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oxford diffraction Xcalibur Series User Manual

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User Manual
Xcalibur
Point detector operation
May 2004
Version 1.2
Oxford Diffraction Limited
68, Milton Park, Abingdon,
Oxfordshire. OX14 4RX. UK
Tel: +44 (0)1235 443630
Fax: +44 (0)1235 443631
http://www.oxford-diffraction.com

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  • Page 1 User Manual Xcalibur Point detector operation May 2004 Version 1.2 Oxford Diffraction Limited 68, Milton Park, Abingdon, Oxfordshire. OX14 4RX. UK Tel: +44 (0)1235 443630 Fax: +44 (0)1235 443631 http://www.oxford-diffraction.com...
  • Page 2 Important Information This user manual applies to the Xcalibur systems manufactured in Poland by Oxford Diffraction. It is a supplementary document to accompany the full Xcalibur User Manual regarding the installation and use of a point detector fitted on an Xcalibur 2 diffractometer.

  • Page 3: Table Of Contents

    Contents Contents................. 2 Table of Figures ..............3 1. Health and Safety Information ......... 4 1.1 General ............................4 1.2 Electrical Safety ......................... 5 1.3 Mechanical Handling Safety ...................... 6 1.4 Safe Mechanical Practice ......................6 1.5 Moving Parts ..........................6 1.6 X-ray Radiation ..........................

  • Page 4: Table Of Figures

    4.7 Dc Movie - Replay of Data Collection Movie ................23 4.8 Absorption Correction ......................23 4.9 GRAL - Space Group Determination ..................24 5 Glossary of point detector commands ......25 Table of Figures Figure 2.1 The universal theta arm ..................... 2 Figure 4.1 Optical alignment of the crystal ..................

  • Page 5: Health And Safety Information

    Xcalibur should only be operated and maintained by authorised operators of the system. An authorised operator is a person who has undergone specialist radiation training and has been trained in the use of Xcalibur by Oxford Diffraction personnel. XcaliburPD Version 1.1 XcaliburPD v1.2.doc...

  • Page 6: Electrical Safety

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

  • Page 7: Mechanical Handling Safety

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

  • Page 8: X-Ray Radiation

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

  • Page 9: Extreme Temperatures

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

  • Page 10: Normal Operation Using A Point Detector

    OPERATION 2. Normal Operation Using a Point Detector This section of the manual describes the installation and operation of a point detector on an Xcalibur diffractometer fitted with a universal theta arm. For information regarding the use of a CCD detector, refer to the main Xcalibur operators manual. 2.1 Installation of the point detector If a CCD camera is currently installed, determine the orientation matrix of the standard crystal before removing the CCD camera from the diffractometer (this will save a lot of time): Mount...

  • Page 11: Figure 2.1 The Universal Theta Arm

    OPERATION 4. Drive the goniometer to theta = 90 deg (GT T 90), and drive the camera distance to 60 mm (GT D 60). 5. Unplug all the connectors to the CCD head, note which fibre optics cable is connected to which socket;...
  • Page 12 OPERATION WARNING The point detector interface cable carries a high voltage 9. Switch the interface back on and issue the command GON REINIT. Check that no error messages appear. Drive all angles back to zero (GT a 0 0 0 0). 10.
  • Page 13 OPERATION 13. If the orientation matrix and unit cell are unknown find them using peak hunting (for example: PH S 25 10 20 -60 -20 0 359). NOTE to find a cell more rapidly, it may be better to increase the size of the slits from the front of the detector.
  • Page 14 OPERATION correction for theta and horizontal using the ZC A command. This command will examine the peak from two opposite directions and will output a suggested correction in the history window. Apply the suggested correction by copying the line of text from the history window and pasting it into the command line and pressing return.

  • Page 15: Removal Of The Point Detector

    OPERATION was originally designed to deal with CCD data, the refinement may become unstable due to the small number of observables. 8. Note the calculated corrections for omega, theta and kappa and add the new values to the parameters by issuing the command ZC S do dt dk NOTE the only way to measure the correction for horizont (4.th parameter) is ZC A.

  • Page 16: General Commands

    OPERATION 3 General Commands 3.1 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 go to angles with values omega (om), theta (th), kappa (ka) and phi (ph) gt o om go to omega angle ‘om’...
  • Page 17 OPERATION the scan), psistart (starting psi angle for a sequence of scans), psistep (psi step angle for measuring a sequence of scans) sm s steps time step scan with a number steps (steps) and an exposure time (time) sm ao om th ka ph scanwidth time Single measurement omega scan with angles om, th, ka and ph are the omega, theta kappa and phi settings in degrees...

  • Page 18: Commonly Used Unit Cell/Indexing Commands

    OPERATION sequence sm t startangle scanwidth time theta scan 3.4 Commonly used unit cell/Indexing commands um f [lengthdeviation angledeviation Automatic unit cell determination (indexation, 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.

  • Page 19: Peak Table Commands

    OPERATION 3.5 Peak table commands clearing of the peak table pt clear pt a add a peak to the peak table pt e Peak table edit pt expand n mmin mmax intmin dmax dmin Peak table expand 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...

  • Page 20: Writing To Disk

    OPERATION 3.7 Writing to disk Current machine parameters, images and the contents of peak hunting tables can be written to disk wd p write disk parameter settings. Saves the current machine parameters to disk wd ph write disk peak hunting. Saves the current contents of the peak hunting table to disk wd t write disk table.

  • Page 21: Standard Point Detector Experiment

    OPERATION 4 Standard Point Detector Experiment In order to use the point detector (PD), the correct parameter file must be loaded. This is due to subtle changes between the layout of the GUI for the CCD experiments and the PD experiments.

  • Page 22: Figure 4.1 Optical Alignment Of The Crystal

    OPERATION 4. Mount the xyz goniometer head with crystal attached to, for example a glass fibre or nylon loop with oil or glue. 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.

  • Page 23: Setting The Data Collection Parameters

    OPERATION 4.2 Setting the data collection parameters • Two theta range The two-theta range may be set by the command TR tthmin tthmax (where TR = theta range, tthmin is the minimum value of 2 theta and tthmax is the maximum 2 theta value) typical values are: TR 4 60 or TR 4 80 for Mo radiation.
  • Page 24 OPERATION (0.004768≤Vmin ≤1.5). The most typical mode of scan is an integrating stepscan with prescan. This skips reflections that have I/Sigma(I) values worse than 3.0, whilst trying to obtain I/Sigma(I) ≤25. This should give an R1 factor of the refined structure ≤5% For example: MO S 1 55 3 25 0.015 MO S 1 60 1 10 0.0050...
  • Page 25 OPERATION where s is the total number of scan points. • Index limit The index limit command IL hmin hmax kmin kmax lmin lmax sets the index limits for the data collection. The range is dependent upon the unit cell lengths. Signs are dependent on the crystal system (unique reflections set) and on the crystal orientation.

  • Page 26: Figure 4.2 The Reflections Conditions Programme

    OPERATION ‘negated’ option, allowing the measurement of, for example, forbidden or mistakenly skipped reflections. Figure 4.2 The reflections conditions programme NOTE One has to be very careful not to create contradicting extinction conditions (the conditions are always logically interpreted by "and"). •...

  • Page 27: Peak Hunting

    OPERATION 4.3 Peak Hunting The detector aperture is determined by two sets of manually exchangeable slits which are inserted in the front of the detector. The inserted combination of slits is expressed in degrees (DH and DV for the horizontal and vertical apertures, respectively). NOTE The detector aperture parameters are vital in the centring, zero corrections and peak hunting procedures.

  • Page 28: Figure 4.3 The Peak Hunting Process

    OPERATION NOTE All peaks found will be appended to peak table, so in the case of a new data collection, any existing peaks should be erased first by using the PT CLEAR command. 3. Start the peak hunting procedure either by using default values, using the command PH S, or by using custom settings by typing the command PH S n T1 T2 K1 K2 P1 P2 •...

  • Page 29: Unit Cell Determination

    OPERATION Figure 4.4 The centring procedure 5. The top intensity Int is the number of counts recorded in one second. The angles are converted to reciprocal coordinates x(1),x(2) and x(3) and these are compared with the coordinates already stored in the peak table. A new peak is said to be found, when the table does not contain a peak with coordinates y(1) , y(2) and y(3).

  • Page 30: Data Collection

    OPERATION 4.5 Data Collection 1. If the orientation matrix of the crystal is known, you may import an existing peak table. Alternatively, you may input the matrix using the command line. Then using sequence: GT R (go to reflection), CE 1 (centre reflection) and PT A (add to peak table) fill the peak table with approximately 10 reflections, refine the existing matrix and skip to point 4.

  • Page 31: Figure 4.5 Dataproc Programme Opened By Using The Dc Redpd Command

    OPERATION • Cut off multiplier – This will clean the output file by removing reflections below a certain I/sigma value. Tick the radio button to apply the cut-off and click on the box to edit the limit. Data may also be corrected for absorption: •...

  • Page 32: Dc Movie - Replay Of Data Collection Movie

    OPERATION 4.7 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 reflections. 1. Type either dc redpd or dc moviepd and select the relevant *.dc1 file 2.

  • Page 33: Gral - Space Group Determination

    OPERATION The absorption correction incorporated into the CrysAlis software package can be summarised into the following five steps: 1. Record a jpeg movie of the crystal sample 2. Build / modify a 3-D model of the crystal sample 3. Refine / optimise the 3-D model against the X-ray diffraction data 4.

  • Page 34: Glossary Of Point Detector Commands

    GLOSSARY 5 Glossary of point detector commands Command Meaning Example abs display View movie recording and build absorption abs display correction routine abs grab Initiate movie recording routine for absorption abs grab correction af i Applies an attenuation filter af i af o Removes the attenuation filter af o...
  • Page 35 GLOSSARY chi = chi angle in deg. phi = phi angle in deg. gt o goto omega gt o om om = omega angle gt t goto theta angle gt t th th = theta angle gt k goto kappa angle gt k ka ka = kappa angle gt p...
  • Page 36 GLOSSARY ph extractprofiles extract profiles from data collection ph extractprofiles ph help help overview of ph commands ph help ph s Peak hunting start ph s ph reconstruct reconstruct the peak table with current ph reconstruct instrument model pt clear clearing of the peak table pt clear pt a...
  • Page 37 GLOSSARY at = attenuation filter use: 0,1 ( 0 = filter out , 1 = filter in ) scale3 abs Initialise absorption correction shape scale3 scale3abs optimisation routine scale3 pack Initialise scale3pack data scaling plug-in scale3 scale3pack script start a script. A script is an ASCII file with the script [[filepath]filename] extension *.mac and contains a sequence of CrysAlis commands, which will be, executed...
  • Page 38 GLOSSARY steps = number of steps for scan time = exposure time in sec per step sm t 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...
  • Page 39 GLOSSARY ub matrices for data reduction of twinned data. Arraynum (0..7) storage buffers for unit-cell matrices Ub11 … ub33 unit-cell ub matrix um u activates the procedure to refine the crystal um u orientation automatically wd i Write disc image wd i [[filepath]filename] [[filepath]filename] –...
  • Page 40 APPENDIX 1 – HIGH PRESSURE WORK Appendix I - High Pressure Crystallography using a DAC on an Xcalibur system This is intended as a short guide to setting up a DAC for a data collection on an Xcalibur diffractometer. The user is assumed to be familiar with the CrysAlis software and commands and their use for data collections from crystals in air.
  • Page 41 APPENDIX 1 – HIGH PRESSURE WORK 1. Select Tools|Setup file/Xcalibur1PD.par 2. Exit from Tools|Setup 3. Exit from program (en) 4. Restart Crysalis CCD from desktop Switch to DAC mode (sw s 2) and set the DAC opening angle to 40deg (or to the value corresponding to your DAC (sw a angle).
  • Page 42 APPENDIX 1 – HIGH PRESSURE WORK Xcalibur 2/Xcalibur 3 etc. Follow the procedure as above except use the alignment position using the F12 key and the remote pilot. Align the DAC by eye so that it is perpendicular to the beam. Align the aperture in the XY direction using the video microscope and then align along the beam axis as above or use the beam rocking method below.
  • Page 43 APPENDIX 1 – HIGH PRESSURE WORK I.3.1 UB matrix known from previous measurement Copy the peak table from the previous measurement. Use the Windows file browser to copy the *.tab file to the current working directory (rd t). Or input values into the command line (um s u11 u12 u13 u21 u22 u23 u31 u32 u33).
  • Page 44 APPENDIX 1 – HIGH PRESSURE WORK Exit from the peak table editor and expand the peak list by Laue symmetry (pt l n) (if you do not know n for your Laue group then type pt l to obtain a list). At this stage you need 20-30 strong reflections (pt e). Edit the peak list to remove reflections with low kappa angle: •...
  • Page 45 APPENDIX 1 – HIGH PRESSURE WORK Method 1 takes less time, but method 2 is often more reliable. Both alternatives are described below: Method 1 - 8-position centering • Find a strong reflection with Eulerian chi > 80 gt r h k l •...
  • Page 46 APPENDIX 1 – HIGH PRESSURE WORK Save parameters (it is useful to call this something like orient.par) wd p Start data collection (use a distinct filename such as orientn) where n indicates the iteration through this process dc s When data collection is complete, export the data to a dca file Open the Crysalis Reduce software and type dc redpd on its command line.
  • Page 47 APPENDIX 1 – HIGH PRESSURE WORK Exchange brass slits on detector. Update values in software: da 1.33 0.5 then um u. Save peak table to disk wd t. On the Xcalibur 1 system, Install the additional slits on detector arm. Screw down the slits onto the carrier on the dovetail.
  • Page 48 APPENDIX 1 – HIGH PRESSURE WORK • Select Xcalibur.par as the instrument parameter file. • Check the scans are ok and centered; Use Integrate | Manual Profile Fit to review the dataset • Integrate the data and refine the structure Xcalibur DAC Data Collection...

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