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CrysAlisPro - Agilent Technologies

1. 7 3 6 Groups CrysAlis r USER MANUAL 35 LATTICE WIZARD i iw 13012 w i 4945 we 5501 1328 alo o E oo o s o o Figure 24 Groups window in Ewald Explorer The groups box can be populated with up to 20 different groups Within these groups lattice peaks may be either Indexed or Wrong Wrong indicated that they are un indexed by the lattice Figure 24 Lattice peaks belonging to each group will be displayed when the tick boxes are selected To hide specific groups or indexed wrong reflections deselect the relevant tick boxes Once assigned to a group the lattice peaks will take on the colour designated by the Color box To change the colour click on the group colour and choose the appropriate shade 7 4 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 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 5 Lattice transformation Click on the Lattice transformation button to open the lattice reduction window It is possible to select the particular cell settings and Bravais lattice from a list of likely cells The arrow button to the right of the main button gives the lattice transformation with user matrix option so that the user can manually enter and a
2. D Unwarping A Precession images gt Log window EI 9 Figure 17 Main lattice wizard window 7 1 Peak hunting Click on the Peak hunting icon to automatically search through all frames and select peaks above a threshold level Once finished it will return to the main lattice wizard screen where there will be a report on how many peaks have been extracted To access advanced peak hunting options 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 CrysAlis re USER MANUAL 30 LATTICE WIZARD 7 2 Unit cell finding Click the unit cell finding icon to automatically determine the unit cell The best fit unit cell and associated errors 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 options allows the user to set search limits on the minimum and maximum axis lengths e Selecting unit cell from list of found cells 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 e B
3. CrysAlis Data Collection and Processing Software for Agilent X ray Ditfractometers User Manual Revision 5 2 January 2013 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 Agilent Technologies DOCUMENT REVISION LOG Document revision log Person s responsible l Update of new features from W Paneer software release 171 36 24 Revision Date Approval Reason for update CrysAlis re USER MANUAL Contents 1 2 Jude lee 1 1 1 Eo eca a e Gaerne ne ee ee ee eee ee 1 StALATION oo cecesceccescsscsecsecseceecencsecseceecsecsuseecsuceessuseesenseuseuseeceussuseuseuseusenseuseusenseesenseusensensensensensensnsensensensensnees 2 2 1 BEER 2 ZDNET Select EE insna aaa AAA ARS 3 2 2 Close Lpnvs lsfm EEE Ea Enean aa 4 2 9 GUlintenace ert cc atitece see srtccsttercesctiecr teetitetentdeecesctiece tewetee teen dete etecn aii 4 2 4 PO TA Up ect cee cet ces tect et cect en cet ck ceca es cet ek cee ges cece etek geet ot 5 Hardware WG Tu Ve hs eae eee E 6 3 1 Doveo Kei Let 6 CEO Shutter Closed e WE 6 Al X ray Mo tu 6 SE E EK 0 eer eer ee 6 A ABO E 6 Sab gf dE 6 SSMN 8 ey E A 8 3 2 EMT E 8 3 9 Command CMD Shell oo ccc csssscsessssssesscsesesecsesececsesesaesesessssesessesesassusesassesessesesaesusesaesesessasesasenes 8 3 4 SE 10 Standard small Molecule exvperment 12 4 1 BES e E 12 MW We EK
4. 5 For either Mo or Cu or both click on either the Strategy 1 or Strategy 2 button Select Edit runs and then import the generated strategy Figure 16 6 Select the installed cryodevice and click Settings Clicking on the Add button allows the user to input each temperature point separately and define which strategy to use Each experiment will be stored in clearly labelled folders with a temperature suffix List of temperatures for cryo experiment List view summary Total of temperature points Total of temperature points with experiment List Temperature unit File Clipboard Copy selected SCH ERS VETI Kelvin Append Clipboard ETE wm wm Figure 16 Window showing temperature list for multi temperature wavelength experiment 7 For the last temperature it is useful to tick the Is end point box which allows for automatic warm up and shutdown of the cryodevice after all data has been collected 8 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 Single image The single image tool allows manual collection of images with goniometer movements controlled by the user Clicking on the Single images icon on the left hand side of the screen 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 CrysAlis re USER MANUAL 28
5. For more difficult samples it is possible to tune the peak search parameters to obtain a better indication of the unit cell This is described in more detail in the online help manual Unit Cell This section contains information about the Laue class and symmetry of the system Clicking on the Unit Cell link opens a window where the unit cell parameters may be modified for example in the case of a twin This is described in more detail in the online help manual Quality The diffraction power and mosaicity of the crystal is examined here The information contained in here will influence the parameters for the full data collection Please note that the suggested resolution is sometimes underestimated and exposure times overestimated especially for the Single scan and Fast screening options If a full data collection is not required the Next crystal button may be selected which opens up the screening window again If data collection is required select Go to strategy 5 2 Data collection Full experiment The strategy window has many parameters which may be altered to optimise the data collection This is discussed in more detail in Section 4 3 5 3 Data reduction Once the strategy has been optimised selecting Start Experiment will begin the automatic data collection and reduction The default option for the automatic data reduction in CrysAlis e means that data reduction begins after 25 frames and is updated after every subsequent 25 fra
6. Please follow the below procedure for all computers covered by your licence 1 CrysAlis re yv171 36 20 or higher must be installed in order to interface with AutoChem2 If not already installed the latest version of CrysAlis re can be downloaded from the Current Release section under Software Downloads and user manuals on the XRD forum 2 Install the AutoChem2 9 version of Olex2 Go to the XRD forum and download the 32bit or 64bit installer depending on your operating system version If you dont know which you have you may use the 32 bit version or help can be found here http windows microsoft com en GB windows 32 bit and 64 bit Windows frequently asked questions Run the installer by double clicking on it and following the on screen prompts 3 Open Olex2 by selecting the Olex2 1 2 ac2 icon from the Start Menu 4 Your licence code should already have been emailed to you please paste this code into Olex2 command line at the bottom of the screen under the molecular viewer and press return Olex2 will now verify your licence online and download some additional files When it has finished follow the prompt to restart Olex2 This may take a few minutes depending on your internet connection speed 9 Open or restart CrysAlis and the AutoChem icon should appear on the left hand side of the main window This indicates successful installation For systems where an older version of Olex2 or AutoChem has been in use it may
7. USER MANUAL 8 HARDWARE CONTROL time and can be resized Close the command shell by clicking on the button located in the bottom right hand corner of the window Shell command window Crtl interrupts i Pro a Command shell CG Aus RED ccp VW Foce auto saol M Transparent Telcom to the Crys lis system CCD Version 11 171 36 20 release 27 06 2012 Crys lisi 7i MET compiled Jul 11 012 15 39i22 Plugin Dr abs odplugin loaded Plugin 1 gral odplugin loaded Plugin 2 nada odplugin loaded Plugin 3 odbench2 cdplugin loaded Plugin 4 powder odplugin loaded Plugin 5 scale3 odplugin loaded Image format 1 sapphire dll loaded Your current setup file is C Documents and Settings agriffin besktop SinFiles saim SN par No flood field image loaded because Elood field switch off Goniometer type ER km gonio dll simulator Ho flood field image loaded because flood field switch off Switching to new EH4 collision model Atlas SuperNova Dual Cu at Zero Cu active extended big CG Collision model EM4 gonio Atlas model MCS beametop gemini Cu GERSU INFO Entering pCheckStarctupConsistencyGENsSv GEASW INFO Cu model in Gemini ODBENCH SUPEBRBN INFO Open client create thread 1 users Options CCD Close Figure 6 Command shell window Options CCD RED This button provides access to the machine and software setup There are many tabs which control the functions of the hardware and software It
8. 03 2 V 994 5 9 Constrained c a 5 9693 9 ER Ge 18 MALES e 90 0 V 994 5 5 Symmet e E Laue c SE 2 m2 m2 a P lattic JESS SS PEAK TA uS fit de th 2 tes otal 308 SET ime rel o se on e pi ray wa elength x cen 1024 Lie SE cen 1024 0000 distance 60 0000 ge beam 0 0000 e DI P P e OLEX2 s o E ge n D D ER D Crystals e D 2 bw Kl e 8 Data Collection Data Reduction E Agilent Technologies Ga F CECD DODO O OO O OOE Figure 2 Main window of CrysAlis re software Note that some icons are greyed out inactive during data collection and can only be accessed in the offline mode of the software The main features include A Power tools access to the lattice wizard command shell refinalisation features as well as links to structure solution software for full list of icons see Section 9 2 CrysAlis r USER MANUAL 4 INSTALLATION B Main window shows current frame in online mode and selected frame or precession unwarp image in offline mode C Layout and controls allows user to scroll through frames get peak information change brightness and use peak profile tools for full list of features see Section 9 1 D Device control Only shown in the online mode of the software and shows status of shutter which source Is in use and provides access to CCD cryo device X ray tube information E Information tabs Provide information about the current unit cell data coll
9. 51 24 2012 Thu May 10 12 26 32 2012 Thu May 10 12 32 58 2012 Thu May 10 12 31 32 2012 Thu May 24 12 20 27 2012 Thu May 24 12 14 05 2012 Fri Jul 20 09 42 10 2012 Fri Jul 20 09 54 02 2012 Fri Jul 20 09 56 56 2012 Fri Jul 20 10 02 12 2012 Fri Jul 20 10 02 55 2012 Fri Jul 20 10 05 01 2012 Wed May 11 10 29 51 2011 Wed May 11 10 42 40 2011 Thu Jul 1912 15 43 2012 Tue Sep 20 08 46 42 2011 Tue Sep 20 09 08 15 2011 Tue Mar 13 17 15 59 2012 Tue Sep 20 12 42 27 2011 Mon Feb 06 16 10 38 2012 Mon Feb 06 10 01 34 2012 Fri Mar 23 13 55 42 2012 Tue Mar 20 09 13 07 2012 Tue Apr 24 17 27 42 2012 Tue Apr 24 17 16 34 2012 Thu May 10 12 26 32 2012 Thu May 10 12 34 49 2012 Thu May 10 12 31 43 2012 Fri Jun 01 08 34 15 2012 Thu May 24 12 17 42 2012 Fri Jul 20 09 44 17 2012 Fri Jul 20 09 54 16 2012 Fri Jul 20 09 57 29 2012 Fri Jul 20 10 02 36 2012 Fri Jul 20 10 03 09 2012 Fri Jul 20 10 32 31 2012 Wed May 11 10 31 15 2011 Mon Feb 06 10 00 09 2012 Hide pre experiments Hide screenings Displaying information e Standard List Name of list ES rm Custom columns Volume laue wavelength Rint redundancy Multiple addition Protein screening Figure 1 The experiment list window The list may be refined by using the tick boxes for Hide pre experiments and Hide screenings The lists may be defined for an individual or over a set time period using the gt gt button in Name of list will open a window which will allow
10. MANUAL 51 APPENDIX Xcealibur root typically C Xcalibur Corrections directory corrections Site directory sitename contains ffi poar ccd and geo correction files These files describe the machine setup Log directory log log contains the applications error logs which are important to trace application errors Macro directory macro mac contains the CrysAlis macros for task automation Applications root CrysAlisXXX contains the CrysAlis executables and drivers exe d vxd sys Darkimages directory darkimages contains the CrysAlis img dark images which are acquired during a CrysAlis CCD session Initialisation and user defined setup files directory CrysAlisINI contains initialisation user defined setup files for CrysAlis ODBench and ODShell programs ODShel software directory ODshelEXE is an executable folder which contains the ODShel software This is a shell program for structure solution and refinement 9 42 Experiment file structure A typical experiment folder will have the following directory structure Experiment root C Xcaliburdata expname contains important experiment definition files such as Dat mun ffiinffit ffi tab rrpprof ccd geo gon sum ct ins hkl etc all of which are required in order for the experiment to open and function properly Expinfo directory expinfo contains ini files with information regarding some of the uni
11. OTHER DATA COLLECTIONS 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 CrysAlis r USER MANUAL 29 LATTICE WIZARD 7 Lattce Wizard The lattice wizard contains all the tools necessary for finding the unit cell and Laue group Figure 17 The tools within the lattice wizard group are discussed in turn below Lattice wizard 1 0 32 ef gr Lattice wizard LATTICE fo Peak hunting Current cell CSD install i 5 9591 4 9 0344 6 18 3940 12 89 989 5 89 988 5 89 995 5 990 27 11 gt Constrained current cell I 5 9589 2 9 0361 2 18 3911 5 90 0 90 0 90 0 990 27 5 Lattice reduction selected cell S 5 9592 9 0344 18 3930 89 9813 89 9917 89 9948 oP 32 reciprocal space reduced cell g 5 9592 9 0344 18 3930 89 9813 89 9917 89 9948 990 2 PEAK TABLE fine Peak hunting table nstrument model UB fit with 2371 obs out of 2377 total 5314 skipped 2937 99 75 gt INSTRUMENT MODEL Goniometer winning Incommensurates beam 0 14228 alpha 50 04022 beta 0 01206 multi crystals Ain Quasi crystals om zero 0 14382 th zero 0 10518 ka zero 0 02427 gt G g Detector x rot 0 43283 y rot 0 17213 x cen 1027 48527 y cen 1038 04976 distance 49 96486 ea Load Wavelength Cu Ang A1 1 54056 A2 1 54439 B1 1 39222
12. are 50kV and 0 8mA The generator will reach the desired values in a stepwise and controlled manner NOTE If you close the window before the ramp process is complete then only the values at closure will be reached The Fault and Status indicators provide feedback for the state of the generator In normal operation only the Status indicators should be active The Fault indicators can be used as guides for 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 the experiment and this can be viewed at any time by clicking the Plot button For automatic generator ramping control go to CMD gt CCD options and click on the Generator tab see section 3 3 CrysAlis re USER MANUAL 7 HARDWARE CONTROL 3 1 6 Level 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 3 1 7 10 This IO device control button brings up a window with access to software control of the cabinet lights and resetting of the emergency stop button 3 2 Status Display The status display located underneath the device control provides information on the activity of the instrument and software processing see Figure 5 CCO Ready RED Ready Figure 5 Status d
13. 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 9 Log window Additional information about the calculations being performed can be seen by clicking on the Log window button The arrow next to the button gives the option to always show the log during computations CrysAlis r USER MANUAL 38 INSPECTION AND MANIPULATION OF DATA 8 Inspection and Manipulation of Data On completion of an experiment the data reduction tab within the main CrysAlis e window displays key data processing statistics For more detailed information use the Inspect data reduction results and refinalize with user corrections button on the left hand side of the screen 1 The Data reduction File contents area contains a summary of cell dimensions and the 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 2 The Data reduction output tab contains the full log of the automatic data reduction process Starting with the generator settings and data col
14. group extinctions that are detectable 8 3 Running GRAL in interactive mode The space group determination module GRAL can be run in interactive mode This is very helpful in cases where the X ray data are weak and the automated procedure fails Interactive GRAL is enabled by clicking on the Options button next to the Space group determination tick box When interactive GRAL launches the user is presented with a series of windows showing data relevant to space group determination and various options relating to the space group determination The program will automatically choose appropriate options at each stage but the user can override these at any time Clicking on Apply accepts the selection and the user is moved to the next window 0 Settings not automatically shown the user can change limits for identical lattice parameters systematic absence test centring selections and space group preferences 1 Load displays the hkl file to be used and the unit cell parameters Centring statistics on lattice exceptions for each centring option Niggli a Niggli reduction is applied to the data and the user is provided the opportunity to apply a transformation matrix to the original cell Lattice a selection of Bravais lattices are shown with corresponding Rint values Centring the centring statistics are re examined after the Niggli reduction lt E2 1 gt E statistics are shown to help determine whether the structure is centrosymmetri
15. hits may be deselected using the tick boxes or the Select all and Deselect all buttons may be used CrysAlis USER MANUAL 14 STANDARD SMALL MOLECULE EXPERIMENT It is possible to view the selected hits either in Mercury if you have a CSD license installed locally on the PC by clicking View in Mercury or on the WebCSD again a license is required by clicking Go To WebCSD Mercury Is a program distributed by the CCDC Visit www ccdc cam ac uk for more information 4 1 2 Local database It is also now possible to create your own local database of structures to search against when using the CellCheckCSD feature To activate simply click on the Options button in the Check CSD window and tick Enable local database search Clicking on the Create from lists button will search through all previous experiments that have been run on the PC and then add the results to the database It is also possible to browse any folder containing res ins cif files Databases from other PCs can be merged using the Import xml button Any previous experiment or stored res ins cif file that matches the current unit cell settings will now appear in the drop down list Green entries are local experiments and can be accessed by double clicking on them which brings up a new offline instance of CrysAlis e A red entry indicates an experiment which is currently open in CrysAlis Any local entries that are black indicate that the Original experiment
16. is not available 4 2 Pre experiment Before the main data collection a pre experiment is run to better determine the unit cell parameters diffraction symmetry and the other properties of the diffraction pattern required to calculate a suitable collection strategy During the pre experiment an information card will appear on the right hand side of the screen displaying the user defined settings from the previous dialog and the unit cell of the crystal being measured By default 15 frames are recorded when using molybdenum and 30 with copper radiation 15 low angle and 15 high angle Once the first frame has been measured the software will attempt to find the unit cell crystal lattice and evaluate the average sigma spread to a set resolution This information will be updated after every frame Using this information a suitable strategy will be calculated The Start experiment button will become active and the user can choose to start the main experiment using the information present in the pre experiment card The default action is to wait for the completion of the pre experiment and for the user to check the details of the experiment in the strategy window If the Interactive strategy after pre box is not checked the software will automatically launch the full experiment CrysAlis r USER MANUAL 15 STANDARD SMALL MOLECULE EXPERIMENT 4 3 Strategy calculation On completion of the pre experiment a strategy window opens automaticall
17. list generator for Dectris 9 3 2 Rigaku CrysAlis e supports processing of Rigaku d trek image format frames via the command dtrek createrunlist Figure 29 Run list and aliases file generator for DTREK data collections i This dialog allows you to quickly generate a run file and aliases file for the data reduction of a DTREK data set 1 You select image name UU mg 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 will 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 DTREK data set added to the experiment list NOTE Using CrysAlisPro you can process only DTREK images from Diamond Rigaku detectors First de DTREK de file 1001 img Last de DTREK de file Browse n a pees Help Cancel Save d Figure 29 Run list generator for d trek image format 93 3 SAXI Data from Bruker AXS SAXI formats can also be processed with CrysAlis e via the command saxi createrunlist Figure 30 CrysAlis re USER MANUAL 50 APPENDIX Run list and aliases file generator for SAXI data collections my kd This dialog allows you to quickly generate a run file and aliases file for the data reduction of a SAXI data set 1 You select image name_1_1 sax or name01 001 or name_01_0001 sfrm 2 You sel
18. method for determining the background correction can be changed from the standard Average method to a Smart correction For datasets in which the background is non uniform using the Smart method is often beneficial since it additionally takes into account the local environment of each reflection This however is more computationally expensive so may not be desirable for routine samples on older computers Typical starting values are to set the frame range to 5 but will be dataset dependant 5 Outlier rejection the choice of outlier rejection is usually based on the chosen Laue group of the crystal but can be altered 6 Output details about the output including CrysAlis r USER MANUAL 19 STANDARD SMALL MOLECULE EXPERIMENT e re naming the output files useful if performing several data reductions on the same data e the choice of automatic or manual space group determination via GRAL see Section 8 2 e the option to perform structure determination if AutoChem is installed e whether to perform completeness calculations e automatic generation of unwarp precession images NOTE there is the option to refinalize a dataset if the user wishes to improve the data further without having to re process the images This is significantly faster than repeating the whole data reduction procedure and is covered in Section 8 46 Structure solution Once the user is happy with the data reduction results there is a choice of s
19. o ange peiod width Angle Period Widtkr ERR Operations Kb Move selected to Group h Figure 22 Selection Lattice It tab in Ewald Explorer CrysAlis re USER MANUAL 34 LATTICE WIZARD The Selection tools offer three options which relate to the function of the mouse in the viewer window e None The mouse defaults to rotating and zooming of the lattice e Rubber band Using the LH mouse button it is possible to put a rectangle around a section of lattice peaks Lattice peaks will become green once selected e Lattice It This option allows the user to select lattice peaks which appear in evenly spaced parallel lines Figure 23 b5 Ewald Explorer 1 0 1 Bik Cy saic Crystal Filters Selection Lattice It Figure 23 Example of Lattice It function in Ewald Explorer Hovering over the lattice viewer will adjust the angle and distance from the centre of the lattice Pausing at a particular place forces the viewer to calculate all parallel positions at a regular period The type of calculation can be controlled by using one of the three options in the drop down box find period refine angle refine period or give me period where click Once a good position has been found a LH mouse click confirms the position and the lattice peaks may be selected using the three buttons at the top of the tab Once selected lattice peaks may be moved into a specific group see section 7 3 6
20. offline window and click on the Powder power tool icon Click OK in the pop up window and a powder diffraction graph will be generated The Options button allows various output files to be selected and a range of correction to be applied to the data 6 3 Variable temperature wavelength experiments This facility allows the user to queue up experiments for collection at a variety of temperatures and wavelengths if using a dual source system It is best used with a pre defined strategy and so it is recommended that the user carries out a pre experiment beforehand Temperature Wavelength experiments dialog 3 0 1 exp e yg XcaliburData Mo experiment in folder C XcaliburData exp_9 Mo Cu experiment in folder C XcaliburData exp_9 Cu Use temperature device control Options Iw Data reduction during data collection W Mo Runlist KV 50 00 mA 0 80 w Cu Strategy 1 Runilist ooo mal 0 00 ku 50 00 mA 0 80 i User message Figure 15 Multi temperature wavelength experiment window 1 Conduct a pre experiment as normal CrysAlisP e USER MANUAL 27 OTHER DATA COLLECTIONS 2 Define up to two strategies to collect as much data required for full evaluation at the different temperatures 3 Save the strategies as run files by clicking Export in the Edit runs window and then close the strategy window 4 Click on the Multi temperature wavelength icon on the left hand side of the main screen
21. parameters to be selected so only certain experiments appear in the defined list These lists may be deleted or removed More experiments may be added to the list by selecting the Multiple addition option or an individual experiment may be found by clicking Browse experiment The displayed information may be changed to one of the pre set views choose between Standard or Volume laue wavelength Rint redundancy or Protein screening or Custom columns may be set CrysAlis re USER MANUAL 3 INSTALLATION 2 2 Close CrysAlis re To close CrysAlis re click on the X icon in the top right corner of the CrysAlis screen When in CCD mode a prompt will appear regarding generator ramping control For micro focus systems in particular it is recommended that users ramp the generator down when the diffractometer is not in use This will leave the generator running in stand by mode with minimal power settings to help extend the lifespan of the X ray tube 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 2 3 GUI interface guide Figure 2 highlights the features of the main software window These are covered in greater detail throughout this document e e K S Lesser Ges d Deeg nd Mon Oct 01 16 43 58 2012 RED Pro ng exp_12 run 1 image 18 575 peaks A H Crystal o g exp_i2 pion Les nor done 2 del 3 eerie 18 SEH 90 04 4 90 05 3 90
22. rays or Closed green meaning the sample is not exposed to X rays 3 1 2 X ray Mo Cu This button is only visible on a dual wavelength system The source is automatically selected according to the machine defaults upon system start up Clicking on this button switches between sources Selecting Yes on the pop up window will switch wavelength and force ramping up of the generator to the standard data collection power selecting No will switch wavelength but keep the generator at the standby values selecting Cancel will stop any wavelength changing 3 1 3 CCD This opens the software device controller for the CCD head The display will show the running temperature of the CCD and the power being used to maintain this temperature 3 1 4 Cryo Clicking this icon will open the device controller window for cryodevices if there is one installed Right clicking this icon allows the appropriate cryodevice to be selected Devices supported include Cobra Cryojet Cryostream 600 and 700 Helijet and Hotjet Within this menu it is possible to display the current sample temperature in the image window by selecting Display current sample temp 3 1 5 Xray Clicking the X ray generator controller icon opens a window to display and control generator settings The Read Values box displays the actual Voltage kV Current mA Power kW and Temperature C of the system The Set values box displays the target power of the source and its on off status
23. recommended If this is the case the user can select Different time for each theta position It is also possible to change the scan width which is useful for collecting weak reflections or to help separate out close overlapping peaks E Current Strategy details the number of frames and length of the experiment If any changes are made to sections A B C or D the user will need to click on the Calculate New Strategy button to update the experiment details Advanced users may wish to create their own run list which can be accessed via the Manually Edit Run List button the online help for more details F Coverage graphs or tabulated views of the proposed data collection showing the completeness and redundancy values for the chosen Laue group and for the full sphere of reciprocal space P1 G Settings Options there are three buttons in this section The Data collection Dark button lets the user change settings regarding correlation prevents problems with zingers at long exposure and dark current measurements The CCD processing button allows the correction and binning mode of the CCD to be changed The Autochem Movie Cryo Red button lets the user choose to record a movie of the crystal input the expected chemical formula set AutoChem to attempt automatic structure solution if the relevant license has been purchased There is also a useful feature that will automatically shut down any hot cryo device being used once the experiment is finis
24. reduction only you will need to have an Oxford Diffraction Agilent Technologies data set situated on your machine in the absence of data locate the file deal small am from within the help folder of this installation this will contain a dummy experiment allowing you to start The program will present a message box Red fatal system start up asking you locate the par file of the aforementioned experiment Click on Yes and locate the par file 2 1 Open CrysAlis Pre To start CrysAlis re either double click on the icon on the windows desktop or navigate to Start gt All Programs gt Xcalibur Agilent Technologies gt CrysAlis e for Windows XP 7 Please note that there are two icons on your desktop for CrysAlis one online and one offline data reduction only When the program is started on a PC connected to an Oxford Diffraction Agilent Technologies diffractometer CrysAlis re will start up in online mode This means the program will connect to the diffractometer CCD and other devices 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 The windows header carries the text online CrysAlis r USER MANUAL 2 INSTALLATION When a second version of CrysAlis e is started or if CrysAlis e is opened on a standalone PC this offline version wil
25. reduction will be performed using the current unit cell settings so the user must make sure they are happy with the cell before continuing To change the settings used by the profile fitting data reduction click on Start Stop and select Data reduction with options There are six windows and the most commonly used settings are discussed below 1 Orientation Matrix the user can choose which lattice extinctions to filter out There are also options to choose unit cells from any twin components that have been assigned or to use any q vectors determined for incommensurate structures via Ewald ro Section 7 3 These will be automatically highlighted when these features are used 2 Experiment run list by default the full run list is used during data reduction but entire runs or individual frames can be removed using this window with good reason as removing too many will reduce completeness of data 3 Basic algorithm parameters there are three levels for following crystal movement during a run moderate sample wobble significant sample wobble and discontinuous jumps This window also gives the user the option to clear any data generated from previous data reduction runs and also to edit several special sample movement parameters e Auto select optimal prediction approach on run basis e Follow significant sample wobbling 2 cycle 3D peak analysis e Follow sudden discontinuous changes in sample orientation 4 Background evaluation the
26. small molecule mode Once the PX tick box has been selected the default settings are shown in the SM PX window The Edit options button allows default settings to be optimised to meet the user s requirements For example checking the MTZ export for use in CCP4 allows automatic generation of the correct MTZ output file Other settings are discussed in more detail in the online help 5 1 Data collection screening To begin a new experiment press START STOP and select New experiment This opens a screening tool which allows sample mounting screening and if required full data collection and automatic data reduction Once New experiment is selected a screening window appears as in Figure 13 The window is comprised of five sections A In the Compound Sample Description section it is possible to enter the sample name in the Compound box and a description about the sample in Comment The user can change the root folder experiment list or experiment performer in the Edit description box B In the Control section use Mount sample to activate the video camera and controls for mounting and centring the crystal on the goniometer head Video snap takes one image of the sample and Saves it as a jpg file for future reference Screening tool 1 0 3 Pro Crystal Screenin j g ca N Compound Sample Description Control Experiment list Standard A Root folder C XcaliburData Experiment performer H Comment i Pathisc Path C Xcalibur
27. solution programs within WinGX 4 6 3 Olex launcher This button launches the crystallographic structure solution and refinement software Olex2 where installed Assuming the data have been processed the ins hkl and et od files will be imported into a directory within the main data directory with the path struct olex2_ samplename These files are CrysAlis r USER MANUAL 20 STANDARD SMALL MOLECULE EXPERIMENT 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 Olex version 1 2 is fully supported by CrysAlis r The user can also install several versions in parallel The version which is currently used is selected in the CCD RED Options panel in the Programs tab 4 6 4 Crystals launcher When installed this button launches Crystals structure solution and refinement software from the University of Oxford 4 6 5 Jana launcher When installed this button launches Jana a crystallographic program focused on solution refinement and interpretation of difficult especially modulated structures Developed at the Institute of Physics in Prague this software is the industry standard when working with incommensurate modulated structure data sets CrysAlis r USER MANUAL 21 DATA COLLECTION FOR PROTEIN CRYSTALLOGRAPHY 5 Data collection for protein crystallography The logo in the bottom right hand corner allows the user to switch between protein and
28. 18 Ewald Explorer tool bar part 1 31 Figure 19 Ewald Explorer tool bar part JI 32 Figure 20 Crystal tab in EwaldP o oo cccssscssssscsssscsrssscsssecsesssssesessessusassesseseesansesseseesaasassesensansassesensansassesensansasees 32 Figure 21 Filters tab in the Ewald Explorer 34 Figure 22 Selection Lattice lIt tab in Ewald EXxplore f iiiisisctcinssstannstannncinnntnanninnnennanaiamnnaistnanw 34 Figure 23 Example of Lattice It function in Ewald Explorer 35 Figure 24 Groups window in Ewald Explorer 36 Figure 25 Data reduction finalizing WINdOW s ssesesssesenesnnsrersrerururununenurarararurannnrnrnrursrurururenararararunnnnnrererersrerenns 40 Figure 26 Twin data finalisation vwindow 41 Figure 27 Abs display window showing crystal image and face indexing details 44 Figure 28 Run list generator for Decttis cccesssssssscsscerssecscsecerssecacsecsessesaesessesessaasecsesensansassesensansassesensansatees 50 Figure 29 Run list generator for d trek image format 50 PIQUE OU Puni oen roro E 51 Figure 31 Run list generator for MAR 51 Tables Table 1 Control buttons in CrysAlisP oo ccssssssssssssssessessessessessessesessessessessessessessessessessessessesaesaesesnsnsansans 45 Ee Re Le E 49 CrysAlis r USER MANUAL INTRODUCTION 1 introduction CrysAlis ro 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
29. C11H10 502 C11H10 502 C11H9S02 C10 H9 5 02 C11H10 502 C10 H9 5 02 C11H10 0251 C11H10 0251 Cel match voume a fb Le Lage beta gamma Formula Symm_ Origin name Prim V_ More info J P212 P212 P212 2 m2 P212 P212 2 m2 P212 P212 P212 exp exp_15 exp exp_14 exp exp_3 exp pre_exp_14 exp exp_1 exp exp_9 exp pre_exp_15 exp exp_5 CSD MSULINOS CSD MSULINO1 Local exp Cu gr Local exp Cu gr Local exp Mo o Local exp Cu pr Local exp Mo oz Local exp Mo o Local exp Cu pr Local exp Mo o ccDCCheckCell ccDCCheckCell 15 99 9 989 3 2 m2 exp pre_exp_7 Local exp Mo pi 4 b Information Searching completed CSD tools ctall Deselect all Go To WebCSD license required Figure 11 Check CSD window The window may be re sized to view the data more easily The drop down menu allows various cells current constrained average and final to be used as the search Two buttons can be used to start or stop manual or automatic searching of the CSD and alongside these is an Options button Clicking Options opens a window to allow the search parameters to be altered according to your requirements The window displays the hits which are most closely matched to the cell and the most likely has the highest cell match value The formula symmetry and Refcode are displayed but are not used as search parameters Individual
30. CrysAlis r USER MANUAL 6 HARDWARE CONTROL SuperNova Device Control bol wiel Read values Firrwere version 22 20 Final_Rev4i4_PCee Voltage kV Curren mA Power WJ Temperature Sei values Voltage k 50 000 Coupen br i 0 800 ce egen ey Emergency X RAY Of Set kma Xray Auto Ramp On GO DKV D 6mA Status Device connected SSES Fouts Status Ce H Intesfockc cl sts Ei EE Temperature limit 43 0 Gent merock closed ie water ok VIENS EE O Pump ON C 6 Satety shutter open ei O Fast shutter open OQ Lomp status O Calibration run Usage time 1798 h Moray stop C Number of cycles 54 Conditioning C Logfile TT ire Figure 4 Example of SuperNova device control window The Emergency X RAY OFF button quickly shuts the generator down and stops the production of X rays in an emergency After such an event the hardware interface needs to be reinitialised switched off and on before setting the next Voltage and Current In dual source systems the Second lamp button displays the status of the non active source The Start Stop button initiates or ends communication between the software interface and the generator Use the Set kV and mA X ray button to alter the power of the tubes 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 Micro focus systems Mova and Nova standard generator settings
31. Data exp_1 exp_1 Edit description Screening Experiment Options e Single scan C runs 1 frames 2 distance 52 0 Remeasure overflown frames Two scans wi Correlate images e Fast screening Reliable resolution limit and exp time prediction ke lies Hare D Custom scans Edit orientation s Distance not closer than mm Exposure time 20 0 D Edit exp options Resolution 290 ng Frame multiplier 1 Export in other formats 0 5 XDS Mosfim Denzo Scan width deg Total experiment time 02m 11s Figure 13 Crystal screening window for PX experiment CrysAlis re USER MANUAL 22 DATA COLLECTION FOR PROTEIN CRYSTALLOGRAPHY C The Screening Experiment section allows the choice of one scan two scans or custom scans e The Single scan option consists of two frames each scanning 0 5 in omega at phi 0 e The Two scans option consists of four frames for fast screening or eight frames for Reliable resolution limit and exp time prediction Half the frames are collected at phi 0 and the other half at phi 90 e Custom scans has an Edit orientation s button which allows the user to select any phi value and number of frames The user may also select the closest allowed distance the desired resolution the scan width the exposure time and any frame multiplier Using the above information a total experiment time will be displayed D The Options section allows the user to decide if the software should remeasure fram
32. S D orenen att cnetnast AAAA EE A E AAA AAAA EE A AE 14 SCHRETT 15 4 2 BLOMUS eee ee eer 15 4 3 Cae Cal Cll Al e 16 4 4 Data CONC COON EE 17 4 5 Bata rode Orea E EA E AE E A 18 4 5 1 Automatic data processing cccseccesssssssccssssssseseesessesauseesessesanseesesonsaaseesesonsauseesesonsansensesonsanseses 18 4 5 2 Data reduction WIth optons 19 4 6 Suc re de EE 20 eM MMU Cu EEN 20 CONTENTS EE ege ergeet ZU luchen ZU AOA IEN Ee E 21 409 AANA ell 21 5 Data collection for protein crystallography ssesssesssrerssesrseersrenurusrsrunurunrsrunurunnsrnnurunnnrnnurunnnnnnnnnnnnrnrnrnnrsrernns 22 5 1 Data collection screening 22 5 2 Data collection Full experiment 24 5 3 BR eg E 24 5 4 EXPONUNG MNCS EN 24 5 5 Advanced data collection modes 24 6 Htergater GOEN 26 6 1 Special Append data collecton 26 6 2 Powder CIITA CT OM E 26 O22 POWGErOXDE LINE EE 26 O22 POWGER Datel ClO QUO Nl EE 21 6 3 Variable temperature wavelength experiments seeessssesssiserersrersurururisisisisisisinnnnnnnnnrnrnennnnnnsnnas 27 6 4 SMAN asuna aa 28 EEN 30 7 1 Peak RUNNUM EE 30 1 2 MFI ec anO te EAS A N EAE EAE AEA AE R RE AE AE AA tat hae tad tat A 31 1 3 ANYO EE 31 kol TOB EE 31 de AEN 32 Toa IR EE 32 Tot al E 8 ee or 33 KS SECUN Ua EEN 34 TOG GROUNDS EEN 35 74 Refine instrument model 36 1 5 Reger iere d E EE 36 7 6 EATING Ir EE EE 36 1 1 Ia ell Ven TE MI E nn anonn aana OU OUAR UODO UGRA 37 1 8 Precession
33. a options including editing of the chemical formula 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 refinalized to impose the change see Section 8 The Data Collection card provides real time progress feedback displaying the current positions of the omega theta kappa phi axes and the detector distance A progress bar and the expected end time for the data collection are also shown The end time is updated during the data collection to take into account required frame re measures the percentage of which Is approximated during the early part of the experiment but then continuously updated Other information such as the CCD Peltier chiller parameters generator settings max and min exposure times etc are recorded here The Data Reduction card displays top level feedback of the progress and results of data reduction and Space group determination The feedback contains information regarding e Absorption correction e Scaling 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 frame
34. ata collection and can only be accessed in the offline mode of the software 4 Figure 3 Device control for the Xcalibur Gemini system left and the Supernova system right 6 Figure 4 Example of SuperNova device Control vwipndouw 7 Figure 5 Status E E 8 Breif EEEE E e 9 Figure 7 CCD Options vwipndouw nae 9 Figure 8 Full calibration experiment Window cccceccsscesscscsscscsecsssecsececseceesnsassesaesecsusessusessusassesateesaneesensasensass 11 Figure 9 Pre experiment screening window for small molecule ExperiMent ccccsccececersssseeeeersseeeeees 12 Figure 10 Full screening window with strategy options highlighted s s sseseseseseserenenerererererersrnrererererererrrens 13 Figure 11 Check CSD wmdow ssssssseseserererersrsrsrererursrarararunnsrsrsrsrurururururanarararununnnnnrrursrunsnanenanananananannnnrensrnrnn nae 14 Figure 12 Experiment strategy window with each information section Tabelle 16 Figure 13 Crystal screening Window for PX experiment e esesesssesesererererirerinrsrsrsrursrursnurerarararurnnnnrrersrsrsrerenns 22 Bref OR SChECUING AD a aR E oe 23 Figure 15 Multi temperature wavelength experiment vwipndouw 21 Figure 16 Window showing temperature list for multi temperature wavelength experiment 28 Figure 17 Main lattice Wizard WINKOW ccccccssescesssssssssesessecsesessecsssassecsessnsaasecsesersaasassesersaasassesensansansesensansatees 30 Figure
35. ated data unmerged and unscaled The last step of the data reduction process is finalization in which a hkl and mtz 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 hkl and mtz files 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 1 Chemical Formula edit the proposed chemical formula and Z value for the sample 2 Outlier Rejection change the outlier rejection method used during refinalization based on Laue groups CrysAlis r USER MANUAL 39 INSPECTION AND MANIPULATION OF DATA 3 Absorption Correction A face indexed absorption correction can be applied provided the crystal shape has already been determined by ticking the Apply absorption correction box in the top right corner of the window A spherical absorption correction can also be applied by ticking Apply next to the Spherical abs button and then entering a suitable value for p r where ris the average radius of the crystal 4 Sigma calculation control Possible to change the sigma error model and rejection criteria for overlapped reflections 5 Limits filters amp lattice extinction filters set a negative intensity sigma limit change the resolution lim
36. be necessary to update the AutoChem program location in CrysAlis to point to the correct version of Olex2 namely Olex2 1 2 ac2 This is accessible by opening the CMD window pressing the Options CCD button and selecting the Programs tab N B A standard licence code covers 2 computers CrysAlis r USER MANUAL 53 Agilent Technologies Inc Printed in Poland January 2013 E Agilent Technologies
37. c centric or non centrosymmetric acentric The numbers in each theoretical list are highlighted with lt gt to show the closest match to the experimental data 7 Space group systematic absence exception statistics are shown to help the user decide on an appropriate space group from the list below By default only the most likely space groups are shown but all can be shown D Inside input the Z value and chemical formula for the ins file creation Data on the formula weight density etc is given on the right hand side CrysAlis r USER MANUAL 42 INSPECTION AND MANIPULATION OF DATA 8 4 Filtering data The Filters menu enables the user to omit specific runs frames intensities theta values o values and a variety of other measures from the refinalized data It is accessed from the data reduction finalizing window 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 problems may be the reason for removing an outlier 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 problems use the same filter with two conditions F
38. data Based on the CrysAlis CCD and RED programs the CrysAlis e software provides greatly increased automatic functionality CrysAlis provides direct visual access to data collection and reduction as well as other functions all of which in a single multi threaded program can be performed in parallel This manual is designed to be a brief introduction to CrysAlis and its features For more in depth information the on line help which is embedded into the CrysAlis e software or the XRD forum www agilentxrdforum com should be consulted The use of CrysAlis re is limited to owners users of Agilent Technologies Oxford Diffraction equipment and their collaborators If you are interested in using CrysAlis e but are not an existing Agilent equipment user please contact xrdapplications agilent com 1 1 Contacts List CrysAlis re users are greatly encouraged to report any software bugs by sending details to xrdsoftware 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 features for future editions of CrysAlis For specific crystallographic enquiries use the xrdapplications agilent com e mail address and for general queries try the forum www agilentxrdforum com Hardware support xrdsupport agilent com Software support xrdsoftware agilent com Crystallographic quer
39. e 6 Clicking on Mount sample opens up a new window which activates the video camera and is used to align the crystal in the beam more details can be found in Section 8 5 From that window the Exit amp Screen button starts the screening experiment 7 By default ten images of the sample will be recorded which can be used to check sample quality and determine the details of the pre experiment see Figure 10 If the crystal quality is too poor the user can simply click on Mount sample again and repeat the process to quickly check through several candidate crystals Information about crystal quality and suggested unit cell parameters is shown next to the accumulated diffraction image SS Gees e Ka Pre experiment CO Alig Path and user Sample Experiment performer Name exp_29 Experiment exp_29 in folder C XcaliburData exp_29 Expected crema form oes ox KOR ox henrscai fe D ZA coment kx A Fast screening Delete cel Screening Lookup Progress of screening table Screening information well diffracting sample Diff limit beyond 1 22 theta res limit for I sige2 0 Mosaicity elel 3 e201 3 e301 1 deg Isoul 23 deg Detector distance 52 0mm Scan width 1 0deg Movie on ayo shutdown off Strategy mode Complete data default mode Exposure time 1 0s 4 0s Total Pre experiment Time 0 05 No Runs Frames 6 30 Experiment Finish Fri Jan 18 13 38 48 2013 Type of experiment C
40. e 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 9 1 13 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 9 1 14 Help The Help icon gives access to online help features version news and the command reference list 9 1 15 View The View icon switches between views Press the view icon re
41. ect the last image to be considered It is assumed that all frames between these two are available 3 Save the file Al You wiil 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 SAXI data set added to the experiment list NOTE Using CrysAlisPro you can process only SAXI images from APEX1 and APEX2 detectors First de SAI de file _1_1 sax or 01 001 of _01_0001 sfrm Last de SAX de file Browse n a Help Cancel Figure 30 Run list generator for SAXI 9 3 4 MAR Data from MAR image plates and some MAR CCD detectors e g MARCCD 165 may be processed with CrysAlis e via the command mar createrunlist Figure 31 8 m Run list generator for MAR data collections M o This dialog allows you to quickly generate a run file for the data reduction of a MAR data set 1 You select image 2 You select the last image to be considered It is assumed that all frames between these two are available 3 Save the file First de MAR de file _001 mar ext J Last de MAR dc file Browse n a Help Cancel Figure 31 Run list generator for MAR 9 4 File structure The correction files and experiment data are stored in different locations on the PC 9 4 1 Directory file structure The CrysAlis program system is installed in the following directory structure CrysAlis re USER
42. ection progress and a summary of the data reduction Additional features can be accessed via the gt buttons F SM PX button allows the user to switch the software between small molecule and protein modes 2 4 Software updates CrysAlis re is continually updated with new features and bug fixes Beta test versions of the software are in constant use by Agilent Technologies employees and the most stable of these is released for customer use approximately every six months Releases can be downloaded from the XRD forum Each new edition of CrysAlis ro is released with details of bug fixes and additions since the previous issue This information can be found in the Help menus under Reference section Version news It is possible to install a new version of CrysAlis e without having to uninstall the previous release If required older versions may be uninstalled using the standard windows remove programs procedure CrysAlis r USER MANUAL 5 HARDWARE CONTROL 3 Hardware Control 3 1 Device Control The Device control is only available when CrysAlis r is in online mode In offline mode only the status area Is shown Shutter K ray Shutter Closed Mo Closed S sg cw mje 10 Figure 3 Device control for the Xcalibur Gemini system left and the Supernova system right 3 1 1 Shutter Closed Open This icon indicates the current status of the X ray shutter this can either be Open red meaning the sample is exposed to X
43. ections Select Start to begin the pre experiment 4 1 1 CellCheckCSD The Cambridge Structural Database CSD is a database containing many molecular crystal structures and is populated by structures submitted to the Cambridge Crystallographic Data Centre CCDC Developed in collaboration with the CCDC CellCheckCSD is a freely available plug in via www ccdc cam ac uk for CrysAlis e Every time a cell is found or updated CellCheckCSD searches for hits or structures closely related in unit cell parameters to the found unit cell The CSD link appears in various places in CrysAlis software and Is a useful tool for spotting structures which are already in the public domain It is particularly useful during the screening process to check that the crystal isn t an unwanted starting reagent The number of hits is displayed within the link and clicking this link opens a window as shown in Figure 11 I Check CSD and local database ORNs Current cell oP V 993 1 5 97 9 05 18 38 90 0 90 0 89 9 34hits E Current cell Lattice centering oP 5 98 2 9 053 15 18 43 7 89 8 2 89 7 3 89 8 2 997 5 Data sent to CSD Lattice centering oP 5 969 8 9 052 5 18 383 11 89 99 5 89 97 7 89 89 7 993 2 cl See SEET en 117 O 19 O 18 11032 133 1 C16 O 26 0O23 M 12 M 10 100 0 100 0 99 9 99 9 99 9 99 9 99 9 99 9 99 9 99 9 991 9 991 9 991 9 992 4 991 8 991 7 992 3 991 3 991 6 989 9
44. elled A Unit cell for Strategy Calculation contains the proposed unit cell calculated from the pre experiment The user has the option to analyse the pre experiment data and change the unit cell by clicking on the Lattice Wizard button Full details on the features within the Lattice Wizard can be found in Section 7 B Strategy parameters it is possible to set the maximum resolution of the data collection choose how the strategy is collected by Laue symmetry or by the sphere of reciprocal space and set the detector distance If the sample is suspected to be of chiral nature the Friedel mates box should be un checked The Advanced button allows for greater control over the experiment setup and is discussed further in the online help C Strategy mode includes options such as complete redundant and time limited collections Clicking on the IUCr limit button reduces the coverage to 98 5 which is the minimum required for publication in an IUCr journal CrysAlis re USER MANUAL 16 STANDARD SMALL MOLECULE EXPERIMENT D Time prediction shows the predicted exposure times based on the pre experiment data and desired sigma value usually set to 15 for good quality data These values can be overridden by the user The strategy can be optimized based either on achieving a relevant sigma level or time constraint When collecting with copper radiation it is usually necessary to collect for a longer time at higher angles a ratio of 1 4 is
45. es 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 9 1 7 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 9 1 8 Zoom in This option 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 9 1 9 Zoom out This option 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 9 1 10 Zoom localiser The zoom localiser is a floating semi transparent window which display
46. es with overflow correlate the images and whether or not or use dark images For typical screening experiments with exposure times less than 60 seconds none of these options are required The Edit exp options button contains some advanced settings which are further discussed in the online help E The Export in other formats section allows the user to export images from the screening experiments in formats suitable for external programs The options here are XDS Mosflm and Denzo HKL 2000 Once the screening experiment has been optimised press Start The data will be collected and the sample will be automatically evaluated and displayed in the Crystal Screening tab Figure 14 Crystal Screening 3 PEAKS UB fit with 6F obs out of 67 total 67 skipped 0J 100 000 UNIT CELL PG 1 anorthic triclinic P 26 65907 30 8102 33 636 16 69 3405 72 623 67 7804 Me 24243 20 QUALITY Fredicted resolution inf Suggested exposure time for I s1g 10 0 11 2 sec deg Mosaicity 1 0 46 ef 0 52 3 0 53 deg Is0 0 50 deg partials used 15 Overlap area 0 00 scan wi dth 1 0 dd 52 0 EEE Go to strategy Figure 14 Crystal screening tab CrysAlis r USER MANUAL 23 DATA COLLECTION FOR PROTEIN CRYSTALLOGRAPHY There are three sections to be considered Peaks Unit Cell and Quality Peaks shows the percentage of the found peaks or spots which fit the unit cell Selecting the Peaks link opens up a Peak search window
47. eserve the tube life by lowering the voltage and current settings to stand by values after a period of non use Programs direct CrysAlis to the location of your favourite structure solution program E mail set up hardware software and experiment status notifications emailed directly from your system e g low N level generator trip Laue group change end of experiment 3 4 Service This power tool collects those service commands most commonly accessed by the user into one defined area It is recommended that they are only used under guidance from Agilent employees These commands include e Shutter to manually control the opening and closing of the shutter e CCD options to reinitialise or reset the CCD or remove the dark images e Goniometer for direct goniometer control and home flag search e Image control CCD pars to change any CCD parameters and record diffraction images e Configuration file paths points the software to specific CCD setup file par file and Correction files geo ffi ffinf and ccd files e Instrument calibration to start new or resume calibration experiments 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 e Align SuperNova optics should not be used unless the user has been appropriately trained e Tools the Make zip is a useful feature for z
48. f 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 Point click on the outer corners of the crystal shape The first point will be a red cross and subsequent points will be yellow crosses To finish outlining this view of the crystal click again on the red cross Rotate the crystal and repeat until a suitable shape Is defined CrysAlis r USER MANUAL 43 INSPECTION AND MANIPULATION OF DATA 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 Any face marked with an are redundant and may be deleted Refinement of the defined crystal shape can be carried out by clicking on the Scale3 abs button in the Data reduction results window A movie which clearly demonstrates the face indexing process with a worked example is available to download from the XRD forum STARTISTOP GOES ep CECD 9990 0 000 0 0000 0 0 Ss Figure 27 Abs display window showing crystal image and face indexing details CrysAlis re USER MANUAL 44 APPENDIX 9 Appendix 9 1 Layout and control
49. g any external frame formats the first and last frames need to be provided and some additional information about the setup some parameters are taken from frame headers where possible We do not offer full support for this feature since it relies on data formats and detector parameters which are outside of our control For any queries with these features contact xrdapplications agilent com 9 3 1 Dectris CrysAlis e supports processing of Dectris detector frames via the command dectris createrunlist At the moment only the detector for Swiss Light Source instrument 6M is implemented The detector gaps of the Dectris detector are automatically handled Figure 28 CrysAlis re USER MANUAL 49 APPENDIX Bun list and aliases file generator for DECTRIS data collections ed Se 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 name cht 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 will 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 m First de DECTRIS de file 0001 cbf Last de DECTRIS dc file Browse n a Ee Help Cancel le Figure 28 Run
50. gles 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 9 1 5 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 Lin 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 CrysAlis r USER MANUAL 46 APPENDIX 9 1 6 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 objects and remov
51. gnifying glass button resets the zoom and the slider allows zooming in or out The CrysAlis r USER MANUAL 31 LATTICE WIZARD compass button calculates nice views of the lattice Le views where most empty space can be seen Movement of the slider scrolls through all of the nice views Figure 18 Figure 19 Ewald Explorer tool bar part 2 Thea hand e buttons show views along directions of the lattice The R R switches between the regular and reciprocal axes Selecting the unit cell button toggles the unit cell in the lattice view window The arrow next to this allows selection of different or more than one unit cells in the case of twinning The spanner or wrench button allows editing of the visual settings within Ewald Explorer and the views button changes between orthogonal stereographical and gnomic projections Figure 19 7 3 2 Lattice viewer window This window displays the peaks found during the peak hunting process It is possible to rotate the view by holding down the left hand mouse button and moving the mouse To zoom hold down the right hand mouse button and move the mouse To rotate the display in the plane of the page hold down the left hand mouse button and with the Ctrl key 7 3 3 Crystal tab The crystal tab allows control of the lattice Here you are able re index peaks carry out lattice transformations and also search for and index both twinned and incommensurate samples The distribution histograms pr
52. hed Click on Start Experiment to begin By default a movie is taken of the crystal for later reference or for face indexing see Section 8 5 and after reference dark images are recorded the experiment will start 44 Data collection During the data collection it is possible to stop the experiment at any point by clicking on the Start Stop button and selecting Stop All The experiment can be resumed from this point at a later time assuming the crystal has not been taken off the goniometer head by clicking on Start Stop and selecting Resume All Whilst the experiment is running access is available to three information cards on the right hand side of the screen Crystal Data Collection and Data Reduction A fourth card named AutoChem will appear if the relevant software has been installed and license purchased see Section 9 6 The different cards can be maximized by clicking on the relevant card name Additional options for the cards are found by clicking on either the card name when maximized or the gt buttons The Crystal card displays the current unit cell information the sample chemical formula Z value and machine model parameters Also displayed will be the Average unit cell from Proffit CrysAlis s cell CrysAlis r USER MANUAL 17 STANDARD SMALL MOLECULE EXPERIMENT refinement algorithm and the Final unit cell for selected space group Clicking on the arrow symbol at the top of the card gives access to several extr
53. ies xrdapplications agilent com General information and resources www agilentxrdforum com CrysAlis r USER MANUAL 1 INSTALLATION 2 installation To install CrysAlis re you will first need to obtain a copy of the CrysAlis e executable file and the Corrections folder from your diffractometer PC The executable comes in the following form CrysAlisPro171_XX_YY exe where XX current version number and YY the current release number Step 1 Double click on the CrysAlisPro171_XX_YY exe program Follow the on screen instructions Step 2 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 Step 3 Once installation is complete double click on the CrysAlis e icon which has been installed on the desktop Step 4 If this is first installation of CrysAlis on your computer the user has to choose between two scenarios of first use There will be a message box saying Choose start up mode Do you want to set this application for Data Collection Yes The computer is a data collection machine connected to Oxford Diffraction Agilent Technologies hardware This will open the CrysAlis setup par file generator The dialog will guide you through a multi step procedure to collect all system relevant information It will require you to have the media with all correction files ready No Your computer is intended for data
54. iffraction experiment to be performed or in offline mode the ability to convert a collection into a 2D powder pattern 6 2 1 Powder experiment Load a powder sample onto the diffractometer and align using the standard method Samples may be mounted on a loop using a small amount of mineral oil or in a capillary Click on the Powder power tool icon A window will appear with various options e Path change the output file name e Options choose to export the data in XYE or GSAS format if required e Experiment Movements add constraints for the scans to be used CrysAlis r USER MANUAL 26 OTHER DATA COLLECTIONS e Target set the detector distance and resolution to collect to e Exposure Time set the exposure of the frames e There is also an option to use a cryodevice for the experiment When all options have been configured press the Start with analysis button to begin the experiment A new window will appear which shows the powder diffraction graph for the sample Left clicking on the graph zooms in and right clicking zooms out NOTE when collecting a powder pattern it is important that the machine parameters are well calibrated at the exact detector distance used More information on collecting powder patterns can be found on the XRD forum 6 2 2 Powder pattern creation It is possible to extract a 2D pattern from powder data or generate a powder pattern from a single crystal data collection open up the relevant experiment in an
55. ipping up complete experiments into a single file for easier archiving or to send to the software team for problem resolution WARNING It Is advisable to contact a service engineer or e mail xrdsupport agilent com before attempting manual goniometer control as no collision protection is provided in this mode Calibration Generally calibrations are run for three purposes e Instrument model calibration e Instrument model calibration at specific detector distances useful for powder experiments CrysAlis r USER MANUAL 10 HARDWARE CONTROL e Instrument model calibration with additional flood calibration lf 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 dual wavelength systems the procedure is carried out for both sources In order to save time calibration 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 Figure 8 The calibration can be monitored in the Command Window 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 As the amount of data required for a system calibration is ty
56. is not generally necessary to change any settings however listed below are some usful options which may be employed Fonts Peaktable Colorcodes Beam stop Angular limits Goniometer Run list size CCH Processing User access Distance calibration SM PX Camera Compression Dark Generator Programs E mail Instrument model Instrument modell Monochromator This dialog allows you to modify the instrument parameters for the detector and the goniometer Detector di 0 000 d2 0 000 Org PCS dd 52 000 x 1024 000 i y 1024 000 Pixel size mm 0 Goniometer om 0 000 i th 0 000 ka 0 000 i he oooi L Edit po al 50 000 Edit al T Saveto mastertie on eat prm Figure 7 CCD options window CrysAlis re USER MANUAL 9 HARDWARE CONTROL Fonts use this tab to change the displayed font size in specific windows of CrysAlis Pre Beam stop allows adjustment of the beamstop mask Reflections that fall under the mask are rejected This is set up during installation but can be adjusted here Decreasing the size may help retrieve low angle reflections and can also improve the quailty of the extracted powder patterns Goniometer allows acivation of de icing runs at the end or during data collections This is useful when using a low temperature device coulped with long exposure times Generator here it is possible to set the time for automated generator ramping This will help pr
57. isplay CCD status gives feedback of the current status of the data collection CCD thread only in online mode RED status gives feedback of the current status of the data reduction RED thread Progress bar shows the progress of the current process for example the percentage completeness of the pre experiment or data collection 3 3 Command CMD Shell This button on the left hand side of the main screen opens a history window with an attached command line CrysAlis e may be run automatically through the GUI menus and buttons or manually using commands entered into this command line The user can access all existing and historical functions using manual commands Either the entire experiment may be run completely in this mode or the window may be opened simply to issue specific commands A list of commands and their functions are available in the online help or type COMMAND HELP into the command line The main part of the window contains a history terminal which is always active continuously updated and can be referred to by the user for further information This history window can be viewed in either CCD or RED modes and it is possible to toggle between these using the tabs at the top of the window The CCD tab is only available when CrysAlis is in the online mode When issuing commands it is important that the correct mode is chosen The command shell window can be opened or closed at any CrysAlis r
58. its and apply filters used for discarding outlier peaks and images 6 Data items in hkl file Alter beam path information this can help with absorption correction It is possible to apply this to specific batches or runs 7 User modifications various data export items as well as the option to edit the absorption correction package via the Edit ABSPACK button The user can also choose whether to perform Space group determination via GRAL see Section 8 2 and structure solution via AutoChem if installed The resolution for completeness can also be adjusted Any re finalized data can be saved under a different name with the Change output name button Clicking on OK will refinalize the data NOTE The best way of maintaining consistency between all files hl mp me cif for a given experiment is to use the Refinalization menu to impose any changes Data reduction finalizing rrp file to hkl file 1 6 6 ml Chemical formula Absorption conection cli eil Ze 4 00 CNA Ach face based absorption correction Outlier rejection Use outlier rejection mmm v C Don t use outer rejection oP 5 96673 9 04502 18 41304 90 02213 89 388678 90 02869 M Use Friedel mates as equivalent TEM _Sphericalabs urj 1 062 Sigma calculation control O verlap twin reject Limits fiters and lattice extinction filters Iw Estimate error model WV Neg intensity sigma limit 20 Override rejection par Edit rej par Resolution Ce Nofite
59. l open in data reduction 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 the experiment database 2 1 1 Opening CrysAlis re in the offline mode opens a window which allows browsing within a list of Select experiment experiments Figure 1 Open CrysAlis experiment 1 0 38 61 experiments available Select experiment Name of list list Leni SC De ech pre exp 15 pre exp 19 exp_20 pre ep 20 exp pre ep Al exp_22 pre ep 22 exp_24 pre_exp 24 pre_exp 26 exp 2 pre_exp 2 exp 28 pre_exp A8 pre ep 20 pre_exp 31 pre_exp 32 pre_exp 27 pre_exp 34 pre_exp 28 pre_exp_4 exp_S Cicaliburbatai Cicaliburbatai Cicaliburbatai Cicaliburbatai CtcaliburData T icaliburData CicaliburData CMcaliburData CMcaliburDatat CMcaliburData CicaliburDatat CicaliburData CMicaliburData CcaliburData CcaliburData CcaliburData CtcaliburData CxcaliburData CcaliburData CcaliburData CcaliburData CcaliburData CcaliburData CMcaliburData Thu Jul 1912 15 43 2012 Tue Sep 20 08 46 19 2011 Tue Sep 20 09 07 52 2011 Tue Sep 20 12 43 01 2011 Tue Sep 20 12 42 04 2011 Mon Feb 06 10 03 15 2012 Mon Feb 06 10 01 15 2012 Tue Mar 20 09 17 42 2012 Tue Mar 20 09 07 46 2012 Tue Apr 24 17 26 05 2012 Tue Apr 24 16
60. lection 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 3 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 4 The Red Graphs window area displays a run by run visual summary of the data scaling coefficients absscale a frame by frame plot of Rint and a number of comparisons regarding the coverage and or completeness of the data 5 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 Cryo device a plot of temperature and flow rates against frame number and two further charts for 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 The data reduction procedure generates a rrpprof file which contains all integr
61. lp and XRD forum 7 3 4 Filters Tab The Filters tab is a feature which controls the reflections used for indexing There are three ways to filter your data by intensity d value or run number see Figure 21 The intensity and d value filters are controlled by firstly ticking the appropriate check box and then selecting a range by dragging the mouse whilst holding down the left hand button The peaks in the selected range turn green and are marked as hidden If a mistake is made use the Undo or Clear buttons To filter using the run list simply de select or hide the runs which are not required CrysAlis r USER MANUAL 33 LATTICE WIZARD Theta i o 38 500 39 39 2 o 43 546 80 80 3 o 104 937 46 46 4 o 104 937 37 37 5 o 104 937 41 41 gies 104 937 81 81 o Hide systematic extinctions for Pattice none Operations K Move hidden to Go sl i Move visible to Figure 21 Filters tab in the Ewald Explorer It is possible to then move either the hidden or visible peaks into a different group Groups are discussed in section 7 3 6 7 3 5 Selection Tab The Selection or Lattice It tools allow easy selection of peaks in the lattice viewer The three buttons allow for different modes of selecting the peaks in the viewer Select All Invert selection and Deselect all Figure 22 Selection Lattice It Select all Invert selection Deselect all Selection tools e None C Rubber band C Lattice It Ei
62. mes The output files are in hkl format and also in CCP4 mtz format if this option has been selected in the SM PX window 5 4 Exporting files If other programs are preferred for data processing using the Export button on the left hand tool bar opens a window with option to generate image files suitable for mosFLM XDS Denzo HKL 2000 or in an Esperanto portable format 5 5 Advanced data collection modes Other data collection modes are accessible from the Start Stop button which are summarised below CrysAlis r USER MANUAL 24 DATA COLLECTION FOR PROTEIN CRYSTALLOGRAPHY e Resume all prompts user to locate a specific run file to continue collecting data and the automatic data reduction This uses both the CCD and RED threads e Resume data collection only prompts the user to locate a specific run file to continue collecting data This uses the CCD thread only e Append data collection prompts the user to locate a run file relating to the completed experiment Once selected a strategy window appears allowing the user to add additional runs to the experiment to expand the data collection CrysAlis r USER MANUAL 25 OTHER DATA COLLECTIONS 6 Other data collections 6 1 Special Append data collection On completing an experiment in certain cases it can be 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 facili
63. omplete data for publication Lag 15 0 Resolution 0 837 I Interactive strategy after pre I Attempt AutoChem Goniometer Omega Theta Kappa Phi Distance Generator e 106 1 35 0 70 0 0 0 52 0 50 0kV 0 80mA WW keen tart Figure 10 Full screening window with strategy options highlighted 8 There are three details to consider when deciding whether a crystal is suitable for data collection e Peaks The number of peaks that fit the proposed unit cell is shown e Unit Cell Details of the point group and lattice parameters are given based on the screening data collection The user has the option to access the CSD module at this time to compare the unit cell with other structures present in the database see Section 4 1 1 for further details e Quality Estimates of the sigma values are given out to various resolution values and a guide is given as to how well the sample diffracts The diffraction limit and mosaicity of the sample is also estimated CrysAlis re USER MANUAL 13 STANDARD SMALL MOLECULE EXPERIMENT 9 Details of the calculated pre experiment are shown at the bottom of the screen with the option for the user to define what strategy they would like to aim for with regards to the actual experiment Figure 10 To override the suggested settings the slider allows for a manual adjustment of the exposure time and the drop down menu offers different types of experiments such as complete redundant or time limited coll
64. or 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 NOTE Filtering data will inevitably lead to a loss of completeness For this reason filters should only be used when absolutely necessary 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 image can be rotated by pressing the Page Up or Page Down keys Figure 27 shows the window with an example of a modelled crystal shape 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 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 The faces may be indexed either by using the Drag or Point methods Drag click and hold the left mouse button moving the mouse 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 o
65. orption corrections e Filters and merging e Space group determination including specific control using the space group options window DC PROFFITRRP TWIN 1 0 9 Twin data finalization rrpprof files For twin Finalization Chemical formua Component 1 E KC4H506 i 9 00 Component 2 EIER exp_S11_twin2 rrpprof oP 7 612 7 790 10 652 90 00 89 96 89 97 Gomponent 3 None LATTICE 3 Lattice symmetry Use Friedel Gomponent 4 Remove Noe LATICE 4 SS mm sl KE Se Twin finalization log File From previous run exp_511 twinlog equivalent Twin decomposition scale3 abspack scaling uniformity empirical absorption Full overlap threshold 0 800 Tdl tdCS dek Common scales for all twin components JV Use ABSPACK Edit ABSPACK Remove exp_511_twin1 rrpprof oP 7 614 7 789 10 653 90 02 90 03 89 97 Corrections Override overlap threshold for HKLF4 export 0 800 Separate scales for all twin components Numeric and spherical absorption correction Apply absorption correction Gfaces 14corners 21 edges 2 Apply nja Grystal with 0 045600smnms t eq 0 221 95mm rel p O 61544mm 1 Export options Data items in hk Files HKLF4fAKLES A A Filters and lattice extinction filters ayauetAnay inte O71 z Ents D k F St res T Beam path information for absoprtion correction special Formats Resolution Zeta dea 0 00 60 00 TS Ce No fiter use filter for P tattice v o active fite
66. ovide a visual plot for determining the quality of indexation Figure 20 Crystal Log window LATTICE CSD install 5 9591 4 9 0344 6 18 3940 12 89 989 5 89 988 5 89 995 5 V 990 27 11 oP index 98 8 Overlay off Activate multicrystal Activate incommensurate peaks Distribution histograms 2 vectors projection 0 1 2 Figure 20 Crystal tab in EwaldPre CrysAlis r USER MANUAL 32 LATTICE WIZARD Lattice opens a menu giving the following options e Auto unit cell finding in shown peaks e Refine unit cell e Custom unit cell finding in shown peaks e Lattice improvement with tolerance e Modify lattice type e Modify lattice type with user matrix CSD opens up the CellCheckCSD window to check your cell against database entries see Section 4 1 1 Overlay off Toggles on off the unit cell lattice in the viewer window Activate multi crystal Selecting this link shows a menu with the following options e Automatic twin finding e Custom twin finding e Find next component in wrong peaks e Find next component in shown peaks e Custom component in wrong peaks e Custom component in shown peaks e Goto UM TWIN UB matrix setup for twins Twinning and the use of the multi crystal tools are described in more detail in the online help and XRD forum Activate incommensurate peaks This link allows the addition of modulation vectors Incommensurate indexation tools are described in more detail in the online he
67. peatedly to cycle through the CCD RED and USER displays The header window bar is updated to show which view is being displayed 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 the computer is not connected to the diffractometer 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 CrysAlis r USER MANUAL 48 APPENDIX 9 2 Key to power tool icons Strategy tool 2 WinGX launcher if installed e man lex her if installed D Second instance of CrysAlis r Crystals launcher if installed e Powder diffraction AutoChem if installed apane Multi Temperature Wavelength T 100 IK e Table 2 Power tool icons 9 3 External detector frame formats It is possible to process external detector frame formats in CrysAlis and this is done via commands in the command shell When loadin
68. photo reconstruction tannanna nannan 37 1 9 LOGANA et 38 8 Inspection and Manipulation of Data 39 8 1 REIMANA O DEEN 39 8 2 TWIN data Tnalzaton anana 41 CrysAlis r USER MANUAL CONTENTS 8 3 RUNMING EC Se Bleu Le TE 42 8 4 FL FIA data EE 43 8 5 Crystal shape modelling face mdevmg 43 Si HIE 45 9 1 Layout and controls eriin ia 45 Jkl mage li EE 45 TIZ De ei re EE 45 Ia wld Peers eege EE 46 9 1 4 Header information K goniometer angles ccccsessescsessesssesscscsessssesececsesecessesesseesessesesasenes 46 eee Cut IM EE 46 JLO Lookup EE 41 Ee E o o e EE 4 e OOO 47 ed OOM E 47 9 1 10 TAALA ETEA ro a ner a AA A A PP PP A 47 9 1 11 MESOMION TING E 47 9 1 12 RR SE ee UE 48 9 1 13 3D Peak profile Rocking Curve ccc ccescesscsssssscsesesscsesecscseseceesesecsssesessesesassesesaesesassesesatenes 48 9 1 14 Eerst erer eiert eerste 48 FIIS TEE 48 9 2 Key CO OWE ee te EE 49 9 3 Extermmakdetectorirame OKT 49 OSC E WE KE 49 LOE ue TEE 50 Sg Ee 50 dE E VT eee ee 51 9 4 EENE EE 51 9 4 1 Directory file structure 51 942 Expernment nle get EE 52 9 5 le CSD IS tal Er EE 53 9 6 AutoChem IS tal ACO EE 53 CrysAlis r USER MANUAL CONTENTS FIGURES Figure 1 The experiment list WINdOW ccceccessscsssscsrssssssescsessesseecsessesaesessesausacsesensaesassesensausassesensansassesensansasees 3 Figure 2 Main window of CrysAlis e software Note that some icons are greyed out inactive during d
69. pically less than that required for a structure determination an option is included to collect additional frames for those users who wish to refine structures from calibration data for system benchmarking Name a_63 Settee aC XcaliburData mere Experiment in folder C XcaliburData calib_a_63_Fri Jan 18 13 31 16 2013 Basic system Sege Generator at end of experiment Gain Mo 90 00 double correlated divide by 2 Gain Cu 40 00 double correlated divide by 2 Dd No change zero Mo 12 00000 Dd zero Cu 12 00000 Overflow threshold 230000 Beam stop support Wee Gen orientation gemini Atlas 2x2 binning 1024x1024 pixels Dark subtraction on Flood correction off Pu Options Calibration mode Crystal viid Lattice type P attice v Lattice min 2 max 30 e Optimal C Manual f User C Constraint ar Dig Collect extra data for better structure refinement Exposure time same ta positions 2 0s Detector distance 55 00 Scan kv 50 00 mA 0 80 range 40 0 Scan width 2 0 Far Exposure time the same for all theta positions 2 0s Detector distance 115 00 Scan L Cut kV 50 00 mA 0 80 z SSES idth 2 0 Cu far Automatic flood field correction calibration Run flood calibration ar Collect extra data for better structure refinement Exposure time the same for all theta positions 2 0s Detector distance 55 00 Scan Monear kV 50 00 mA 0 80 E 20 0 Scan width 1 0 Mo near Far Exposure time the same for all the
70. pply a matrix to apply to transform the unit cell 7 6 Twinning multi crystals The options available in this button are now also included in the Ewald gt Activate multi crystal It is recommended that the twinning tools are used from within this window CrysAlis r USER MANUAL 36 LATTICE WIZARD 7 7 Incommensurates Quasi crystals As with the Twinning tools the incommensurate tools are now best implemented from within the Ewald Explorer gt Activate incommensurate peaks 7 8 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 If required adjust the number of runs frames used in the unwarp reconstruction by clicking on the relevant run in the main text box The whole line occupied by that run should be highlighted in blue Now click on Edit start num of selected run or Edit end num of selected run Enter the desired parameters Setting the start 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
71. que settings for this experiment Frames directory frames contains all the frames in img format Log directory log contains logs for CCD RED and USER threads in txt format Movie directory movie contains jpg images collected as a rotated movie of the crystal Plots de directory plots_dc contains information logged from the various hardware components of the system dat files blots red directory plots_red contains information on scaling Rin and other integrated data output functions dat files Struct directory struct is set aside for storing structure solution and refinement files CrysAlis r USER MANUAL 52 APPENDIX 9 5 CellCheckCSD installation CellCheckCSD works during the Pre experiment and data collection and automatically provides close unit cell matches from the Cambridge Structural Database CSD A variety of information is freely available and if you have a local CSD or WebCSD license you can view the full details directly in Mercury or WebCSD To make use of this tool you need CrysAlis version 35 or later and download CellCheckCSD from the CCDC website www ccdc cam ac uk tree_services cellcheckcsd Here you will need to register which is free for anyone and download the licence and CellCheckCSD files Once installed direct CrysAlis to the installed location by clicking on CCD RED Options gt Programs and browsing for the correct file 9 6 AutoChem installation
72. r use filter for tee Data items in hkl file for use in external programs User modifications I Beam path information for absoprtion correction special formats Export ev file eege Export Stoe crs Export sadabs _1 raw I Batch number Each run gt 1 batch Edit hatch W Export CIF file Add hkl data to CIF Update overwrite hkl file in WinGX and Olex2 subfolders struct _exp_475 provided Scaling and empirical absorption that output hkl file is compatible with existing structure V Space group determination GRAL Use overlap rejection F Use twin rejection 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 Output file name C X lt caliburD ata Ylid exp_475 exp_475 Structure solution AutoChem _ AutoChem options a ZE Figure 25 Data reduction finalizing window CrysAlis re USER MANUAL 40 INSPECTION AND MANIPULATION OF DATA 8 2 Twin data finalization As with standard data sets twinned data can be altered by changing the settings in the Twin finalization module Figure 26 This button 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 Multi scan absorption and scaling e Application of face indexed abs
73. re experiment 3 1 3 E ee ee Pro amp Pre experiment Leg Fath and user Sample Experiment performer Name exp_3 Experiment exp_3 in folder C XcaliburDatalsim exp_3 Path is ok Browse root folder C icaliburData sim Expected chemical formula Get Last used formula Comment Sample description Mount sample Fast Screening Configure Pre Manually Screening Experiment options Information ro Omega Thee kapa Phi og 60 0 2L 2AL 0 0 0 0 0 05 mA Figure 9 Pre experiment screening window for small molecule experiment 4 Inthe Path and user Sample section input the sample name and path for storing the data files If known enter the Expected chemical formula which is used for absorption corrections and assisting in structure solution and add a comment about the sample The last used formula can be recalled with the Get Last used formula button The user running the experiment can be set with CrysAlis re USER MANUAL 12 STANDARD SMALL MOLECULE EXPERIMENT the Set user button and additional details about the sample can be recorded using the Sample description button 5 The user now has three options to proceed to the Mount sample screen to align the crystal to go Straight on to Fast Screening of the sample with setup options configurable from the gt gt button or to setup the pre experiment manually via the Configure Pre Manually button The default choice for most users will be Mount sampl
74. rs Merging JV Export CIF file Add hk data to CIF HKLF4 only E Use Friedel mates JV Space group determination Options V Merge data using Te the same Laue class as Equivalent IT Remove outliers different Laue class Jun Gompleteness 0 60 Ang I Update overwrite hk files in WinGX Olex2 or and AutoChem folders I Structure solution AutoChem Weel Figure 26 Twin data finalisation window One feature here which is unique to twin data finalization is the full overlap threshold setting 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 CrysAlis re USER MANUAL 41 INSPECTION AND MANIPULATION OF DATA The Separate scales for all twin components option allows for the application of different scaling models for each set of twin reflections 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 differences in the volume fraction of each twin 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 hklf4 file provided your sample has space
75. rute force indexation of known cell allows the user to input cell dimensions and search using a specified number of reflections The Stop if gt figure should be set to no greater than 30 50 for the best chance of success e Set orientation matrix by hand using prior knowledge about the unit cell and matrix it is possible to manually adjust the orientation matrix e Search for smaller unit cell volume forces the search to look only for cells with a smaller volume ZA Ewald ro Ewald re has been designed as a replacement for the existing reciprocal lattice viewer Ewald explorer as of v36 20 The new interface has been designed to provide easier access to peak manipulation and indexing tools whilst adding some new features such as groups This tool is useful for indexing difficult diffraction patterns such as twins or incommensurates but describing its use for this purpose is beyond the scope of this user manual These features will be shown using examples in the online help and XRD forum The small arrow next to Ewald Explorer in the Lattice Wizard allows access to Peak table editing control over Peak table flags Axial photo generation and the Old Ewald explorer The large Ewald Explorer button opens a window containing the features described below 7 3 1 Tool Bar Figure 18 Ewald Explorer tool bar part 1 The three X Y and Z buttons rotate the lattice around each axis axes of rotation are denoted by the arrows The ma
76. s gt Ce Look up table CG Zoom localiser window Resolution rings 2D Peak profile a line profile X 3D Peak profile rocking curve B pee m f E mae heater information ae View CCD RED USER Table 1 Control buttons in CrysAlis r 9 1 1 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 9 1 2 Predictions Once the unit cell has been determined sensible predictions can be overlaid 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 CrysAlis r USER MANUAL 45 APPENDIX 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 CrysAlis re GUI The predictions overlay a cross rhombu
77. s 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 This behaviour is the default setting of the auto mode however should the user need to re evaluate the data they can at a later stage If AutoChem is installed structure solution will also be attempted every 25 frames 4 5 Data reduction 4 5 1 Automatic data processing To reprocess data after data collection with automatically determined settings first open a second offline version of CrysAlis e 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 peak hunt and find the unit cell parameters before processing and scaling the data It will then determine the space group and output the ins and CrysAlis r USER MANUAL 18 STANDARD SMALL MOLECULE EXPERIMENT hkl files If the user has found the unit cell by hand using the Lattice wizard click on Start Stop and select Automatic data reduction 4 5 2 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
78. s or diamond and square to show 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 9 1 3 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 values 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 background 9 1 4 Header information K goniometer an
79. s 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 9 1 11 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 CrysAlis r USER MANUAL 47 APPENDIX 9 1 12 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 peak can be obtained to aid the user in the evaluation of the quality of th
80. ta positions 2 0s Detector distance 115 00 Scan wl S wl ve SE Morar Automatic flood field correction calibration Run flood calibration User message Ready UE Se End of calibration Fri Jan 18 15 00 27 2013 1h29min Figure 8 Full calibration experiment window CrysAlis re USER MANUAL 11 STANDARD SMALL MOLECULE EXPERIMENT 4 Standard small molecule experiment This section explains the main features involved in performing a single crystal diffraction experiment for small molecule samples from the initial screening of samples to analysing the data from the pre experiment devising a suitable data collection strategy and finally to the data collection reduction and structure solution Before beginning an experiment it is useful to have some knowledge of the chemical composition of the sample to select the appropriate system parameters e g wavelength temperature detector distance 4 1 Screening 1 Check that the appropriate X ray source is selected if using a dual source system and that the generator settings are correct see section 3 1 5 2 Ensure the software is running in small molecule mode by checking that the CrysAlis r icon on the bottom right of the screen has the suffix SM If not then click on this icon and select small molecule mode in the SM PX window 3 Click on Start Stop and select Start new experiment The pre experiment window will appear see Figure 9 Agilent automode p
81. tructure solution and refinement plugin programs to run If installed correctly corresponding icons will appear on the left hand side of the main screen 4 6 1 AutoChem2 AutoChem2 is an updated integrated feature designed specifically for CrysAlis e version 171 36 20 and higher Developed exclusively for Agilent Technologies by the authors of Olex2 QlexSys UK AutoChem2 represents a significant advancement over the original AutoChem program and is seamlessly integrated into CrysAlis for automated real time structure solution and refinement during data collection experiments AutoChem2 is not included in CrysAlis e as standard and must be installed as a separate software plugin If you have purchased Auto hem as part of a new system installation an applications scientist will install AutoChem2 for you or provide instructions For all other installations including trial licences limited to 30 structures please refer to the guide on the XRD forum 4 6 2 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 CrysAlis e are automatically loaded Assuming the data has been processed the ins hkl and cif_od machine cif files will be imported into a directory within the main data directory with the path struct wingx_samplename The user can then solve the structure using a choice of
82. ty 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 obtain a complete data set to publish such data it may be necessary to collect more of the Friedel pairs 1 On completing the experiment click on the Start Stop button and choose Append data collection 2 Select the run list used for the experiment you want to add to run file 3 In the 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 4 The user can then change the strategy details to collect more data either by increasing the resolution redundancy or by changing the coverage 5 Click Calculate new strategy The software will then provide the user with a suitable experiment to collect the extra data required 6 If further changes are required Undo Strategy must be selected before the extra changes are applied and Calculate new strategy selected This avoids overwriting the previously collected data 7 Click Start Experiment to collect the extra frames 6 2 Powder diffraction The Powder power tool icon on the left hand side of the main screen allows in online mode a powder d
83. will take 3 Click on the Browse for output dir button and create a new folder where the reconstructed images will be stored 4 To generate the three most common layers hk0 WU 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 5 To generate a specific layer click the New layer button The user can then 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 to accept the details for the layer 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 the 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 6 If required click on the tick box marked background subtraction Click on Next 7 Apply any data corrections including a scale factor by clicking on the Edit user scale H Click on Finish CrysAlis r USER MANUAL 37 LATTICE WIZARD 9 The defined layer or layers will now be reconstructed A process
84. y Note that this can also be accessed directly by clicking on Start Stop and selecting Start New no pre experiment if no pre experiment is required The window has several different components Expenment Strategy LLS sutomode suggests exposure time t Leer scan F Unit ce for Strategy Csiadston CSD not dane Celt 5 970 2 9 056 2 18 397 9 89 99 3 89 98 3 89 98 2 994 617 oP Pisto 100 00 157 of 157 reflections i Time prediction based on data to 0 800 9 ee re a on Are z Bescher res ZThets 0 300 R ome os preoa e merged S pana Fi Lisigma 1o Jas zs Dusas O mm E The same tme for al theta postons jV Foede mates are equvalent uncheck for hgh quality absolute canfigureton data Different sme for each feta postions FC ER ae Detector Distance 60 00 Predicted resotuton bevond 0 80 er vee Scanwidte 100 Strategy mode Compiete data default mode k D imat 200 0 IVC ima Max 99 61 ett EEN Settings Optors Generates runs thet reech C completeness limit CCD process Current Strategy No runs frames 2 140 Total experiment time Oh 12m Expected experiment finish time Thu Jul 12 11 14 40 2012 Completeness Coverage curves Completeness Coverage tables Completeness in mmm ris SI 3 60 4 F rio Completeness Coverage abe 18009 10 Huepunpay ee 10 ssaUa 3 duI09 10 Luepunpay Figure 12 Experiment strategy window with each information section lab

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