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Agilent Technologies CrysAlis Pro User Manual

1. A ne User settings C User settings Predefined instruments 3 dE Geometry Kappa 0 z Image rotation 90 y Predefined instruments Typical Mar345 scanner h Beamstop orientation Bonom A Polarisation z Polaisction n a Edt Help Cancel OK Figure 40 Run list generator for MAR CrysAlisPro USER MANUAL CrysAlis_Pro_manual_v4 Page 66 APPENDIX Appendix Directory Structure The CrysAlis program system is installed in the following directory structure Windows program files directory typically C Xcalibur root typically C Xcalibur Corrections directory corrections Site directory Asitename ffi par ccd and geo correction files These files describe the machine setup Log directory Mog log This 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 Applications root CrysAlisXXX 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 Initialisation and user defined setup files directory CrysAlisINI This directory contains initialisation user defined setup files for CrysAlis ODBench and ODShell programs ODShel software directory ODshe
2. e CCP4 launcher if installed e Olex launcher if installed 3415900000850 a C rysAl i gPro CrysAlis_Pro_manual_v4 Page 11 USER MANUAL CRYSALISPRO0 LAYOUT AND CONTROLS e Crystals launcher if installed e Jang launcher if installed e Autochem if installed Figure 4 Key to power tool icons 4 4 2 Lattice Wizard The lattice wizard icon launches a dialog from which all lattice related functions can be accessed using a GUI The lattice wizard allows both semi automatic and manual operation of lattice related functions for when the automatic process fails The GUI provides for e Peak hunting e Unit cell finding e Reciprocal space visualisation using Ewald Explorer e Indexation with known cell e Refine instrument model e Lattice transformation e Twinning and multi crystals e Incommensurates Quasi crystals e Loading and saving your work e Precession photo reconstruction As can be seen from the screenshot below the GUI provides buttons for each of the above Clicking on the buttons such as peak hunting will perform this function automatically using the default settings If the user wishes to use non default settings or change the range of frames etc then clicking on the arrow to the right of the button offers a greater number of options Full details regarding use of the lattice wizard can be found in Chapter 7 4 4 3 Command line This opens a history
3. 6 2 Append data collection On completing an experiment in certain cases it is useful to collect some extra data Providing the crystal has not been removed from the diffractometer frames can be added to the existing data set This facility is particularly useful in cases where a crystal is unexpectedly non centrosymmetric and the original strategy was calculated so that the Friedel pairs were considered to be equivalent In order to publish such data it may be necessary to collect more of the Friedel pairs 1 On completing the experiment go the START STOP button and choose Append data collection 2 Inthe resulting strategy window select the Advanced button and make sure the Lock State says Locked This means that the frames already collected are still part of the strategy but are considered done and locked Any new strategy calculation will take these into account and then add any necessary frames 3 For the example described keep everything else the same but uncheck the Friedel mates are equivalent box 4 Click Find experiment and a message will appear at the bottom of the window saying x run s were considered locked for the finding of experiment y run s were added 5 Click Start Experiment to collect the extra frames 6 3 Multi Temperature Wavelength experiments This facility allows the user to queue up experiments for collection at a variety of temperatures and back to back Cu and Mo wavelengths It is best us
4. efine instrument model a Incommensurates A Sec x rot 0 27626 y rot 0 01947 x cen 522 67600 y cen 504 95401 distance 50 53688 Wavelength Mo Ang A1 0 7093042 0 71359 B1 0 63229 Refinement res 0 009828 da 0 004550 sx 0 001956 sy 0 002076 h 0 004718 k 0 004778 l 0 004761 ref 6004 skipped 0 op Load Save Cer SE Precession images Additional command information E Ge UM TTTSOLUTION E 20 458jsub EES d 3 1298 1674 2235 90 00 90 55 90 01 pr 4858 59 UM TTTSOLUTION 7 21 462 sub 5658 al HP 22 9 2235 2237 8 37 90 01 89 98 119 43 pr 3644 91 Peak table 500 sub 6115 al Best cell 482 indexed Nigali oP 32 3 6 44 8 UM TTTSOLUTION 1 22 482 sub 6004 al OP 32 3 6 44 8 37 11 27 90 00 UM TTTSOLUTION 2 23 480 sub 6037 al NP 22 9 1287 1298 8 37 90 UM TTTSOLUTION 3 24 474 sub 5912 all oP 32 3 8 37 11 27 19 30 89 Log window de est cell deved Nigol oaa 3 644 837 11 27 90 00 89 97 89 98 prim 607 39 red 60 E TTT INFO JE Primitive unit cell refinement SE check Figure 21 Lattice wizard panel including log window 7 1 1 Peak hunting Click on the peak hunting icon and the computer will go through all the peaks and extract all those above a threshold level When this has finished it will return to the main lattice wizard screen In the window there will be a report on how many peaks have been extracted To access user settings such as thresholding and smart peak hu
5. 2 RED thread this thread can be used to view whole or partial data collections The RED thread can be used to view data as the diffractometer is collecting as long as the automatic data reduction is not C rysAl i gPro CrysAlis_Pro_manual_v4 Page 16 USER MANUAL CRYSALISPR LAYOUT AND CONTROLS active When automatic data reduction is active then the RED thread allows the user to visualise the data reduction in progress 3 USER thread this thread provides for the user to look and analyse images data while both the CCD and RED threads are actively employed in data collection and reduction respectively All functionality should be accessible in this thread 4 7 Status area Shutter Open Closed This icon simply reflects the current status of the X ray shutter Open Red with X rays exposed or closed Green with no X rays exposed X ray Mo or Cu button This button is only visible on the Gemini system It automatically selects the source when it starts up depending upon what default has been set up To change sources just click on the button and press OK on the pop up window When the power switches from one generator to the other it will ramp to default figures of 20kV and 5 mA The power must then be manually raised to the desired operational settings Figure 6 Status indicators CCD status This provides feedback of the current status of the CCD thread RED status This provides feedback of the current status of the
6. A usually helps The Calc button will bring up a window which will estimate the volume and cell dimensions of the unit cell based on a supplied chemical formula and crystal system Click on OK and the two or more cells output by the cell finding routine will be displayed in the left hand window These should be more or less identical Twin indexation is carried out as part of the automatic process C rysAl i gPro CrysAlis_Pro_manual_v4 Page 55 USER MANUAL TWINNING 5 The cells are automatically stored in the Twinning multi crystal utility The relationship between the cells is displayed in this window as a rotation Rot UB1 UB2 x deg around a b c rec a b c dir 6 The relationships between all of up to 4 components are displayed 7 One of the best methods of assessing the quality of twin lattice finding is visual inspection using the Ewald explorer module See section 9 3 below 9 2 Manual twin lattice indexation In the case that the user would like to impose a user defined cell which is not found by the automatic multiple cell finding routine use the following steps 1 Once data collection has finished carry out peak hunting using the peak hunting icon 2 Find a suitable unit cell using the various cell finding tools see section 7 1 3 The chosen cell will be printed in the left hand window of the lattice wizard Save the first twin matrix to memory by clicking on the Twinning multi crystals icon in the lattice
7. Chiral only Comment m Experiment m Detector settings and targets Scan width and exposure time Resolution Theta C 2Theta 0 837 Auto run list Scan width deg 1 00 Detector distance mm 54 9 TE Target ier en The same time for all theta positions sec deg 5 00 i i Different time For each theta positions sec deg p Run list info theta 1 theta 2 Total Pre experiment Time 0 17 5 00 20 00 Experiment Finish Wed Jun 09 16 16 46 2010 No Runs Frames 6 30 Custom run list L Editrunlist m Automode settings C Auto start IT Cryo shutdown post data collection Experiment fuse Laue Symmetry JM Record movie during de Step in deg 6 J Set total time min 15 0 J Attempt AutoChem E EE E 9 Pre experiment setup dialog window 3 Click on the Mount Sample button to mount a sample A WARNING Press STOP on the remote control on the keyboard to stop movement of the equipment in an emergency Mechanical movement of the goniometer and CCD detector may be performed using the remote control e Pressing the mount sample button releases control from the computer to the remote control unit in the diffractometer cabinet e Press the 0 and HOME buttons on the remote control to drive the goniometer angles to the zero home position e Mount the xyz goniometer head with attached crystal Typically the crystal is glued on top of a glass fibre e Press Lower on the remote control This will dri
8. If the formula is edited here during a data collection the user must wait for the next cycle of data reduction this occurs every 25 frames in order for the changes to take effect If the formula is changed at any other time the data must be refinalised to impose the change see Chapter 8 4 3 3 Data collection When connected to the diffractometer and collecting data the data collection information card provides real time progress feedback displaying the current positions of the omega theta kappa phi axes and the detector distance Also displayed are a progress bar and the expected end time for the data collection The end time is updated during the data collection to take into account required frame remeasures the percentage of which is approximated during the early part of the experiment but then continuously updated Information is collected in the data collection tab during data collection In offline mode this collected information is displayed For example e CCD Peltier maximum and minimum during experiment e KV and mA maximum and minimum from the generator if connected e Cryojet maximum and minimum temperature e Overflowed and remeasured reflections e Maximum and minimum exposure time e Date time etc 4 3 4 Data reduction The information displayed on this card depends on the data reduction being performed The Data Reduction information card displays top level feedback of the progress and results of data reduction
9. O e 3 AontTechnologies Figure 1 CrysAlis layout and controls 2 4 1 Start stop The main control button within the CrysAlisPro GUI is the START STOP button The function of this button changes depending upon the current process but in general it provides access to a range of automatic functions including e Automatic data collection and concurrent automatic data reduction e Stop All functions C rysAl i gPro CrysAlis_Pro_manual_v4 Page 4 USER MANUAL e Start Data reduction only e Full auto analysis cell red e Special data collection e Append special data collection e Resume data collection pre experiment e Resume all data collection and reduction 4 2 Image control icon bar 4 2 1 Key to image control icons CRYSALISPR LAYOUT AND CONTROLS image list Y Image list Previous run Jump back 10 frames Previous image a Play stop image movie Next image Jump forward 10 images Next run Predictions Pixel area information Image header information goniometer angles Find hkl 4 e Look up table 4 e Colour table Zoom in copo oboo Zoom out CrysAlisPro USER MANUAL CrysAlis_Pro_manual_v4 Page 5 CRYSALISPR0 LAYOUT AND CONTROLS e Zoom localiser window Resolution rings 4 e 2D Peak profile a line profile e 3D Peak profile rocking curve 4 4 e 000
10. Red thread Progress bar This shows the progress of the current process for example the percentage completeness of the pre experiment or data collection 4 8 Device control 4 8 1 Key to device control icons cco e CCD detector head controller cryo e Cryodevice controller e 0 device control SuperNova systems only Level e Liquid nitrogen level indicator controller e X ray generator controller Figure 7 Key to device control icons C rysAl i gPro CrysAlis_Pro_manual_v4 Page 17 USER MANUAL CRYSALISPR0 LAYOUT AND CONTROLS 4 8 2 CCD detector head controller Clicking on this icon opens the software device controller for the CCD detector head The display should show the running temperature of the CCD and the power being used to maintain this temperature The temperature should normally be about 40 to 45 degrees Celsius and the power between 40 and 65 4 8 3 Cryodevice controller Clicking on this icon opens the software device controller for whichever Cryodevice is installed with the system A right click of the mouse button on this icon allows the cryodevice to be changed allowing control of Nitrojet Cryojet Cryostream 600 and 700 Cobra Helijet and Hotjet devices The most commonly used device is the Cryojet On the top of the display window the actual temperature at the Cryojet head is monitored in degrees Kelvin along with the Heater power output in as well as Heate
11. Y Use twin flag wo Je Ee Bl IT Neither Lattice Lo Show twin lattice ra Fe E E r Twin cell view along KA CS 2 C SH p SCH H Wavelength Mo Colorlegend b green blue Intensity skip off Note Beware of triklinic samples gt Dragindex only works in planes isolated in the stereographic projection view Figure 33 Ewald explorer twin flags and lattice visualisation 9 4 Data reduction of a twinned data set 1 Click on the START STOP button and select Data reduction with options Twin 2 The Twinning multi crystal menu will already be activated with boxes ticked for as many components as have been defined Switch off components to be integrated as required 3 Select a suitable follow model option see Section 6 5 1 This may prove to be quite important because the center of mass of individual twin components may not lie at the center of mass of the externally visible crystal 4 Continue with data reduction as normal remembering to Clear data from previous run when prompted 5 Click on Finish and data reduction will begin 6 The frames will be processed repeatedly once for each twin component 7 On completion of twin data reduction a variety of top level information is displayed in the data reduction tab Figure 16 This includes the twin ratio including the number of reflections associated with each component plus Rin and l sig statistics for both isolated and overlapped reflections hkIf
12. collection strategy as much as you like selecting different exposure times scan widths or completely different data collection ranges When you have finished click on OK to exit this window and return to the strategy window To see the effect your changes have had click on the Update Completeness button The graphs and table of statistics should be updated When satisfied with your changes to the Strategy click on Start Experiment to begin data collection 5 4 1 Strategy calculation tips The strategy module is a remarkably powerful tool and can be used in many different ways Mastering the manipulation of data collection strategies is the best way to collect the best possible data Here are a few tips related to common scenarios e Particular attention should be given to the exposure times used for data collection Occasionally CrysAlisPro will overestimate the times required due to pre experiment data being of low intensity particularly at higher angles The count times can be adjusted in terms of seconds or I sig values For Cu data sets collected to 0 84 A good data for IUCr publication exposures for a high angle theta setting will generally need to be 3 or 4 times the value of those for the low theta setting For high resolution Mo data the same applies The strategy module will use the same time for all theta positions as standard so this must be changed by the user All scaling of data to account for two or more differing exposure times
13. experiments are often run without frame correlation or overflow re measurements both of which can be switched on off in the Calibration Experiments window The experiment can be further optimised by changing the resolution and exposure times The calibration can be monitored in the Command Shell and an output message is generated upon finishing which details the instrument parameters test crystal unit cell dimensions and the percentage fit for indexed reflections From the service power tool we can access the automatic instrument calibration tool Generally calibrations are run for two purposes e instrument model calibration e instrument model calibration with additional flood calibration Often the performance of the standard sample is a characteristic fingerprint of the machine performance But the R1 statistic is really a function of the data completeness To make the results comparable an option has been added that will append to the calibration frames normal data collection frames to produce a complete data set C rysAl i gPro CrysAlis_Pro_manual_v4 Page 44 USER MANUAL POWER TOOLS Full calibration expenment dialog 2 0 3 Path wes I zeng PE Expermentin folder CipxcalbuDatalcalb_a_14_Tua Jun 22 10 06 37 2010 Basic system parameters Generator at end of experiment EE gel No change zeroio 19 90000 Od nee cu theeshold 730000 Beam stop support ME nae eS having ee Dark subtraction on Flood correction
14. is handled automatically C rysAl i gPro CrysAlis_Pro_manual_v4 Page 31 USER MANUAL NORMAL OPERATION The strategy module will automatically adjust the scan width of the frames depending on the unit cell axis dimensions mosaicity and overlap parameters found in the pre experiment The scan width can also be easily adjusted by the user Generally speaking for Mo radiation cell axes greater than 40 A are often best collected with a scan width of less than 1 Longer wavelength Cu radiation can easily cope with much greater axis lengths If twinning is suspected reducing the scan width can significantly improve the chances of obtaining good quality data When collecting data using an overnight time slot it is often worth adding redundancy to a data set so that the whole amount of time is used In order to add extra data click Complete redundant data in the Strategy mode drop down menu choose a suitable redundancy multiplier e g 5 and click Calculate New Strategy Check the expected end time and recalculate as necessary Having a higher redundancy means a better signal to noise ratio for the data and higher quality determination of frame scale factors and empirical absorption correction Some cryo devices perform better than others and in humid conditions small amounts of ice can form on the metal pin below the crystal This problem is enhanced when long exposure times are used and the goniometer head sits in or near the cold stream for a s
15. list generator for d trek image format C rysAl i gPro CrysAlis_Pro_manual_v4 Page 65 USER MANUAL FRAME FORMATS 11 3 SAXI Data from Bruker AXS saxi formats can also be processed with CrysAlisPro Run list and aliases file generator for SAXI data collections SH xt This dialog allows you to quickly generate a nm file and aliases file for the data reduction of a SAX data set 1 You select image name_1_1 sax or name01 001 or name_01_0001 zm 2 You select the last image to be considered It is assumed that all frames between these two are available 3 Save the file 4 You wal be prompted for entering some critical parameters usually default values are OK as they are taken from image headers 5 Finally a new CrysAlisPro instance will be launched with the SAX data set added to the experiment list NOTE Using CrysAlisPro you can process only SAXI images from APEX1 and APEX2 detectors y First de SAXI de file _1_1 sax or 01 001 or _01_0001 sfrm Browse E data bruker ylid yid_01_0001 sfrm r Last de SAXI de file EA data bruker yidyid_03_0112 stim Help Cancel Save run file Figure 39 Run list generator for SAXI 11 4 MAR Data from MAR image plates and some MAR CCD detectors e g MARCCD 165 may be processed with CrysAlisPro CrysAlis experiment setup for MAR data collections 1 0 3 x This dialog allows you to quickly generate all necessary files for a CrysAlisPro experiment descriptio
16. loss of completeness For this reason filters should only be used when absolutely necessary 8 4 Applying absorption corrections A face indexed absorption correction can be applied provided the crystal shape has already been determined see section 8 4 by ticking the Apply absorption correction box in the top right corner of the window The absorption coefficient p is not always calculated automatically and so this can be done by setting the formula and Z value in the Show face list button A spherical absorption correction can also be applied by ticking Apply next to the Spherical abs button and then entering a suitable value for ur where r is the average radius of the crystal The transmission factors resulting from the absorption correction are output in the cif file generated by refinalization 8 5 Crystal shape modelling face indexing The Abs display button opens the crystal movie window display provided that a movie of the crystal has been previously recorded The crystal can be rotated incrementally by pressing the Page Up or Page Down keys C rysAl i gPro CrysAlis_Pro_manual_v4 Page 53 USER MANUAL INSPECTION AND MANIPULATION OF DATA The crystal shape is defined with respect to both hkl and xyz values The hkl indices relate to the cell defined at the time of face indexing However as the cell is also defined by standard xyz coordinates if the cell is changed in any way the orientation of the model will not
17. often be fixed by selecting Card reinit or Reset FIP and Start More details on the service utility features may be found in Chapter 7 A N WARNING The mgcutil Expert control window is the only place within CrysAlisPro where there is no goniometer collision protection Although warning messages will appear when driving the circles using mgcutil the facility should only be used by experienced users or qualified Agilent employees C rysAl i gPro CrysAlis_Pro_manual_v4 Page 14 USER MANUAL CRYSALISPR0 LAYOUT AND CONTROLS 4 4 7 Powder diffraction The powder diffraction power tool performs different functions depending on the CrysAlisPro operating thread CCD RED USER When in CCD view a powder experiment dialogue box opens Here the user can specify settings such as detector distance exposure time resolution and phi scan constraints to generate a run list for a powder diffraction experiment To begin the experiment click the Start with analysis button at the bottom of the window When the experiment is complete a powder graph will be automatically generated from the correlated diffraction images If the powder diffraction button is clicked when in either RED or USER threads a dialogue box appears asking if the user would like to extract the powder pattern from the current experiment This function allows the user to generate a powder diffraction image generated from the frames of a single crystal diffraction experime
18. often highly symmetrical and so many different cell and space group combinations are possible the added presence of satellite reflections makes this even more difficult One simple technique for identification of the parent lattice is to filter the reflections based on intensity in order to filter out the weaker satellites This can be done in the Ewald explorer module 1 Use the Skip filter and select Intensity 2 Tick the Remove weak reflections box and raise the threshold The weak reflections will gradually disappear 3 To skip the removed peaks choose Mark invisible skip in the Flags menu The skipped flag will be placed next to the reflections concerned the peak table and they will not be used in any unit cell determination 4 Attempt to find a suitable unit cell with a high fit accounting for the maximum number of unskipped reflections The Gnomonic view in the Ewald Explorer module combined with the Drag indexing function can also be used when it is difficult to distinguish between different cells Initially perform a standard data reduction and attempt to solve and refine the structure as normal This will be the average structure with no treatment of modulation taken into account Incommensurate data sets with q vectors in up to 3 directions can be handled Samples that are both incommensurate and twinned can also be dealt with The best method for searching for potential satellite peaks is by using the q vector over
19. olex2 exe C Program Files Olex2 WinGX executable wgxMain exe or wingx32 exe C Program Files xraysoft wingx F Savetomesterfie on ext MENETAN TE CH Figure 27 Programs tab of CCD setup options panel C rysAl i gPro CrysAlis_Pro_manual_v4 Page 47 USER MANUAL POWER TOOLS Provided that you have installed AutoChem you will have access to the AutoChem control panel We support at the moment the following solution methods ShelXS smtbx charge flipping and ShelXD As refinement methods we support ShelXL and smtbx refine Within Olex2 you can also install SuperFlip and SIR as a solution method Figure 28 AutoChem settings panel Both AutoChem and Olex2 now share the same structure folder This makes it easier to review an AutoChem structure after concurrent data reduction As a result of this we now have to halt the Autochem operation in concurrent data red while Olex2 is open For this reason you might observe the following states on the AutoChem tab e Launch Resume AutoChem Figure 29 AutoChem information card C rysAl i gPro CrysAlis_Pro_manual_v4 Pa ge 48 USER MANUAL POWER TOOLS C rysAl i gPro CrysAlis_Pro_manual_v4 Page 49 USER MANUAL INSPECTION AND MANIPULATION OF DATA 8 Inspection and Manipulation of Data On completion of an experiment the data reduction tab within the main CrysAlisPro window displays various output information However for more detailed results the Insp
20. temperature for Eos Atlas and Titan detectors FIP60 the same plot for Sapphire Ruby and Onyx detectors Cryojet a plot of temperature and flow rates against frame number and two further charts for the XrayChiller and CCDChiller If data reduction has been carried out several times and saved under different filenames statistics for each can be observed by locating the appropriate file in the drop down menu at the bottom of the window 8 1 Refinalization If the user wishes to re process the data the Refinalize button will activate a new window through which many aspects of the data reduction process can be fine tuned Figure 14 Laue symmetry and outlier rejection can be applied as well as limits filters and lattice extinctions The data reduction procedure generates a rrpprof file which contains all integrated data The last step of the data reduction process is finalization in which a hkl file is generated from the rrpprof file by applying the Laue symmetry space group multiscan absorption correction and frame scaling both using the ABSPACK module Data can be Refinalized repeatedly using differing parameters generating several hkI files y NOTE The best way of maintaining consistency between all files hkl ms cif for a given experiment is to use the Refinalization menu to impose any changes C rysAl i gPro CrysAlis_Pro_manual_v4 Page 50 USER MANUAL INSPECTION AND MANIPULATION OF DATA Dit a E
21. the experiment database This will also be the case where no diffractometer is connected 3 2 Closing CrysAlisP o To close CrysAlisPro click on the X icon in the top right corner of the CrysAlisPro screen When in CCD mode a prompt will appear regarding generator ramping control For microfocus systems in particular it is recommended that users turn the generator power down when the diffractometer is not in use For all other systems it is up to the users individual preferences as to the power settings used when the system is not in use C rysAl i gPro CrysAlis_Pro_manual_v4 Page 3 USER MANUAL CRYSALISPR LAYOUT AND CONTROLS 4 CrysAlisPro layout and controls The CrysAlisPro GUI is comprised of a number of different areas These include 1 START STOP button Image control icon bar Information cards P fo ba Power Tools 5 Diffraction Image display window Status area 7 Device control 1 lali STARTISTOP cco cro xray Lover CCD Colecung 6 355 engrwes Sep 24 09 47 54 20101 D FED prof t wating or new data Cue Sep 20 22124 kass Bra Crystal a Data Collection a Peopass milo de 6 165 200 030 Sep 29 09 47 54 2010 Imaga fo sr 0 1 image J neg Thota Kapps mu 2910916 1920s 70000 07 0000 Distance sosom siama EE gres Sc Gr a SEH SC en we Plier ane as Lien E ER a CJ iel e PA CA E E e SEN Ee EE 20 wu CCCDDDDO O O O O OOOO O
22. ticked Click on OK C rysAl i gPro CrysAlis_Pro_manual_v4 Page 41 USER MANUAL POWER TOOLS 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 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 corner of the Ewald Explorer window All the skipped peaks including the intensity skipped peaks should now be visible as red dots 7 1 4 Indexation with known unit cell It is possible to re index the peak table using the currently loaded unit cell This applies a round of least squares and shows the results in the lattice window More options are available using the arrow button to the right of the icon These include e Indexation with known unit cell and criterion e Non integer indexation e Twin indexation The first of these options allows the tolerance for indexation to be changed set to within 0 125 of an integer value as defa
23. values for Voltage and Current and the appropriate filament current A and power limits kW for each particular system The Emergency X ray Off button quickly shuts the generator down and stops the production of X rays in an emergency The hardware interface needs to be reinitialised switched off and on after such an event before setting the next Voltage and Current The Start Stop button initiates or ends communication between the software interface and the generator If not in communication already click on START to connect to the generator Use the Set kV and mA X ray button to set new values Typical settings for both Molybdenum and Copper fine focus tubes Xcalibur and Gemini systems are 50 kV and 40 mA although some users prefer 40kV and 40mA for Copper For Microfocus systems Mova and Nova standard generator settings are 50kV and 0 8mA The generator will reach the desired values in a stepwise and controlled manner If you close the window before the ramp process is complete then only the values at closure will be reached In the bottom half of the X ray window display there are Fault and Status indicators that provide feedback for the state of the generator In normal operation only the Status indicators should be active Use the Fault indicators as guides to investigating hardware issues should there be any trouble with the generator A log file for the generator output is automatically recorded from the beginning of th
24. vector coordinates are refined and output information is available under the peak table menu on the left of the lattice wizard window The key points to note are a Has the of indexed reflections increased b How many Main reflections q1 satellites are there The second third fourth etc orders can now also be investigated by returning to the q vector overlay tool and raising the value of m max for the q1 satellites Use visual inspection of the overlay spots as well as the histograms on the right of the window to decide whether or not the specified order makes sense 1 Raise the value of m max by a single integer 1 to 2 2 Return to the lattice wizard and refine the q vector values in the same way as before 3 Look to see if the of indexed reflections has increased C rysAl i gPro CrysAlis_Pro_manual_v4 Page 63 USER MANUAL INCOMMENSURATES 4 Observe the By order output to see how many 2 4 order satellites are present 5 If this value is zero 274 order satellites are probably not present Reset the value of mmax to 1 and refine again 6 However if 2nd order satellites are present use the same approach to look for 3 then 4t order satellites etc Crystals with more than a single q vector are relatively rare Samples with three q vectors 3 d quasi crystals are extremely rare and so in most cases single q vectors possibly with a satellite order higher than 1 are most worthy of pursuit in the first instance Once a
25. wizard 4 Click on the radio button Component 1 then select the Current UB to twin button The UB matrix will be printed in the bottom window Click on OK 5 Click on the Ewald explorer icon and radio button Show wrong and only the wrongly indexed reflections will be shown 6 The indexed reflections need to be skipped in order to index the second twin component Click on the zoom button to zoom out until all reflections are within the screen Click on the Drag radio button and then hold the left mouse button down and drag a box around the reflections Right click and select Mark selection skip and they will turn red Click on the pull down menu Flags and select Invert used and skipped Click on the radio button Show all followed by OK and then click on the unit cell finding icon in the lattice wizard 7 When the 2 cell has been found it will be printed in the left hand window of the lattice wizard 8 Click on the Twinning multi crystals icon to store the second lattice as component 2 Select Component 2 and click on the radio button Current UB to twin You now have two twin components saved to memory 9 Click on OK to exit the UM TWIN window 10 Index and refine the two cells by clicking on the arrow to the right of the twinning multi crystals icon and selecting Twin indexation Make sure the radio buttons 01 R1 02 and R2 are selected then click on OK The cells will be refined and printed in the lattice wizard window On promptin
26. 0900 Help CH CH 4 o View CCD RED USER Figure 2 Key to image control icons Stepping forward and backward between diffraction images can be controlled by using the image control icons but also by using the mouse wheel 4 2 2 Image list The image list allows the user to open and save diffraction images Options include Open image with explorer Save image to save the current diffraction image Save image as to save the current diffraction image under a new name Save jpg to save a jpeg graphic image of the currently displayed diffraction image and Save bitmap to save a bitmap format graphic image of the currently displayed diffraction image Bitmaps and jpegs can be saved with resolution rings and or predictions displayed Zoomed areas of the images can be saved by choosing Save visible part of image as bitmap or jpeg 4 2 3 Predictions Once the unit cell has been determined sensible predictions can be overlayed on the diffraction image Clicking on the predictions icon in the image control tool bar switches predictions on and off Note that these may take a few seconds to display especially when this function is used in conjunction with the movie control buttons such as play where the calculations are all done in advance If in doubt check the status area in the top right hand corner of the CrysAlisPro GUI The predictions overlay a cross rhombus or diamond and square to show
27. 3D Peak profile Rocking une 8 4 2 15 Hel WEE 8 4 2 16 VUEN 8 4 3 AA A A A ea paaa aA EASE aiaia 9 4 3 1 Pre Ex periment E E E E E E E OTE 9 4 3 2 REI EE 10 4 3 3 Data collection cia 10 4 3 4 Data TedUCION iii id a dd dd dd AEN 10 4 4 Power tool sicts li a ee et de ad o o 11 4 4 1 Key to power Tool eons a a a ES 11 4 4 2 Ee TEE 12 4 4 3 Command lines iconos coladas Sheds 12 4 4 4 Inspect data collection and reduction results 13 445 Launch Znd instance of CrysAliSPTO a cccccnnnnnnnnnnnnnnnnnnnnnnnnonononnnnnnnononononononenenenenenenos 13 4 4 6 VIC A A eg Ee ee Tae Ok Bien 14 4 4 7 Powder diffracti n ca id Ee a da cotas 15 4 4 8 Multiple Temperature Wavelength Experiment cccccccccececececececeeeeeseseseceeeeeseeess 15 4 49 elle UN 15 4 4 10 WINGX Jauncher conoce no nonono nono no nono no nono nononononononon 15 4 4 11 CGPA launcher EE 15 4 4 12 Olex2 lAUNCH EN esst d egog A Ee AE E 16 4 4 13 Giystals lauUnGhe reese ste ege id ee EEN 16 4 4 14 Jana launched AA AAA geld dee ee dE 16 CrysAlisPro CrysAlis_Pro_manual_v4 Page ii USER MANUAL CONTENTS 4 4 15 Autochem launcher sss 29 eebiee ated ashes ad cd 16 4 5 Diffraction image display window ccccccccccececececeeeseeeeeeeeeeeeeeeeeeeeeeeseseeeeeseeeeeeeeeeeeeess 16 4 6 Window hed der bat snieter niei iaai EE iii a id did 16 4 7 ET e eee o ad o reos faro oo de Meta e dE 17 4 8 Device Control il anida 17 4 8 1 Key to device Control ICONS unicida
28. 4 and hklf5 Twin data reduction outputs a single HKLF4 file per twin lattice Each one is clearly labelled as name_twin1_hkIf4 hkl name_twin2_hklf4 hkl etc These hklf4 files are standard data files and are to be used for structure solution The best chances of success come from structure solution using the major component data file which is usually twin1_hklf4 hkl however this will depend on which cell was found first and stored as component number 1 C rysAl i gPro CrysAlis_Pro_manual_v4 Page 58 USER MANUAL Data Reduction FRAMES RUNS In run list 188 3 used 188 3 3D PROFILE ANALYSIS twin component 1 Frames done 188 Reflections tested 10323 used 5129 Avg mosaicity in ES 3 run s el 0 88 e2 0 88 e3 0 9 3D INTEGRATION amp FITTING twin component 1 Frames done 188 Fitted 10511 overflow 0 hidden 769 Outliers rejected 0 FINALIZATION INPUT FILE Filename tenerife SCALING NUMERICAL ABSORPTION Empirical abs e 2 0 0 min 0 97 max 1 03 Frame scales 1 scale min 0 95 max 1 04 TWIN ANALYSIS Component Ratio Isol E ee 1 0 52 4506 2 0 48 2897 4506 DECOMPOSED TWIN DATA STATISTICS lt 0 80 overlap Component Redundancy Ee Rint 5 0 0 078 2 0 10 ci 0 082 EE limit for HKLF4 export 0 80 TWIN HKLF5 STATISTICS FOR OVERLAPPED OBS Components Redundancy F2 sig F2 Rint 1 2 1 8 17 4 0 039 SPACE GROUP DESCRIPTOR P2 1 n Group 14 3 SG found no data coverage DATA REDUCTION OPTIONS 3D pr
29. CONTROLS 4 2 11 Zoom localiser The zoom localiser is a floating semi transparent window which displays the full diffraction image regardless of the zoom used in the main diffraction image The zoom localiser window can be switched on and off by repeated clicking on the icon in the image control icon bar Within the zoom localiser window the zoomed area of the main diffraction window is outlined by a wire frame box which can be moved over the zoom localiser window As the wire frame box is moved over the image the zoomed area in the main diffraction image window is updated Use in combination with the zoom in and zoom out 4 2 12 Resolution rings Resolution rings can be switched on off by clicking on the button in the image control icon bar This displays lines of constant d value on the diffraction image to enable a quick visual check of diffraction limits angular resolution The default is with resolution rings switched off Additional settings can be accessed by clicking on the arrow to the right of the resolution ring icon These settings include the selection of a greater number of rings of constant d value selectable between the default 3 and the maximum of 12 the display of labels on the rings and the display of rings in black or white 4 2 13 2D Peak profile Peak profile allows the user to drag a line through an object in the main diffraction window and obtain a 2D plot of the object In this way a profile of a reflection
30. CrysAlisPro Data Collection and Processing Software for X ray Diffractometers User Manual Read the main diffractometer user manual in particular the Health and Safety information before operating CrysAlisPro with the diffractometer Version 4 September 2010 Agilent Technologies XRD Products 10 Mead Road Yarnton Oxfordshire 0X5 10U UK Tel 44 0 1865 291600 Fax 44 0 1865 291601 http www agilent com chem E eS Agilent Technologies CONTENTS Contents 1 2 2 1 A A A Installation of CrysAliSP ccssceescesscesneeeneeeneeeneeenseonsenenessnenenes 2 Software Ta EE E EE E E E A E E 2 Starting and Closing CrysAlis ccssccesscesscenecenssenssnssensseeeeeed 3 1 Starting Cs Ali gedoe dn eee aiaa nae aie Fee ain 3 3 2 RI RK EE 3 4 CrysAlisPro layout and Controls 0scceseceseceeecenscenssenssenseenseenseesd 4 1 Start 7 Stop d a 4 4 2 Image control Icon bar tii A a 5 4 2 1 Key to image Control ICONS ioiai oaran aa aai aa aaa a aa aaar a KAE a aN 5 4 2 2 Mart EE e T 6 4 2 3 RE Wee EEN 6 4 2 4 PCMCIA MN HEEN 6 4 2 5 Header information K goniometer anglesl nn nccnn 7 4 2 6 Sir Dr A A is 7 4 2 7 LOOK UP iii tna ad ran 7 4 2 8 Colourtables cosa ta lolas 7 4 2 9 ZOOM EE 7 4 2 10 O E 7 4 2 11 Zoom localis r cisat ii dd AA di a aid 8 4 2 12 ResolutionjringS 28 3st tention aia hed tia aaa dee sie LA eN 8 4 2 13 2D Peak tel UE 8 4 2 14
31. NUAL POWER TOOLS For qualitative powder patterns the dark current is not essential You can uncheck the Use darks check mark under Options to get faster powder experiments For calibration powder experiments you can use the Expand theta positions in range check mark which will insert into the run list more overlapping theta positions to see the same ring under different conditions 7 4 Single Images Clicking on the single images icon displays a box with options to e Record a still image e Make a phi scan e Make an omega scan e Make a rotation photo e Axial photographs e Screening data collection Only the axial photographs option is clickable when working off line It allows you to calculate the position at which you might take a photograph Click on an option to select it and then click on the start button 7 5 AutoChem Olex2 version 1 1 is fully supported by CrysAlis The user can also install several versions in parallel The version which is currently used is selected in the tools options panel Programs as shown in Figure 28 CrysAlis CCD program options 1 0 40 2 x Color codes Beam stop Angular fimits Goniometer Run list size cep Processing User access Distance calibration SMPX Instrument model Instrument modelil Monochromator Fonts Peaktable Camera Compression Dark Generator Programs This dialog allows you to set paths to extemal programs Olex2 executable
32. O EU H GC Chemical formula c15h16 n4 02 2 200 Outlier rejection Use outlier rejection 2 m bunique C Dontuse outher rejection mP 4 36299 10 30879 15 22940 90 03883 95 00234 89 96577 IV Use Friedel mates as equivalent Apply Sigma calculation control Overlap twin reject Limits erz and lattice extinction filters I Estimate error model Negintensity sigma imt 3 0 Override rejection par Edit rej pa F Resolution d IF Use overlap rejection dit overtap re Nofiter use filter for I Use twin rejection C Edit twin re WET o active titers Data items in hk file User modifications I Beam path information for absoprtion correction special formats I Esport equ file I Export sadabs _1 raw Batch number Each run gt 1 batch L Edit batch I Export CIF file Add hkl data to CIF Export MTZ file I Update overwite hkl file in WinGX and Olex2 subfolders struct _compound2 Y Use ABSPACK I Space group determination IZ Tip You may change the output name and directory to keep results of data reductions under different parameter sets Limits sigma parameters I Completeness 0 84 Ang Edit res Output file name C XcaliburD ata compound compound2 compound2 I Structure solution AutoChem tions Change output name Fre Figure 30 Data reduction refinalisation GUI 8 2 Running GRAL in interactive mode The space group determination module can be run in interactive mod
33. UAL CrysAlis_Pro_manual_v4 Page 26 NORMAL OPERATION Hext with options Figure 12 Screening information card The Peaks button invokes the peak hunting dialog box Here you can quickly tune the peak hunting parameters in case of difficult samples k hunting for proteins 1 0 2 Protein peak hunting Figure 13 Protein peak hunting panel The 2D drag tool gives an estimate of the expected d values and possible lattice repeat distance which could be one of the lattice constants C rysAl i gPro CrysAlis_Pro_manual_v4 Pa ge 27 USER MANUAL NORMAL OPERATION Period 95 582 Decke 7 sa 7220 700 240 500 SG 160 4200 2 10 a0 PO 1400 40 0 00 0 60 120 La 20 30 SOOO OOOO OOOO O enn Hitt Figure 14 d value tool CrysAlisPro CrysAlis_Pro_manual_v4 Page 28 USER MANUAL 5 4 Strategy NORMAL OPERATION The strategy module will automatically pick up the Laue class detector distance resolution target and exposure time from the pre experiment and will determine an optimum data collection strategy with these and the unit cell in mind The default strategy is that required to obtain 100 complete data However a number of alternative modes are available These include e 100 completeness e Specified global redundancy with incompleteness allowed e Specified global redundancy with 100 completeness e Specified constrained experiment time with incompleteness allowed e Specified constrained exper
34. _ File Clipboard Figure 18 Multi Temperature Wavelength utility 4 Click on the Multi temperature wavelength icon 5 For either Mo or Cu or both click on the Strategy button Select Edit runs and then import the generated strategy C rysAl i gPro CrysAlis_Pro_manual_v4 Page 35 USER MANUAL NON STANDARD OPERATION 6 Select the installed cryodevice and click Settings By choosing start and end temperatures and a number of steps a series of experiments will be run one after the other For example starting at 100K and ending at 300K with 5 steps will run experiments at 100K 150K 200K 250K and 300K These are stored in clearly labelled folders with a temperature suffix 7 The data is processed concurrently but it is often useful to reprocess data in order to help correctly identify any changes in cell parameters over the given temperature range 6 4 Data reduction non concurrent To reprocess data after data collection but using automatic settings first open a second offline version of CrysAlisPro Click on the START STOP button and select Load Experiment Select the experiment you are interested in from the experiment database list Click on the START STOP button again and select Full auto analysis cell red the program will find the unit cell including peak hunting etc and process the data scale the data find the space group and output the ins and hkl files If you have found the unit cell by hand using th
35. ackground 4 2 5 Header information K goniometer angles The Header information K goniometer angles icon switches on a window at the top of the diffraction image This window displays different information depending on whether the computer is offline or online with goniometer When the computer is offline the window displays the current image name and the angles at which it was collected When the computer is online the window displays the image name and its collection angles and also the current angles of the goniometer The window provides real time feedback of what is happening on the machine 4 2 6 Find hkl Once you have an indexed unit cell click on the find hkl icon A dialog box will open Input the desired H K L in the box at the top of the dialog Click on Search If the current run list contains this HKL then the frame s on which this reflection occur will be listed in the box at the bottom of the dialog By clicking on a particular line item in this bottom box the main diffraction window will update with the relevant frame image where the HKL in question is marked with a on the image If the is difficult to see use the xy pixel position to help 4 2 7 Look up table The look up table affects the main diffraction image display This is the viewing level above or intensity threshold above which reflections or image information are displayed Going to a higher look up level displays higher intensity obj
36. ael eak hunting SE Unit cell finding a Gees kl Reindexation with transformation H Incommensurates heated 1 Go to the Ewald explorer module click on Show in the menu bar and select Show twin flags and twin lattice Figure 15 This will bring up a new window with toggle boxes for up to 4 components Ticking the Use twin flag box will enable the user to toggle each component on or off according to its twin flag The flags themselves can be seen in the peak table which is accessible through the small arrow icon next to the Ewald explorer icon 2 The Show twin lattice box enables the user to switch each lattice overlay on and off individually 3 The Twin cell view along tool means that the sphere of data can be rotated to view along any axis of up to 4 components 4 Ifthe user is interested to see if the found components account for the majority of the ordered reflections switch on the Neither reflections only By looking at these reflections on their own it is usually easy to see whether or not it is worth attempting to search for further twin components CrysAlisPro USER MANUAL CrysAlis_Pro_manual_v4 Page 57 TWINNING sphere 1 3 20 x Exit Show Flags Tum90deg Turn SOdeg ClearDrag Cell Properties Tools Windows Help Rotation axis x CSC Cat gt Siow rotation 4 0 200 Fastrotetion x Sa e HR 1 300 Twin flags and lattice window Twin
37. an be made the structure should be refined using the twin data file HKLF5 In the ins file the HKLF4 command must be changed to HKLF 5 A BASF batch scale factor command must also be inserted into the file along with a number which defines the ratio of the twin components This number will refine but an initial value is output by CrysAlisPro and is found as the last item in the command shell In cases with more than 2 components more than one BASF number is required Details of what to include can be found in the command shell CrysAlisPro USER MANUAL CrysAlis_Pro_manual_v4 Page 59 TWINNING Ey NOTE Structure solution cannot be performed using a HKLF5 file A HKLF4 file containing the information of only a single lattice must be used for this purpose 9 5 Twin data finalization As with standard data sets twinned data can be altered by changing the settings in the Twin finalization module This is the bh power tool and is only available if twin data reduction has been carried out All the standard features are available here including e Chemical formula editing e Laue symmetry and Friedel mates manipulation e Multiscan absorption and scaling e Application of face indexed absorption corrections e Filters and merging e Space group determination including specific control using the space group options window One feature here which is unique to twin data finalization is the full overlap threshold s
38. an also adjust intensity thresholds lattice extinctions and d spacing thresholds to select peaks Information on using the Ewald Explorer to find multiple lattices in twinned crystals can be found in Chapter 9 7 1 3 1 Drag indexing a unit cell 1 Click the Ewald explorer button 2 The Ewald explorer allows you to scan the reciprocal space of your data collection for lattice planes The image can be rotated by holding down the left mouse button whilst the pointer is positioned over the image and rotating it 3 Try to find a plane by rotation about x y z A lattice overlay can be shown by ticking the Lattice tick box 4 Click the radio button Drag then the radio button DragIndex This will allow you to specify three non collinear vectors to define a UB matrix and thereby a unit cell 5 Click on the button b order radio button and then left mouse click on the lattice and drag out a vector The corresponding d value is shown below the b order button Count the diffraction orders you covered and enter the value by clicking on the button order b 6 Repeat the previous bullet point for a order rotate and repeat for the c order 7 Click on the button UM S to set the UB matrix based on the DragIndex vectors and exit the Ewald explorer using the OK button and select Yes if you are happy with your results 8 Index the reflections by pressing the button index with known cell and repeat if necessary A percentage figure of merit for th
39. and space group determination The feedback contains information regarding e Absorption correction scaling C rysAl i gPro CrysAlis_Pro_manual_v4 Page 10 USER MANUAL CRYSALISPR LAYOUT AND CONTROLS e Space group e Information of face indexed absorption corrections e Multi component information from twin data reduction e Results in terms of Rint sig Redundancy Completeness etc e Mosaicity During the automatic data collection and reduction process this window will only display feedback after the first 25 frames have been collected since data reduction will not start until this point This is so that a good estimate of the average background can be established requiring 25 consecutive frames The automatic data reduction will process newly collected data in batches of 25 frames and will update the feedback area accordingly so that by the time the last frames are collected almost all data has already been integrated This behaviour is the default setting of the auto mode however should the user need to re evaluate the data they can do so by using the power tools 4 4 Power tools 4 4 1 Key to power tool icons e Lattice Wizard ES e e Command line D e Strategy tool e Data finalisation e Twin data finalisation CrysAlisPro Service utility e Powder diffraction Multi Temperature Wavelength e Single images e Shell launcher e WinGX launcher if installed
40. bottom and far left hand side of the image If you deselect the stereographic projection radio button the lattice lines should be lined up and the drag index function should be easier to use C rysAl i gPro CrysAlis_Pro_manual_v4 USER MANUAL Page 61 INCOMMENSURATES 10 Incommensurates An incommensurate or modulated structure derives from data where there is periodic distortion of the atomic positions modulation and or of the occupation probability of atoms density modulation This gives rise to satellite reflections present in addition to the main lattice Satellite reflections are often of very weak intensity and so are not always clearly observed The best chance of observing as many satellite reflections as possible is to collect data with a reduced scan width 0 5 and with a significant exposure time Collecting data of increased redundancy is also beneficial A movie demonstrating some of the incommensurate data processing utilities with a worked example is available to download from the Agilent X ray user forum This can be accessed at forum oxford diffraction com Users will find the movie particularly useful when using incommensurate tools for the first time Successfully identifying the parent lattice in an incommensurate crystal is often the key to treating incommensurate data sets Finding the parent main unit cell can be as simple as finding a standard cell but on occasions it can be quite difficult Structures are
41. change However the hkl indices of the faces will change according to the new cell and may no longer be integer values Initially the crystal centre must be defined by right clicking in the appropriate place and choosing Define center Clicking the left mouse button and dragging will drag out two vectors for principle and mirror faces The vector needs to be dropped so that it is coincident with a face with the face perpendicular to the screen The hkl values for the drawn vector are displayed at the bottom of the window The face can be added to the list by right clicking on the window and selecting the Add face or add mirror faces option in the pop up window Ideally natural faces should have natural indices 1 0 0 0 1 0 etc However it is more likely that faces such as 1 0 10 and 22 0 3 will be observed These are in fact 0 0 1 and 1 0 0 but due to the errors involved the vectors do not correspond exactly to the natural face The user can manually edit the face list as well as control more aspects of the indexing process within the Faces tab of the Crystal movie configuration window Once enough faces have been added to define a 3D shape the shape model will appear superimposed over the movie image Clicking on a face in the Faces tab will highlight it in red on the image allowing for simple identification and editing Refinement of the defined crystal shape can be carried out by clicking on the Scale3 abs button in the Data reduction re
42. cified number of reflections The Stop if gt figure should be set to no greater than 30 50 for the best chance of success 7 1 3 Reciprocal space visualisation using Ewald Explorer The peak table can be displayed by selecting the appropriate option which appears after pressing the small button next to the Ewald Explorer tool Optionally the peak locations can be cast in terms of diffractometer setting angles Cartesian coordinates or coordinates in the detector frame of reference Peak table editing 1 0 6 D 0 02905 e i 2 70086 0 10570 A 0 75711 0 26644 a 1 01909 0 1ss s E S 1 89762 0 25690 H 0 39750 0 05430 R 0 78843 6 11143 1 1614 6 11705 A i 0 30700 0 13630 e 4 38232 4 18039 S Laera 0 20505 6 1 20724 0 15521 S 8 9 91331 0 06635 KR 6 51557 0 24054 RP 0 839675 0 17116 e 6 70033 0 16174 6 1 36576 6 01723 A KR 6 83772 01439 KM lt 0 67316 0 08S24 N i 6 59636 8 22692 1 29063 0 13920 0 62764 29013 t 3 4 s D H D 3 e A A A A A LA Ext ed Copy to cp sortes VOS 5 re E Pako Coda Cas Figure 22 Peak table panel Alternatively the current contents of the peak 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 C rysAl i gPro CrysAlis_Pro_manual_v4 Page 40 USER MANUAL POWER TOOLS reflections for peak indexing The user c
43. creening tool 1 0 2 e Screening NORMAL OPERATION xl Conk Path D idatalexp_371lexp_371 Control Mount sample Edit description SII Single orientation screen Two orientations screen N orientations screen T Distance not dloserthan 191 mm Resolution 2 00 Ang Scan width fos deg Figure 11 Protein screening dialog Protein screening normally involves exposure times significantly longer than those for small molecule Options runs 1 frames 2 distance 122 0 IV Correlate images IV Use darks Edit orientation s Exposure time 20 0 s Frame multiplier E Total experiment time 02m 08s I Remeasure overflown frames Edit exp options Gol Ee experiments For this reason the collection of dark frames at the beginning of a screening experiment can take a disproportionately long time compared to the frame of data itself Unchecking the Use darks box will force the system to proceed immediately with the first frame of data For the most accurate intensity data dark current subtraction should be always used However for qualitative work sample screening unit cell determination the skipping of dark currents can significantly speed up your work The screening results are summarized in the screening tab figure 25 and there are hyperlink buttons on the screening tab to enable quick access to unit cell finding related functions CrysAlisPro USER MAN
44. d acaba 17 4 8 2 CCD detector head Controller cccccccccceccccceeeeeeeeeeeeeeeeeeeeeeeseeeeeeeseeeeeeeeeeeeeseseneess 18 4 8 3 Cryodevice controller das 18 4 8 4 X ray generator controller 0 0 i i i i i i i i ii nananana nananana nananana nananana 18 4 8 5 ID duet geet A A A WO Oa ea Eed 19 4 8 6 Liquid nitrogen level controller nann nnnnnn annann nananana 19 4 8 7 Right Mouse Controls ooooonococccnnnncccncnnononcnnnnnnnnnnnnnoncnnnnnnnn nano nnnnnnnnnnnn anne nn nn nnnnnnnnnnnnnes 19 5 Normal operatpon ee RE RE REN REN RE REENEN EEN EE EE e ue d 5 1 Crystal mounting and centring EI 21 5 2 Rei AEII E E E A E E E A 21 5 3 Protein Screening ii 26 5 4 SHALE GY EET T E EE E E ETS 29 5 4 1 Strategy Calculation cia 31 5 5 Data collectionie a EEN 32 5 6 Stop all prO ES ES a ad 33 5 7 Resume experiment pre experiMent ccccccccnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnonenenenenenenenenes 33 6 Non standard Operation cssccesecesecesecnseensecnsenenenenseeessenssess OF 6 1 Start special collecti n a a eR hols eee aes 34 6 2 Append data collection 34 6 3 Multi Temperature Wavelength experiments nnnnnnnnnnnnnnnnrnnnrnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn nn 34 6 4 Data reduction NON Concurrent tt ttttsrt rrtt ttnt rs rrtt ttrt annn ttrt nn nnn tn mnene 36 6 5 Data reduction With Options cosest in aie a aaan a aa a A aa a a maa aa aeania 36 6 5 1 Tracking Crys
45. differences in the volume fraction of each twin You can also use interactive GRAL in conjunction with twin data The options Remove lattice absent reflections from output HKL file and Remove space group absent reflections from output HKL file will help assure that you have more complete data in your hkIf4 file provided your sample has space group extinctions that are detectable ET NOTE It is often a good idea to reconstruct some precession images to directly observe the extent of the overlap between twinned reflections This is also a fantastic teaching aid for presentations focussed on twinned data sets C rysAl i gPro CrysAlis_Pro_manual_v4 Page 60 USER MANUAL TWINNING DC PROFFITRRP TWIN 1 0 9 En Twin data finalization H Chak rrpprof files for twin finalization 7 Chemical Formula Component 1 EPT o exp_511_twinl rpprof oP 7 614 7 789 10 653 90 02 90 03 89 97 ESE DO ASADO Component 2 A exp 511 twinzarrpprof oP 7 612 7 790 10 652 90 00 89 96 89 97 Component 3 Browse None LATTICES Component 4 None LATTICES Eesen tes Fries Twin Finalization log file from previous run exp_S11 twinlog View foo equivalent Corrections m Twin decomposition scale3 abspack scaling uniformity empirical absorption Full overlap threshold ld Common scales for all twin components I Override overlap threshold for HKLF4
46. e Service Ulla id A ika a iaa A daian aiaa a ai 14 Figure 6 gt Status Nd A OTS Eed ia at ates 17 Figure 7 Key to device control eons tt ttnnnsat ttrt ttntt antt rtnn nanta nErenn mnnn 17 Figure 8 Generator ramping Control 19 Figure9 Pre experiment setup dialog window ccccceeeeeeeeeeeeeeeeseeeeeeeeeeeseeeeeeeeeeeeeeeeeeeseeeeeeeseeeeeees 22 Figure 10 CrysAlisPro GUI with active Pre experiment information Card cccccceeeeeeseeeeeeeeeeeeeeeeeeeeeeeees 25 Figure 11 Protein screening dialog ccceeceee cece ee ee ee nees ee eet anar eee eee aaa aaa aa eee eee aaa cece e ee eeeeeeeeeneees 26 Figure 12 Screening information Card 27 Figure 13 Protein peak hunting panel nono no nana 27 RU CEET 28 Figure Strategy Mod ule cvs A a scene eb devin ee it 29 Figure 16 Strategy advanced options pang 30 Figure 17 Strategy panel settings options subdialog ooooocccnnnnnnnnococcccncncconanononccnncnn canon cnn nn nnnn anar rn 31 Figure 18 Multi Temperature Wavelength ul 35 Figure 19 Enabling Manual Interactive Space Group Determination during data reduction 000001111004 37 Figure 20 Follow model options during data reduction oooooccncnnnncococccnconcnonnnonnnccnnnnn cnn nnn cn cnn nrnn anar ncnnnn 38 Figure 21 Lattice wizard panel including log windouw nana rn n cc nn 39 Fig re 22 Pealotable pan ls vio di ye ieee 40 Figure 23 Setup Calibration Experiments ccccccccccccccecec
47. e This is very helpful in cases where the X ray data are weak and the automated procedure fails Interactive GRAL is enabled by opening the Space Group Determination Options panel from the Data Reduction Finalizing window Figure 31 and clicking the appropriate radio button C rysAl i gPro CrysAlis_Pro_manual_v4 Page 51 USER MANUAL INSPECTION AND MANIPULATION OF DATA Space erpup determination options ry Refinalize data using space group cell Laue or lattice type required for consistent cif od_cif mtz output Iw Remove lattice absent reflections from output HKL file l Remove space group absent reflections from output HKL file C Run GRAL in silent mode E M Run GRAL in interactive mode Figure 31 Space group determination options When interactive GRAL launches the user is presented with a series of panels showing data relevant to space group determination The upper portion of the panel presents the experimental data Along the bottom are a series of radio buttons One of these options must be selected before moving on to the next panel When a panel first appears one radio button will have been selected automatically by the program The user must either confirm this choice or select his own choice based on his interpretation of the experimental data shown in the upper portion of the panel This process is continued until the space group has been assigned and the unit cell contents established A detailed listing of t
48. e Lattice wizard click on START STOP and select Automatic data reduction 6 5 Data reduction with options For problematic data sets it is often useful to process data with some manual influence over the settings used The data reduction will be performed using the unit cell in the memory at the time and so the user must make sure they are happy with the cell before continuing 1 If you would like to change the settings used by the profile fitting data reduction then click on START STOP and select Data reduction with options 2 The wizard allows the user to add lattice extinctions omit frames from specific runs and apply a variety of algorithm parameters and background calculations If the data is weak or has a high varying background the data can be improved by incorporating the Smart background tool A range of frames over which more localised background averages are applied must be chosen odd numbers only 3 When performing data reduction with manual settings ensure that you click the button marked Clear all data from previous runs 4 Sample wobbling in the beam can be accounted for by choosing options for either moderate or significant wobble 5 The edit special pars window contains some specialist options for high pressure experiments and enables the user to override the size of integration masks in cases where reflection overlap or mosaicity cause problems in the integration 6 Outlier rejection is not important at this s
49. e cell is displayed in the lattice wizard window 9 Sometimes a negative and non standard cell will result so we apply a lattice reduction by using the arrow button under the lattice transformation window 7 1 3 2 Drag Selection of Reflections and Marking them as Skipped 1 Make sure that the Select radio box and the Drag radio button are 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 Any skipped reflection will not be used when unit cell finding 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 e Unindexed reflections are now shown 7 1 3 3 Intensity Selection of Reflections and Marking them as Skipped 1 Select Skip filter from the top menu and select Intensity 2 A new 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 intensity filter box is
50. e experiment and this can be viewed at any time by the Plot button C rysAl i gPro CrysAlis_Pro_manual_v4 Page 18 USER MANUAL CRYSALISPR LAYOUT AND CONTROLS CrysAlis RED program options 1 0 31 i ax ccD Processing User access Distance calibration Instrument model Instrument model Il Monochromator Fonts Peak table Color codes Beam stop Angular limits Goniometer Runlistsize SEN Camera Compression Dark Generator Expi PA Cu Y Use generator ramping control at end of experiment exluding scripts After end of Exp a Aftertime MN 45m m Change generator state while ramping a Turn down C Turn off Apply for all future experiments Figure 8 Generator ramping control Clicking the right mouse button on the X ray button gives access to Generator options Figure 19 This menu controls automatic generator ramping before and after experiments The generator can be turned down or off either immediately after an experiment or after a period of inactivity If desired the generator will also turn itself up to operational settings user defined when a new experiment begins This facility is particularly recommended for Micro focus systems where keeping the tube at a standby power setting when not in use will prolong the lifetime of the tube 4 8 5 10 device control This 10 device control button brings up a window with access to software control of
51. ect data reduction results and refinalize with user corrections 4 power tool button utility contains a wealth of information about the completed experiment The Data reduction File contents area contains a summary of cell dimensions and orientation matrix used for integration along with a run by run listing of scan type angle ranges exposure time detector distance and the number of reflections collected in each run The Data reduction output tab contains the full log of the automatic data reduction process Starting with the generator settings and data collection temperature information is provided on any re measured frames profile fitting parameters outlier rejection scaling space group determination and final merging statistics allowing for a thorough inspection of all aspects of the data reduction process The Data collection output tab gives information obtained during the experiment specifically relating to remeasured frames and overflows Any problems encountered during the experiment will also be displayed in this log The Red Graphs window area displays a run by run visual summary of the scaling coefficients absscale a frame by frame plot of Rint and a number of comparisons regarding the coverage and or completeness of the data The Devices Plots tab contains graphical hardware information This includes Spellman SuperN a log of voltage and current values for users with a software controlled generator CCDSCAM a plot of CCD
52. ectory C Xcalibur data folder The user can choose to change both the root directory where the data are collected and the experiment name by clicking on the Browse for root directory button and typing the experiment name in the text box next to the label Name Pressing Return at this point may start the experiment It is not possible to overwrite existing experiments however the button Clear folder allows the folder to be removed such that the experiment name can be re used In the browse dialog usual windows operations such as rename delete etc are accessible under the right mouse button If you have any prior knowledge regarding the crystal it is a good idea to enter it in this window The chemical formula for instance will be carried through the program and used in the absorption correction ins file and summary report The chemical formula will recognise brackets and common abbreviations such as Me Et Ph C rysAl i gPro CrysAlis_Pro_manual_v4 Page 21 USER MANUAL NORMAL OPERATION OD Automode pre experiment 1 1 4 Pl Figure 92 Pre experiment AR m Path and user wn IER Cie ETT Experiment exp_1 in Folder C win32 exp_1 Setuser Experiment performer Sample Type Video Sample type Well diffracting GEET Coon BEEE crr Expected chemical formula Movie J Limit space groups taken into consideration Allnoncentrosymmettic
53. ects and removes lower background effects from the displayed image The look up table can be changed to increasing levels by repeatedly clicking on the icon which will cycle around to level 1 again after level 13 or by clicking on the arrow to the right of the icon This will activate a pop up menu from which the desired look up level can be selected The currently selected look up table is denoted with a tick mark on the left of the list 4 2 8 Colour table The colour table icon allows the user to select from the 11 different colour schemes used to display the diffraction image Repeated clicking on the colour table icon will cycle through the 11 options or the arrow to the right of the icon can be clicked on to provide a pop up menu for selection of a particular colour table The current colour table is highlighted with a tick to the left of the list entry 4 2 9 Zoom in Zoom in magnifies the main diffraction image Repeated clicking on this icon magnifies the diffraction image in x2 steps to a maximum of x8 magnification By default the image zooms to the top left hand corner of the image Use in combination with the zoom localiser 4 2 10 Zoom out Zoom out de magnifies the main diffraction image Repeated clicking on this icon de magnifies the diffraction image in x2 steps to a maximum of x1 8 magnification Use in combination with the zoom localiser C rysAl i gPro CrysAlis_Pro_manual_v4 Page 7 USER MANUAL CRYSALISPR0 LAYOUT AND
54. ed with a pre defined strategy and so it is best to carry out a pre experiment beforehand 1 Conduct a pre experiment as normal C rysAl i gPro CrysAlis_Pro_manual_v4 Page 34 USER MANUAL NON STANDARD OPERATION 2 Define a strategy to collect as much data as is required for full evaluation at various temperatures More data than normal may be needed in order to take account phase changes and other temperature effects 3 Save the strategy as a run file by clicking Export in the Edit runs window Temperature Wavelength experiments dialog 3 0 1 Path name SE See Mo experiment in folder C XcaliburData exp_20 Mo V Use temperature device control Information Number of temperature points 5 number of experiments which will be made for proper temperature points 2 Cryojet X Settings Options e Data reduction while collection data lv Mo Runlist Number of runs 4 total number of frames 331 detector distance 60 00mm time of Strategy E experiment 02h 14m e User message Tine fexerinr osh im List of temperatures for cryo experiments 2 0 1 List view summary Total of temperature points 5 Total of temperature points with experiment 2 Temperature Shield flow It min Sample flow It min Heater Do Exp Auto wait Wait Time 190 0 4 0 4 0 ON YES YES 15 0 190 0 4 0 4 0 ON YES YES 15 0 190 0 4 0 4 0 ON NO YES 15 0 0 0 0 0 OFF NO NO 0 0 Temperature unit
55. eeececeeeeeceeeeeeeeesesseseeseseeeeeseeeseeeseseseeeeeeeeeeeeeees 45 Figure 24 Experiment Archiving Facility nc nn cnn nn nana nn nn nn cnn rn nannnn rca 45 Figure 25 Powder power tool dalog nn a aa aE nnn nn nn cnn rn rra aa Rae 46 Figure 26 Powder power tool exposure time subdialon nn ncnncnn 46 Figure 27 Programs tab of CCD setup options pang 47 Figure 28 AutoChem settings pang 48 Figure 29 AutoChem information and 48 Figure 30 Data reduction refinalisation GU 51 Figure 31 Space group determination Options ccccccccccccecececececececececeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeseeeeeeeeeeeeaes 52 Figure 32 Lattice Wizard panel showing twin miormaton nano nc nncn rra nana nrncnnnnn 57 Figure 33 Ewald explorer twin flags and lattice visualtsatton nana 58 Figure 34 Data Reduction Tab Showing Twin Statistics 2 cccecccceeeeeeeeeeeecaeeeeeeeeeseeacaeeeeeeesetensnnaeess 59 Figure 35 Twin data finalization panel ccccccceeeeeeneceeeeeeeeeeeanaeceeeeeeeseceaeaeceeeeeeeseeacaeeeeeeeeeseesnaness 61 Figure 36 Ewald explorer with q vector overlay tool 63 Figure 37 Run list generator for DeCtris 0 cccccceeeeeeeneeceeeeeeeeeeeanaeceeeeeeescaaaaeceeeeesesecaaaeeeeeeeeeseneaaeess 65 Figure 38 Run list generator for d trek image Tomat 65 Figure 39 Run list generator for GAN 66 Figure 40 Run list generator for MAR 66 CrysAlisPro CrysAlis_Pro_manual_v4 Page v USER MANUAL INTRODUCTION 1 Introduc
56. egy intensity statistics and a proposed exposure time for the data collection which are all dependent on the initially specified resolution and sig values These can be altered during the pre experiment thereby updating the proposed strategy During data collection of the complete experiment the pre experiment result can be viewed by clicking on the arrow symbol on the data collection information card The pre experiment itself can be re opened at any time by locating it in the load experiment dialogue window or locating the pre experiment name par file in the experiment folder 4 3 2 Crystal Following the pre experiment and during automatic data collection the Crystal information card displays the current unit cell information the sample chemical formula and z value and machine model parameters Also displayed will be the Average unit cell from Proffit CrysAlis s cell refinement algorithm and the Final unit cell for selected space group This is important as for example in cases where the data collection strategy is based on a monoclinic cell with the B angle very close to 90 it is highly likely that an orthorhombic space group will be chosen and therefore the cell will be transformed as appropriate This window can be minimised and maximised as with the pre experiment information card Clicking on the arrow symbol at the top of the card gives access to several extra options including editing of the chemical formula
57. es 0 80 dd 55 00 I sig 20 00 DC Frames Runs in list 30 6 done 30 6 scan width 1 00 Max resolution curve lt ca Figure 16 Strategy advanced options panel The Advanced button opens an additional dialog window from which you can apply angular constraints on kappa theta etc used during the determination of a data collection strategy Cell centring can also be applied The strategy can also be limited to only use omega or phi scans The existing strategy can also be locked and added to and different exposure times can be chosen for each theta position especially useful for high and low angle positions when using Cu radiation After making changes click on OK followed by Calculate New Strategy in the main Strategy window This will cause the strategy module to re compute the best data collection based on the updated parameters The Single phi scan option found on the Advanced tab will produce a run with one phi scan in it The strategy computation will adjust the scan starting point and range so that the highest possible completeness is reached in the shortest amount of time It is intended primarily for proteins Also on the Advanced level you can specify a Reduction list for the hkl generator In this way you can collect data for a specific set of reflections provided you know their reflection indices You can generate the list internally or load it from a user file CrysAlisPro USER MANUAL CrysAlis_Pro_ma
58. etector mm button 8 The Scale exp time button allows the user to apply a scaling factor to the exposure time which is automatically chosen by the strategy software The Scale Exp Time theta shells button allows separate scale factors to be applied to pre experiments where there is more than one theta setting This is most important for Cu or high resolution Mo experiments For example if the exposure time is 5 seconds for all 6 runs of a Cu experiment collected to 0 84 A setting scale factors of 2 and 8 will give 10 and 40 second exposures for low and high angle theta positions respectively C rysAl i gPro CrysAlis_Pro_manual_v4 Page 23 USER MANUAL 10 11 12 13 14 NORMAL OPERATION The automode settings area of this window allows the user to put some restraints constraints on the final data collection strategy The Auto Start tick box when selected instructs the software to automatically continue with the full data collection at the end of the pre experiment Record Movie during dc if activated will automatically record a movie of the crystal at the start of the data collection This movie can be used later for face indexed absorption correction if required The goniometer is driven to the lower position such that the phi axis and crystal are orthogonal to the video microscope A series of jpeg images are then recorded at intervals user defined between 1 and 6 degrees 6 being the default about phi givi
59. etting The Full Overlap Threshold defines the overlap level below which partially overlapped reflections of twins are partitioned into their component contributions The parameter can be set to anything between 0 and 1 with 0 8 as the default value Changing this threshold may help in cases where no structure solution can be obtained or in cases where refinement with the HKLF5 twin data file yields no improvement A good example is a case where two lattices are present but look to have little or no impact on one another In one such case with 15 000 reflections divided between two components only 110 of these were overlapped in some way However this was enough to cause problems in refinement of the Flack parameter for assignment of absolute configuration Setting the overlap thresholds to zero and using only the HKLF4 file of the major component for structure refinement fixed the problem completely This was effectively accepting no overlap of any kind and so removing any effected reflections from the HKLF4 data file Additional features unique to twins are as follows The Separate scales for all twin components option allows for the application of different scaling models for each twin For some twins this results in a significant improvement of data quality The Output multi HKLF4 file option will attempt to produce a complete data set by combining reflections from the twin components The reflection intensities are suitably scaled so as to reflect
60. export 0 500 Seperate scales For al twin components m Numeric and spherical absorption correction T Apply absorption correction Oferes i4comers Zledues 2Z T Apply nja Crystal With Ne dreemt Helga Show face list Export options m Data items in hkl files HKLF4 HKLFS Filters and lattice extinction filters m HKL file options dyalielfna mi O71 gt IT Beam path information for absoprtion correction special Formats T Resolution heat En DOE Fist res its r Use reflections component 1 only ST Nofiter use filter for Pastice Output mukti HKLF4 file Dace ter Re R iwae Merging E Export CIF Fle 7 Add hid data to CIF HKLF4 only SE IV Merge data using the same Laue class p Dee friedel metes I rima as equivalent IV Space group determination Options Fins I Remove outliers different Laue class kee zj F Gompleteness 0 80 48 Edt res d I Update overwrite hkl files in WinGX Olex2 orfand AutoChem Folders T Structure solution Autochem ESTES r Figure 35 Twin data finalization panel 9 6 Indexing problem twins If the automatic algorithms fail to index the twinned compound try to index it manually using the drag index feature described in the Ewald module To help you the stereographic projection provides a clear way of finding lattice planes Rotate the stereo projection diagram around using the arrow keys until a lattice line is aligned vertically or horizontally A maximum will appear in the histogram bars at the
61. g click Yes Once the twin components are found information about them is displayed in the lattice wizard main panel C rysAl i gPro CrysAlis_Pro_manual_v4 Page 56 USER MANUAL Lattice wizard 1 0 32 Lattice wizard LATTICE Current cell f 1522 7 2 2304 8 9 1822 8 f 67M 8 20 25K 8 78 142 9 422 217 Lattice reduction selected cell 6 1581 8 3304 9 1824 66 6703 99 3563 78 1421 2P 31 reduced cell 6 1581 8 3304 9 1824 66 6703 89 3563 78 1421 422 0 Twin information 1 6 1583 8 3310 9 1814 66 668 39 34 78 134 422 0 2 6 1630 8 3379 9 1886 66 689 39 348 78 110 423 0 1 Total 59401 52 5 Separate 4987 48 5 Overlapped 414 4 0 2 Total 4050 48 1 Separate 4536 44 1 Overlapped 414 4 0 Unindexed 348 3 4 PEAK TABLE Peak hunting tahle UB fit with 5400 obs out of 10285 total 10285 skipped 3 52 50 INSTRUMENT MODEL Goniometer beam 0 07329 alpha 50 10899 beta 0 02536 om zero 0 04783 th zero 0 13434kazero 0 14880 Detector xrot 0 30412 y ot 0 96001 x Cen 1038 07954 y cen 294 65209 distance 54 95368 Wavelength Cu Ang Al 1 54056 A2 154439 B1 1 99222 Figure 32 Lattice Wizard panel showing twin information 9 3 Visualising twin components To visualise twin matrices TWINNING wald explorer ciprocal space fine instrument model winning ao Leno oad zeg Save E information E information a a Inwarping oo images BI window gt lis G
62. ge tables Completeness in 1 Full sphere P1 2 2 F 100 2 100 20 2 1 8 a 18 5 g 80 2 80 a 2 e Z ais S g 60 as 60 2 9 al S SU 14 S S 40 14 8 4 3 S E 3 20 1 E 20 12 g E fil bd D T 1 0 B D T 1 0 0 200 400 600 800 1000 1200 1400 0 200 400 600 800 1000 1200 1400 Frame Frame WOREN RER The strategy module displays two graphs The one on the left depicts completeness and associated redundancy related to the Laue class for the calculated strategy and the one on the right illustrates the total coverage of the full sphere and associated redundancy CrysAlisPro USER MANUAL CrysAlis_Pro_manual_v4 Page 29 NORMAL OPERATION These provide a quick and easy graphical feedback Alternatively you can display the corresponding statistics tables by pressing the appropriate radio button just above the graphs The chosen exposure time and corresponding scan width are displayed in the top bar of the window The strategy module provides access to a number of user parameters which can be edited These parameters include resolution target max resolution of the data Laue class Friedel mates are equivalent and detector distance If you change any of these parameters you must then click on the Calculate New Strategy button which will cause the strategy module to re compute the best data collection module based on the updated parameters Friedel mates are equivalent should not be ticked if the sample is known t
63. he content of each panel and possible user responses follows 1 First the lattice centring is determined A table of statistics allows the user to check the selection If the user wishes to choose an alternative then the relevant radio button can be selected by clicking on it and then Apply can be clicked to move to the next step 2 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 3 The space group power tool provides a list of possible Bravais lattice and highlights in blue the programmes preferred choice Clicking on Apply will accept the choice however any one of the alternatives may be selected by clicking on the option in the text box and then clicking Apply 4 Following Niggli reduction the centring of the cell is re examined Click on Apply 5 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 button and clicking on Apply C rysAl i gPro CrysAlis_Pro_manual_v4 Page 52 USER MANUAL INSPECTION AND MANIPULATION OF DATA 6 Space group now examines the systematic absence exceptions where applicable and provides a statistical table for user confirmation of its preferred choice of space group The user can accept the preferred choice which is highlighted choice by clicking on Apply or select from one
64. he exposure times generated for the main data collection before proceeding 15 16 17 If Autochem is installed this can be activated for concurrent data collection and structure solution refinement by ticking the box in the pre experiment window When screening crystals to avoid inputting pre experiment settings multiple times use the Recall previous Pre experiment settings button in the bottom left of the window Then either clear the folder or change the experiment name and click Start Click on the Start button to continue e The dialog will close the pre experiment data collection will begin and a pre experiment information card window will open on the right hand side of the GUI Within this card window are displayed the user defined settings from the previous dialog and the unit cell of the crystal being measured e Ae soon as one frame has been measured the software will attempt to find the unit cell crystal lattice and evaluate the average sigma spread with resolution this last is used to determine the best exposure time for the data collection Each of these will be displayed in the Pre experiment information card and will be updated after every frame C rysAl i gPro CrysAlis_Pro_manual_v4 Page 24 USER MANUAL NORMAL OPERATION e At the end of the pre experiment the strategy module will open and will display the preferred data collection strategy based on the unit cell detector distance Laue class
65. he k direction so both together define the hk0 layer Define a name for the image in the Output name box and then click OK It is possible to define several layers to be generated as part of the same process 7 If required click on the tick box marked background subtraction Click on Next 8 Click on Finish 9 The defined layer or layers will now be reconstructed A process box appears and the reconstruction can be seen in the image area when you press the layer radio button The process box disappears when the process is complete Images can be opened for viewing in the image list menu on the image control icon bar A reciprocal lattice grid can be overlaid on procession images by clicking on Unwarp reciprocal lattice grid in the drop down menu next to the CCD RED USER button in the image control icon bar 7 2 Service The service utility window also provides access to the diffractometer calibration experiment tool This facility should not be needed other than during installation and service visits but if persistent problems are encountered the user may be advised to recalibrate the instrument If required an automated procedure is normally used with data collected at two different detector distances near and far on a test crystal an ylid test crystal is provided with the system With Gemini and dual wavelength SuperNova systems the procedure is carried out for both molybdenum and copper sources In order to save time calibration
66. his information can be found in the Help menus under Reference section Version news CrysAlisPro users are greatly encouraged to report any software bugs by sending details to XRDSupport agilent com Only by receiving bug reports from experienced users can these be successfully identified and repaired Ideas for software improvement are also very much welcomed and all are considered when creating new modules for future editions of CrysAlisPro C rysAl i gPro CrysAlis_Pro_manual_v4 Page 2 USER MANUAL STARTING AND CLOSING CRYSALISPRO 3 Starting and Closing CrysAlisPro 3 1 Starting CrysAlisPro To start CrysAlis double click on the icon on the windows desktop When the programme is started on a PC connected to an Agilent diffractometer CrysAlisPro will start up in CCD diffractometer control mode online and will include the functionality for control of the CCD device control and CCD status feedback On start up the software initialises the hardware Commands cannot be accepted until all hardware initialisation procedures are complete Wait until the CCD status is shown as ready before issuing commands If a second version of CrysAlis o is started when a version of CrysAlisPro is already open and controlling the diffractometer the second version will open in data reduction offline mode only without control of the devices and diffractometer control and will ask the user to select the experiment that they want to work on from
67. ignificant amount of time When long exposure times are used e g greater than 60 seconds employing a kappa limit of 80 to 80 degrees will prevent any ice which may have formed getting close enough to the beam in order to be seen in diffraction images Simply select One kappa range restriction in the Advanced strategy window and then calculate a new strategy In most cases this will not affect the total data collection time but will dramatically reduce the chances of ice diffraction Various methods can be used in order to minimise the time taken for data collection One of the most effective is to slightly reduce the complete data limit Clicking on IUCr limit will reduce the figure from 100 to 98 5 This may seem a small drop but it has a dramatic effect In most cases the time for data collection will be reduced by approximately 20 30 This is because the extra reflections required for 100 completeness are in extreme places requiring many extra frames to be collected Adopting this tactic will also significantly reduce the redundancy figure so although it is a good time saving technique it is better to collect 100 data if time permits 5 5 Data collection The data collection will start automatically using the strategy or user constraints After 25 frames the data reduction will automatically start followed by automatic frame scaling automatic absorption correction automatic space group determination and ins file creation The
68. image to be considered It is assumed that all frames between these two are available 3 Save the file 4 You wil be prompted for entering some critical parameters usually default values are OK as they are taken from image headers 5 Finally a new CrysAlisPro instance will be launched with the DECTRIS data set added to the experiment list p First de DECTRIS de file 0001 ima C dota Piatus inO 1d _s 3 inO1d_s 3 00001 cbf r Last de DECTRIS de fle Browse CA data Pilatus inO1d_s_3 inO1d_s_3 00720 cbf Help Cancel Save run fe Figure 37 Run list generator for Dectris 11 2 Rigaku CrysAlisPro now supports processing of Rigaku d trek image format frames Run list and aliases file generator for DTREK data collections Th dialog allows you to quickly generate a run file and aliases fils for the data reduztion of a DTREK date sell 1 You select mage name1001 img 2 You select the last image to be consicered Itis assumed that all frames between these two ars available 3 Save the file 4 You will bs prompted for entering some crtica paramsters usualy default values ae OK as they are laken from mage headers 5 Finally a new Cys lisPro instance will be launched with the DTREK data set added to the experiment list NOTE Using Crys lisPro you can process only OTREK images fron Diamond Rigaku de ectors y First de DTREK de file 1001 img y Last de DTREK de file Figure 38 Run
69. iment time with 100 completeness e Complete data for twins Experiment Strategy 1 1 4 automode suggests exposure time t 8 7sec scan width 1 0 deg Experiment Strategy Pro IS Figure 15 Strategy module Unt cell For Strategy Calculation Cell 8 791 8 9 818 8 11 378 13 105 00 8 103 30 9 104 49 8 872 1 aP P lattice Y 100 00 54 of 54 reflections r Strategy parameters m Time prediction based on data to 0 80 Ang default individual merged Resolution Theta 2Theta 0 800 The same time for all theta positions time Yjsigma I sigma C Different time for each theta positions e7 20 00 Tas ol e Ge soi N Filtime individual meraed Fillifsigma Hammer Hee v Y Friedel mates are equivalent uncheck For high quality absolute configuration data 40 96 40 96 ESCH Detector Distance 55 00 Advanced s1 00 111 00 bee bes 23 53 Strategy mode Total I sigma 20 00 30 18 Scan width 1 00 Complete data default mode y Accuracy depends on R t plan t pre t aver scan time Here R 1 3 For R gt 30 consider repeating pre exp with longer t or limit 100 0 wc men max 100 00 O tao Lao Generates runs that reach p Settings Options p Current Strategy No runs frames 26 1582 Calculate New Strategy Total experiment time 10h 20m Expected experiment finish time Sat May 08 00 36 52 2010 Completeness Coverage curves Completeness Covera
70. lEXE This is an executable folder which contains the ODShel software This is a shell program for structure solution and refinement A typical experiment folder will have the following directory structure Experiment root C Xcaliburdata expname This directory contains important experiment definition files such as par run ffiinffit ffi tab rrpprof ccd geo gon sum cif ins hkl etc all of which are required in order for the experiment to open and function properly Expinfo directory expinfo This contains ini files with information regarding some of the unique settings for this experiment Frames directory Contains all the frames in img format Log directory Contains logs for CCD RED and USER threads in txt format Movie directory This contains jpg images collected as a rotated movie of the crystal Plotsdc directory C rysAl i gPro CrysAlis_Pro_manual_v4 Page 67 USER MANUAL APPENDIX dat files contain information logged from the various hardware components of the system Plotsred directory dat files contain information on scaling Rint and other integrated data output functions Struct directory This is set aside for storing structure solution and refinement files Tmp directory C rysAl i gPro CrysAlis_Pro_manual_v4 Page 68 USER MANUAL Agilent Technologies Inc Printed in Poland September 2010 2 Agilent Technologies
71. lay tool in the Ewald Explorer module 1 In the menu bar click Windows and select Show q vector overlay window Figure 17 2 Up to 3 q vectors can be defined To begin click on Set overlay for q1 and either Edit the a b and c coordinates with max m order as 1 to start or use the Interactive adjustment to move the purple overlay spots in the Ewald image 3 The q vector should be defined so that the overlay spots line up well with what are considered to be satellite reflections C rysAl i gPro CrysAlis_Pro_manual_v4 Page 62 USER MANUAL INCOMMENSURATES 4 Once an initial overlay has been set drop back to the lattice wizard and select the Incommensurates Quasi crystals icon The order m max hkl integer tolerance crithkl and q vector coordinates from the defined overlay are already input so simply click on OK Exit Show Skip filter Flags Tum 90deg Turn 90deg Clear Drag Cell Properties Tools Windows Help P R H Rotation axis xO cyl Ct Slow rotation 4 gt 0 200 Fast rotation mm Zoom BR Histograms Along a Set overlay for Y ql 0 184 0 000 0 321 m 4 Edit Along b Color legend a red b green c blue daa n ction views Intensity skip off Ge Note Beware oftriklinic samples gt Dragindex only works in planes isolated in the stereographic proje Figure 36 Ewald explorer with q vector overlay tool The values of the q
72. list 4 2 16 View The View icon switches between views Refer to section 4 6 for more information Press the view icon repeatedly to cycle through the CCD RED and USER displays The header window bar is updated to show which view is being displayed C rysAl i gPro CrysAlis_Pro_manual_v4 Page 8 USER MANUAL CRYSALISPR0 LAYOUT AND CONTROLS In CCD view the images coming off the machine are displayed but it is not possible to do anything with them when collecting data In RED view visual feedback of the data reduction is displayed but it is not possible to do anything with the images when collecting or reducing data In USER view you can read in an individual image or play through a movie and perform various analysis tasks whilst data collection and reduction are being performed and updated If computer is offline then only RED and USER are available Reference frames if collected the beamstop mask a reciprocal lattice grid overlay for precession images and background subtraction options can be viewed by clicking on the arrow to the right of the CCD RED USER icon 4 3 Information cards al 2 The information cards appear as tabs located on Ho information available the right hand side of the screen To select a card click on the text The arrow symbols on each information card gives access to several extra features Crystal Edit chemical formula Edit comment Show crystal movie Edit crystal shape Add experimen
73. mal operation CrysAlisPro is designed to work in automatic mode The automatic mode consists of the following three major components 1 Pre experiment a short experiment to determine the X ray diffraction quality of the crystal 2 Strategy determination of the best method of collecting the data under certain settings 3 Data collection data reduction and finalisation Before running a pre experiment it is advisable to check the generator settings and the Cryojet control to ensure that the hardware is optimally configured for an experiment To check these settings click on the Cryo and X ray buttons 5 1 Crystal mounting and centring F12 To mount and centre a crystal press the F12 key This transfers goniometer control from the PC to either the manual control box inside the cabinet or to the abs pilot module in SuperNova systems Centring of the crystal is easiest when the goniometer is in the lower position This same facility can be accessed by clicking the Mount Sample button in the pre experiment window A detailed procedure for crystal mounting is described below 5 2 Pre Experiment 1 To start the auto mode click on the START STOP button in the top right corner of the GUI A dialog will open giving the user a range of options 2 Click on START NEW and a set up window will open By default an incremental experiment name such as Exp_1 Exp_2 etc will be assigned and a new data folder will be created in the root dir
74. ment and in terpretation of difficult especially modulated structures Developed by Vaclav Petricek at the Institute of Physics in Prague this software is the industry standard when working with incommensurate modulated structure data sets 4 4 15 Autochem launcher Autochem is a CrysAlisPro plugin for automatic structure solution and refinement and is a purchasable option Autochem is designed to work concurrently during data collection but it can also be activated post data collection by clicking on the power tool icon Autochem data files are located in the autochem_experimentname folder within the Struct directory More details on using AutoChem are found in Chapter 7 4 5 Diffraction image display window The majority of the CrysAlisPro GUI is taken over by the image display area which provides for the display of X ray diffraction images These can be displayed in a variety of sizes accessible through the zoom in out functions 4 6 Window header bar The window header bar is used to display the current thread displayed in the main diffraction window There are 3 threads in CrysAlisPro 1 CCD thread used by the diffractometer New diffraction images are displayed in this thread as they are collected and read out from the CCD detector Whilst the diffractometer is collecting data functionality in this thread is limited to adjusting the colour table look up table resolution rings STOP and viewing the information cards
75. n of a MAR data set 1 You select an image name_001 mar_ext 2 You select the last image to be considered It is assumed that all frames between these two are available 3 Optional repeat 1 2 for 2nd theta setting 4 Optional change parameters relevant for the experiment compare with your experiment note header info 5 Press OK to create run and par file and new experiment description and launch new instance of Crys lisPro m Theta 0 D Data Mar Roche b2 b2_1_001 meed f Theta settings Header MARMCCD 0 0 00 t 0 00 k 0 00 pe DI E 1 00 dd 86 00 w 0 70 0x 1536 00 0y 1536 00 pixs 0 07324 Theta deg 0 00 Edit ko 57 00 kt 0 00 kk 134 00 kp3 0 00kpe 1 00 D Data Mar Roche b2 b2_1_360 meed Header MARMCCD 0 0 00 t 0 00 k 0 00 ps 359 00 pe 360 00 dd 86 00 w 0 70 0 1536 00 oy 1536 00 pixs 0 07324 ko 57 00 kt 0 00 kk 134 00 kps 359 00 kpe 360 00 r Theta n r Theta settings _ Browse 1st _001 mar ext n a n a Theta deg n a Edit Browse last n a of runs n a Edit n a of runs 1 Edit r Special notes Informations Image correction will be done with width of 10 Detector distance mm 86 000 ASE No MCCD header Please update missing values Pixel size mm 0 073 Edit Mest det Le ce Name of the experiment b21 Beam origin X pix 1536 000 Edit Wavelength Ang 0 700 Edit Edit Beam origin Y pix 1536 000 Edit r Experiment interpretation
76. ng 360 degrees of photos around the crystal Set max time allows the user to put a maximum time constraint on the data collection For instance if 15 hrs is input the data collection will be limited to finish within 15 hours Note this does not take into account the additional time incurred by overflow remeasurements Experiment type The default here is Use Laue symmetry where this means use the automatically determined strategy giving 100 completeness The user can also select hemisphere sphere or quadrant Target resolution This is the maximum angular resolution or d value to which the data will be collected Set target I sigma This is the target sigma required for the data being collected and impacts the estimated exposure times required for data collection The I sigma estimate is based on an analysis of the intensities of reflections recorded during the pre experiment and on theoretical predictions of the scattering power of the sample as a function of resolution The purpose of including the theoretical data is to correct the overestimation of count times observed in those cases where intensities close to the resolution limit chosen for the pre experiment are very weak or not observed at all This can happen when the count time used for the pre experiment is too short NOTE EJ It is always best to choose a reasonable pre experiment exposure time plus it is advisable to always check t
77. noncnnnnnannnnnncnononnnnannnnnnnnonnnannnnnnnnnnnnnnnnnrnnnnanenos 53 8 5 Crystal shape modelling face indexing 2 s ecceceeeeeeeeeeenceeceeeeeseeeeaeaeeeseeeseeseneeeeeeeess 53 AAA tatoo as diaclemoet ngs sean aabentae E 55 9 1 Automatic twin lattice finding 0 ccceceececneceeeeeeeeeceaeaeeeeeeeeeecaaeaeeeeeseseseneaeaeeeeeeeeeeeenaees 55 9 2 Manual twin lattice mdexvatton tn tnneertrn rt rtnnasrn ttrt rtnnrnnn nt tnnnnnn tnne nenna 56 9 3 Visualising twin components cinc 57 9 4 Data reduction of a twinned data set 58 9 5 Twinkdata finalization 2 iaa 60 9 6 Indexing problem Iwins nn nn Ennn nn nAnn Annn EnEn Ennn nananana nnna 61 10 WG mime SUN ACES ois ii ee Eege 62 11 External Detector Frame Formats c sccssccsseeeseeseeeseneseneneneeenees 65 11 1 Decidir aie atone cies EE 65 11 2 e WE EEEE EE EEEE E EEE A EATE T e TEE ET S E mean 65 11 3 SAM AS A EE een 66 11 4 MAR a ns rd de Ee ain tact ed et cee Led 66 PA eee ee ee ee 67 Ne eleng TC 67 CrysAlisPro CrysAlis_Pro_manual_v4 Page iv USER MANUAL CONTENTS Table of Figures Figure 1 CrysAlisPro layout and Controls 0 csscseseseseseeeseseseseseseseeeeeeeeeeeeseeeeeeeseeeeeeeeeeseeeeeeeeeeeeseeees 4 Figure 2 Key to image Control ICONS oooononccccncnnncncnnononcnnnnncnnnnnnnnncnnnnnnnnnnnn nn rn carr nn enn nn nn nr nn rana mn nc nn rra 6 Figure Information Cards iii i 9 Figure 4 Key to power Ool EONS ic dadas 12 Figur
78. nt An image is built up as the frames are processed and a powder graph is displayed upon completion Specialist commands that can be used to process specific areas of a powder diffraction image include powder azim and powder radial The areas defined with the command will be greyed out on the diffraction image concerned Full details of how to use these commands are available in the CrysAlisPro help utility under Command Overview Any output powder plots are stored in the experiment root directory as an experiment_powder dat file This is in text format and can be input into many specialist powder applications More details on powder diffraction features can be found in Chapter 7 4 4 8 Multiple Temperature Wavelength Experiments This icon accesses a module where experiments can be set up combining multiple temperatures and both Mo and Cu wavelengths The facility is very simple to use and full details are given in Chapter 6 4 4 9 Single images When using the CCD thread this utility allows the user to take still images omega and phi scans as well as axial photographs When in either RED or USER threads only the Axial photographs option is available More details on the features available in single image mode can be found in Chapter 7 4 4 10 WinGX launcher This icon sends a command to launch the crystallographic structure solution and refinement software WinGX where installed The current experiment name and folder defined in Cry
79. nting press the arrow button to the right of the main peak hunting icon The menu options are e Peak hunting with user settings e Auto analyse unit cell Under the peak hunting with user settings menu the Smart peak hunting option is particularly useful This will generally find 20 30 more peaks but without picking up too much background noise CrysAlisPro USER MANUAL CrysAlis_Pro_manual_v4 Page 39 POWER TOOLS 7 1 2 Unit cell finding Use the unit cell finding icon after you have finished peak hunting Press the unit cell finding icon and the computer will automatically determine the unit cell Information will appear in the top left of the window More options are accessible by pressing the arrow button to the right of the main unit cell finding icon These include e Unit cell finding with cell options e Solution selection unit cell finding e Search for known unit cell e Set orientation matrix by hand e Search for smaller unit cell volume Unit cell finding with options allows the user to set limits on the minimum and maximum axis lengths to search for This is also the utility used for twin lattice finding see Chapter 9 Solution selection unit cell finding gives a list of cells considered by automatic unit cell finding If looking for a specific cell which is not output by automatic cell finding it can often be found in this list Search for known unit cell allows the user to input cell dimensions and search using a spe
80. nual_v4 Page 30 NORMAL OPERATION If you have bypassed the pre Experiment but wish to set up crystal movie generation and AutoChem you may do so by launching the Strategy module and pressing the Autochem Movie Cryo Red button located in the Settings options block of the Strategy panel Experiment options 1 0 1 FJ xj m Parameters Expected chemical formula C23 H17 N 02 E Attempt AutoChem IV Record movie during dc Step in deg 6 Auto ervojhot device shutdown on experiment completion Y Data reduction while collection data after 25 of frames Information Figure 17 Strategy panel settings options subdialog If you are planning to process the image frames using an independent data processing software such as MOSFLM you will need to ensure that the frames are always collected such that the scan rotation axis is perpendicular to the beam The easiest method of ensuring this is either to select omega scans only or to fix the kappa angles To do this click on the Advanced button and tick on use kappa limits Click the one range radio button In the min box type the number 0 and in the max box type the number 0 000001 Click on OK which will close the window Now click on Calculate New Strategy to calculate the updated data collection strategy If you want to change the automatically determined strategy click on the Manually Edit Run List button This will open the runlist editor From here you can alter the proposed data
81. o be or suspected of being chiral non centrosymmetric This is particularly important in cases where absolute configuration is the main focus of the experiment Strategy Advanced Options 1 0 9 EN xj Constraints gt Axes UB scaling T Use phi scan I Use axes I Use constraints c Constraint cell 8 48 9 40 10 94 90 0 90 0 90 0 CF ER NOTE The used UB is symmetry constraint Volume is not scaled E Lockstate c tric Unlocked Locked runs in edit runs are kept strategy appends new runs c Unlocked runs in edit runs are destroyed default mode Symmetry options i 40 0 0 0 I Use additional theta I Use theta constraints Overlap evaluation JetjHP Cell Reduction list I Use JetShadow Use reduction list e Overlapped area area of E P overlapped reflections area of all ia Generate C EES reflections bone Range res T Evaluate overlapped area Fr Lond nin ma Pre experiment inf gt 1 LD CELL Nigg 44 amorthic triclinic P e an Mosaicity from preexp 100 000 54 54 Single phi scan recommended for proteins Resolution Current max res 0 792 max full res 0 818 in dd 55 00 Max res is not computed yet e1 110 e2 1 11 e3 11 76 Mosaicity defined by user 8 791 8 9 818 8 11 378 13 105 00 8 103 30 9 104 4X8 Y 8721 INT N 141 min 0 80A max 6 314 Ysig 21 53 obs 62 4 I sigo 33 78 strategy predicted time for I sig 20 00 9 3 TIME initial time column predicted for r
82. o the computer and prevent use of the remote control 4 Click on Movie or Video Snap if you want to record a movie of the crystal as it is rotated through 360 or a picture of the crystal 5 The information on whether the crystal is a protein or small molecule the crystal size cell volume diffraction limits and if it is a low temperature data collection are used to adapt the pre experiment which will be collected you can see the changes being made in the experiment area in the middle of the dialog window By defining the crystal sample as Protein or Small molecule certain default parameters are employed throughout the pre experiment data collection and data reduction For example by choosing Protein a Smart background calculation is employed in data reduction whereas for Small molecule the default is for an Average background calculation Protein data reduction also involves a default 2 cycle 3D data reduction 6 The pre experiment will typically carry out a 5 20 minute data collection in order to determine the crystal quality and to gather information required to design a suitable data collection strategy For Mo this pre experiment employs 3 orthogonal runs of 5 frames each For Cu where typically several theta settings are employed there are more runs and more frames to collect 7 The pre experiment run list can be edited by hand using the de editruns button A preferred detector distance can also be chosen by clicking on the D
83. of the alternative choices when present 7 Finally a ins file is prepared for use with structure solution programs The user can edit the molecular formula and Z number in the relevant boxes Clicking on Test allows the user to check the formula weight absorption correction p 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 Finish creates the ins and hkl file and closes the power tool 8 3 Filtering data The Filters menu enables the user to omit specific runs frames intensities theta values Lie values and a variety of other measures from the refinalised data In the filters menu click Add and then set up a filter using the rejection condition and specific value The most useful and commonly used filters are for Run Run frame d value and Rint To omit a particular run simply use the equals condition and choose the run number that you would like to remove Severe data scaling may be the reason for removing a run and so the run number can simply be read from the absscale plot To omit a single frame use the run frame filter run number frame number To omit blocks of frames perhaps due to icing use the same filter with two conditions For example to omit frames 11 to 20 of run 2 use the condition gt 2 10 but then add a second condition lt 2 20 y NOTE Filtering data will inevitably lead to a
84. of typical usage are available by typing COMMAND HELP in the command line power tool There is also an options button included which provides access to the machine and software setup The command line power tool can be closed by clicking on the Close button located in the bottom right hand corner of the window 4 4 4 Inspect data collection and reduction results By opening the Data finalisation window the user can access the results of the automatic data reduction process via five tabbed window panels The Data reduction File contents area contains a summary of cell dimensions and orientation matrix used for integration along with a run by run listing of scan type angle ranges exposure time detector distance and the number of reflections collected in each run The Data reduction output tab contains the full log of the automatic data reduction process Starting with the generator settings and data collection temperature information is provided on any re measured frames profile fitting parameters outlier rejection scaling space group determination and final merging statistics allowing for a thorough inspection of all aspects of the data reduction process The Data collection output tab gives information obtained during the experiment specifically relating to remeasured frames and overflows Any problems encountered during the experiment will also be displayed in this log The Red Graphs window area displays a run by run visual summar
85. ofile fitting used Figure 34 Data Reduction Tab Showing Twin Statistics TWINNING In the data reduction tab above there is the line Overlap limit for HKLF4 export 0 8 This means that any reflection which is greater than 80 overlapping with another reflection is discarded from the HKLF4 files This aids structure solution as some reflections are so severely corrupted that it makes finding a solution almost impossible The 80 figure works well in most cases but this can be changed by performing twin finalization see section 9 5 The Decomposed twin data statistics give Rint values for each component but these values are sometimes higher than might be expected This is due to the effect of removing badly overlapped reflections The Rint value given under Twin HKLF5 statistics for overlapped observations gives a very realistic indication as to the success of the twin data reduction A more detailed output can be found in the Command Shell Here Rint values are displayed for both isolated and overlapped reflections in the HKLF5 output file This file is labelled name_twin1_hkIf5_merged hkl As with HKLF4 files the twin data file incorporates an overlap threshold of 0 8 or 80 default value However no reflections are discarded but this is the limit at which reflections are either treated separately or as one single entity Once a structure solution has been obtained and refinement is at the point where no further improvement c
86. on in CCD C tumo Calibration mode T Lattice typa Kaz Leen 2 max cx Narie of rafiettions to find 2000 1007 for iori cid rason sees Constraint E Colect extra data for better structure refinement 7 IRSCH A Exposure tine the same for al theta positnns 2 05 Detector dstancesi65 00 Scan Wien H JE renger40 0 Scan width 2 0 e man 100 Epoo tre tho same for al theta postions 2 0 Detector gen 9 Scan me renge 40 D Scan width 2 0 Automanc Food field correction calbraton F Bun flood calbration Fle C xcallbur corrections e_14 Aoodcu_turnel_inf_s_14_050908 ffi i Exposure time the same for al theta positions SE Tee deg d z un same el ewf Sp af SE e Exposure time the same for al theta positions 2 05 Detector distance 2 00 Scan j w SH i di e angen Scan att ER A Automate flood field correction calibration E Run flood calbeation Fie C yicalbur corrections a_14 floodmo_tunnet_inf_a_14_050906ffi User message Ready TE Er o catbration Tue dun 22 11 51 58 2010 tht nin a Em Figure 23 Setup Calibration Experiments There is also a Make zip tool Users can zip up complete experiments into a single file for easier archiving or to send to the software team for problem resolution Experiment back up for service analyse 1 0 9 Source Experment ties Type of scenario E Batic cod geo par run first frame RED CCO compac
87. on the run file for the experiment making sure to distinguish between the run files for the pre and main experiments C rysAl i gPro CrysAlis_Pro_manual_v4 Page 33 USER MANUAL NON STANDARD OPERATION 6 Non standard operation 6 1 Start special collection This utility is located under the menu accessed from the START STOP button and is used for experiments generated without a pre experiment For example if the user would like to use a previously generated run list this can simply be imported and re used Generally speaking it is always best to conduct a pre experiment with any new crystal But in certain circumstances especially when the same experiment is repeated under differing conditions pre experiments are not required To use this facility effectively a cell must be defined or a previously generated strategy imported For the latter this is achieved through the Edit runs utility by simply selecting Import If the strategy has been used before the frames will be considered done and so this must be reversed Select Refer to all runs then click Invert done runs Return to the strategy window and choose Completeness to view your strategy To find a previously defined cell click on the Lattice Wizard button and either load a peak table or parameter file from a previous experiment The cell finding tools can then be used as normal On returning to the strategy module the chosen cell will be quoted at the bottom of the screen
88. peak can be obtained to aid the user in the evaluation of the quality of the crystal Ideal peaks should have a narrow sharp profile with no obvious humps on the side The profile is displayed in a separate semi transparent window which defaults to display in the top left corner of the diffraction window This window can be resized by dragging out in the bottom right corner of the window It can be closed by clicking on the X in the top right corner and it can be moved by holding down the right mouse button with the cursor over the window and moving the mouse The profile can be saved as a bitmap or jpeg via the floppy disc image in the top right corner of the semi transparent window The data can also be saved as a text file or copied to the clipboard by clicking on the arrow symbol The semi transparent window means the profile of peaks can be drawn through the window i e of peaks on the diffraction image behind 4 2 14 3D Peak profile Rocking Curve This is similar to the 2D peak profile but with the profile taken through consecutive frames The user needs to define the box size and range around the peak The box size and range are accessed through the arrows to the right of the icon The box size needs to be fitted to the size of the reflection A data file can be saved or data copied to the clipboard by clicking on the arrow symbol 4 2 15 Help The Help icon gives access to online help features version news and the command reference
89. positions where the software expects reflections to be if the unit cell is correct It is therefore used as a visual check of the unit cell and crystal quality The cross highlights positions where a reflection would be expected to be centred in this frame the rhombus or diamond shows reflections centred in the previous frame and the square reflections centred in the next frame Warning if a peak search and indexation have not been carried out yet a default unit cell will be displayed which is obviously not correct 4 2 4 Pixel area information The pixel area information icon switches on and off a semi transparent information display window which appears on the main diffraction window This window tracks the cursor about the diffraction image highlighting information about the image at the current cursor position This information includes the current X and Y pixel position the Int ensity at that position the H K L indices the L orentz T heta and R esolution C rysAl i gPro CrysAlis_Pro_manual_v4 Page 6 USER MANUAL CRYSALISPR0 LAYOUT AND CONTROLS If the left mouse button is depressed and held a wire box can be drawn around an area object in the diffraction image window and a semi transparent window displays the following information about the enclosed area window start position in pixels window size end position and dimensions in pixels maximum and minimum intensity and sigma values for the image and the b
90. progress of data reduction is shown in the data reduction information card Data reduction will then wait 25 frames then repeat this process using all the data collected up to this point This process will continue until the end of data collection Clicking on the external application power tools WinGX Crystals Olex2 at any point during the data collection will copy the latest ins and hkl files into the Struct folder and open a project using these files ready for structure solution C rysAl i gPro CrysAlis_Pro_manual_v4 Page 32 USER MANUAL NORMAL OPERATION 5 6 Stop all processes Working On Line 1 Press the START STOP button 2 A dialog window appears with the option Stop All Press Stop ALL and all processes will stop NOTE EJ Stopping all processes is also achieved by pressing the CTRL key on the bottom left of the keyboard e To pause an experiment open the Command Shell and click DC pause When ready to resume the experiment click Yes on the dc pause dialogue box Working Off Line 1 Press the START STOP button 2 A dialog window appears with the option Stop Press Stop and all processes will stop If you do not want to stop all processes when the dialog box appears then press the x icon in the top right corner to cancel 5 7 Resume experiment pre experiment In order to resume an incomplete experiment 1 Click START STOP and Resume experiment Pre experiment 2 Click
91. r voltage V Below these are indicators about the current set values for the temperature K heater status on off and the flow rates for the shield and sample flows It min To set a new temperature first click on the Start button if the device is not connected yet then click on the Set button on the right which allows you to input a new set temperature turn the heater on or off and set the desired sample and shield flow rates In typical operation 10 It min is used for both the sample and shield flow rates when cooling to a new temperature once the setpoint is reached the flow rates are reduced to 6 It min To warm up the Cryojet to room temperature flow rates of 3 It min are used All operations normally have the heater switched on The status line updates the state of communication between the software control panel and the Cryojet The Log file and Start Log buttons give the user complete control over recording the temperature throughout experiments however the temperature is automatically logged from the beginning of data collection by default The COM Settings button allows for changing the communication port settings manually should there be a need 4 8 4 X ray generator controller Clicking the X ray generator controller icon allows the user access to the generator settings On the top of the display the actual Voltage kV Current mA and Power kW is monitored Below these are indicators for the current set
92. s available to download from the Agilent X ray user forum This can be accessed at forum oxford diffraction com Users will find the movie particularly useful when using the twin data processing tools for the first time 9 1 Automatic twin lattice finding Searching for twin lattices is a remarkably simple procedure to the extent that it is worth exploring the possibility that crystals are twinned whenever problematic data sets are encountered To access the automated multiple lattice finding tool select the Unit cell finding with options utility under Unit cell finding in the lattice wizard 1 Select the Twin multicrystal radio button and then choose the number of components to search for It is often best to look for two lattices at first and then look for further cells if this seems necessary on further inspection of remaining un indexed reflections The Force identical lattice for all components box is ticked automatically If the routine still finds two very different lattices the crystal is unlikely to be a twin Certain crystals will output suspiciously large cells due to the presence of false long axes caused by superimposed twin lattices In order to prevent this twin lattice finding can be conducted with added cell axis constraints The worked example in the twinning movie is one such case where constraints are required in order to find cells of a reasonable size In most cases choosing an upper limit of 20 30
93. sAlis are automatically loaded Assuming the data has been processed the ins hkl and et od machine cif files will be imported into a directory within the main data directory with the path struct olex2_samplename The user can then solve the structure using a choice of solution programs within WinGX 4 4 11 CCP4 launcher When installed this button launches the CCP4 suite of programs for protein crystallography C rysAl i gPro CrysAlis_Pro_manual_v4 Page 15 USER MANUAL CRYSALISPR0 LAYOUT AND CONTROLS 4 4 12 Olex launcher This button launches the crystallographic structure solution and refinement software Olex where installed Assuming the data have been processed the ins hkl and cif_od files will be imported into a directory within the main data directory with the path struct olex2_samplename These files are imported directly into the program and the structure can then be solved using the tools on the right hand side of the screen The new Olex2 version 1 1 is fully supported by CrysAlisPro The user can also install several versions in parallel The version which is currently used is selected in the tools options panel Programs 4 4 13 Crystals launcher When installed this button launches Crystals structure solution and refinement software from David Watkin at the University of Oxford 4 4 14 Jana launcher When installed this button launches Jana a crystallographic program focused on solution refine
94. suitable peak table has been obtained this can be saved specifically by choosing Save specific peak table only under the Save information button The data must then be integrated by using Data reduction with options under the START STOP menu 1 On the first screen check that the correct q vector and order are already defined for Single q vector cases 2 In more specialist cases select Other reduction list and Generate an hkl list 3 The data reduction module will output an hklm file for single q vector cases hklmn for 2 d and hklmno for 3 d Other highly specialist tools are also available in the Generate window 4 Progress through the Data reduction with options choices as normal giving the output a suitable systematic name 5 Click Finish 6 All output files are compatible with Jana see section 4 4 15 for modulated structure refinement C rysAl i gPro CrysAlis_Pro_manual_v4 Page 64 USER MANUAL FRAME FORMATS 11 External Detector Frame Formats 11 1 Dectris CrysAlisPro now supports processing of Dectris detector frames At the moment only the detector for Swiss Light Source instrument 6M is implemented The detector gaps of the Dectris detector are automatically handled Run list and aliases file generator for DECTRIS data collections ux This dialog allows you to quickly generate a run file and aliases file for the data reduction of a DECTRIS data set 1 You select image name0001 img 2 You select the last
95. sults window A movie which clearly demonstrates the face indexing process with a worked example is available to download from the Agilent X ray user forum This can be accessed at forum oxford diffraction com C rysAl i gPro CrysAlis_Pro_manual_v4 Page 54 USER MANUAL TWINNING 9 Twinning A twin is formed when two or more crystals of the same material intergrow The unit cells of the two or more components are related to one another by symmetry The lattices may completely coincide in all three dimensions merohedral twinning or in fewer than three dimensions non merohedral twinning A twin may be suspected for a number of reasons Re entrant faces on the sample Non uniform polarisation of light when examined by microscope Peaks which appear split in the diffraction pattern Difficulty with indexing or a low percentage of indexed peaks Difficulty solving and refining the structure to a decent Ri value Two or more clearly visible lattices in the Ewald explorer 3 dimensional lattice viewer If a twin is suspected before data collection it is often beneficial to move the detector further back than you would for a standard data collection This will help to separate the spots from each twin component Consider using slightly longer exposure times and collecting higher redundancy than normal to increase the number of data points A movie which clearly demonstrates the twin data processing utilities with a worked example i
96. t data reducto r Info es GE TED compact data in this scenario E Peak table tab re oes OM ls EE Kater lr scenario all neccessary F deeg votre 4 X Whole expesiment in this scenaioal E Pre esperiment files par run first fame es data beet by Cas folder E stored Whole files in this scenario al files wil GC be added to zi fle F can log files not older tharr days E Experiment log folder F Startup log fler C wain32 pro ex_exp3 Code ciysaks debug E Exp ray log fies Ces Sa m Taget Destinaton lolder Zip fie name E Datawane exp_511 0 51 1_copy E Open destination folder alter zip Figure 24 Experiment Archiving Facility C rysAl i gPro CrysAlis_Pro_manual_v4 Page 45 USER MANUAL POWER TOOLS 7 3 Powder Diffraction When in CCD mode in CrysAlisProthe Powder power tool allows you to design powder experiments Powder experiment dialog 1 0 8 Path is ok Options sya Jenee ma mmm Coe MET Edit runs list 4 Start with analysis Exit Figure 25 Powder power tool dialog The user selects a detector distance and target resolution and the power tool sets up the experiment Then the Exposure time control panel is opened so that the exposure time may be set Exposure time dialog for powder experiments Figure 26 Powder power tool exposure time subdialog C rysAl i gPro CrysAlis_Pro_manual_v4 Pa ge 46 USER MA
97. t performer Add notes txt file Data Collection Show data collection graphs Show pre experiment result Data Reduction Show twin log file if available Create report rtf or html Data Collection gt Data Reduction gt Figure 3 Information Cards 4 3 1 Pre Experiment This information card is only displayed during the automatic pre experiment and is launched once Start has been clicked on from the pre experiment set up dialog Displayed on the right hand side of the CrysAlisPro GUI the pre experiment window can be minimised by clicking on the data collection information card Clicking on the pre experiment header will maximise this window The pre experiment window provides direct feedback of the unit cell intensity statistics and the defined user set up for the automatic data collection to follow As soon as one frame has been collected the automatic software will attempt to find the unit cell Once a unit cell has been successfully found it will be displayed in the pre experiment window along with information relating to the quality of the cell e g of reflections indexed the cell centring and the Laue class As additional frames are recorded the unit cell is re determined and the pre experiment is updated with the new or C rysAl i gPro CrysAlis_Pro_manual_v4 Page 9 USER MANUAL CRYSALISPR0 LAYOUT AND CONTROLS improved unit cell Also displayed are information on the proposed data collection strat
98. tage as this can be changed by Refinalizing later However non centrosymmetric cases should have the Friedel mates box unchecked 7 Space group determination can be done in either automatic or manual interactive mode by clicking the appropriate radio button on the last panel which appears Using interactive mode can be very helpful in C rysAl i gPro CrysAlis_Pro_manual_v4 Page 36 USER MANUAL NON STANDARD OPERATION ambiguous cases For example where an orthorhombic cell is found but is transformed by the user to a monoclinic cell with the B angle very close to 90 automatic space group selection will often choose an orthorhombic space group and transform the cell accordingly Interactive space group selection can also be enabled from the Refinalization tool See Chapter 8 n CrysAlis datared ction assistant 9 0 23 Profile fitting data reductior Step E Output Tip You may change the output name and directory to keep results of data reductions under different parameter sets UB supercells Output file name C XcaliburD ata compound compound2 compound2 Change output name Finalization options IV Space group determination Automatic e Manual Automatic structure solution AutoChem cl5h6n4o2 Z 200 Iw Completeness computation Rae EK Es WW Figure 19 Enabling Manual Interactive Space Group Determination during data reduction 6 5 1 Tracking crystal movement Occasionally a crystal will change orienta
99. tal movement nnne 37 7 N TOONS A A OO 7 1 Lattice Wizards EE 39 Figure 17 Lattice wizard panel including log window ooooonnninnininnnnnnnnnnnnnn ee ee ee ee ee eeeeeeeeeeeeeneees 39 7 1 1 Peak Hunting EE 39 7 1 2 Unit COl fining caia cs EE EAR eg 40 7 1 3 Reciprocal space visualisation using Ewald Explorer 40 7 1 3 1 Drag indexing a unit cell deresi NNN EES EEN 41 7 1 3 2 Drag Selection of Reflections and Marking them as Skipped oooooninonocccnnnnccncnccnos 41 7 1 3 3 Intensity Selection of Reflections and Marking them as Skipped n0nnnnnnnnnn0n0nnaaa 41 7 1 4 Indexation with known unit cell cocccccccncncncncncnnncnononononononononononononcnnnnnonononononnos 42 7 1 5 Refine instrument model 42 7 1 6 Lattice transformati A ta 42 7 1 7 Twinning multi CryStalS ooococccononononononononono nono nonononanannno nono no nono no nono no nono nononononononon 42 7 1 8 Incommensurates Uuasl cnmstals nananana 43 7 1 9 Precession photo reconstrucHon tt tittsettrt tt tternnr tnnt rtnn nnn rnrn ne nnna 43 7 2 TEE 44 7 3 Powder Dur e Da XG Model Seeded cc a ice oca 46 7 4 elle Uu 47 7 5 A A tege eege bieles ege 47 CrysAlisPro USER MANUAL CrysAlis_Pro_manual_v4 Page iii CONTENTS 8 Inspection and Manipulation of Data conccocccocnconnconnconncnanenanenano 50 8 1 EE 50 8 2 Running GRAL in interactive mode 51 8 3 A O NN 53 8 4 Applying absorption corrections cocooononnccnn
100. the cabinet lights and resetting of the emergency stop button 4 8 6 Liquid nitrogen level controller The liquid nitrogen level controller icon brings up a window panel indicating the level of liquid nitrogen in the tank if there is an autofill connection The level is expressed as a percentage with 100 indicating that the tank is full 4 8 7 Right Mouse Controls Right mouse controls only work if the image control icon pixel area information is NOT selected Using the right mouse button on the diffraction image displays a menu with various options C rysAl i gPro CrysAlis_Pro_manual_v4 Page 19 USER MANUAL CRYSALISPR0 LAYOUT AND CONTROLS e Pixel integration Select a peak by hovering over it then right click Information such as integrated sigma and so on is displayed so that you can check that you have the correct exposure time e Single frame peak hunting Select this to find all peaks in the frame and add them to the peak table e Add peak To pick out individual peaks to add them to the peak table put the cursor over the peak and right click to add the peak e Pixel value replacement e Copy selection e Remove background This clears the background noise from the diffraction image e Semi transparent windows on off This switches all semi transparent windows between non transparent and semi transparent C rysAl i gPro CrysAlis_Pro_manual_v4 Page 20 USER MANUAL NORMAL OPERATION 5 Normal operation In nor
101. thm parameters 1 Follow significant sample wobbing 2 cycle 3D peak analysis T Follow sudden discontinuous changes of sample orientation Orientation search range may 10 dea NT Sesh steps dea mar 10 E Edit special pars CEN EW WO Figure 20 Follow model options during data reduction 5 If successful the Ewald Explorer will show one single and good quality lattice There should also be a remarkable improvement in Rint statistics C rysAl i gPro CrysAlis_Pro_manual_v4 Page 38 USER MANUAL POWER TOOLS 7 Power Tools 7 1 Lattice Wizard The lattice wizard contains all the tools necessary for finding the unit cell and Laue group The tools within the lattice wizard group are discussed in turn below Lattice wizard 1 0 32 Lattice wizard LATTICE Current cell 6 4365 4 8 3715 5 11 2783 7 90 011 5 90 005 5 90 009 5 607 71 7 Constrained current cell 6 4341 3 8 3722 3 11 2816 4 90 0 90 0 90 0 607 71 7 Lattice reduction selected cell 6 4365 8 3715 11 2782 90 0119 90 0062 90 0091 oP 32 reduced cell 6 4365 8 3715 11 2782 90 0119 90 0062 90 0091 607 7 PEAK TABLE Peak hunting table UB fit with 6004 obs out of 6115 total 6115 skipped D 98 18 INSTRUMENT MODEL Goniometer beam 0 01067 alpha 50 13011 beta 0 02787 om zero 0 15946 th zero 0 31579 ka zero 0 06394 Detector aaa xj Cronk rysAlis SW Peak hunting tet Unit cell finding dia a SEN E Ewald explorer Core space
102. tion CrysAlisPro has been designed to provide a user friendly simple to use graphical user interface for data collection and data reduction of single crystal X ray diffraction data Based upon the CrysAlis CCD and RED programmes the CrysAlisPro software provides greatly increased automatic functionality CrysAlis ro is a single multi threaded programme which combines the functions of the old CCD and RED and can perform each in parallel CrysAlisPro provides direct access to automated data collection and reduction and the most commonly used functions in a single multi threaded programme which can perform each in parallel Added to this is a command line interface and history window which can be switched on off and allows access to the complete range of historical and indepth CrysAlisPro functions C rysAl i gPro CrysAlis_Pro_manual_v4 Page 1 USER MANUAL INSTALLATION OF CRYSALISPRO 2 Installation of CrysAlisPro To install the CrysAlisPro software on your diffractometer PC you will need the following programme saved to your computer CrysAlisPro171 xx yy exe Where 171 xx yy is the current version number and the xx and yy values change with each new software update You will also need the correction files which are specific to your diffractometer Without these files the CrysAlisPro software is not fully functional To obtain these files copy to your computer the entire Corrections folder from the PC attached to your diffrac
103. tion during a data set This is usually related to glue which is not properly set or sometimes needle like crystals mounted on fibres or loops with insufficient points of contact Crystal movement is easily observed by looking at reference frames from a data set any change in the reference frames denotes a movement in the crystal or crystal decomposition Also if a crystal has moved the Ewald Explorer module will show two or more lattices which appear to be in different orientations also a sign of non merohedral twinning However such data sets can be recovered using a tool which looks for changes in orientation matrix from one run to the next 1 Peak hunt on the first run only or possibly the pre experiment only and use the cell finding tools to find the initial cell and orientation matrix 2 Peak hunt over the full data set but do not attempt to index all the reflections using the initial cell 3 Choose Data reduction with options in the START STOP menu C rysAl i gPro CrysAlis_Pro_manual_v4 Page 37 USER MANUAL NON STANDARD OPERATION 4 At step 3 tick all three boxes the most important of which is Follow sudden discontinuous changes in sample orientation Set the Orientation search range and Steps per degree to suitable figures higher values mean a longer processing time but a greater chance of success Proffit CrysAlis data reduction assistant 1 0 24 xi Profile fitting data reduction _ E i Step 3 Basic algori
104. tometer 1 Double click on the CrysAlisPro171 xx yy exe programme Follow the on screen instructions When asked to select the program elements required for installation click on the box next to PRO and HELP only a tick appears in the box and click on Next 2 Once installation is complete double click on the CrysAlisPro icon which has been installed on the desktop The programme may ask you for a set up file if this is the first installation of CrysAlisPro on your PC If required locate the Corrections folder which you saved to disk earlier and select the file par Click on OK When installing CrysAlisPro on a PC remote from your diffractometer use the process described above The programme will ask to be pointed towards a data set on launching for the first time so copy some data onto your remote PC and locate the parameter file par when prompted 2 1 Software updates CrysAlisPro is continually updated with new features and bug fixes Major releases incorporating significant new features are available approximately every six months In between major releases bug fixed versions are also available The latest releases can be downloaded from the Forum website forum oxford diffraction com Please register on the Forum to access this feature It is recommended that customers monitor the website and use the latest software Each new edition of CrysAlisPro is released with details of bug fixes and additions since the previous issue T
105. u Sep 17 15 46 00 2009 Service_Thu Sep 17 15 46 00 2009_1 x Ea Service i GC rysAlis Shutter control y ECD Control pGoniometer control Image control Re initialize Re initialize Record single static image C Reset Expert control Record single phi or omega scan C Remove darks Position gonio Iv Save images to service directory C Xcalibur corrections a_20 a_20_160209 par Exp back up for analysis Information Image info Omega Theta Kappa Phi Distance 21 5000 21 5000 0 0000 0 0000 55 0000 Figure 5 Service utility 4 4 6 Service This power tool collects those service commands most commonly accessed by the user into one defined area These commands include shutter open and close control goniometer reinit ialisation CCD reinit ialisation Clearing dark image buffer card clear Dark direct goniometer control and home flag search Mgcutil It also provides for the definition of the machine parameter setup file If the system interface is ever switched off it will be necessary to reinitialise the goniometer using the service facility by simply selecting Gon reinit and Start Problems involving homing of the circles and detector require the Mgcutil or Expert Control facility However it is advisable to contact a service engineer or email XRDSupport agilent com before attempting manual goniometer control as no collision protection is provided CCD problems can
106. ult 7 1 5 Refine instrument model This facility enables the user to manually calibrate the diffractometer s instrument model However this tool should only be operated by specifically trained personnel CAUTION IN Manual calibration of the instrument should only be carried out by an expert The calibration of the diffractometer may be lost if an invalid model exists 7 1 6 Lattice transformation Click on the main button to open the lattice reduction window This allows you to select the particular cell settings and Bravais lattice from a list of possibilities The arrow button to the right of the main button gives the lattice transformation with user matrix option so that a matrix to apply a transformation to the unit cell can be entered 7 1 7 Twinning multi crystals A twin is formed when two or more crystals of the same material intergrow The unit cells of the two or more components are related to one another by symmetry The lattices may completely coincide in all three dimensions merohedral twinning or in fewer than three dimensions non merohedral twinning A twin may be suspected for a number of reasons e Re entrant faces on the sample C rysAl i gPro CrysAlis_Pro_manual_v4 Page 42 USER MANUAL POWER TOOLS e Non uniform polarisation of light when examined by microscope e Peaks which appear split in the diffraction pattern e Difficulty with indexing or a low percentage of indexed peaks e Difficult
107. umber 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 number of a selected run to zero will prevent that run being used in the reconstruction Click on Next NOTE The greater the number of runs data employed the longer the reconstruction will take 4 Click on the Browse for output dir button and create a new folder where the reconstructed images will be stored 5 To generate the three most common layers hk0 h0l and Oki click on Generate layers Changing the order to 1 will also generate the 1 and 1 layers giving 9 in total Set the resolution and click OK 6 To generate a specific layer click 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 C rysAl i gPro CrysAlis_Pro_manual_v4 Page 43 USER MANUAL POWER TOOLS To set up the layer to reconstruct define the plane using the L1 and L2 boxes L1 1 0 0 defines the h direction and L2 0 1 0 defines t
108. user constraints resolution etc H the Auto Start option was ticked on then this strategy window will automatically close and the data collection begin Otherwise the window will remain open until user intervention e Clicking on the start full experiment in the pre experiment information card window at any time will accept the currently displayed unit cell and jump to the strategy module without finishing the pre experiment e ee Pro online Gemini ultra system Mo wavelength active CCD view urData Jordan ao_screenshot pre_ao_screenshobipar E ale x 3 STARTISTOP ccoo cvo Xray Levei cco waiting COOL RED DC AUTO INFO Waiting for new data Wed Sep 29 10 42 58 2010 Pre experiment a d dee 35 98 8 62 83 menselini AGN D I Ee ER ere qe H 114 22 10 69 759 KE S FAS 0 848 Zo EE si EE ap ae iy Thu Sep Hg Eer 2010 25h 04m avg mosaicityr0 30 deg partials used 93 pre 1 24A exp 1 004 Experimenttype Targettesolition bau Ang Res C Th C 2th Target l sig e Geer SE EISES T Totalexp time 5500 DEI IT ago stan Data Collection a lis Cra Image st v E E SDAD a DO OO OOA A A cop E Agilent Technologies Figure 10 CrysAlis ro GUI with active Pre experiment information card C rysAl i gPro CrysAlis_Pro_manual_v4 Page 25 USER MANUAL 5 3 Protein Screening The protein screening features can be accessed from the START STOP menu 0D s
109. ve the goniometer to the correct orientation to allow optical alignment of the crystal CrysAlisPro CrysAlis_Pro_manual_v4 Page 22 USER MANUAL NORMAL OPERATION NOTE EJ The settings lower and upper refer to the glass stick position on the video monitor e 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 e 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 by approximately half the distance moved and in the opposite direction to the movement Press 0 and repeat this procedure until rotation gives no movement of the crystal e Repeat the above process rotating between 90 and 270 degrees e Press Upper on the remote control The goniometer will now move to the upper position such that the goniometer head is located behind the collimator If the vertical height of the crystal has changed adjust as above and return to the lower position Repeat until the vertical position is unchanged between the upper and lower positions e Press Lower and check alignment of the crystal on rotation between 0 and 180 90 and 270 degrees e Press 0 and Home to return the goniometer to its zero position e Exit the alignment procedure by clicking close on the computer screen This will return goniometer control t
110. window and attached command line From here the user can access all of the existing historical and new commands allowing for maximum flexibility and control The entire experiment and processing can be run completely in this mode or the window can be opened simply to issue specific individual commands The main part of the window is taken over by a history window which is always active This means that even in the fully GUI controlled and automated mode this history window is being updated and can be referred to by the user for further information When online using commands which result in image output will display the image in the view corresponding to the command line window tab which is selected Thus commands from the RED tab will display images in only the RED view and commands from the CCD tab will display images in only the CCD view The user has to manually select the proper view to correspond with the selected command line tab So to control the diffractometer and move the angles to 30 30 30 30 the user would click on the CCD tab click in the command line and type the gt a 30 30 30 30 command The command line window can be opened or closed at any time and can be resized An in depth manual explaining all available commands can be accessed by typing HELP from the command line Alternatively descriptions of individual C rysAl i gPro CrysAlis_Pro_manual_v4 Page 12 USER MANUAL CRYSALISPR0 LAYOUT AND CONTROLS commands and illustrations
111. y of the scaling coefficients absscale a frame by frame plot of Rint and a number of comparisons regarding the coverage and or completeness of the data The Devices Plots tab contains graphical hardware information This includes Spellman SuperN a log of voltage and current values for users with a software controlled generator CCDSCAM a plot of CCD temperature for Eos Atlas and Titan detectors FIP60 the same plot for Sapphire Ruby and Onyx detectors Cryojet a plot of temperature and flow rates against frame number and two further charts for the XrayChiller and CCDChiller This window is the point of access for all post data reduction data manipulation functions This facility is labelled Refinalization and includes the application of numerical face indexed absorption corrections Laue setting changes space group manipulation data filtering and data truncation Inspection and Manipulation of Data is described in detail in Chapter 8 4 4 5 Launch Znd instance of CrysAlisPro This opens a second offline version of CrysAlisPro and transfers all current settings such as experiment name machine set up and unit cell information to the second programme to allow for an independent off line processing of the data that is separate from any work done in the on line window C rysAl i gPro CrysAlis_Pro_manual_v4 Page 13 USER MANUAL CRYSALISPR LAYOUT AND CONTROLS Service GUI 1 0 18 C XcaliburData ylidtest frames ServiceTh
112. y solving and refining the structure to a reasonable Ri value If a twin is suspected before data collection it is often beneficial to move the detector further back than you would for a standard data collection This will help to separate the spots from each twin component Consider using slightly longer exposure times and collecting higher redundancy than normal to increase the number of data points Twin data decomposition is discussed in detail in Chapter 9 7 1 8 Incommensurates Quasi crystals An incommensurate or modulated structure derives from data where there is periodic distortion of the atomic positions modulation and or of the occupation probability of atoms density modulation This gives rise to satellite reflections present in addition to the main lattice Satellite reflections are often of very weak intensity and so are not always clearly observed CrysAlisPro s utilities for incommensurate data processing are described in detail in Chapter 10 7 1 9 Precession photo reconstruction This power tool allows the user to reconstruct precession photographs This is achieved via a wizard that guides you through the process and can utilise either the complete data set or specific runs and frames 1 The guided wizard is started by clicking on the icon Unwarping Precession images in the lattice wizard 2 The current orientation matrix is loaded Click on the Next button to proceed to the next step 3 If required adjust the n

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