosphor should be as thin as possible to provide resolution as thick as possible to absorb the incoming photons and as bright as possible to provide a high system gain The most commonly used phosphor for Cu and Mo radiation is Gd202S Tb whi
65. 286 E Ready Iv Show tool window Help Exit Ready lo ooo T ooo0 k ooo P 0 000 EE E stan AU A E amp Mail Summary Mein E Xcalibur version 1 3 CrysAlis RED C F 0449 Figure 6 5 22 Screenshot of crystal movie screen 4 Click on Browse and select the directory path and filename of the movie you recorded in step 1 above 5 Select the Preferences menu Click on Edit Scale Pix mm This should have a value of 0 002 Pix mm for the small magnification 6 Click on the movie window and define the centre of the crystal Do this by right clicking on the centre of the crystal image and select Define center Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 59 USER MANUAL OPERATION CrysAlis RED CCD camera data reduction user interface m _ E Edit ColorT pay H m mms Crystal movie configuration gt Fie Faces Log Utities Preferences Crystal movie Inverted video image amp etup alor m Zoom 1x poo 11an X130 4 Edit Y 248 poo o wu H Pix mm 0 002174 Edit Edit T Crystal back Priorimage Page up Units of 0 1mm 7 ie He oa e Add face r Draw r oe front X 373 Y 284 ree ex fo 0000 T 0000 K 000 Fon i T 08 36 0 0 709 3 294 1 717 L 0 33 T 10 90 R 1 88 Biccrysalis RED C E Xcalibur version 1 3 Hf abs mp Paint X 450 Y 158 Int sfstan ADE gt I e Figure 6 5 23 Screen
66. 32 0930 4460 L009 T 1380 RTT o 0000 T 0000 K 0000 09080 O Figure 6 5 9 Rotation photograph 2 Type wd ito save the image to disk 6 5 3 2 3 Axial rotation photographs 6 4 Axial photographs can be taken along the a b or c axis of the crystal These allow the crystallographer to determine if any symmetry is present in the sample This requires that the unit cell has been determined 1 Type gt orient This allows the crystallographer to select axial photographs along a b c or a b c 2 Click on calculate and then either sym ao or sym all 3 Change the exposure time and press the return key Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 45 USER MANUAL OPERATION onenter Axial and Burger images Vector Direchon Co Cb Co C Towards source x C hki C Towards beametop x C Towards front y Ca Cb Ce Towards back y C ww Towards top 2 C Towords bottom 2 mer Towards video camera Pst 0 00 Edit psi C Towards any vector Edit calc options Calcujate Help Cancel 1D J Thornas orientation calculation Wed Sep 27 23 13 02 2000 Ej Solution 1 GTa 0274 0 000 46 539 79 430 Omega scanning range 132 000 B6 726 45274 SM ao 2726 0 000 46 539 7 0 ime ISM ao 86726 DO 16539 79 430 132 000 ime GTa SM eo sym SM eo ell Figure 6 5 10 Screenshot of axial photograph orientation screen 4 Type wd i to save the image to disk 6 5 3 3 Unit Cell Determina
67. 4 Xcalibur Manual v1 4 Xcal l b u r Page 104 USER MANUAL MECHANICAL CHANGEOVER OF DETECTORS AND X RAY SOURCES 4 Drive the detector distance to 100 mm gt d 100 and the theta arm round to 90 degrees gt t 90 N WARNING During the following steps take care not to allow the camera to slide into the kappa block as the slider has very low friction The Onyx is a delicate electronic instrument If dropped it may be damaged and warranty will be invalidated Due to the construction of the Onyx camera cannot be mounted in exactly the same way as the Sapphire 2 and 3 cameras The camera must be rotated on it s mounting bar in order to prevent the front face of the camera colliding with the universal mount during the mounting procedure 5 Onthe underside of the Onyx the mounting rail is attached by three screws Before attempting to mount the camera remove the front and middle screws and slightly loosen the back screw Rotate the rail by about 20 as shown in figure 7 1 3 1 WARNING The Onyx CCD is heavy and it s weight must be supported by holding onto the CCD head as well as the mounting rail The Onyx is a delicate electronic instrument If dropped it may be damaged and warranty will be invalidated Figure 7 1 3 1 Mounting the Onyx CCD rotated mounting rail with screw positions 6 The rail can now be pushed into the universal theta arm of the Xcalibur with the Onyx camera held at an angle as shown in Figure 7
68. 459 Figure 6 5 25 Screenshot of crystal movie screen 10 Now repeat the above process to add the opposite edge of this face 11 Rotate the crystal to a face perpendicular to the first Drag out the four edges of the crystal defining 4 new faces including the top and bottom faces Do this as describe above NOTE E You need at least six faces to define a closed shape NOTE E In building an absorption model first define a rough envelope of the crystal This will give better results than trying to perfectly model the crystal on the first attempt 12 In the tool window select the button Crystal front A wire frame model box will appear on the crystal movie image The screenshot below shows a first approximation of the crystal shape Version 1 4 Xcalibur Manual v1 4 Xcal i b u r Page 61 USER MANUAL OPERATION Crys Alis RED CCD camera data reduchon user intorisoe Crystal movie Fis Foces Log Usitins Preferences r meea Zoom 6 1x Cx CA Rer puc x3m a gt Ed fes v 83 ajej Edit Soo Pix mrm 0002174 Edit Units of 0 1mm 7 Edit TON F Crystolirom Crystal back 6 P F Fac exes 3 HEL 0 00 0 00 100D 0 17390 X 206 Y 392 F Showtool window Help Ext k450Y 150Int 0 0709 3294 1717 L0 33 T 10 90 c1 60 lo 0000 fT 0000 k 0 000 P 0 000 E rs RBicrysatis nED C BB xeaiburversion 1 3
69. 8kV2mA0 1sec 11 Mount an xyz goniometer head with attached steel ball provided by the manufacturer this is mounted on top of a glass fibre attached to a brass pin and optically align 12 Drive the CCD detector to the zero position using the command gt a 0 0 0 0 within the CrysAlis CCD software application WARNING Take extreme care when working with Xcalibur with the interlocks defeated as exposure to X ray radiation is possible Do not allow any part of the body to intersect the X ray beam Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 122 USER MANUAL MAINTENANCE INSTRUCTIONS 13 Use the sm i 0 1 command to take a single image of the X ray beam on the CCD The image of the beam should show the beam with a shadow of the steel ball if the X ray beam is correctly centred on the sample position Using adjustment screws 1 and 4 adjust the vertical position of the X ray beam 14 Using screw 2 adjust the horizontal position of the X ray beam and record a single image of the beam using the command sm i 0 1 15 Repeat steps 13 to 14 until the image of the X ray beam is coincident with the sample position and shows a shadow of the steel ball Save a single image to disk when aligned using wd i 16 Enhance is now aligned Mount the beam stop and adjust using the 3 point adjustment See section Screw 1 Vertical shift Screw 2 Horizontal Figure 9 9 2 Enhance X ray source collimator adjustments front
70. ANUAL 10 11 12 13 14 Key Version 1 4 MECHANICAL CHANGEOVER OF DETECTORS AND X RAY SOURCES Disconnect the top water pipe at the rear of Enhance X ray tube shield and position a receptacle to catch the water contained within the tube shield Wait until the water has drained out of the Enhance X ray tube shield and then disconnect the bottom water pipe Disconnect the earth cable from the back of the Enhance X ray tube shield Pull out the Fischer connector cable from the back of the Enhance shutter located on the side of the X ray tube shield Remove the front plate from the Enhance by loosening the two grub screws holding it to the optic housing Disconnect the temperature sensor from the front of the X ray tube Remove the beam stop by unscrewing it from the top of the Enhance Remove the collimator from the optic housing Underneath the rear of the Enhance X ray tube shield note the two opposing horizontal adjustment screws Figure 7 2 1 unscrew both of these screws so that the Enhance X ray tube shield is no longer held by them gt o A o Front view of Enhance Rear view of Enhance Retaining nut holding Enhance X ray tube on to base plate and 3 Horizontal adjustment and N retaining nuts Xcalibur Manual v1 4 Xcal i b u r Page 109 USER MANUAL Figure 15 16 17 18 19 20 21 22 23 24 25 26 2T 28 29 30 31 32 33 34 35 Version 1 4
71. ATION Run list optimizer x Instrument p Run list experiment Crystal x0 519 3 y0 510 8 dd 52 9 d1 0 5 d2 0 1 o0 0 0 t0 0 2 k0 0 1 al 50 2 be 0 0 b2 0 0 wave 0 709 L 0 050 not used peak 10 not used beam stop 15 0 3 0 not used Sr 11 081 5 662 12 187 90 0 117 0 30 0 681 6 Res 0 800 Laue P2 m2 m2 m Friedel yes Current run i i Show 1 0 540 510at 30 0 25 0 260 0 C Run list C Help Optimize Duplicate Delete Add Coverage Coverage Clipboard vs resolution Completeness under Laue symmetry Coverage under Pl Res Data Theory Redundancy Total Data Theory 10 85 1 72 131 131 100 0 3 5 465 339 554 61 2 1 72 1 36 144 145 99 3 3 2 454 329 556 59 2 1 36 1 20 149 149 100 0 2 8 423 312 556 56 1 1 20 1 09 152 152 100 0 2 5 379 281 556 50 5 1 09 1 01 142 146 97 3 2 6 366 272 556 48 9 1 01 0 95 14 150 98 05 2 3 343 257 556 46 2 0 95 0 90 137 150 91 35 2 2 300 227 556 40 8 0 90 0 86 130 147 88 4 2 3 295 219 556 39 4 0 86 0 83 134 149 89 9 2 2 297 229 556 41 2 0 83 0 80 125 149 83 9 2 1 266 207 558 37 1 10 85 0 80 1026 1076 95 45 3 5 3588 2672 5560 48 1 Finished at Fri Sep 28 11 30 21 2001 Figure 6 5 64 Screenshot of Run List Optimiser Coverage Statistics 12 Select run 2 from the Current run drop down menu and click optimize Select theta and kappa for optimisation and click on OK This gives 98 2 completeness c NOT
72. Component Dimensions eee 141 13 2 2 Electrical Drawings iere erede en PERS 143 14 CE Conformity HOLl CB 2 ieu oiii tetti cces eese ie era teco 145 APppendiCeS ee M p REE 146 Appendix 1 X ray Tubes Wave Lengths ssssssssseeeeenn emen 146 Appendix 2 Standard Crystal Parameters sss 146 Appendix 3 Temperature Scales Conversion ssssssssssssseeeeee re rnrn 146 Appendix 4 Maintenance Records ssssssssssssssssssseeee ener enne neret 146 Appendix 5 Example of Local Rules for the Xcalibur System Set Up at Oxford Diffraction 151 Version 1 4 Xcalibur Manual v1 4 Xcal i b ur Page vi USER MANUAL Table of Figures Figure 4 1 1 Components of the Xcalibur system sssssseeene emen 14 Figure 4 1 2 View of the diffractometer ssssssssesseeenenene eene 15 Figure 4 2 1 Schematic of a fibre optic coupled CCD detector for x rays ssssssssss 16 Figure 4 3 1 Goniometer phi kappa omega and theta axes 19 Figure 4 4 1 C3K5 X ray Generator front panel 20 Figure 4 4 2 DF3 X ray Generator front panel sssssessssseeeeeeneene mener 20 Figure 5 2 1 Xcalibur installation procedure sssssseen enne 28 Fig re 6 1 1 Eocatioriof SwItChes iit mo orti been in ned dae Pata dit E a 32 Figure 6 5 1 Screenshot of Image selection and Zoom sse 37
73. D Detector Theta and Resolution Ranges 10 3 3 4 OnyX GCD Detector rci ie cma cR E tie pedet 11 3 3 4 1 Onyx CCD Detector Theta and Resolution Ranges sessssss 11 3 9 5 PC CCDXInte rface 5 ete e Re ed e pa tee dedo del evi aes 12 3 3 6 Four circle Kappa Geometry X ray Goniometer sssssseeeeen en 12 4 4 Electrical Data teh eheu e uM 13 A Technical Deseriplionhi ee odruccc s euccc aes ecos es e ocac kk cce ieu PEEL PBAP 14 CABOS 14 4 2 CCD Detector Technology orriari aai R A A ARTEARI 15 472 1 Berylliam Window ein d DH e d gie Tode ee 16 Ae 2 PNOSPINOK RESE em 17 4 2 3 Fapema iid iad ie eee dea i eA a ale ea 17 42 4 Dunne n eiie Melee a 17 4 2 5 Readout Speed e tee rite eR ERR ARRA RR RR RT o Ate RIT ERA BRE ART NAR FRRR AR RATER ESAE 17 Version 1 4 Xcalibur Manual v1 4 Xcal i b ur Page iii USER MANUAL 4 2 6 BING i edet in aay E ei a ee raton 17 4 2 7 Dark Current and MPP Mode ssssssssssssssssee eene eren 18 4 2 8 Radiation Damage oap etg d eerte d Gln desee iid ind niet dling dd ned dd ite 18 4 2 9 Full Well Depth and 18 bit Digitisation s mm 18 4 2 10 Anti bloomilhg 5 e Item i Pte Perth dtm ee ud Dun a dta e e had 18 4 211 Vacuum a e itt oq it e ER A Lese etes addet 18 42 12 East Shutter uoa iiti iiti eae Le libata al 18 4 2 13 Zingers and Cosmic Ray Events sssssssssssseeee emnes 19 4 3 Four Circle Kappa G
74. E Use the Coverage clipboard button to get the data to a graphing program like Excel via cut and paste This allows us to visualize the data collection progress by plotting frame vs coverage completeness redundancy It is sometimes astonishing how much time is spend to get 5 more coverage completeness 13 Version 1 4 Finally we need to optimise the scan range In dc editruns we set run two start end omega to 0 1 and in dc opti we optimize phi From 180 To 180 Steps 10 and the scan range omega From 170 To 170 Steps 10 range 30 enlarge 10 Click on OK This will find the optimal phi and the optimal portion in omega which may not be the full range The result is 1 o 124 0 430 at 32 0 30 0 0 0 and 2 o 70 0 20 0 at 28 0 80 0 120 0 This uses 257 frames to get 99 5 completeness Task complete save your work by clicking on Export Xcalibur Manual v1 4 Xcal i b u r Page 86 USER MANUAL OPERATION Optimisation of 100 Coverage Using the final run list from above Try to work through the following example of how to optimise a run list to get 100 coverage which is the same as P1 with Friedel not equivalent 1 Click on Optimise and select theta kappa and phi Enter the following values for theta From 35 To 35 Steps 5 kappa From 90 To 90 Steps 10 and phi From 180 To 180 Steps 10 and set general properties to 100 coverage The computation takes a while We start from 58 and after
75. E E The C3K5 ItalStructures X ray generator will not switch on unless the voltage and current setting dials are returned to the zero position The DF3 Spellman X ray generator will not switch on unless some pre set values have been applied To do this switch on the generator by depressing the button marked CONTROL POWER ON Next depress and hold the X RAY OFF button Using the relevant dials set the filament amperes to 3 8 and kilowatts to 3 02 Now set the dials milliamperes to 20 and kilovolts to 10 Release the button marked X RAY OFF 6 The X ray tube generator chiller will now switch on 7 Switch on Xcalibur goniometer interface using the red power on off switch This is located inside the electronics cabinet on the left hand side of the interface panel All the LED lights should illuminate indicating that the power supplies are on 8 Switch on power supply to fibre optic lights This is located inside the protective enclosure mounted on the support arm 9 Set required voltage and current on X ray generator see third party manual observing maximum values quoted for the X ray tube and also X ray safety regulations 6 3 X ray Tube Warm up Procedure A N WARNING When handling and using X ray tubes particular care should be taken to avoid injury caused by exposure to the X rays exposure to high voltages possible implosion of the vacuum tube and contact with Beryllium and
76. ECHANICAL CHANGEOVER OF DETECTORS AND X RAY SOURCES 7T Mechanical Changeover of Detectors and X ray Sources 7 1 Interchange of CCD Detectors The universal theta arm on the Xcalibur diffractometers facilitates rapid interchange between detectors The following sections describe the removal and installation procedures for the Point detector and the Sapphire 2 and Sapphire 3 detectors 7 1 1 Installation of a Sapphire 2 and Sapphire 3 CCD detectors 1 In the pull down menu tools setup file of the CrysAlis CCD and CrysAlis RED programs change the setup par file to that corresponding to the correct Sapphire 2 or Sapphire 3 CCD camera 2 Turn the interface on using the red switch on the front 3 Restart the CrysAlis CCD and CrysAlis RED programmes and check that the correct correction files are loaded in the tools correction files pull down menu 4 Drive the detector distance to 100 mm and the theta arm round to 90 degrees Slide the CCD camera onto the slider on the theta arm WARNING Take care not to allow the camera to slide into the kappa block as the slider has very low friction 5 Turn the end fixing plate clockwise by 180 degrees and fix the CCD slider into place using two screws Connect the fibre optic cables and water pipes to the top of the camera 6 Turn the CCD camera on by turning the key on the front of the KMW200CCD chiller clockwise The red light on the top of the camera will start to flash
77. ENSOR CABLE 2 EC 04 06 001 A C3K5 X RAY GENERATOR SAFETY SWITCH 2 Version 14 Xcalibur Manual v4 Xcalibur Page 143 USER MANUAL ADDITIONAL INFORMATION EC 24 07 001 A GONIO68332 SAFETY CONNECTIONS 5 GONIO68332 SAFETY MODULE CONNECTIONS 2 XCALIBUR GONIOMETER ELECTRICAL DIAGRAM 2 Version 1 4 Xcalibur Manual v1 4 Xcal ib u r Page 144 USER MANUAL 14 CE Conformity notice DECLARATION OF CONFORMITY This Declaration of Conformity is suitable to the European Standard EN 45014 General criteria for supplier s declaration of conformity The basis for the criteria has been found in international documentation particularly in ISO IEC Guide 22 1982 Information on manufacturer s declaration of conformity with standards or other technical specifications Oxford Diffraction s liability under this declaration is limited to that set forth in the current Oxford Diffraction s Terms and Conditions of Sale Applied Council Directive s 89 336 EEC Electromagnetic Compatibility Directive EMC and amending directives 91 263 EEC 92 31 EEC 93 68 EEC 73 23 EEC Low Voltage Directive and amending directive 93 68 EEC We The Manufacturer Oxford Diffraction Ltd 20 Nuffield Way Abingdon Oxfordshire OX14 1RL declare under our sole responsibility that the following equipment Xcalibur Serial Number From Oxford1 2000 XCALIBUR to which this declaration relates are in conformity with the relevant provisions of the
78. UCTIONS Figure 9 10 1 Adjustment screws of Enhance Ultra Figure 9 10 2 Schematic showing the rotated beam stop dashed line shows up position and solid line shows down position 1 Set X ray generator settings to 30 kV and 1mA 2 Flip the beam stop to the UP position see Figure 9 10 2 3 Setthe CCD detector distance to 60 mm Using the CrysAlis CCD application software type KM4 detector 60 4 Drive the CCD to be directly in line with Enhance ULTRA x ray beam Using the CrysAlis CCD application software type gt t 0 5 Remove the Enhance ULTRA front face panel Using a 3mm Allen key completely undo the screw 1 see Figure 9 10 1 and lift off the front face panel 6 Release the grub screws 2 see Figure 9 10 1 and pull off the collimator 7 Unscrew the optic alignment x tilt i e screw 5 2 y tilt i e screw 5 1 and the x pivot i e screw 3 and y pivot i e screw 4 see Figure 9 10 1 Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 125 USER MANUAL MAINTENANCE INSTRUCTIONS Using the CrysAlis CCD application software type the command card raw on 0 5 to take a 0 5 sec uncorrelated uncorrected CCD image Repeat points 8 10 until the image from the CCD looks like Figure 9 10 3 Atthis point we are imaging the direct x ray beam without use of the optics The optic is completely mis aligned Figure 9 10 3 Image of direct X ray Beam 10 11 12 13 14 15 The image you obtain shoul
79. USER MANUAL
80. UTION Have a receptacle ready to receive water from the pipes and X ray tube shield 3 Disconnect water pipes from back of Enhance Ultra X ray tube shield These are attached with quick release connectors 4 Remove the Enhance ULTRA front face panel Using a 3mm Allen key completely undo the Screw 1 see Figure 9 4 1 and lift off the front face panel 5 Unscrew the temperature sensor from the front plate metal base with label of the X ray tube WARNING Do not touch the Beryllium windows in the X ray tube Beryllium is a potentially toxic material 6 Release the two screws holding the X ray tube in place and withdraw the X ray tube from the X ray shield Do this by holding the front plate metal base with label and pulling towards the front of the Enhance ULTRA Ensure that the X ray tube is held level and withdraw parallel to the X ray shield 7 For disposal of used X ray tubes see the DISPOSAL chapter of this manual WARNING Do not touch the Beryllium windows in the X ray tube Beryllium is a potentially toxic material 8 Replace the x ray tube with an identical specification Cu X ray tube Holding by its metal base remove the new X ray tube from its protective box N WARNING Ensure that the X ray tube is correctly mounted Incorrect mounting may result in exposure of personnel to X ray radiation Red plastic spacers may need to be removed to ensure perfect fit of X ray tube 9 From th
81. X Mo 12x04 long fine focus Ceramic glass X ray tube Copper anode CX Cu 12x04 long fine focus Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 138 USER MANUAL DISPOSAL INSTRUCTIONS 12 Disposal Instructions 12 1 X ray Tube and CCD Detector The X ray tube and CCD detectors have beryllium windows Dispose of Beryllium in accordance with local government regulations 12 2 Third Party Equipment Refer to third party manuals for information about disposing of third party equipment Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 139 USER MANUAL ADDITIONAL INFORMATION 13 Additional Information 13 1 Third Party Information Information marked optional is only supplied when that option is fitted to Xcalibur Title Supplier 3K5 X ray Generator Ital Structures optional DF3 X ray generator Spellman optional Material Safety Data Sheet M10 Beryllium Brushwellman KMW200CCD chiller manual Oxford Diffraction optional KMW3000C chiller manual Oxford Diffraction optional Cryojet User Manual Oxford Instruments optional Cryostream User Manual Oxford Cryostreams optional Helijet User Manual Oxford Diffraction optional Hotjet User Manual Oxford Diffraction optional Version 14 Xcalbur Manual v4 Xcalibur Page 140 USER MANUAL ADDITIONAL INFORMATION 13 2 Drawings 13 2 1 Mechanical Drawings Drawing no Title Number of pages OD 01 00 15 C Xcalibur Suggested Layout 1 OD 01 00 01 System and Com
82. Xcalibur September 1 2003 Version 1 4 Oxford Diffraction Limited 20 Nuffield Way Abingdon Oxfordshire OX14 1RL UK Tel 44 0 1235 532132 Fax 44 0 1235 528005 http www oxford diffraction com Single Crystal Diffractometers QS oxford diffraction Important Information This user manual applies to the Xcalibur systems manufactured in Poland by Oxford Diffraction Product XCALIBUR2 XCALIBUR 3 XCALIBUR PX and XCALIBUR PX ULTRA Model Type CCD PD Electrical Ratings 1 N AC 230 V 50 60 Hz 4200 Watts Before attempting to operate the system PLEASE READ THE INSTRUCTIONS This product should only be used by persons legally permitted to do so If the equipment is used in a manner not specified in the User Manual the protection provided by the equipment may be impaired Important Health and Safety Notice When returning components for service or repair it is essential that the item is shipped together with a signed declaration that the product has not been exposed to any hazardous contamination or that appropriate decontamination procedures have been carried out so that the product is safe to handle Care has been taken to ensure the information in this manual is accurate and at an appropriate level Please inform Oxford Diffraction if you have any suggestions for corrections or improvements to this manual Xcalibur service and support is available for technical and operationa
83. a satisfactory absorption correction model Repeat dc rrp tick the top right hand corner tick box marked Apply absorption correction and output the absorption corrected data with a new file name 6 5 3 7 6 Example absorption corrections This example is based on a UB matrix obtained for a GaAsO crystal and using the point detector The crystal was indexed using the sample movie and its shape found to be non crystallographic As a result real face indices were used Crystal movie x aX pa z x 13 50 0 05820 2 02 0 04117 2 88 0 04123 5 10 0 03650 2 6 910 02532 8 01 0 09085 4 92 0 03794 12 68 0 08337 4 90 0 07046 10 39 0 06441 5 267002381 2 330 02720 7 71 0 04584 6 49 0 05403 X XO YO vo 2 20 l5faces 26comers 39 with Ve 0 00043mm 3 TS es 00K 10O P 78 00 nt t ores E x v 10 Add shop Edt mu Optimised shape with real indices Optimised shape with real indices Rint without abs 0 12472 Rint with abs 0 04167 after optimisation Version 1 4 Xcalibur_Manual_v1 4 Xcal l b u r Page 64 USER MANUAL OPERATION Mu mm 1 18 00000 transmission factors min max 0 25061 0 44904 Figure 6 5 29 Example of absorption correction Absorption correction has a marked effect as shown above Rint has fallen from approximately 12 596 to 496 6 5 3 8 GRAL Space Group Determination NOTE E Data reduction must have been completed with a hkl and p4p file generated prior to space group d
84. acuum pump ideally 70 Litres sec turbo is required to periodically evacuate the Cryojet head and the heater leg To demonstrate the operation of the Cryojet 100 litres of liquid nitrogen are required The customer should supply a suitable rack for both the ILM and the Cryojet controller 5 2 1 6 CCD Camera Pumping A suitable high vacuum pump ideally 70 Litres sec turbo 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 9996 grade helium gas in order for the operation of the Helijet to be demonstrated Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 27 USER MANUAL OPERATION 5 2 2 Setting to Work 5 2 2 1 Equipment Required 8 Table for computer for integration with system 9 Engine hoist portable lifting device with soft slings capable of lifting 100 kg 10 1 set of Allen keys 11 Phillips screw drivers assorted sizes 12 Flat headed screw drivers assorted sizes 5 2 2 2 Personnel Required for Installation 5 persons for lifting of heavy components 5 2 2 3 Setting up Procedures Oxford Diffraction personnel normally perform installation The duration of the installation is typically 3 working days with an additional 1 day for the low temperature option This followed by 2 days training from an Oxford Diffraction crystallographer The numbers on Figure 5 2 1 refe
85. al i b ur Page iv USER MANUAL 6 5 Normal Operation i Ie et et e t ere bet t md D ee ee ns 37 6 5 T General Commande ares 2 roce eerte dre curet ae A eet aae Ea Res ud edd ke Enos 37 6 5 2 Changing Xcalibur Settings mener nnns 39 6 5 3 Standard Diffraction Experiment sss 43 6 5 3 1 Crystal Mounting and Alignment sssesseeen nennen 43 6 5 3 2 Diffraction Photographs to Determine Crystal Quality esssssss 45 6 5 3 3 Unit Cell Determlnatlori 2 itn it Rr RU it C e cn tee 46 6 5 3 4 Data Collection ttt tette edet ticae de eee ina 48 6 5 3 5 Data Processing and Reduction sssssseeeee eene 49 6 5 3 5 1 Orientation Matrix asie eriein eenaa Ea AAEN emnes 50 0 5 3 5 2 Rufi EE ert t eed e leitet e en 51 0 5 3 5 3 Scan WIG 2 5 eee epit T em ii 52 6 5 3 5 4 Background Evaluation ssssssessseeeeee eee 52 6 5 3 5 5 Special Correction Spini ana tnai seem 53 6 5 3 5 6 Outlier Reject n innritan aie trii eed eee died 54 0 5 3 5 7 Output Format 5 c pee au dude n c t fedes 55 6 5 3 6 Changing the Output Format from Data Reduction sssseese 56 6 5 3 7 Absorption C orrectlOrn 2 2 e ede e ee ed dte ee ri eee de 57 6 5 3 8 GRAL Space Group Determination ssssssssssssseeeenees 65 6 5 3 9 Structure Solution and Refinement sse 71 6 5 4 Ewald exploter 5 2 ia tem ee
86. ame Compound formula Cell constants Appendix 3 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 The attached record sheets are provided as examples of the type of records of maintenance checks that should be completed for Xcalibur These records are to show only that maintenance has been Version 1 4 Ylid 2 Dimethylsulfuranylidene 1 3 indandione C10H1002S a 5 947 A b 9 026 A c 18 399 subtract 32 from F then multiply by 5 9 a y 90 multiply by 9 5 then add 32 add 273 15 first convert F to C then add 273 15 Xcalibur_Manual_v1 4 Page 146 C 5 9 F 32 F 9 5C 32 K C 273 15 Xcalibur USER MANUAL completed as directed in this manual Other maintenance records should be kept as required by any local national or international regulations Weekly Maintenance Record Sheet Week Date of Name of person Signature Comments No maintenance performing test 1 2 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 147 USER MANUAL Weekly Maintenance Record Sheet Week Date of Name of person Signature Comments No maintenance performing test
87. and safe operation of equipment N WARNING Xcalibur should only be operated and maintained by authorised operators of the system An authorised operator is a person who has undergone specialist radiation training and has been trained in the use of Xcalibur by Oxford Diffraction personnel Version 1 4 Xcalibur Manual v1 4 Xcal i b u r Page 1 USER MANUAL HEALTH AND SAFETY INFORMATION 1 2 Electrical Safety In normal use the user is protected from the dangers associated with the voltage current and power levels used by the equipment Only personnel qualified to work with the voltages and currents used by this equipment should attempt to disconnect dismantle or modify the equipment 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 electric shock electric burn fire of electrical origin electric arcing 1 2 2 Recommended Precautions WARNINGS 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 and procedures Do not defeat interlocks remove connectors disconnect equipment open
88. ant arrow button m o o e Current image run 3 frame 6 CAMy Documents xtldata BaTh Se18 ph BaTh Sel8ph Q 10 lt lt STOP 10 gt gt t dr o x Play s Iv Lattice T Statistics at o Play control e p Continuous C Delayed sec 1 000 9 Forwards C Backwards a a H F J Help o a P 0 Ka i o Run 3 Omega scan 28 000 43 000 15 frames 10 000 sec at th 28 198 ka 24 852 ph 0 000 4 HKL list info 248 refl 0 shortened x Ready o 33 000 r 28000 k 25 000 P 0000 Amm Hsen 26 S OHE gt O yin amp o eju amp c Ego Min fic E geso m QT du 9 102 Figure 6 5 51 Screenshot of Data Collection Movie with Unit Cell Predictions Overlayed 3 Ifthe unit cell has previously been determined index efc then predictions of reflection positions can be overlayed on the movie images To do this simply click on the box marked Lattice until a tick appears and then Play The images should then look like the one in figure 6 5 51 NOTE E reflection in the previous frame O reflection in the next frame X reflection in the current frame 4 Click on Exit to finish data collection movie playback Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 77 USER MANUAL OPERATION 6 5 6 Reconstruction of Precession Photographs CrysAlis RED allows the user to reconstruct precession photographs This is achieved via a wizard that guides you through t
89. as 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 Gas cylinders become dangerous projectiles if they are ruptured or the valve is knocked off They can break through thick walls or travel hundreds of metres by rocket propulsion 1 10 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 A N WARNING 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 11 Modifications and Service The manufacturer will not be held responsible for the safety reliability or performance of the equipment unless assembly operations extensions re adjustments modifications and repairs are carried out only by persons authorised by the manufacturer It should be stressed that those parts of the equipment which are interchangeable and which are subject to deterioration during operation
90. as the camera starts its cool down procedure 7 Drive all angles back to zero GT a 0 0 0 0 8 Setthe detector distance to 130mm GT D 130 and open the cabinet door Drive theta to 90 degrees GT T 90 and 90 GT T 90 and check that there are no potential collisions with the cabinet Move the goniometer if necessary NOTE You may not collect data until the camera has cooled down fully and the green light is visible on top of the camera Once the camera is fully cooled collect a short data collection Xcalibur calibration run and refine the machine parameter file as described in section 6 5 12 CAUTION The wd cal command will overwrite the current diffractometer set up file Calibration of the diffractometer may be lost at this point if an invalid model exists Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 103 USER MANUAL MECHANICAL CHANGEOVER OF DETECTORS AND X RAY SOURCES 9 When a good model has been refined store the new detector offset by typing ZC detector dd where dd is the expected detector distance e g 50 0 mm this will type a detector distance offset into the parameter file then save the remaining parameters by typing wd cal NOTE E Back up files of the parameter file are automatically created of format bup 7 1 2 Removal of a Sapphire 2 and Sapphire 3 CCD detectors 1 Switch off the CCD camera by turning the key anticlockwise on the front panel of the KMW200CCD
91. asted into the following um sarray command and thereby assigned to a memory buffer 8 buffers numbered 0 to 7 are available 1 Version 1 4 These twinned unit cell matrices should be stored in consecutive buffers Assigning UM S matrices to a memory buffer is achieved using the following command structure um sarray 1 ub11 ub12 ub13 ub31 ub32 ub33 The first UB matrix has now been assigned to the buffer 1 Re enter the Ewald explorer using the command pt ewald and drag index the second twin unit cell Exit the Ewald explorer and index the new UB matrix via the command um i Once again typing ty u will output the current NEW UB matrix to the history window Assign this new UB matrix and unit cell to the second memory buffer by using the UM S matrix output via ty u and pasting it into the following command um sarray 2 ub11 ub12 ub13 ub31 ub32 ub33 Having defined two or more twinned unit cells and their UB matrices we can now reduce the twinned dataset via the dc red command During data reduction the number of active buffers with unit cell UM S matrices assigned are automatically recognised by the data reduction module Follow the procedure for data reduction as described in section 6 5 8 On reaching STEP 5 Special corrections click on the button Special corrections properties A window like the one in figure 6 5 64 should open Click on the tab marked Peak finding Here you will be offered the choice of applying various corr
92. at pixel position to output statistics at that pixel position 6 5 1 2 Gt Goto Angles Commands When Xcalibur is not collecting data the goniometer axes can be driven to accessible positions using the following commands gt a om th ka ph goto angles with values omega om theta th kappa ka and phi ph gt o om goto omega angle om gtt th goto theta angle th gt p ph goto phi angle ph Version 1 4 Xcalibur Manual v1 4 Xcal ib u r Page 37 USER MANUAL OPERATION 6 5 1 3 Sm Single Image Commands Single image omega phi and theta scan photos can be recorded using the following commands sm o starfomegaangle scanwidth time omega scan sm p startphiangle scanwidth time phi scan sm t startthetaangle scanwidth time theta scan 6 5 1 4 Ty Type Details Commands The ty command allows the user to print a variety of current settings to the history window ty p print current Xcalibur parameter settings tyu print current UB matrix ty print current unit cell and lattice settings tyt print current contents of peak table ty imageinfo print information about the current image 6 5 1 5 Card CCD Image Commands On occasions the user may wish to record single diffraction CCD camera images without the collection of dark images This can be achieved using the following commands card raw time Single CCD image without X rays time in secs card raw on time Single CCD i
93. be 90 degrees oniometer Area Detector Model x r Refinement control Refinement weigths Cycles Diffraction angle 1 00000 Spot position 1 00000 Levenberg Marquarct 0 00000 hkl 1 00000 Ewald sphere 1 00000 r Crystal LAT_ABC M a 13 16414 Edita V b 14 01379 Edit b M c 14 08749 Editc Iv al 76 91934 Edit al M be 8442057 Edit be I ga 80 91906 Edit ga FEE ERE Ww r 5545564 Edit rl M r 72 64273 Edit r2 M r3 73 54286 Editr3 W Goniometer M b2 0 08283 Edit b2 mes moooi Edith I el 4934087 Edit al T be 0 00065 Editbe M o 0 26653 Edit o0 M t0 0 63198 Edit t0 T k 0 06821 Edit k0 T ipo monaoa Editt CW Detector wdi 0 49103 Edit d1 Iv d2 019800 Edit d2 mies ttt Eqifd Cancel IV x 50474444 Editx IV y 53110288 Edity M dd 5307038 Editdd Figure 6 5 70 Screenshot of Refine Model Constraining all Unit Cell Lengths to be Equal Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 92 USER MANUAL Figure 9 10 11 OPERATION x Goniometer Area Detector Model LS Refinement control Refinement weigths Cycles 10 Diffraction angle 1 00000 Spot position 1 00000 Levenberg Marquardt 0 00000 hkl 1 00000 Ewald sphere 1 00000 Edith F c JENE Crystal LAT AAA Sa MV a 13 16414 Edita Fb5 TET Edit ANG_ALBEGA hd M al 76 91934 Edital Ww be 8442057 Editbe Iv ga 80 1906 Edit ga Ww rz 5545564 Edit rl M r 7264273 Editr2 M r3
94. below KMW200CCD 55 38 x 54 x 75 Centre of unit At the four corners and from below KMW3000C 56 38 x 54 x 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 Cryojet 15 15 x 35 x 15 head only Centre of component From below or parts using handles whilst supporting transfer tube ILM210 5 44 x 10 x 30 Centre of unit By hand from below ITC502 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 Version 1 4 Xcalibur_Manual_v1 4 Xcal ib u r Page 24 USER MANUAL OPERATION 5 1 3 2 Boxed Weights Dimensions and Lifting Points on Delivery Box Item Length Width Height Weight kgs No cm cm cm 1 Goniometer 85 65 70 135 2 Accessories 85 60 60 80 3 Protection cabinet 140 120 60 200 4 Electronics rack 96 94 106 170 5 Helijet 92 60 96 55 6 KMW 3000C Chiller 110 56 80 100 7 PC 66 56 47 13 8 KMW200CCD Chiller amp CCD 90 66 80 140 camera 9 160L LN2 dewar 70 72 155 119 10 17 Monitor 57 52 48 18 11 Cryojet 70 79 189 143 12 X ray generator 91 65 45 80 The weights and dimension above are 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 15cm clearance from floor to the base of each box It is recommended that a fork lift truck is available to
95. ble pt clear pta add a peak to the peak table pta pt ewald Initiate Ewald explorer pt ewald pte Peak table edit pte pt expand Peak table expand pt expand n mmin mmax intmin dmax dmin n number of reflections required mmin min order of difference 1 for CCD 3 Point detector mmax max order of difference 1 for CCD 3 Point detector intmin Intensity threshold dmax max d spacing dmin min d spacing pt I add reflections to the peak table according to PT L lauecode their Laue symmetry lauecode The following codes can be selected 1 1 2 2 m 3 mmm 4 4 m B 4 immm 6 3 Ta 3m1 8 31m gx 6 m 10 6 mmm 11 m 3 12 m 3m ptsa add reflections from a different setting position PT SA settingno settingno The settingno refers to the basic measurement settings rd flood Read flood field image from file rd flood rd help help overview of rd commands rd help Version 1 4 Xcalibur_Manual_v1 4 Xcal l b u r Page 97 USER MANUAL OPERATION rd iheader Read in an area detector image file header rd iheader filepath filename filepath filename Optionally you can put the path and filename on the command line Note that you have to use quote for filenames with spaces rd jpg JPEG image rd jpg filepath filename filepath filename Optionally you can put the path and filename on the command line Note that you have to use quote for filenames with spaces rd p rd ph Read parameter fil
96. ce assembly X ray tube and temperature sensor Mount Enhance or Enhance ULTRA and secure with fixing screws WARNING Ensure tube shield is properly aligned with the fast shutter Incorrect mounting may result in exposure of personnel to X ray radiation Holding by its metal base remove the X ray tube from its protective box WARNING Do not touch the Beryllium windows in the X ray tube Beryllium is a potentially toxic material From the front of the Xcalibur insert the X ray tube into the tube shield and secure WARNING Ensure a perfect fit of the X ray tube Remove red plastic spacers if necessary Incorrect mounting may result in exposure of personnel to X ray radiation Secure temperature sensor to base of X ray tube Mount Front face panel or X ray source and secure in position using fixing screws From back of Xcalibur insert the power cable from the X ray generator into X ray tube shield and secure Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 29 USER MANUAL OPERATION 9 Mount CCD detector Slide detector onto graduated mount from right hand side of Xcalibur from front and secure at 60 mm WARNING Do not touch the Beryllium window at the front of the detector Beryllium is potentially toxic material 10 Mount beam stop and collimator where applicable Screw into position the beam stop WARNINGS 1 Do not touch the Beryllium window at the front of the detector
97. ch has a very high stopping power due to its high density and a very good light output Its emission wavelength 550nm is well matched to the sensitivity of CCDs A screen of 0 1mm thickness will yield an absorption of gt 90 and has FWHM of approx 2x its thickness 4 2 3 Taper The fibre optic taper reduces the light image obtained from the scintillation screen to the CCD A taper is composed of bundles of 10 15um fibres which are fused together to form 95mm and 165 mm diameter tapers These fibres have been drawn under heat to give a reduced image at the small end with a reduction ratio of typically 2 5 1 The light loss of the taper image transformation is proportional to the square of the reduction ratio 4 2 4 CCD The acronym CCD stands for charge coupled device Essentially a CCD detector is an array of silicon based capacitors Light photons generate in the CCD silicon matrix photo electric effect Each pixel is covered with electrodes which allow shifting the charges generated in the CCD matrix towards the readout node The shifting is a two step process First the charges are shifted by a parallel shift to the serial register a kind of one dimensional CCD row at the edge of the matrix Secondly this row is read out sequentially through the read out node at the end of the serial register The readout node is a field effect transistor FET which has a typical sensitivity of 1uV electron The signal from the FET is subsequently ampl
98. chiller 2 Drive the goniometer to theta 90 deg GT T 90 and drive the camera distance to 60 mm GT D 60 3 Unplug all the connectors to the CCD head note which fiber optics cable is connected to which socket mark them if necessary to save time when reconnecting The order of the water pipes is not important NOTE E Take care when disconnecting water pipes to prevent drips of water landing on the camera 4 Unscrew the two upper M4 screws connecting the slider to the lead screw which defines the camera distance Turn the end plate of the slider anticlockwise by 180 degrees Remove the camera from the slider carefully and place in the storage box NOTE E Take care not to allow the CCD head to collide with the beam stop or kappa block as the slider has very low friction 7 1 3 Installation of the Onyx CCD camera WARNING Two people are needed for this procedure The Onyx camera is heavy The Onyx is a delicate electronic instrument If dropped it may be damaged and warranty will be invalidated 1 In the pull down menu tools setup file of the CrysAlis CCD and CrysAlis RED programs change the setup par file to that corresponding to the correct Onyx CCD camera 2 Turn the interface on using the red switch on the front 3 Restart the CrysAlis CCD and CrysAlis RED programmes and check that the correct correction files are loaded in the tools correction files pull down menu Version 1
99. cl 3201646 86 28120 16 18849 139 71279 110 24717 33 93904 Ge ey 1 E umigue 1 UmIBuE 1 cumipue Iv Use Friedel mates as equivalent r Sigma calculation control Overlap twin reject I Override machine error TEE I Override rejection par mood F Use overlap rejection TUTO T Use twin rejection moooi r Limits and lattice extinctions T Photon zihesstyeg 2theta EO GGG Don tuse lattice extinctions a C Use lattice extinctions m Data items in hkl file m User modifications T Beam path information for absoprtion correction direct j ES 2 F Don tuse scan speed rescaling D Export Stoe crs Exportxprep p4p Expartsadabs 1 raw Tip You may change the output name and directory to keep results of data reductions under different parameter sets Limits sigma parameters Output file name C My Documentskxtldata Customer Demos Evain BaTh Sel 8 de BaTh 7Sel8a Change output name Figure 6 5 20 Screenshot of data reduction finalisation window Version 1 4 P Xcalibur Manual v1 4 Xcal l b u r Page 56 USER MANUAL OPERATION 6 5 3 7 Absorption Correction As X rays pass through the crystal sample a percentage of the X rays will be absorbed by the sample The degree of absorption is related to the distance travelled through the sample and also the composition of the sample To minimise absorption a spherical crystal is ideal however this is often unobtainab
100. cooling system is required to dissipate the heat produced by the X ray tube A closed circuit cooling system should be installed to minimise the effects of particles low pressure and water temperature fluctuation on the performance of the system from local tap water The KMW3000C Chiller is a closed circuit cooling system suitable for this purpose It is supplied with two hoses 10 metres long and 10mm in diameter The maximum distance between the KMW3000C chiller and the system is 10 metres The distance between the water supply and the chiller is not limited but the supply must deliver 0 5 5 bar gauge pressure with a minimum 5 litres min flow and a gravity drain with an elevation that does not exceed 1metre The supply should have a wall mounted shut valve If the X ray tube and generator are not cooled by the KMW3000C Chiller the cooling system selected must have a flow sensor and thermal switch to monitor the cooling and act as safety devices for the X ray tube and generator It must also meet the following requirements Flow rate 4 0 Litres min Pressure 0 3 0 8 bar gauge Temperature stability 1 C Temperature range 10 20 C CAUTION There is no flow sensor or thermal switch inside the system to protect internal components against improper cooling These are provided inside the KMW3000C The X ray tube warranty does not cover damage due to improper cooling water 5 2 1 5 Low Temperature Option A suitable high v
101. corner of the Ewald Explorer window All the skipped peaks including the intensity skipped peaks should now be visible as red dots E la x x He Rotation axis a Cx C yO e 2 Slow rotation E EU E Skip filter intensity x Min 4 0 Min Step Max v mimi 3000 Max Sep FS pores se intensity iter UB fit i iy filter UB J J M F Show L C all C used skip C wrong i v Wavelength 0 70930 Mo pt ewa OK I liz Intensity skip off ee Ready O 43 280 T 30 000 K 25 000 P 260 000 a waster A A e HE P orde muno 4 xcelibur l CrysAri Be markinvi apos eT ya 2 3 0148 Figure 6 5 50 Screenshot of Ewald Explorer Skip Filter Intensity Window Version 1 4 Xcalibur_Manual_v1 4 Xcal l b u r Page 76 USER MANUAL OPERATION 6 5 5 Dc Movie Replay of Data Collection Movie The CrysAlis software package enables the user to examine the whole of the data collection as a movie The user can move back and forth through the data frames in single frame steps or play a continuous movie If the unit cell has been determined then predictions of reflection positions can also be overlayed on to each frame 1 Type dc movie and select the data collection run file A control window will appear 2 Click on the Play button and a continuous movie will be played of the data collection Select forwards or backwards play of the movie by the relev
102. d ideally have a regular square shape turned through 45 degrees This image should have sharply defined edges If one or more edge is ill defined fuzzy adjust the relevant tilt or pivot screws until it is sharp Place the mouse cursor over the 45 degree square Right mouse click and select integration at pixel position Record the intensity figure displayed in the history window of CrysAlis CCD application software Adjust the height pivot screw 3 see Figure 9 10 1 and type card raw on 0 5 Repeat points 11 12 to give a maximum intensity whilst retaining the sharply defined 45 degree square image Adjust the tilt screws 5 1 and 5 2 see Figure 9 10 1 and type card raw on 0 5 Place the mouse cursor over the centre of the 45 degree square image Right mouse click and select integration at pixel position Record the intensity figure from the history window Repeat point 5 13 until a maximum intensity has been obtained whilst retaining the sharply defined 45 degree square image The x ray beam is now aligned and shining directly through the centre of the Enhance ULTRA 9 10 2 Optic Alignment of Enhance Ultra 1 The position of the optic must be adjusted in order to focus the raw non monochromatised x rays Adjust the x and y tilt screws Type card raw on 0 5 in CrysAlis CCD Repeat points 2 3 until the image consists of 4 separate spots The left hand spot will be very much more intense than the others see Figure 9 10 4
103. d using the relevant stopper 11 Switch of vacuum pump and disconnect pipes 12 Unscrew T tool and replace access plate of CCD detector 13 Re attach the water pipes to the CCD detector and switch on water supply KMW200CCD chiller unit NOTE E It doesn t matter which pipe goes on which connection 9 15 Dismantling Xcalibur Task Time When Personnel This procedure is normally performed by specially trained Oxford Diffraction Personnel Tools Engine hoist portable lifting device with soft slings capable of lifting 100 kg 1 set of Allen keys Phillips screw drivers assorted sizes Flat headed screw drivers assorted sizes NOTE E Refer to the Setting to Work procedure of this manual for more detailed information about the way in which parts are attached to the system Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 131 USER MANUAL MAINTENANCE INSTRUCTIONS Procedure WARNING When components have been removed from the system ensure that they are put in a safe place to prevent injury to personnel and or damage to the components 1 Perform the Normal Shutdown Procedure 2 Leave the system for 20 minutes to allow X ray tube to cool down 3 Drain water out of the CCD detector cooling system and the X ray tube and generator cooling system 4 Turn off mains power and disconnect the mains power cables 5 Remove the low temperature option if fitted
104. data reduction default is 1 often this should be increased 3 If needed click on the tick box marked User max mask and click on the button Edit max mask This defines the maximum size of the mask used in data reduction 4 Click on OK Removing negative peaks from data reduction 1 Click on Special Corrections and select the tab marked Skip filters 2 Click on the tick box marked Photon limit and then click on the button marked Edit Photon Limit default is 1x10 rang 1x10 to 1x10 3 Input a positive value e g 10 Click on OK 4 Click on OK Limiting the 2 theta range Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 53 USER MANUAL OPERATION Often when data reduction is unsatisfactory this is due to the fact that the crystal does not diffract to high angle The default setting for maximum 2 theta threshold is 180 degrees 1 Asa guide examine a number of diffraction images and place the mouse cursor on the diffraction image at the position where diffraction is essentially zero Read off the theta value at this from the bottom of the CrysAlis RED window Theta is marked as T number 2 Return to dc red Click on Special Corrections and select the tab marked Skip filters 3 Click on the tick box marked 2 Theta max threshold Click on the button marked Edit 2 theta max 4 Enter 2 x the maximum theta value which you determined from analysis of the diffraction images Click on OK 5 Click on OK 6 5 3 5 6 O
105. del is correct Check that this number is falling towards zero Type um i to refine the unit cell parameters You should see an improvement in the parameters eg The angles tend towards 90 degrees Type the command refine model and press Enter Check that the dd distance has refined to a sensible value Click on the tick box marked Detector until the box contains a tick Click on OK The detector parameters will are now refined and details are output to the history window Type um i to refine the unit cell parameters Xcalibur Manual v1 4 Xcal i b u r Page 93 USER MANUAL OPERATION 17 Type refine model and click on the tick box marked b2 which describes the X ray beam orientation Click on OK When refinement finishes type um i to refine the unit cell parameters 18 Type refine model and click on the tick boxes marked o0 t0 and k0 These define the omega theta and kappa axis zero corrections respectively Click on OK Once refinement is complete check the history window output as above Type umi to refine the unit cell parameters These should have improved CAUTION Al and be parameters should ONLY be refined using data collected from the Xcalibur calibration run If not using this run then skip step 19 below The Calibration of the diffractometer may be lost at this point if an invalid model exists 19 Type refine model and click on the tick boxes al and be and then OK At the end of refinement check the history win
106. details of specific CCD detector Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 129 USER MANUAL MAINTENANCE INSTRUCTIONS Sapphire 2 Access plate of Sapphire 2 CCD detector removed Secured by one screw at centre Pump out port with T tool attached Sapphire 3 Access plate of Sapphire 3 false front to head spring loaded Secured by 4 grub Screws at corners 2 shown y he Pump out port with T tool attached Onyx Pump out port with cover unscrewed Figure 9 14 1 View of the access plates and pump out ports of the Sapphire and Onyx CCD detectors 4 Screw into place the T tool Version 1 4 Xcalibur Manual v1 4 Xcal i b u r Page 130 USER MANUAL MAINTENANCE INSTRUCTIONS 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 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 remove stopper Secure plunger in place 9 Leave under vacuum for 16 hours 10 Depress T tool plunger to replace stopper and unscrew plunger CAUTION Do not turn off the vacuum pump until the CCD detector has been seale
107. directory contains the applications error logs which are important to trace application errors Macro directory macro mac This directory contains the CrysAlis macros for task automation Run directory run run This directory contains the CrysAlis run files for setting up data collections Applications root VCrysAlisXXX exe dll vxd sys This directory contains the CrysAlis executables and drivers Darkimages directory darkimages img This directory contains the CrysAlis dark images which are acquired during a CrysAlis CCD session Formats directory Mormat dll hlp This directory contains the CrysAlis image formats which describe the formats of different detector types sapphire Help directory format hip chm This directory contains the CrysAlis online help Plug ins directory plug ins hip dll This directory contains the CrysAlis plug ins Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 21 USER MANUAL TECHNICAL DESCRIPTION 4 5 2 Basic Menu Philosophy The CrysAlis programs interact with the user in various ways Basic commands The basic tasks are stored in the order that they are likely to be carried out Expert mode commands A link to all the available commands is available here NOTE E Every command has a short cut code for instance dc s for data collection start The toolbar The toolbar contains short cuts to the most important tasks The command line The experi
108. dit run Delete run Import run list Export run list Clear run list Clear done runs Selection to new Change frame width Change exposure Change theta Check collisions Edit done number m New runs Choose a scan type Type of run list Data collection frames C Reference frames omegetieta dyi Mega theta iked Figure 6 5 11 Screenshot of Edit data collection runs 3 Start data collection by typing dc s Complete experimental data when prompted and leave to collect data NOTE EI Data collection may be interrupted at any time using the Ctrl key or the Stop menu To resume data collection type dc r When data collection is complete 4 Type ph s to start peak hunting 5 If required change on screen parameters The default values for peak and threshold are 1000 and 20 Typical values for peak 7x7 threshold values are 150 and 5 for fast unit cell data where weak data with background subtraction are used and 500 and 20 to 2000 and 20 for full data collection If background subtraction is used typical values for background frames interval are 25 and 30 25 frames are for 1 frame width NOTE E To determine the minimum value for peak threshold examine a number of images and right click on a weak reflection Select Integration at pixel position Read off the intensity value and set the peak threshold in peak hunting below this
109. dow output The Residual value should ideally be between 1 396 Refine the unit cell parameters using um i CAUTION The wd cal command will overwrite the current diffractometer set up file Calibration of the diffractometer may be lost at this point if an invalid model exists 20 When a good model has been refined store the new parameters by typing wd cal NOTE E Back up files are automatically created of format bup 6 5 12 Glossary of CrysAlis Commands Command Meaning Example abs display View movie recording and build absorption abs display correction routine abs grab Initiate movie recording routine for absorption abs grab correction afi Applies an attenuation filter afi afo Removes the attenuation filter afo card cleardark erasing of the dark image data base card cleardark ccd par Change ccd settings binning ccd par card raw Collection of a dark image with the current card raw rawtime shutteronoff parameters The image will be stored in the dark image buffer DARK The dark image will rawtime image integration image in seconds be collected as a double correlated image to shutteronoff ON or OFF default OFF reduce measurement error card dark Acquisition of dark current map card dark darktime destination image darktime Time of dark image integration in sec destination image destination image buffer where the default is set to DARK card help H
110. e Read peak hunting table from file rd p filepath filename filepath filename Optionally you can put the path and filename on the command line Note that you have to use quote for filenames with spaces rd ph filepath filename filepath filename Optionally you can put the path and filename on the command line Note that you have to use quote for filenames with spaces rdt Read peak table from file rd t filepath filename filepath filename Optionally you can put the path and filename on the command line Note that you have to use quote for filenames with spaces rdi Read disc image rd i filepath filename filepath filename Optionally you can put the path and filename on the command line Note that you have to use quote for filenames with spaces rd jpgheader JPEG image header rd jpgheader filepath filename jpg filepath filename Optionally you can put the path and filename on the command line Note that you have to use quote for filenames with spaces refine model Refine diffractometer geometry model refine model refine export Export details of model refinement to file refine export rr reference reflections PD RR rr num interval om tol int tol h k l at h k I at h k at rr_num number of reference reflections 0 lt rr num lt 3 if rr num gt 0 interval interval between reference reflections measured 1
111. e 6 5 2 Screenshot of CCD parameters window 6 5 2 2 Changing Beam stop Mask During data processing the area of the CCD which is obscured by the shadow of the beamstop is ignored This is because a mask has been defined in this area The user can change the default values of this mask to suit their experimental needs To visualise the current beam stop mask first read in a data image using the command rd i Type dc beamstop this will overlay a semi transparent shaded rectangle over the diffraction image this is the beam stop mask E CrysAlis RED CCD camera data reduction user interface File Edit ColorTables LookUpTables Zoom Datareduction Commands Stop Test Tools Help STIS om 0 00 th 28 20 ka 24 85 ph 0 00 aj Beam stop polygon 31 206 31 511 82 511 82 206 X 2193Y 213Jnt 0 4 564 0 263 6 441 L 0 38 T 11 55 R 1 77 O 33 000 T 28 000 K 25 000 P 0 000 HAsen 6 5 oH a BC erc ERA AES gasyosmlQT v 8a 3 1045 Figure 6 5 3 Screenshot of CrysAlis RED showing a diffraction image with beam stop mask To re define this mask type setup options This will open a window which allows the machine parameters to be edited Click on the tab marked beam stop settings Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 40 USER MANUAL OPERATION lel x le CrysAlis RED program options 21x PH and PT size l Color codes Beam stop settings G
112. e Control and drive goniometer Control must be released from computer Enclosure Lights Switch Right side of electronics rack Illuminate inside of enclosure Fibre optic lights Switch Inside enclosure see figure Illuminate crystal sample 6 1 1 Power Control Type Location Effect Xcalibur Red switch Interface front panel left Power on off to goniometer goniometer Inside front door of electronics interface rack X ray Generator Turn MAINS Generator front panel Inside Power on off to X ray key switch front door of electronics rack generator DC power supply Switch Inside enclosure see figure Power on off to CCD 6 1 1 detector Version 1 4 Xcalibur Manual v1 4 Page 31 Xcalibur USER MANUAL OPERATION Fibre optic light control box front with switch on underside DC power supply rear with Switch on underside Figure 6 1 1 Location of switches Indicator Location Meaning Orange light Outside top right of the protective enclosure X ray power is on Red light Outside top right of the protective enclosure X ray shutter open Green Light Outside top right of the protective enclosure X ray shutter closed 6 2 Initial Switch on Procedure Safety devices in Xcalibur protect against damage to the system and the operator during start up The following initial switch on procedure should be followed 1 Switch on the computer controlling Xcalibur 2 Switch on DC power
113. e front of the Enhance ULTRA insert the X ray tube into the tube shield and secure with two screws E uos X ray tube must be inserted the correct way up See figure 9 3 1 10 Secure temperature sensor to base of X ray tube 11 Remount the thermocouple and the Enhance ULTRA front face panel and secure in place using a 3mm Allen key and the screw 1 see Figure 9 10 1 Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 118 USER MANUAL MAINTENANCE INSTRUCTIONS 12 Reconnect water supply to back of Enhance ULTRA X ray tube shield 13 Xcalibur system KMW200CCD and KMW3000C chiller units 14 Align X ray optics as described below 9 5 X ray Beam Stop Alignment Task Time 5 min When As necessary Tools Special tool 1 Procedure 1 Set the X ray generator to 20 mA and 10 kV 2 Ensure that the X ray shutter is closed and then fit the X ray beam stop N WARNING Ensure the body parts are kept away from the X ray beam Back scattered radiation from the scintillation detector screen is inevitable during this process 3 Flip the beam stop to the DOWN position see figure 9 10 2 4 Drive the detector to a distance of 60 mm using km4 detector 60 5 Image the x ray beam and beam stop shadow using the command card raw on 0 5 We are attempting to avoid any straight through x ray beam manifested as an intense spot on the image The ideal alignment will give an image where the b
114. e interlock key switch A continuous signal buzzer should be heard 5 Position the computer monitor such that the screen can be clearly seen from the Xcalibur WARNING X ray radiation is exposed at this time Take care not to move body parts into the beam 6 Record a single image of the X ray beam using the command sm i 0 1 in CrysAlis CCD At this point do not worry about the position of the X ray beam image on the Sapphire CCD 7 Drag out a wire frame box around the X ray beam image on the computer screen Click the right mouse button and select Area statistics Write down the X Y XW YW values from the right hand window in CrysAlis CCD 8 Using the following command will cause the X ray shutter to open and close 100 times with an X ray exposure of 0 1 sec each time The integrated intensity across the defined box use the X Y XW YW values recorded in step 7 will be output to the screen for each exposure xx is 0 1 100 X Y XW YW 9 Standing to the left of the X ray tube from front of Xcalibur adjust screws 1 and 2 on figure 8 4 2 use Allen key during 100 exposures step 6 Adjust to give maximum integrated intensity as output on computer screen 10 Stop the xx is command preventively using Ctrl key on computer Retake a single image with smi 0 1 NOTE Kd Use wd i to save the image for later comparison Save the image in a directory with a name like enhancealigndata and a filename like enhancebeam2
115. eam stop creates a shadow which is perfectly positioned in the centre of a circle of background scatter 6 Adjust the beam stop position using the horizontal and vertical adjustment screws see Figure 9 5 1 and the special tool 1 See figure 9 1 2 provided 7 Repeat points 4 to 5 8 Now increase the exposure time for the image Card raw on 5 Make adjustments as necessary 9 If aligned then increase exposure time to 10 secs card raw on 10 Make adjustments as necessary 10 If aligned then increase exposure time to 30 secs card raw on 30 Make adjustments as necessary 11 If aligned then increase the generator settings to 30 kV and 20 mA and repeat points 3 7 12 If aligned then increase the generator settings once more to 50 kV and 40 mA and repeat 3 7 Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 119 USER MANUAL MAINTENANCE INSTRUCTIONS Vertical adjust screw Horizontal adjust screw Figure 9 5 1 Beam stop adjustment screws 13 Repeat steps 5 and 6 until the X ray beam is centred on the scintillation detector screen 14 Check the position using the CCD detector 15 The X ray optics should now be aligned and ready for experimental use 9 6 Changing the Collimator of Enhance Task Time 1 min When Different sizes of collimator may be necessary for different experiments Three standard collimators of sizes 0 5 0 8 and 1 0mm are provided with the Xcalibur system A 0 3 mm standard le
116. eciprocal space visualiser 5 Next the lattice centring is determined Figure 6 5 34 shows a table of statistics which allows the user to check the plug in s selection If the user wishes to choose an alternative then the relevant radio box can be selected by clicking on it and then Apply can be clicked to move to the next step Here we can see that the table of statistics reflects the P rimitive lattice selected by GRAL ix T Settings E Load eg Centering Lattice exceptions P A B C I F Obv Rev All N total 0 2520 2522 2524 2513 3783 3362 3353 5042 N int gt 3sigma 0 1967 1926 1989 1952 2941 2568 2572 3699 Mean intensity 0 0 a Fa BEA TT 0 205 T1 i0 8 11 3 TI Tr Mean int sigma 0 0 25 6 24 7 24 1 2525 24 8 25 6 25 5 2503 Lattice type iz CA CB c cl CE C Obv C Bev Intensity divided by 1000 Cancel Apply Help Figure 6 5 34 Screenshot of the GRAL plug in Centring Window 6 A Niggli reduction is applied to the data and the user is provided the opportunity to apply a transformation matrix to the original cell Click on Apply Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 67 USER MANUAL OPERATION Ce 2 x T Settings Load fe Centering p Niggli m Original cell a 5 96570 b 9 03330 C 18 40670 o 90 01 050 B 90 0120 Y 90 03130 m Transformation matrix from original cell to Niggli cell fmm 2 0000 o 0000 1 0000 1 0000 0 0000 o c000 0 0000 1 0000
117. ections Click on the box marked Use twin overlap check Note Use overlap check box will automatically be selected You now have the option to adjust the twin overlap fraction This is achieved by clicking on the box marked Edit twin frac The default for this parameter is 0 25 range 0 0 to 0 5 Click on OK and follow the dc red wizard as in section 6 5 8 Xcalibur USER MANUAL Xcalibur Manual v1 4 Page 89 OPERATION CRYSALIS data reduction special corrections Figure 6 5 65 Screenshot of Data Reduction Special Corrections Editing twin overlap fraction Figure 6 5 66 Screenshot of Data Reduction Editing of Twin Overlap Fraction 6 5 10 Extracting Data from Powder Samples The Xcalibur and Sapphire CCD can be used to collect powder ring data see figure 6 5 67 Simple powder patterns can be extracted from the images using the powder extract command The data which is extracted from the powder image is output to the history window and also to the clipboard allowing its transfer to a spreadsheet program for plotting Version 1 4 Xcalibur_Manual_v1 4 Xcal i b u r Page 90 USER MANUAL OPERATION 1 CrysiAlis RED CCD camera data reduchon user interlace File Edit ColorTebles LookUpTobles Zoom Dotereduction Commands Test Tools Help H ss ed to clipboard o small for area statistics Bk ad ARA aR AAP Tink 24 ID WRENIN AARATI NAATIN RAA 1750 T amn X nnm P nam O Figure 6 5 67 Screenshot of Powde
118. ed 20 frames and have 2 3 more coverage Click on Export This is still not 100 To achieve this we need five runs 1493 1502 99 4 720 frames With average redundancy 1 8 use Laue P1 no Friedel Meaning we measure on average every reflection two times 6 5 8 Indexing and Data Reduction of Incommensurate Samples The CrysAlis RED program provides the user with the ability to examine and analyse incommensurate crystal structures Incommensurates with q vectors in up to 3 directions can be handled Samples that are both incommensurate and twinned can also be dealt with Version 1 4 Xcalibur_Manual_v1 4 Xcal l b u r Page 87 USER MANUAL OPERATION We must first achieve indexation of the parent main unit cell This can be achieved by a number of methods In many cases the strongest reflections can be used in conjunction with pt ewald direct editing of the peak table using pt e or um f Once the correct unit cell has been selected either use the command um clearskipd or enter the Ewald explorer using pt ewald and select from the Flag menu Mark all used Exit the Ewald Explorer Re index the unit cell against all the reflections by typing um i Now examine the peak table by typing pt e An examination of the hkl values should enable you to determine a rough estimate of the q vector note this down and exit the peak table by clicking on Exit Type Nada qvector mmax crithkl q1 q2 q3 q1 q2 q3 q1 q2 q3 where mmax is the maximum order o
119. elp overview of card commands card help card reinit Re initialisation of CCD detector head card reinit interface ccd help Help on CCD commands ccd help ce center a peak CE n HP n setting number n 0 current angle setting i e do not recover standard setting during refinement n 1to8 standard settings default 1 n HP string carry out centering procedure in 8 symmetrical positions to calculate the crystal displacements from the sphere of confusion of the goniometer as described by A Ross in Rev in Miner amp Geochem 41 2000 559 596 Version 1 4 Xcalibur_Manual_v1 4 Xcal l b u r Page 94 USER MANUAL OPERATION da detector aperture setting DA dh dv dh horizontal slit in deg dv vertical slit in deg dc help help overview of dc commands dc help dc applycorrections Application of data reductions corrections on current frame dc applycorrections typeofcorrection L P A W S L lorentz correction P polarization correction A air path correction W window absorption correction S scintillator correction dc beamstop Beam stop visualization dc beamstop dc hkl Import hkl file and apply outlier rejection dc hkl dc movie Data collection inspection dc movie dc oneframe Fixing the integration peak mask dc oneframe filepath filename run frame filepath filename The filename eventually with path may be given on the command
120. enced user may find the command line the quickest way to interact with the system 4 6 KMW200CCD Chiller Information about the KMW200CCD Chiller is in a separate manual supplied with this equipment 4 7 KMW3000C Chiller Information about the KMW3000C Chiller is in a separate manual supplied with this equipment 4 8 Low Temperature Option If a cryogenic cooler is fitted to the Xcalibur system then the correct adapter must be used to mount the cooler on the stand for optional equipment Further details can be obtained from Oxford Diffraction 4 9 Safety Features In normal operation the X rays are generated and projected in a totally enclosed cabinet constructed of glass WARNING The enclosure does not prevent the escape of X ray radiation It is provided to restrict access to hazardous areas Xcalibur has magnetic switches mounted at the base of the front doors of the protective enclosure During normal operation i e interlocks applied the X ray shutter will not open unless the front doors are closed If the doors are then opened whilst the X ray shutter is open the X ray shutter is immediately caused to close Access to the interior of the cabinet via the front doors is required when changing samples When the doors are opened during sample change and alignment the X ray generator remains on for optimum performance Indicator lights mounted on the outside of the enclosure show when the X ray generator power is on o
121. eneric goniometer settings Instrument model Instrument model II Monochromator Fonts This dialog allows you to modify the instrument parameters for the detector and the goniometer Detector di 0 079 d2 0118 Edit d2 dd 62079 Edit dd x 517 470 Editx y 493 032 Edity Pixel size mm 0 0611 Goniometer om 0 049 Edit o0 th 0 143 Editt0 ka 0 071 Edit k0 al 50 153 Edital be 0 007 Edit be 4 SETUP OPTIONS SETUP OPTIONS SETUP OPTIONS OK Cancel Help La zi Ready O 0000 T oooo k oooo P ooo DENEN gAsten A E RED gt S Gn xcelibur manus M Listot Crysis f Crysis RE Bajema Tu R3 08 55 Figure 6 5 4 Screenshot of CrysAlis program options Instrument model I CD ci lel x CrysAlis RED program options x Instrument model Instrument model II Monochromator Fonts PH and PT size Colorcodes Beam stop settings Generic goniometer settings This dialog allows you to modify the beam stop settings Beam stop support orientation C Bottom C Let Right Left45deg C None C Beam stop dimensions 15 000 EditX stop 3 000 Edit stop dia 4 SETUP OPTIONS SETUP OPTIONS SETUP OPTIONS F Ready O 0000 T oooo K ooo fP ooo ERES HA Start ud euge ro F Xcalibur 1 Fe List of Cry Bi CrysAii Hf setup opti poule QT a ut 0856 Figure 6 5 5 Screenshot of CrysAlis program options beam stop settings A number of options are available for edit
122. eometry Goniometer ssssssssssssssssseeeeeneeeen 19 4 4 X ray Generator dice eec eoe agg dee ioc ade ie E debe ed ee de eed ida 20 4 5 SOftWale 6er eoe eco ect avesse catu ole e Tie eru ele s a tai cet alee 21 4 9 1 Directory Structure e eden ei ene ete ds 21 4 5 2 Basic Menu Philosophy 2 tti Lebe tete tein heisse tto Deep ard ede hebes eR E era td 22 4 6 KMW200CCD hiller 22 2 rd tt rate temo den ed de egt err renta 22 4 7 KMW3000G Chiller 2 2 coca edente eed pce einen cte ene d et nidis 22 4 8 Low Temperature Option sssssssssssssessseseeeeeeeerenen ener eer tenth nn nennen Eea 22 4 9 Safety FeatUures i nion bte nion ibit nii me pita RE en 22 5 Handling Installation Storage and Transit Information 23 5 T Reception and Handling eene t e RR ne p a tete edis 23 51 1 DellVeryacs etn etant uma t 23 5 1 2 Unpackinig 2 oh NA AiE ENA EAE deed ed dee se e ue d e edid 23 5 1 3 Mechanical Handling nemen 24 5 1 3 1 Weights Dimensions and Lifting Points sssee 24 5 1 3 2 Boxed Weights Dimensions and Lifting Points on Dee ii ei trstmitt oe ibn o ne teca miei ettet iat te itte tea fier 25 5 2 Installation and Setting to Work meieni arri aenea EA EEEa EA TEE enm eene nenne 25 5 2 1 Preparation of Site and Services ssssssssssssssesseesseeeen enne 25 5 2 1 1 Environmental Requirements sssssssssssssseeeeeneem 25
123. er Disconnect the fibre optic cables interface cables and water pipes from the rear of the detector Mark the position of the fibre optic cables The order of the water pipes is not important NOTE E Take care not to allow drips of water from the water pipes to fall onto the goniometer or camera Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 107 USER MANUAL MECHANICAL CHANGEOVER OF DETECTORS AND X RAY SOURCES N WARNING During the following steps take care not to allow the camera to slide into the kappa block as the slider has very low friction The Onyx is a delicate electronic instrument If dropped it may be damaged and warranty will be invalidated Due to the construction of the Onyx camera it cannot be removed in exactly the same way as the Sapphire 2 and 3 cameras The camera must be rotated on it s mounting bar in order to prevent the front face of the camera colliding with the universal mount during the removal procedure Underneath Onyx the mounting rail is attached by three screws as shown previously in figure 7 1 3 1 3 Unscrew the two upper M4 screws connecting the slider to the lead screw which defines the camera distance Turn the end plate of the slider anticlockwise by 180 degrees N WARNING The Onyx CCD is heavy and it s weight must be supported by holding onto the CCD head as well as the mounting rail The Onyx is a delicate electronic instrument If dropped it may be da
124. er from table obtained by typing um c C11 c12 c13 c31 c32 c33 direct space transformation matrix um reduce Apply Niggli reduction of unit cell um reduce umr refine UB under symmetry constraint um r symmetrycode symmetrycode The necessary code can be obtained by just typing um r um sarray Store the defined ub unit cell matrix to a buffer Um sarray arraynum ub11 ub12 ub13 ub31 ub32 ub33 array 8 available Used to define a number of ub matrices for data reduction of twinned data Arraynum 0 7 storage buffers for unit cell matrices Ub11 ub33 unit cell ub matrix umu activates the procedure to refine the crystal umu orientation automatically wdi Write disc image wd i filepath filename filepath filename Optionally you can put the path and filename on the command line Note that you have to use quote for filenames with spaces wd bitmap Current image as 8 bit bitmap wd bitmap filepath filename filepath filename Optionally you can put the path and filename on the command line Note that you have to use quote for filenames with spaces wd flood Save current image as flood image wd flood wdt Write peak table to file wd t filepath filename Version 1 4 Xcalibur_Manual_v1 4 Xcal l b u r Page 100 USER MANUAL OPERATION filepath filename Optionally you can put the path and filename on the command line Note that you have to use quote for filenames with spaces wd p
125. ers from disk rd i read disk image Reads a stored image from disk rd ph read disk peak hunting Reads a stored peak hunting table from disk rd t read disk table Reads a stored peak table from disk 6 5 1 10 Exiting the CrysAlis CCD program To exit the CrysAlis CCD program the command en should be issued This drives the goniometer axes to their home zero positions and exits the CrysAlis CCD program 6 5 2 Changing Xcalibur Settings 6 5 2 1 Changing CCD Binning The Sapphire CCD chip typically operates in 2x2 binning mode However the CrysAlis CCD program allows the user to switch between 1x1 2x2 and 4x4 binning It is also possible to switch off flood field dark corrections and spike suppression In CrysAlis CCD type ccd par Click on the drop down menus and select the required setting e g 2 for Sapphire 3 2048 x 2048 binning followed by OK Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 39 USER MANUAL OPERATION cco EES a Fe CCD parameters x Operational parameters Corrections m c2 Dark On C Ot ic igh Flood field r On Off 1 1 1024 1024 Spike suppression C none Comeletion C Filler MPP yes Defouits Resdoutnode C A 1x1 full 2x2 full 4x4 full 8x8 full 8x8 center free ea 1048576 pix 4199168 bytes 340Y 794Int 0 0 546 1 640 2 706 L0 16 T 9 44 R 2 16 0000 T 0000 K 0000 0000 x gesund 6 S ONEG mw moo Rios Rs gc un poet v E 101 Figur
126. etermination The CrysAlis RED GRAL plug in wizard guides the user through space group determination At all points the plug in makes suggestions regarding choice and these are based upon a set of parameters The tolerances of these parameters can be adjusted at any point by returning to the settings window This is achieved by clicking on the settings tab at the top of the window Figure 6 5 30 shows a screen shot of the settings window and the parameters which can be adjusted GRAL E 3 x Settings amp Load m Cell parameters are supposed to be identical if differences in amp b c arelessthan fo 007 00 andin p vy are less than 1 00100 r Parameters for systematic absence test Max No of forbiden refl 5 Max mean I ofl 3 93000 Min l a l gap 4 86000 r Far selecting space group use only reflections with p Err parameter for lattice selection I lt 4 c l o lt o 06000 1 00000 Err lt 0 55000 Use experimental r Space Group preferences weights of parameters CCDC 0 ICSD O Rint 2 0 Set default parameters Figure 6 5 30 Screenshot of the GRAL plug in Settings 1 Inthe CrysAlis RED program type Gral go and press Enter 2 On initialisation of the plug in click on the Load button and select the relevant hkl file Click on the tick box Read parameters from file to load the associated unit cell and radiation parameters Alternatively these can
127. f Unwarp Wizard Step 4 Background Evaluation 8 Click on Finish Version 1 4 Xcalibur Manual v1 4 Xcal i b u r Page 81 USER MANUAL OPERATION Step 5 Data corrections M Use scan speed renormalization m Correction rescaling Scale 1 00 Edit user scale lt Back Cancel Figure 6 5 59 Screenshot of Unwarp Wizard Step 5 Data Corrections The defined layer will now be reconstructed An example of a reconstruction layer follows Figure 6 5 60 An Example of a Reconstructed layer 6 5 7 Dc opti Optimisation of Data Collection Strategy The CrysAlis system contains a powerful module for determining an optimal data collection strategy This module is accessed through the command dc opti NOTE EI An optimal data collection is calculated to meet the following user defined constraints Time exposure time and complete experiment Completeness this is a fractional value expressing the ratio of measured vs measurable reflections in a given resolution range This uses the specified Laue Version 1 4 Xcalibur_Manual_v1 4 Xcal l b u r Page 82 USER MANUAL OPERATION group to determine equivalent reflections Coverage this is a fractional value expressing the ratio of measured vs measurable reflections in a given resolution range using no symmetry Redundancy multiple measurement of equivalent reflections Resolution this describes the maximum and minimum d value included in a
128. following instructions in the relevant third party manual 6 Empty the chiller water reservoirs 7 Disconnect cables 8 Disconnect halogen cabinet lights Remove fibre optic lights cabinet vents and Xcalibur remote control 9 Remove the video telescope camera 10 Remove the video monitor 11 Remove the fibre optic power supply 12 Remove the DC power supply 13 Remove the video tower WARNING Do not touch the Beryllium window at the front of the detector Beryllium is potentially toxic material 14 Remove the beam stop and collimator 15 Remove the CCD detector WARNING Do not touch the Beryllium windows in the X ray tube Beryllium is a potentially toxic material 16 Remove the X ray tube shield X ray tube and temperature sensor 17 Remove the X ray generator NOTE ET 3 persons are required to perform this step 18 Remove cable guide and fibre optic light arm 19 Remove support arm 20 Remove protective cabinet frame and top NOTE Version 1 4 Xcalibur_Manual_v1 4 Xcal l b u r Page 132 USER MANUAL MAINTENANCE INSTRUCTIONS E 4 persons are required to perform this step 21 Remove goniometer 22 Remove tabletop 23 The Xcalibur system is now fully dismantled Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 133 USER MANUAL TROUBLE SHOOTING 10 Trouble Shooting Symptom Fault Solution X ray shutte
129. ge theta Check collisions Edit done number New runs Choose a scan type Type of run list Data collection frames C Reference frames omega Figure 6 5 12 Screenshot of Edit data collection runs 2 Press Import run list and select a pre defined run list e g typical data collection run for hemisphere data collection If necessary adjust exposure time or frame width using the relevant buttons Alternatively define an optimised data collection run list using the dc opti command described in section 6 5 7 NOTE E Disk space available and required is displayed at the top of the window Please ensure there is enough disk space available for data collection 3 Start data collection by typing dc s Complete experimental data when prompted click on re start and leave to collect data NOTE E Data collection may be interrupted at any time using the Ctrl key or the Stop menu To resume data collection type dc r 6 5 3 5 Data Processing and Reduction Data processing and reduction is achieved using the CrysAlis RED application This allows the conversion of raw experimental data into a format that is compatible with today s crystallographic solution and refinement software Data reduction cannot proceed until you have determined the unit cell parameters During data reduction you will have the option to apply extinction laws special corrections such as local background least squares and theta fi
130. gt O AwordDo B xcelibu Figure 6 5 45 Screenshot of Ewald Explorer Skip reflections invisible Hlskipped PgpomumiqeT a 4 ig 4 0120 6 5 4 2 Intensity Selection of Reflections and Marking them as Skipped 1 With the Select radio box selected use the mouse to select Skip filter from the menu bar at the top of the window Select Intensity from the drop down menu glx Rotation axis Cx s so Slow rotation 0 200 Edit Fast rotation 3 000 Edit Zoom sk Ee 0 700 Edit ES gt v Latice T B ag Drag Select C Draglndex d iren 3 ren E f rene Show ell C used C skip C wrong v Wavelength 0 70930 Mo pt ewa Intensity skip on Ready O 43 280 T 30 000 k 25 000 P 260 000 gwuuEE waster A E E gt DNorde muno RE xcelibur l crysati Sr stereopro apos QT 9 a 01 44 Figure 6 5 46 Screenshot of Ewald Explorer Skip Filter Intensity Menu Selected o 2 Anew window entitled Skip filter intensity should appear By clicking on the Max left and right arrows decrease or increase the intensity threshold As you increase the threshold using the right arrow you should see reflections disappearing in the main Ewald Explorer window The Min left and right arrows also allow the minimum threshold intensity to be adjusted Adjust the Max and Min settings to remove the unwanted reflections from view ensuring that the Use intens
131. he following procedure explains how to load software updates CAUTION The following upload procedure will overwrite the current Xcalibur MGC interface software Xcalibur control information including slit positions may be lost To install the MGC interface software you will need the following programs saved to your computer WinZip packaging software Hyper Terminal program Mgc_111 zip where 111 is the current version number 1 Copy the file mgc_111 zip file onto your hard disk Using WinZip unpack the file mgc_111 hex 2 Start the program Hyper Terminal usually this is part of the Windows system and can be found under Accessories Communication tool Open a new communication and name the connection MGC upload Set the COM port to 1 check the back of the PC to see this is the COM port to which the interface is connected and the transmission parameters as Baud speed 19200 Bits 7 Parity Even Stop bit 1 Flow control None 3 Switch off the Xcalibur interface using the red ON OFF button mounted on the front panel Xcalibur goniometer interface 4 Depress and hold the red EMERGENCY button located on the front panel of the Xcalibur goniometer interface 5 Switch on the Xcalibur interface and release the red EMERGENCY button after 3 seconds 6 The Hyper Terminal window on the PC should now display a hash mark 7 Within the Hyper Terminal program select Transfer or Send Transfer from the drop dow
132. he process and can utilise either the complete data set or the unique data 1 The guided wizard is started by typing dc unwarp 2 Figure 6 5 52 shows Step 1 in the unwarp wizard The current orientation matrix is loaded Click on the Next button to proceed to Step 2 i CrysAlis unwarp assistent crystal lattice reminder Figure 6 5 52 Screenshot of Unwarp Wizard Step 1 Orientation matrix 3 In step 2 the user must load the relevant data collection run file This can be done by clicking on the button marked Browse for run list and selecting the relevant folder and run file Open Xcalibur datacollection run files zeli l BaTh7Se18 Xcalibur datacollection file run Version 1 4 Xcalibur_Manual_v1 4 Xcal i b u r Page 78 USER MANUAL OPERATION Figure 6 5 53 Screenshot of Unwarp Wizard Step 2 Open Run List 4 If required adjust the number of runs frames used in the unwarp reconstruction by clicking on the relevant run in the main text box The whole line occupied by that run should be highlighted in blue Now click on Edit start num of selected run or Edit end num of selected run Enter the desired parameters Setting the start num of a selected run to zero will prevent that run being used in the reconstruction Click on Next NOTE E The greater the amount of runs data employed the longer time reconstruction will take CrysAlis unwarp assistent run list x Step 2 Experiment ru
133. hed to your Xcalibur 1 If required double click on the CrysAlisBaseOD exe program icon This is a self extracting installation program Follow the on screen instructions 2 When complete run the CrysAlis171 exe program Again follow the on screen instructions When asked to select the program elements required for installation click on the box next to CrysAlis RED only a tick appears in the box and click on Next CrysAlis CCD is only useful if the computer is being used to drive the Xcalibur 3 Onceinstallation is complete double click on the CrysAlis RED icon which has been installed on the desktop The program will ask you for a set up file Locate the Corrections folder which you saved to disk earlier and select the file par Click on OK 6 4 3 Changing Machine Correction and Set up Files To analyse and reduce data recorded on a different Xcalibur diffractometer you MUST obtain a copy of the corrections folder for that machine Save this folder to your computer Open the program CrysAlis RED and select Tools Set up files from the menu bar Click on the button marked Set up file par locate the new corrections folder and select the relevant par file Click on Open and then OK From the menu bar select Tools gt Correction files You should see that all geo ffi and ccd have all changed to those for the new Xcalibur set up Click on Cancel If the files listed are incorrect click on the buttons marked Geo fi
134. heldrick s solution and refinement software Available free to academics Further information available at http shelx uni ac gwdg de SHELX index html XSTEP and WINCSD Stoe solution and refinement software SADABS George Sheldrick s area detector absorption correction program Crystals free download from the University of Oxford at http www xtl ox ac uk download html 6 5 4 Ewald explorer The current contents of the peak peak hunting table can be visualised using the Ewald Explorer reciprocal space visualiser Ewald explorer allows the user to rotate reciprocal space zoom in and out drag index and select reflections for peak indexing The user can also adjust intensity thresholds lattice extinctions and d spacing thresholds to select peaks 1 To initialise the Ewald explorer type pt ewald and press Enter 2 The Ewald explorer allows you to scan the reciprocal space of your data collection for lattice planes For example you can rotate the diffraction pattern about three axes and you can choose between a slow and fast rotation 3 Try to find a plane like the following by rotation about x y z Click on the desired Rotation axis radio button marked x y or z to define the direction of rotation Use the Slow or Fast Rotation arrow buttons A lattice overlay can be shown by clicking on the Lattice tick box until a tick appears NOTE E The lattice overlay will be the program default cubic cell of ca
135. hms Fit a line voltage regulator if the power supply voltage fluctuates more than 10 95 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 unreliable an uninterruptible power supply UPS is recommended The UPS should have specifications of 10 kVA with 3 phase input and single phase output Description Voltage Frequency Maximum Main Maximum V Hz mains fuse power current A Ww A X ray generator 1 N AC 230 10 50 60 24 32 4200 CCD detector amp 1 N AC 230 410 50 60 1 1 6 300 KMW200CCD cooler Kappa geometry X ray 1 N AC 230 10 50 60 2 5 6 3 400 goniometer video monitor halogen lamp fibre optics Computer and 100 240 50 60 10 10 peripherals Cryojet controller 100 240 50 60 2 25 5 ILM201 100 230 50 60 0 6 0 8 1 6 KMW30000C Cooler 1 N AC 230 10 50 60 1 2 6 3 300 Version 1 4 Xcalibur Manual v1 4 Xcal i b u r Page 26 USER MANUAL OPERATION 5 2 1 4 Water Supply CCD detector Cooling The CCD detector is water cooled by the KMW200CCD Cooler Ten metre long water pipes are supplied with the system The minimum distance required between the back and the side of the casing for KMW200CCD and electronics rack is 30 cm X ray Tube and Generator Cooling A
136. hot of the GRAL plug in Load Window File loaded from DC GAINS HKL 66 Figure 6 5 33 Screenshot of the GRAL plug in Load Window Reciprocal space visualiser 67 Figure 6 5 34 Screenshot of the GRAL plug in Centring Window eee 67 Figure 6 5 35 Screenshot of the GRAL plug in Niggli Window sem 68 Figure 6 5 36 Screenshot of the GRAL plug in Lattice Window e 68 Figure 6 5 37 Screenshot of the GRAL plug in Centring Window After Niggli Reduction 69 Figure 6 5 38 Screenshot of the GRAL plug in lt E2 1 gt Window see 69 Figure 6 5 39 Screenshot of the GRAL plug in Space Group Window sss 70 Figure 6 5 40 Screenshot of the GRAL plug in INS File Window ee 70 Version 1 4 Xcalibur Manual v1 4 Xcal ibu r Page vii USER MANUAL Figure 6 5 41 Screenshot of Ewald explorer screen sssssesseeee 72 Figure 6 5 42 Screenshot of Ewald explorer screen with vector shown sssseesss 72 Figure 6 5 43 Screenshot of dialog box displayed when exiting the Ewald explorer 73 Figure 6 5 44 Screenshot of Ewald Explorer Drag Selection of Reflections and Marking Skip 73 Figure 6 5 45 Screenshot of Ewald Explorer Skip reflections invisible ccccccseeeeeeeeeees 74 Figure 6 5 46 Screenshot of Ewald Explorer Skip Filter Intensity Men
137. ibur Manual v1 4 Xcal l b u r Page 17 USER MANUAL TECHNICAL DESCRIPTION 4 2 7 Dark Current and MPP Mode The silicon base of the CCD chip generates a so called dark current The dark current is material property of the silicon and it is due to spontaneous generation of electron hole pairs in the silicon lattice due to thermal excitation Cooling the CCD chip reduces the dark current At the typical operating temperatures of 45 to 50 C the dark current is 0 2 electrons pix s The low dark current is archived by a special mode of operation of the CCD chip The MPP mode MPP stands for multi pinned phase and describes the fact that each pixel has a special boron implant under a part of the active area which pins the electrons under it without having to use the actual gates under tension used for the readout transfer 4 2 8 Radiation Damage CCD chips as all unprotected Silicon devices are sensitive to radiation damage The glass taper which is in front of the CCD absorbs all incoming radiation and thus protects the CCD from radiation damage 4 2 9 Full Well Depth and 18 bit Digitisation The full well depth is the number of electrons that a CCD pixel can hold The typical value of the full well depth for a MPP mode operated CCD is 300 400k electrons for a single unbinned pixel In order to take full advantage of the full well offered by the CCD chip the readout electronics have to match the resolution of the CCD chip 16 bit readout 65k
138. ield Re insert the high voltage cable in to the back of the Enhance X ray tube shield Reconnect the water pipes to the back of the Enhance X ray tube shield Reconnect the temperature sensor to the base of the X ray tube Replace the front cover plate on the Enhance X ray tube shield and tighten the grub screws which hold it to the optic housing At the rear of Enhance X ray tube shield screw in the horizontal adjustment screws 2 and 3 in Figure 7 2 1 so that they are pushing on the Enhance X ray tube shield Open the mains water supply Turn on the water chiller KMW3000C and ensure that cooling water is flowing correctly Replace the collimator in the optic housing The X ray generator may now be switched on Switch on the Xcalibur interface using the red ON OFF button Xcalibur Manual v1 4 Xcal l b u r Page 110 USER MANUAL MECHANICAL CHANGEOVER OF DETECTORS AND X RAY SOURCES 36 The horizontal adjusting screws under the rear of the X ray tube will need readjustment to align the optics with the crystal 37 The vertical adjusting screws may need to be readjusted one large screw under the plate near the front of the tube shield and two on either side of the tube shield near the rear to optimise the vertical position of the beam on the crystal 38 Follow Enhance alignment instructions in section 9 of this manual 39 If the beam cannot be aligned horizontally with the crystal then the plate underneath the tube shield is not ideally po
139. ified and digitised 4 2 5 Readout Speed Unlike normal video CCD chips the CCD chips used in the X ray CCD camera are optimised for slow scan operation The readout nodes designed for a typical readout speed of 50 100kHz to give optimal noise performance A typical top grade CCD chip has a readout noise of 3 4electrons under these conditions You may also readout these chips at a faster speed like 0 25 1Mhz but the read noise quickly increases to 8 20electrons For the X ray diffraction application low system noise is of utmost importance for the measurement of weak diffraction signals 4 2 6 Binning Binning is an operation mode of a CCD chip which allows grouping together several pixels There is parallel and serial binning In parallel binning more than one row is shifted at once into the serial register This means that the charges of the pixels in the direction of the parallel shift are summed together in the serial register The same can be done in the serial register Instead of reading out every single pixel the charges of more than one pixel are dumped into the readout node Binning reduces the resolution of the CCD camera But is also reduces the readout noise due to less readouts per unit area and readout time The 1k CCD chips typically used in X ray diffraction are typically read out in 2x2 binning mode as to give a faster readout time lower noise and as to match the front end pixel size to approximately 100x100um Version 1 4 Xcal
140. ill be assumed by the program as center of the scanning area st 7 measurement time of one scanning point sec s1 number of scanning points in the U1 V1 W1 direction sw1 increment of scanning angle for U1 V1 W1 direction Deg U1 V1W1 indices of the first scanning direction s2 number of scanning points in the U2 V2 W2 direction sw2 increment of scanning angle for U2 V2 W2 direction Deg U2 V2 W2 indices of the second scanning direction filename optional filename smr measure a single reflection SM Rh kl psistart psiend psistep h k I reflection index may be fractional psistart optional psi angle psiend optional psi start angle for measuring a sequence psistep optional psi step angle for measuring a sequence sms single step scan SM S steps time steps number of steps for scan time exposure time in sec per step smt theta scan sm t startangle scanwidth time system dos Open MSDOS prompt in current directory system dos system explorer Open current windows directory system explorer system help Help overview of system commands system help Qvector Refine incommensurate q vector qvector mmax crithkl q1 q2 q3 q1 q2 q3 q1 q2 q3 tr theta range TR tthmin tthmax tthmin minimal two theta tthmax maximum two theta 0 0 deg lt tthmin lt tthmax lt 180 deg ty help help overview of ty commands ty help tyl Print lattice information to history tyl typ Print parameter file to history typ ty
141. in how to interface to the equipment e list performance characteristics of the equipment 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 100 Angstrom in any direction for small molecule Xcalibur diffractometers and 500 Angstrom for macromolecular Xcalibur 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 Oxford Diffraction to enable use of these devices Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 6 USER MANUAL SPECIFICATIONS 3 Specifications 3 1 Environmental Requirements Ambient temperature during operation 18 28 C Stability of ambient temperature during 1 C operation Storage temperature Relative humidity Location Floor covering Floor strength gt 10 C lt 40 C 80 non condensing Clean dust free environment gt 2m from air conditioning or heating units Cond
142. ing The beam stop support orientation would not normally be changed from the default top setting To change the crystal to beam stop distance click on the button marked Edit X stop Enter the required values in the range 5 100 mm default value is 15 To change the diameter of the beam stop mask click on the button marked Edit stop dia Enter the required values in the range 0 1 10 mm default value is 3 When you have finished editing click on OK Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 41 USER MANUAL OPERATION To visualise the new beam stop mask type dc beamstop To remove the mask type dc beamstop a second time CAUTION The wd cal command will overwrite the current diffractometer set up file Calibration of the diffractometer may be lost at this point if an invalid model exists Once you are happy with the new settings you must save them to disk using the command wd cal 6 5 2 3 Peak table profiles The peak hunting table contains the raw peak hunting coordinates A true peak may be composed of several peak hunting profile steps These can be visualised via the peak table editor profile inspector In order to do this the setup option Save 32x32 image copy in peak hunting table must be selected in the Setup options This is achieved as follows 1 Type Setup options From the resulting setup window select the tab marked PH and PT size and click on the tick box Save 32x32 image cop
143. ion data Whilst the refinement may show a marked improvement in terms of Rin values this improvement may not be reflected by the physical shape of the crystal model Examine the crystal model to see if the refined optimised shape is a good fit with the crystal s physical shape 1 Type the command abs display to start the absorption correction module and rotate the image If the model can still be improved repeat steps 2 4 Adding new faces where necessary The final result in this case provided a crystal model which was optimised to a pseudo ball E NOTE The command um shape allows you to visualize the shape model without video overlay You may enter the absorption coefficient there or compute it based on the known chemical information Version 1 4 Xcalibur Manual v1 4 Xcal i b u r Page 63 USER MANUAL OPERATION lal File Edit Color EESE F m Crystal movie ina Hj zis Goniometer ty abs display Message from O 57 00 T 30 00 K 134 00 P 165 00 HKL 0 00 8 00 X 579 Y 353 o Ready M Help PK 450 Y 158 Int 0 0 709 3 294 1 717 L 0 33 T 10 90 P 1 88 fo 0000 r oooo K o000 Pon iT gistan 1 2 A gt A E Ef crysatis RED c Be xeeriburtversion 13 f abs7bmp Paint e ons Figure 6 5 28 Screenshot of crystal movie screen 6 5 3 7 5 Step 5 Apply Absorption Correction to Full data Once you have determined
144. ional equipment like high or low temperature attachments System software installed on PC workstation A water chiller for the CCD detector type KMW200CCD D cv ode ov a A water chiller for the X ray tube and X ray generator type KMW3000C Note The numbers on this diagram refer to the numbered list above Figure 4 1 1 Components of the Xcalibur system The diffractometer and CCD area detector are mounted inside a cabinet The cabinet experiment area is mounted on top of the electronics rack Water chillers for the CCD detector and the X ray generator are positioned to the side of the instrument The PC workstation is located close to the instrument to allow a clear view of the diffractometer and convenient access to it The diffractometer consists of an X ray tube a 3 axis Kappa goniometer omega kappa and phi axis for sample orientation and a detector arm theta axis which has a universal mount capable of supporting any Oxford Diffraction CCD area detector or scintillation point detector The CCD area detector and the point detector are used to measure the X quanta diffracted from the sample Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 14 USER MANUAL TECHNICAL DESCRIPTION il J 5 S Ex m L ERU 2 p i x H 1 ym m y Key 1 X ray tube 4 Collimator 2 4 circle Kappa goniometer 5 Beamstop 3 X ray Shutter 6 Beryllium Window Figure 4 1 2 View of the
145. ity filter box is ticked Click on OK Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 74 USER MANUAL 5 um c 1 UB fit UB ex EN v Wavelength 0 70930 Mo T eae ees l mm TM Ok OPERATION Rotation axis Oxo Oy amp 2 lesu entation Edit gt 0 Min Step Edit Max Fee qux pa 2E Show al C used C skip C wrong ll Intensity skip on Ready HAStar AUG HE gt o E O 43280 T 30 000 k 25 000 P 260 000 mE y orde munro m Xcalibur Hi CrysAii Hf intensity fi 2 Spouse v Qe i3 01 45 Figure 6 5 47 Screenshot of Ewald Explorer Skip Filter Intensity Window Use Intensity Filter 3 From the menu bar select the Flags menu and then Mark invisible skip A window will appear asking you Do you want to mark all invisible peaks skip Click on OK The invisible reflections which have been selected using the intensity filter have now been skipped Hs Ewald sphere explorer x Hl Exit Show Skipfilter Flags Tum90deg Tum S0deg ClearDrag Properties Help Mark all used Rotation axis tae Invert used and skip Cx C y 6 20 i v Wavelength 0 70930 Mo pt ewa X vo z TEENS siete Jl xl Slow rotation 4 gt 0 200 Edit Fast rotation 4 gt 3 000 Edit de Gis Sate Zoom eee ah at CANS dm RG oa a gt 0 700 Edit E Iv Lattice M Blereog M Drag I DASE Sse
146. l uum low level for the counting chain 0 0 2 55 mab matrix boundary PD MA B n 1 1 n 1 2 n 1 3 n 2 1 n2 2 n 2 3 n 3 1 n 3 2 n 3 3 or MA B lt predef set no gt n matrix elements 32 lt n i j lt 32 predef set no The following codes can be selected 5 4 mmm T 3m1 8 31m 10 6 mmm 11 m 3 12 m 3m mob mode of background PD f background parameter 0 01 lt f lt 2 0 mos mode of scan PD MOS ms n1 n2 Vmin m mode of scan 0 lt m lt 2 0 BPB scan 1 continuous integrative step scan 2 stationary step scan S number of scan steps not for m 0 10 lt s lt 1024 n1 minimum accepted l sigma l and n2 requested l sigma l 3 lt n1 lt n2 lt 50 Vmin Minimal rescan speed 0 004768 Deg Sec lt Vmin lt 1 5 Deg Sec phe ph extractprofiles edit peak hunting table extract profiles from data collection phe ph extractprofiles ph help help overview of ph commands ph help Powder extract1D ph profile Extract powder pattern data to clipboard to be used in any spreadsheet program transform peak locations to peak profiles powder extract1d bins thetamindeg thetamaxdeg ph profile phs Peak hunting start phs ph reconstruct reconstruct the peak table with current instrument model ph reconstruct pt clear clearing of the peak ta
147. l class PC Pentium IV class PC gt 1 GHz gt 2 4 GHz gt 256Mb RAM gt 1 0 Gb RAM 17 colour display 21 colour display 3 3 6 Four circle Kappa Geometry X ray Goniometer Type Sphere of all axes coincidence Maximum load Phi axis Resolution Scanning speed range Scintillating detector angular range CCD detector to sample distance Shutter opening and closing time 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 90 to 167 deg 45 to 150 mm 3 ms Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 12 USER MANUAL 4 4 Electrical Data SPECIFICATIONS DF3 X ray 3K5 X ray Sapphire 2 Sapphire 3 X ray Generator Generator CCD Onyx CCD Goniometer Power connection 1 N AC 198 1 NAC230V 1 NAC230V 31 NAC230 1 NAC230V to 242V 1096 1096 V x 1096 1096 50 60 Hz 50 60 Hz 50 60 Hz 50 60 Hz 50 60 Hz Maximum power 4300 W 4200 W 150 W 200 W 250 W consumption Maximum mains 19A 24A 1 0A 1 7A 1 2A current Main fuse 32A 32A 1 6A 4 0A 6 3A Ground terminal 6 mm Cu 6 mm Cu 2 5 mm Cu 2 5mm Cu 2 5mm Cu Version 1 4 Xcalibur_Manual_v1 4 Xcal ibur Page 13 USER MANUAL TECHNICAL DESCRIPTION 4 Technical Description 4 1 Overview The Xcalibur system consists of 1 Akappa geometry 4 circle diffractometer A CCD area detector An instrument cabinet with electronics rack A stand for opt
148. l issues as indicated below e E mail support oxford diffraction com e Phone 44 0 1235 532132 between 8 a m and 4 30 p m UK time Monday to Friday e Fax 44 0 1235 528005 This users manual has been written according to standard 89 392 EEC and further modifications Xcalibur is a trademark of Oxford Diffraction Limited in some jurisdictions and a registered trademark of Oxford Diffraction Limited in other jurisdictions Oxford Diffraction acknowledges all trademarks and registrations Copyright 2003 Oxford Diffraction Limited All rights reserved No part of this document may be reproduced or distributed in any form or by any means or stored in a database or retrieval system without prior written permission of Oxford Diffraction Xcal l b u r Xcalibur_Manual_v1 4 Version 1 4 USER MANUAL Page ii Contents 1 Health and Safety Information eeeseuss 1 UuEC USCI ELLE 1 1 2 Electrical Safety antin dee eg ed epi Radia pi n dag o ede eek eA 2 1 2 1 Potential Electrical Hazards 2 ececccceccece cece eecencae cece cece cecceaeeeeeeeeesecacenaeeeeeetenseeseaeees 2 1 2 2 Recommended Precautions sss nennen 2 1 2 3 FITSE AI itti etin ignea e Hi rises 2 1 3 Mechanical Handling Safety arae AE E R 3 1 4 Safe Mechanical Practice ssssssssssssssssssesessseeenee nennen nennen nennen sten 3 19 sez
149. le geo Flood file ffi and CCD file ccd in turn and locate the new corrections folder and the relevant file Click on OK Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 36 USER MANUAL OPERATION 6 5 Normal Operation 6 5 1 General Commands 6 5 1 1 Image Area Statistics Zoom and Histograms Position the Mouse cursor over the diffraction image window Hold down the left mouse button and drag out a wire box around the area of interest Click the right mouse button and select from various zoom options area statistics histograms area pixel value replacement The result is output to the right hand window t CrysAlis RED CCD camera data reduction user interface _ x File Edit ColorTables LookUpTables Zoom Datareduction Commands icp Test Tools Help aie jx Area Statistics Area Histogram Zoom 2x Zoom 4x x v Area drag Line drag Copy selection Area pixel value replacement rd i P rd i C My Documents xtldata Customer Demos york sample 1XdclNdc 1 117 img Zoom factor too high for selected area set to 1 x 251 XW 32 Y 396 YW 41 Int 56 2 537 2 090 4 496 0 45 T1617 R 1 2 O 4000 T 30 000 k 79000 P 0 000 g stn d E e amp 1MeiSummer Bxcalibutvers Bii Crys Aris n geo mST Ou 054 Figure 6 5 1 Screenshot of Image selection and Zoom Position the mouse cursor over a reflection of interest and click the right mouse button Select Integration
150. le As a result the diffraction data is often corrected for absorption The absorption correction incorporated into the CrysAlis software package can be summarised into the following four steps 1 2 3 4 Record a jpeg movie of the crystal sample Build modify a 3 D model of the crystal sample Refine optimise the 3 D model against the X ray diffraction data Examine 3 D model Repeat steps 2 4 until a satisfactory model and absorption correction have been obtained 6 5 3 7 1 Step 1 Record a jpeg movie of the crystal sample Once data collection has been completed and before removing your sample from the diffractometer record a jpeg movie of the crystal sample This is achieved as follows Version 1 4 1 On the Xcalibur system switch on the fibre optic lights and arrange the lighting to give the best sample background contrast Now in the CrysAlis CCD application type abs grab and click on OK This will initiate the ABS plugin Crystal movie Right click on the ABS plugin Crystal movie window and select Overlay picture Click on Movie This should open a new window titled ABS Acquisition of movie See the screenshot below Xcalibur_Manual_v1 4 Xcal l b u r Page 57 USER MANUAL Figure 6 5 21 Screenshot of ABS Acquisition of movie screen OPERATION CrysAlis RED CCD camera data reduction user interface Ele Edit ColorT gm ey E 7
151. lease connectors 4 Remove the front plate from the Enhance by loosening the two grub screws holding it to the optic housing 5 Unscrew the temperature sensor from the front plate metal base with label of the X ray tube WARNING Do not touch the Beryllium windows in the X ray tube Beryllium is a potentially toxic material 6 Release the two screws holding the X ray tube in place and withdraw the X ray tube from the X ray shield Do this by holding the front plate metal base with label and pulling towards the front of the Xcalibur Ensure that the X ray tube is held level and withdraw parallel to the X ray shield 7 For disposal of used X ray tubes see the DISPOSAL chapter of this manual WARNING Do not touch the Beryllium windows in the X ray tube Beryllium is a potentially toxic material 8 Holding by its metal base remove the new X ray tube from its protective box Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 116 USER MANUAL MAINTENANCE INSTRUCTIONS WARNING Ensure that the X ray tube is correctly mounted Incorrect mounting may result in exposure of personnel to X ray radiation Red plastic spacers may need to be removed to ensure perfect fit of X ray tube 9 From the front of the Xcalibur insert the X ray tube into the tube shield and secure y NOTE X ray tube must be inserted the correct way up See figure 9 3 1 Water In AX Water MSN
152. low 5x20mm F2 8150 PCB Xcalibur Manual v1 4 Xcal l b u r Page 137 USER MANUAL SPARES Bulbs Device Location Description Fast shutter Front panel MultiLED T5 5 RED 12V 25mA Swisstac Sapphire CCD Top panel of CCD MultiLED T5 5 RED 12V 25mA Swisstac camera MultiLED T5 5 GREEN 12V 25mA Swisstac Protective enclosure illumination Inside top protective Halogen 12V AC 35W Osram type enclosure 44865WFL Fibre optic lights Inside light source box Halogen 12V 75W Osram type 64617 DF3 Spellman X ray generator Front panel CONTROL Lamp T1 3 4 Mid groove 28V 1 12W Farnell POWER ON X RAY ON and X RAY OFF button warning lamps Service kits and spares Part Number XZ 02 00 001 A XZ 02 00 002 A XZ 02 00 003 A XZ 02 00 004 A XZ 01 00 001 A XA 00 00 052 A XA 00 00 054 A XS 00 00 000 A UC 01 01 001 A UC 01 02 001 A UC 02 01 000 A UC 02 02 000 A Description Service kit bulbs and fuses Service kit o rings and seals Protective cabinet service kit bulbs and fuses Video microscope service kit XYZ Goniometer head HR4 647 Hampton XYZ Goniometer head Huber XYZ Heated goniometer head Hampton Fast shutter assembly Metal glass X ray tube Molybdenum anode FK61 04 fine focus short anode Metal glass X ray tube Copper anode FK61 04 fine focus short anode Ceramic glass X ray tube Molybdenum anode C
153. lters reject outliers and specify output format and absorption correction Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 49 USER MANUAL OPERATION The following files are created during data reduction Y Filename hkl reflections data file optionally including reflection direction cosines or Schwarzenbach psi and short summary of integration process Filename Ist detailed listing of the data processing and outlier rejection process Filename sum short summary file containing the most important data about crystal unit cell measuring conditions and data collection and processing history A wizard can perform automatic data reduction Here data reduction is separated into seven steps 1 Orientation matrix Run list Scan width 2 3 4 Background 5 Special corrections 6 Outlier rejection 7 Output format The data reduction procedure is as follows 1 Start the application CrysAlis RED 2 Load the relevant unit cell parameters from disk using the command rd p 3 Start data reduction by typing dc red This will start the automatic data reduction wizard Follow on screen instructions 6 5 3 5 1 Orientation Matrix The first step gives the current unit cell and orientation matrix There is also an option to apply lattice extinctions which is particularly useful for larger unit cells showing overlap problems and to apply refined q vectors for data reduction of incommensurate samples 1 Click
154. lue resembles the normal constant scanwidth on conventional diffractometers 0 7 1 0 for good samples 1 0 4 0 for bad samples Scan width 1 00 Edit Scan width Cancel Figure 6 5 15 Screenshot of CrysAlis data reduction screen scan width 6 5 3 5 4 Background Evaluation The CrysAlisRED program uses a global background evaluation For an accurate evaluation of integrated intensities a good background determination is essential The evaluation range Re and the repeat frequency Fr values can be edited Since the background evaluation process is very memory consuming you may reduce the load by binning several pixels together This is less accurate but 4x4 binning is usually sufficient Select 4 Click on Next CrysAlis data reduction assistent background evaluation Step 4 Background evaluation Background evaluation frequency For an acurate evaluation of integrated intensities a good background determination is essential Two parameters control this evaluation The evaluation range Re and the repeat frequency Fr Re 25 Edit Re Fr 25 Edit Fr Binning for background evaluation Binning may reduce the memory requirements for the background evaluation Default is 1 You may use 2 or 4 in case of lack of physical memory on your machine risk of swapping Required disk space for background evaluation 12 5 Mb amp 1 s C4 Iv Reduce background accumulation to SHORT type saves memory T Snap background
155. mage with X rays time in secs 6 5 1 6 Reinit Card and Goniometer Reinitialisation Commands If for any reason there is a communication problem between the Sapphire CCD or the Xcalibur goniometer and the control computer then communication may be reinitialised via the commands card reinit reinitialise CCD to PC communication gon reinit reinitialise goniometer to PC communication 6 5 1 7 System commands The following commands may be issued to access the Windows system operations System dos spawns a MSDOS window with the current directory path being used in the CrysAlis program System explorer spawns an Explorer window with the current directory path being used in the CrysAlis program Version 1 4 Xcalibur_Manual_v1 4 Xcal l b u r Page 38 USER MANUAL OPERATION 6 5 1 8 Writing to disk Current machine parameters images and the contents of peak hunting tables can be written to disk wdp write disk parameter settings Saves the current machine parameters to disk wdi write disk image Saves the current image to disk wd ph write disk peak hunting Saves the current contents of the peak hunting table to disk wd t write disk table Saves the current contents of the peak table to disk 6 5 1 9 Reading from disk Machine parameters images and peak tables can be read from disk using the following commands rd p read disk parameter settings Reads stored machine paramet
156. maged and warranty will be invalidated 4 Slide the Onyx camera backwards until the middle screw underneath the mounting arm is visible Remove the middle screw and loosen the last screw 5 Push the Onyx camera forward until the front screw is visible Remove the front screw 6 Rotate the rail by about 20 and carefully slide the camera backwards and off the mounting rail making sure that the front face will not catch or collide with the theta arm as it is removed Take care to support the entire weight of the camera by holding both the camera and the support rail 7 Once removed place the camera on a sturdy surface Rotate the support arm so it is once again parallel with the camera and replace the screws in the holes underneath the support arm Place the Camera in the storage case 7 2 Procedure for Interchange of the Molybednum and Copper Enhance X ray Source 1 Turn off the X ray generator using the X RAY OFF followed by CONTROL POWER ON button or turn the MAINS ON OFF key switch to the off position Turn off the water chiller KMW3000C Isolate the mains water supply Turn off the Xcalibur interface using the red ON OFF switch on the front panel a Boo DN Disconnect the high voltage cable inserted into the back of the Enhance X ray tube end CAUTION Have a receptacle ready to receive water from the pipes and X ray tube shield Version 1 4 Xcalibur_Manual_v1 4 Xcal l b u r Page 108 USER M
157. may significantly affect the safety of the equipment Version 1 4 Xcalibur_Manual_v1 4 Xcal l b u r Page 5 USER MANUAL SPECIFICATIONS 2 Introduction 2 1 Scope This manual applies to the Xcalibur systems designed and manufactured by Oxford Diffraction 2 2 How To Use This Manual This manual is aimed at operators and maintenance personnel of the Xcalibur system Operators of the system should be computer literate familiar with X ray diffraction techniques have had training in the use of the Xcalibur system by Oxford Diffraction staff and have had training about radiation safety 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 expla
158. me umr refine UB under symmetry constraint um r symmetrycode symmetrycode 7 The necessary code can be obtained by just typing um r ums set UB matrix or enter known orientation um s ub11 ub12 ub13 ub31 ub32 ub33 sub11 sub12 sub13 matrix Sub31 sub32 sub33 ub11 ub12 ub13 ub31 ub32 ub33 orientation matrix sub11 sub12 sub13 sub31 sub32 sub33 sigma of orientation matrix um shape View absorption correction model wire frame um shape less movie overlay um showskipd show skip list um showskipd um skipd add item to skip list um skipd um setqvector set incommensurate q vector um setqvector q1 q2 q3 mmax q1 component of q vector along a q2 component of q vector along b q3 component of q vector along c mmax maximum satellite order um f Automatic unit cell determination indexation um f lengthdeviation angledeviation fractionindexed refinement reduction lengthdeviation angledeviation fractionindexed The defaults are 0 05 0 1 0 7 You can loosen this condition in case of an unsuccessful indexing typically 0 3 0 3 0 5 umi Index and refine unit cell um i indexrejectioncriterion indexrejectioncriterion 7 rejection criterion which determines the maximum allowed deviation for which a reflection is considered indexed um c Change orientation matrix um c change c11 c12 c13 c31 c32 c33 change transformation numb
159. n menu and select Text File Locate and select the file mgc 111 hex 8 The file should now begin uploading to the Xcalibur goniometer interface During upload the Hyper Terminal window will display strings of asterix 9 When upload is complete the Hyper Terminal window will display a forward slash terminating a string of asterix 10 Switch off the Xcalibur interface using the red ON OFF button mounted on the front panel Xcalibur goniometer interface 11 Save communication parameters in Hyper Terminal for future use and exit program NOTE E If you encounter problems in the above procedure turn the interface off and on and open and close communication from the Hyper Terminal menu Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 35 USER MANUAL OPERATION 6 4 2 2 CrysAlis Software If you are installing the CrysAlis software for the first time you will need the following two programs saved to your computer CrysAlisBaseOD exe CrysAlis171 exe Where 171 is the current version number If you already have CrysAlis installed on your machine you will NOT need the CrysAlisBaseOD exe These files can be downloaded from the Oxford Diffraction web site You will also need the correction files which are specific to your Xcalibur diffractometer Without these files the CrysAlis software is not fully functional To obtain these files copy to your computer the entire Corrections folder from the PC attac
160. n list for unwarping Current run list C My Documents xtldata BaTh Se18 dc BaTh7Sel8a Browse for run list img v Current image dir C My Documents xtldata BaTh Sel8 de Browse for image Experiment information type start end width exposure omega detector kappa phi start end l o 54 00 51 00 0 76 20 00 e 30 00 25 00 260 00 1 129 2 o 54 00 10 00 0 76 20 00 30 00 25 00 20 00 0 0 3 o 54 00 61 00 0 76 20 00 Ex 30 00 25 00 180 00 0 0 4 o 54 00 10 00 0 76 20 00 30 00 25 00 270 00 0 0 By defaultthe whole experiment will evaluated To modify this Belting Geese behaviour edit the run list gt Edit end num of selected run Cancel Figure 6 5 54 Screenshot of Unwarp Wizard Step 2 Run List Loaded 5 Click on the Browse for output dir button and create a new folder where the reconstructed images will be stored Version 1 4 Xcalibur_Manual_v1 4 Xcal l b u r Page 79 USER MANUAL OPERATION Step 3 Creation of a layer list Layer reconstructions may create a lot of files Try to organize them into a sub directory of your data directories Output base name paTh7SelBa 9 n Output path n a gt use Browse for output dir Button to specity Browse for output dir Lookin 3 4 0 sal el es cl l File nome Qpen q Files of ype directory browse z Cencel d Select Dw di dc Bock x Cencel Ready 46 400 T 30 000 k 25 000 P
161. nc gon reinit Xcalibur goniometer re initialisation gon reinit hv high voltage of photomultiplier HV hv hv high voltage for the counting beam monitor chain KM4 100 0 1000 0 V il Index limits Il hmin hmax kmin kmax Imin Imax ip add ip add destination buffer source1 buffer source2 buffer ip addlong ip addlong destination buffer source buffer longvalue ip convolution ip convolution destination buffer source buffer ip copy ip copy destination buffer source buffer ip correlation ip correlation destination buffer source1 buffer source2 buffer ip help Help overview of ip commands ip help ip histogram Image histogramming whole ip histogram min max visualizationlevel min minimum level for the histogramming range max maximum level for the histogramming range visualizationlevel 1 9 logarithmic high scaling ip imagestatistics Evaluates the mean standard deviation and skewness of the whole image area ip imagestatistics ip median Median filtering of the whole image area ip median destination_buffer source_buffer ip multiplydouble ip multiplydouble destination_buffer source_buffer ip noiseadd ip noiseadd noisetype level destination buffer name noisetype UNIFORM GAUSS POISSON NO level level at which the noise is computed destination buffer name ll Low level of the photomultiplier LL II Hm Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 96 USER MANUAL OPERATION I
162. ngth collimator and a short 0 3 and 0 5 mm collimator for use in high pressure experiments are available by special order Tools None Procedure 1 Ensure that the X ray shutter is closed and all interlocks are in place 2 Nosample should be mounted on the goniometer WARNING Do not touch the Beryllium windows in the X ray tube Beryllium is a potentially toxic material 3 The collimator housing is spring loaded Pull out the collimator from its housing pulling from the right hand side Be careful not to touch the beamstop or CCD detector 4 Select the required size of collimator and push into position on the Xcalibur such that it is flush to the housing surface The collimator should be inserted such that the flat edge is uppermost WARNING Ensure that the collimator is correctly mounted Incorrect mounting may result in exposure of personnel to X ray radiation Version 1 4 Xcalibur Manual v1 4 Xcal i b u r Page 120 USER MANUAL MAINTENANCE INSTRUCTIONS 9 7 Changing the Collimator of Enhance Ultra Enhance Ultra is supplied with only one size of collimator 0 3mm It is therefore not applicable to describe changing collimators 9 8 Aligning the X ray Collimator of Enhance The X ray collimator is factory aligned via the collimator housing This means that re alignment is not needed when changing between the collimators supplied by Oxford Diffraction If collimator re alignment is requi
163. nshot of crystal movie screen 9 The Crystal shape add face window is now displayed Select the desired hkl values real integer or custom It is up to the crystallographers judgement to choose real integer or custom On nicely shaped samples one should use custom and find the custom index with the lowest common denominator e g 6 0 12 would be 102 Click on Add face rysAlis RED CCD camera data reduction user interlace s oa z amp xj Ele Edit ColorT E fer Pa Crystal movie configuration Fie Faces Log Utiities Preferences F Inverted video image sewpealar m Zoom 1x s C dx C Bx Crystal shape add face x m Center X 376 4 Edit ET FETS pg Y 283 4 Edit Scale 5 Pix mm 0 002174 Edit Units of 0 1mm 7 Edit p Draw T Crystal front Crystal back m Index selection 1 297 9 912 0 254 nteger hil 1100 C Custom hkl 1100 Distance selection Measured distance 0 11957 C Custom distance 11957 T Birectexes T Rec axes cr Message from HKL 1 30 9 91 0 25D 0 11957 X 430 Y 282 Show tool window Help Exit O 57 00 T 30 00 K 134 00 P 174 00 a X 431 Y 284 Ready fo 0 000 fT 0000 k 0000 P 0 000 a afe sten Were Mail Summary Mai FA Xcalibur version 1 3 ff CrysAlis RED Wf abs3 bmp Paint QT 0
164. number in the text box This will be highlighted in blue 6 Click on the button Profile A window like Figure 6 5 7 should appear Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 42 USER MANUAL OPERATION CrysAlis profile inspector Exit ColorTables LookUpTables Measured data Reflection scan info __ x y projection r l omega profile hkl es Abe d value 3 884 2 theta 10 479 Omega 31 500 frame wath 1 000 max frame 6 Kappa 40 000 gt Phi 0 000 6 atomega 31 593 Alpha x omega projection y omega projection min 162 max 408483 Omega all 31 467 Cursor on measured data Xy 20 8 143 0 xy 181722143 xy32 158 17 0 Int 408483 Aleha Omega al2 31 557 hkl 2 018 0 995 3 981 m 211 1424 gt 0 06597 xy32 121 164 1 01667 Figure 6 5 7 Screenshot of CrysAlis profile inspector window 6 5 3 Standard Diffraction Experiment A standard crystallography experiment consists of 8 main steps 1 DC OO S oom 8 Crystal mounting and alignment Diffraction photographs to determine crystal quality Unit cell determination Data collection Data processing Absorption correction Space group determination Structure solution and refinement The procedure for a standard experiment follows 6 5 3 1 Crystal Mounting and Alignment WARNING Press STOP on the remote control or Ctrl on the keyboard to stop movement of the equipment in an emergenc
165. nyx CCD CELE CONS EDT 130 Xcalibur DimMeEnSiOns isi ae ei ele el i a as Sa es 142 KMW3000G DIMENSIONS S12 oti e Ete ieee ee edet lle hoo le 142 KMW200CCD DimensiOhs eei tono sh sneeshesavansbebsineededesteesiawetuessseaaueedadevautsaeever 142 Version 1 4 Xcalibur_Manual_v1 4 Xcal i b u r Page ix USER MANUAL 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 should be aware of potential hazards which exist in and around equipment of this type and the ways of avoiding possible injury and equipment damage which may result from inappropriate ways of working A description of such potential hazards and how to avoid them is given in this section This manual adopts the following convention WARNING Indicates a potential hazard which may result in injury or death CAUTION Indicates a potential hazard which may result in damage to equipment Warning symbols on the equipment are Protective conductor terminal Earth ground terminal CAUTION Risk of electric shock CAUTION Refer to accompanying documents WARNING Radiation Hazard gt gt Pir GB See original manufacturers manuals for further safety data on third party equipment supplied with the system A list of these is given in this manual WARNING Do not take risks You have a responsibility to ensure the safe condition
166. ocedure We would like to measure a sample with monoclinic Laue symmetry or higher to full completeness and 1 0 resolution We assume that Friedel pairs are equivalent We also choose only omega scans as they are the most precise 1 Start CrysAlis Red 2 Setthe UB matrix to that of a standard cubic sample in order to sample the Ewald sphere homogeneously type um s 0 1 0 0 0 0 1 0 0 0 0 1 3 Select the required detector distance Type setup options and Edit dd in Instrument model l Enter the value 58 mm 4 Create a default run Type dc editruns Create a new file The run list should be empty Now click on Omega in the bottom left of the window to create a default omega run Click on OK Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 83 USER MANUAL OPERATION 5 Start the run list optimiser by typing dc opti If the current run is not present click on the import button and located the relevant run file In the run list optimiser window click on the crystal button and select Laue group 2 m and resolution 1 0 A Click on OK NOTE E Due to the rectangular nature of the area detectors reflections will also be measured beyond this resolution but these will not be to the same completeness Run list optimizer Figure 6 5 61 Screenshot of Run List Optimiser Figure 6 5 62 Screenshot of Run List Optimiser Crystal Properties 6 Click on the coverage radio buttion to see the current result A pitiful 8 5
167. on Next to proceed to step 2 Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 50 USER MANUAL OPERATION CrysAlis data reduction assistent crystal lattice Figure 6 5 13 Screenshot of CrysAlis data reduction screen crystal lattice 6 5 3 5 2 Run List In this step the wizard requests the name of the run list and the image type 1 Click on the button Browse run list select the relevant data collection file and click on Next It is also possible to evaluate only a sub range of the data set by selecting a run and editing the start and end numbers CrysAlis data reduction assistent run list Figure 6 5 14 Screenshot of CrysAlis data reduction screen run list Version 1 4 Xcalibur_Manual_v1 4 Xcal i b u r Page 51 USER MANUAL OPERATION 6 5 3 5 3 Scan Width The scan width is linked to the mosaicity of the sample The default values are selected for a crystal of average quality This number may need to be increased for a poor quality crystal Click on Next NOTE EJ This number is not the frame width used during the run list editing CrysAlis data reduction assistent scan width Step 3 Scan width for the reflection profile prediction The orientation matrix allows to predict all potential reflection positions AIl profiles have a certain intrinsic width in which they may appear This depends on the intrinsic reflection size The intrinsic reflection width is computed from the scanwidth value This va
168. ponent Dimensions 1 OD 01 00 15 C Xcalibur Suggested Layout z x 208 240V SINGLE PHASE g 2 x 1B 2D8 240V SINGLE PHASE SEE SHT D 01 00 014 C 3l f E YS ao NP d WATER SUPPLY ILLL AL LLULL 4 x 100 24DV Meist 9 B XCALIBUR STAND sj ra wo V EH SS E Se H X RAY DIRECTION ba oe E Era 2 ij uj i 100 115 of 3D 38 38 50 TABLE NOT SUPPUED OXFORD DIFFRACTION XCALIBUR SYSTEM DESCRIPTION SUGGESTED LAYOUT TRANNE NOMEER 0D 01 00 015 C DRAWN OD 01 00 01 System and Component Dimensions Version 1 4 Xcalibur_Manual_v1 4 Xcal l b u r Page 141 USER MANUAL ADDITIONAL INFORMATION Xcalibur Dimensions I 116 y y 115 200 9l Y O COODDOOOO000000000000000000000000 TDNDODDODONDCODOCODNODONNDNON COOODODOO000000000000000000000000 OODODO0000000000000000000000000000 je 80 KMW3000C Dimensions 54 YS KMW200CCD Dimensions D d LJCJICCCAI 54 RM 100 DUNDONDDODOOOCOCODOTDIDIOODOCDUDUU DIOC QOO DOC OC OE COODDIOOO0000000000000000000000000 OODODI0000000000000000000000000000
169. r Rings and Line Profile Extraction of powder pattern data is achieved using the following command powder extract1d bins thetamin thetamax The powder data shown in figure 6 5 67 was extracted from the powder image using the command Powder extract1d 5000 0 26 The clipboard contents were then pasted into a spreadsheet program for plotting see figure 6 5 68 Zhat rea y h 0 07281 279 844 U7RU 760 AF01 PRT 5 0 2222 0 2482 F x ae 700 0 4043 0 4563 600 0 73128 128 0 3643 500 O 7163 0 7064 400 Series 0 204 Series a 0 3244 300 5i T Series3 200 i EI 100 Wiss 0 0 23526 v i n244as B m 1 638 1275 1912 2549 3186 3823 4460 81 382402 58 LI uc 2575 76 BIRIT 795 3223 75 3399 242 75 73 71539 29 zh NERA 12 A 29 Vut m M 4 WY Sheet f Raest shee Id gt zen NM Figure 6 5 68 Screenshot of Powder Pattern Data Plotted via a Spreadsheet Program 6 5 11 Refining of Machine Parameter File 1 Mount and optically align the orthorhombic ylid test crystal C49H4905S See normal operation 2 Inthe Crysalis CCD program type dc editruns Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 91 USER MANUAL OPERATION 3 Import run list named Xcalibur calibration run and adjust exposure time if required Click on OK 4 Start data collection by typing dc s 5 Once data collection has finished typically 1 3 hours t
170. r 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 Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 3 USER MANUAL HEALTH AND SAFETY INFORMATION 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 WARNINGS 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 equipment to perform regular radiation checks as per any laboratory rules Use only genuine firmware X ray tubes X ray generato
171. r the satellites crithkl is typically 0 05 and q1 q2 q3 etc define the rough q vector This q vector value will then be refined against the reflections in the peak table A listing of the q vector refinement is output to file and also to the history window By scrolling back through the output the user can view the number of indexed peaks with their associated order 6 The second third forth efc orders can also be investigated by using the command Nada qvector mmax crithkl q1 q2 q3 q1 q2 q3 q1 q2 q3 where mmax is 2 3 or 4 etc Refinement is an iterative process At the end of a cycle of refinement the current refined q vector is output to the history window Cut and paste this command into the command line and press Enter When you are happy with the unit cell save it to disk using the commands wd p wd ph and wd t assigning a unique filename Typing um setqvector q1 q2 q3 mmax or cutting and pasting the command from the history window where it was displayed at the end of refinement will set the q vector and order for use in data reduction Data reduction of an incommensurate then follows the normal data reduction procedure described in section 6 5 8 On initialisation of the data reduction wizard by typing dc red the first window should display the set q vector values in the bottom right corner Final output of the reduced data will be in hklm format compatible with Jana2000 6 5 9 Indexing and Data Reduc
172. r to the step numbers in this section These notes provide installation guidance only Figure 5 2 1 Xcalibur installation procedure Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 28 USER MANUAL OPERATION 1 Install electronics rack Use 2 persons to lift electronics rack into position on a level floor see environmental requirements 2 Mount table top Remove vented front back and side panels at the top of the electronics rack Screw table top into position from below and at the four corners Check that the table top is level 3 Mount goniometer Use 5 persons to lift the goniometer to the centre of the table top Position goniometer on feet provided 4 Mount protective cabinet frame and top Use 4 persons Each person supports one of the four side struts of the cabinet frame Attach and secure the frame uprights Remember to secure corner screws Once base is securely positioned around the tabletop attach cabinet top Remember to secure corner screws 5 Mount support arm Mount in position shown and secure fixing screws 6 Attach cable guide and video camera arm Use appropriate screws to attach in positions shown 7 Insert X ray generator Use 3 persons to insert the X ray generator Insert from front of electronics rack 2 persons lifting third person guiding cables through to back of rack This requires removal of back and side panels of electronics rack 8 Mount Enhance or Enhance ULTRA X ray sour
173. r will not open 1 Protective cabinet doors are not closed properly Close doors properly 2 X ray generator signal light defective Check light connections and bulb Replace bulb 3 Shutter open and or shutter closed lights defective Check light connections and bulbs Replace bulbs 4 Protective cabinet doors were opened whilst the shutter was open and safety circuit was activated In CrysAlis CCD type sh c to close the shutter Then re start experiment Continuous high pitched buzz Interlock circuits defeated triggering signal buzzer Switch off interlock override using turn key switch X ray generator won t switch on 1 Check that the chiller unit KMW3000C is attached to generator and X ray tube and Switched on Connect chiller unit and turn on using MAINS turn key switch 2 Water leak Check connections and water pipes for leaks and correct 3 kV and mA settings are not zero Set kV and mA settings to zero and press X R ON button Goniometer Detector collision 1 Collision of the goniometer with the CCD detector Turn off the KMW200CCD chiller this will disable the collision sensors great care should be taken while the machine is in this state as considerable damage could be caused In CrysAlis CCD type KM4 MGCUTIL and press enter Click on parameters and the two Edit deg buttons Set both to 1 0000 and click on
174. range 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 shutter 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 Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 22 USER MANUAL HANDLING INSTALLATION STORAGE AND TRANSIT INFORMATION 5 Handling Installation Storage and Transit Information 5 1 Reception and Handling 5 1 1 Delivery Carry out the following steps on delivery of the system and before unpacking Xcalibur 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 Oxford Diffraction immediately Check that shock watch and tilt indicators fitted to the outside of the packing cases have not been activated If the indicators have been activated notify Oxford Diffraction immediately Check the number of delivered items against the packing list If any items are missing contact Oxford Diffraction within 3 days WARNING 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 CAUTION Do not
175. red please contact Oxford Diffraction for assistance 9 9 Aligning the Enhance X ray Source Task Time 30 mins When After mounting a new X ray tube or collimator if necessary Tools Set of Allen keys Figure 9 9 1 Enhance X ray Source mounted on Xcalibur 2 The Enhance X ray source provides approx 2 5 times the intensity of a traditional sealed tube This intensity increase having been measured on a diffracted X ray beam of 0 8 mm diameter Based on traditional sealed tube technology the Enhance incorporates a built in monochromator fast shutter and specially selected optics Enhance comes complete with interchangeable collimators of sizes 0 8 and 0 5 mm Enhance is available as an upgrade to the Xcalibur system and can be ordered using the part number below Enhance Mo part number XA 04 00 000 A Enhance Cu part number XA 10 00 000 B Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 121 USER MANUAL MAINTENANCE INSTRUCTIONS Procedure Alignment of the Enhance X ray source has been greatly simplified from the traditional sealed tube Set up The procedure is as follows 1 Set X ray generator settings to 28kV and 2mA or lowest possible generator settings where these are not obtainable see third party manual The voltage rating is at about the threshold to excite characteristic radiation 2 Remove the beamstop 3 Ensure that the collimator is mounted 4 Defeat the safety interlocks using th
176. rs monochromators goniometer heads and collimators as recommended by your Xcalibur supplier Use of other products may compromise the performance of the shielding and safety system and may invalidate your warranty 1 7 Extreme Temperatures WARNINGS 1 Systems fitted with the low temperature option use liquid nitrogen and or liquid helium as a coolant Liquid nitrogen and liquid helium are cryogenic liquids and can cause cold burns Wear gloves when handling cryogenic liquids and use eye protection Refer to the information supplied with the equipment for more information 2 During operation both the X ray tube and the heat sink of the CCD power supply become hot In normal use they are located inside a cabinet and hot parts are not accessible During maintenance periods however it may be necessary to override the interlock so that adjustments can be made Therefore great care must be taken to avoid touching either the X ray tube or the heat sink of the CCD power supply when they are operating and for a period of 20 minutes after operation Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 4 USER MANUAL HEALTH AND SAFETY INFORMATION 1 8 Vacuum WARNING 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 1 9 High Pressures WARNING Know the law about high pressure g
177. rsonnel Estimated task Estimated duration elapsed time 1 Refine machine parameter file Authorised Operator 4 5 hours 4 5 hours 2 CCD detector pump out Authorised Operator 1 hour 16 hours vacuum Version 1 4 Xcalibur Manual v1 4 Xcal ibu r Page 113 USER MANUAL MAINTENANCE SCHEDULES 8 6 10 000 Hours Maintenance Schedule Tools and Materials Set of Allen keys Set of flat headed screwdrivers Water receptacle e g Bucket Special tools special tool 1 and special tool 2 see section 8 for identification Action Personnel Estimated task Estimated duration elapsed time 1 Changing the X ray tube Authorised Operator 1 2 hours 1 2 hours 2 Alignment of X ray optics Authorised Operator 2 3 hours 2 3 hours 3 Monochromator alignment Authorised Operator Version 14 Xcalbur Manual v4 Xcalibur Page 114 USER MANUAL MAINTENANCE INSTRUCTIONS 9 Maintenance Instructions WARNINGS 1 Read and understand the Health and Safety Information section of this manual before performing any maintenance procedures 2 Follow any local national or international rules and guidelines that apply to this equipment when performing maintenance tasks 3 When performing maintenance tasks that require safety interlocks to be overridden ensure that there is no unauthorised access to Xcalibur 4 Maintenance tasks must only be performed by authorised operators of Xcalibur 9 1 Special Tools
178. s The mouse driven menu bar commands are arranged into Basic Commands and Expert mode commands in both cases the short cut commands are also listed The basic commands are listed in the order in which they are likely to be performed Extensive on line software documentation is provided with the CrysAlis software and can be accessed using the application CrysAlis User Guide or by typing help in the CrysAlis programs NOTE E Please take the time to read the screen messages provided in the CrysAlis dialog and menu Reading the displayed information helps to conduct the data evaluation efficiently Scanning through the Basic Commands sub menu in the Commands menu provides a simple mneumonic A I D Use the laminated short guide as support material Read section 6 5 before operating the software 6 4 1 Software Updates Information about CrysAlis software updates is available from the website http www oxford diffraction com software html Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 34 USER MANUAL OPERATION 6 4 2 Software Installation 6 4 2 1 MGC interface software The Xcalibur goniometer interface is mounted in the electronics cabinet of the Xcalibur diffractometer system The interface contains an programmable EPROM and serves to translate the signals received from the diffractometer control PC and CrysAlis CCD into machine operations As with any software the firmware loaded on this EPROM has version updates T
179. shot of crystal movie configuration screen 7 Using the Page Up and Page Down buttons rotate the crystal image such that a crystal face normal is in the plane of the screen This means that you are not looking onto the face but glaze its surface 8 Depress the left mouse button with the cursor over the crystal image Drag out the resultant lines to define the edge of the crystal face right mouse click and select add face NOTE Use the h k I values displayed at the bottom of the Crystal movie window and also rotation of the image to get these close to integer values E CrysAlis RED CCD camera data reduction user interface E Eile Edit ColorT gags Fie Faces Log Utilities Preferences F Inverted video image Seti calor Zoom 6 dx C 2x SS E MMMM 1 X376 gt Es Y 283 Edit ee Pix mm 0 002174 Edit Units of 0 1mm 7 Edit p Draw T Crystal front T Crystal back T Directexes PREC exes Sa Grass hat Status Goniom Help Hide abs di Message from 0 57 00 T 30 00 K 134 00 P 174 00 HKL 130 991 0 25 D 0 11957 X 431 Y 284 a X 431 Y 284 Help Ready lo oooo r 000 K ooo P ooo iT stan ADO gt A E amp Mail Summary Mei E xoaliburtversion 13 f Crysatis RED abs2 bmp Paint eet 0456 Version 1 4 Xcalibur Manual v1 4 Page 60 Xcalibur USER MANUAL OPERATION Figure 6 5 24 Scree
180. sitioned and the following steps should be made 40 Repeat steps 1 18 in order to remove the Enhance X ray tube shield 41 Loosen the four screws holding the plate to the pillar 42 Rotate the plate in the direction thought necessary to bring the beam towards the crystal 43 Retighten the four screws holding the plate 44 Repeat steps 21 38 in order to replace the Enhance X ray tube shield and then align it Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 111 USER MANUAL MAINTENANCE SCHEDULES 8 Maintenance Schedules 8 1 Introduction Various maintenance tasks must be performed to ensure that the Xcalibur system continues to operate safely and reliably These tasks are detailed in the maintenance schedules given below WARNINGS 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 Xcalibur 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 safet
181. slow Version 1 3 Xcalibur_Manual_v1 4 Page 134 Xcalibur USER MANUAL TROUBLE SHOOTING Click enter Select Detector and drive relative Click on Start This will move the detector away from the goniometer axis in 1mm steps This should be repeated several times until there is a clear gap between the detector and the goniometer axis Turn on the KMW200CCD chiller Follow steps 2 9 from Power loss to goniometer below Goniometer lost angle positions 1 Collision of the goniometer See above 2 Power loss to goniometer 1 Restore power to Xcalibur restart the PC and CrysAlis CCD program 2 Switch off the Xcalibur interface wait 5 seconds and then switch on 3 In CrysAlis CCD 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 Por 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 Version
182. some time we have 81 896 Click on the Stop button to keep the current best result 2 Repeat step 1 for run 2 select run 2 from the Current run drop down menu selecting only kappa and phi for optimisation This gives 84 396 coverage Click on Export 3 Type dc editruns and add a new omega default run 4 Type dc opti and optimize run 3 with theta and omega scan range selected This allows a suitable scan portion to be found first Resulting coverage is 85 8 Now optimise kappa phi and omega scan range We now have 89 coverage with 519 frames Not bad Add another omega run and repeat step 4 In dc editruns set all omega ranges to 0 1 and in dc opti only optimize the scan ranges of all four runs The coverage result is 96 0 with 600 frames Task completed Click on Export NOTE E Computation takes time Remember it scales with volume consider volume scaling with um c 0 9 0 0 0 0 9 0 0 0 0 9 NOTE E The step width chosen determines the speed 5 We still do not have 10096 coverage With the current settings we will measure 2173 reflections of which 1442 are unique in P1 no Friedel pairs and 1502 are measurable i e 96 0 To improve this we need to make the kappa angle higher This gives us 650 frames with 1485 1502 98 9 coverage One more cycle of dc editruns with all scan ranges set to zero folowed by only optimization of the scan range of all four runs gives us 1477 1502 98 396 with 580 frames This is nice we have sav
183. sssseee 106 Figure 7 1 3 4 Mounting the Onyx CCD replacing the rear screw sss 106 Figure 7 2 1 Location of Enhance retaining and adjustment nuts sss 110 Faure NP eoo E 115 Figure 9 1 2 Special too 1 oun D REIR Ee RHOD euet 115 Figure 9 3 1 Position of the X ray source sssssssseseeee ene ene enne 117 Figure 9 5 1 Beam stop adjustment screws ssssessse eene 120 Figure 9 9 1 Enhance X ray Source mounted on Xcalibur 2 ssessseee 121 Figure 9 9 2 Enhance X ray source collimator adjustments front view ssessssss 123 Figure 9 9 3 Enhance X ray source adjustments front view ssssse 123 Figure 9 9 4 Enhance X ray source adjustments top view sem 124 Figure 9 10 1 Adjustment screws of Enhance Ultra sssssssm 125 Figure 9 10 2 Schematic showing the rotated beam stop dashed line shows up position and solid line Shows down positlon eti oet rh eee e Ce tree iet urbt Pl aeu fue eee tb Ple pepe dd 125 Figure 9 10 3 Image of direct X ray Beam ssssssssseee eene enne nennen 126 Figure 9 10 4 Image during optical alignment of Enhance Ultra ssseeeee 126 Version 1 4 Xcalibur Manual v1 4 Xcal ibu r Page viii USER MANUAL Figure 9 14 1 View of the access plates and pump out ports of the Sapphire and O
184. t Print peak table to history tyt ty imageinfo Print image information to history ty imageinfo um crec change orientation matrix in reciprocal space um crec c11 c12 c13 c31 c32 c33 c11 c12 c13 c31 c32 c33 reciprocal space transformation matrix um clearskipd clear skip list um clearskipd um help help overview of um commands um help um hppolynomial UM HPPOLYNOMIAL dO d1 d2 d3 d4 d5 d6 d7 d8 Version 1 4 Xcalibur Manual v1 4 Page 99 Xcalibur USER MANUAL OPERATION d0 d9 polynomial coefficients um ip indexing with peak table printing um ip indexrejectioncriterion indexrejectioncriterion rejection criterion which determines the maximum allowed deviation for which a reflection is considered indexed um ir indexing with real indices um ir um overlayskipd overlay skip list um overlayskipd um pointdetector generate goniometer angles from peak table um pointdetector um predict predict reflection positions um predict markertype L H latticetype A B C I F R markertype L H As default the prediction is shown in inverted colour you may use the low or high colour of the current palette latticetype A B C I F R In the presence of lattice extinctions it is useful to remove the extinct reflections from the prediction n reflection in the previous frame reflection in the next frame x reflection in the current fra
185. t aeneis 71 6 5 5 Dc Movie Replay of Data Collection Movie sseenm nn 77 6 5 6 Reconstruction of Precession Photographs ssssseee een 78 6 5 7 Dc opti Optimisation of Data Collection Strategy ssseene 82 6 5 8 Indexing and Data Reduction of Incommensurate Samples ssssss 87 6 5 9 Indexing and Data Reduction of Twinned Samples sese 88 6 5 10 Extracting Data from Powder Samples seen 90 6 5 11 Refining of Machine Parameter File sse eene 91 6 5 12 Glossary of CrysAlis Commands ssssssseeeeneenenen eene 94 6 6 Normal ShutdoWri chien or e rte tette ie tice eec site bieten lab tete dete s 101 o z Emergenecy Sbu tdOoWn nei tc RD RU ER GR Si ERR EG HR HERE RR tad 101 6 7 1 Emergency Shutdown Procedure ssssssssseeeeeeeeenen nennen 102 7 Mechanical Changeover of Detectors and X ray Sources 103 7 1 Interchange of CCD Detectors sssssssssseeneeeneeenee nnne nennen nnne nennen nns 103 7 1 1 Installation of a Sapphire 2 and Sapphire 3 CCD detectors suuusss 103 7 1 2 Removal of a Sapphire 2 and Sapphire 3 CCD detectors ssususss 104 7 1 3 Installation of the Onyx CCD camera ssssesseeeeeneemeenemen 104 7 1 4 Removal of the Onyx CCD camera sss eene 107 7 2 Procedure
186. ter head is located behind the collimator If the vertical height of the crystal has changed adjust and return to the lower position Repeat until the vertical position is unchanged between the upper and lower positions 10 Press Lower and check alignment of the crystal on rotation between 0 and 180 90 and 270 degrees 11 Press 0 and Home to return the goniometer to its zero position 12 Exit alignment procedure by selecting OK on the computer screen This will return goniometer control to the computer and prevent use of the remote control Version 1 4 Xcalibur Manual v1 4 Xcal i b u r Page 44 USER MANUAL OPERATION 6 5 3 2 Diffraction Photographs to Determine Crystal Quality 6 5 3 2 1 Single photograph Single diffraction images can be taken of a crystal to determine its quality These diffraction photographs are taken without goniometer movement 1 Type sm i time time exposure time in secs NOTE E Images are always taken as double exposures to allow correction for zingers 2 Type wdi to save the image to disk 6 5 3 2 2 Rotation photographs A rotation photograph can be recorded in which the sample is exposed to X ray radiation as it is rotated about the Phi axis 1 Type sm rp This will automatically record a 30 second exposure CrysAlis RED CCD camera data reduction user interface ajx Fle Edt ColorTables LookUpTables Zoom Dotareduc on Commands Test Tools Help J RIS Lint 11 11
187. tion A short data collection typically of 5 minutes duration is collected to enable fast unit cell determination of a crystal Data collection is carried out in three sets of omega scans These scans sample reciprocal space so as to independently define the three crystal axes Each set of scans consists of 5 frames taken at one degree intervals 1 2 In the program Crysalis CCD type dc editruns and follow the on screen instructions When a window such a figure 6 5 9 is displayed click on Import run list and select the pre defined run list unit cell in 5 min run If required adjust the exposure time or frame width using the relevant buttons c NOTE The disk space available and required is displayed at the top of the window Please ensure there is enough disk space available for data collection Version 1 4 Xcalibur Manual v1 4 Xcal i b u r Page 46 USER MANUAL OPERATION Edit datacollection runs Detector distance 53 13mm x Name of experiment fesi Help Clipboard Data collection directory C My Documents xtldata Browse Total of frames 0 Disk space required Mbytes 0 00 DC frames 0 Disk space available Mbytes 14084 56 Ref frames 0 Approximate data collection time h min 0 00 run scan pars type start end width time speedratio gonio pars omega detector kappa phi to do done Activate reference frames reference runs frequency 1 per 0 dc frames Change ref freq E
188. tion of Twinned Samples When you suspect a twinned sample visualise the reflections using the Ewald explorer using the pt ewald command 1 Using the Ewald explorer it should be possible to see that a number of unit cells are present Either by Drag indexing or by skipping reflections and auto indexing determine one of the unit cells 2 Exitthe Ewald explorer and type ty u to print the current UB matrix to the history window Version 1 4 Xcalibur_Manual_v1 4 Xcal l b u r Page 88 USER MANUAL UB matrix OPERATION 0 003995 0 052494 0 013353 0 000129 0 000118 0 000116 0 016664 0 003653 0 049665 0 000123 0 000113 0 000111 20 053339 0 001014 0 008949 0 000129 0 000118 0 000116 QR decomposition of UB U matrix 0 071313 0 995604 0 060715 0 297441 0 036875 0 954028 0 952073 0 086094 0 293504 B matrix 0 056024 0 005795 20 005300 0 000000 0 052311 0 010693 0 000000 0 000000 0 050819 M matrix 0 003139 0 000325 0 000297 0 000014 0 000009 0 000009 0 000325 0 002770 0 000529 0 000009 0 000012 0 000009 0 000297 0 000529 0 002725 0 000009 0 000009 0 000012 UM S 3 9952638E 003 5 2494081E 002 1 3353473E 002 1 6663957E 002 3 6526877E 003 4 9664814E 002 5 3339399E 002 1 0139163E 003 8 9492647E 003 This unit cell UB matrix can now be assigned to a memory buffer Above is an example of the output from the ty u command To the right of the UM S command can be seen the UB matrix This can be p
189. u Selected 74 Figure 6 5 47 Screenshot of Ewald Explorer Skip Filter Intensity Window Use Intensity Filter 75 Figure 6 5 48 Screenshot of Ewald Explorer Mark Invisible Skip ceececeeeeeeeesecteeeeeeeeees 75 Figure 6 5 49 Screenshot of Ewald Explorer Mark All Invisible Peaks Skip 76 Figure 6 5 50 Screenshot of Ewald Explorer Skip Filter Intensity Window sssss 76 Figure 6 5 51 Screenshot of Data Collection Movie with Unit Cell Predictions Overlayed 77 Figure 6 5 52 Screenshot of Unwarp Wizard Step 1 Orientation matrix ssssssss 78 Figure 6 5 53 Screenshot of Unwarp Wizard Step 2 Open Run List ccceceeeeseeeeeeeeeeeees 79 Figure 6 5 54 Screenshot of Unwarp Wizard Step 2 Run List Loaded ssssssss 79 Figure 6 5 55 Screenshot of Unwarp Wizard Step 2 Select Output Directory 80 Figure 6 5 56 Screenshot of Unwarp Wizard Step 3 Creation of a Layer List 80 Figure 6 5 57 Screenshot of Unwarp Wizard Step 3 Add a Reconstruction Layer 81 Figure 6 5 58 Screenshot of Unwarp Wizard Step 4 Background Evaluation 81 Figure 6 5 59 Screenshot of Unwarp Wizard Step 5 Data Corrections sssssssss 82
190. uctive or if carpeted covered with electrostatic mats Able to bear system weight of 450 kg 3 2 Services 3 2 1 Electrical Supply Total power requirements Number of outlets required Voltage fluctuation Location of outlets Protection 230 V 10 95 63A 3 phase 2 single phase outlet 16A for Xcalibur system 1 single phase outlet 32A for X ray generator 4 single phase outlets for temperature attachments lt 10 with line voltage regulator fitted if necessary On wall behind system Circuit breaker to be fitted to all outlets 3 2 2 Water Cooling Min flow rate Pressure Temperature stability 1 8 l min 0 5 5 bar gauge 5 C Version 1 4 Xcalibur_Manual_v1 4 Xcal l b u r Page 7 USER MANUAL SPECIFICATIONS Temperature range 10 20 C Composition Filtered without deposits chemically neutral and optically clear 3 2 3 Helium Gas Supply where applicable Purity 99 99 Regulator low pressure regulator Minimum pressure 0 5 bar gauge Flow rate 30 40 cm min ATP 3 3 Performance Data 3 3 1 X ray Tube Typical Operating Conditions Tube Voltage kV setting Current mA setting Resulting power kW Cu 2 2kW tube 40 55 2 2 Mo 2kW tube 50 30 1 5 Mo 3kW tube 55 40 2 2 Ag 2kW tube 60 25 1 5 Maximum radiation dose due to scattering 0 6 uSv h with Mo 3 kW tube operating at 2 2 kW radiation at outside surface of the
191. utlier Rejection The reduced data set may contain outliers detected by comparing symmetry equivalent reflections 1 Using the drop down menu marked mmm here select the Laue group 2 For monoclinic cells select the unique axis then click on Next NOTE Outlier rejection is not related to merging The data output from CrysAlis RED is S always unmerged NOTE The selected reduced cell is shown as a reminder for the selection of the corrected Laue class The initial setting off the drop down menu is based on this Niggli cell Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 54 USER MANUAL OPERATION CrysAlis data reduction assistent outlier rejection N t Banaue E LGSITITGIULES Figure 6 5 18 Screenshot of CrysAlis data reduction screen outlier rejection 6 5 3 5 7 Output Format Select the required format of the output file and then click on Finish to start data reduction CrysAlis data reduction assistent output format P GITE GHGTSGEITE S Si Stiwerenvccn pel es el rfe pig Figure 6 5 19 Screenshot of CrysAlis data reduction screen output format During data reduction text information is output to the computer screen and listing of selected outlier rejection file filename Ist The summary file is filename sum The final output is that of resolution statistics an example of which is shown below Version 1 4 Xcalibur Manual v1 4 Xcal i b u r Page 55 USER MANUAL OPERATION
192. when the system is not being used for extended periods store Xcalibur in accordance with the environmental conditions for temperature and humidity stated in the SPECIFICATIONS section of this manual Always store Xcalibur in a secure room Version 1 4 Xcalibur Manual v1 4 Xcal l b u r Page 30 USER MANUAL 6 Operation Xcalibur is a computer controlled system All functions are controlled from the computer terminal except when control is released from the computer terminal to the remote control unit Power is switched on and off via manual switches located on Xcalibur OPERATION The KMW200CCD chiller must be connected to Xcalibur before operating the system WARNING Local rules and regulations may apply to the use of Xcalibur If these exist refer to these local rules before operating the system 6 1 Controls and Indicators WARNING Do not activate the interlock override during normal operation of Xcalibur as this could result in exposure of personnel to X ray radiation The interlock is a safety device and must not be overridden Control Type Location Effect Interlock Override Turn key Front right corner of Overrides door safety switch electronics rack interlocks and activates continuous warning buzzer Emergency Stop Red button Front left corner of electronics Shutdown X ray generator rack power Remote Control Key pad Inside protective enclosur
193. with basic faces or similar 6 5 3 7 3 Step 3 Refine optimise the 3 D model against the X ray diffraction data Before refining our absorption model the collected diffraction data in form of a hkl file needs to be in a particular format This is achieved in the following way 1 Use the command dc rrp to finalize an already performed data reduction If you haven t done a data reduction of your sample proceed to section 6 5 8 Select the radio button Use outlier rejection Check the Beam path information box followed by the radio button Schwarzenbach psi abs plug in Click on change output name and save the hkl file under a new name e g absorption hkl Once data finalisation is complete start the crystal model shape optimisation plugin This is achieved by typing the command scale3 scale3abs Select the absorption hkl file Click on load edit shape and define the mu value for the crystal sample Click on OK Now adjust the l sigma value to give approximately 1000 reflections this is because shape optimisation is CPU intensive Typically l sigma for a strongly diffracting sample would be 100 and for a weakly diffracting sample about 20 Click on OK The shape of the crystal will now be optimised Details such as Rint with and without absorption correction are output to the screen and to a log file 6 5 3 7 4 Step 4 Examine 3 D model We have now refined the absorption correction model against the collected diffract
194. ws the user to check the formula weight absorption correction mu density etc against the molecular formula and Z number The current contents of the ins file are displayed on the left hand side of the screen Clicking on Apply creates the ins and hkl file and exits the GRAL plug in ixl G Settings Ez Load E Centering Niggli fh Lattice E8 Centering B lt E2 1 gt L Space Group ins Ins File TITL DC GAIN8 in P2 1 2 1 2 1 CELL 0 71073 5 9657 9 0333 18 4067 90 0105 90 0120 90 031 ZERR 4 00 0 0009 0 0014 0 0022 0 0111 0 0111 0 012 LATT 1 cii H10802 SYMM x 1 2 y z 1 2 SYMM x y 1 2 z 1 2 SYMM x 1 2 y 1 2 z SFACCHSO UNIT 44 00 40 00 4 00 8 00 Formula wt 206 27 Mu um 1 0 29 Density 1 381 F 000 432 00 At vol 10 33 4 element s C 11 00 64 05 H 10 00 4 90 1 00 15 54 0 2 00 15 51 E Cancel Apply Help Figure 6 5 40 Screenshot of the GRAL plug in INS File Window Version 1 4 Xcalibur_Manual_v1 4 Xcal i b u r Page 70 USER MANUAL OPERATION 6 5 3 9 Structure Solution and Refinement Data can be output from CrysAlis in the following formats crs ins hkl cif raw img mosFLM compatible p4p These can be read into the following solution and refinement programs These are free software and have NO connection with Oxford Diffraction Jana 2000 free download from http www xray fzu cz jana jana html ShelX 97 George S
195. y Mechanical movement of the goniometer and CCD detector may be performed using the remote control Version 1 4 Start the CrysAlis CCD application Press F12 key to release control from the computer to the remote control unit Press the 0 and HOME buttons on the remote control to drive the goniometer angles to the zero home position Mount the xyz goniometer head with attached crystal Typically the crystal is glued on top of a glass fibre Xcalibur Manual v1 4 Xcal i b u r Page 43 USER MANUAL OPERATION 5 Press Lower and 0 on the remote control This will drive the goniometer to the correct orientation to allow optical alignment of the crystal NOTE E The settings lower and upper refer to the glass stick position on the video monitor Upper Setting Lower Setting Figure 6 5 8 Optical alignment of the crystal 6 Use the tool provided with the goniometer head to adjust the vertical height and horizontal position of the crystal such that the crystal is in the centre of the video monitor screen 7 Press 180 on the remote control to rotate the crystal through 180 degrees If the crystal s horizontal position has moved on rotation adjust the position Press 0 and repeat this procedure until rotation gives no movement of the crystal 8 Repeat the above process rotating between 90 and 270 degrees 9 Press Upper on the remote control The goniometer will now move to the upper position such that the goniome
196. y features The user s authorised service representative should carry out other tasks If in any doubt about the performance of the Xcalibur contact Oxford Diffraction 8 2 Weekly Maintenance Schedule Tools and Materials None Action Personnel Estimated task Estimated duration elapsed time 1 Check door safety interlocks Authorised Operator 2 minutes 2 minutes 8 3 Monthly Maintenance Schedule Tools and Materials Radiation meter Action Personnel Estimated task Estimated duration elapsed time 1 Check Emergency Stop Authorised Operator 10 minutes 10 minutes 2 Check X ray radiation levels Authorised Operator 20 minutes 20 minutes Version 1 4 Xcalibur Manual v1 4 Xcal ibu r Page 112 USER MANUAL MAINTENANCE SCHEDULES 8 4 Six Monthly Maintenance Schedule This maintenance schedule should also be completed after adjustment of beam collimator CCD detector position etc Tools Ylid test crystal C49H44SO Action Personnel Estimated task Estimated duration elapsed time 1 Refining machine parameter Authorised Operator 4 5 hours 4 5 hours file 2 Check alignment of video Authorised Operator 1 hour 1 hour telescope and cooler if fitted 8 5 Yearly Maintenance Schedule Tools and Materials Ylid test crystal C49H418O Special T tool Phillips screw driver Rotary vacuum pump capable of obtaining a pressure of 1x10 mbar Vacuum tubing and adaptor Action Pe
197. y in peak hunting table 2 Finally click on OK to return to the main program CrysAlis CCD program options Instrument model Instrument model II Monochromator Fonts PH and PT size Color codes Beam stop settings Generic goniometer settings This dialog allows you to change the sizes of the peak hunting table and peak table Note that with the reallocation you will loose all information in both tables Use WD PH and or WD P to save your work Peak hunting table The peak hunting table contains the raw peak hunting coordinates A true peak may be composed of several peak hunting profile steps These can be visualized in the KM4CCD profile inspector Typically the of ph entries should be 2 3 bigger than the pt of pt entries 10000 Edit ph num Memory requirement 41 2 Mb Peak table The peak table contains Cartesian peak coordinates They are derived from the strongest profile step They can be visualized with PT EWALD and edited with PT E Edit pt num Memory requirement 2 3 Mb 482 Y 558nt 0 0 038 0 555 0 631 L 0 06 T 2 41 P 8 43 O 0000 T 0000 k coco P ooo NNUS AStarn AC oO gt 3i BL BX Mc Hela ic Ss aespo med t Shy 3 10 44 Figure 6 5 6 Screenshot of CrysAlis program options PH and PT size 3 Start peak hunting using ph s see section 6 5 3 3 4 Once complete edit the peak table using the pt e command 5 Select the reflection of interest by clicking on its entry
198. ype ph s to start peak hunting 6 Find the unit cell parameters by typing um f or by Drag indexing using the Ewald Explorer accessed via the pt ewald command 7 Type refine model The resulting new window enables the user to edit and refine all the machine set up parameters oniometer Area Detector Model x Refinement control Refinement weigths Cycles uy Diffraction angle 1 00000 Spot position 1 00000 Levenberg Marquardt 0 00000 hkl 1 00000 Ewald sphere 00000 Crystal LAT ABC i M a 13 16414 Edita M b 14 01379 Editb Mv c 14 08749 Editc ANG_ALBEGA W al 7691934 Edit al W be 8442057 Edit be Ww ga 80 91906 Edit ga Mri 55 45564 Edit rl M r2 72 64273 Edit r2 M r3 7354286 Edit r3 ERE gt Goniometer VM b2 008283 Edit b2 H ag tjitItItIFJE Edith I al 49 94087 Edit al I be 0 00065 Editbe Iv o 0 26653 Edit o0 Iv t 0 63198 Editt T k 0 06821 Edit k miro mooiii Edita M Detector V dl 0 49103 Edit d1 WM d2 019800 Edit d2 FdE tiriritirjt Editdg IV x 50474444 Editx IVy0 53110288 _ Edity Iv dd 5307038 Editdd Cancel TE Figure 6 5 69 Screenshot of Refine Model Window 8 Editing and refining of these parameters should be done bit by bit When using the cubic Alum test crystal select LAT AAA and ANG 909090 from the drop down menus located in the Crystal region of the window This constrains all cell lengths to be equal to A and all angles to

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