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M86-E00078 APEX2 User Manual.book

1. Figure 4 11 Sample locked window Program Start Up and Shutdown 4 3 Client Computer Shutdown NOTE The order of stopping these programs is important If you attempt to close the database before APEX2 is stopped the database will remain open until APEX2 is stopped 4 3 1 Stopping APEX2 1 For Windows or Linux systems click on the X in the upper right corner of the window or click on File gt Exit in the upper left It is not necessary to disconnect from the instru ment 4 3 2 Stopping the Database la For Windows systems click on Start gt Pro grams gt Bruker Nonius Programs gt Stop Database or click on the Stop Database icon s 1b For Linux systems in a terminal window enter bnrun stopdb or click on the Stop Database icon APEX2 User Manual A window will appear and quickly disappear and the Start Database window will close Start Database DEBUG checkpoint record is at 073275080 redo record is at M 3275888 5 undo record is at 07 0 shutdown TRUE next transaction id 21669 next oid 83108 z database system is read G pq_recubuf recu smart whutdown request Figure 4 12 Stop database screen NOTE Occasionally the windows won t disap pear and the Start Database window will display a smart shutdown request see Figure 4 12 This message means that the database is wait ing to close until applications that it might write to are closed Exit APEX2 t
2. colorramp Colored SCD ICM This is the typical BAXS orange display The most frequently used other color choices are Black On White SCD ICM White On Black SCD ICM The Blues ANY ICM Other color ramps are in Windows C bn src gui intensitycolormaps Linux ust local bn src gui intensitycolormaps M86 E00078 E 3 Config APEX2 User Manual This 1s how user positions can be defined userpos1 name Zero dx60 type n dx 60 0 theta 0 omega 0 chi 0 phi 0 0 i If you want angles other than zero the import projtls and del projtls must be used import projtls userpos2 name Chi45 dx90 type n dx 90 0 theta 10 0 projtls degrees omega 5 0 projtls degrees chi 45 0 projtls degrees phi 180 0 projtls degrees del projtls i Acceptable CCD temperature ccdtemperaturerange 65 55 E 4 M86 E00078 APEX2 User Manual Config Auto connect to the instrument when needed This is a protected varialble that is controlled by the System Administrator autocomnect 1 i The following five values define matrix runs perpendicular matrix runs 2theta 30 Set the 2 theta for the matrix measurement perpendicular matrix runs distance 41 Set the detector distance for the matrix measurement perpendicular matrix runs nr sweeps 3 Do three sweeps or runs perpendicular matrix runs sweep 6 Each run will be 6 degr
3. 6 No Operation No Operation Yes le No Operation Yes a No Operation Yes 10 No Operation Yes 11 No Operation Yes 112 No Operation Yes 113 No Operation Yes 14 No Operation Yes 15 No Operation Yes 16 No Operation Yes 17 No Operation Yes zl Append Strategy Append Matrix Strategy Validate Execute Ages Figure 6 23 Experiment view with strategy appended In Version 1 26 and later the Execute and Resume buttons are separated Execute will force the collection of all data Resume will start at the point where the data collection was interrupted M86 E00078 6 19 Data Collection NOTE At the top of the experiment window are controls for data collection Usually the default values are correct For data collection times of less than five seconds correlation can usually be turned off If new dark frames are required APEX2 will automatically collect them Checking Generate New Darks will force the collection of darks before every run In Figure 6 23 the time and width are explicitly set for each run so changing the default width and time will have no effect If the explicit time or width for a run is deleted so that the box is empty the word default appears and the default values at the top right will be used 5 Click Execute Resume The focus will shift to Monitor Experiment and images
4. smb Unix only Where samba will mount shares made available from other HOSTS smtphost type string default localhost Host of a machine that can be addressed via SMTP to send E malls statuslines type integer default 1000 2 temperaturerampspeed type integer default 240 The speed to use for ramping the temperature of a low temperature device in K per hour universalfnprotocols type tuple of strings default smb file Allowed protocols to exchange files with the BIS Should be 7smb file when BIS is running on the same machine and smb 1f BIS is running remotely userposl type scan default Not set userpos2 type scan default Not set p userpos3 type scan default Not set gt userpos4 type scan default Not set calibweaklevel type integer default 10 Minimal I sigma for peaks to be used in calibration routines M86 E00078 E 17 Config APEX2 User Manual E 18 M86 E00078
5. Delete Selected finalized at save Delete Non Visible finalized at save Intensity Filter Reflection Size Zoom Export Visible Spots to P4P Figure A 14 View with most of the lattice lines selected Lines to the top and bottom are not selected M86 E00078 A 11 RLATT APEX2 User Manual Hit Page Up to add lines to the outside of the previously selected lines in this example the top and bottom Page Down will remove lines from the outside Now all visible lines are selected Note that the selected reflections are turquoise rad db y Editing Tools C Box Lattice Overlay Single Spot Circle C None rotate Selection Helpers Select Weak Reflections Select Current Group Invert Selection Grouping Tools Current Group E Group 1 y Add To Current Group Remove From Current Group Select Visible Groups v None Deletion Helpers Delete Selected finalized at save Delete Non Visible finalized at save Intensity Filter Reflection Size Zoom Export Visible Spots to P4P Figure A 15 A view with all layers selected A 12 M86 E00078 APEX2 User Manual RLATT Click on Invert Selection in the Editing Menu RLATT gt Edit under Selection Helpers All of the spots that do not touch the layer lines are now selected Editing Tools C Box f Lattice Overlay C Single Spot Circle None rotate Selection Helpers Select Weak
6. SAINTPLUS APEX2 User Manual B 4 M86 E00078 Appendix C Using CELL_NOW CELL_NOW is an extremely powerful tool for determining unit cells for difficult crystals lt ana lyzes a list of reflections to find a cell and orien tation matrix despite the presence of several twin domains or other problems In initial search mode the program tries to find sets of reciprocal lattice planes that pass close to as many reflections as possible The corre sponding real space vectors are sorted on a fig ure of merit 1 0 being a perfect fit After the vector list has been output CELL_ NOW attempts to suggest a suitable cell This will not necessarily be the conventional cell so it should be checked using XPREP Once a cell is found it may be rotated to locate further twin domains iteratively using only the reflections that have not yet been indexed If CELL_NOW fails to suggest a sensible cell either something is seriously wrong with M86 E00078 the reflection list e g a wrong detector dis tance or a cell axis is longer than the given search range C 1 Running CELL_NOW CELL_NOW must be run from the command line It requires a list of reflections exported from the APEX software a p4p file 1 Open a Command Prompt window 2 Change directories to the folder containing the exported reflection list 3 For Windows or Linux enter the command cell now After the command is entered the terminal will print out an ex
7. 0 050 acire maoe oad nite id F 3 Intensity Sigma Upper Limit for LS Model Profile Fit 8 000 Lower Resolution Limit for LS Model Profile Fit A 3993 000 Beam Monitor J Enable Beam Monitor Normalization Profile XYZ Half widths fa Ja E 7 Normalize each Run Separately More Options Cancel Figure 7 10 Integration Options window Data Integration and Scaling The default values in the Model Profiles window are usually good Model Profiles Blend Profiles from All Detector Regions Intensity Sigma Lower Limit for Model Profile Update 10 000 Fraction of Model Profile Maximum for Simple Sum Mask 0 050 IntensitySigma Upper Limit for LS Model Profile Fit 8 000 Lower Resolution Limit for LS Model Profile Fit 6 3999 000 Profile XYZ Halwidths 4 4 4 Figure 7 11 Model Profiles window For weakly diffracting crystals it is sometimes helpful to change some options in the Model Profiles window Reducing the Intensity Sigma ratios from 10 and 9 to for example 5 and 4 or 3 gives the profile fitting algorithm more reflec tions to model Increasing the profile blending by clicking on Blend Profiles from All Detector Regions can also help with weakly diffracting crystals 4 Click on More Options This results in an expanded window see Figure 7 12 and gives access to several other useful fea tures in particular Active Mask see Figure 7 13 Algorithm see Figure
8. DISABLED M86 E00078 APEX2 User Manual RLATT Figure A 20 A view that zooms in on the Unit Cell tool Almost all spots lie on the lines and planes defined by the unit cell To the left and right are two weaker reflections black dots that do not fit M86 E00078 A 17 RLATT A 3 Defining Groups Selected reflections can be grouped This tool is most useful for examining twinned split in grown and otherwise problematic crystals For Figure A 21 alternate rows were selected with the Lattice Selection tool In the Grouping Tools section of the tool boxes to the right the current group was Set to Group 1 red Click on Add to Current Group to turn these rows red Then the other rows and Group 13 white were selected o o o o o o eS G Y DY Y DD DD YD ee Y Y Y Y Y Y Y Y Y DD DY DD Y DD DD Y Y Y Y es amp SY Y Y Y Y DY DS DD Y Y DD Y 8 6 SS Figure A 21 Reflections selected for different groups APEX2 User Manual and added The box tool was used to select the reflection to the top left and these were put in Group 3 the yellow group Finally some of the reflections to the top and bottom were selected and added to Group 5 the blue group This example of using the color groups generates a flag type display For twinned crystals etc the groups would be used to denote different com ponents see Figure A 22 Selection Helpers Select Weak Reflections Select Current Group Invert S
9. Omega o 00 Chi Kappa 0 00 IV Constrain Angle Zeros Display Image matrix_01_0001 sfrm y Show Observed Spots Show Predicted Spots Fit More Tolerant 5 929 A 8 981 A 18 348 A Total Spots 259 Spots Fit 93 89 955 89 811 89 953 RMS Y mm 0 00 RMS Angle 0 00 Volume 976 9 A 3 Symmetry Constraint View Histograms Triclinic v Refine Bravais Transform Orientation Matrix Figure 6 13 The Refine menu with histograms displayed M86 E00078 APEX2 User Manual The YLID test crystal should have an ortho rhombic primitive cell with approximate cell dimensions of a 5 95A b 9 03A c 18 38A and a P y 90 2 Click View Histograms The histograms show how observed data compares to the data calculated using the current unit cell The HKL values should be close to integers and the rotation angle differences should not be significantly larger than the step size used to collect the matrix frames Click Refine several times Check the Constrain Distance and Con strain Beam Center boxes NOTE Check the constraints to fix the parame ters listed Uncheck the constraints to allow the parameters to refine Uncheck Constrain Pitch Roll and Yaw Click Refine several times 7 Uncheck Constrain Distance and Constrain Beam Center and check Constrain Pitch Roll and Yaw 8 Click Refine several times M86 E00078 Data
10. 10000 00 Na on o ma 8000 00 6000 00 S ewBbis Belsa y 4000 00 Average spot intensity 2000 00 0 00 7 12 M86 E00078 APEX2 User Manual In this full view the Integrated Spots window looks much like the image viewer used previ ously At the bottom of the window is an entry box that can be used to change the display fre quency of the Integrated Spots images The default is to display every fifth image im Integrated Spots TS BY xj Scan 4 Integration gt All Components y O Progress Statistics O Integration progress O Per lmage Statistics 2 Spot shape correlation E Spot intensity and Sigmafl O Spot intensity lt 2 Sigmall C Number of reflections harvested E E Spot position overlay ef x Y Z error HO X Y Z RMS difference O xX Y Z spot size tL Queue extent used O Primary beam intensity O Periodic Statistics 2 Profile snapshots O A axis ESD O B axis ESD O C axis ESD O Alpha angle ESD O Beta angle ESD Gamma angle ESD O Cell volume ESD 2 LS goodness of fit iL LS Residuals O x Y Z crystal translation X Y beam center O Distance correction O Pitch Roll Yaw correction iO Angle zeros p O Coverage Statistics O oaran torann Corowa torann O Harvested reflections 1 10 100 1000 10000 100000 1000000 O Completeness and redundancy O Bijvoet pairs Description 1 Image type Phi Scan Image Start position Distance
11. HS2 36 3 K 2N 4928 LAr 49 3 mons 69 1 Koni O7e2 1 3ne 60645 This percentage information is useful for identifying supercell problems Typically the percentages should be 30 or higher for the 2n values and 50 or higher for the 3n values but problem crystals or crystals with heavy atoms in special positions can make the values lower Low values for a particular class of reflections can suggest that an axis is double 2n or triple 3n its correct length New cell from list number reorientate R accept A or quit Q A A 9 Enter A or just hit lt Enter gt to accept this cell The program will ask for a name for a p4p file Enter the name of the p4p file for this solution in this example domain1 p4p C 6 M86 E00078 APEX2 User Manual Using CELL_NOW p14p or spin file to write domain to domainl p4p RLATT color coding employed in file domainl p4p White indexed for first domain Red not yet indexed 877 reflections within 0 250 of an integer index assigned to domain 1 877 of them exclusively 122 reflections not yet assigned to a domain 122 reflections approximately 1 10 of the data have not yet been indexed assigned to a domain This is more than might be expected for random noise peaks A search for an additional domain makes sense The domain 1 cell will be rotated to locate further twin domains iteratively using only the reflec tions that have not yet been indexed Re refine initial cell R search
12. Suffix Descending Figure 9 15 Atom Labelling box 4 The two selected atoms need to be changed to oxygen atoms Do this one of two ways e Click on the Element field and type in the element symbol case does not matter e Click on the El button to the right of the Ele ment field This will open a periodic table Left click on the appropriate element sym bol to select it the periodic table will auto matically close Structure Solution and Refinement APEX2 User Manual Periodic Table 00 T fels elelelel 9 02 2 jefe we oe om v mm roo ca m oo noe ca e 10m 562 cif 03 oo afm w oe r omfon cfc fm Cancel a a aA jeje siete ala elelelelEl E E elele ale lo e slo Figure 9 16 The periodic table for selecting atom types 5 Once the element type is set correctly click on Relabel to number the peaks sequen tially in the order they were selected start ing with the number in the First Sequence field 9 12 M86 E00078 APEX2 User Manual Structure Solution and Refinement 6 Seeing the color of atoms can be difficult in the Wireframe view used so far Right click in the background with no atoms selected to get a slightly different action menu In this menu highlight and left click on Pipes This makes the bonds thicker and makes it obvi ous that there is an incorrectly labeled atom This will be corrected when the carbon atoms are labeled wir
13. changed to 0 75 M86 E00078 Data Integration and Scaling At the bottom of the window are two buttons for defining the data collection runs to be inte grated Find Aung Import Runs from Esperiment Figure 7 5 The Find and Import Runs buttons The Import Runs button determines the runs to be integrated from the experiment that has just been submitted Using this button allows the user to start integration while the data is still being collected NOTE SAINT will integrate all of the data cur rently measured and then will wait for the next image integrate that wait for the next etc The Find Runs button is used to browse to the set of runs to be integrated This button is nor mally used when the data collection is finished Data Integration and Scaling 1 Click on Find Runs The following window will open Usually it will have the correct directory and base name as the defaults If these are not correct then use the Browse button to find the runs for the data col lection of interest 2 x Find Runs in Directory Je struc guest data_manual ylid_manual Image Base Mame plid_manual Browse Cancel Figure 7 6 Find Runs tool view Both the Import Runs from Experiment and the Find Runs buttons will generate a list of runs as shown in Figure 7 7 Space Group Pree g Starting Image Filename 1 C Astruc guest data_manual ylid_manualylid_ manual 739 structures data_for_manual ylid_manual work
14. the Cen ter module M86 E00078 2 Crystal quality check from the APEX2 Server the Simple Scans module See Section 6 for 3 Cell determination from APEX2 the Cell Determination module 4 Data collection setup from APEX2 the Strategy module 5 Data collection from APEX2 the Experi ment module The first steps mounting aligning and screen ing a crystal are performed on the server com puter Crystal Orientation 5 1 Mount the Goniometer Head on the Instrument 1 Open the enclosure doors Push either of the rectangular green Open Door buttons on the side posts This will release the door locks for approximately five seconds During this time pull out on one or both of the han dles to physically open the doors 2 Inthe APEX2 Server GUI under Setup click on Center Crystal The centering buttons will appear and the video window will open Center Crystal ml ES Manual Y Motorized 1 spin Phi 30 spin Phi 180 Mount Left Top Right Center Figure 5 1 The Center buttons APEX2 User Manual The bottom five buttons will drive the goniome ter to various pre defined positions that are designed to simplify crystal centering The top two buttons will drive phi by either 90 or 180 degrees 3 Click on Mount to mount the goniometer head 4 Carefully remove the goniometer head con taining the crystal from its case MN CAUTION Use extreme care when handling t
15. ylic_n CAstuctguestidata_manuallid_ manual lid manua tetructurestdata for_manualylid_ manualworkplid_n C Astruc quest data_manual ylid_manualiylid_manua vetructurestdata_ftor_marnualblid_rmarnaal work ylid_n CAstuctrguestidata_manuallid manual ulid_manua etructures data_for_manualhwlic_manualwork ylid_n Figure 7 7 Completed runs list NOTE To integrate runs from a CD or DVD browse to the device and find the runs to be integrated APEX2 will automatically write the result in the work directory for the current project APEX2 User Manual M86 E00078 APEX2 User Manual Figure 7 8 shows a run list entry being modified A shows the original run information B shows the run with the starting image number changed to 51 C shows the number of frames to process changed to 111 Double click on any of the fields in this list to open up that value for editing A C stuckquesthdata manualiplid manualiylid manual 74 manualwlid manualtlid manual O4 OO01 str Ge BR Eststuciguestidata_manualplid_manualplid_manua manuallid manualPpulid manual 04 161 struc guestdata_manualwlid_manualwlid_manua C Cystucquest data manual old manuabuld_ mana Figure 7 8 Example of manually editing a run list 2 Check the refinement defaults The two buttons on the bottom far left are used to change the default options for the refinement of the data M86 E00078 Data Integration and Scaling The default values are genera
16. 114 fo 85 8200 A 0 6561 0 1836 0 3232 sp3 0 0 05 15 Joi 66 1600 0 0 5674 0 1814 0 2395 sp3 0 0 05 Q15 64 7300 0 0 8062 0 4621 0 2409 sp3 0 0 05 17 oie 54 7300 0 0 9493 0 1856 0 1563 sp3 0 0 05 18 017 40 2200 0 0 52 0 989 0 237 sp3 0 0 05 Print Figure 9 7 Atom information screen At the bottom right of the main window is a slide bar which is used for deselecting peaks The arrow can be moved by left clicking and drag ging the arrow or by left clicking on either side of the arrow Left clicking to the left of the arrow i e where the mouse cursor is pointed in Fig ure 9 8 will remove peaks Residual Difference Fourier Q Peaks o Ho of QPeaks 22 Figure 9 8 The Q peak slider M86 E00078 Structure Solution and Refinement 6 Slide the pointer down while watching the molecular display Change the number of Q peaks to 15 Structure Solution and Refinement APEX2 User Manual At 15 the molecule is much cleaner but there Click left on the slider until you find a reasonable are still peaks that do not make sense model Figure 9 9 Image after the number of Q peaks was Figure 9 10 Image with all noise peaks removed changed to 15 7 Put the cursor over the bonds to check dis tance The distance will be displayed at the bottom right 9 8 M86 E00078 APEX2 User Manual Structure Solution and Refinement 9 3 2 Label the Atoms 1 Label the atoms and set the atom types Left click
17. 2Theta 30 00 Omega 31 mae Detector Corrections Distance mm 0 00 Horizontal Beam Center mm fono Vertical Beam Center mm 0 00 Image Header Tool Editor Cursor Position Figure 6 8 Image viewer with indexing tool M86 E00078 Data Collection Data Collection 2 The name of the first image is already entered Click on Harvest Spots NOTE All other options are gray at this point because no reflections are available A blue progress bar will appear as the software determines the best background level to use for harvesting Then a window with two sliders will appear hy Harvest Spots 20x More Spots Image pgs da pa Fewer Spots 1 Cancel Figure 6 9 Indexing sliders The right slider selects which image is dis played The left slider increases or decreases the I s l the cutoff criteria for accepting reflec tions Generally the defaults are acceptable APEX2 User Manual 3 Change the run number in the First Image box to matrix_02_0001 and click on Harvest Spots The run number is 02 The image or frame number is 0001 4 Change the run number in the First Image box to matrix_03_0001 and click on Harvest Spots At this point you should have 100 to 300 reflec tions harvested NOTE If you have started harvesting before all of the matrix runs were collected a window may pop up that says Do you want to continue with the images that cou
18. 7 3 Scale The scaling process uses the SADABS program to put all of the measured data on the same scale This process involves five steps 1 Set up input files Parameter refinement Error model refinement 2 3 4 Display diagnostics 5 Exit 7 3 1 Set up Input Files 1 Click on Scale gt Scale in the task bar Fig ure 7 24 shows a portion of the initial Scale work area The defaults and file names are typically correct Base yidmanual Output hkl file yid_manual Omak Diagnostic Plots File Name yiid_manualmeps Title of Diagnostic Plots yid mana SS Log File yid manualmabs V Use only centrosymmetric point groups Point Group mmm ad Additional Spherical Absorption Correction Mur of Equivilant Sphere IV Lambda 2 Correction Correction Factor 0 001 5 Allow for crystal decomposition Noe S by B value refinement None z Extra Linear Correction to be Applied Noe to Each Reflection wns Figure 7 24 Input setup window APEX2 User Manual Click Next and check that the defaults are correct Generally the Absorber Type is the only value that might be changed Set it to indicate the expected absorption of the sample If in doubt use the default Use the help arrow to get information regarding individual items M86 E00078 APEX2 User Manual 7 3 2 Parameter Refinement 1 Click on Refine Figure 7 25 shows refinement result The R values are Data Integration and Scaling a typical r
19. All Atoms window Lnrormaction on All ALO Add Hydrogen atoms Hybridize All Calculate Hydrogens Figure 9 39 Calculate Hydrogens button 9 24 M86 E00078 APEX2 User Manual 4 Click on the Refine button to launch the least squares refinement program The out put window will open and a summary of the results of individual cycles of refinement will appear Refine GooF S 0 482 Restrained GooF 0 482 for 0 restraints Mean shift fesd 0 506 Maximum 2 502for y Cii at 11 53 17 Max shift 0 011 A for H11B Max dU 0 000 for C1 wR2 0 0781 before cycle 3for 2445 data and 129 129 parameters GooF S 0 475 Restrained GooF 0 475 for 0 restraints Mean shift esd 0 034 Maximum 0 243 for U13 C4 at 11 53 17 Max shift 0 001 4 for H11B Max dU 0 000 for C5 wR2 0 0781 before cycle 4 for 2445 data and 129 129 parameters GooF S 0 475 Restrained GooF 0 475 for 0 restraints Mean shift esd 0 009 Maximum 0 070 for tors H114 at 11 53 17 Max shift 0 001 4 for H11B Max dU 0 000 for C5 WR2 0 0781 before cycle Sfor 2445 data and 2 129 parameters 0 475 GooF Restrained GooF 0 475 for 0 restraints Ri 0 0284 for 2315 Fo gt 4sig Fo and 0 0303 for all 45 data WR2 0 0781 GooF S 0 475 Restrained GooF 475 for all data Ri 0 0291 for 1440 unique reflections after merging for Fourier Highest peak 0 25 at 0 7757 0 3500 0 2034 0 81 A from C2 Deepest hole 0 16 at 0 192
20. Full Matrix T Conjugate Gradient Refinement Cycles la Number of residual peaks zo Sigma Cutoff Sigma Resolution Cutoff 2 Theta E Invert structure Late stage refinement options Refine all non H atoms anisotropically Use suggested weights Squared Term Jo co0000 Linear Term Refine extinction parameter Generate ACTA CIF information file Refine Edit File Cancel Figure 9 20 The Refine menu M86 E00078 Structure Solution and Refinement After a few seconds a Refine window will open with output results for the calculation WR2 0 2818 before cycle 3for 2445 data and 57 57 parameters GooF S 2 496 Restrained GooF 2 496 for O restraints Mean shift esd 0 686 Maximum 2 456 for y Cii at 11 50 43 Max shift 0 015 A for C11 Max dU 0 001 for C2 WR2 0 2787 before cycle 4 for 2445 data and 57 5S parameters GooF S 2 Restrained GooF 2 473 for O restraints Mean shift esd 0 180 Maximum 0 854 for y 02 at 11 50 44 Max shift 0 004 A for 02 Max dU 0 000 for C4 WR2 0 2783 before cycle Sfor 2445 data and 2 57 parameters GooF S 2 470 Restrained GooF 2 470 for O restraints Ri 0 0879 for 2315 Fo gt 4sig Fo and 0 0918 for all 2445 data WR2 0 2783 GooF S 2 470 Restrained GooF 2 470 for all data Absolute structure probably wrong invert and repeat refinement Ri 0 0932 for 1440 unique reflections after merging for Fourier Highest peak 1 18
21. GUI will open 4 Use of SAINTPLUS is described in appen dix A 5 The output from a multicomponent integra tion is a mul file rather than the normal raw file This file will be processed with TWIN ABS Processing Twinned Data APEX2 User Manual D 2 Scaling with TWINABS 1 In the same command window change directories to the work directory and enter the command TWINABS er D WINDOWS system32 cmd exe struc guest MRtwi n gt twi nabs TWINABS Bruker Nonius scaling and corrections f Figure D 1 Starting TWINABS at the command prompt 2 Set the number of reflections to process and the output file The defaults are usually correct TWINABS Bruker Nonius scaling and corrections for twinned crystals V1 05 Maximum number of reflections allowed 500000 Enter listing filename twin abs 3 Check the Laue group carefully It always defaults to 2 and is often incorrect In this case the unit cell is monoclinic and the correct answer is 2 Laue group numbers 1 1 8 3m rhombohedral axes 2 2 m Y unique 9 31m 2 unique 3 mmm 10 3m1 Z unique 4 4 m Z unique 11 6 m Z unique 5 4 mmm Z unique 12 6 mmm Z unique 6 3 rhombohedral axes 13 m3 7 3 Z unique 14 m3m 0 to write list of equivalent indices for Laue point groups to listing file Enter Laue group number 2 2 D 2 M86 E00078 APEX2 User Manual Processing Twinned Data 4 The default values for th
22. Groups Sometimes a complete group of options need to be changed to get a specific functionality For these Cases there are function Calls that change a number of variables at once Due to the default like nature of these function calls they should probably be used only in the site wide configuration files and even there only at the beginning but this is not enforced Tre aval lable unectltons are default protein This switches from the default small molecule parameters to more protein like parameters At this time the following parameters are ser chiralonly 1 autochiralpointgroup 1 resomode 1 resolution 2 5 default noprotein This sets the defaults back to small molecule values E 8 M86 E00078 APEX2 User Manual Config The following variables in alphabetic order can be set in a configuration file anglemargin type floating point default 1 0 Do not change autochiralpointgroup type boolean default 0 This selects whether point groups are preferably chiral This can be useful in a protein setting autoconnect type boolean default 0 TE Chis 1s Set to ly the connection to Eine BIS server will be created automatically without user intervention whenever required This variable can only be changed in the system wide configuration file see protectedvariables axcrit type floating point angle default 0 2 degrees This is the criterion used by the automatic cell reduction algorithm to deci
23. M86 E00078 Data Collection Data Collection NOTE COSMO will use information from cell determination to set defaults You can modify the suggested values 2 Check the inputs for defining the data col lection 2 1 Set the data collection distance For SMART APEX II systems this should be set to the actual detector distance For Kappa APEX II systems there is a variable DX and the distance will default to the shortest reasonable dis tance For the APEX II detector the dis tance in millimeters should generally be about the same as the longest cell dimension in angstroms Typically dis tances ranging from 35 to 45 are rea sonable 2 2 Set the exposure time and press Enter For normal crystals on an APEX Il five seconds is a reasonable time 2 3 Click Same to set all of the times to be the same NOTE If the Same feature is not chosen the times for shells can be set to collect high angle data more slowly than inner shell data APEX2 User Manual 2 4 Set the desired resolution 0 75 is a rea sonable value 2 5 Check the other values Laue class Lattice etc 2 6 Each time a value is changed COSMO recalculates the statistics for the runs The results are displayed in the column labeled Current 2 7 Below the Target and Priority columns is a pull down menu with several differ ent strategies Choose the one that best meets the needs of the experiment e g Best in 2 hours for the exa
24. The beamstop catches the remainder of the direct beam after it has passed the speci men The beamstop has been aligned to minimize scattered X rays and to prevent the direct beam from hitting the detector The entire collimator assembly is supported by a collimator support assembly which has been precisely aligned to guarantee that the X ray beam passes through the center of the goniometer Video Camera The video camera an essential part of the sys tem allows you to visualize the crystal to opti cally align it in the X ray beam It also allows you to measure the crystal s dimensions and index crystal faces The camera is interfaced to the computer and is operated through the VIDEO program The VIDEO program includes several computer generated reticles and scales to make it easy to center and measure the crystal M86 E00078 Hardware Overview 2 1 3 Radiation Safety Enclosure with Interlocks and Warning Lights A common component of all systems in the D8 family is the radiation safety enclosure This new design is fully leaded i e leaded windows leaded metal sides and panels to protect you from stray radiation The enclosure also includes warning lamps a government require ment that alert you when X rays are being gen erated As a special feature the enclosure also incorporates interlocks for both hardware and software an automatic system interruption device that senses when the doors and panels are open and preve
25. a run This icon is vis ible only when an image is displayed 2 Select previous image This icon is visible only when an image is displayed Table 3 2 Tool icon bar options M86 E00078 APEX2 User Manual Icon Description Select next image This icon is visible only gt when an image is displayed bl Select the last image in a run This icon is vis ible only when an image is displayed TF Go down one run PaA Go up one run Draw a resolution circle This icon is visible C only when an image is displayed Draw a plotting line This icon is visible only when an image is displayed Change the part of the image displayed while zoomed in This icon is visible only when an image is displayed Table 3 2 Tool icon bar options M86 E00078 Software Overview Icon Description Select a region of the image This icon is visi o ble only when an image is displayed Table 3 2 Tool icon bar options Software Overview Task Bar The task bar provides menus for all of the options in the APEX2 Suite crystal evaluation and indexing Evaluate Crystal data collection Collect data processing Integrate and Scale and instrument setup Instrument Center Perform crystal centering func tions Describe Specify crystal size color shape etc Evaluate Crystal and Bravais lattice type A Determine Unit Cell Determine unit cell Pi a Recipr
26. a test for merohedral twinning are very useful tools M86 E00078 APEX2 User Manual 8 6 Simulated Precession Images 1 Click on Precession Images under Examine in the task bar Precession Images provide an undistorted view of layers of the recipro cal lattice APEX2 generates simulated pre cession images by finding the appropriate pixels in a series of sfrm images You must specify the images to examine and the zones to calculate 2 To open the File Selection window left click on the folder beside the file name Choose the sets of images that you want to use for the calculation by clicking on the check boxes see Figure 8 22 ba python Aux Look in A c struc guest data_manual ylid_manual y Ef EE sE EJ mai Run E O matris_01_ HH 1 12 O matrix_02 HH 1 12 matrix_03 HH 1 12 E ylid_manual_O1_ 1 739 E ylid_manual_02_ 1 153 E ylid_manual_03_ H 1 74 E yliid_manual_04_HHHH 1 161 a work a matrix_01_ E bn event log E matrix_01_ E communication log 20040502 gz E matrix_O1_ 23 matrix_01_0001 sftm 23 matrix_01_ 3 matris_01_0002 sftm E matrix_O1_ E matrix_01_0003 sfm E matrix_02_ E matrix_01_0004 sfrm E matrix_02_ E matrix _01_0005 sfrm E matrix_02_ E matris _01_0006 sfrm 3 matrix_02_ gt Directory ylid_manual Cancel File type Figure 8 22 File Selection window with matrix runs deselected M86 E0
27. as wide frames 7 1 3 Image Queue mage Queue Active Image Queue Halttwidth Images 7 4 Figure 7 15 The Image Queue tool The Image Queue sets the number of frames being used to determine profiles For crystals with high mosaic spread large wide reflec tions increasing the queue size can improve integration 5 Click on the Start Integration button on the far right of the bottom row This will start the integration and will open the SaintChart win dow for monitoring the integration 6 Examine the output Double click on any of the output entries for one additional tool the Is button at the far right of the line see Figure 7 16 This will open the SAINT list ing file for that integration run M ualyid manualrworkylid_manual_04 1aw 15 Figure 7 16 Using the runs list Is tool M86 E00078 APEX2 User Manual Data Integration and Scaling 7 2 SaintChart SaintChart is a powerful tool for monitoring the progress of the calculation and for graphically presenting the results of the integration process 7 2 1 Monitor the Progress of the Integration Run l0 x E SaintChart Chart Windows Bes is Spot Shape Correlatio lolx Scan 1 Integration i Average Spot Intensity 1 00 oo Tt 10000 00 AN Components xl o SE 0 80 2 8000 00 D Progress Statistics ae o ae Lf Integrati 5 90 50 v 6000 00 ntegration progress oo E o O Pe
28. at 0 2500 0 3358 0 2419 0 51 from 1 Deepest hole 0 75 at 0 1606 0 2830 0 2403 0 51 from 1 AA RA AA AA A AA A AA A A A A A A A A AA HFEF E HFEF ylid_res75 finished at 11 50 44 Total CPU time 0 3 secs HA A A A A A A A A A A QK Figure 9 21 Isotropic refinement output In the output displayed above note that the R1 value is 0 08 This is typical for a preliminary iso tropic refinement for an organic molecule with data to a resolution of 0 75 and no hydrogen atoms included The refinement program also indicates that the model needs to be inverted to get the correct absolute structure NOTE This indication of the absolute configura tion is usually reliable but all assignments of absolute structure should be confirmed later in the refinement process by including TWIN and BASF cards in the instruction input Structure Solution and Refinement 2 Click on OK to return to XShell The mole cule display will refresh with the results of the least squares calculations APEX2 User Manual Figure 9 22 The model after isotropic refinement The peaks in the diagram represent difference in the electron density between the refinement model and the experimental electron density as defined by the measured data Many of these difference peaks are near the sulfur and oxygen atoms Refinement of all atoms anisotropically should improve the model 3 Inthe refinement box click on Invert St
29. con troller the power settings can be adjusted within the APEX2 software This is usually not neces sary as the software automatically increases the power to the user defined values at the begin ning of an experiment and lowers them when the instrument is inactive Timing Shutter and Collimator On SMART APEX II systems the monochro matic X ray beam then passes through the laby rinth the timing shutter and the incident beam collimator before striking the specimen On Kappa APEX II systems the monochromatic X ray beam passes through a small labyrinth the timing shutter a secondary labyrinth and the incident beam collimator before striking the sample e The labyrinth is a device that ensures that the collimator and shutter are tightly con nected to prevent X ray leakage e The timing shutter is a device which pre cisely controls the exposure time for each frame during data collection lts status lamps indicate when the shutter is open ON and closed OFF For SMART APEX Il systems this assembly also houses an automatic attenuator Kappa APEX II sys tems do not have an attenuator e The incident beam collimator is equipped with pinholes in both the front near crystal and rear near source These pinholes help M86 E00078 APEX2 User Manual to define the size and shape of the incident X ray beam that strikes the specimen Col limators are available in a variety of sizes depending on your application e
30. eee 7 8 TAS MACS QUESO aes dase eed a edhe es EDR Ae ee eee was 7 8 Dae SANA AU rs Sa cals sh Sees St Nand ata va nh ato hee cs ee 7 9 7 2 1 Monitor the Progress of the Integration RUN 0 0c ee ee 7 9 7 222 Examine Final RESUS coria Mews ash oe oa Ute nee ea 7 14 D9 DCA Oras Bie Adapt A BAHN aban saad me a cee eee Be 7 16 7 0 SLU INPUT FICS arar Ot ai ete ia ed Pee eke Ones wa ie adie 7 16 7 3 2 Parameter Refinement 2 0 00 eee eee 7 17 7 3 Error Model Rene Menta ale Corea ee bee A eres a 7 18 7 3 4 Examine Display Diagnostics 0 0 ccc eee ees 7 19 TSE A idas Ce ee ee ii 7 23 9 EXamine Data marcar datada dd dees daa di 8 1 A A A Aa ahi Stag a teas ane rcs ahead ace See Sheree Se 8 1 8 2 apace Group Determination surtir ara eek eu ketene aos 8 2 8 3 Reflection Statistics 2 2 erami nea eaa eee eee eee 8 4 8 4 Applying High Resolution Cutoff 0 0 0 0 eee eee 8 5 8 5 Preparing an Output Files secs sec cc e il A ates a hea A A a ens Selene OES Sas 8 7 8 6 Simulated Precession IMages 0c eee eee teens 8 9 9 Structure Solution and Refinement 000 c eee eee eee 9 1 2 2 a er er ee e da da Vos ee ee ai 9 1 9 2 Solve the SIUCTUTO dosvitads de dra a ia aes 9 2 g3 AONE eects es si ds dol ds tea dal le io e dia Bs a Oho e ad e 9 4 9 3 1 Refine the SUuctwre ue 5 042084 a ia is A A es ex de 9 4 3 3 2 LEADING ATOMS ms dosis as da a e bai 9 9 9 3 3 Refine the M
31. fitness for a particular purpose No part of this publication may be stored in a retrieval system transmitted or reproduced in any way including but not limited to photocopy photography magnetic or other record without prior written per mission of Bruker AXS Inc Address comments to Technical Publications Department Bruker AXS Inc 5465 East Cheryl Parkway Madison Wisconsin 53711 5373 USA All trademarks and registered trademarks are the sole property of their respective owners Printed in the U S A Date Changes 0 2 05 Original release ii M86 E00078 1 05 Table of Contents NOCO nuran oir ap Sco ee E hs nis ea ar Rodent Bde ap eae ii ENE UCI rias 1 1 1 1 APEX Il Systems for Chemical Crystallography 0 0 00 cece eee 1 1 1 2USer Manual Features sede sac atid ocd cx a A ee es ea es alee ates 1 2 Md AANA AIC tactile asses ce Soe Ns is Sa oe UN 1 3 2 Hardware Overview 6 iii A A A ea ete eee 2 1 21 SYSTEM COMPONEN varia a Saree ra ee Wh nae eon dare 2 1 2 ALVA EX IDO rra a ae Se ae aoe ee ee ea 2 3 2 die GONIOMECICN areen pita aU oor et oe ea ee Cae ads Eee eee Ae da 2 3 2 1 3 Radiation Safety Enclosure with Interlocks and Warning Lights 2 7 e ADS Gon toledo Sal beak a Satine da ta 2 7 2 1 5 Refrigerated Recirculator for the Detector 0 no 2 8 2 16 COMPUTER S a0 4 4 oes Lee ee eo Se bo we dee aa a a 2 8 2 1 ACCESSOMOS rr WS ee Ah Gk BONES Se aaa MG ES AE RE Mo
32. for next domain S quit Q or choose new cell from list enter number S S 10 Enter S to search for another orientation of the newly chosen cell Cell for domain 2 12 s6972 11 016 14 648 89 70 90 95 90 00 Figure of merit 0 643 0 1 69 7 0 2 97 5 0 3 98 4 Orientation matrix 0 00598966 0 00402327 0 06807401 0 083567313 0 06180340 0400480114 Oo OPOGI202 D SUSO TA Ts O 2002210359 Rotated from first domain by 179 7 degrees about FSEIPrTOCAL axis 1 000 0 00L 0 032 sand real axis 1000 0 002 0 010 Twin Law to convert hkl from first to 0 999 0 004 0 019 this domain SHELXL TWIN matrix 0 003 1 000 0 004 0 064 0 006 0 999 M86 E00078 C 7 Using CELL_NOW APEX2 User Manual CELL_NOW has identified an additional domain that fits 97 5 of the data with a tolerance of 0 2 The relationship between this domain and the first domain and the SHELXL TWIN matrix are reported This example is for a rotational twin about the a axis The output shows a suitable cell with its orientation matrix figure of merit and the deviations of the input reflections from integer indices This deviation is used to determine which reflections fit this cell and which are left for further searches for new domains 11 Enter the maximum deviation from integer index cutoff typically the default is reasonable Maximum deviation from integer index 0 25 12 Enter the name of the p4p file for this solution in this example domain
33. have a CFOM of 0 06 or less 4 Highlight and click on Direct 3 to set up an extreme run with two instructions ESEL 1 0 and TREF 100000 By adding ESEL 1 0 more reflections are used in the solution process Increasing the number of tries in the TREF command to 100000 runs until ended by clicking on the STOP button is particularly useful for acentric triclinic struc tures and for pseudo symmetric structures There is only one pre defined option for the dual space calculations and also only one for the heavy atom Patterson methods Structure Solution and Refinement At the end of the direct methods runs the output display will look like Figure 9 2 Good figures of merit are near 1 0 for Sigma 1 and M abs and less than 0 06 for Ralpha and the CFOM Struc tures can be solved with figures of merit that deviate from these numbers but they may require more effort If the initial model looks reasonable click OK in the output display and Exit in the Solutions plug in The next step is structure refinement using XShell APEX2 User Manual 9 3 XShell 9 3 1 Refine the Structure The structure solution step produced statistics indicating that a solution had been found The real proof however is in the initial model that is produced XShell provides the tools to view and refine the model A quick glance at the results of the direct methods run is often all that is needed to see that the results make chemical sense Control of the
34. image Still 360 Phi Marrow 0 5 Wide 2 0 Drive Scan Figure 5 18 Simple Scans menu APEX2 User Manual M86 E00078 APEX2 User Manual The sliders and data boxes at the top can be used to position the detector The buttons in the middle provide easy access to common movements There are four possible user defined buttons The Drive button initiates the requested move ment If it is gray an impossible movement has been requested The buttons and boxes at the bottom set up scans In Figure 5 18 the Drive Scan button is grey and therefore inactive because no scan has been requested 2 Click on Zero and then on Drive 3 Set the distance 3 1 On Kappa APEX II systems check that the moveable beamstop is pushed in and set the desired position typically 45 mm for Distance in the data win dow 3 2 On SMART APEX II systems with mov able DX set the desired position typi cally 50 mm for Distance in the data window 3 3 On SMART APEX II systems with fixed DX check that the distance displayed is the same as the actual distance in mm on the detector arm M86 E00078 Crystal Orientation 4 Click 360degree Phi and set the desired exposure time The default of 15 seconds is usually sufficient 5 Click Drive Scan Since these are evalu ation scans there is no need to request cor related images or new darks The resulting Phi 360 image is shown in Figure 5 19 The crystal di
35. intensities and to scale all of the data M86 E00078 Los Data Integration and Scaling APEX2 User Manual 7 1 Integration 1 Click on Integrate in the task bar 2 Click on the Integrate Images icon The fol lowing window will open Resolution Limit 4 0 651 Space Group Images Dutput Filename Starting Image Filename zi Refinement Options Integration Options Find Runs Import Runs from Experiment Start Integration Figure 7 1 Initial integration window 3 Check the default values There are two items of interest at the top of the window the Space Group tool and the Resolu tion Limit value Space Group Pee E Figure 7 2 The Space Group tool 7 2 M86 E00078 APEX2 User Manual The Space Group tool allows the user to set the symmetry for integration Typically this value is correct when the Integration window opens Group P222 Starting Triclinic lA N Monoclinic E Orthorhombic a La Tetragonal I P2221 E Rhombohedral a n Panama OA 2 Cubic TEE Figure 7 3 Choosing P2 1 2 1 2 1 with the Space Group tool The Resolution window on the upper right sets the upper limit of resolution for integration Resolution Limit 0 750 Figure 7 4 The Resolution tool The APEX2 Suite will suggest a resolution cut off In this case the suggested value has been
36. now ready to collect data M86 E00078 Data Collection Data Collection 6 4 Data Collection Run Experiment 1 Click Collect gt Experiment 2 Go back to the experiment window and delete the three matrix runs if they are still there First Aun 1 TBa Copy A Paste 7 Clear Figure 6 22 Deleting the matrix runs 3 Click Append Strategy APEX2 User Manual M86 E00078 APEX2 User Manual Data Collection 4 The program changes the name to the name of the current project in this example ylid_manual Esstruc quest data_manual ylid_manual ylid_manual_01_0003 sftm al lt a gt DH See a Sy a Setup Experiment Monitor Experiment Image location Ic struc quest plid_manual I Attenuate if topped Default time hr 0 000 sec frame y Filename or prefix ylid_manual IV Correlate Frames Default width fo 500 degrees z First Run 1 J Generate new Dark Images Detector Format 512x512 v Operation Active Distance mm 2Theta deg Omega deg Phifdeg Chifdeg Time sec _ width deg Sweep deg Direction _ 1 PhiScan Yes 35 000 22 000 286 99 358 39 3 83 5 00 0 50 369 50 automatic FE Omega Scan Yes 35 000 32 000 27 75 27 75 99 47 5 00 0 50 76 50 automatic 13 Omega Scan 35 000 7 000 26 26 26 26 55 59 5 00 0 50 37 00 automatic 14 Phi Scan 40 000 28 000 14 31 14 31 34 09 5 00 0 50 81 automatic 5 En Yes i of
37. of the next steps are performed with APEX2 on the client computer Crystal Orientation 5 2 2 For a SMART APEX II System NOTE If the image of the crystal is difficult to see illuminate the sample with a high intensity lamp and or temporarily place a light colored piece of paper on the front of the detector 1 Click the Right button The crystal and goni ometer head will be positioned perpendicu lar to the microscope To center the sample make adjustments to the height with the Z axis adjustment Figure 5 11 Initial mounted crystal 2 Click the Center button Move the crystal so that it is centered in the microscope reticle by adjusting the X or Y axis translation adjustment screw that is perpendicular to the microscope axis and facing you see Figure 5 3 and Figure 5 4 APEX2 User Manual Figure 5 12 Initial center position Figure 5 13 Initial X or Y axis translation ajustment 3 Click Spin Phi 90 Remove half of the differ ence with the adjustment screw that is fac Ing you Figure 5 14 Spin Phi 90 M86 E00078 APEX2 User Manual 4 Click Spin Phi 180 Remove half of the dif ference with the adjustment screw that is facing you 5 Click Spin Phi 180 again 5 1 If the crystal is centered click Spin Phi 90 5 2 If the crystal is not centered adjust to remove half of the difference and click Spin Phi 180 Repeat until the crystal is centered Click Spin Phi 90 5 3 If c
38. on Connect 3 Click on Append Matrix Strategy at the bot tom left of the window M86 E00078 Data Collection Data Collection Setup Expedment Mordor Esperar his kee ston Cda pedal rr lisas on prados Port Mum fi 2 APEX2 User Manual A icc PA Diedecica comas mas a La K CE Pre Scan Ye iii nooo 5 000 0 000 MEME 3 Predcan ras 40 000 W 060 0 121000 AT dell Y Ph ean iai 4610000 noon ETE la Ma Open Te a Ma lpm TE Aa pea Te m Ma Opes Te a Ma pees TE a Ma lpm Te 10 Ma pastor 01 it Ma Upa TEL az Ma pea Te 13 Ma pear TE a Ma Opes Te 119 Ma pastor Te i Ma Opes TE VF Ao pasto is Chel 6 000 pei dl LU porfas ll 6 000 prins Figure 6 4 Append matrix runs 4 Adjust the scan time and scan width if desired The default values are usually good The default time of 10 seconds works for most samples but shorter times will not adversely affect most experiments 5 Click on Execute The view will shift to the Monitor Experiment view see Figure 6 5 The program will collect a series of three runs with twelve frames per run This typi cally takes less than ten minutes The images will stop changing when the experi ment is done It is not necessary to wait for all runs to complete before proceeding to the harvesting step step 6 2 2 NOTE Adjust the time upper right to match the scattering ability of the crystal i e shorter exposure times for str
39. or if the com pound is known to be chiral enter that infor mation see Figure 8 6 Generally it is sufficient to press Enter to start the space group determination Figure 8 6 Space Group options M86 E00078 Examine Data 5 XPREP has chosen the crystal system O see Figure 8 7 Press Enter to accept Figure 8 7 Choose the crystal system 6 XPREP has chosen the crystal lattice P see Figure 8 8 Press Enter to accept Figure 8 8 Choose the lattice 7 XPREP evaluates the data and looks at the systematic absences for all possible glide planes and screw axes see Figure 8 9 These are displayed across the middle of the figure By examining the number of reflections with I gt 3 sigma l the mean intensities and the mean int sigma which should all be very small for a systematic absence XPREP derives a suggested space group P2 1 2 1 2 1 Press Enter to accept Examine Data 8 3 Reflection Statistics Figure 8 9 Systematic absences and a suggested space group 1 XPREP returns to the general menu seen previously see Figure 8 5 This time D is chosen to evaluate the data set Press Enter to accept 2 There are multiple choices for data manipu lation see Figure 8 10 S chooses a dis play of statistics 3 XPREP Ver 6 14 W95 98 NT 2000 ME Copyright Bruke lata Filename or Source of Data current dataset Figure 8 10 The data manipulation menu APE
40. ray Tube Monochromator Goniometer Figure 2 4 SMART goniometer components M86 E00078 Hardware Overview Hardware Overview APEX2 User Manual X ray Source Three components make up the X ray source a shielded X ray tube an X ray safety shutter and a graphite crystal monochromator The sealed tube X ray source with a molybde num Mo target produces the X ray beam used by the system The X ray safety shutter is built into the X ray tube shield The shutter opens upon initiation of a set of exposures and closes upon the end of collection Status lamps on the shutter housing indicate when the shutter is open red or closed green The shutter is also interfaced to the controller and to the safety interlocks A tunable graphite crystal monochromator selects only the K line A 0 71073 A emitted from the Mo X ray source and passes it down the collimator system K780 X ray Generator The K780 X ray generator is a high frequency solid state X ray generator that provides a sta ble source of power for operations up to 60 kilo volts kV and 50 milliamps mA Typical maximum power settings for the APEX II system with a fine focus tube are 50 kV 40 mA Either copper or molybdenum tubes may be used on APEX II systems For both types of tubes the kV setting should not exceed 50 kV and the power kV x mA should not exceed the power rating given on the tube cap Because the generator is interfaced to the
41. refinement process is quite straightforward using XShell 1 Start XShell the molecular viewing and refinement plug in by clicking on Refine Structure in the Task Bar and then on the Structure Refinement icon 2 This will open a window to select files for XShell In usual operations the file name will be pre selected If a different file is desired select Browse E E ba Select Files For XShell Tx RES file C sstructguestiplid_manualwworkiplid_reso75 res a Figure 9 4 The Select Files tool M86 E00078 APEX2 User Manual Structure Solution and Refinement 3 Click on OK to open a molecular display window XShell 6 2 C frames quest cust work ylid_Om res File Refine Disorder Constrain Model Render Preferences Help EIS je ees ee ao ae SELECT ATOMS Element Name Component Include f Exclude Numeric Component Include fo to jaa Exclude to Trailer Component Include f Select Components Exclude oo Deselect Components Clear Current Selection OK Cancel Residual Difference Fourier Q Peaks T Legend Atom Name x Y 2 Height Bond No ofQPeaks 20 Figure 9 5 Initial view of the YLID molecule M86 E00078 9 5 Structure Solution and Refinement APEX2 User Manual 4 Right click in the background to open a pop up window with options to change the Image lt wireframe Ball And Stick Thermal Ellipsoid Pipes Selec
42. the image display e g Black On White right click in the intensity bar to the right of the image display see Figure 6 6 List Ref Le am ASC i BB e Black On White 11 Colored CUSTOM DIFFER Life 1000 MONG Trichi PRINT om a ee g E Rainbow Rainbow Step The Blues Tie Dye v16 vas va VIDEO white On Black Custom Figure 6 6 Color too NOTE After the first run is completed there is usually sufficient information to start the index ing step APEX2 User Manual 6 2 2 Harvest the Reflections 1 Left click on Evaluate Crystal gt Determine Unit Cell FF Determine Unit Cell Figure 6 7 The Determine Unit Cell Indexing icon M86 E00078 APEX2 User Manual This will open the image viewer but with a tool bar to the right for indexing see Figure 6 8 The plug in initializes with the first run e g matrix_01 First Image Gtrix_O1_0001 shm Ga le Number of Images 12 Clear All Reflections Harvest Spots Index Refine List Reflections i O Reflections Unit Cell A 10 000 4 o 30 000 B 10 000 4 B 30 000 C 10 000 4 vw 30 000 Volume 1000 0 4 3 Sommet Triclinic Lattice P 2 H l 1 LEENI l EEEL l EEEL l EEEL l 1 LEENI l EEEL 100 1000 10000 100000 1000000 10 Description 1 Image type Phi Scan Image Start position Distance 40 00 2T heta 30 00 Omega 315 1 13 End position Distance 40 00
43. with other Bruker products Other members of this new generation of instruments include the D8 ADVANCE and D8 DISCOVER and the D8 GADDS systems for general diffraction Docu mentation on some of these common hardware and software components is available in the user manuals for the D8 family of instruments APEX2 User Manual 1 2 User Manual Features This user manual and associated YLID test data are intended to provide you with a step by step guide to data collection and processing using the APEX2 software program The test data supplied was collected on a Kappa APEX II diffractometer with graphite monochromated molybdenum radiation from a sealed tube generator The high quality data resolution 0 75 A allows easy refinement of the hydrogen atom positions and determination of the absolute structure of the sample NOTE Before using this manual check that your system is in proper working order e g the optics and goniometer are aligned and that the APEX2 suite is properly installed M86 E00078 APEX2 User Manual 1 3 X ray Safety X ray equipment produces potentially harmful radiation and can be dangerous to anyone in the immediate vicinity unless safety precautions are completely understood and implemented All persons designated to operate or perform maintenance on this equipment need to be fully trained on the nature of radiation X ray generating equipment and radiation safety All users of the X ray equipment are r
44. 0 0 4763 0 0236 1 29 A from C O EEF FEF ylid_res75 finished at 11 53 17 Total CPU time 0 5 secs HA A A A A A A A A Figure 9 42 Refinement results The value for R1 0 029 is typical for an aniso tropic refinement with riding hydrogen atoms and a data set measured to 0 754 Since the mean shift esd is less than 0 01 the model is not changing significantly Since the highest peak and the deepest hole in the difference map are similar there are probably no missing atoms The resulting difference electron density map appears rather ugly This is because the number of difference peaks to be displayed has been left at 20 M86 E00078 Structure Solution and Refinement Figure 9 43 Difference peaks in a well refined model 9 3 7 Final Refinement for Publication Obtain a view that is much easier to interpret by reducing the number of difference peaks in the Refine menu see Figure 9 44 1 For the final cycles of refinement reduce the number of peaks to be displayed to five and turn on Use Suggested Weights and Generate ACTA CIF Information File as shown in the next two figures NOTE If the suggested weights vary signifi cantly from 0 06 and 0 00 then change the val ues to 0 06 and 0 00 Number of residual peaks ls Y Figure 9 44 Reduce the number of difference peaks Structure Solution and Refinement Late stage refinement options Refine all non H atoms anisotrop
45. 0000 1000000 Narowtos ween Distance 40 00 2T heta 0 00 Omega 0 00 Phi 0 00 Chi 0 00 Distance 40 00 2T heta 0 00 Omega 0 00 Phi 2 00 Chi 0 00 Instrument Figure 3 3 Simple Scans window M86 E00078 3 3 Software Overview 3 2 The Client Computer The client can be any computer on the same network as the server For SMART APEX II sys tems it is usually the same computer as the server The main portion of the APEX2 suite the APEX2 client runs on the client computer The client is a GUI with multiple plug ins or modules for different aspects of an experiment The client includes a database which stores relevant data from each step in the experiment Details of the functions available in the GUI will be explained in more detail later in the manual 3 2 1 Database and Database Connection As currently configured the database is used internally by the APEX2 Suite and is not avail able for user customization or manipulation It must be running before the APEX2 Suite is started and it should be stopped before the computer is shut down see Section 4 3 2 The database is used for the storage of data generated by the Bruker APEX2 software APEX2 User Manual M86 E00078 APEX2 User Manual Software Overview 3 2 2 APEX2 GUI e Window Tool Bar The APEX2 GUI has one main window see Fig ure 3 4 This window is divided into four sec tions Tool Icon Bar e Task Bar e Task Display Area File In
46. 000001 0010122100122211 256 256 Phase sets refined best is code 917713 with CFOM 0 0597 Fourier and peaksearch N RE 0 154 for 14 atoms and 467 E values Fourier and peaksearch RE 0 140 for 14 atoms and 467 E values Fourier and peaksearch FEFAFEFEEEF EEF EEEAEEFEEEF EEE EEFA EEF EEF vlid_reso 5 finished at 07 46 22 Total elapsed time 0 9 secs Figure 9 2 Structure Solution output 3 Click on the arrow to the right of Direct 1 in the Method box see Figure 9 3 This gives three choices for structure solution using direct methods Method E Direct 1 c Dual Space 1 Patterson 1 r i Structure Expansion Computing Effort log scale _ _ gt ooooPVom Figure 9 3 Method box M86 E00078 Structure Solution and Refinement In most cases the default values will give a good initial model but there are several other options available for more difficult problems 1 Chose the solution method by clicking the appropriate radio button on the left in the Method box 2 Highlight and click on Direct 1 to set up a default run with a simple TREF instruction 3 Highlight and click on Direct 2 to set up an extended run with TREF 10000 By adding 10000 to the TREF command more attempts are made to determine a solution This will take more time but if you see a good solution in the output window it is pos sible to stop at that point by clicking on the STOP button Good solutions typically
47. 0078 Examine Data 3 Check the default input value Modify as needed and press Calculate Calculating more zones does not significantly increase the calculation time In the example 1kl h1l and hk1 have been added to the defaults of Okl hOl and hkO Fractional values e g 0 5kl are allowed Reducing the resolu tion may speed the calculations slightly The thickness defines the range of pixels above and below the requested range For example if the Okl zone is requested with a thickness of 0 1 then the simulation is looking for all pixels that have 0 1 lt h lt 0 1 and any value including frac tional values for k and I Planes ok AOLAkO AKT TE htl Images from Iruc quest data_manual ylid_manual 1127 image files in 4 runs best resolution 0 77 Thickness 0710 Calculate Created files hi Figure 8 23 Detail of the input section Examine Data APEX2 User Manual 4 Aprogress bar will appear Figure 8 24 and 5 Use the simulated patterns to check space after approximately 5 10 minutes depend group symmetry see Figure 8 25 Figure ing on the number of sfrm files read an 8 26 and Figure 8 27 and to find signs of image will appear on the screen Display twinning see Figure 8 28 other planes by clicking on the calculated images to the bottom right of the work area or by browsing as usual with the View plug in Figure 8 24 Progress bar Figure 8 25 The Okl plane for the test YL
48. 187 Karlsruhe Debug BIS Samie MEO FTES 27 S08 Phone No 49 0 721 595 6348 Fax No 1 608 276 3015 Fax No 49 0 721 595 6561 Email bugs bruker axs com Email software bruker axs de Internet www bruker axs com Internet www bruker axs de C Delft Japan Bruker Nonius B V Nihon Bruker AXS K K Customer Support Customer Support Delft The Netherlands Japan Phone No 31 152 152 574 Phone No 81 298 52 1236 Fax No 31 152 152 500 Fax No 81 298 58 0322 Email service bruker nonius com Email kuroda bruker co ip Internet www bruker nonius com Internet www bruker axs com Figure 3 2 BCP main window M86 E00078 APEX2 User Manual Software Overview 3 1 3 APEX2 Server The APEX2 Server provides tools for aligning and screening samples There are two main items Align Crystal and Simple Scans see Fig ure 3 3 E Apex2Server 1 0 3 Simple Scans 3 Eile Instrument Windows y 1 x R2 CNDOCUME 1 ADMINI TSLOCALS 1 Temp s_01_0001 sfrm gt ca 4 gt Os MO Distance mm ao 4 2Theta Omega _ Phi Chi Zero Current Phi 0 Phi 90 Align Crystal DE y Scan Axis Phi Omega Scan Range 2 00 Image Width jo Exposure Time fio y secs image y m Scan Options I Correlate 2 images J New dark image 1 1 I D A AL 1 I Perret 1 ee Still 360 Phi 100 1000 10000 10
49. 2 32 56 00 07 53 All 684 1127 HEE 22 32 56 00 07 53 Figure 7 19 Integration Progress display M86 E00078 Data Integration and Scaling Data Integration and Scaling APEX2 User Manual 2 Click on Spot Position Overlay in Per Image Statistics to add one of the most powerful windows for monitoring the progress of the integration Pull up on the Window Tool Bar for Integrated Spots the cursor arrow is pointing to this tool bar in Figure 7 20 to display the entire window see Figure 7 21 Je S JO x Scan 3 Integration O 35 00 All Components O Progress Statistics 30 00 O Integration progress O Per Image Statistics E Spot shape correlation E Spot intensity and 1 Sigmall J Spot intensity lt 2 Sigmall O Number of reflections harvested E Spot position overlay E x Y Z error HO X Y Z RMS difference 15 00 ro A Y Z spot size O Queue extent used 2 Primary beam intensity 10 00 O Periodic Statistics E Profile snapshots O A axis ESD 2D B axis ESD l l Image EO C axis ESD Intensity sigma O Alpha angle ESD O Beta angle ESD i Integrated Spots LE Gamma angle ESD 3 iC Cell volume ESD oO LS goodness of fit O LS Residuals HO x Y Z crystal translation O x Y beam center O Distance correction Pitch Roll Y aw correction O Angle zeros O Coverage Statistics C Harvested reflections J Completeness and redundancy O Bijvoet pairs 14000 0 12000 00
50. 2 p4p p4p or spin file to write domain to domain2 p4p RLATT color coding employed in file domain2 p4p White indexed for first domain Green current domain but not in a previous domain Red not yet indexed 691 reflections within 0 250 of an integer index assigned to domain 2 LUG or hem exclusively 3 reflections not yet assigned to a domain Re rerine initial Gell R y search for next domain 8 GULE 0 or choose new cell from list enter number Q 13 Enter lt q gt to exit CELL_NOW C struc guest twin gt NOTE At this point CELL_NOW has indexed a two component twin The orientation matrices for the two components are in the domain2 p4p file discussed below Typically the next step in processing is to integrate using SAINTPLUS with the multi component p4p file in this case domain2 p4p used as the matrix file C 8 M86 E00078 APEX2 User Manual Using CELL_NOW C 2 CELL_NOW output In this example in addition to the terminal output described above and the example _cn listing file writ ten to disk CELL_NOW has written two p4p files domain1 p4p and domain2 p4p The second of these is a multicomponent p4p for a two component twin It is shown below The following entries appear twice once for each domain CELL ORT ORTZ ORTS ZHROES ADCOR CELE ORTIZ ORTZZp ORTIZ LCEROESZ y ADCORZ This will eventually trigger SAINT to treat this data set as a twin FILEID SAINT V6 43A 4 00 06 19 03 09 3
51. 2268 7964 O O O for all composite Run 2 theta 1 28 0 UY 2 28 0 0 3 28 0 0 4 28 0 0 Statistics Run 2 theta 1 28 0 0 2 28 0 0 3 28 0 0 4 28 0 0 Statistics Run 2 theta 1 28 0 0 2 28 0 0 3 28 0 0 4 28 0 0 M86 E00078 R int 1018 AL 1184 OTSO Incid 0907 2962 0 968 NOS Factors DiItkr SOS 1 002 O AS 1 000 MAD 1 014 IA 6 1 0 966 reflections Factors Dirirs OS dei 0ga 026 0 986 OZ TOEL abe o e7 0 946 factors Sd 1 126 a Meg 1 172 factors 1 factors gee Ss Ted LO Teed 128 L29 TZ Mes Daz 128 124 096 O O O O O O O O O O O O s033 629 084 662 8632 608 038 MOT KELL 032 617 47 06 Total L gt 285 GUI Z133 A22 1827 898 1024 TELG EAA 340 Total L gt 281g 1 2666 A223 LOS 906 LTOZ T855 893 316 Total L gt 52S GAL 1955 2343 SEA 604 1058 Laal ZO 402 Processing Twinned Data APEX2 User Manual Statistics for all single and composite reflections Run 2 theta R int Incid factors Diffr factors K Total T2919 1L Te 2820 De LS 07 1300S Le 002 Lsizs 0 636 7374 SATO 2 BROS AA E 10 AS OSOS My 26 Geal 10789 4796 3 28x0 20 1500 OS a 2 062 TEOLL LANAS 0 664 4261 1880 Ae FAS ie LITO Cec oy 0 T Od le OLA te G2 O 2679 2408 L123 su K Sgrt sigma 2 1 g lt I gt 2 where sigma I is estimated by SAINT The above statistics are based on all non rejected data ignoring
52. 3 For Windows enter the command bnrun c bn src plugins saint Saintplus pyc see Figure B 1 M86 E00078 4 For Linux enter the command bnrun usr local bn src plugins saint Saintplus pyc es Command Prompt bnrun c bn src plugins saint saintplus pyc struc guest ephe lt gt cd N Ned struc guest ephe 1t Nstruciguestrephe 1t gt bnrun c bn sre plugins saint saintplus pyc Figure B 1 Starting SaintPlus SAINTPLUS APEX2 User Manual After the command is executed the SaintPlus window will open see Figure B 2 sitos S 10 x Resolution Limit A fi 700 Images Matrix Filename utputFilename 222 File Options Utilities Space Group P1 hd Starting Image Filename 1 3 ES 4 5 6 7 o Refinement Options Integration Options Figure B 2 Initial integration window Find Runs Replace Matrix Files This window is like the Saint window discussed previously Section 7 but with the following dif ferences e Defaults are not determined by previous knowledge of the sample e There is a button to replace the matrix files 5 Click Find Runs Browse to find the images to integrate F Find Runs ES Find Runs in Directory EE Image Base Name IS Figure B 3 Find Runs window ee z Start Integration 7 Click on Replace Matrix Files and browse to find a p4p or spin file to use Replac
53. 3 Ifthe hydrogen atoms in Figure 9 49 are large change their size 3 1 Click on Preferences in the Window Tool Bar and choose Atom Prefer ences i Atom Preferences Figure 9 50 Atom Preferences tool M86 E00078 Structure Solution and Refinement At the top of the box that is opened there are three values that can be changed to adjust the size of atoms and the bonds to them ATOM PREFERENCES Element Atom Radius Bond Radius PeriodicTable Ho lo 12 lo 22 Figure 9 51 Default atom preferences 4 Change the hydrogen radius to 0 08 and the bond radius to 0 15 to make the hydrogen atoms smaller i ATOM PREFERENCES Element Atom Radius Bond Radius PeriodicT able Ho oos lo 15 Figure 9 52 Modified atom preferences Figure 9 53 Thermal ellipsoid plot with smaller hydrogen atoms Structure Solution and Refinement 5 Position atom labels by right clicking on the atom and choosing Position Label Delete Atom Hide Atom Labelling Set Pivot Point Hide Label Position el Change Part Figure 9 54 Position Label menu Figure 9 55 Positioned labels 6 Convert this image into a high quality jpg file for inclusion into reports by clicking on render in the Windows Tool Bar and choos ing Black and White to High Quality JPEG file 9 28 APEX2 User Manual Constrain Model Render Preferences Help Black and White To Printer Ctrl T Eke HighQuiality JPEG
54. 35 00 2Theta 28 00 Omega 48 51 Phi 57 End position Distance 35 00 2Theta 28 00 Omega 48 51 Phi 58 4 gt Image Header Show every 5th image Figure 7 21 Full view of the Spot Position Overlay M86 E00078 Data Integration and Scaling Data Integration and Scaling APEX2 User Manual 7 2 2 Examine Final Results At the end of integration examine this text criti text as indicated by the position of the cally In particular look at the Overall Rsym the mouse cursor in Figure 7 22 Coverage Statistics and the Unconstrained Unit Cell refinement 1 Setup to view SAINT text output At the bot tom of the SaintChart window is a scrolling 2 Examine the final results 2 1 Overall Rsym and Coverage Statistics Figure 7 22 text window that displays the text output The overall Rsym is usually less than 8 from SAINT This window can be expanded Higher values may indicate problems with by dragging the horizontal bar above the absorption twinning or poor crystal quality _ g o m Spot Shape Correlation f ol x i eh ey Mi Aigi coefficient a co El 25 000 Fairs Uri Merg 225 lt I gt lt 5igq gt lt B gt Bem JII dI 12956 1442 1451 12948 17 3 4707 540 27 07 0 000 a Overall Centric Fairs Urii Merg fs lt I gt lt 5iq gt Bg gt Eswym dI I dls 0 000 2413 447 454 2407 21 5 7064 4427 39 39 3 08 0 033 0 000 0 1 000 overage Statistics for ylid m
55. 6 24 mraa SITEID RufM Ruf TITLE REOOCECIO INTHE in CHEM C40H58Cr2C1402 CELL 126913 OTTO 14 6480 Sd POA 90 9494 9020010 20422695 CELLSD O 007 3 0 0022 O AS 93 00 0 0300 00300 LOZA ORT1 0001643376 0003574040 0 0068 1 63L086 ORTA 0 034171116 0 08L POLLS 00003900211 ORT3 0s 070988722 00394033979 0 000980361 ZEROS OOOO 0000 On82489 754 0 0041494 00000 0 0000 0 0000 ADCOR LIZ 20 00 47 00003 O 0 III 0 0123 020 937 CELL2 LLO 918 IT Odo 14 6480 Sd 7011 90 94 94 90 0010 204 P0295 CELLSD2 020025 0 0022 D029 040500 0 0300 20390 LOZ 4 ORT12 O00 S593 96 63 02004023272 0 068074010 ORT22 O 03367 3126 0 0891803404 0 004801138 ORT SZ CeO 70993027 1 0 03914 ki 27 O 002210349 ZEROSZ 0 0000000 0 3249754 0 0041494 0 0000 0 0000 0 0000 ADCOR2 Ze DOO 0 00 04 7 O s 0 00 3 6999 DOLLZ On O37 SOURCE Mo Oa TOTS Os 70930 On LS 2 00000 50 00 40 0 M86 E00078 C 9 Using CELL_NOW APEX2 User Manual C 10 M86 E00078 Appendix D Processing Twinned Data D 1 Integration with SAINTPLUS The multicomponent p4p file written by cell_now is processed using SAINTPLUS 1 Open a Command Prompt window 2 Change directories to the folder containing the exported reflection list 3 Depending on your operating system enter the command to start SAINTPLUS M86 E00078 Windows bnrun c bn src plugins saint saintplus pyc Linux bnrun usr local bn src plugins saint saintplus pyc After the command is entered the SAINTPLUS
56. 7 14 and Image Queue see Figure 7 15 APEX2 User Manual M86 E00078 APEX2 User Manual Data Integration and Scaling Integration Options Active Mask File F_am y Figure 7 12 The Integration Options window with More Options selected M86 E00078 7 7 APEX2 User Manual Data Integration and Scaling 7 1 1 Active Mask E Generate Mask Fractional Lower Limit of Average Intensity 0 000 f Use Pre Esisting Mask Active Mask File _aml na Figure 7 13 The Active Mask tool The Active Mask is used to mask out areas that are covered by the beamstop low temp nozzle or other obstructions Typically a value of 0 7 is good here SAINT will determine an active mask for each run NOTE If this option is set the user should examine the active mask images that are written into the work directory with the name basename_am_ sfrm There is one for each run These images can be opened with the image viewer They should be blank except for an area in a different color showing the shape of the obstruction typically the beamstop 7 1 2 Algorithm Algonthm f Use Narrow Frame Algorithm f Use Wide Frame Algorithm Figure 7 14 The Narrow Wide Algorithm tool The algorithm buttons are used to change from narrow to wide frame integration Frames col lected with narrow scan widths less than one degree should be integrated as narrow frames Those greater than one degree should be inte grated
57. 96 44 686 4 POs angle correlation to Oo Oe 2g SAS HIS LOO GO S096 99 Dons os IU LSO 99 PA 193 ASA Ze TOS ee OE 569 SO DO TASES OO dio Goa Tawa LOS LOAD 0 480 0 484 65 465 80 Cd 0 3 999 DO G90 92 JIo 2a AOS 99 O92 Oe Wat 97 BOW IIa ZOO Dis IEY 0 487 AGO Gos 299 899 698 899 898 O 399 Tod 465 components previous vectors se O 475 491 TOAN 2200 446 lt 3 20 496 128 248 O SOs 14 493 dz 414 402 Ll 915 2332 3200 AS 1 LS LN LS 20k 432 182 211 s64 668 109 999 OAT 7059 M86 E00078 APEX2 User Manual Using CELL_NOW LS OL AOS AO LO Lo O 07 Das Usado O32 C2524 0409 0469 00469 De d6 14 648 0 684 18 jodo O Ad DI O90 gt 142633 o 0025 Sl US AUes Deo One 029 20 2 OO ll Masa 0603 0 9096 Dedos 9 Dia o Oar DADO 0 0350 0 4424 After the vector list has been output CELL_NOW attempts to suggest a suitable cell This will not nec essarily be the conventional cell so it should be checked using XPREP without an hkl file taking the lattice type found with CELL_NOW into account lf necessary this conventional cell may then be input in specified cell search mode to find the orientation matrix The following cells would appear to be plausible but should be checked using XPREP because they are not necessarily the conventi
58. ART APEX II system M86 E00078 APEX2 User Manual 2 1 1 APEX Il Detector The APEX II detector is specific to this system Status lamps on the top of the detector housing indicate when the detector is on green and off red On Kappa APEX II systems the detector is mounted on a motorized 2 theta track The cam era distance is computer controlled a typical distance for the camera is 40 or 50 mm On SMART APEX II systems the detector is mounted on a 28 dovetail track The track has a scale that is calibrated in mm to indicate the dis tance from the crystal to the phosphor window a typical distance for the camera is 40 or 50 mm An optional motorized DX track is available for the SMART APEX ll M86 E00078 Hardware Overview 2 1 2 Goniometer The goniometer module and APEX II detector make up the unique hardware of the system This is the part of the instrument that actually performs the experiment Several components make up the goniometer module with APEX II detector e Goniometer 3 axis or 4 axis e APEX Il detector e X ray source including shielded X ray tube X ray safety shutter and graphite crystal monochromator e K780 X ray generator e Timing shutter and incident beam collimator with beamstop e Video camera Hardware Overview Kappa APEX Il Goniometer The Kappa goniometer uses a horizontally ori ented Kappa goniometer with 2 theta omega kappa and phi drives and a motorized DX tra
59. Collection NOTE In most cases the angle zeroes are close to zero and should not be refined The crystal should now be aligned so refinement of the crystal center is not necessary Data Collection 6 2 5 Determine the Bravais Lattice 1 After refining click Bravais Lattice and look for other unit cell choices i e look at fit val ues hal Choose Bravais Lattice 4 Asis B Avis A C Avis A Alpha Beta t Gamma Volume 4 3 _ Orthorhombic F 0 59 5 96 9 04 18 42 29 94 Monoclinic E 89 97 89 90 992 Temse IRC s so eo CE o a7 Cancel A Figure 6 14 Bravais lattice display Note that even though monoclinic has a slightly better fit the software makes the correct choice data collection strategy of the higher symmetry cell 2 Click on the appropriate Bravais lattice in this case Orthorhombic Press OK to accept the suggested lattice settings Refine again Refine for several more cycles changing the constraints one or two at a time APEX2 User Manual Now you have a unit cell ready for determining a M86 E00078 APEX2 User Manual 6 3 Determine the Data Collection Strategy APEX2 includes a powerful algorithm COSMO for determining an efficient strategy that fully uti lizes the flexibility of your instrument 1 Left click on Collect gt Data Collection Strat egy or AUN AUN AUN LL Figure 6 15 The strategy display il if l
60. File Ctri u Figure 9 56 Generate JPEG NOTE A message may appear that the font file needs to be defined Please set your font direc tory for the first time for opengl rendering If this happens click on Preferences gt OpenGL Pref erences Then click on the TrueType font For OpenGL In Windows browse to C bn xshell fonts or in Linux go to usr local bin xshell fonts Choose a font M86 E00078 APEX2 User Manual XShell 6 2 c struc guest data_manual ylid_manual work ylid_resoG res A590 ae se aaa Figure 9 57 The final rendered thermal ellipsoid atomic displacement parameter plot M86 E00078 Structure Solution and Refinement Structure Solution and Refinement APEX2 User Manual 9 30 M86 E00078 Appendix A RLATT RLATT is a very powerful tool for viewing the harvested reflections in a reciprocal lattice This section will cover only a few of its features RLATT is best learned through use This example has over 3300 reflections This is not the typical case generally only 300 or 400 reflections are examined Using extra reflections will make the examples easier to see M86 E00078 A 1 Open RLATT 1 Start RLATT from the Task Menu under Examine Crystal 2 Click on the Start icon to read the reflections from the database into RLATT A n E A a Lo P m A Reciprocal Lattice Wiener Figure A 1 RLATT icon RLATT Figure A 2 is a typical unoriente
61. ID 8 10 M86 E00078 APEX2 User Manual Examine Data Figure 8 26 The hOl plane for the test YLID Figure 8 27 The hkO plane for the test YLID M86 E00078 8 11 Examine Data APEX2 User Manual Figure 8 28 A plane from a rotationally twinned crystal showing the two lattices 8 12 M86 E00078 9 Structure Solution and Refinement 9 1 Overview You are now ready to solve and refine the crys tal structure The various steps in solving and refining the structure are carried out within the APEX2 GUI XPREP has prepared the input files for a standard direct methods run There are two files ins and hkl In this example the two files are ylid_res75 ins and ylid_75 hkl M86 E00078 These files are all that is required to begin the structure solution and refinement process The various steps of solving and refining the struc ture are carried out using the Solve and Refine functions of the APEX2 Suite Structure Solution and Refinement APEX2 User Manual 9 2 Solve the Structure 1 1 If you entered a correct formula in the display GUI then you are ready to start The process of obtaining an initial model of the a normal direct methods run compound is started by clicking in the Task Bar o o on Solve Structure and then on Structure Solu 1 2 If the formula is incorrect change it in tion the formula window and press Return PER The input file will update 1 This will open the Structure Solution GUI Check t
62. Image Widtl Exposure Ti Scan Opti I Corre 5 1 Ty 10 Narro D Cursor be Position pixels 353 365 i Intensity counts 35 f HKL index n a n a Ax _ A AAA NNNNNX lt A i Resolution A 0 93 O O E 1 Theta 191 44 97 100 1000 10000 100000 1000000 Figure 5 22 A 2 phi scan on a high quality crystal at 2 theta of 30 The cursor is pointing to an area between the two reflections shown in the 2D box The cursor info at the bottom left shows the resolution is 0 93 and 2 theta is 45 M86 E00078 Crystal Orientation Crystal Orientation APEX2 User Manual 5 4 Examples of Poor Screening Figure 5 23 A 360 phi scan on a poor quality crystal The Figure 5 25 A 2 phi scan on a poor quality crystal at plus spot shape is poor and the spots tend to run together The 90 in phi The spot shape is poor and the spots are very obvious bands on the image suggest that the crystal is close together nearly aligned on an axis Figure 5 24 A 2 phi scan on a poor quality crystal The Figure 5 26 A 360 phi scan on a small crystal The spot shape is poor and the spots are very close together diffraction power of the crystal is small but with slower scans this is clearly a reasonable candidate for data collection 5 14 M86 E00078 6 Data Collection The data collection process is carried out on the client computer using APEX2 Once data collec tion is started exit APEX2 optional Da
63. M86 E00078 APEX2 User Manual 9 3 5 Sort Atoms 1 Right click on the background and click on Sort to sort the atoms into a sensible order e Hydrogen Labels e Labels Grow Pack Figure 9 31 Choose the Sort option A box will appear to the right of the molecule display Since S1 O1 and O2 are in a reason able order only the carbon atoms need to be ordered M86 E00078 Structure Solution and Refinement SORT ATOMS Sort Bin Atom List lt Top of List gt Sorti Alpha Wumeric Sorti Mumeric Alpha Insert Selected 4fter gt Insert All Ofber gt lt Move Selected Atoms To Sogt Bin lt Move All Atoms To Sort El Cancel Figure 9 32 Selecting carbons for sorting NOTE Generally it is easier to sort and number atoms before adding hydrogen atoms 2 Highlight the atoms to be sorted i e left click and drag over the atoms and move them to the Sort Bin i e left click on Move Selected Atoms to Sort Bin Structure Solution and Refinement APEX2 User Manual Sort Bin 4 Highlight O2 and click on Insert All After as in Figure 9 34 Sort Bin Akom List lt Top of List gt Sorki Alpha Mumeric i Figure 9 33 Carbon atoms in Sort Bin 3 After the atoms are in the Sort Bin click on Sort Alpha Numeric Sort Alpha Numeric to get them into a nor satis UEP mal O rde r Insert Selected After Insert All AFter Figure 9 34 Sorted atoms with i
64. Reflections Select Current Group Invert Selection Grouping Tools Current Group MA Gopi Y Add To Current Group Remove From Current Group Select D Groups v None Deletion Helpers Delete Selected finalized at save Delete Non Visible finalized at save Intensity Filter Reflection Size Zoom Export Visible Spots to P4P Figure A 16 The selected spots are now the little ones between the layers The spots in the layers are grey and the selected spots are turquoise M86 E00078 A 13 RLATT APEX2 User Manual Click on Delete Selected finalized at save to mark the selected reflections to be deleted and turned black Alternatively these selected reflections can be added to a group and then hidden using Select Visible Groups Editing Tools C Box f Lattice Overlay C Single Spot E Circle None rotate 211 7 Selection Helpers Select Weak Reflections Select Current Group Invert Selection Grouping Tools Current Group MA Group 1 y Add To Current Group Remove From Current Group Select Visible Groups vI None Deletion Helpers Delete Selected finalized at save Delete Non Visible finalized at save Intensity Filter Reflection Size Zoom Export Visible Spots to P4P Figure A 17 Selected reflections are blacked out A 14 M86 E00078 APEX2 User Manual Save the file by clicking the disk icon Figure A 18 or use F
65. SS UKER BRUKER ADVANCED X RAY SOLUTIONS APEX2 User Manual version 1 27 USER MANUAL M86 E00078 2 05 SS UKER BRUKER ADVANCED X RAY SOLUTIONS APEX2 USER MANUAL M86 E00078 2 05 This manual covers the APEX2 software package To order additional copies of this publication request the part number shown at the bottom of the page References to this manual should be shown as APEX2 User Manual O 2005 Bruker AXS Inc 5465 East Cheryl Parkway Madison WI 53711 All world rights reserved Notice The information in this publication is provided for reference only All information contained in this publi cation is believed to be correct and complete Bruker AXS Inc shall not be liable for errors contained herein nor for incidental or consequential damages in conjunction with the furnishing performance or use of this material All product specifications as well as the information contained in this publication are subject to change without notice This publication may contain or reference information and products protected by copyrights or patents and does not convey any license under the patent rights of Bruker AXS Inc nor the rights of others Bruker AXS Inc does not assume any liabilities arising out of any infringements of patents or other rights of third parties Bruker AXS Inc makes no warranty of any kind with regard to this material including but not limited to the implied warranties of merchantability and
66. T CTRL 16x speed Selection Tools SHIFT left click CTRL left click remove spots from current selection UP DOWN LEFT RIGHT move selection tool add spots to current selection hold SHIFT 4x speed during movement only hold CTRL 1 4 speed during movement only hold SHIFT CTRL 16x speed during movement only add slice lattice tool only remove Slice lattice tool only PGUP add Extension lattice tool only PGDN remove Extension lattice tool only ALT left click lock onto spot lattice tool only adjust intensity slider adjust intensity slider change axis modes change colorization method invert selection toggle distance measurement during lattice selection tool toggle Null Resolution Mode change 2D Projection Scale mode toggle Unit Cell Tool A a I M N S U Figure A 6 Shortcut keys and commands M86 E00078 Fl 100 along a F2 0 10 along b F3 00 1 along c F4 unoniented identity matrix FS user defined orientation 1 F6 user defined orientation 2 F user defined orientation 3 F8 user defined orientation 4 SHIFT F5 store user defined orientation 1 SHIFT F6 store user defined onentation 2 SHIFT F store user defined onentation 3 SHIFT F8 store user defined orientation 4 add slice remove Slice PGUP add Extension PGDN remove Extension hold SHIFT ALT left click action
67. X2 User Manual 3 The data can be merged in several ways Choose the Merge ALL equivalents includ ing Friedel opposites option A see Figure 8 11 Press Enter to accept NOTE This merge will not average the reflec tions in the final data file It is only for the calcu lation of statistics Figure 8 11 The merge data menu 4 A table of statistics appears see Figure 8 12 Examine the data presented Is the completion near 100 Is the redundancy good Are Rint and Rsigma small and increasing smoothly from top to bottom In particular look at the last two lines which compare all of the data with the high resolu tion data The completion should be near 100 for both the high resolution shell and the complete data set The redundancy and Rint should be similar for the two The Mean Intensity and the Mean l sigma l will usually be quite different The Mean l sigma l for the high resolution data should be greater than 3 0 M86 E00078 APEX2 User Manual For this data set when integrated to 0 67A reso lution the difference between the Rint for the high resolution data and the complete data set is slightly larger than expected Press Enter to continue Sl XPREP Ver 6 14 W95 98 NT 2000 ME Copyrig Figure 8 12 Intensity statistics 8 4 Applying High Resolution Cutoff NOTE For the YLID crystal if the resolution limit for integration was changed to 0 75 as sug gested on Page 7 3 then there will b
68. a file 1 file fusr local lib7bn contig py 2a file the initial Character ror the normal Iis comand 8 file bn config an Windows these files bn config py in the bDn conf ig py in the bn contig in the current folder On are wW N e If none of these files is present Just been installed change a single configuration parameter on config in your home directory which renders this file invisible SystemDrive US HR PROM MGR all parameters are using built in defaults Please note your Current directory folder folder the situation when the program has TO creates or edits one of the three files and put in a value for the parameter to be customized You should put a parameter in 1 all Users put Lt in 2 want to use other values project The configuration files are read as M86 E00078 if it should be the system default for if it is your own default DUE LE AT and other people might S LE 1E us only required Tor a single Python programs and therefore Config APEX2 User Manual syntax is very important The best way to use 1t is to only use variable assignments or function Calls as described below If required you Can comment out lines from your configuration file by preceding them with a character Note Leading space is significant Start all assignments in the first column Variable names are Case sensitive FunctLonality
69. al to 2n or 3n resp 10 7 If the default minimum and maximum distances are acceptable hit lt Enter gt again Minimum and maximum allowed values for cell edge 5 40 NOTE Usually CELL_NOW is used to search generally for a cell but if the cell is known choose the specified cell option and enter the cell dimensions CELL_NOW will then search for a matching cell After some period of time a list of real space vectors sorted on a figure of merit 1 0 being a perfect fit will be output These are followed by the percentages of reflections that fit within 0 1 0 2 and 0 3 times the interplanar separation the components a1 a2 and a3 of the vector the angles to previous vectors and a cross figure of merit to previous vectors The latter should be larger for reflections belonging to the same twin component Cosines of angles between vectors a and b can also be calculated from the components by a1 b1 a2 b2 a3 b3 a b M86 E00078 C 3 Using CELL_NOW APEX2 User Manual Length fom Followed by IZ 2692 D LIgUl6 Os 9040 Os TOS 1628020 O Ie AO IES AO Os 19 De 209 T6805 Us Logs AD Os 142 0 739 za 0 La OO 0673 0 657 Ake TOL Oe 166 66 6 0 687 0 6539 242o Oa REISS Se ESO dl UEa Doa too Os da LAL 0 596 0 605 Susto Ue hits 902 30 S91 20 836 24 819 ZO SS 0 688 741 19 Ie BALAS E 06309 00616 T96 43 Ad ANO 0 620 0 645 122 45 cd IO 06309 00600 688 35 Gra US 025
70. anual Om raw Angstrms Ob s Theory Compl Pedund Baym Pairs Pairs Pshell fSigma lt 2s to 1 615 178 178 100 00 11 78 0 032 178 100 00 0 032 92 97 4 7 to 1 282 327 328 99 70 11 38 0 033 327 99 70 0 038 31 34 2 6 to 1 120 473 475 99 58 10 95 0 034 473 99 58 0 039 21 81 7 6 to 1 018 614 616 99 68 10 71 0 034 614 99 68 0 045 13 70 11 0 to 0 945 760 763 99 61 10 29 0 035 759 99 48 0 050 9 88 13 5 Coverage to 0 889 597 903 299 34 10 03 0 035 8968 99 22 0 063 7 32 18 9 to 0 845 1033 1036 99 71 9 77 0 036 1031 99 52 0 076 4 84 28 1 to 0 808 1183 1189 99 50 9 44 0 037 1181 99 33 0 083 4 45 30 9 to 0 777 1317 1320 299 77 9 18 0 037 1313 99 47 0 098 3 34 40 3 to 0 750 1451 1452 99 93 28 93 0 038 1442 99 31 0 116 2 65 50 8 Figure 7 22 Final SAINT Overall Rsym and Coverage Statistics 7 14 M86 E00078 APEX2 User Manual The coverage statistics are reported by resolu tion shells The values in the Rsym column give the cumulative agreement of equivalent reflec tions The Rshell values give agreement within a particular shell These change faster than the Rsym values The lt 2s column is useful for checking where the weak data becomes pre dominant greater than 50 or 60 The Sigma column gives the average l sigma for each shell If that number is less than 1 5 or 2 then little sig nificant data is being measured in that shell Unconstrained global unit cell refinement Data Integration and Scaling 2 2 Unconstrained Unit Ce
71. bsorption correction Enter lt ER gt Lt none Average Friedel opposites in output file Y or N Y 13d IMPORTANT Specify that only component 1 should be used for the HKLF 4 file Use component N only recommended 0 to use all 1 913 Corrected reflections written to Tile twin Ashkl Reflections merged according to point group 2 m Ratio of minimum to maximum apparent transmission 0 807218 13e Output an HKLF 5 format file for refining the structure Note TWINABS has automatically changed the default to type 5 It is now possible to generate a HKLF 4 format file with crude intensities for structure solution or a more accurate HKLF 5 format file for refinement Repeat R write shkil File 4 or 0 Of Quite 0 Los Average equivalent reflections Y or N Y 13f Set the output file to reflect that this is a HKLF 5 type file For example name it hkIf5 or twin_5 Enter name of output hkl file twin hkl twin 5 Mu r of equivalent sphere for additional spherical absorption correction Enter lt CR gt ack none Average Friedel opposites in output file Y or N Y M86 E00078 D 9 Processing Twinned Data APEX2 User Manual 13g IMPORTANT Note well that the default will output only component 1 You can enter 0 for all data Experience has shown however that only writing single or composite reflections to the hkl file when a given component e g 1 is present usually gives a better structure and r
72. cidad me done ae eee ate 4 7 5 Crystal Onientauon iento Soar ten hei tae 5 1 5 1 Mount the Goniometer Head on the Instrument 0 0 0 cee eee ee 5 2 5 2 Center and Align the Sample 0 0c cc eee eee eens 5 5 52 Fora Kappa APEX ILSYS EM era ira iaa Sinan exceed tase baad abe wes 5 5 5 2 2 Fora SMART APEX ll System 0 0 06 ee eee 5 8 Do SIMPIC SCANS begins ache ail cate eo A Slee eg AAA ee 5 10 5 4 Examples of Poor Screening 0 0 cc eee eee eee een aes 5 14 6 Data CONGCUON caros A heeds ks oes 6 1 6 1 Start a New Project and Describe the Sample 0 0 0 cece eee eee 6 1 6 2 Determine the Unit Cell 0 4 lt 0 5 503 34uieee deans deeb deeeana de eee is a 6 3 6 20 1 CONCCLIMAGES sustancia ae erate dan Dees eee aaa gee ae 6 3 6 2 2 Harvest the MelCCIONS 25 3 un Retreat a Rie ies Nokon a A 6 6 6 2 3 Index the Reflections sisi rica oe cS ek da oe SS ee ee 6 9 6 2 4 Refine the Unt Cell sx cia a a na A 6 10 6 2 5 Determine the Bravais Lattice o ooooooooononona ee 6 12 6 3 Determine the Data Collection Strategy nannaa cc nea 6 13 6 4 Data Collection Run ExperiMent o o o oooo eee ees 6 18 gt M86 E00078 APEX2 User Manual Table of Contents 7 Data Integration and Scaling o ooooooooornarnan 7 1 7 ANMCOANON nicas cidade eibar de idas 7 2 A AA ada oem eee ned bad lw eed bed 2H 7 8 Tale ALGO MI ada awe SA een Re a tee we ae sare ee eit ee we eee
73. ck for setting the detector distance lt includes mounting points for the video camera and for optional attachments such as the optional low temperature attachment Timing Incident Beamstop Shutter Beam Safety Collimator Goniometer Sealed X ray Shutter Head Tube APEX II Detector Monochromator Kappa Stage Kappa Goniometer Figure 2 3 Kappa 4 axis goniometer components With the kappa angle the crystal can be ori ented at chi from 92 to 92 This leaves the top of the instrument open for easy access Kappa can be positioned so that the phi drive which has unlimited rotation can be swung under the incident beam collimator allowing free rotation in omega APEX2 User Manual M86 E00078 APEX2 User Manual SMART APEX II Goniometer The SMART APEX II system uses a horizontally oriented D8 goniometer base with 2 theta omega and phi drives dovetail tracks for the X ray source and detector and an additional mounting track for accessories such as the video camera and optional low temperature attachment The 3 axis system incorporates a fixed chi stage with chi angle of approximately 54 74 and a phi drive with 360 rotation which is so compact that it swings under the incident beam collimator allowing free rotation in omega Rotary Beamstop Incident Shutter and Beam Fixed Chi Goniometer Collimator col Safety Stage Head ee Shutter APEX II Detector Sealed X
74. d view after import The gray circles are more intense reflec tions i e those with higher l sigma l The black dots represent less intense reflections The intensity key slider at the bottom of the window can be used to change the selection criterion gt t ATA i te a 0 ee ete E 4 4 Figure A 2 Unoriented RLATT view Other tools can be accessed by right clicking on the background to give the Quick Tools menu Figure A 3 and by clicking on RLATT in the menu bar Figure A 4 Le Rotate Select Measure Figure A 3 Quick Tools menu APEX2 User Manual RLATT Rotate Edit Orientation Unit Cell Tool Measure Distance Measure Angle Visualization Figure A 4 Full menu tools Additional context sensitive information is avail able by left clicking on the What s This help arrow in the menu bar Figure A 5 The What s This help arrow For example clicking on the help arrow and then clicking in the work area the gray area to the right of the lattice display gives the display of shortcuts shown in Figure A 6 Clicking on the blue background gives the hints shown in Figure A 7 M86 E00078 APEX2 User Manual RLATT RLATT Keyboard Commands Onentations Rotate amp Zoom UP DOWN rotate along x LEFT RIGHT rotate along y INS DEL rotate along z zoom hold SHIFT 4x speed hold CTRL 1 4 speed hold SHIF
75. de whether two axes coincide Do not touch badcolor type tuple of three integers default 255 190 190 Color in the GUI that is associated with bad situations busycolor type tuple of three integers default 240 240 96 Color in the GUI that is associated with busy situations bgdone type tuple of three integers default 96 240 96 Color in the GUI that is associated with done situations bgerror type tuple of three integers default 240 96 96 Color in the GUI that is associated with error situations M86 E00078 E 9 Config APEX2 User Manual bgimpossible type tuple of three integers default 240 240 96 Color in the GUI that is associated with impossible situations bgpossible type tuple of three integers default 96 240 96 Color in the GUI that is associated with possible situations bgtodo type tuple of three integers default 96 240 96 Color in the GUI that is associated with todo situations bgwarning type tuple of three integers default 240 240 96 Color in the GUI that is associated with warning situations bishost type string default is not set The name or IP address of the BIS server computer ccdtemperaturerange type tuple of 2 integers default 60 40 Acceptable range minimal maximal of temperatures in deg C for the detector chiralonly type boolean default 0 If set to 1 only chiral point groups will be used at any momen
76. diffraction open in a new window All other plug ins open patterns It also displays the runs for data collec in the Task Display area of the GUI tion and solution and refinement For version 1 22 Eile Instrument Windows View 19 x B s Be Evaluate Crystal Distance mm 37 50 d Al 0 77 Collect Mosaicity 0 40 2Theta 54 97 Image Width 0 23 sin t 148 0 65 Bijvoet Pairs merged Laue Class 1 y Lattice Type P A Axis Alpha B Axis Beta C Axis Gamma co o Completeness A2uepunpay Experiment Total Reflections Unique Driented Scans 12 i Runs 67 Images Resolution A Req Disk Space 7361 MB Completeness Y Redundancy Exposure Times s Inf A 1 374 0 714 0 504 0 414 0 374 F y 60 30 120 150 0 004 0 36 4 0 7044 0 9974 1 2274 1 3644 fio zo ao 3 zo 30 q zo a 30 3 Same Extend Reduce Reset w o Aduepunpey Completeness 8 Current Target Priority A Completeness 99 52 fi 00 00 100 Integrate Redundancy 46 12 fi 00 00 PODER Time h 10618 fiaco fro Solve Structure Strategy Custom Refine Structure Execute Refine Strategy z Instrument 3 10 M86 E00078 4 Program Start Up and Shutdown As mentioned previously the APEX2 Suite is composed of several programs All of the pro grams are started in a similar fashion For ease of use there is usually a desktop icon for
77. e Matrix Files ax New Matrix aN Cancel Figure B 4 Find Matrix window 8 This defines the information on the runs but the defaults for space group and resolution have not been updated Click on Space Group and select the correct space group in this case Pmmm Actually it is the Laue symmetry that is important here you will note that Pmmm is starred in the list indi cating a preferred choice see Figure B 5 M86 E00078 APEX2 User Manual F1 Fmm Triclinic Pmc2 1 Monoclinic L01_0002 ps Prriaz Tetragonal I os Pca2 1 Rhombohedral E Price Hexagonal C Prn2c1 Cubic r o re sion Integration Option Priaz 1 Phin Figure B 5 Space group tool 9 Double click on the Resolution Limit and enter an appropriate value NOTE If the starting values for SAINT need to be changed frequently change the default by modifying the SAINT ini file Consult the SAINT manual 269 0175xx for further information M86 E00078 SAINTPLUS 10 Use the Refinement Options and Integration Options buttons to set up the SAINT run In this case Generate Active Mask has been turned on and set to 0 7 Active Ma Generat Mask Fractional Lower Limit of Average Intensity 0 700 FC Use Pre Existing Mask Active Mask File _aml a Figure B 6 Active Mask tool 11 Click on Start Integration to start the calcu lations and open the SaintChart window for monitoring the results
78. e next two inputs are usually correct Treat Friedel opposites as equivalent for parameter refinement Y or N Answering N halves the data to parameter ratio and is not recommended unless you have a high redundancy and know what you are doing Y 5 Supply the name of the data file to be scaled Often this is a Om mul file In this case the file is twin mul Read reflection files written by EVALCCD with extension sam specified or by SAINT extension mul default if no extension Either individual files for each scan or a single merged file may be read It is important that all files are from the same crystal and that reflections have been indexed consistently i e that the orientation matrices are similar no rows with signs reversed Enter filename if no more twin mul 2 twin components present Mean and maximum errors in direction cosine check function 02000 0 002 The mean error should not exceed 0 008 and is usually caused by matrix changes during data processing Maximum 2 theta 56 63 deg Approximate wavelength 0 71066 Angstroms M86 E00078 D 3 Processing Twinned Data APEX2 User Manual 6 Model the systematic errors Check the defaults They are usually correct but in some cases the error model can be improved by changing some or all of the defaults PART 1 Refinement of parameters to model systematic errors 9701 data 3680 unique involve component 1 only mean I sigma Zak 9653 daba 1 3649 u
79. e no need to apply a High Resolution Cutoff at this point M86 E00078 Examine Data 1 Since the difference between the Rint for the high resolution data and the complete data set is slightly larger than expected it is reasonable to apply a high resolution cutoff using the H option in the data manipulation menu see Figure 8 13 Type H and press Enter Figure 8 13 Requesting a high resolution cutoff 2 Enter a high resolution limit of 0 75 see Fig ure 8 14 and press Enter to accept the low resolution cutoff of infinity Figure 8 14 The resolution cutoff menu Examine Data APEX2 User Manual 3 Applying the cutoff removes approximately 5 After the cutoff all of the statistics look bet 3000 reflections from the data set see Fig ter see Figure 8 16 Press Enter to con ure 8 15 The next step is to see if the cut tinue off has improved the statistics Type S and fesolution Data Theory Complete Redundancy Mean I Mean I s Rint Rsigma press Enter E XPREP Ver 6 14 W95 98 NT 2000 ME Copyrig Index Data Filename or Source of Data lt current dataset Figure 8 16 Statistics after high resolution cutoff Figure 8 15 Requesting statistics after applying a high 6 This response will return to the data manip a EUa ulation menu see Figure 8 10 Figure 8 13 4 As in step 3 of Section 8 3 enter A to or Figure 8 15 The default answer should merge all equivalents be E for Exit Press Ente
80. e running ANY or ALL all products SCD single crystal XRD powder XRE fluorescence M86 E00078 E 15 Config APEX2 User Manual protectedvariables type map default protectedvariables 1 autoconnect 1 A selection of variable names and a limit to which configuration files Can be used to change them This can be used to make sure users do not overwrite system defaults like is done by default for the autoconnect variable resolution type floating point default 0 77 Default resolution to go for in an experiment 0 77 is reasonable for standard small molecule experiments scanrepr type integer default 1 Determines how scans are represented in text 1 scan angle from x to y length y x Os scan angle length y x starting from x l scan angle from x to y scanwidthtolerance type floating point angle default 0 003 Tolerance in degrees that determines whether two scans are equal Do not touch fileserver type tuple of strings default Where experiment data files should be stored by default First element in the tuple is the host name second the share name and the rest are successive folder names inside the share fileserverprotocol type string default smb The protocol that should be used to address the file server Should be either file local file or smb network drive E 16 M86 E00078 APEX2 User Manual Config smbroot type string default
81. educed and the Mean Weight increases Typical final values are 3 4 for the R values and 0 95 0 98 for the Mean Weight Gs File Instrument Windows BY ax ID co El Evaluate Crystal Collect Integrate _ foot F CI of Groups E js ta No mua o Mean lisigma Examine Data Solve Structure Alincid A diffr Refine Structure Instrument Figure 7 25 XScale window after refinement M86 E00078 Diagnostics Direction Cosines Mean error fo 000 Maximum error fo 001 Data Statistics Maximum 2 8 feses wavelength 4 foz1074 Reflections 8331 Unique 2788 Data per frame p 59 Input of Data 0 98 Mean I a l threshold 0 9798 0 9796 0 9794 Factor g for initial weighting scheme 0 9792 E Restraint esd for scale factors 0 002 y ey 0 979 Absorption Type Weak Absorber y Number of refinement cycles 50 Mean Weight Refine E Finish Start Over Exit AXScale High resolution threshold Data Integration and Scaling APEX2 User Manual 7 3 3 Error Model Refinement Figure 7 26 shows typical Error Model results Irati Frederic Total Irch fe boksing babies Number of Reflections e i 10 0002 006 031 03901 1 044 0473 67H 0004 El 0 DEI 064 1053 0545 106 041 15 145 W 3 7 0 00075 0057 0318 094 1027 0550 mm 1 4 fal 00h 034 0513 055 TO 045 1615 1451 Detenmine Error Model Flepeat Parame
82. educes the statistical underestimate of the parameter esd s Output only reflections containing component N 0 to output all 1 O 12829 COrErected reflections written to file EwiB 0 6kI Reflections merged according to point group 2 m Ratio of minimum to maximum apparent transmission 0 807218 14 Typically accept the default Q and exit twinabs It is now possible to generate a HKLF 4 format file with crude intensities for structure solution or a more accurate HKLF 5 format file for refinement Repeat KR write sikl fale 4 0 3 Or quit Oy JOJ Integration and scaling with the multicomponent p4p file written by cell_now is complete Use the stan dard APEX2 GUI and the twin_4 hkl data typically copied or renamed to match the ins file to solve the structure Use the twin_5 hkl data typically copied or renamed to match the ins file to refine the structure D 10 M86 E00078 Appendix E Config The APEX2 Suite includes the ability to custom ize many features of the program Most custom ization should be left to the site administrator but some introduction is appropriate The exam ple below is a color coded example of an actual Python file It gives an introduction to configur ing the program M86 E00078 In the following text Red denotes comments that result from comments e Green denotes comments between triple quotes e Black denotes actual Python code Config APEX2 User Manual Examp
83. ees long perpendicular matrix runs frametime None The frame time is left to be the default Setup to get some debug messages for scans This is useful if resume is failing if debug goniometer scan debug expt findresolution i M86 E00078 E 5 Config APEX2 User Manual Hardware profile used by the data collection strategy planner bishost bruker server hardwareprofile Kappa A PEX II euler hrd bishost smart apex hardwareprofile SMART APEX II hrd IP address or DNS name of the file server used for storing images followed by the name of a network shared folder on that server Add additional path segments as comma separated and quoted strings To find out the DNS name For Linux type hostname atthe command prompt For Windows type echo computername atthe DOS prompt it fileserver x8 client frames Supported file name protocols Currently these are smb for files that are accessed over a MS Windows network and file for local files universalfnprotocols smb file H E 6 M86 E00078 APEX2 User Manual Config Configuration of the APEX amp PROTEUM programs The appearance and working of this can be modified by a configuration a seires of configuration files in specification ina later file overwrites a setting in an earlier Om unix these files are Suite of programs file The programs read the folowing order As described below
84. eframe Ball And Stick Thermal Ellipsoid Select at ms Hide Part s Show all Atoms Disassociate Atoms Unit Cell Hydrogen Labels lt lt Labels Or Grow Pack Trim Zoom Out Toggle Pan And Rotate Restore Deleted Atoms Find Duplicate Labels Information on All Atoms Figure 9 17 Choose the pipes view 7 Left click on the remaining peaks in the order that you want them labeled NOTE If working on YLID test data look at Fig ure 9 18 and click on the peaks to give the same order as used here Right click and choose 8 9 Labelling Select Carbon and apply the labels In the Labelling tool change the element type to C carbon The starting atom num ber will change to 1 the first available number for carbon atoms Click Relabel 10 Click Cancel to close the window M86 E00078 Structure Solution and Refinement APEX2 User Manual 9 3 3 Refine the Molecule The labeled YLID molecule is now ready for refinement Figure 9 18 Correctly labeled model 1 Left click on the Refine icon in the tool icon bar the cursor is pointing to it in Figure 9 19 or Type Control R or go to Refine in the Windows tool bar Figure 9 19 The Refine icon 9 14 M86 E00078 APEX2 User Manual This will open the Refine Box Click on Refine to launch XL the least squares refinement pro gram using the default parameters as given REFINE Least squares options e
85. election Grouping Tools Current Group MN Group 5 y Add To Current Group Remove From Current Group Select Visible Groups pr Deletion Helpers M86 E00078 APEX2 User Manual Figure A 22 A more practical use of the selection and color groupings in RLATT The two components of a rotational twin are colored yellow and red M86 E00078 RLATT RLATT APEX2 User Manual A 4 Measuring Distances and Angles Right click on the background and choose Mea sure to get tools for measuring distances and angles The Measure Distance tool gives two lines much like the lines in the Lattice Selection tool that can be oriented and dragged to get lattice spacings see Figure A 23 Use the Alt key to lock on spot centers for easier orientation and more accurate measuring po a Figure A 23 Using the Measure Distance tool A 20 M86 E00078 APEX2 User Manual With the Measure Angle tool left click hold and drag a line on a lattice layer ending on the spot that will become the vertex of the angle When the mouse is released that point becomes the pivot point for a new line Moving the mouse with no buttons depressed gives angle mea surements see Figure A 24 As described the angle measurements will be done in 2D mode br RLATT i e the angle between the two lines displayed To measure an angle in 3D mode hold the Alt key while selecting spots as above The tool will then lock on
86. em area M86 E00078 APEX2 User Manual 7 3 5 Exit 1 Click on Exit AXScale to close the scaling GUI Exit 45 cal Figure 7 33 Exit AXScale NOTE Scale is one of the few GUIs where it is necessary to exit using a special Exit button This avoids an error message indicating that SADABS has exited improperly M86 E00078 Data Integration and Scaling Data Integration and Scaling APEX2 User Manual M86 E00078 8 Examine Data In this step the space group for the sample is determined and optional simulated precession photographs are calculated to further evaluate the overall quality of the data APEX2 provides two tools for this XPREP for space group deter mination and Precession Images for looking at undistorted slices of reciprocal space This is the final step before beginning the structure solution and refinement process 8 1 XPREP 1 Clickon XPREP Space Group Determina tion under Examine in the task bar 2 Check that the two files in the pop up win dow are correct see Figure 8 1 and click OK M86 E00078 21xi PAP file quest data_manual ylid_manual work ylid_manual_Om p4p_ g HKL file f guest data_manual ylid_manual work ylid_manual_Om hk 152 Cancel Figure 8 1 Select files for XPREP input NOTE In this example the scaling process has created two files ylid_manual_0m p4p contain ing the final unit cell parameters from integration and ylid_manual_Om hkl containing the cor rec
87. entered adjust the height If not cen tered repeat steps 2 through 5 until it is centered Figure 5 15 Height adjusted 6 Click the Left button Adjust to remove half of the difference Adjust the height M86 E00078 Crystal Orientation Figure 5 16 Check Left 7 Click the Right button Adjust the height Adjust to remove half of the difference Figure 5 17 Check Right 8 Ifa height adjustment was made in step 6 or 7 repeat those steps to check the height If the height is adjusted repeat steps 2 to 5 to check the centering If no height adjustment was made the crystal is centered The crystal is now centered on the instrument All of the next steps are performed with APEX2 on the client computer Crystal Orientation 5 3 Simple Scans The Simple Scan plug in provides the tools for rapid screening of the sample to check sample quality It allows the user to quickly set up scans to measure a 360 degree phi rotation as well as still thin 0 5 degree and thick 2 0 degree Images 1 Click on the Simple Scan icon The menu shown in Figure 5 18 will open Distance mm 45 2 Theta 19 Omega i 0 2l Phi las 4 Chi is 4 HL Zero Current Phi 0 Phi 90 User Usen Users User 4 Drive Scan Axis f Phi Omega Scan Range Image Width Exposure Time 10 Y secs image Y Scan Options Correlate 2 images New dark
88. equired to accurately monitor X ray exposure by proper use of X ray dosimeters For safety issues related to the operation and maintenance of your particular X ray generator diffractometer and shield enclosure please refer to the manufacturer s operation manuals or your Radiation Protection Supervisor The user is responsible for compliance with local safety reg ulations M86 E00078 Introduction Introduction APEX2 User Manual 1 4 M86 E00078 2 Hardware Overview The two hardware platforms for the APEX II sys tems are the Kappa APEX II the four axis advanced research instrument and the SMART APEX II the three axis laboratory instrument Software functionality is essentially the same for both platforms M86 E00078 2 1 System Components The system Figure 2 1 and Figure 2 2 consists of the following basic components APEX II CCD detector 4 axis Kappa or 3 axis SMART goniometer K780 X ray generator Radiation safety enclosure with interlocks and warning lights D8 controller Refrigerated recirculator for the detector Computer s two for the Kappa APEX II and one for the SMART APEX II Video microscope Accessories high and low temperature devices Hardware Overview APEX II Detector Power Supply Figure 2 1 Kappa APEX Il system APEX2 User Manual APEX II Detector Power Supply Optional LT Controller Optional LT Controller Electronics Figure 2 2 SM
89. ess Statistics O Integration progress gt O Per lmage Statistics 40 00 2 iE Spot shape correlation Spot intensity and Sigmaf o Spot intensity lt 2 Sigma 30 00 Number of reflections harvested Spot position overlay x Y Z error x Y ZAMS difference x Y Z spot size Queue extent used O Primary beam intensity O Periodic Statistics if Profile snapshots A axis ESD B axis ESD C axis ESD Alpha angle ESD Beta angle ESD Gamma angle ESD Cell volume ESD LS goodness of fit LS Residuals x Y Z crystal translation x Y beam center Distance correction Pitch Roll Yaw correction O Angle zeros D Coverage Statistics iO Harvested reflections O Completeness and redundancy O Bijvoet pairs 50 00 Connected V Integration in Progress Y v Stop Integration M86 E00078 APEX2 User Manual To the right of the image area are a series of check boxes that select the displays 1 Click on the check boxes to add or remove displays Click on Integration Progress to add the new display seen in Figure 7 19 When the integration is complete the blue progress bars will be full and the remaining time will be zero ix Integration Progress 0 x images Progress ETA Remaining plid_manual_01_0001 sfrmm 684 733IMMMMN 22 25 28 00 00 24 lid manual_02 0001 sfren 0 153 22 28 08 00 03 05 ylid_manual_03_0001 sfrm 0 74 22 30 13 00 05 09 ylid_manual_04_0001 sfrm 0 161 2
90. f the experiment storage of raw frame data integration of the data and solution and refinement of the struc ture The computer or computers are often attached to a network of similarly configured computers with access to local and or network printers NOTE Connection to the external network must be done with care Consult with local security experts APEX2 User Manual 2 1 7 Accessories Various devices can be mounted on the goniom eter base These include optional low and high temperature attachments Both instruments can be used with diamond anvil cells M86 E00078 3 Software Overview This section presents an outline of the system server and the client execute on the same com software including a brief description of the soft puter but their functionality remains separate ware layout as well as the graphical user inter The flowchart in Figure 3 1 shows the software face GUI layout For both Kappa APEX Il and SMART APEX II systems the server and client commu APEX2 runs on two computers the server and nicate using TCP IP protocol the client For SMART APEX II systems the APEX2 Suite Server TCP IP Connection Client Hardware Control BIS l Data Collection Crystal Orientation and Evaluation APEX2 Server APEX2 GUI Figure 3 1 APEX2 software diagram M86 E00078 3 1 Software Overview 3 1 The Server Computer The server computer communicates with the hardware allowing the user to co
91. ffracts nicely with lots of sharp spots Figure 5 23 shows a Phi 360 scan with a bad crystal Figure 5 19 A 360 Phi scan on a good quality crystal 6 Click on Wide 2 0 change the scan range to 2 0 and set the desired exposure time A time of 5 to 15 seconds is usually sufficient Crystal Orientation Click Drive Scan The resulting 2 degree scan is shown in Figure 5 20 The spots are sharp and clean There are no peaks that are very close together Figure 5 24 shows a 2 degree scan with a bad crystal Figure 5 20 A 2 phi scan on a high quality crystal The spots shapes are well defined and the spots are well separated 8 9 Click Phi 90 in the middle row of boxes Click Drive Scan The resulting 2 degree scan is shown in Figure 5 21 This image is measured 90 degrees from the previous one giving a view of the diffraction pattern from a different perpendicular direction Figure 5 25 gives a similar view for the poor crystal APEX2 User Manual Figure 5 21 A 2 phi scan at plus 90 in phi on a high quality crystal The spots shapes are well defined and the spots are well separated 10 Set 2Theta to 30 This will allow evaluation of the diffraction at higher angles M86 E00078 APEX2 User Manual 11 Click Drive Scan The resulting image is shown in Figure 5 22 Distance m 2Theta Omega bal 3D View PI Scan Axis Phi Scan Rang
92. fig Program Start Up and Shutdown 4 2 Client Computer Start Up On the client computer two programs are also required the database and APEX2 It is best to start the database before starting APEX2 NOTE For the SMART APEX Il there is typi cally only one computer for the client and server software 4 2 1 Starting the Database 1a For Windows systems click on Start gt Pro grams gt Bruker AXS Programs gt Start Database or click on the Start Database icon on the desktop q FER 1b For Linux systems open a terminal window and type bnrun startdb or click on the Start Database icon A window should appear that says the database system is ready E Start Database z database system was interrupted at 2004 04 30 15 64 36 CDT checkpoint record is at M 3275B00 redo record is at 073275000 undo record is at 6 6 shutdown FALSE next transaction id 21669 next oid 83168 z database system was not properly shut down automatic recovery in progre ReadRecord record with zero length at 073275040 redo is not required database system is ready Figure 4 6 The database is ready APEX2 User Manual You can minimize this window If the database has not previously been closed properly e g after a power failure a window will appear see Figure 4 7 that states that another postmaster is running If this happens stop the database and then start it again E Start Database ii rdatar
93. for rejection 4 0 8b Input the weighting terms to use in determining rejection sigmas G value for use ane su t2 sigma 2 g lt 1 gt 2 sigma LL trom SAINT This is only used for rejections not for final sigma 1 values 0 04000 24832 total and 9829 unique reflections left after I lt I gt su test 9 Examine the results They are acceptable if the number of rejected reflections is reasonable Typi cally it is reasonable to reject less than half of your data In this case there were 9829 unique reflec tions before applying rejections and the same number after Repeat parameter refinement P repeat rejections R or accept A A D 6 M86 E00078 APEX2 User Manual Processing Twinned Data 10 If the suggested g value is reasonable 0 02 to 0 09 accept the suggested value g 0 0610 gives best error model Enter new value for g or lt CR gt to accept 11 Examine the statistics for the twin components comparing the R int values for various runs and components In general each class of statistics should stay about the same for all of the runs and components Accept if they are reasonable Statistics for singles for twin component 1 for singles R int DO oe bP al ye oh 2466 Incid 0 907 40162 0 968 0 964 factors OOS 1026 g 1 012 ll 062 Diffr T0072 00 993 1 014 00967 for twin component 2 Rint UDAZ 1249 1447 SLOG Incid 0 907 2962
94. g with the reflection list e g a wrong detector distance or a cell axis is longer than the given search range In specified cell search mode the program tries to find the best cell within the specified ranges The reflections that fit this cell within a specified fraction of all three interplanar spacings may be flagged as indexed and a new p4p or spin file written in which they have the H flag so that they can be displayed in a different color with RLATT Then the cell may be rotated to locate further twin domains iteratively using only the reflections that have not yet been indexed WARNING the exhaustive search employed in this program is VERY SLOW so a CPU clock frequency of AT LEAST 3GHz is strongly recommended AN C 2 M86 E00078 APEX2 User Manual Using CELL_NOW CELL_NOW will then request the name of the input file and will suggest a name for the output file 4 Enter the name of the input file For the output file hit lt Enter gt to accept the default Full name of p4p spin or drx file to read example p4p 999 reflections read in Listing Pike examples Cn 514 reflections read in Lkstindg tute examples cm 5 Hit lt Enter gt to start a general search Initial Search lt sEnter gt or specified cell search S5 6 Ifthe default superlattice threshold is suitable hit lt Enter gt Superlattice threshold an axis will be rejected if less than this percentage of reflections has indices not equ
95. gure 8 17 Defining and checking the unit cell contents 3 The next default action for XPREP is to write out the files necessary for the structure solution process see Figure 8 18 Press Enter to accept Current dataset Wavelength Original cell Esds Current cell Matrix Crystal system Space group Formula Formula wt Density at vol a Mu ren 1 Figure 8 18 Requesting output files Examine Data 4 The program asks for an output file name Since this data has been cut off at a resolu tion of 0 75A it makes sense to change the output file name to ylid_res75 to reflect the cutoff see Figure 8 19 Press Enter to accept F 000 Figure 8 19 Changing the file name 5 After entering the file name or hitting Enter to accept the default file name an input file for the structure solution module is created and displayed on the screen and the pro gram asks Do you wish to over write the intensity data file ylid_res75 hkl Since the file name has been changed this question must be answered with a y see Figure 8 20 APEX2 User Manual R Figure 8 20 The input file for structure solution and a final question 6 Exit XPREP see Figure 8 21 Press Enter to exit the program R Figure 8 21 Exit XPREP from the general menu NOTE There are many other features in XPREP that can be accessed from the general menu reciprocal space plots simulated powder patterns and
96. hardwaretype type integer default 4 If different hardware types are supported this can be used to select which one should be used 4 BIS Do not touch detectorsizemargin type floating point default 0 1 DO NOG TOULE MN eventlogfile type file name default bn event log File in which important events are logged during program runs fontsize type integer default None GUI font size in points groupcolors type tuple of color names default gray7 5 red green yellow blue magenta cyan white gray25 brown forest green khaki midan1ight plue violet turquoise gqray50 guicolor type tuple of three integers making a color default 0xd4 0xd0 0xc8 guistyle type string default windows The style of the GUI Do not touch hardwareprofile type file name default None The hardware profile to be used by COSMO for strategy calculations hashfilepattern type string default DO ROG COUCH E 12 M86 E00078 APEX2 User Manual Config headerdisplay type default not set ES imageextension type string default sfrm DO Toe Ouch imagemask type int default 0 value of a mask used in viewing powder frames inhibitgc type boolean default 0 Inhibit garbage collection Do not touch localfilemap type map default None A map of network drives translating local file names to equivalent netw
97. hat there is a reasonable formula in the formula window nstructions Y Listing Y Results TITL ylid_ reso75 in P2 1 2 1 2 1 Base ylid_teso75 5 CELL 0 71073 5 9634 9 0449 18 3942 90 000 90 000 30 000 ZERR 4 00 0 0005 0 0010 0 0021 0 000 0 000 0 000 Formula C11H12025 SYMM 0 5 X Y 0 5 Z Statistics SYMM X 0 5 Y 0 5 Z Reflections 12251 Unique 1423 SYMM 0 5 X 0 5 Y Z i SFACCHOS j Rejected 75 Observed 11363 UNIT 44 48 8 4 Alint 3 57 Observed 95 TEMP 0 TREF s Observed HELF 4 De ae in 1 1 1 24 Shell 179 END Method E Direct 1 c C J Structure Expansion Computing Effort log scale _ MMMM M lt AN Solve Structure STOP Reset Exit Figure 9 1 Default Solve Structure view 9 2 M86 E00078 APEX2 User Manual 2 Click on Solve Structure to start the calcula tions and open an output window This win dow can be used to monitor the progress of the direct methods calculations a Structure Solution Log Window 172 Reflections and 3346 unique TPR for R alpha 465 Unique negative quartets found 465 used for phase refinement 110 Unique NOR employed in phase annealing 128 Parallel refinements highest memory 3822 44055 Try Ralpha Nqual Sigma 1 M abs CFOM Seminvariants 1890781 0 064 0 770 0 946 1 154 0 064 Freq 00097130000000010010100100121111 128 917713 0 060 0 799 0 946 1 151 0 060 Freq 001 201 25000
98. he Intensity Filter slider bottom left has been moved slightly to the left M86 E00078 A 5 RLATT With additional rotations the layers of reflec tions can be further oriented so that stacks of reflections become visible Sometimes it is quite useful to right click on the background and choose Z rotations from the rotation options The 2D profiles on the top and to the left are a valuable aid in this process With practice the ES i Intensity Filter Reflection Size Y Figure A 10 An oriented lattice view The Visualization menu is to the right The 2D profiles are to the left and to the top APEX2 User Manual 2D profiles can be organized into clusters As shown the 2D profiles are counting intensity The counting mode can be changed to spot count or turned off completely using the Visual ization menu RLATT gt Visualization or by hit ting the s key to cycle through the counting modes Axis A Reciprocal Space Direct Space Laboratory None Colorization Method C By Group C ByACHS Flags C By Intensity Light Direction and Colors 2D Projection Scale S f By Intensity Count C By Spot Count C None Null Resolution Nj DISABLED M86 E00078 APEX2 User Manual The distance between layers can be measured by clicking on one of the clusters of lines in the 2D view and then dragging to the next cluster If you drag over three clusters then the dis
99. he goniometer head to prevent damage to the sample on the end of the small glass fiber 5 Place the goniometer head onto its base on the phi drive Line up the slot on the bottom of the goniometer head with the pin on the mounting base see Figure 5 2 Line up this slot with the pin on the mounting base View of the bottom of the goniometer head Figure 5 2 View of the bottom of the goniometer head M86 E00078 APEX2 User Manual Crystal Orientation 6 Screw the head s collar to the base so that the head does not move Do not overtighten it finger tighten only Crystal Sample ih Mounting Screw bh Extender 4 optional Sample Z axis Lock Mounting Collar Lomo Sie Collar 2 Z axis Adjustment Screw Y axis Lock Y axis Adjustment Screw X axis Adjustment Screw X axis Lock x axis Lock Figure 5 3 Huber goniometer head in detail M86 E00078 5 3 Crystal Orientation APEX2 User Manual Crystal Sample Mounting Screw Z axis Lock Z axis Adjustment Collar Y axis Adjustment Screw X axis Adjustment Screw Figure 5 4 Standard goniometer head in detail 5 4 M86 E00078 APEX2 User Manual 5 2 Center and Align the Sample To obtain accurate unit cell dimensions and to collect good quality data align the center of the sample with the center of the X ray beam and maintain this alignment for the entire experi ment Your video camera should be aligned so that the crosshairs of the
100. ically IV Use suggested weights Squared Term fo 0s8s00 Linear Term fo co0000 I Refine extinction parameter JV Generate ACTA CIF information file Refine Edit File Cancel Figure 9 45 Select weights and request ACTA output Figure 9 46 shows a difference map with the number of peaks set at five Figure 9 46 Difference peaks 2 Click on Edit File choose INS and click OK to open the instruction file for XL This allows you to add instructions that are not directly available in the GUI APEX2 User Manual Edit File Open File for Editing ylid_reso67 INS LST Cancel Figure 9 47 Open the ins file for editing 3 Check that the temperature card is correct 4 Iftorsion angles are of interest add a CONF confirmation card see Figure 9 48 TEMP 23 conf mola 12 cl c2 c3 c4 c5 c6 c7 cB c9 sl ol of clo cll mola 6 c4 c5 c6 c7 cB c9 cl c2 cS of of s1 c10 ell mola 5 c8 c9 cl c2 c3 c4 c5 c6 c7 ol of s51 c10 ell mola 10 cl c2 c3 c4 c5 c6 c7 cB c9 s51 ol of clo cll Figure 9 48 Add instructions in the ins file 5 If planarity and angles between planes are of interest add mpla cards M86 E00078 APEX2 User Manual 9 3 8 Generate an Atomic Displacement Thermal Ellipsoid Plot 1 Remove difference peaks with the slider tool 2 Right click on the background and select Thermal Ellipsoids Figure 9 49 Thermal ellipsoids with large hydrogen atoms
101. ile gt Save to remove the reflection from the reflection list Hiding a group with Select Visible Groups does not remove it from the reflection list Either way the resulting RLATT image is much cleaner and easier to interpret Figure A 19 te Crystal tLIo Figure A 18 Save File icon M86 E00078 RLATT RLATT Enable the Unit Cell tool to put a colored box in the view This allows you to see if reflections are actually falling on the corners of the box see Figure A 19 and Figure A 20 There are multi ple options in the Unit Cell tool Select a Visible Plane displays individual planes Select Plane ms eee PP o sasaaa amm a amma m A le o N ob LL ella J de shins L A epee rae EA Intensity Filter Reflection Size K Figure A 19 A view of the reciprocal lattice after the non fitting reflections were deleted and with the Unit Cell tool enabled APEX2 User Manual Size determines the boundaries of the planes and the number of unit cells displayed Grid Planes mode displays planes as grids with spacings determined by the lattice Unit Cell Tool 11 ENABLED Select Unit Cell Tool Style FC Planes Grid Planes Single Box f Layered Box Select amp Visible Plane to alona ae b ys c f alonab a vs c f along c a vs b ia b c fall planes Select Plane Sizes e b _ e k1 1 10 20 Link Sizes
102. inement 9 3 6 Add Hydrogen Atoms At this point refine the hydrogen atoms either by renaming the Q peaks using the Labelling tool as before and then including them in the refinement or include the hydrogen atoms in fixed idealized positions riding on the atom to which they are attached In this manual we will illustrate the latter fixed idealized method NOTE In some cases e g hydrogen atoms on hetero atoms or on geometrically strained car bon atoms it is better to refine the hydrogen atom positions A general rule is to refine if there is some doubt about the position of the hydro gen atom and there is difference electron den sity present 1 Using the slider tool remove all of the Q peaks Structure Solution and Refinement APEX2 User Manual 2 Right click in the background and click on 3 The following warning will appear indicating Hybridize All that the hydrogen atoms have been provi sionally added and that the final addition with naming will take place when the least squares calculations are started Click OK Add Hydrogen ators Figure 9 38 Hybridize button The colors of the atom labels will change to indi iD SHELL has only assigned atom types Correct labels Se Will be generated during the next refinement cycle cate the atom hybridization NOTE If the atom hybridizations are hard to see right click on the background and open the Figure 9 41 Hydrogen atom warning Information on
103. ld be read If this happens and only one or two frames are needed to com plete the run wait and then process the entire run However if you have a hundred or more spots and there are several frames yet to be col lected you can skip step 3 or 4 and go to Sec tion 6 2 3 Then return to Section 6 2 2 and harvest the spots before refining M86 E00078 APEX2 User Manual 6 2 3 Index the Reflections 1 Click on Index in the tool bar to the right of the image viewer A window will open ba Index Spots 24x Select Spots For Indexing Reduced Unit Cell More Spots Resolution From 9999 00 A Resolution To 0 69 A Axis 10 000 gt B Axis 10 000 Y Spots Must Be Isolated C Axis 10 000 T Spots Must Span Images Spots Must Be Whole Alpha 90 000 Total Spots 259 Beta 90 000 Selected Spots 244 Gamma 90 000 Indexed Spots n a Filter Tools Fewer Spots O O Volume 1000 0 A 3 o Index Harvested Images matrix_O1_O0001 sfrm Me e Show Observed Spots C Show Predicted Spots Figure 6 10 Indexing tool The defaults are usually acceptable Use the slider to omit reflections with lower l sigma from the calculations If indexing is difficult try reduc ing the number of reflections used If indexing is difficult use the RLATT tool This tool is described in Appendix A 2 Click on Index M86 E00078 Data Collection After approximately 30 seconds the Index wi
104. les of configuration changes The following is a collection of examples of possible changes to the configuration files for Apex2 and Proteum2 These files control the look and feel of the GUI Configuration variables the system adminstrator wants to set globally for all users go into a file called bn config py that resides in C for Windows or usr local lib for Linux Individual users can set their own preferences for most configuration variables in a file in their home directory This file is named bn config py for Windows and bn config for Linux Under Windows at a command prompt type echo UserProfile to find out where the user version of bn config py should be located Additionally configuration variables can be set for a specific sample using a file in the sample directory This file is bn config for Windows and Linux These files are read in the order given above so values set globally are replaced by individual values and global and individual values are replaced by specific values A few notes about Python comments Three quotation marks in a row on a line start a comment section The next three quotation marks end the section The text you have just read is in a comment section mono end of commenting out a section with triple s E 2 M86 E00078 APEX2 User Manual Config Pound or Number starts a simple comment This can be anywhere on a line The default color scheme for the image display
105. line to another row as shown in Figure A 13 Let go of the but ton If you want to start over click on another spot and repeat the process Using the Alt key is optional but it makes alignment of the lines eas ier and more accurate Linux users may find that the Alt key has operating system functions M86 E00078 RLATT RLATT APEX2 User Manual Editing Tools C Box f Lattice Overlay Single Spot Circle None rotate Selection Helpers Select Weak Reflections Select Current Group Invert Selection Grouping Tools Current Group E Group 1 y Add To Current Group Remove From Current Group Select Visible Groups v None Deletion Helpers Delete Selected finalized at save Delete Non Visible finalized at save Intensity Filter Reflection Size Zoom Export Visible Spots to P4P Figure A 13 Two lattice lines selected M86 E00078 APEX2 User Manual RLATT Hit the plus key to add lines between the two you have marked Hit the minus key to remove lines Editing Tools C Box Lattice Overlay Single Spot Circle None rotate Selection Helpers Select Weak Reflections Select Current Group Invert Selection Grouping Tools Current Group MMM Group 1 y dd To Current Group Remove From Current Group Select Visible Groups Group 6 Group 8 Group 9 Group 10 Group 11 Group 13 Deletion Helpers
106. ll Refinement Figure 7 23 Check the angles in the unconstrained unit cell refinement to get a quick confirmation that the initial lattice determination was correct In the unconstrained refinement angles that are required to be 90 or 120 are allowed to refine If they differ considerably from the expected value then the data should be checked care fully O8 0e 04 22 32 31 Performing final unit cell least squares on file d i structures data for manualyylic Input file contains 5552 reflections Global Pefinement single component data Maximum allowed reflections 99393 One reflection will be stored in memory per l reflection s read Orientation least squares component 1 5552 input reflections Wavelength relative uncertainty 0 7107300 Reflection Summary o 0000089 RLY Excl are reflections excluded after cycle 1 because BLY error exceeded O 025C Component Input BLY Excl Used WorstRes 1 EDZ T ELZ 3 1065 Orientation UB matrix 0 0584509 0 0333484 0 0483062 O 0005328 0 1049404 0 0175150 O 1573586 0 0121009 O 0180036 A E E Alpha Beta 5 9872 9 0273 18 3668 20 088 59 999 o 000l o 000z o 0004 0 001 0 001 Corrected for goodness of fit o 0005 o 0003 o 012 0 005 0 005 Figure 7 23 Unconstrained unit cell refinement M86 E00078 Best Hes Min TE Max Th 0 7584 5 0Z5 53 580 Gamma Yol 40 033 an Fe o 00l ad 05 o 005 a ZZ Data Integration and Scaling
107. lly very good There is seldom any need to change those in the Refine window Refinement Options E 21 x Per lmage Refinement Damping Factor 1 000 Initial XYZ Box Size 0 994 fo 994 fo 994 Global Refinement IV Enable Global Refinement M Enable Orientation Refinement JV Enable Box Size Refinement Periodic Refinement IV Enable Periodic Refinement IV Enable Initial Passes Frequency Images 50 Max Number of Reflections asas 3 Constrain Metric Symmetry of Unit Cell to Space Group P222 Constrain Metric Symmetry of Unit Cell to Space Group P222 Crystal System Orthorhombic 7 C Crystal System f Orthorhombic Refinement Parameters La Refinement Parameters a O Detector Horizontal Beam Center Vertical Beam Center A Vertical Beam Center E Distance H E Distance E Pitch E Pitch A Roll A Roll iE Yaw iLE Yaw D Unit Cell D Unit Cell EEA Anaa Hl EER Anaa ha Figure 7 9 Refine Window 3 Change the default options for the integra tion in the Integration Options window The Integration Options window has a few val ues that are changed more frequently Integratica Options 21x m Model Profiles m Background Update IS Ao Uni cla Pate Po I Blend Profiles from All Detector Regions Intensity Sigma Lower Limit for Model Profile Update 10 000 Image Queue Fraction of Model Profile Maximum for Simple Sum Mask
108. mple used here At this point if all of the runs available were col lected it would take 183 98 hours and have a redundancy of 452 86 Clearly this is not desir able 3 Click on Refine Strategy 4 A list of options will appear Click on Refine Strategy again Execute Refine Strategy Penei A a DM La or Completeness Figure 6 16 Click on Refine Strategy M86 E00078 APEX2 User Manual NOTE The objective in Refine Strategy COSMO is to get good completion 98 or better with high redundancy in a reasonable amount of time When COSMO is first started it will tell you the completion redundancy and time for all of the available runs It is almost never necessary to let COSMO run to comple tion Typically it should be stopped when com pletion is greater than 99 and the time is close to what is desired M86 E00078 Data Collection 100 co 12 A A 60 102 2 5 g2 E 2 e 40 E o o 5 20 4 2 0 1 4 12 1 0 8 Resolution Completeness Y Redundancy 100 10 80 g 8 m A a 50 2 2 D 6 3 pur o x z Q 40 E 2 D 4 1 Time h Figure 6 17 Completeness and Redundancy chart In this example as shown in Figure 6 17 the completion is 99 76 and the time is approxi mately 2 33 hours 15 Data Collection NOTE Time estimates are approximate They depend on the number of rescans general instrument overhead backlash compensation etc If estimated times a
109. n dow will display a possible cell and the OK but ton will no longer be gray The values shown in Figure 6 11 are reasonable for the YLID crystal Reduced Unit Cell A Apis 5 929 B Axis 8 981 C Asis 18 345 Alpha 59 955 Beta 89 8511 Gamma 29 953 Volume 976 9 4 3 Figure 6 11 The unit cell The spot statistics are also acceptable with 98 e 238 244 x100 of the selected spots indexed Total Spots 259 Selected Spots de Indexed Spots 0 Figure 6 12 Focus on the spot results There are often a few reflections that are not indexed You can use the reciprocal lattice viewer to look at the spots used in the indexing but refine this cell first 3 Click on OK to accept the indexing results Data Collection 6 2 4 Refine the Unit Cell There is not a correct order for the following steps Use this procedure as a guideline with the main goal of creating a stable converged refinement 1 Click Refine in the Indexing Tools menu The Refine Unit Cell window will open hy Deviation Histograms 20 x 100 80 APEX2 User Manual ba Refine Unit Cell 21x Detector Corrections Distance mm 0 00 I Constrain Distance Beam X mm 1 44 Beam Y mm 0 36 I Constrain Beam Center Pitch 0 34 Roll 0 65 Yaw 0 09 IV Constrain Pitch Roll Yaw Crystal Position x mm fo 00 Y mm fo 00 Z mm fo 00 Y Constrain Crystal Position Goniometer Angle Zeros
110. nd composite reflections that contain at least one contribution from domains 1 2 4150 single and 1483 overlapped reflections used for parameter fitting Effective data to parameter ratio 269 R int 0 0532 selected reflections only before parameter refinement Cycle AR CLnGid R diffr Mean wt a Oe Oa 0 0504 0 9393 0 0496 0 0496 0 9417 3 0 0495 0 0496 0 9419 4 0 0495 0 0496 0 9420 5 0 0496 0 0496 0 9420 29 0 0497 0 0497 0 9419 30 0 0497 0 0497 0 9419 R int 0 0497 selected reflections only after parameter refinement 7 Examine the results and accept them if they are reasonable i e if the Rint is lowered and the mean weight has increased to approximately 1 Repeat parameter refinement R or accept A A M86 E00078 D 5 Processing Twinned Data APEX2 User Manual 8 Reject reflections that don t fit outliers and establish the error model The defaults are usually acceptable PART 2 Reject outliers and establish error model Rejected reflections are ignored in the statistics and Postscript plots except the detector diagnostics and in the output hkl files All statistics and error estimates refer to total intensities of single or composite reflections only Before applying rejections there are 24833 total and 9829 unique reflections assuming Friedel s law 8a Input the resolution and rejection criteria Typically the defaults are fine High resolut non Limit Lost I lt I gt su ratio
111. nique involve component 2 only mean I sigma 2 4 5479 data 2500 unique involve 2 components mean I sigma Soo 6a Set the treatment of twin components With limited data as in this example 2 is recom mended but given more data 0 is often used Enter N to fit component N and apply to all data e g when one component dominates N for one parameter set to fit equivalent singles and composites that contain at least one contribution from domains 1 N or O to fit each component separately 2 2 6b Set the cutoffs and initial weighting scheme Enter mean I sigma threshold must be positive 3 Highest resolution for parameter refinement 0 1 Factor g for initial weighting scheme w 1 sigma 2 1 g9g lt 1 gt 2 where sigma I is estimated by SAINT and lt I gt is mean intensity 0 04 6c Set up the treatment of weak moderate or strong absorbers The following restraint esd should be increased for strong absorbers Restraint esd for equal consecutive scale factors 0 005 Suitable spherical harmonic orders are 4 1 for weak absorption and 8 5 for strong Highest even order for spherical harmonics 0 2 4 6 or 8 6 Highest odd order for spherical harmonics 0 1 3 5 0 7 372 6d For fast computers increase the number of refinement cycles D 4 M86 E00078 APEX2 User Manual Processing Twinned Data Number of refinement cycles 15 30 Refinement of a single parameter set to fit all single a
112. nsert after atom 02 selected 5 Click on OK to accept the sorting Figure 9 35 OK button 9 22 M86 E00078 APEX2 User Manual The resulting list of atom information is easier to examine Information On All Atoms INFORMATION ON ALL ATOMS r mwe lx e fz_ iero e Si 0 0000 5 0 8097 0 1815 0 2405 sp3 0 0 0353467 12 Jor D 0000 0 0 3345 0 3026 0 1765 sp3 0 0 04722 13 Joz 0 0000 0 0 8432 0 890 0 1287 sp3 0 0 0488033 mc D 0000 0 4329 0 1949 0 1500 sp3 0 0 0335967 Is c2 0 0000 C 0 6354 0 1245 0 1726 sp3 0 0 0332767 16 cs 0 0000 0 6896 0 8 0 1251 sp3 0 0 03449 A CA D 0000 0 4862 0 891 0 76 sp3 0 0 0486733 l8 es 0 0000 0 2978 0 620 D 378 sp3 0 0 0566333 a cs 0 0000 0 1496 0 502 D 228 sp3 0 0 0549167 io c7 D 0000 0 1756 0 1410 0 377 sp3 0 0 0462133 u c 0 0000 C 0 3591 0 1141 0 827 sp3 0 0 03482 112 co 0 0000 0 5093 0 24 0 679 sp3 0 0 0371967 ia cio 0 0000 C 0 8345 0 3779 0 2289 sp3 0 0 04692 14 cil 0 0000 0 6496 0 1778 0 3230 sp3 0 0 0572667 Figure 9 36 Sorted atoms The Ueg are reasonable if there are e lower values for the sulfur atom and the five member ring e higher values for the terminal atoms meth yls and carbonyls e sensible numbers for the six member ring lower for C8 and C9 higher for C5 and C6 and in between for C4 and C7 M86 E00078 Structure Solution and Ref
113. ntdx type floating point default 5 The default crystal to detector distance for the aligned images plugin If given as a negative number it is counted from the back of the dx sled orientdegreetime type floating point default 10 0 Default scan time in seconds per degree for an aligned image orientscanwidth type floating point default 5 0 Default scan angle in degrees for an aligned image overlapcolor type color string default red M86 E00078 APEX2 User Manual Config overlaycolor type color string default green peakradiusfactor type floating point default 2 2 How many times the single sigma spot radius should be used as integration radius Do not touch planes type string default 0k1 h01 hk0 List of precession planes that is suggested as default planes for the calculations planethickness type floating point default 0 1 Default thickness of precession images precessionmargin type integer default 1 How many pixels at the outer edge of the detector that is to be ignored in precession calculations prefereulerian type boolean default 1 1 prefer eulerian geometry over kappa geometry O prefer kappa geometry over eulerian geometry This should not be changed after installation preferreddirection type integer default 1 E productline type string default ANY A selection of the features in the program suite based on the type of application we r
114. ntrol the instru ment The server computer runs software for aligning the system as well as software for aligning and screening samples 3 1 1 Bruker Instrument Service BIS BIS provides the link between the hardware and software Once a connection is established BIS executes hardware commands sent by the APEX2 software The instrument service can also be used as a service tool displaying diag nostic messages during operation APEX2 User Manual 3 1 2 Bruker Control Program BCP BCP is used to configure BIS as well as to pro vide instrument control and alignment tools See the online help within BCP for more information BrukerInstrument ini BCP Bruker Configuration Program File Edit view Tools Help DEGONFIG DBTOOLS D O Generator RA Ctrl ShFt G Detector Bias Gtr eshft B Gane Wika Ratemeter Ctri Shft R Half beam Ctri Shft K T HI STAR grid Ctrl Shft H paz Test Frame Ctrl ShFt T Configuration Dark Current Ctrl ShFt D fument Administrator Bad Pixels Ctrl ShFt P i Spatial Ctri Shft 5 ToN Gonio Heads Flood Field Ctreshfe r oca Attenuator GtrlShft A Fax no f dy Imagemeter Ctri Shft 1 A Robot amp Dewars Manual Ctri Shft M Limits Ctri Shft L Collision recovery Ctrl Shft C jth World wide Update home Ctri Shft U Bruker AXS Gmbh Encoder Offsets Ctrl Shft E Customer Support Log Test Security Ctrl L Destliche Rheinbrueckenstr 50 Exenci n beck D 76
115. nts data collection and use of the shutter until you close the doors 2 1 4 D8 Controller The D8 controller is an electronic module enclosed in the rack behind the front panel of the instrument It contains all of the electronics and firmware for controlling the generator open ing the X ray shutters and monitoring other instrument functions such as safety interlocks generator status and detector status For SMART APEX II systems the goniometer is controlled by the D8 controller For Kappa APEX Il systems there is an additional module the Kappa controller for positioning the Kappa goni ometer angles and adjusting the detector dis tance by driving the detector along its track Hardware Overview 2 1 5 Refrigerated Recirculator for the Detector To minimize dark current in the APEX II detec tor dual Peltier devices are used to cool the CCD chip to approximately 58 F 50 C The refrigerated recirculator uses an ethylene glycol water mixture to absorb the heat from the Peltier devices 2 1 6 Computer s The Kappa APEX II system uses two high speed computers The server controls the instrument and is used for crystal centering and screening The client collects the data stores the raw frames processes the data and solves and refines the structure The two computers are linked via a hub and communicate with each other via TCP IP protocols The SMART APEX II system uses a single high speed computer for control o
116. o solve this problem If the message still appears use the Task Man ager to check for other processes that may still be running e g COSMO M86 E00078 APEX2 User Manual 4 4 Server Computer Shutdown Stop APEX2 Server before BIS It is accept able for the order to be reversed Generally BIS is never stopped 4 4 1 Stopping the APEX2 Server 1 Click on the X in the upper right corner of the window or click on File gt Exit in the upper left It is not necessary to disconnect from the instrument 4 4 2 Stopping BIS It is almost never necessary to stop and exit BIS If necessary click on the Stop BIS button on the bottom of the BIS window and then click on the Exit button at the bottom of the window M86 E00078 Program Start Up and Shutdown Program Start Up and Shutdown APEX2 User Manual M86 E00078 5 Crystal Orientation We are now ready to begin data collection with the instrument It is assumed that your system manager has set up the system properly and that all system default parameters have been set appropriately The data collection process is divided into five steps which will be covered in Section 5 and Section 6 The steps in Section 5 are performed using the APEX2 Server software on the server computer The steps in Section 6 are performed using the APEX2 program on the client com puter See Section 5 for 1 Centering aligning the crystal on the diffrac tometer from the APEX2 Server
117. ocal Lattice Viewer 3D visualization z of lattice projected in reciprocal space View Images View collected frames Table 3 3 Task bar options APEX2 User Manual Data Collection Strategy Simulated data collection and determination strategy Experiment Sequence editor for data col lection experiments T t Oriented Scans Measure different images AE with the crystal aligned along the axes Integrate Images Integration of different data Scale Scale intensities and perform absorption correction Table 3 3 Task bar options M86 E00078 APEX2 User Manual Examine Data XPREP Space Group Determination prep Run XPREP Precession Images Create synthesized precession images based on measured frames Solve Structure Structure Solution Solve the phase prob lem to get an initial model Refine Structure Structure Refinement Use least squares to improve the model x Run XCIF to generate a report Table 3 3 Task bar options M86 E00078 Software Overview Software Overview APEX2 User Manual Task Display Area The Task Display area is the main area for space group determination SaintChart output tasks user input and selected output This area XSHELL refinement and XCIF report genera displays images the reflections used in index tion do not use the Task Display Area they ing and the observed and predicted
118. od Sa aes 2 8 3 Software Overview iia eee hada ee cere poet ee eke as 3 1 3 1 Th Server Computer osi anea oe edi Bae ear e ead ecb da e Sede ce Se dale des 3 2 3 1 1 Bruker Instrument Service BIS 0 06 cc eee 3 2 3 1 2 Bruker Control Program BCP 0 0 0 0 3 2 Odo Ee SENE sae Sd Races wy wee un a ae eee er tio ele oe eee es 3 3 9 2 MeGllentCGOMputer evi ala ene eer deat od tra pios wed Ge ORO Sass 3 4 3 2 1 Database and Database Connection 0 0 eee 3 4 S22 AE Ee GUI A Stee Eee eee ee BO hee eb eae oe tia 3 5 M86 E00078 1 Table of Contents APEX2 User Manual 4 Program Start Up and Shutdown 000 cece ee 4 1 4 1 Server Computer Star UD 2 2544 h52s6 teas diia barrera a de 4 1 4 1 1 Starting Bruker Instrument Service BIS o o oooooooooonon nono 4 1 4452 Stanting Ihe APEX2 SONO last daa 4 3 4 2 Client Computer Start Up o o o ooooooor eee eens 4 4 4 2 1 Starting he Database 26 vcd eke heed ene 4 4 AD 2 SMN AREAS caia a al Tae Md eke eee KOE dee ete Bake Re 4 4 4 3 Glient Computer SHUIdOWN 12 2064008 ia A da asd oe Re he ea ee ae 4 6 431 STOPDING AAP EA 20d 40 de a AS nd da a nN ie ede Jal oe Sees wba 4 6 4 32 SIOPping the Database oi scarats da bee ees FOO REY E nE ee Oe ewww eA aes 4 6 4 4 Server Computer Shutdown 0 00 ccc eee ee eee ees 4 7 4 4 1 Stopping the APEX2 Server 0 ccc eens 4 7 44A 2 STOW OIG BIS mrss mifare dad ene ede dad
119. olecule o oo ooocooonon eee eee nes 9 14 9 3 4 Look at Atomic Displacement Parameters Thermal Ellipsoids 9 19 93 5 SOM LOIN tt a de es a Sr eS a een as a ds tl eee es 9 21 M86 E00078 3 Table of Contents APEX2 User Manual 953 0 AGG AY OhOGenAlOMS sa A A 9 23 9 3 7 Final Refinement for Publication 0 0 0 cee eens 9 25 9 3 8 Generate an Atomic Displacement Thermal Ellipsoid Plot 9 27 Append A PRLS I vaste ia a o dida a eee A 1 AO RA arts atoms detente eric da a Aa ee ue E A 1 AZ Onentnda VICWS sexsi atin ia ii a Ri A A 5 AS Deining GrOUDS a AA E AS A 18 A 4 Measuring Distances and Angles o ooooooooron eee eee eee A 20 ASWANG APAD ING S44 O A 22 Appendix B SalntPlUS 225 darsaiad rra das deena ne eed B 1 Appendix C Using CELL_NOW 2 ccc es C 1 Gal Running CELL NOW ctas ds e o ted a al kN ell aah alee id e oe es C 1 C2 CELL NOWeQUIPUl prada AS tea aoe es we Ewes C 9 Appendix D Processing Twinned Data o o o oooo oooooooo D 1 D 1 Integration with SAINTPLEUS wt eas A See a A A AA D 1 D 2 SCaling with TWINAB S csse srana A A a D 2 Appendix E Conn rden E 1 4 M86 E00078 1 Introduction 1 1 APEX Il Systems for Chemical Crystallography Bruker AXS Kappa APEX Il and SMART APEX Il systems are the newest members in the Bruker Nonius product line of instrumentation for single crystal X ray diffraction These sys tems
120. on atoms to select them Left click on the peaks for the two oxygen atoms Q2 and Q5 in this example Figure 9 11 View of model with the probable oxygen peaks selected M86 E00078 9 9 Structure Solution and Refinement APEX2 User Manual 2 If it is difficult to see the color and labels change the color scheme by left clicking on Preferences and then right clicking on Background Color Choose colors and click Apply Click Cancel to exit the background color mode Note that the selected peaks are blue in Figure 9 13 Preferences Help Atom Preferences Ctrl F El OpenGL Preferences Ctrl G BAY shel cur style al Color Ctrl B SELECT BACKGROUND COLOR Solid f Gradient Foreground Background Apply Cancel Figure 9 12 Selecting the background color 9 10 M86 E00078 APEX2 User Manual Figure 9 13 New background color 3 Right click to view a pop up menu and select Labelling Delete Atoms Hide Atoms Information Labelling Set Pivot point Sort Show All Labels Show Hydrogen Labels Zoom In Change Parts Plane Weighted Plane Associate Connected Atoms Grow Move to Symmetry Equivalent Site Pack Trim Deselect All Constrain Model Add hydrogen atoms Figure 9 14 Select Labelling M86 E00078 Structure Solution and Refinement The Atom Labelling box will open ATOM LABELLING IN ORDER OF SELECTION Element Ic E First Sequence ft Ascending
121. onal cells FOM within 0 2 a gamma volume and lattice type for potential unit cells he SO BOO 2 09 LLSOmto 1404 89 10 90393 90 00 BOA oe 1 E Cell for domain 1 2s 6 OZ TIOS 14 648 89210 Oa DO 90200 Figure of merit 0 619 GA ar 83 SOARE EIR aUo hE O CELL_NOW has identified a domain that fits 85 3 of the data with a tolerance of 0 2 M86 E00078 C 5 Using CELL_NOW APEX2 User Manual The output shows a suitable cell with its orientation matrix figure of merit and the deviations of the input reflections from integer indices This deviation is used to determine which reflections fit this cell and which are left for further searches for new domains Orientation Matrix O 0UTO64330 0 00337404 0 06816519 0 034 7112 008170117 000385047 DeO JOUIZ TZ Us 035940339 0 000 98056 Maximum deviation from integer index 0 25 8 Enter the maximum deviation from integer index cutoff Typically the default is reasonable Hit lt Enter gt Percentages of reflections in this domain not consistent with lattice types A 50 1 B 49 9 C 45 0 I 48 9 F 72 5 O 64 3 and R 65 85 Lattice information given as of relevant reflections that do not fit a particular lattice should be used in XPREP to determine the conventional cell Typically for a lattice to be present the inconsistent should be less than 10 but problem crystals can make the value higher Percentages of reflections in this domain that do not have
122. ong diffractors and longer times for weak diffractors If the exposure times are five seconds or less click on the check mark by Correlate Frames to turn off this feature Frame correlation takes two exposures for each frame each typically having half the duration of the full exposure and then combines the two together This is usually not necessary with shorter exposure times M86 E00078 APEX2 User Manual NOTE The format for frame names is shown in Figure 6 5 APEX2 assigns every frame a name For this figure the name is ylid_manual_01_005 sfrm This means that the frame is for the project ylid_manual and that this is the fifth image of the first run La Apex2 y1 0 20 User quest File ylid_manual Experimer lt 4 Eile Instrument Windows 18 x 658 JC tramestguestiylid_manualiylid_manual_01_0005 sfin y a 4 bm l pa O NN Sy Setup Experiment Monitor Experiment Evaluate Crystal Collect Left and ri Up and down arrows move arrows move between frames between runs Experiment Oriented Scans A O O 100 1000 10000 100000 1000000 Integrate Description Phi Scan Image Examine Data it Distance 35 00 2Theta 338 00 Omega 286 99 Phi 3 61 Chi 3 83 Solve Structure iti Distance 35 00 2Theta 338 00 Omega 286 99 Phi 4 11 Chi 3 gd Refine Structure Instrument Figure 6 5 Monitor Experiment view M86 E00078 Data Collection Data Collection To change the color of
123. ork names On Windows machines this is set automatically On unix this should represent a copy of the relevant parts of the samba CONTLIQUEat Lona lowcurrent type floating point default 5 Tube current in mA to set when an experiment finishes lowvoltage type floating point default 20 Tube voltage in kV to set when an experiment finishes mailfrom type string default Not set The From address of E mails sent by the software e g bug reports mailfromdomain type string default Not set The domain of the From address of E mails sent by the software This will only be used if mailfrom is not set The user name will be prepended M86 E00078 E 13 Config APEX2 User Manual matrixstrategy type list of scans default 3 specific scans The measurement strategy that is to be used to find a unit cell minimalpowerfraction type floating point default 0 5 The minimal generator power as fraction of the maximal power that will be considered as sufficient to make a measurement mosaicity type floating point angle default 0 4 Expected normal width of a reflection in degrees nominalpowerfraction type floating point default 0 9 The normal generator power as fraction of the maximal power that the generator should be set to before a measurement nominalvoltage type map default MO 60 CU 45 AG 60 A definition of the nominal tube voltage in kV as a function of the target element orie
124. planation of the program Read this a copy is on the next page as it has useful information about what the program is doing Using CELL_NOW APEX2 User Manual CELE NOW analyses a List Of ter lecti ns to find a cell and orientation matrix despite the presence of several twin domains or other Junk In initial search mode the program tries to find sets of reciprocal lattice planes that pass close to as many reflections as possible The corresponding real space vectors are sorted on a figure of merit 1 0 would be a perfect fit In the output these are followed by the percentages of reflections that fit within 0 1 0 2 and 0 3 times the interplanar separation the components al a2 and a3 of the vector the angles to previous vectors and a cross figure of merit to previous vectors The latter should be larger for reflections belonging to the same twin component Cosines of angles between vectors a and b can also be calculated from the components by al bl a2 b2 a3 b3 a b After the Vector Tist as Deen Output CELL NOW attempes Co suggest a Sultable cell This will not necessarily be the conventional cell so it should be checked using XPREP without an hkl file taking the lattice type found with CELL NOW 11to account Lf necessary this conventional cell may De reinput un specified cell search mode to Tind the orientation Matrix TE CELE NOW fails to suggest a sensible cell either something is seriously wron
125. plot should have a constant resolution lE 11 is a strong indicator of centric and acentric space groups The two horizontal lines indicate the expected values for centric top and acentric bottom space groups This plot clearly suggests an acentric space group Intensity statistics for ylid_manual Riini blue Risigea ved Riint ce Risigena Resolution dL A IE 1 for general hk of 21 L amp La L I LO on 0 5 Resoludon d A Figure 7 28 Intensity Statistics APEX2 User Manual The plots of Chi Squared values for the data as a function of resolution and intensity should be mostly flat Values below one are not unusual for weaker high resolution data The plots shown in Figure 7 29 are typical Chi squared distributions for ylid_manual Chi squared Mean of N Sum l lt L gt N L Sur su L N equivalents BF 21 1 5 1 2 1 0 0 9 0 8 07 Resolution d Chi squared ba 0 1 0 2 0 3 0 4 0 5 0 6 0 7 0 8 0 9 Intensity quantiles Figure 7 29 Chi squared M86 E00078 APEX2 User Manual The Spatial Distribution plots are generated for each data collection run They indicate using red and blue dots points of average intensity for a particular reflection after scaling The actual intensity measured at that spot on the detector may vary by more than three standard devia tions Figure 7 30 shows two spatial distribution plots side by side This is the way they are t
126. postmaster pid already exists Is anoth e postmaster Cpid 17882 running in rdata Figure 4 7 Database failure message 4 2 2 Starting APEX2 1a For Windows systems on the client com puter click on Start gt Programs gt Bruker Nonius Programs gt APEX2 or click on the APEX2 icon on the desktop e aj 1b For Linux systems open a terminal window and type bnrun apex2 or click on the APEX2 Icon M86 E00078 APEX2 User Manual 2 A window will prompt you to log in to the database by entering a user name and password see Figure 4 8 2 1 If the system manager has set up the system to automatically enter the user name and password step 2 is skipped TR ES User Password Figure 4 8 Login request 3 An empty start up window will appear see Figure 4 9 ba Apex2 v1 0 20 User guest 0 x File Instrument Windows ID a mie Figure 4 9 APEX2 start up window M86 E00078 Program Start Up and Shutdown 4 Click on File ba Apex v1 0 Eile Instrument w eogi Logout 7 New gt Open Mi Figure 4 10 File menu 5 Use the options in this menu to create a new project or to open an existing project 6 If the window in Figure 4 11 appears then APEX2 thinks the database is already in use Answer Yes to close the window ha Sample locked xl i This sample is locked by another session Do you want to unlock the sample
127. provide the tools for complete small mole cule structure determination The hardware and software are completely redesigned The soft ware features a new start to finish graphical user interface GUI The hardware features a new CCD detector based upon four port readout of a 4K chip and a choice of two goniometers APEX II systems are enclosed in a radiation safety enclosure system The Kappa APEX II system features the Kappa 4 axis goniometer Two computers are used for experiments One computer the server controls the goniometer The other computer the client M86 E00078 controls all other aspects of the experiment from data collection through report generation The SMART APEX II system is an enhanced version of the SMART APEX fixed chi system A single computer controls the data collection and solution and refinement of the structure From a software and operational viewpoint the APEX II systems use the GUI of the APEX2 software suite to control all operations from crystal screening to report generation for a typi cal crystallography study This is a complete departure from the command driven function ally separate modules of SMART SAINTPLUS and SHELXTL Enhanced versions of the proven and widely accepted programs used by these modules e g SAINT SADABS XPREP XS XM XL etc underlie the GUI and provide powerful tools Introduction From a hardware viewpoint APEX II systems share common hardware components
128. r Image Statistics Zz 0 40 SE 4000 00 A Spot shape correlation 8 00 gt 2000 00 E Spat intensity and l Sigmall qX Spot intensity lt 2 Sigmall 0 00 0 00 Number of reflections harvested MEARE aa Pane pay pe pa O Spot position overlay 2 4 6 8 2 E 3 al Gi Y x Y Z enor Image Image 0O x Y ZAMS difference Correlation coefficient e Intensity sigma Oo X Y Z spot size O Queue extent used il O Primary beam intensity D Periodic Statistics iE Profile snapshots B amp Average Difference Bet 0 20 0 10 A axis ESD 0O B axis ESD 0 00 tf C axis ESD Alpha angle ESD O Beta angle ESD 0O Gamma angle ESD 0O Cell volume ESD oO LS goodness of fit 0O LS Residuals HO X Y Z crystal translation O X Y beam center 0 10 0 20 0 30 Error pixels C Distance correction 2 Pitch Roll Yaw correction Y Sirap shot al O Coverage Statistics iO Harvested reflections O Completeness and redundancy W O Bijvoet pairs 1669 3 11 3 0 o 0 o o 0 69 0 71 0 60 1 4 sfrm 13 0 13 0 17 0 08 0 31 0 34 0 18 849 75 6 31 0 81 18 0 69 0 71 0 60 1 000 S sfrm 12 0 14 0 26 0 13 0 37 0 45 0 18 1862 1 9 25 0 78 15 0 69 0 71 0 60 1 000 6 sfrm 9 0 03 0 09 0 04 0 15 0 26 0 16 1288 8 7 33 0 78 24 0 69 0 71 0 60 1 000 7 sfrm 14 0 04 0 08 0 07 0 54 0 15 0 24 9361 1 31 14 0 87 20 0 69 0 71 0 60 1 000 Connected 7 Integ
129. r bar 2 Right click on the background and select Thermal Ellipsoids WireFrame Ball And Stick Figure 9 27 Selecting Thermal Ellipsoids M86 E00078 Structure Solution and Refinement Figure 9 28 Thermal Ellipsoid plot Alternatively a list of Ueq s equivalent isotropic displacement parameters can be generated by requesting information on all of the atoms Examining these values for outliers is good practice 3 Right click on the background and click on Information on All Atoms Find Duplicate Labels Information on All Atoms d Hydrogen atoms Figure 9 29 Selecting Information on All Atoms Structure Solution and Refinement APEX2 User Manual This produces the table in Figure 9 30 Information On All Atoms h INFORMATION ON ALL ATOMS E E e jo oss oas ore o ras a je omo oase oso otz7s8 o noses eje ome osa ona oss o onse sje ome onse 002 ozas o oos eje ome oe oa orsi o ons aja ome oseo oso osoo o Dosser eje ome os oz oss o oons e je ome oes 012 ozs o oos ajo ome oase oaao oars o ooer mjo ome ness oaro ozas o omes js ome oza oz osr o nossas aje ome ose oa ozs o osea see ome nesse oarra asza o 0057267 Print Figure 9 30 List of parameters with Ueq to the right Examining the values here is difficult because the atoms are not in order 9 20
130. r to accept this default and return to the general menu 8 6 M86 E00078 APEX2 User Manual 8 5 Preparing an Output File 1 Inthe general menu chose C to define the unit cell contents 2 A window will open displaying the current formula Z the density and the atomic vol ume see Figure 8 17 In this example the formula is incorrect and Z has been set to six to try to achieve a reasonable density and atomic volume Since this formula is incorrect it must be modified now The cor rect chemical formula for the YLID crystal is 2 1 At Select Option do not accept the default answer of E Type in F to enter a new formula 2 2 In response to the question Enter For mula type the correct formula C11 H10 O2 S1 and press Enter 2 3 Check that the information is correct Check that Z seems reasonable for the space group that the density is as expected 1 1 to 1 4 for organic mole cules higher for inorganic compounds and that the atomic volume is around 17 or 18 Significant variation from the expected values may indicate an incor rect molecular formula or missing counter ions or solvates The values at the bottom of the window look fine for the YLID Press Enter to accept M86 E00078 Examine Data E XPREP Ver 6 14 W95 98 NT 2000 ME Copyrig Current dataset Wavelength Original cell Esds Current cell Matrix Crystal system E Formula Formula wt ES Density AG VOl Mu ren 1 Fi
131. ration in Progress TY 8 sfrm 17 0 06 0 22 0 02 0 20 0 35 0 13 5251 3 19 18 0 94 19 0 69 0 71 0 60 1 000 v Stop Integration Figure 7 17 SaintChart view M86 E00078 7 9 Data Integration and Scaling As shown in Figure 7 17 when the SaintChart window opens the graphs are small and under Linux the text area is large If desired change the view Change the text area by clicking and dragging on the line between the text and image areas APEX2 User Manual Expand the windows to fill the available image area by clicking on the four square icon B in the upper left see Figure 7 18 o SaintChart loj x Chart Windows SB m t Spot Shape Cora on TAZAZA4S AS AB A ZAB AS 17 0 08 D 583 sfrm 11 0 13 0 02 0 5384 sfrm 9 0 08 0 03 0 585 sfrm 8 0 05 0 08 0 536 sfrm 12 0 04 0 06 0 587 sfrm 9 0 02 0 14 0 Figure 7 18 SaintChart view with graphical area expanded 14 11 13 18 che 13 Snapshot after image 3638 8 4624 6 6412 5 10489 1246 6 2330 8 nin LL 1 22 zl 30 3 15 35000 00 30000 00 25000 00 20000 00 15000 00 o 10000 00 Average spot intensity 5000 00 0 00 Intensity a o Xx amp 0 00 o wi O h o o z o S ny o D 94 138 0 90 11 0 95 25 0 93 17 0 91 11 0 91 s9090 cosooo Sea ee Dee wa oe do pol xj Scan 1 Integration 60 00 arcomponents xi O Progr
132. re consistently longer or shorter modify the COSMO hardware profile 5 Click Stop when the completeness nears 100 and the time and redundancy approach the desired values It is not neces sary to wait until the refinement reaches 100 Current Target Priority 93 76 hooo fro 748 oo o B 4 233 jeo fho 2 Figure 6 18 Strategy Status and Priority control 6 Click Refine Strategy 7 A list of options will appear Click on Sort Runs for Completeness Execute Refine Strategy Refine Strategy Sort Runs for Completeness Figure 6 19 Choose Sort Runs for Completeness Completeness 100 co Oo 1 4 Ta 1 Resolution A Completeness Redundancy APEX2 User Manual Aduepunpey o A2uepunpay Time h Figure 6 20 Completeness and Redundancy charts after sorting for completeness M86 E00078 APEX2 User Manual 8 To look at the actual runs chosen go to View gt Detailed Strategy This will open a window that shows the runs to be collected see Figure 6 21 1 Strategy 35 00 22 00 206 99 358 39 3 83 Phi 2 Strategy 35 00 32 00 24 79 27 75 99 47 Omega Strategy 35 00 7 00 4 01 26 26 55 59 Omega 4 Strategy 35 00 28 00 48 51 14 91 34 09 Phi Ez Figure 6 21 Runs to be collected NOTE If for some reason it is necessary to start over change the distance slightly by 0 02 for example and press Return COSMO will reload all of the possible runs You are
133. reflections after merging for Fourier Highest peak 0 49 at 0 8141 0 0816 0 2288 0 95 A from C10 Deepest hole 0 24 at 0 6815 0 3980 0 1149 1 21 A from C3 FEEFEEEAFAFEFEFEFEAFEFEFEFEEFEFEFEFEAEEFEFEFEAEEFEFEFEFEE A ylid_res75 finished at 11 52 34 Total CPU time 0 5 secs PARRA AA AA A E A A AA A AA A AA A A A A A A A A A EEF Figure 9 24 Least squares refinement summary The value for R1 0 047 is typical for an initial anisotropic refinement with no hydrogen atoms included Since the mean shift esd is greater than 0 1 the model is still changing Since the highest peak in the difference map has a height of 0 49 and is 0 5A from C10 there are certainly some hydrogen atoms to be included M86 E00078 Structure Solution and Refinement Structure Solution and Refinement APEX2 User Manual Examination of the difference peaks in the resulting difference electron density map shows that the top difference peaks all correspond to hydrogen atoms Figure 9 25 Difference peaks correspond to expected hydrogen atom positions 9 18 M86 E00078 APEX2 User Manual 9 3 4 Look at Atomic Displacement Parameters Thermal Ellipsoids It is generally good practice to examine the dis placement parameters at this point in structure determination 1 Remove difference peaks with the slider tool Residual Difference Fourier Q Peaks 1 Hoof QPeaks oO Figure 9 26 Removing all Q peaks with the slide
134. reflections without equivalents when estimating R int and K Repeat parameter refinement P repeat rejections R or accept A A 12 Output the diagnostics plots and look at them The plots have the same information content and meaning as in the scaling section of the main manual The defaults are usually fine PART 3 OUEDUL Postscript diagnostics and corrected data 12a Set up the diagnostic output Typically the defaults are fine Write Postscript duagnestio fale Yor N IO Enter name of Postscript file twin eps Short lt 21 chars title for Postscript pots Tests Spatial display of I lt I gt su greater than 3 0 0 for none 13 Examination of the diagnostic plots is recommended before writing the hkl data files 13a Output an HKLF 4 format file for solving the structure It is now possible to generate a HKLF 4 format file with crude intensities for structure solution or a more accurate HKLF 5 format file for refinement Repeat R write hkl file 4 or 5 OY guit 0 14 Average equivalent reflections Y or N Y D 8 M86 E00078 APEX2 User Manual Processing Twinned Data 13b Change the output file to reflect that this is a HKLF 4 type file For example name it hkIf4 or twin_4 The extension hkl is added automatically Enter name of output hkl file twin hkl twin 4 13c Enter spherical absorption and Friedel averaging Mu r of equivalent sphere for additional spherical a
135. ruc ture and Refine All Non H Atoms Anisotropi cally as in Figure 9 23 Number of residual Cipeaks fo Sigma Cutoff D n Sigma Ez Resolution Cutoff 2 Theta a Jw Invert structure Late stage SaaS opkions p Refine all non H atoms anisotropically Figure 9 23 Inverting and choosing anisotropic refinement M86 E00078 APEX2 User Manual 4 Click on the Refine button to launch the least squares refinement program The out put window will open and a summary of the results of individual cycles of refinement will appear GooF S 1 627 Restrained GooF 1 627 for 0 restraints _ Mean shift esd 1 801 Maximum 15 000 for U13 si at 11 52 34 Max shift 0 010 A for CS Max dU 0 004 for C5 WR2 0 1427 before cycle 3 for 2445 data EE 127 127 parameters Goof 1 257 Restrained GooF 1 257 for 0 restraints Mean shiftfesd 0 503 Maximum 2 462 for ae 1 at 11 52 34 Max shift 0 005 A for C5 Max dU 0 002 for C6 WR2 0 1408 before cycle 4for 2445 data and 127 127 parameters GooF S 1 236 Restrained GooF 1 236 for 0 restraints Mean shift esd 0 095 Maximum 0 561 for U33 C6 at 11 52 34 Max shift 0 001 A for C7 Max dU 0 000 for C5 WR2 0 1407 before cycle Sfor 2445 data ee 2 127 parameters GooF S 1 233 Restrained Goof 1 233 for 0 restraints Ri 0 0468 for 2315 Fo gt Sa and 0 0489 for all 2445 data wR2 0 1407 GooF S 1 233 Restrained GooF 1 233 for all data Ri 0 0505 for 1440 unique
136. rystal centered Figure 5 7 Spin Phi 90 2 Adjust the height with the Z axis screw 5 Click Spin Phi 180 and adjust the screw fac ing you as needed Adjust to remove half 3 Adjust the translation with the X or Y axis of the difference screw whichever is facing you 4 Click Spin Phi 90 and adjust the crystal position using the X or Y axis screw Adjust to remove half of the difference Figure 5 8 Spin Phi 180 5 6 M86 E00078 APEX2 User Manual 6 Click Spin Phi 180 and Spin Phi 90 making adjustments until the crystal stays in the same place in the microscope 7 As needed repeat step 2 through step 5 to keep the crystal in the same place in the microscope 8 Click the Left button and note the height The goniometer drives to place the fiber horizontal and to the left 9 Click the Right button and check that the crystal height stays in the same place in the microscope 9 a If the height is in the same place you are done 9 b If the height is not in the same place adjust to remove half of the difference and repeat step 8 and step 9 Figure 5 9 Check the crystal height M86 E00078 Crystal Orientation 10 Click the Top button Click Spin Phi 180 a few times to verify that the sample stays in the same position If it is not centered go back to step 2 Figure 5 10 The crystal is centered 11 Go back to the Center position The crystal is now centered on the instrument All
137. strument Windows Window Tool Bar Tool Icon Bar Jo BN Setup i OS COS Describe Task Display Area Evaluate Crystal Solve Structure Refine Structure Figure 3 4 APEX2 GUI M86 E00078 Software Overview Window Tool Bar The tool bar provides pull down menus for a variety of file operations image tools and help files Symbol Use this menu to select the following Restore Move Size Minimize Maxi mize and Close File Use this menu to select the following Login Logout New Open Save Close Import Spatial Export p4p file and Exit Instrument Use this menu to select the following Connection Status Toggle Shutter and Abort Windows Use this menu to select the following Cascade and Tile RLATT Use this menu to select the following available when Rotate Edit Orientation Unit Cell Tool you select Measure Distance Measure Angle and Reciprocal Visualization Lattice Viewer View Use this menu to select the following available when Detailed Strategy you select Data Collection Strategy Table 3 1 Window tool bar options APEX2 User Manual Tool Icon Bar The tool icon bar provides shortcuts to the options available through the window tool bar Icon Description 7 Create a new file gt Open a file IZ Save a file k What s this Context sensitive help Open an image Hi Select the first image in
138. t Do not touch colorrcampy type ile nane detault Colored CDs LCM Default color ramp used by the image display tool communicationlog type file name default communication log File name used for logging all communication between application and BIS If unset no logfile will be kept E 10 M86 E00078 APEX2 User Manual Config componenticolor type string color name default green component2color type string color name default blue component3color type string color name default yellow datcoldx type floating point default 35 0 Default sample to detector distance for data collections dbtype type string default postgresql Type of database engine used Do not touch Gbhost typesstring detaule 127 050 1 Name or IP address of the server running the database The default is to run the database on the same host as the rest of the software hence the default that refers to the local host dbport type string default 5432 IP port to use to address the database Normally dependent on database installation dbname type string default testdb Name of the database Do not touch debug type tuple of strings default This is a list of all modules that are to be debugged This should not be touched except if a developer asks you to add something here to help track a problem M86 E00078 E 11 Config APEX2 User Manual default
139. t atoms Hide Partis Show all Atoms Disassociate Stoms Unit Cell e Hydrogen Labels v Labels Sort Grow Pack Trim Zoom Out Toggle Pan 4nd Rotate Restore Deleted Atoms Find Duplicate Labels Information on All Atoms Add Hydrogen atoms gt Figure 9 6 XShell menu 5 Click on the Information On All Atoms option to open a window displaying a list of the peaks and their heights see Figure 9 7 The drop in height between Q13 the last real peak and Q14 the first noise peak is typical of a correct solution Click on OK to close this window 9 6 M86 E00078 APEX2 User Manual formation On All Atoms INFORMATION ON ALL ATOMS 0 8105 0 1820 0 2401 sp3 e gum WOT RCE A A T 51 0 0000 0 05 2 for 161 0300 0 6925 0 10 0 1253 sp3 0 05 5 0 Q 0 a Q2 158 7400 Q 0 3333 0 3057 0 1756 sp3 0 0 05 14 lo 155 9800 0 0 4332 0 1961 0 1488 sp3 0 0 05 5 los 141 7900 0Q 0 5055 0 3 0 685 sp3 0 0 05 6 los 141 6800 0 0 8344 0 898 0 1307 sp3 0 0 05 7 los 140 8200 0 0 6372 0 1262 0 1726 sp3 0 0 05 8 jaz 140 6700 0 0 3537 0 1161 0 834 sp3 0 0 05 la Jos 127 0800 0 0 1821 0 1416 0 360 sp3 0 0 05 10 fo 109 9200 9 0 8324 0 3761 0 2281 sp3 0 0 05 11 foro 109 4100 0 0 1499 0 486 0 244 sp3 0 0 05 12 fon 104 8200 0 0 2908 0 615 0 380 sp3 0 0 05 113 foz 98 8900 Q 0 4789 0 856 0 93 sp3 0 0 05
140. ta col lection will continue regardless M86 E00078 6 1 Start a New Project and Describe the Sample 1 In APEX2 left click on File gt New 2 In the window that appears enter the sam ple name ba New Sample E E Hame yid marna Template ho Folder C fames quest ylid manual El Figure 6 1 The New Sample window 3 Click OK 4 The task bar will appear with the Setup sec tion open Left click on Describe Data Collection 5 Enter the requested information into the Describe window Setup Describe Center Crystal Name vlid_manual Compound Test ylid for manual Formula fer H100251 Appearance Intensity Primary Color Secondary Color Crystal Color translucent pale green y yellow Crystal Dimension 0 22 x 0 25 x 0 23 mm Crystal Shape Oblated sphere Figure 6 2 Describe window 6 Close this module The data will automati cally save to the database APEX2 User Manual M86 E00078 APEX2 User Manual 6 2 Determine the Unit Cell 6 2 1 Collect Images 1 Inthe task bar left click on Collect and then Experiment If there was no connection to the instrument when this module was started the program will either automatically connect or it will recognize that it needs to connect in order to collect images and will ask to connect see Figure 6 3 3 Instrument Connection Host Name MAMAS Figure 6 3 Instrument Connection window 2 Click
141. tance as measured would need to be multiplied by three 17 57 A 5 964 A Figure A 11 RLATT display with measured distances in the 2D views The Orientation menu allows easy orientation if the cell is indexed Hit the F1 F2 or F3 key or click on the appropriate button M86 E00078 RLATT RLATT APEX2 User Manual Pre Designated Orientations 100 along a F1 01 0 along b F2 001 along c F3 unoriented F4 9 277 User Designated Orientations Orientation 4 F5 Load Save Orientation B F6 Load Save Orientation C F7 Load Save Orientation D F8 Load Save Layers Layer Mode DISABLED Layer KL s CAEL Thickness e HK 0 0 40 5 41 0 Visible Run Scans v Scan Intensity Filter Reflection Size Zoom Figure A 12 An aligned image with the Orientation menu to the left A 8 M86 E00078 APEX2 User Manual 1 Select reflections with the Lattice tool The Lattice tool is one of the most useful editing tools Activate it from the Edit menu or by click ing on the background and choosing Select gt Lattice When initially activated nothing appears Hold down the Alt key to lock on a cen troid and then left click and hold on a spot Now drag the mouse and line up the line that is tied to your spot on a row Choose a longer row and align carefully Now while still holding the left mouse button drag the second
142. ted intensities Typically these are the files to use for determining space groups but you can browse to choose other files Examine Data 8 2 Space Group Determination 1 XPREP evaluates the data and looks at the mean intensities and the mean int sigma Since these are large for all groups except P XPREP suggests that the lattice is P see Figure 8 2 Press Enter to accept E XPREP Ver 6 14 W95 98 NT 2000 ME Copyright Bruk Figure 8 2 Lattice statistics 2 XPREP determines the reduced cell based on the lattice entered above Since the lat tice was primitive and the magnitudes of the cell dimensions were proper a lt b lt c the original and reduced cells are the same see Figure 8 3 Press Enter to search for a higher symmetry cell APEX2 User Manual W XPREP Ver 6 14 W95 98 NT 2000 ME Copyright Bruke Original cell Figure 8 3 Reduced cell For the YLID no higher symmetry cell is found The program has determined that the YLID crys tal has an orthorhombic primitive lattice see Figure 8 4 Press Enter to accept Figure 8 4 Higher symmetry cells M86 E00078 APEX2 User Manual 3 The next logical step is to determine the space group XPREP suggests this see Figure 8 5 Press Enter to determine the space group E XPREP Ver 6 14 W95 98 NT 2000 ME Copyright Bruke urrent dataset Wave length Original cell Figure 8 5 Determine the space group 4 If the space group is known
143. ter Mefinement l cra Figure 7 26 Error Model results If the R values in one run are significantly higher than the others you can repeat the entire scal ing calculation with that run omitted Click the check box by the bad run and then click Repeat Parameter Refinement 7 18 M86 E00078 APEX2 User Manual Data Integration and Scaling 7 3 4 Examine Display Diagnostics The Scale Variations plot Figure 7 27 shows the overall variation in Scale and R int for the individual frames The Scale plot should be flat for highly absorbing irregularly shaped crystals it will probably be sinusoidal and the R int plot should not show large variations more than 1 Click Finish to produce a series of diagnos 2 tic plots Some of these are reviews of the plots that have already been displayed The Display Diagnostics provide valuable insight into the quality of the data and possible problems with the data Click on the tabs at the bottom of the screen to view diagnostic data pap YY Parral Yo cnet YY Dipoi a Overall scale and R int variations for ylid_manual Normalized Scale Factor Smoothed R int Run Frame gt Figure 7 27 Overall Scale and R int variations M86 E00078 7 19 Data Integration and Scaling The Intensity Statistics plots look at R int and IE 11 as a function of resolution Typical plots of R int versus resolution increase to the right as seen in Figure 7 28 An E 11
144. the folder containing these programs and desktop icons linked directly to these programs How ever the Start gt Programs gt Bruker path is always available This more explicit method will be used in this discussion M86 E00078 4 1 Server Computer Start Up Two programs must be running Bruker Instru ment Service and APEX2 Server NOTE For Kappa APEX II systems the pro grams will be on the server computer in the goniometer cabinet For SMART APEX II sys tems there is typically only one computer 4 1 1 Starting Bruker Instrument Service BIS 1 Click on Start gt Programs gt Bruker AXS Programs gt Bruker Instrument Service or click on the BIS icon on the desktop Program Start Up and Shutdown After a brief initialization period a window will appear see Figure 4 1 On Kappa APEX II sys tems the goniometer will move to reference positions ll EIS Escher Instrument Serve BIS 1 204 15 Ap 21 Y Command DJ Fie Y smn Widows Serce Manager Conard File Sin Command Fie Suba instal Sence femore Seaca Dee o O Ces 9 0 cat ue bh 00080m Che O Clee ee a E p Fae NOCPERATION mn 000 z da Cas o O w 00 em Co Message BS He i j sons w smo Figure 4 1 The BIS window If a small pop up window appears that says This second instance of BIS is exiting see Fig ure 4 2 BIS was already running Click on OK to clear this informational message Ins
145. to spot centroids and the angle will be calculated using spot coordinates This elimi nates errors that might result from measuring using the 2D projection of the current orienta tion al A A A A E a PS ARIAS A AA A koai A A ni il is is a a ee ee ee F F F O A E O A ET TT G E E E O O E A pE F T T F T O E T TT TETT TP TETT ee a T T T T T TT E UD E T T i iii Tina TE TT T TT T re TUE rit TF a a a h po ca TEE E a Pr ea ee A el e a A A a a A dk E TP Pra A A a a Figure A 24 Using the Measure Angle tool M86 E00078 RLATT A 5 Writing a p4p File At the bottom of the Edit menu there is a button for exporting all visible reflections to a p4p file The p4p file is a text file of crystal instrument and reflection information If the cell and crystal orientation is known that information is included also otherwise dummy values are included The sequence of cleaning up a set of reflections using RLATT and then exporting the results for input to CELL_NOW is a useful tool for dealing with hard to index crystals APEX2 User Manual M86 E00078 Appendix B SaintPlus Occasionally it is necessary to integrate images outside of the APEX2 GUI Usually this is nec essary in order to import a matrix p4p file SaintPlus executed from a command window is designed for this purpose 1 Open a Command Prompt window 2 Change directories to the folder of interest
146. trumentService x IN This second instance of BIS is exiting Figure 4 2 BIS exiting message APEX2 User Manual NOTE With a Kappa APEX II the kappa goni ometer will home and the kappa server will acti vate when BIS is started This may take a minute or two The Kappa server is a service tool and should not be used to control the instru ment M86 E00078 APEX2 User Manual 4 1 2 Starting the APEX2 Server 1 Click on Start gt Programs gt Bruker Nonius Programs gt APEX2 Server or click on the APEX2 Server icon on the desktop A window will appear see Figure 4 3 Figure 4 3 Initial APEX2 Server window M86 E00078 Program Start Up and Shutdown 2 In the top left corner click on the Instrument pull down menu see Figure 4 4 Li Apex25 erver 1 0 19 File Instrument Windows Status E E Toggle Shutter Abork Center Crystal Figure 4 4 Connecting to the instrument 3 Click on Connection and a new window will appear see Figure 4 5 The name of your server should already be filled in 4 Click on Connect a E lb g Instrument Connection Host Name Figure 4 5 Connection window NOTE If the host name is wrong then the instrument is not properly configured and you should consult your system manager It is pos sible to configure the instrument to automatically connect so that this window will not appear This is discussed in Appendix E Con
147. video camera coincide with the center of the goniometer and the center of the X ray beam see manual M86 Exx024 for instructions on aligning the microscope to the center of the instrument If the microscope is not centered you can still align the sample the key to crystal centering is that the crystal stays in the same place in the microscope s field of view in all orientations NOTE Use the thin end on the goniometer wrench to unlock the X Y and Z locks at the beginning of the centering process and to lock them at the end locking needs only a very slight touch The other end of the wrench is used to move the adjustment slides Do not overtighten M86 E00078 Crystal Orientation NOTE Centering is often easier if the crystal is rotated to give a good view before the actual centering process is started e g down an edge for a plate To do this drive to one of the cen tering positions loosen the screw that locks the crystal mounting pin rotate the crystal to a suit able orientation and then tighten the screw again 5 2 1 For a Kappa APEX Il System 1 Click the Center button the crystal and goniometer head will be positioned perpen dicular to the microscope To center the sample make adjustments in the height with the Z axis adjustment and with the translation screw that faces the front of the diffractometer Figure 5 5 Crystal initially mounted Crystal Orientation APEX2 User Manual Figure 5 6 C
148. will start to appear This may take a minute or two if new darks are being collected NOTE When resuming after a power failure APEX2 will automatically skip images that were previously collected with matching angles and generator settings Otherwise it will ask if you want to overwrite the images APEX2 User Manual NOTE After data collection is started the experiment window can be closed and APEX2 can be stopped The server computer must be left on If communications are lost between the client and the server frame data is stored on the server Typically they will be in the directory C frames They should be copied to the correct project directory before starting integration E hai Apex2 v1 0 20 User guest File ylid_manual Experiment 3 Ele Instrument Windows g x 0 c amp tah dalmMdpml vs OvrG C frames quest ylid_manual ylid_manual_01_0005 sfrr Evaluate Crystal Setup Experiment Monitor Experiment Integrate Phi Scan Image Examine Data fi ition Distance 35 00 2Theta 338 00 Omega 285 99 Phi 3 61 Chi 3 83 Solve Structure 13 End position Distance 35 00 2Theta 338 00 Omega 285 99 Phi 4 11 Chi 3 83 Refine Structure Instrument Figure 6 24 Monitor Experiment view M86 E00078 7 Data Integration and Scaling Before the data can be used to solve and refine the crystal structure it is necessary to convert the information recorded on the frames into a set of integrated
149. x 10 lock onto spot e Measurement ALT lock onto spot locking onto all left chck three calculates the angle in 3D RLATT APEX2 User Manual 3D Reciprocal Lattice View In this window is the three dimentional display of the reciprocal lattice using OpenGL for hardware rendering Left click and drag to rotate the view or use a selected feature Double left click on a reflection to bring up a little statistics window Click on the statistics window to make it disappear ee and drag to change the zoom ratio 5 n the mouse wheel to adjust the reflection sizing Right click to make a quick menu of special features available Figure A 7 Help for the 3D display obtained by clicking the What s This arrow on the blue display background A 4 M86 E00078 APEX2 User Manual RLATT A 2 Orienting Views By sliding the intensity key at the bottom of the display it is easy to deselect weak reflections In Figure A 9 the reflections between the layer lines all go black when the intensity filter is moved to the left Move the mouse to rotate the RLATT display It is possible to easily see rows and non fitting peaks see Figure A 8 Intensity Filter Reflection Size Zoom Figure A 8 RLATT display looking down layers of a N gt gt gt gt 45 reflections Figure A 9 RLATT display looking down layers of reflections Weaker reflections i e those with smaller sigma l are black because t
150. ypi cally output by the scaling process Spatial distribution of 1 lt 1 gt su for yhd_manual Spatial distribution of L lt L gt su for yhd_manual Sean L detector 2 theta 22 00 lt gt gt 3 0054 red blue errors black Scan 2 detector 2 theta 32 00 lt i gt 3 0050 red blue errors blac rd A Spatial Distota ton Figure 7 30 Spatial distribution M86 E00078 x Data Integration and Scaling Data Integration and Scaling Figure 7 31 shows a single plot so that the dots are easier to see Note that the points of dis agreement are spread fairly evenly over the entire detector face Spatial distribution of lt 1L gt 5u for ylid_manual San detector ea 2200 Ls 53 00 red bue errors black 50 100 150 200 240 HF 350 00 150 N gt Figure 7 31 A single Spatial Distribution APEX2 User Manual If the spots are clustered in an area or if there are significantly more spots of one color than there are of another then the data should be examined critically Figure 7 32 is from another data set where the Active Mask was not used during integration and the reflections collected in that area are consistently smaller than expected This kind of problem may affect the final results Scan 1 detector 2 theta 12 00 1I lt l gt 1 gt 3 00su red blue errors black 50 100 150 200 250 300 350 400 450 X gt Figure 7 32 A Spatial Distribution plot showing a probl

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