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M86-E01078 APEX2 User Manual.book - X

1. Table 6 1 Collect Data menu items 6 8 M86 E01078 APEX2 User Manual Harvest Spots First Image Number of Runs Go to Image Min sigmall Excluded Shells Store A4 b rw Frames quest ylid_example matrix_01_O001 strm gt fa Images per Run 12 CA Frames guestiylid_exampleimatrix_01_0001 sfrrn More Spots Fewer Spots v Smooth images Add 1 30 1 92 222 229 E dit 3 63 3 79 Delete Delete All E Group 0 270 reflections J Save only reflections that span images Figure 6 7 Harvest Spots menu M86 E01078 Harvest Cancel Data Collection Menu Item Function Select the first image in the group of First Image images to be examined for spots Number of Runs Number of runs to be examined Number of images to be examined in Images Per Run each run Select a frame filename from this drop Go to Image down menu to display the frame in the Image Information Area Adjust the criterion for harvesting a spot based on its pixels intensity ver l l sus their standard deviation Slide the Min l sigma l slider between More Spots and Fewer Spots to vary the minimum l sigma l A Gaussian filter is applied to the frames prior to harvesting which reduces the noise and eliminates Smooth images falsely harvested pixels For very weak data however the Smooth images function can interfere
2. Bravais Lattice FOM ala et c ari eri vr a 5 954 b 9 024 c 18 35 a 90 00 B 90 00 y 30 00 V 98B5 Orthorhombic P 0 01 21 31 21 31 21 31123 30 60 96147 57 0 01 1930 10 81 20 46 68 40 31 37 80 23 000 595 302 1836 90 00 90 00 90 00 0 01 5 95 902 18 36 90 00 90 00 30 00 RhombohedralR 0 01 5 95 1081 5613 94 35 35 08123 41 0 01 595 902 3828 76 37 81 06 90 00 0 01 595 902 1836 90 00 90 00 90 00 0 04 595 1900 37 20 87 13 99 20108 25 38 28103 63 98 94 90 00 3 02 30 00 90 00 18 36 90 00 100 595 902 18 36 90 00 90 00 90 00 Menu Item Initial Unit Cell Function Use the Unit Cell Combo Box to select a unit cell to which to assign a Bravais lattice type Bravais Lattice This list shows the 14 Bravais lattice types for the selected unit cell parame ters For each entry the list contains from left to right the Bravais lattice type the figure of merit ranging from 0 0 to 1 0 with 1 0 being perfect agree ment and the six unconstrained unit cell parameters for that Bravais lattice type Bravais lattices that are in agreement with the unit cell are displayed in green which those that do not are displayed in red The most likely Bravais lattice type is chosen automatically If necessary you may override the program s deci sion by clicking on a different entry Go to the previous step in the unit cell A Lau determination process iaht Go to t
3. aaa 5 7 532 For SMART APEX II Systems vss RR ees o erre 5 13 5 4 Simple SCAN cra Patav eR A A oae ipi due aux 5 18 5 5 Examples of Poor Quality Crystals 0 00 e ee eene 5 22 6 Data Colection koh xd wid axes acie ae he keene hee wee 6 1 6 1 Creata New Sample iio dara daa teens 6 2 62 Determine the Unit Cell 34 259 2 372 x5 et eh ee eee ee eae eee on 6 4 62 1 Automate Mode sio emot HORROR SE Eod Ie ooo a eee 6 6 0 2 2 NanUal Mod aia ss daa 6 7 6 3 Determine the Data Collection Strategy 0o ooooooooooonmonmo 6 16 6 3 1 Operation and Initial SettingS o o oooooooooonor ooo 6 16 6 3 2 Refining the Strategy 0 eee eens 6 18 6 3 3 Looking at the Current Strategy llle 6 21 6 4 Data Collection Run Experiment 0ccocccocccoc ee 6 23 7 Data Integration and Scaling l l 7 1 M86 E01078 vii Table of Contents APEX2 User Manual viii UE ccu IL AA AAA A ee RE 7 2 7 1 1 Check the Refinement Defaults o oooooocoocoonoo nono 7 5 7 1 2 Check the Integration Options 0 0 0 eee 7 6 FASS Sta INICOMAUOWN tiara a p dg ai Ge ta SES du aee Col bed a eon ae 7 7 Te ANTAL Dart 5 tasado ol ll arm ds are a 7 8 7 2 1 Monitor the Progress of the Integration 0 00 cee eee 7 9 Tee EXamMine Final RESUNS start Aa 7 11 1 0 Scale Data ascos iaa EX kee eee deni ee ee eee ee 7 14 TSL 9erUplnpUt
4. Mone 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 Deletion Helpers Delete Selected finalized at save Delete Non Visible finalized at save Intensity Filter Reflection Size Zoom E port Visible S pots to P4P Figure A 14 View with most of the lattice lines selected Lines to the top and bottom are not selected M86 E01078 RLATT RLATT Use the Page Up key to add lines to the out side of the previously selected lines in this example the top and bottom Page Down removes lines from the outside Now all visible lines are selected Note that the selected reflec tions are turquoise Intensity Filter Reflection Size Figure A 15 A view with all layers selected APEX2 Editing Tools Box Lattice Overlay Single Spot C Circle C None rotate Selection Helpers Select Weak Reflections Select Curent Group Invert Selection Grouping Tools Current Group mm Goo y Add To Current Group Remove From Current Group Select Visible Groups E Group 13 Deletion Helpers Delete Selected finalized at save Delete Non Visible finalized at save Zoom Export Visible Spots to P4P User Manual M86 E01078 APEX2 User Manual RLATT Click Invert Sele
5. 20 2 theta 04 theta1 05 theta2 O omega D phi X chi y gamma Table 1 2 Greek and Roman text M86 E01078 APEX2 User Manual 1 23 Warnings Cautions and Notes This User Manual contains notices that you must observe to ensure your own personal safety as well as to protect the product and con nected equipment These notices are high lighted in the User Manual by a warning triangle and are marked as follows according to the level of danger The word WARNING alerts the reader to an immediate or potential hazard that can result in death severe personal injury or substantial property damage The word CAUTION alerts the reader to a potential practice or condition that could result in minor personal injury or damage to the product or property NOTE The word NOTE in bold capital letters draws your attention to particularly important information on the product or handling of the product or to a particular part of the product documentation M86 E01078 About This User Manual 1 3 Referenced Documentation Table 1 3 contains a list of documentation refer enced in this User Manual It is recommended to have this additional documentation available as you work with this User Manual Documentation itl Part Number s 269 0175xx SAINT Software Reference Manual M86 Exx024 Microscope Focus and Sample Alignment M86 Exx043 BCP and BIS Installation Notes M86 Exx045
6. An oriented lattice view The Visualization menu is to the right The 2D profiles are to the left and to the top A 6 M86 E01078 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 distance as measured would need to be multiplied by three 17 574 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 Press the F1 F2 or F3 key or click the appropriate button M86 E01078 RLATT RLATT 9 277 A Intensity Filter Reflection Size es Figure A 12 An aligned image with the Orientation menu to the left APEX2 User Manual Pre Designated Orientations 100 along a F1 01 0 along b F2 001 along c F3 unoriented F4 User Designated Orientations Orientation A F5 Load Save Orientation B FB Load Save Orientation C F7 Load Save Orientation D F8 Load Save Layers Layer Mode DISABLED Laver Thickness Visible Run Scans v Scan Zoom M86 E01078 APEX2 User Manual 3 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
7. unconstrained global unit cell refinement 05 30 06 18 17 01 Performing final unit cell least squares on file cC sFrames sqguest ylid example wwork wyylid al ma Input file contains 4325 reflections Refinement includes 1 sample sample 1 contains component 1 Global Refinement for sample 1 of 1 single component data Maximum allowed reflections 6955 one reflection will be stored in memory per 1 reflectionts read orientation least squares component 1 in sample 1 in integration 4325 input reflections wavelength relative uncertainty Q 7107300 OO 0000085 Reflection summary RLv Excl are io excluded after cycle 1 because RLV error exceeded 0 0250 Component Input RLW Excl Used wWworstRes BestRes Min 2Th Max 2Th 1 4325 o 43425 4 1954 D 7 6572 4 450 35 184 orientation C UB J matrix 0 0005223 0 06524560 0 0450134 0 1250715 O 0572444 0 0203780 0 10716558 0 0686201 0 0247583 A B E Alpha Beta Gamma wol 3 9608 9 03476 18 3909 ao 997 90 001 90 002 990 76 D 0005 0 0007 0 0014 o 001 0 001 D 001 0 23 orrected for goodness of fit O 0002 0 0003 0 0007 0 000 0 000 0 000 0 11 Crystal system constraint o Unconstrained Parameter constraint mask G Eulerian angles 65 108 117 084 134 154 Figure 7 19 Unconstrained unit cell refinement YLID unit cell shown M86 E01078 7 13 Data Integration and Scaling 7 3 Scale Data The scaling process uses
8. Figure 6 1 New Sample window 3 Click OK The Task Bar appears with the Setup section open 4 Click Describe 5 Enter the requested information into the Describe window APEX2 User Manual M86 E01078 APEX2 User Manual Data Collection bg APEX2 v2 1 RC7 User quest Sample ylid example Licensed to Applications Lab at Bruker AXS Describe Sample Instrument Windows Help 15 x 1654 100x e Name yid example Compound vub Formula ci H10 02 51 Appearance Intensity Primary Color Secondary Color Crystal Color r n a y n a y yellow n a Y Center Crystal Crystal Dimension o 3 x 0 3 x o 3 rm Crystal Shape spec This is an example YLID for the APEX2 Version 2 User Manual Notes Figure 6 2 Describe window 6 Close the Describe module by clicking the X button on the right hand side of the Menu Bar APEX2 will automatically save the data to the sample database M86 E01078 6 3 Data Collection 6 2 Determine the Unit Cell Unit cell determination is performed in several steps e Data collection e Harvesting of reflections from collected frames e Indexing of harvested reflections e Bravais lattice type determination e Refinement In APEX2 Version 2 these steps are integrated in the Determine Unit Cell module located in APEX2 s Evaluate category which also con tains a one click solution for fully automated unit cell determinat
9. HKL file C Frames guest ylid_example work ylid hkl Figure 8 1 Select files for XPREP input NOTE In this example the integration process has created two files ylid example Om p4p containing the final unit cell parameters from integration and ylid hkl containing the corrected intensities Typically these are the files to use for determining space groups but you can browse to choose other files Examine Data 8 1 1 Determining Space Groups 1 Lattice type 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 Figure 8 2 Press Enter to accept FAFA A A A A AA A A AA A E A A A A AA A A AA A A A AA A A AA A A A AA A A A AA A EHE AA A A A AA E RP HP HR A A A 40 4 XPREP Reciprocal space exploration Version 2005 2 for Windows COPYRIGHT c 2005 Bruker Axs ll Rights Reserved TEMERE ERE EHEHEH EHEHEHEH HEHH EHH HEHH EE HEC EE HE EE EE EHE EE EHE HE EE ERE E ER HP P E RR HP RR ET Screen size 1280 x 1024 Window size 6430 x 923 Font size 8 x 16 125 x 178 Number of colors 256 When xprep is started without a filename on the command line the filename is prompted for and then the type of data SHELX SCALEPACK XDS or XENGEN requested To generate ideal data a SHELX ins or res file if necessary made from a PDB file using SHELXPRO or XPRO should be given Xprep name reads a SH
10. 9 2 1 Options for Direct Methods Clicking on the arrow to the right of Direct 1 in the Method box Figure 9 3 gives three preset choices for structure solution using direct meth ods Direct 1 r Dual Space 1 Patterson 1 r i Structure Expansion Computing Effort log scale AA _ gt _ __ _ A _ _ Figure 9 3 Method box In most cases the default values will give a good initial model but several other options are avail able for more difficult problems Chose the solu tion method by clicking the appropriate radio button on the left in the Method box Structure Solution and Refinement Preset Description Standard settings which should be appropriate for a wide range of circumstances Direct 1 Sets up a default run with a simple TREF instruction Brute force method with a higher number of direct methods attempts Sets up an extended run with TREF 10000 By adding 10000 to the TREF command more Direct 2 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 possible to stop at that point by clicking on the STOP but ton Good solutions typically have a CFOM of 0 06 or less Brute force method with even more direct methods attempts Sets up an extreme run with two instructions ESEL 1 0 and TREF 100000 By adding ESEL Direct 3 1 0 more reflections are used in the solution process Increasing the number
11. 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 9 removes peaks Fesidual Difference Fourier Q Peaks o Ho of GPeaks 22 Figure 9 9 The Q peak slider M86 E01078 APEX2 User Manual Structure Solution and Refinement 7 Slide the pointer down while watching the molecular display Change the number of Q peaks to 15 At 15 the molecule is much cleaner but there are still peaks that do not make sense Figure 9 11 Image with all noise peaks removed 8 Put the cursor over the bonds to check dis tance The distance is displayed at the bot tom right Figure 9 10 Image after the number of Q peaks was changed to 15 Click left on the slider until you find a reasonable model M86 E01078 9 9 Structure Solution and Refinement APEX2 User Manual 9 3 1 Label the Atoms 1 Label the atoms and set the atom types Left click atoms to select them Left click the peaks for the two oxygen atoms Q2 Pe oo i and Q5 in this example P ORE ARR TNI Figure 9 13 Selecting the background color Figure 9 12 View of model with the probable oxygen peaks selected 2 fitis difficult to see the color and labels change the color scheme with Preference
12. C 2 M86 E01078 APEX2 User Manual Using CELL_NOW 4 CELL NOW requests the name of the input file and suggests a name for the output file Enter the name of the input file For the output file press Enter to accept the default Full name of p4p spin or drx file to read example p4p 999 reflections read in Listing file example _cn 514 reflections read in Listing file example _cn 5 Press Enter to start a general search Initial search lt Enter gt or specified cell search S 6 Ifthe default superlattice threshold is suitable press Enter Superlattice threshold an axis will be rejected if less than this percentage of reflections has indices not equal to 2n or 3n resp 10 7 fthe default minimum and maximum distances are acceptable press Enter 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
13. EM 1 10 20 Link Sizes DISABLED Intensity Filter Reflection Size Zoom y AAA r Figure A 19 A view of the reciprocal lattice after the non fitting reflections were deleted and with the Unit Cell tool enabled A 16 M86 E01078 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 E01078 As17 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 Add to Current Group to turn these rows red Then the other rows and Group 13 white were selected 221 1X2 ZIlXI PgDRXIBIINBIBIBLBIRLZIIAlL LA DD DDD DD Y c a A Y Y Y Y Y Y Y Y Y YD Y SD DD DD DD Y Y Y Y 222 Y Y Y Y Y YD SD Y Y DY 2 22 222 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 add
14. in unit cell refinement Huber goniometer head Hybridize All command Hydrogen atoms adding in XShell Index 3 11 6 24 3 14 2 6 2 1 2 6 9 20 5 2 5 6 1 1 2 3 1 2 A 18 3 1 3 7 1 4 7 15 6 15 5 4 9 21 9 20 Index 3 Index l sigma l in unit cell determination 6 9 6 11 Image width 6 8 Index 6 11 Information on All Atoms 9 8 9 16 Integrate Images module 3 12 Integrated intensities 7 1 Integration Progress display 7 9 Intensity Statistics 7 18 Interlocks 2 8 Isolated reflections 6 11 Isotropic displacement parameters 9 16 J JPEG output 9 25 K K780 generator 2 6 Kappa angle 2 4 Kappa APEX II 1 1 2 1 centering the crystal 5 7 Goniometer overview 2 4 L Labyrinths 2 7 Lattice type XPREP 8 2 License Manager 4 5 Licenses 4 5 Login 3 9 3 10 4 4 Index 4 APEX2 User Manual Logout 3 9 M Manual unit cell determination 6 7 Mean Weight 7 15 Menu Bar 3 7 Merge all equivalents in XPREP 8 4 Monochromator 2 3 2 6 Mosaicity 6 4 Mount position 5 3 Movie view for frames 3 11 N New Sample 3 11 6 2 No active sample 3 12 Noise peaks removing in XShell 9 9 Nonius goniometer head 5 5 Normals in Face Indexing B 4 Notes 1 3 defined 1 3 Numerical Absorption Correction From Face In dices B 8 O Omega free rotation 2 4 2 5 Online and Offline Operation 4 2 Open in XP 9 6 M86 E01078 APEX2 User Manual Open in XShell 9 6 Open sample 3 11 OpenGL rendering alert 9 26
15. theta 10 0 projtls degrees omega 5 0 projtls degrees chi 45 0 projtls degrees phi 180 0 projtls degrees del projtls Acceptable CCD temperature ccdtemperaturerange 65 55 Auto connect to the instrument when needed This is a protected variable that is controlled by the System Administrator autoconnect 1 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 degrees long perpendicular matrix runs frametime None M86 E01078 D 3 Configuring APEX2 APEX2 User Manual The frame time is left to be the default Setup to get some debug messages for scans This is useful if resume is failing debug goniometer scan debug expt findresolution Hardware profile used by the data collection strategy planner bishost bruker server hardwareprofilez Kappa APEX 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 F
16. C Define unit cell CONTENTS P Contour PATTERSON sections F Set up shelxtl FILES H Search for HIGHER metric symmetry R RECIPROCAL space displays 5 Determine or input SPACE GROUP U UNIT CELL transformations 4 Absorption powder SIR SAD MAD etc T Change TOLERANCES M Test for MEROHEDRAL TWINNING 0 Self rotation function L Reset LATTICE type of original cell Q QUIT program Select option Q f Output file name without extension ylid manual Om A Figure 8 13 Defining and checking the unit cell contents 5 The next default action for XPREP is to write out the files necessary for the struc ture solution process see Figure 8 14 Press Enter to accept Current dataset ylid_manual_Om hkl Wavelength 0 71073 Chiral Original cell 5 957 9 027 18 366 90 00 90 00 90 00 Vol 987 7 Esds 0 001 0 001 0 002 0 00 0 00 0 00 Lattice P Current cell 5 957 9 027 18 366 90 00 90 00 90 00 Vol 987 7 Matrix 1 0000 0 0000 0 0000 0 0000 1 0000 0 0000 0 0000 0 0000 1 0000 Crystal system Orthorhombic Space group P2 1 2 1 2 1 19 chi Laue 3 Formula C11 H12 O2 51 Formula wt 208 27 Z 4 00 Density 1 401 At vol 17 6 F 000 440 00 Mu rm 1 0 30 D Read modify or merge DATASETS C Define unit cell CONTENTS P Contour PATTERSON sections F Set up shelxtl FILES H Search for HIGHER metric symmetry R RECIPROCAL space displays 5 Determine or input SPACE GROUP U UNIT CELL transformations 4
17. Closed Displays whether the faces you have defined encapsulate a closed volume Dimensions of the crystal calculated Size mm according to the defined faces Table B 2 Face list B 4 B 3 1 Depending on the color and reflectivity of the crystal and background you may want to adjust the display colors Set View Options 1 Right click in the image display area and select Configure Overlay from the menu The Overlay Configuration menu appears Figure B 5 hy Overlay Configuration 24x IV Show crystal edges wike 3 Show backside Show crystal faces Crystal Labels Y Show crystal labels Font size pt fi 2 E x center pixels 287 E Y center pixels fi 81 B Titande fo 4 Cancel Figure B 5 Overlay Configuration menu M86 E01078 APEX2 User Manual B 3 2 Specify Crystal Faces 1 Use the dial control at the bottom of the screen or use the mouse wheel to rotate the crystal until one of the faces is parallel to the microscope axis as in Figure B 6 Note that because Show T Tool and Show possible face normals are selected APEX2 suggests possible faces whose indices are within the Max Miller Index parameter with dotted lines Figure B 6 Face parallel to microscope axis 2 Move the mouse cursor to the dotted line that is perpendicular to the face The mouse cursor snaps to the possible face normal A line appears to show the possible face This
18. Figure 6 21 Monitor Experiment tab M86 E01078 Er 33333 Earn 333333 Data Collection Unit cell a 5 99 b 9 104 c 18 50 a 90 00 B 90 00 y 90 00 V 1008 Orthorhombic P Data Collection APEX2 User Manual M86 E01078 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 intensities and to scale all of the data M86 E01078 Data Integration and Scaling APEX2 User Manual 7 1 Integration 1 Under Integrate in the Task Bar click Integrate Images The initial integration window opens bg APEXZ v2 0 2 User quest Sample ylid example Temporary license 74 days remaining Integrate Images EJ Sample Instrument Chart Windows lej x 058 00 x lt lt lt sy mages Oupk ras Resolution Limit A 0 622 Unit Cells a 5 99 b 9 104 c 18 50 a 30 00 B 30 00 y 90 00 V 10084 Orthorhombic P ntegrate Images Refinement Options Integration Options Find Runs Import Runs from Experiment instrument o7 Figure 7 1 Initial integration window 7 2 M86 E01078 APEX2 User Manual 2 The Resolution Limit parameter in the upper right sets the upper limit of resolution for integr
19. Ihe From address of E mails sent by the software e g bug reports mailfromdomain type string default Not set Ihe 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 pre pended D 10 M86 E01078 APEX2 User Manual Configuring APEX2 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 b 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 orientdx type floating point default 5 The default crystal to detector distance for the aligned images module 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 sc
20. M86 E01078 A 1 Open RLATT 1 Under Evaluate in APEX2 s Task Bar click Reciprocal Lattice Viewer RLATT The Reciprocal Lattice Viewer module opens a A m a LS P mm em Reciprocal Lattice Viewer Figure A 1 RLATT icon 2 RLATT will automatically read in the reflec tions from the current project and display them as a reciprocal space plot RLATT Figure A 2 is a typical unoriented 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 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 k 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
21. Pipes Select atoms Hide Park s Show all Atoms Disassaciate Atoms Unit Cell Hydrogen Labels v Labels Sorter Grow Pack Trim Zoom Out Toggle Pan And Rotate Restore Deleted Atoms Find Duplicate Labels Information on All Atoms Add Hydrogen atoms gt Figure 9 7 XShell menu 6 Select the Information on All Atoms option to open a window displaying a list of the peaks and their heights See Figure 9 8 The drop in height between Q13 the last real peak and Q14 the first noise peak is typical of a correct solution Click OK to close this window APEX2 User Manual INFORMATION ON SLL ATOMS 1 l D Dn s BS D Em B Puy spas o n i z 161 000 Q Ug GIO 0 125 ipd 0 0 1 150 7400 Q D 03057 0 1756 pd 0 5 4 155 9600 0 0 4332 Gawi 0 1460 i5pd a 0 06 5 la 141 7900 Q 0 5055 O23 065m3 0 05 e o 141 6800 0 na ose 0130790 a 0 05 oe 140 8200 Q nee BIDS 01726 3 7 0 05 In jar TU B TIXO CE E Bol DAE a EM apa 0 u m e 117 000 Q AI a 0 0 bra TES 0 dimes oxe oza d i A 109 4100 dial 4 Obami a 0 05 i2 ui 104 8200 0 0 2908 0 615 oam y 0 05 13 an mon o nmm 0 85 0 3 o3 a 0 05 ala asno al naai cima OT O 5 0 05 15 ea fib 1800 Cy 0 557 ML AL n zw us n 1 Ds tk fous TEIE D Geet spe 0 0 05 17 los 54 7300 0 9440 858 0 1563 ap a 0 05 i amp jor 40 220014 652 dde obim a 0 06 em Figure 9 8 Atom information screen
22. all users put it in 2 if it is your own default and other people might want to use other values put it in 3 if it is only required for a single project The configuration files are read as Python programs and therefore Syntax 1S very important The best way to use it 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 4 character M86 E01078 D 5 Configuring APEX2 APEX2 User Manual Notes Leading space is significant Start all assignments in the first column Variable names are case sensitive Functionality 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 The available functions are default protein This switches from the default small molecule parameters to more protein like parameters At this time the following parameters are set chiralonly 1 autochiralpointgroup 1 resomode 1 resolution 2 5 default noprotein This sets the defaults back to small molecule values The following variables in alphabetic order can be set in a configuration file anglemargin
23. di O2 L 4 0 AL 1 6 1 3 Lal L O 0 9 0 8 Resolution d 5 4 3 H3 g d U2 0 1 0 2 0 3 0 4 0 5 06 0 7 08 09 Intensity quantiles Figure 7 25 Chi squared M86 E01078 APEX2 User Manual Data Integration and Scaling The Spatial Distribution plots are generated for each data collection run They indicate spots that were either stronger or weaker than expected with a deviation from the mean inten sity larger than three standard uncertainties Figure 7 26 shows two spatial distribution plots side by side This is the way they are typically output by the scaling process Scan L detector 2theta 22 04 IL D 53 0056 pede baci coors black Gan L detector theta 3200 E Dd 53 008 red blue error black 1504 250 13505 0 10 i50 M0 20 300 30 400 430 X 0 Ww 150 00 230 0X0 30 ao 40 X gt Figure 7 26 Spatial distribution plots M86 E01078 7 19 Data Integration and Scaling Figure 7 27 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 I d San l detector 2 1 2200 lt b 230080 rede blue carers black 0 qu 150 m 250 HI 350 EIN 150 A gt Figure 7 27 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 28 is fro
24. from the previous one giving a view of the diffraction pattern from a differ ent perpendicular direction Figure 5 39 gives a similar view for the poor crystal Figure 5 34 A 2 phi scan on a good quality crystal The spots shapes are well defined and the spots are well separated Figure 5 35 A 2 phi scan at phi 90 on a good quality crystal The spots shapes are well defined and the spots are well separated 5 20 M86 E01078 APEX2 User Manual 9 Set 2 theta to 30 This will allow evaluation of the diffraction at higher angles 10 Click Drive Scan The resulting image is shown in Figure 5 36 E Cursor bu Position pixels Intensity counts i HKL index x ___ i Resolution A 0 93 O TT yp ype orgia i Theta 44 97 1 10 100 1000 10000 100000 1000 Image Header _A Tool Editor A Cursor Position Figure 5 36 A 2 phi scan on a good quality crystal at 2 theta 30 The cursor is pointing to an area between the two reflections shown in the 3D View window The cursor position tab at the bottom left shows that the resolution is 0 93 and 2 theta is 45 M86 E01078 Crystal Centering and Screening Crystal Centering and Screening APEX2 User Manual 5 5 Examples of Poor Quality Crystals Puri nA ie 74 PRA ASNS tip JE EM AENA PAPEL Wa Ja IT d Figure 5 37 A 360 phi scan on what is likely a poor quality Figure 5 3
25. gt Programs gt Bruker AXS path is always available This more explicit method will be used in this discussion M86 E01078 APEX2 User Manual Program Startup and Shutdown 4 1 Access to BCP and APEX2 Bruker software allows different user accounts to have different levels of access to the instru ment e Service e Security e Administrator e User e Non user NOTE You need Bruker Instrument Administra tor rights to run BCP and Bruker Instru ment User rights to run APEX2 Typically your system administrator will already have your user account config ured or you will be using the default accounts as provided by Bruker AXS 4 2 Online and Offline Operation APEX can operate in either online or offline mode In online mode APEX2 is connected to BIS in order to communicate with the instrument for performing experiments To use APEX2 in online mode you must start BIS APEX2 and optionally VIDEO In offline mode APEX2 is not connected to the instrument but is still able to analyze and inter pret existing data To use APEX in offline mode you only need to start APEX2 M86 E01078 APEX2 User Manual 43 Startup 4 3 1 Starting Bruker Instrument Service BIS BIS is the link between the hardware and the APEX2 software The BIS software executes hardware commands issued by APEX2 1 To start BIS select Start gt Programs gt Bruker AXS gt Administration gt BIS Fig ure 4 1 fp decai
26. osaa 007 ps mmc osse os oa o a Jeri ooje eee ume oaza o Figure 9 31 List of parameters with Ueq to the right Examining the values here is difficult because the atoms are not in order M86 E01078 0 0353467 004722 a 0488033 0 03482 0 0549167 0 0344 0 0335967 0 0371967 00332767 0 0462133 0 04692 d 0566333 a 04856733 0 05 72667 Structure Solution and Refinement Structure Solution and Refinement 9 3 4 Sort Atoms 1 Right click on the background and click Sort to sort the atoms into a sensible order m Hydrogen Labels m Labels Grow Pack Figure 9 32 Select the Sort option An Atom List box appears to the right of the mol ecule display Since S1 O1 and O2 are in a rea sonable order only the carbon atoms need to be ordered APEX2 User Manual SORT ATOMS Sort Bin Akom List lt Top of List gt Sorti Alpha Mumeric Sorti Numeric Alpha Insert Selected After z Insert All Ofber gt lt Move Selected Atoms To Sort Bin lt Move All Atoms To Sort El Cancel Figure 9 33 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 click Move Selected Atoms to Sort Bin M86 E01078 APEX2 User Manual Structure Solution and Refinement Sort B
27. 22 D D8 Controller 2 8 D8 family of instruments for XRD 2 1 Data Collection Strategy module overview 6 16 Deleting samples from database 3 11 Describe module 3 12 6 2 Determine Unit Cell module 3 12 6 4 Diagnostics messages in BIS 3 4 plots in Scale module 7 17 Diamond anvil cells 2 9 Difference electron density maps 9 22 Difference peaks 9 15 removing 9 16 Direct methods 9 3 Distance optimum detector distance 6 16 Domains in CELL_NOW C 1 Dovetail track SMART APEX II 2 3 Drive Scan 5 19 M86 E01078 APEX2 User Manual Dual Space Methods 9 4 DX track 2 3 2 4 E El button in XShell 9 11 Enclosure 2 1 2 8 opening doors 5 2 Error Model 7 16 Ethylene glycol for recirculator 2 8 Ewald sphere In refinement 6 15 Excluded shells 6 10 Execute 6 24 Exit 3 9 Exiting APEX2 after starting an experiment 6 1 6 24 EXP files 6 23 Experiment module 3 12 loading and saving experiments 6 23 overview 6 23 F Face Indexing 2 7 3 13 Face List B 3 Face normals B 4 Find a Reflection 3 13 Fixed chi 2 5 Formula 9 2 in Describe module 6 3 in XPREP 8 5 Frames frame view controls 3 11 M86 E01078 opening G Generate New Darks Generate Report module Generator automatic ramping K780 description Generators K780 overview Geometrically strained carbon atoms Goniometer Head adjustment sleds Goniometers Greek and Roman Text Groups in RLATT GUI overview H Harvest Spots Help Histograms in Scale module
28. APEX2 User Manual 7 3 2 Parameter Refinement 1 Click Refine Figure 7 21 shows a typical refinement result The R values are reduced and the Mean Weight increases Typical final values are 3 4 for the R val ues and 0 95 0 98 for the Mean Weight of Groups 450 of Groups b ro n3 CO ww Ix c c cn n cn Cx c e ce ce e c c c Mean l sigma 1 8 rr Figure 7 21 Scale window after refinement M86 E01078 Data Integration and Scaling Diagnostics r Direction Cosines Mean error fo 000 Maximum error 0 000 Data Statistics Maximum 2 8 56 51 Wavelength 4 0 71072 Reflections Co Unique Co Data per frame 4 17 Approximate Unit Cell from direction cosines b c o b m a 5 361 3037 18 380 83 381 30 007 30 014 r Input of Data Mean lafl threshold High resolution threshold 0 1 Factor g for initial weighting scheme 0 04 Y Restraint esd for scale factors 0 005 Absorption Type Medium Absorber Number of refinement cycles 50 Data Integration and Scaling 7 3 3 Error Model Refinement 1 Click Next to proceed to the Error Model tab and click Determine Error Model Fig ure 7 22 shows typical Error Model results R int 96 r Reflections after Outlier Rejection Number of Reflections Figure 7 22 Error Model results NOTE If the R values in one run are signifi cantly higher than the others
29. Absorption powder SIR SAD MAD etc T Change TOLERANCES M Test for MEROHEDRAL TWINNING 0 Self rotation function L Reset LATTICE type of original cell 0 QUIT program Select option F i Figure 8 14 Requesting output files APEX2 User Manual 6 The program asks for an output file name Press Enter to accept Current dataset ylid manual Om hkl Wavelength 0 71073 Chiral Original cell 5 957 9 027 18 366 20 00 20 00 20 00 Vol 987 7 Esds Op001 0 001 D 002 0 00 0 00 0 00 Lattice P Current cell 5 957 9 027 18 366 20 00 20 00 20 00 Vol 987 7 Matrix 1 0000 0 0000 0 0000 0 0000 1 0000 0 0000 0 0000 0 0000 1 0000 Crystal system Orthorhombic Space group P2 1 2 1 2 1 19 chi Laue 3 Formula C11 H12 02 S31 Formula wt 208 27 Z 4 00 Density 1 401 At vol 17 6 F 000 440 00 Mu rm 1 0 30 D Read modify or merge DATASETS C Define unit cell CONTENTS P Contour PATTERSON sections F Set up shelxtl FILES H Search for HIGHER metric symmetry R RECIPROCAL space displays 5 Determine or input SPACE GROUP U UNIT CELL transformations 4 Absorption powder SIR SAD MAD etc T Change TOLERANCES M Test for MEROHEDRAL TWINNING 0 Self rotation function L Reset LATTICE type of original cell OQ QUIT program Select option F Output file name without extension ylid manual Om PP Figure 8 15 Changing the file name 7 After entering the file name or pressing Enter to accept th
30. Cake Lun wr Ep A209 USB Serial Dess Rondo Easy OD and DVO Crestor fh c ate al Sc Chei St y El Wee El adobe Reader 7 0 AQ Heroit Moua p Mouse Hesthy Computing mude ml HSN Explorer Se Dakak press r e ow r r F po Homai Aone Set Program Accent and Def mute d 98 ade transfer B ono DA Leerse Manager E Leer Manager Figure 4 1 Starting BIS from the Start menu 2 Once the BIS window appears you may be asked to confirm the detector distance M86 E01078 Program Startup and Shutdown 4 3 2 Starting APEX2 APEX is used to set up crystallographic experi ments and to process crystallographic data 1 Tostart APEX2 select Start Programs Bruker AXS gt APEX2 Abe qu mower Ej Aa USB Serial Drier Qi Roxio Erry CD and DVD Creator f c Startup Lau Sym Cher cut y El Wrap El adobe Reader 7 0 i Mena Mase Kip Mouse Healthy Computing Guida t Hit E clones Tatik Express Erro Piin r e e o To er F fur Figure 4 2 Starting APEX2 from the Start menu Program Startup and Shutdown APEX2 User Manual 2 The Login window appears automatically when you start APEX2 At the Login win NOTE By editing the bn config py configura dow enter your user name and password tion file APEX2 may be configured to As shipped by Bruker AXS the default start without displaying the Instrument account is guest with password guest Connection window In th
31. In order to correct intensity data for absorption B 1 Start the Crystal Faces Module numerically the crystal s faces must be indexed This allows a very exact crystallographic description of the crystal s shape 1 From the Scale category in APEX2 s Task Bar select Crystal Faces Once you have a unit cell for your crystal the Face Indexing module allows you to define faces directly over images of the crystal As you define more and more faces APEX2 automatically determines the dimensions of the crystal The examples in this Appendix use a large crys tal for which the unit cell has already been deter mined M86 E01078 B 1 Face Indexing B 2 Collect a Video Zip Stream To index the faces first collect a video zip stream which is a series of images taken with the video microscope as the crystal is rotated through 360 about the phi axis NOTE For the best results make sure that light ing conditions are optimal for the crystal you are viewing If possible try to illumi nate the crystal for optimum contrast between the crystal and the background Also it may desirable to use multiple light sources to illuminate several faces simultaneously 1 If no video zip stream has been collected for this crystal a dialog appears prompting you to acquire a new video zip stream or load an existing one bg Video Source 121 xi Specify source of video file Acquire New Load Existing Cancel Figure B 1
32. Manual Hardware Overview 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 E01078 2 9 Hardware Overview APEX2 User Manual M86 E01078 3 Software Overview This section presents an outline of the APEX2 software including a brief description of the soft ware layout as well as the graphical user inter face GUI From a software and operational viewpoint the APEX II systems use the GUI of the APEX2 software program 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 APEX2 GUI and provide powerful tools M86 E01078 3 1 Introduction to Client and Server Functions The various programs within the APEX2 Suite have a client server relationship Figure 3 1 in which the server program BIS executes com mands given by one of several client programs APEX2 APEX2Server or BCP Software Overview APEX2 User Manual Client Functions APEX2 APEX2Server Server Functions BIS Instrument Figure 3 1 APEX2 software relationships 3 2 M86 E
33. SMART APEX II goniometer overview omooth images Sort Bin Sort Runs for Completeness Sorting Atoms in XShell Space Group Determination module Space Groups and Statistics Spatial Distribution plots Index 6 3 1 1 4 7 8 C 10 3 6 4 4 3 6 3 9 3 9 3 10 3 9 3 11 3 13 7 14 7 17 7 1 7 14 3 1 2 6 3 10 3 3 5 18 1 1 2 1 2 5 9 18 6 19 9 18 3 13 8 1 3 13 7 19 APEX2 User Manual Spin files importing 3 9 Spin phi 180 5 3 Spin Phi 90 5 3 Spot Position Overlay 7 10 Spot Shape Correlation and Profiles in SAINTChart 7 9 Stack Bar 3 15 Status window 3 10 Strategy module 3 12 Strategy view detailed 6 21 Structure refinement module 3 13 overview 9 13 Structure Solution module 3 13 9 1 overview 9 2 Supercell problems in CELL_NOW C 6 Symmetry higher symmetry cell search with XPREP 8 2 Systematic absences and XPREP 8 3 T Task Bar 3 7 Task Display Area 3 7 overview 3 16 Technical Support 1 4 1 5 Temperature attachments 2 9 Terms and Conventions 1 2 Thermal Ellipsoids 9 16 plots 9 24 M86 E01078 APEX2 User Manual Tic Tac Toe Timing shutter Title Bar Tolerance in refinement Tool Icon Bar Torsion angles and CONF card Transform Unit Cell module Tree View T tool in Crystal Faces module Twinned crystals and APEX2 and precession images multiple orientation matrices Typographical Conventions U Unconstrained Unit Cell refinement Unit Cell Combo Box Unit Cell tool i
34. This Help function M86 E01078 APEX2 User Manual 9 3 Refine the Structure with XShell 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 Structure Solution and Refinement Control of the refinement process is quite straightforward using XShell 1 Under Refine Structure in APEX2 s Task Bar click the Structure Refinement icon This opens the Structure Refinement mod ule which contains tabbed sections for viewing the instructions file listing file results file and a 3D model of the structure Figure 9 4 Structure Refinement module initial view M86 E01078 Structure Solution and Refinement 2 Click the Browse icon a on the right hand side of the Base field A dialog opens in which you can select the desired ins file Pm bg Choose A File Look in 3 C Frames guest ylid_example work lt a CX 31 g File name piid Om ins File type RES and INS files res ins y Cancel A Figure 9 5 Open file dialog 3 Click Open The contents of the ins file and any other files with the same base name are displayed under their respective tabs Also the six buttons in the lowe
35. a license Figure 4 5 No valid license window M86 E01078 4 5 Program Startup and Shutdown 45 Shutdown 4 5 1 Shutting Down APEX2 1 First log out of the sample database by going to Sample gt Logout within APEX2 In the Closing Sample window select whether to save or discard the changes to the sample database Ly Closing Sample A What should happen to your changes to this sample Discard Figure 4 6 Closing Sample window NOTE The Closing Sample window appears even if no apparent changes were made to the sample database because the date and time of the last access are held in the sample database and differ from the current date and time 2 Within APEX2 select Sample gt Exit APEX closes APEX2 User Manual 4 5 2 Shutting Down BIS 1 To stop BIS click the Exit button in the upper right hand corner of the BIS window You may be asked to place the generator into Standby mode 2 Atthe confirmation dialog click OK BIS closes M86 E01078 5 Crystal Centering and Screening We are now ready to begin the process of data collection with the instrument It is assumed that your system administrator 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 Chapter 5 and Chapter 6 The steps in Chapter 5 are performed using the APEX2Serve
36. 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 domain2 p4p p4dp 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 2 119 of them exclusively 3 reflections not yet assigned to a domain Re refine initial cell R search for next domain S quit 0 or choose new cell from list enter number 0 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 C 8 M86 E01078 APEX2 User Manual Using CELL_NOW C 2 CELL_NOW output In this example in addition to the terminal output described above and the exampl
37. by reducing the number of difference peaks in the Refine menu see Figure 9 45 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 values to 0 06 and 0 00 Number of residual peaks ls UN Figure 9 45 Reduce the number of difference peaks Late stage refinement options Refine all non H atoms anisotropically IV Use suggested weights Squared Term o o58500 Linear Term o 000000 Refine extinction parameter IV Generate ACTA CIF information file Refine Edit File Cancel Figure 9 46 Select weights and request ACTA output M86 E01078 Structure Solution and Refinement Figure 9 47 shows a difference map with the number of peaks set at five Figure 9 47 Difference peaks 2 Click 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 Edit File Open File for Editing vlid reso67 INS LST Cancel Figure 9 48 Open the ins file for editing 3 Check that the temperature card is correct Structure Solution and Refinement 4 Iftorsion angles are of interest add a CONF confirmation card see Figure 9 49 TEMP 23
38. choosing Select gt Lattice When initially activated nothing appears Hold down the Alt key to lock on a centroid 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 line to another row as shown in Figure A 13 Let go of the button 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 easier and more accurate Linux users may find that the Alt key has operating system functions M86 E01078 RLATT RLATT APEX2 Editing Tools C Box Lattice Overlay C Single Spot C Circle C None rotate Selection Helpers Select Weak Reflections Select Current Group Invert Selection Grouping Tools Current Group IMM Group 1 y Add To Current Group Remove From Current Group Select Visible Groups Group 12 Group 13 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 User Manual M86 E01078 APEX2 User Manual Press the key to add lines between the two you have marked Press the key to remove lines Editing Tools C Box Lattice Overlay C Single Spot C Circle
39. conf mola 12 cl c2 c3 c4 c5 c6 c cH cB sl ol of cl cll mola 6 cd c5 c amp c cB cB cl c2 c3 ol of sl c10 ell mola 5 c8 c9 cl c2 c3 cd c5 c amp c of of sl c10 ell mola 10 cl c2 c3 c4 c5 c6 c cH cB s51 ol of clo cll Figure 9 49 Add instructions in the ins file 5 If planarity and angles between planes are of interest add mpla cards APEX2 User Manual 9 3 7 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 50 Thermal ellipsoids with large hydrogen atoms 3 If the hydrogen atoms in Figure 9 50 are large change their sizes by going to Pref erences gt Atom Preferences in XShell s Menu Bar Atom Preferences Figure 9 51 Atom Preferences tool M86 E01078 APEX2 User Manual 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 o 12 n 22 Figure 9 52 Default atom preferences 4 Change the hydrogen radius to 0 08 and the bond radius to 0 15 to make the hydro gen atoms smaller Click Apply DS ATOM PREFERENCES Element Atom Radius Bond Radius PeriodicTable Ho p 06 p 15 Figure 9 53 Modified atom preferences Figure 9 54 Thermal ellipsoid plot with smaller hydrogen atoms M86 E
40. from the general menu NOTE There are many other features in XPREP that can be accessed from the general menu resolution cutoff recipro cal space plots simulated powder pat terns and a test for merohedral twinning are very useful tools M86 E01078 Examine Data 8 2 1 Under Examine in the task bar click Precession Images The Precession Images module provides an undistorted view of layers of the reciprocal lattice APEX2 generates simulated precession images by finding the appropriate pixels in a series of sfrm images You must specify the images to examine and the zones to calculate Simulated Precession Images 2 To open the File Selection window click 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 18 bd python El xi Look in E C Frames guest ylid_example ex EE s Eg a E matris_01_0009 sftm matrix_01_0001 sfrm 3 matrix_01_0010 sfrm E matrix_01_0011 sftm Es matrix_01_0012 sfrm O matrix 01 fitit 1 12 O matis 02 itttittt 1 12 O matis 03 HHH 1 12 mai 01 QD02 sfm E matis D2 DOOl sm A D ERA matrix Q1 O003 sfrm ls matrix_02_0002 sftm AC BRIT pL l EN matrix 01 OD04 sfrm matrix 01 0005 sfrm matrix _01_0006 sfrm matrix 01 O007 sfrm matrix 01 O008 sfrm 3 matrix_02_0003 sfrm E matrix_02_0004 sfrm Ed matris_02_0005 sftm ls matrix_02_0006 sfrrn E matri
41. iguxer BRUKER ADVANCED X RAY SOLUTIONS APEX2 Version 2 USER MANUAL M86 E01078 6 06 M86 E01078 BRUKER ADVANCED X RAY SOLUTIONS APEX2 Version 2 User Manual M86 E01078 APEX2 User Manual This document covers the APEX2 software program References to this document should be shown as M86 Exx078 APEX2 User Manual O 2006 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 publication 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 perfor mance 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 fitness for a particular purpose No part of this publication may be stored
42. in a retrieval system transmitted or reproduced in any way including but not limited to photocopy photog raphy magnetic or other record without prior written permission 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 Revision History Revision Date Changes 0 2 05 Original release 1 6 06 Revised and expanded for APEX2 Version 2 BRUKER AXS INC BRUKER AXS GmbH BRUKER NONIUS B V ISO 92001 2000 MOODY 5465 EAST CHERYL PARKWAY STLICHE RHEINBR CKENSTR OOSTSINGEL 209 2612 HL DELFT MADISON WI 53711 5373 49 THE NETHERLANDS USA D 76187 KARLSRUHE scu 15250205 DU A TEL 1 800 234 XRAY SEBMANY FAX 31 15 215 2500 CERTIFICATION les M e m TEL 449 721 595 2888 E mail info 9 bruker nonius com 1 608 276 FAX 49 721 595 4587 www bruker axs nl Ey AOGO Mandy lateinationsh inc USA E mail info bruker axs com E mail into brukeracde www bruker axs com www bruiker axe de iv M86 E01078 Table of Contents 1 About This User Manual 0 0 0 no 1 1 1 1 APEX Il Systems for Chemical Crystallography 0ooooooooooooooo 1 1 1 2 Terms and Conventions Used in this User Manual 1 2 1 2 1 Typographical Conventions curd dee ode ne era e AA ee 1 2 1 2
43. integer index 0 25 8 Enter the maximum deviation from integer index cutoff Typically the default is reasonable Press Enter Percentages of reflections in this domain not consistent with lattice types AS SUG Be 2929 Gi dos 0 I 48 9 F 72 5 O 64 3 and R 65 8 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 h 2n 36 3 k 2n 49 8 1 2n 49 3 h 3n 69 1 k 3n 67 2 l 3n 66 4 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 0 A A C 6 M86 E01078 APEX2 User Manual Using CELL_NOW 9 Enter A or just press Enter to accept this cell The program asks for a name for a p4p file Enter the name of the p4p file for this solution in this example domain1 p4p p4p or spin file to write domain to domainl p4p R
44. lt I gt lt sig gt zBg o 000 5853 1259 1400 6759 6 3 5521 869 345 57 2 53 Ue Overall Reym centric Pairs unig Merg lt 2s lt I gt lt 57q gt lt B gt Rsym 0 000 1424 330 428 1370 13 3 7973 527 63 33 2 67 0 020 1 000 Coverage Statistics for ylid om ETC Sel Das sous Angstrms obs Theory Compl Redund Rsym Pairs Palrs Rshell 5igma lt 2 to 1 615 179 150 99 44 f 2f 0 019 1 8 98 89 0 019 103 49 3 95 1 283 332 332 100 00 7 30 0 020 329 566 10 0 024 42 35 2 3 1 121 ars 47a 99 79 7 01 0 021 472 58 4 0 026 29 81 2 2 1 019 618 619 564 84 6 61 0 021 606 97 90 0 030 19 90 4 9 Coverage D 946 768 769 99 87 6 15 0 021 7 45 46 88 0 037 15 78 Fle D 890 909 510 99 89 5 85 0 022 875 96 15 0 045 11 91 2353 3 0 845 1044 1045 99 90 5 56 0 022 992 04 03 0 059 9 13 9 2 0 8059 1192 1196 94 6 5 30 0 023 1118 93 48 0 060 5 08 12 0 D 778 1320 1328 99 40 5 08 0 023 1220 91 87 0 064 6 54 19 2 Dora 1400 1462 95 76 4 69 0 023 1259 86 11 0 06 1 64 12 6 Figure 7 18 Final SAINT Overall Rey and coverage statistics 7 12 M86 E01078 APEX2 User Manual Data Integration and Scaling Unconstrained Unit Cell Refinement 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
45. microscope reticle If the crystal does not appear in the same Crystal displaced position approx 2 ticks to the left 3 1 Use the adjustment screw facing you to remove half of the difference shown in the reticle Figures 5 9 and 5 10 3 2 Click Spin Phi 180 3 3 Repeat steps 3 1 and 3 2 until you are satisfied that the crystal remains in the Figure 5 9 Example error in Y axis same position in the micro scope reticle when rotated by 180 After removing AAA half the error NOTE If the crystal consistently fails to appear crystal displaced in the same position when rotated by approx 1 tick to 180 the position of the microscope the left reticle may need adjustment For more information refer to M86 Exx024 Micro scope Focus and Sample Alignment Figure 5 10 Example error removed by half 5 8 M86 E01078 APEX2 User Manual Crystal Centering and Screening 4 Click Spin Phi 90 Phi rotates so that the X axis adjustment is facing forward Any error in the crystal s position along the X axis will now appear in the microscope Figure 5 12 X axis error after spinning phi 90 5 Center the crystal in the video microscope reticle by making adjustments to the X axis adjustment screw Figure 5 11 Center position X axis adjustment screw Figure 5 13 Centered crystal after X axis adjustments M86 E01078 5 9 Crystal Centering and Screening APEX2 User Manual 6 Alternatel
46. of 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 sleds Do not overtighten the locks 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 click Center to drive to the initial center ing position loosen the crystal mounting screw rotate the crystal to a suitable ori entation and then tighten the screw again M86 E01078 APEX2 User Manual Crystal Centering and Screening 5 3 1 For Kappa APEX Il Systems 1 Click the Center button The goniometer head drives so that its Y and Z translation axes are positioned perpendicular to the microscope The Y and Z axis adjustment screws should be facing the front of the dif fractometer If they are not click Spin Phi 180 Figure 5 7 Crystal initially mounted 2 Center the crystal in the video microscope reticle by making adjustments to the Y and Z axis adjustment screws Figure 5 6 Center position Y and Z axis adjustment screws Figure 5 8 Centered crystal after Y and Z axis adjustments M86 E01078 5 7 Crystal Centering and Screening APEX2 User Manual 3 Click Spin Phi 180 and check that after rotating 180 the crystal appears in the same position in the
47. of tries in the TREF command to 100000 runs until ended by clicking on the STOP button is particularly useful for acentric triclinic structures and for pseudo symmetric structures Table 9 1 Direct Methods presets 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 Raja and the CFOM Struc APEX2 User Manual 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 Structure Solution module APEX2 automatically switches to the Display tab and displays the initial solu tion The next step is structure refinement using XShell Section 9 3 9 2 2 Options for Dual Space Methods Two predefined options are available for the Dual Space method Dual Space methods are good for larger organic molecules and polypeptides More information on Dual Space methods and their use within APEX2 is available from the What s This Help function 9 2 3 Options for Patterson Methods Two predefined options are available for Patter son methods Patterson methods are good for finding heavy atom positions In general Patterson methods favor a small number of strong scatterers More information on Patterson methods and their use within APEX2 is available from the What s
48. sample Describe Specify crystal size color shape etc Center Crystal Perform crystal centering functions Table 3 7 Setup Evaluate S Determine Unit Cell Determine unit cell ms and Bravais lattice type by Table 3 8 Evaluate Transform Unit Cell Transform a unit cell APEX2 User Manual Evaluate P gh Heciprocal Lattice Viewer 3D visualization of the lattice projected in reciprocal space View Images View and analyze diffraction images Table 3 8 Evaluate Collect N Data Collection Strategy Simulate data collection and determine strategy Experiment Sequence editor for data collection experiments Oriented Scans Measure diffraction frames with the crystal aligned along axes Table 3 9 Collect Integrate Integrate Images Integrate diffraction data Table 3 10 Integrate M86 E01078 APEX2 User Manual pg Crystal Faces Determine Miller indices a and distances of single crystal faces Scale Scale intensities and perform absorption correction Table 3 11 Scale Examine Data gt Phase ID optional Display and integrate single and multiple frames Space Groups and Statistics Determine the space group Compare Unit Cells Compare unit cells to find twin laws
49. shortcuts shown in Figure A 6 Clicking on the blue background gives the hints shown in Figure A 7 M86 E01078 APEX2 User Manual RLATT RLATT Keyboard Commands Rotate amp Zoom Onentations UP DOWN rotate along x Fl 100 along a LEFT RIGHT rotate along y F2 0 10 along b INS DEL rotate along z F3 00 1 along c zoom F4 unoriented identity matrix hold SHIFT 4x speed FS user defined orientation 1 hold CTRL 1 4 speed F6 user defined orientation 2 hold SHIFT CTRL 16x speed F user defined orientation 3 Selection Tools FS user defined orientation 4 i SHIFT F5 store user defined orientation 1 SHIFT s add spots to current selection SHIFT F6 store user defined orientation 2 CTRL left click remove spots from current selection SHIFT F7l store user defined orientation 3 UP DOWN LEFT RIGHT move selection tool 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 add slice lattice tool only remove Slice remove Slice lattice tool only PGUP add Extension add Extension lattice tool only PGDN remove Extension PGDN remove Extension lattice tool only hold SHIFT action x 10 ALT left click lock onto spot lattice tool only ALT left click lock onto spot Angle Measurement ALT lock onto spot locking onto all left chck three ca
50. 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 the reflection list e g a wrong detector dis tance or a cell axis is longer than the given search range M86 E01078 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 explanation of the program Read this as it has useful information about what the program is doing Using CELL_NOW APEX2 User Manual CELL_NOW analyses a list of reflections 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 ang
51. 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 Ihe name or IP address of the BIS server computer M86 E01078 D 7 Configuring APEX2 APEX2 User Manual ccdtemperaturerange type tuple of 2 integers default 65 35 Acceptable range minimal maximal of temperatures in deg C for the detector This is used only to indicate a red or a green status light for the CCD temperature in the status window chiralonly type boolean default 0 If set to 1 only chiral point groups will be used at any moment Do not touch colorramp type file name default Colored SCD ICM 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 not set no logfile will be kept componentlcolor type string color name default green The component color variables are obsolete Use groupcolors instead component2color type string color name default blue The component color variables are obsolete Use groupcolors instead component3color type string color name default yellow The component color variables are obsolete Use groupcolo
52. with successful harvesting Table 6 2 Harvest Spots menu items Data Collection Menu Item Function Excluded shells Add edit or delete resolution shells to be excluded from the harvesting pro cess for example in the case of rings caused by ice or amorphous diffractors the three inner resolution shells for water ice appear as defaults Excluded shells are defined by their starting and ending resolution which may be found by placing the mouse cursor on a displayed frame and refer ring to the Resolution A field in the Cursor Position Tab The Reflection Group Combo Box shows a list of reflection groups to choose from For each group the group name and number of reflections in the group are displayed If instead of the number of reflections an entry is labeled empty this indicates Store an unassigned entry Choosing the Reflection Group empty entry creates a new group Combo Box instead of appending to the current one A color is associated with each reflec tion group The color is displayed in the box to the left of the group name The color helps in recognizing a group while navigating through the software Right click to edit or clear groups Save only With this checkbox enabled a spot is reflections that only harvested if it is found on multiple span images contiguous frames Go to the previous step in the unit cell x Heaney determination process Table 6 2 Harv
53. ylid_example plid_example_03_0001 sfrm 473 C SFrames quest ylid exam C SFrames quest ylid exam a C AFrames questylid example ylid example O04 O001 sfrm 713 C SFrames questsylid exam Figure 7 5 Runs list with runs imported APEX2 User Manual 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 Figure 7 6 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 any of the fields in this list to open up the value for editing A stmuc questidata manual yld_ manualylid manua manual ulid manualsulid manual 04 OO01 str Ga B Etstuciguestidata_manualplid_maralplid_marua manual ld manual ld manual 04 struc questdata manualvlid rnanualylid manta CAystucquest data manualvlid manualsvlid manua Figure 7 6 Example of manually editing a run list M86 E01078 APEX2 User Manual Data Integration and Scaling 7 1 1 Check the Refinement Defaults Refinement Options 20x Two buttons on the right hand side of the initial be eee integration window are used to change the Fie ieee Ee default options for refinement and integration AO Intil YZ Box Size 0529 oss fosos Periodic Refi
54. you can r Initial Reflections Total 11243 Unique 1482 Dutlier Rejection High resolution limit 0 1 I lt I gt su ratio for rejection a0 g value 0 0400 Total 11248 Rejected ao Unique 1482 Rejected foo Error Model g value Suggested 0 0296 Use fo 0296 Include the following batches Baches 2Theta Rint ves ross bit fects y Tot 7 1 7 0 0 0229 0 948 0 975 0 933 1 047 0 710610 595 40 5 repeat the entire scaling calculation with that run omitted Uncheck the checkbox next to the bad run and then click Repeat Parameter Refinement l gt 2sigl 2 43 5 0 0218 0 909 0 939 0 947 1 031 0 532741 686 3 38 0 0 0217 0 907 0 965 0 940 1 032 0 6444366 4095 4 0 0221 0 910 0 964 0 936 1 032 06395532 5196 APEX2 User Manual M86 E01078 APEX2 User Manual 7 3 4 Examine Diagnostics 1 Click Finish to produce a series of diag nostic plots Some of these are reviews of the plots that have already been displayed The diagnostics provide valuable insight into the quality of the data and possible problems with the data Click the tabs at the bottom of the screen to view the diagnostic data M86 E01078 Data Integration and Scaling The Scale Variations plot Figure 7 23 shows the overall variation in Scale and R int for the individual frames The Scale plot should be flat for highly absorbing i
55. 0 0224 0 0284 0 0298 0 0321 0 0374 0 0402 0 0513 0 0624 0 0569 0 0685 0 0735 0 0850 0 0699 Rsigma 0 0085 0 0084 0 0084 0 0099 0 0104 0 0108 0 0132 0 0159 0 0161 0 0200 0 0231 0 0289 0 0327 0 0313 0 0412 0 0418 0 0488 0 0560 0 0401 0 0120 Inf 2 23 75 77 97 4 7 08 1377 5 2 23 1 73 75 75 100 0 9 09 575 4 1 73 1 47 79 79 100 0 9 28 447 7 1 47 1 32 sl 81 100 0 9 62 246 1 1 32 1 21 76 76 100 0 9 03 211 7 1 21 1 14 77 77 100 0 9 08 227 9 1 14 1 08 79 79 100 0 3 56 124 2 1 08 1 02 66 36 100 0 7 77 98 5 1 02 0 98 78 78 100 0 7 78 105 3 0 98 0 94 95 95 100 0 7 80 TiS 0 94 0 90 103 103 100 0 7 20 62 5 0 90 0 87 89 89 100 0 6 63 46 5 0 87 0 84 99 99 100 0 6 74 38 5 0 54 0 82 89 89 100 0 6 66 43 1 0 82 0 80 82 82 100 0 6 40 30 6 0 80 0 78 93 93 100 0 6 29 30 8 0 78 0 76 100 100 100 0 6 14 27 1 0 76 0 74 26 28 92 9 4 18 28 3 0 84 0 74 425 42 99 5 6 24 33 2 Inf 0 74 1482 1486 99 7 7 57 199 6 Merged A lowest resolution 9 18 Angstroms Enter lt CR gt to continue Figure 8 12 Intensity statistics 5 Press Enter to continue 6 Press Enter again to exit to the main XPREP menu M86 E01078 363 outliers downweighted Examine Data 8 1 3 Preparing an Output File 1 In the general menu choose C to define the unit cell contents A window opens displaying the current for mula Z the density and the atomic volume see Figure 8 13 In this exampl
56. 0 Maximum 0 854 for y O2 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 patameters GooF S 2470 Restrained GooF 2 470 for D 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 at 0 2500 0 3358 0 2419 0 51 A from S1 Deepest hole 0 75 at 0 1606 0 2830 0 2403 0 51 A from S1 THEE EE EHE EE EHE EHE EHE EE EE EE EE EE EHE EE EE EE EE EE EHE ERR ER ERE RE RR RE b RR RR ylid_res75 finished at 11 50 44 Total CPU time 0 3 secs HA A OK Figure 9 22 Isotropic refinement output In the output displayed above note that the R1 value is 0 09 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 assign ments of absolute structure should be confirmed later in the refinement pro cess by including TWIN and BASF cards in the instruction input APEX2 User Manual 3 Click OK to return to XShell The molecule dis
57. 01078 APEX2 User Manual 3 2 Server Functions 3 2 1 APEX2Server APEX2Server is operated on the computer that controls the instrument lt provides functionality for quickly centering a crystal and determining its diffraction quality pa Apri ierre 11 03 gt Simple Sean Were If 0001 ifr z db eh e Ty L tance 0 C ZT het CO Diniga 00 Phe 0 QU D hes UC Ditancrs21 DE 7 retos DET Comcs DIT Phi 00 Chest EL 2 QUO Figure 3 2 APEX2Server s Simple Scans window M86 E01078 Software Overview APEX2Server contains two main modules Align Crystal and Simple Scans see Figure 3 2 APEX2Server is covered in more detail in Chapter 5 Dutanca jaj 10 8 J iTheta p a JL Drags p 4 Phi E icr Sors E Phi C Danga E Scan Flange zm nage wiii zm Exposure Tera 10 VEA mage Sara Uo piens Core Drag Mew dak image on 3 Ph Misses 1015 Wide 210 Dine 5n Software Overview 3 2 2 Bruker Instrument Service BIS BIS acts as a server to the client programs APEX2Server APEX2 and BCP providing a link between the hardware and software Once a connection is established BIS executes hard ware commands sent by the client programs BIS can also be used as a service tool display ing diagnostic messages during operation BIS Bruker Instrument Service 2 0 1 1 14 Dec 2005 a Idle 3 Safety shutter 29 Network Phi de icing Ss Timing shutt
58. 01078 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 Change Part Figure 9 55 Position Label menu Figure 9 56 Positioned labels 6 Convert this image into a high quality jpg file for inclusion into reports by clicking Render in the Windows Tool Bar and choosing Color gt To High Quality JPEG File Structure Solution and Refinement APEX2 User Manual Figure 9 57 Generate JPEG NOTE A message may appear that the font file needs to be defined Please set your font directory for the first time for opengl rendering If this happens click Prefer ences gt OpenGL Preferences and click on the TrueType font For OpenGL Figure 9 58 The final rendered thermal ellipsoid atomic displacement parameter plot In Windows browse to C on xshell fonts In Linux navigate to usr local bin xshell fonts Choose a font 9 26 M86 E01078 Appendix A RLATT RLATT is a very powerful tool for viewing the harvested reflections in a reciprocal lattice This Appendix covers only a few of its features More information on RLATT is available in M86 Exx045 RLATT User Manual 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
59. 14 2 3 3 5 4 2 4 6 4 3 3 3 5 1 5 18 6 23 3 9 3 11 Atom labelling in XShell 9 10 Atomic Displacement Parameters 9 16 Attenuator SMART APEX II 2 7 Audit trails 3 6 Automatic connection to BIS 4 4 Automatic unit cell determination 6 6 AutoStructure 1 1 3 13 Average Difference 7 9 AXScale closing 7 21 B Bad runs 7 16 Base Name 6 8 BCP 3 5 required rights 4 2 Beamstop 2 7 BIS 2 1 3 4 4 2 description 4 3 shutting down 4 6 starting 4 3 Index 1 Index bn config py bn license dat Bravais lattice figure of merit Bruker AXS Service Centers Brukerlnstrument ini C Calibration module Cautions defined CELL NOW Center Crystal module Centric space groups and Intensity Statistics Centroids Chiral compounds specifying in XPREP Chi Squared plots CIF file Client additional computers defined Client and Server Functions Closing Sample alert window Collect data collecting a data set when finding unit cell Collimator Compare Unit Cells Completeness in Strategy module in XPREP Index 2 4 4 D 1 4 5 6 12 6 13 6 13 1 5 3 5 3 14 1 3 C 1 3 12 7 18 A 9 8 3 7 18 9 23 2 8 3 1 4 6 6 23 6 8 2 3 2 7 3 13 6 18 8 4 APEX2 User Manual Computer single computer configuration 2 8 Connection dialog 3 10 4 4 Copy RES to INS 9 6 Correlated frames 6 8 Coverage Statistics 7 11 7 12 Crystal centering 5 1 Crystal Faces B 1 Crystal quality screening images 5
60. 2 EQUIValent Terms eccess senaia a eens os dr ded ano e d ue td 1 2 1 23 Warnings Cautions and NoteS 0 0 00 cc eee 1 3 1 3 Referenced Documentation 000k eee heed ai waa 1 3 TA Atay Sales esc Aveo deed dd eee Ske o SE ee de ed wee 1 4 1 5 APEX2 Help and Technical Support 0 02 ee 1 4 1 5 1 The Whats This Function 0 000 cee ee eee 1 4 Loa Technical SUDDOM uade mctu be eie ta oH Nat Sets artum See eae ew eS a ee 1 5 2 Hardware OVerVIGW p RE LAU EXE REGE RUE Rd UE ade aa ees 2 1 2 4 System COmDODeDlIS seio ue qur fuck nat 2 1 2d APEXIDDOIGGOIOD quio rA se Bo ES e a dre ao o FU AC E EU ERR Ren 2 3 2X ME Cents d T TTCER CER TETTE Ro TETTE 2 3 2 1 3 Radiation Safety Enclosure with Interlocks and Warning Lights 2 8 24 DO CODUDIIGI uu ee pen A dca dense Y ue oed S tabac atu e COR Rog aco E amp 2 8 M86 E01078 Table of Contents APEX2 User Manual vi 2 1 5 Refrigerated Recirculator for the Detector o oo o oooooooooo 2 8 2 15 COMPUTES cener maet baud d oen ded ds au d AU at ose ed 2 8 Zilch ACCOSSOMOS zoom anto SEA A Y 2 9 SoftWare OVELVICW 3 3 3 2 aia id 3 1 3 1 Introduction to Client and Server Functions 3 1 3 2 Server FUNCION Sica A A a a ee 3 3 32d ABPEX2SGIVODLus 19d aaa idas ai iz 3 3 3 2 2 Bruker Instrument Service BIS o o o oooocoooonoononoono 3 4 33 C sHnEFuncliolis ic AI A EA AAA Da dcr ee 3 5 S
61. 4 c 18 264 sigma l needed for a reflection to Store 90 00 B 90 00 30 00 Bs mo Orthorhombic F qualify for indexing Corrections From store From last harvest C Manual Set the resolution range from which Distance nm o Pienti OOO Resolution A spots will be used to index the unit cell Beam Center mm 10 78 Hall 70 00 g bad Reflections must If this checkbox is active overlapping Y Beam Center mm 0 34 Yaw 0 00 i P E be isolated spots will not be used for indexing Methods IV Difference Vectors V Fast Fourier Transform Reflections must If this checkbox is active only spots Least Squares which registered on at least two adja ees span images l i l l cent images will be used for indexing If this checkbox is active spots that have only partially registered on the iS first and e eee d the range from CIR DAN Eee ea pene which they are harvested will not be used for indexing Figure 6 8 Index menu Table 6 3 Index menu items M86 E01078 6 11 Data Collection APEX2 User Manual Menu Item Function Menu Item Function The Unit Cell Combo Box shows a list Finish the sequence of steps in the unit of unit cells to choose from For each Einishs cell determination process beginning unit cell the unit cell parameters are with the current step Perform any displayed as is the unit cell volume tasks that are necessary PI A PICOS Proceed with indexing according t
62. 5 000 2THE TAHIGH 20 000 OMEGALOW 0 000 OMEGAHIGH 0 000 PHILOW 0 000 AXESLIMITS DISTANCE 159 000 2THETALOW 75 000 2THE TAHIGH 20 000 OMEGALOW 0 000 OMEGAHIGH 0 000 PHILOW 0 000 Pais RE b Debug levels Debug level o Detector o Goniometer o v y Exit Send to Help Common commands Hard abort Soft abort Manual mode Filter CHECK and NOOP commands Estimated completion time es sn Clear messages APEX2 User Manual M86 E01078 APEX2 User Manual 3 3 Client Functions 3 3 1 APEX2 Program The APEX2 program is a GUI with multiple plug ins or modules for different aspects of an experiment The APEX2 program includes a sample database that stores relevant data from each step in the experiment Details of the func tions available in the GUI will be explained in more detail later in this User Manual M86 E01078 Software Overview 3 3 2 Bruker Configuration Program BCP BCP is used to configure BIS as well as to pro vide instrument control and alignment tools From the BCP menu see Figure 3 4 default parameters for specific hardware elements can be updated BCP writes these values to the file Brukerlnstrument ini which is read by BIS When changes are saved in BCP BIS automati cally reads in the new values See M86 Exx043 BCP and BIS Installation Notes in addition to the online help within BCP for more infor
63. 6 Stack Bar view In Stack Bar view click one of the Task Bar sec tions labeled Setup Evaluate Collect Inte grate Scale Examine Data Solve Structure Refine Structure Report or Instrument to display only the icons belonging to that section All other Task Bar icons will be hidden M86 E01078 Software Overview Sample Instrument Windows Help JD c l x Er Setup Center Crystal p Evaluate Stack Bar Determine Unit Cell v Transform unit cell i cA i a e Az Reciprocal Lattice Viewer e oe View Images Collect e A Ps t Data Collection Strategy rate Be EN Integrate Images Figure 3 7 Tree View In Tree view sections may be expanded to dis play their Task Bar icons by clicking the plus or minus sign next to the section name Software Overview 3 4 5 Task Display Area The Task Display Area is the main area for tasks user input and selected output This area displays images the reflections used in index ing and observed and predicted diffraction pat terns lt also displays the runs for data collection and solution and refinement Eile Instrument Windows View APEX2 User Manual NOTE In APEX2 Version 2 XShell refinement and XCIF report generation do not use the Task Display Area they open in new windows All other modules open in the Task Display Area of APEX2 s Main Win dow Y ax 0 c q sep Evaluate Crystal Col
64. 6 E01078 Structure Solution and Refinement informacion on All HEDITIS Add Hydrogen atoms Hybridize All Calculate Hydrogens Figure 9 40 Calculate Hydrogens button 4 A warning appears indicating that the hydrogen atoms have been provisionally added and that the final addition with nam ing will take place when the least squares calculations are started Figure 9 41 Click OK Notes Concerning Refinement E3 XSHELL has only assigned atom types Correct labels will be generated during the next refinement cycle Figure 9 41 Hydrogen atom warning Figure 9 42 Model with added hydrogen atoms Structure Solution and Refinement 5 Click the Refine button to launch the least squares refinement program The output window opens and a summary of the results of individual refinement cycles appears GooF S 0 728 Restrained GooF 0 728 for O restraints Mean shift esd 0 693 Maximum 3 778 for y C11 at 19 16 48 Max shift 0 013 A for H118 Max dU 0 000 for C4 wR2 0 0841 before cycle 3for 2389 data and 129 129 parameters GooF S 0 701 Restrained GooF 0 701 for O restraints Mean shiftfesd 0 104 Maximum 0 681 for U13 C4 at 19 16 48 Max shift 0 005 A for H10B Max dU 0 000 for C8 wR2 0 0840 before cycle 4for 2389 data and 129 129 parameters GooF S 0 701 Restrained GooF 0 701 for O restraints Mean shiftfesd 0 043 Maximum 0 265 for y C11 at 19 16 48 Max shift 0 002
65. 8 A 2 phi scan on a poor quality crystal The crystal The spot shape is poor and the spots spot shape is poor and some spots seem split tend to run together The obvious bands on the image suggest that the crystal is nearly aligned along an axis however spots will always apparently run together in a nearly aligned crystal mounting Figure 5 38 is much more convincing proof of a poor quality crystal 5 22 M86 E01078 APEX2 User Manual Crystal Centering and Screening Figure 5 39 A 2 phi scan on a poor quality crystal at plus Figure 5 40 A 360 phi scan on a small crystal The 90 in phi The spot shape is poor and the spots diffraction power of the crystal is small but with are very close together longer exposure times this is clearly a reasonable candidate for data collection M86 E01078 5 23 Crystal Centering and Screening APEX2 User Manual 5 24 M86 E01078 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 Data col lection will continue regardless M86 E01078 Data Collection 6 1 Create a New Sample 1 After starting APEX2 and logging in select Sample gt New 2 Inthe window that appears enter the sample name APEX2 will automatically create a directory for data storage bd New Sample 27x Name ylid example Group Users Folder CAF rames quest ylid_example gt
66. 8 2 1 System Components The system Figure 2 1 and Figure 2 2 consists of the following basic components e APEX II CCD detector e 4 axis Kappa or 3 axis SMART goniometer e K780 X ray generator e Radiation safety enclosure with interlocks and warning lights e D8 controller e Refrigerated recirculator for the detector e Instrument control BIS and crystallo graphic software APEX2 computer e Video microscope e Optional Accessories low and high temperature devices Hardware Overview 0 For both SMART AP external computer E E APEX Il CCD Detector Kappa Goniometer 4 axis Detector I Power Supply gt Refrigerated Recirculator Koen ms en a D8 Controller Figure 2 1 Kappa APEX II system combining Client and Server functionality into a single computer APEX2 User Manual Single Computer EX Il and Kappa APEX II systems this runs BIS APEX2Server and APEX2 ail Il ll o NN TCP IP hub APEX Il CCD Detector f PA D85 Goniometer 3 axis E I I Detector power Supply Refrigerated Recirculator I eL Figure 2 2 SMART APEX II system D8 Controller M86 E01078 APEX2 User Manual 2 1 1 APEX II Detector The APEX II detector is specific to this system Stat
67. 9 91 APEX2 User Manual When automatic unit cell determination is complete the progress list will show a check mark and comments for each com pleted step Figure 6 5 7 Monitor Data Collection 36 images collected Harvested 270 reflection s from 36 image s Indexed 158 out of 270 reflections Found Bravais lattice type Orthorhombic P Refine 6 00 9 09 18 47 90 00 90 00 90 00 zi Figure 6 5 Completed progress list 6 Click the Close button to close the progress list and return to the main Deter mine Unit Cell window The right hand side of the window displays the unit cell parame ters obtained by APEX2 along with options to edit or delete the unit cell and reflection list if you wish to perform additional opera tions in Manual Mode more information on Manual Mode operations is given in Section 6 2 2 M86 E01078 APEX2 User Manual 6 2 2 Manual Mode The Determine Unit Cell Module s Manual Mode functions allow you a great degree of control over unit cell determination Manual Mode con sists of five sections each with its own menu corresponding to the five stages of unit cell determination Collect Data Harvest Spots Index Bravais Refine M86 E01078 Data Collection Data Collection APEX2 User Manual Collect Data Menu Item Function mace Location Location where collected frames will be g saved C Fames guestyid esame T Text string that is ap
68. A for H11 amp Max dU 0 000 for C4 wR2 0 0840 before cycle Sfor 2389 data and 2 129 parameters GooF S 0 700 Restrained GooF 0 700 for O restraints R1 0 0281 for 2262 Fo gt 4sig Fo and 0 0296 for all 2389 data wR2 0 0840 GooF S 0 700 Restrained GooF 0 700 for all data R1 0 0289 for 1418 unique reflections after merging for Fourier Highest peak 0 23 at 0 8218 0 5646 0 1540 0 68 A from C2 Deepest hole 0 19 at 0 1976 0 5182 0 0223 1 26 A from C5 FEEEE EEE EEE EEE EA EEE EEE EEE EEE 2 2 f 2 2 c c c c c c 2 c c c f c c c c c c f f f c f cf cc cc ccc ccc A A vylid Om finished at 19 16 48 Total elapsed time 0 9 secs lazccccccccccccccc cc EF EF c 2 2 2 c 2 C c c c c cc c ccc cc CSS EF EF EP EPEFEE E Figure 9 43 Refinement results The value for R1 0 0281 is typical for an aniso tropic refinement with riding hydrogen atoms and a data set measured to 0 75 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 APEX2 User Manual Figure 9 44 Difference peaks in a well refined model M86 E01078 APEX2 User Manual 9 3 6 Final Refinement for Publication Obtain a view that is much easier to interpret
69. B 11 Face 1 3 2 is incorrect 1 Inthe Face List select the HKL 1 3 2 2 Right click and select Remove The face is removed from the list and the model is improved Figures B 13 and B 13 NOTE Alternatively you can select Clear List to start over or Add and Edit to define your own faces and see where they Figure B 13 Face 1 3 2 removed appear on the crystal M86 E01078 B 7 Face Indexing B 4 1 Scaling With Face Indices When all faces are defined APEX2 has accurate crystal dimensions as shown in the bottom right hand corner At this point you can exit the Face Indexing module and proceed with scaling In the Scaling module be sure to select Numerical Absorption Correction From Face Indices under the Setup tab see Section 7 3 1 APEX2 User Manual M86 E01078 Appendix C Using CELL NOW CELL NOW is an extremely powerful tool for determining unit cells for difficult crystals It 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
70. ELX HELF 4 format file name hkl then tries to find name spin or name p4p to extract the cell dimensions and their esds xprep namel name2 reads namei hkl and name2 p4p or name2 spin Ln on the command line allocates space for 1000000n data default n 4 11249 Reflections read from file ylid hkl Mean I sicgma 20 49 Lattice exceptions P A B C I F Oby Rev All N total 5634 5622 5620 5623 3435 7497 7501 11249 0 5157 5089 5194 5096 7720 6834 6834 10243 0 224 9 214 3 211 3 225 4 216 9 223 9 224 6 220 3 20 7 19 7 20 9 20 5 20 4 20 5 20 5 20 5 N int gt 3sigma Mean intensity Mean int sicma Lattice type P A B C I F O obv R rev rhomb on hex axes Select option P i 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 b cC the original and reduced cells are the same Figure 8 3 Press Enter to search for a higher symmetry cell APEX2 User Manual Current dataset ylid hkl Wavelength 0 71073 Chiral Original cell 5 949 9 018 18 353 20 00 90 00 90 00 Vol 954 6 Esds 0 000 0 000 0 000 0 00 0 00 0 00 Cattices P Current cell 5 949 9 018 18 353 90 00 90 00 90 00 Vol 954 6 Matrix 1 0000 0 0000 0 0000 0 0000 1 0000 0 0000 0 0000 0 0000 1 0000 D Read modify or merge DATASETS C Define unit cell CONTENTS P Contour PATTERSON section
71. Files btt dd Sn 7 14 7 3 2 Parameter Refinement 0 0 0 0 0 ce eee eee 7 15 7 3 3 Error Model Refinement 0 0 0 0 ees 7 16 734 Examine DIAQNOSIICS sg ue uite ara a xe Deor RC 7 17 Fo Eod ue o a Sosa bans dard loe que rs tarde fai ts iter ues 7 21 EXamine Dala danita A a RE 8 1 8 1 Space Group Determination With XPREP 0000 eee 8 1 8 1 1 Determining Space Groups 0 0 cc eee 8 2 9 12 JRCUCCHON SIAUSUCS s aces dq doe RR eee Habe ee ALA 8 4 8 1 3 Preparing an Output Flete nieri tien iea aa a eee 8 5 8 2 Simulated Precession Images eee 8 7 Structure Solution and Refinement 9 1 OA QUOPVIGW Dutra S dcs an ca ora adios ae 9 1 92 Solve the SIFUCIUEG 2 urine RAD CE I REC RC A RUNE UE aa da de 9 2 9 2 1 Options for Direct MethodS o oooooonernonno eee 9 3 9 2 2 Options for Dual Space Methods 0 0 neon 9 4 9 2 3 Options for Patterson Methods llle 9 4 9 3 Refine the Structure with XShell leeren 9 5 M86 E01078 APEX2 User Manual Table of Contents 9 3 1 Label tine ATOITIS d etx eae ds aha wie GA a eae Y 9 10 9 3 2 Reine the Model 2c pete aia Pee RES oe hOB ANSE EES E 9 13 9 3 3 View Atomic Displacement Parameters Thermal Ellipsoids 9 16 9 934 SIE TORIS Sec Pa aduer adi Rar det a ude a Graded ares wt eaten aa ne ae ea 9 18 93 5 Add TIYGIO
72. GeN AIOMS atraido ened EE irf gr 9 20 9 3 6 Final Refinement for Publication 0 0 0 0 ccc eee 9 23 9 3 7 Generate an Atomic Displacement Thermal Ellipsoid Plot 9 24 Appendix A HMEATE ovina dai e A 1 ALL Open RLA TT 005000 dos A E A we e in A OA al el I A 1 A 2 Onen ng VIEWS bailar ais A is ii ii Sa ae A 5 A3 IDETINING GIOUDS 0 ker heb pus da dad a dcs A 18 A 4 Measuring Distances and Angles 0 0oooooooonorornar A 20 A 5 Wing A p4p File us uuu una tt A Re ato No a anro cx ns A 22 Appendix B Facelndexing eleeerlles e B 1 B 1 Start the Crystal Faces Module 0 0 cee B 1 B 2 Collect a Video Zip Stream ouv A ee E m CAE ROO ewe ERE eis B 2 B 3 Using the Face Indexing Module leelelseleeees B 3 Bor Set VIEW ODIONS uda satan adhe a A B 4 B 3 2 Specify Crystal Faces i a idan ee b d opo a cei acd B 5 E 3 5 Eding the Face EISE uu ex a geo ERE etra E Qus Ua Robo Aa B 7 B 4 Scaling Willi Face Indl68S comica RIO DEO ILEEAUEEX eee Lakes See Eu IP E B 8 Appendix C Using CELL NOW eere C 1 M86 E01078 ix Table of Contents APEX2 User Manual Cal Running CELE NOW caderas ERE AA A AR AA C 1 C2 CELE NOW OUIDUEL 2 sui rr ds ia C 9 Appendix D Configuring APEX2 000 es D 1 D 1 Global User and Sample specific Variables D 1 D2 Python Code Examples 92454 24 p
73. LATT 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 for next domain S quit 0 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 12 692 11 016 14 648 89 70 90 95 90 00 Figure of merit 0 643 0 1 69 7 SOZ 97 5 0 3 98 4 Orientation matrix 0 00598966 0 00402327 0 06807401 0 03367313 0 08180340 0 00480114 0207099302 0 03914713 0 00221035 Rotated from first domain by 179 7 degrees about reciprocal axis 1 000 O lt 001 0 032 and real axis 1000 000 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 E01078 Cag 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
74. OL SAPEXZSPEOOEOI S idi dicatae a a a ad E 3 5 3 3 2 Bruker Configuration Program BCP 000 cece eee o 3 5 3 3 8 The Sample Database anaana ccc eens 3 6 34 The APEX2 GUI uunc eap ice ura ee odeur ta ale a epee ee cca se ees 3 7 Su Ge Bab vaca cg See deeds fap ede ORE Bebe IS Ge ee nr tsb o act us Ros CR ay kn a ad DDR 3 8 See A we ee ek ais a mean EA Sed tear ce wives O 3 8 S49 TOONCON 22d 010 sc uted mee a aA deste diosa Sede QE Pn a ure Be Maree a 3 11 2344A ASK Dal sesan obsdn Sp obtu eee erat 3 12 345 Task Display AICO 2 ud o ane Bee Rat wh od ol Me hee D CR ut wc 3 16 Program Startup and Shutdown 4 1 41 Access to BCP and APEXZ iii os max ei a De ew a Cod 4 2 4 2 Online and Offline Operation 0 0 0 ees 4 2 A A A Dee ee 4 3 4 3 1 Starting Bruker Instrument Service BIS o o ooooooooooo 4 3 42 SUAMIING A Ae arcada AAA 4 3 4 4 License Considerations siii a E a A a A 4 5 M86 E01078 APEX2 User Manual Table of Contents AS SNUG OW M A RA ARA RA O E 4 6 45d ihutingDOoWHDmTAPEX2S uu x road ee a as 4 6 4 52 ONNO DOWN Bloc a3 errar EA AR 4 6 5 Crystal Centering and Screening LL 5 1 5 11 Start APEX2SOIVO ia EAE Eu ax m exul RD E Ro Rc o ee a ae 5 1 5 2 Mount the Goniometer Head on the Instrument 5 2 5 3 Center the Crystalis saei gai ad daa 5 6 5 3 1 For Kappa APEX Il Systems
75. Oriented Scans module 3 12 P PAP files CELL NOW output C 8 importing and exporting 3 9 writing from RLATT A 22 Patterson Methods 9 4 Peltier devices 2 8 Phase ID 1 1 3 13 Pink fields invalid entries 3 8 Planarity and mpla cards 9 24 Plotting lines drawing 3 11 Power settings recommended maximum 2 6 Precession Images 3 13 8 7 Publication Generate ACTA CIF Information File 9 23 refinement in XShell 9 23 Python D 1 Q Q peaks unassigned peaks 9 3 9 9 9 16 9 20 M86 E01078 Index H R int variations 7 17 vs resolution 7 18 H1 value 9 14 9 15 9 22 Reciprocal Lattice Viewer 3 12 A 1 Recirculator for detector 2 8 Redundancy 6 18 in XPREP 8 4 Referenced Documentation 1 3 Refine in Scale module 7 15 when determining unit cell 6 14 with XL 9 6 Reflection Group Combo Box 6 10 Reflection Statistics 8 4 Relabel peaks 9 11 Resolution circle drawing 3 11 Restore archived samples 3 11 Rint 8 4 RLATT 3 12 measuring distances and angles in A 20 overview A 1 RMS XY 6 15 Rshell values in SAINT output 7 12 Rsigma 8 4 Rsym overall 7 11 7 12 R values 7 15 7 16 Index 5 Index S SADABS Safety issues SAINT SaintChart SAINTplus Sample database automatic startup and shutdown default account save or discard changes structure Sample Menu Login New Save sample Scale module overview Scale Variations plot Scaling Server defined Shutter safety shutter toggling Simple Scans
76. Precession Images Create precession images based on measured frames Space Group Determination Run XPREP prep Table 3 12 Examine Data M86 E01078 Software Overview Examine Data 150 Find a Reflection Find a reflection in measured frames Table 3 12 Examine Data Solve Structure AutoStructure optional Automatic solu tion and refinement with minimum user input Structure Solution Solve the structure View Molecule Visualize the molecule in 3D Table 3 13 Solve Structure Refine Structure Structure Refinement Run XP XL or XSHELL Table 3 14 Refine Structure Software Overview Generate Report Run XCIF to generate a report Table 3 15 Report System Calibration Make calibration measurements Unwarp and convert images Convert frames between formats Play Tic Tac Toe Play a game of Tic Tac Toe Table 3 16 Instrument APEX2 User Manual M86 E01078 APEX2 User Manual Stack Bar And Tree View Right click in the Task Bar to choose one of two views Stack Bar or Tree View Sample Instrument Windows Help JD c W l e x Collect Integrate Solve Structure S Auto Structure Structure Solution S View Molecule Tree View Refine Structure Figure 3
77. RLATT User Manual M86 Exx087 APEX2 and PROTEUM2 Installation Notes M86 Exx092 User Manager User Manual M88 Exx099 License Manager User Manual Table 1 3 Referenced Documentation About This User Manual 1 4 X ray Safety X ray equipment produces potentially harmful radiation and can be dangerous to anyone in the equipment s vicinity unless safety precautions are completely understood and implemented All persons designated to operate or perform maintenance on this instrument 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 required to accurately monitor their exposure to X rays by proper use of X ray dosimeters For safety issues related to operation and main tenance of your particular X ray generator dif fractometer and shield enclosure please refer to the manufacturer s operation manuals or to your Radiation Safety Officer The user is responsible for compliance with local safety reg ulations APEX2 User Manual 1 5 APEX2 Help and Technical Support 1 5 1 The Whats This Function Context based help is available at any time within APEX2 by simply clicking the What s This icon K Figure 1 1 What s This icon After clicking the icon click any window control or field within APEX to obtain detailed help in a pop up window M86 E01078 APEX2 User Manual About This User Manual 1 5 2 T
78. T goniometer components M86 E01078 2 5 Hardware Overview 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 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 Xayg 0 710730 A for Mo radiation Aayg 1 541838 A for Cu radia tion emitted from the X ray source and passes it down the collimator system APEX2 User Manual 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 e 50 kV 40 mA for Mo radiation e 40 kV 30 mA for Cu radiation 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
79. TL ylid_Om in P2 1 2 1 2 1 CELL 0 71073 5 9617 9 0391 18 3938 90 000 90 000 90 000 0 0002 0 0003 0 0007 0 000 0 000 0 000 X Y 0 5 Z SYMM X 0 5 Y 0 5 Z APEX2 User Manual Check that there is a reasonable formula in the formula window 1 Ifyou have a correct formula in the formula field then you are ready to start a normal direct methods run 2 Ifthe formula is incorrect change it and press Enter The input file will be updated Base vid 0m Formula fer 1H10025 Statistics Reflections sort Unique as Rejected aac Observed 346 Rin 232 Obseved 85 z Observed neama E in 1 1 1 24 Shell Method e Direct 1 y C C Jv Structure Expansion Computing Effort log scale E Solve Structure STOP Reset Exit Figure 9 1 Default Solve Structure view M86 E01078 APEX2 User Manual 3 Click Solve Structure to start the direct methods calculations The upper window displays the Q peaks of the initial model and the text area displays the progress of the calculations Fig 0096 1421 1000000000110102100030021 65 255 Phi sets mbr beet ie code 1627117 wth CFOM 00550 Founer and pesksemch PE 0135 14 aom ond A55 E values Founer and pesk sesch RE 01195 14 aora ond 455 E vues SORTER EEE E TEETH EERE EEE ET ETO ria arrarprnrrntrararrarranrarisntss Figure 9 2 Structure Solution output M86 E01078 Structure Solution and Refinement
80. Video Source prompt 2 Because we have not yet taken a video zip stream for this crystal click Acquire New A save dialog box defaulted to your current project directory appears APEX2 User Manual ba Save Yideo File El Ea File name EXAMENES File type Video Zip Stream vzs y Cancel Figure B 2 Save Video File dialog 3 Click Save If VIDEO is not open it will open with a progress bar showing the video zip stream collection When the video zip stream is fully collected the Face Indexing initial view will appear Figure B 4 osm S 5 4 m 4 Al Acquiring video H i Figure B 3 Progress bar M86 E01078 APEX2 User Manual B 3 Using the Face Indexing Module The Face Indexing module uses a dial at the bottom of the screen to step through the images of the crystal and a tool called the T tool to define faces The Face List shown on the right displays the faces you have defined for the crys tal and their distance from the instrument center bM APEXZ 2 1 RC7 User guest Sample face indexing example Licensed to Applications Lab at Bruker AXS Crystal Faces Sample Instrument Video Windows Help Iv Show T tool Max Miller index 2 3 i O Crystal Face i Miller Indices 1 E EE H Distance mn 00 IV Show possible face normals Dut of plane angle deg 0 70 FF Snap to possible ace roma Instrument Figure B 4 Face I
81. X2 User Manual 432 eZ 2ll 654 668 109 299 Od wie UZ M86 E01078 APEX2 User Manual Using CELL_NOW 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 If 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 conventional cells FOM within 0 2 a gamma volume and lattice type for potential unit cells IL ALO 1993 124692 ATOL 14 049 SFs 70 MU 9D 9000 2047 7 P Cell tor domain s 127592 1 15 016 14 648 O9 20 95 90 00 ErIgqure Of merrt 0 619 SOLES 6025 TLOVE I es Eua CELL NOW has identified a domain that fits 85 3 of the data with a tolerance of 0 2 M86 E01078 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 0 00164333 0 003597404 0 068 16319 0 03417112 0 08170117 O 00365047 007098812 O208 940336 0000990306 Maximum deviation from
82. a RR EE Eau Aag Rd xc e bes D 1 lj ec eL Index 1 M86 E01078 1 About This User Manual 1 1 APEX II Systems for Chemical Crystallography Bruker AXS Kappa APEX II and SMART APEX Il systems are the newest members in the Bruker AXS product line of instrumentation for single crystal X ray diffraction These systems provide the tools for complete small molecule structure determination The APEX2 software features a redesigned start to finish graphical user interface GUI along with the optional Phase ID and AutoStructure software modules The Auto Structure module simplifies structure determina tion more than ever before M86 E01078 The hardware features the APEX Il CCD detector with four port readout of a 4096x4096 CCD chip radiation safety enclosure system and a choice of two goniometers The Kappa APEX II system features the Kappa 4 axis goniometer The SMART APEX II system is an enhanced version of the SMART APEX fixed chi system 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 0 75 resolution data allows easy refinement of the hydrogen atom positions and determination of the absolute structure of the crystal About This Us
83. ailable through the Menu Bar Icon Description Lj Create a new entry in the sample database Open an existing entry in the sample data base Save the current information to the sample database Open the dialog for restoring a previously archived sample Open the dialog for archiving the current sample x e 9 amp E WV Delete samples from the database k What s this Context sensitive help Table 3 5 Tool Icon Bar Menu Bar shortcuts M86 E01078 Software Overview Other icons on the Tool Icon Bar are visible only when a frame is displayed Icon Description Open a frame Select the first frame in a run Select previous frame Sequentially display frames in reverse as a movie If displaying frames as a movie stop the movie Sequentially display frames as a movie Select next frame Select the last frame in a run Adjust the rate of display when viewing frames as a movie Go down one run Go up one run Draw a resolution circle Draw a plotting line Change the part of the frame displayed while zoomed in Select a region of the frame Software Overview 3 4 4 Task Bar The Task Bar provides menus for all of the functions available in the APEX2 Suite NOTE If the Task Bar cannot be seen there is no open sample Click Sample New or Sample Open to open or create a new
84. an angle in degrees for an aligned image overlapcolor type color string default red Color used for overlapping predicted spots overlaycolor type color string default green Color used for predicted spots peakradiusfactor type floating point default 2 2 How many times the single sigma spot radius should be used as integration radius Do not touch M86 E01078 D 11 Configuring APEX2 APEX2 User Manual planes type string default Okl h01 hkO 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 default rotation direction of axes productline type string default ANY A selection of the features in the program suite based on the type of application we re running ANY or ALL all products SCD single crystal XRD powder XREF fluorescence protectedvariables type map default protectedvariables 1 autoconnect 1 A selection of variable names and a lim
85. and for optional attachments such as the optional low temperature attachment Timing incident Peamstop Shutter Beam Safety Collimator Goniometer Sealed X ray Shutter Tube APEX II Detector Monochromator 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 2 4 M86 E01078 APEX2 User Manual Hardware Overview SMART APEX Il 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 addi tional mounting ring for accessories such as the video microscope and optional low temperature attachment The 3 axis system incorporates a fixed chi stage with a 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 Beamstop Rotary Shutter Incident Beam and Attenuator Fixed Chi Goniometer Collimator Assembly Safety Stage Head Shutter APEX II N i C Sealed X minum cm ou Sealed X ray Monochromator D8 Goniometer 3 Figure 2 4 SMAR
86. andle the multiple orientation matrices cor rectly There is no longer a need to use the standalone SAINT program C 10 M86 E01078 Appendix D Configuring APEX2 The APEX2 Suite includes the ability to custom ize many features of the program Most customi zations 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 The following is a collection of examples of pos sible changes to the configuration files for APEX2 and PROTEUM2 These files control the look and feel of the GUI D 1 Global User and Sample spe cific Variables Configuration variables the system administrator wants to set globally for all users go into a file called bn config py that resides in C for Win dows 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 M86 E01078 SUserProfiles to find out where the user ver sion 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 indivi
87. ation The APEX2 Suite suggests a resolution cutoff In this case we will change the selected value to 0 75A Resolution Limit 0 750 Figure 7 2 Resolution Limit parameter 3 On the right hand side of the window are two buttons for defining the data collection runs to be integrated Refinement Options Integration Options Find Runs Import Runs from Experiment Start Integration Figure 7 3 Find Runs and Import Runs from Experiment buttons M86 E01078 Data Integration and Scaling The Find Runs button is used to browse to the set of runs to be integrated This button is normally used when the data collection is fin ished The Import Runs from Experiment button determines the runs to be integrated from the experiment that has just been submitted Using this button allows you to start integration while the data is still being collected NOTE When integrating while collecting data the SAINT integration module will inte grate all of the data currently measured and then wait for the next image inte grate that wait for the next etc 4 Click Find Runs The Find Runs window Figure 7 4 opens Usually the Find Runs window has the correct directory and base name as the defaults If these are not cor rect then use the Browse button to find the runs for the experiment of interest The window pane on the right side displays all of the runs available in the current dire
88. c tory Any combination of runs may be selected by simply checking the check boxes next to the groups and clicking OK Data Integration and Scaling bal python 24x E C Frames quest ylid_example a ef EE s sg Look in Es matris 01 DOD1 sfrm e matrix O1 O002 sfrm 3 matrix 01 0003 sfrm 3 matrix 01 0004 sfrm E matris 01 0005 sftm e matrix O1 OO06 sfrm Es matrix 01 0007 sfrm E matrix_01_0008 sfrm E matrix 01 0009 sfrm E matris 01 0010 sfrm Directory Cancel Directories File type 3 matrix_01_0011 sfim 3 matris 01 0012 sftm e matrix_02_0001 sfrm E matrix 02 0002 sfrm E matri 02 0003 sftm E matris 02 0004 sftm 3 matrix 02 0005 sfrm E matrix 02 0006 sftm Es matrix 02 0007 sfr E matris 02 0008 sfrm E matris 02 0008 sfr gt O matrix O1 i 1 12 O matrix 02 tit 1 12 O matrix 03 Si 1 12 vylid example O1 fti 1 vlid example 02 HHHH 1 vlid example 03 HHHH 1 vlid example 04 fif 1 Figure 7 4 Find Runs window o 64 84 473 719 4 Both the Import Runs from Experiment and the Find Runs buttons generate a list of runs as in Figure 7 5 Setup Y Starting Image Filename C AFrames questylid example ylid example O1 O001 sfrm B4 Dutput Filename C AFrames quest ylid exam C Frames quest ylid_example ylid_example_02_0001 sfrm 84 C Frames quest
89. cation M86 E01078 Hardware Overview e The beamstop catches the remainder of the direct beam after it has passed the crystal 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 colli mator support assembly that has been pre cisely aligned to guarantee that the X ray beam passes through the center of the goni ometer Video Microscope The video microscope an essential part of the system allows you to visualize the crystal to optically align it in the X ray beam It also allows you to measure the crystal s dimensions and index crystal faces with APEX2 s Face Indexing feature The microscope 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 s phys ical dimensions 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
90. ck to the left Crystal displaced approx 2 ticks to the left de e r A Figure 5 26 Example error removed by half Figure 5 25 Example error in X axis 4 Click Spin Phi 180 Remove half of the dif ference with the adjustment screw that is facing you Click Spin Phi 180 again 6 Ifthe crystal is centered click Spin Phi 90 If the crystal is not centered adjust to remove half of the difference and click Spin Phi 180 Repeat until the crystal is cen tered Click Spin Phi 90 8 If centered adjust the height If not cen tered repeat steps 3 through 7 until it is centered M86 E01078 5 15 Crystal Centering and Screening APEX2 User Manual 9 Click the Left button Adjust to remove half of the difference Adjust the height a E E E E E E E E E E f E Figure 5 27 Height adjusted Figure 5 28 Left position Figure 5 29 Check height in left position 5 16 M86 E01078 APEX2 User Manual Crystal Centering and Screening 10 Click the Right button Adjust the height 11 If a height adjustment was made in step 6 Adjust to remove half of the difference 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 Figure 5 30 Right position Figure 5 31 Check height in right
91. ction 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 Lattice Overlay C Single Spot C Circle None rotate Selection Helpers Select Weak Reflections Select Current Group Invert Selection Grouping Tools Current Group MA Group 1 Add To Current Group Remove From Current Group Select e Groups 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 E01078 A 13 RLATT APEX2 User Manual Click 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 Lattice Overlay Single Spot C Circle None rotate 211 Selection Helpers Select Weak Reflections Select Current Group Invert Selection Grouping Tools Current Group EE Group 1 y Add To Current Group Remove From Current Group Select Visible Groups Deletion Helpers Delete Selected finalized at save Delete Non Visible finalized at
92. dancy and Time for all of the available runs It is almost never necessary to let the Data Collection Strategy module run to completion Typically it should be stopped when completion is greater than 99 and the time is close to what is desired M86 E01078 APEX2 User Manual 100 10 80 ES 8 i5 m jm 2 g 2 D a 4 E Q O 20 2 0 100 10 80 3 8 Es 60 c o CE 2 a 40 d 5 zl E Q R 4 O 20 Time h Figure 6 13 Completeness and Redundancy chart In the YLID example shown in Figure 6 14 the Completeness is 99 76 and the Time is approximately 2 33 hours M86 E01078 Data Collection NOTE Time estimates are approximate They depend on the number of rescans gen eral instrument overhead backlash com pensation etc If estimated times are consistently longer or shorter modify the COSMO hardware profile Current Target Priority Completeness 100 00 iono 100 a Redundancy 5 44 50 00 ls 4 Time h ampo fo 3 Strategy Best in 2 hours xy Figure 6 14 Strategy Status and Priority control 4 Click in the Execute field A list of options appears Click Sort Runs for Complete ness Execute Refine Strategy Sort Runs for Completeness Figure 6 15 Click Sort Runs for Completeness Data Collection APEX2 User Manual 100 NOTE If for some reason it is necessary to start 10 over change the distance slightly by 80 0 02 for example and pr
93. dual values and global and individual values are replaced by sample specific values D 2 Python Code Examples In the following text e Red denotes comments that result from comments e Green denotes comments between triple quotes e Black denotes actual Python code Examples of configuration changes Configuring APEX2 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 end of commenting out a section with triple s Pound or Number starts a simple comment This can be anywhere on a line The default color scheme for the image display 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 Cibnisrciguilintensitycolormaps Linux usr local bn src gui intensitycolormaps This is how user positions can be defined userpos1 name Zero Q dx60 type n dx 60 0 theta O omega O chi O APEX2 User Manual M86 E01078 APEX2 User Manual Configuring APEX2 phi 0 0 FIf you want angles other than zero the import projtls and del projtls must be used import projtls userpos2 name Chi45 0 dx90 type n dx 90 0
94. e the for mula is incorrect and Z has been set to six to try to achieve a reasonable density and atomic volume Since this formula is incor rect it must be modified now The correct chemical formula for the YLID crystal is C 1 H49O 3 At Select option do not accept the default answer of E Type in F to enter a new for mula In response to the question Enter For mula type the correct formula C11 H10 O2 S1 and press Enter 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 molecules higher for inorganic compounds and that the atomic volume is around 17 or 18 Sig nificant variation from the expected values may indicate an incorrect molecular for mula or missing counter ions or solvates The values at the bottom of the window look fine for the YLID Press Enter to accept Examine Data Current dataset ylid manual Om hkl Wavelength 0 71073 Chiral Original cell 5 957 9 027 18 366 20 00 20 00 20 00 Vol 987 7 Esds 0 001 0 001 0 002 0 00 0 00 0 00 Lattice P Current ceris 5 957 9 027 18 366 20 00 20 00 20 00 Vol 987 7 Matrix 1 0000 0 0000 0 0000 0 0000 1 0000 0 0000 0 0000 0 0000 1 0000 Crystal system Orthorhombic Space group P2 1 2 1 2 1 19 chi Laue 3 Formula C11 H10 O2 51 Formula wt 206 25 2 4 00 Density 1 387 At vol 17 6 F 000 432 00 Mu rm 1 0 30 D Read modify or merge DATASETS
95. e 8 20 Progress bar 5 Use the simulated patterns to check space group symmetry see Figure 8 21 Figure 8 22 and Figure 8 23 and to find signs of twinning Figure 8 24 M86 E01078 APEX2 User Manual Examine Data Figure 8 21 The Okl plane for the test YLID Figure 8 22 The hOl plane for the test YLID M86 E01078 8G Examine Data APEX2 User Manual Figure 8 23 The hk0 plane for the test YLID Figure 8 24 A plane from a rotationally twinned crystal showing the two lattices 8 10 M86 E01078 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 Om ins and ylid Om hkl M86 E01078 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 9 2 Solve the Structure The process of obtaining an initial model of the compound is started by clicking in the Task Bar on Solve Structure and then on Structure Solution This opens the Structure Solution module nstructions Y Listing Y Results V Structure View TI
96. e Statistics i L Harvested reflections O Completeness and redundancy iC Bijvoet pairs 3 14822e4 003 3 12990e 003 New orientat ion ISen E Frames guest y1 id_example work ylid_Om p4p Refine Structure End global unit cell refinement 05 23 06 10 08 33 ye Connected Is Integration in Progress r vr b Stop Integration Close Figure 7 15 SaintChart view 7 8 M86 E01078 APEX2 User Manual 7 2 1 Monitor the Progress of the Integration Change the text area by clicking and dragging on the line between the text and image areas You can also expand the windows to fill the available image area by clicking Chart gt Tile B in the Menu Bar To the right of the image area are a series of checkboxes that select the displays Click the checkboxes to add or remove displays Average Difference Errors in X Y and Z should be small less than 1 pixel and should not vary during the integra tion of a run Large variations indicate problems with slipping crystals misalignment of the instru ment or other problems Spot Shape Profiles by Detector Region Look for spot shapes that are well contained within the box Split spot shapes indicate diffrac tion from split crystals or twins M86 E01078 Data Integration and Scaling Spot Shape Correlation the Spot Shape Correlation graph is the best indicator for a successful integration After initial passes during the actual integration one expects a high correlat
97. e _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 ORII ORIZ ORIS GEROES ADCOR CELL ORTIZ OR LA ORTS2 ZAEROEBSZ ADCORZ This will eventually trigger SAINT to treat this data set as a twin FILEID SAINT V6 43A 4 00 06 19 03 09 36 24 mraa SITEID RufM Ruf TITLE RCpCrC12 nTHF n CHEM CAO0H58CE2CIA4O02 CELL 2 26908 T0061 14 6480 Ge TULL 90 9494 90 70010 2047 0695 CELLSD Bau 0 20022 0 0029 0 0300 0 0500 Qu QD 1 024 ORT 04001643376 0 003574040 0066 153156 ORTZ Oe DSA ILLES 008170167 0 003850471 ORT OL O07 0956722 0039405379 VL0009603 61 ZEROS 0 0000000 0 3249754 0 0041494 0 0000 0 0000 0 0000 ADCOR 209302 00047 Os DOS OO 00125 O09 37 CELL2 2 09 109 A O oN 14 6480 So OL 90 9494 90 0010 2047 695 CELLSDZ 020025 9 0022 0a 00279 0 0300 0 0300 0 0300 1 024 ORT12 0000989060 0 004023272 0 068074010 ORTZZ sp oU EIA 0 081803404 0 004801138 ORT32 Q0709990Zl O 2039147127 0 002210349 ZEROS2 Q 0000000 0 3249754 0 0041494 0 0000 0 0000 0 0000 ADCOR2 249902 0 0047 0s 0003 08 039 DOT DOS SOURCE Mo Uc LOS D T0930 Ded 2400000 204 00 40 0 M86 E01078 Qs Using CELL_NOW APEX2 User Manual NOTE SAINT users should be aware that APEX2 Version 2 can import p4p files created with CELL_NOW and the Integrate Images module will h
98. e default file name an input file for the structure solution module is created and displayed on the screen and the program asks Do you wish to over write the intensity data file ylid manual Om hkl Since the file name has been changed this question must be answered with a y see Figure 8 16 M86 E01078 APEX2 User Manual Select option F Output file name without extension vlid manual Om ylid_manual_Om File ylid manual m ins set up as follows TITL ylid manual Om P2 1 2 1 2 1 CELL 0 71073 5 9573 9 0270 18 3664 90 000 90 000 90 000 ZERR 4 00 0 0005 0 0008 0 0019 0 000 0 000 0 000 LATT 1 SYMM 0 5 X Y 0 5 2 SYMM X 0 54Y 0 5 2 SYMM 0 5 X 0 5 Y Z SFACCHOS UNIT 44 48 8 4 TEMP D TREF HELF 4 END Do you wish to over write the intensity data file ylid manual Om N y Figure 8 16 The input file for structure solution and a final question 8 Exit XPREP see Figure 8 17 Press Enter to exit the program D Read modify or merge DATASETS C Define unit cell CONTENTS P Contour PATTERSON sections F Set up shelxtl FILES H Search for HIGHER metric symmetry R RECIPROCAL space displays 5 Determine or input SPACE GROUP U UNIT CELL transformations A Absorption powder SIR SAD MAD etc T Change TOLERANCES M Test for MEROHEDRAL TWINNING 0 Self rotation function L Reset LATTICE type of original cell Q QUIT program Select option 0 A Figure 8 17 Exit XPREP
99. echnical Support Users are invited to contact Bruker AXS whenever there are problems or questions related to the sys tem Before contacting Bruker AXS please e If there is a software problem determine the version of the program e Record any error messages e Determine conditions and steps that recreate the problem If the instrument is in North America contact our North American Service Center Bruker AXS Inc Phone No 1 608 276 3087 Customer Support Toll free 1 800 234 9729 5465 E Cheryl Pkwy Fax No 1 608 276 3015 Madison WI 53711 5373 E mail Customer Service bruker axs com U S A Internet www bruker axs com If the instrument is outside North America contact your local Bruker AXS Service Center M86 E01078 1 5 About This User Manual APEX2 User Manual 1 6 M86 E01078 2 Hardware Overview APEX II systems share common hardware com ponents with other Bruker AXS products Other members of this new generation of instruments include the D8 ADVANCE D8 DISCOVER and D8 GADDS systems for general diffraction Doc umentation on some of these common hard ware and software components is available in the User Manuals for the D8 family of instru ments 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 E0107
100. ed hydrogen atom positions Structure Solution and Refinement 93 3 View 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 L o of QPeaks g Figure 9 27 Removing all Q peaks with the slider bar 2 Right click on the background and select Thermal Ellipsoids Wireframe Ball And Stick Figure 9 28 Selecting Thermal Ellipsoids APEX2 User Manual Figure 9 29 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 Information on All Atoms Find Duplicate Labels Information on All Atoms H Hydrogen atoms Figure 9 30 Selecting Information on All Atoms This produces the table in Figure 9 31 M86 E01078 APEX2 User Manual INFORMATION ON ALL ATOMS LEO s os OW oaar ozsa o ot oo Od once oasa 0 b oo Be 059 Nemo o ce oc CET ks oec CTO CI o e oc Bd os spo o A 04x TT 00 bts oc oss oz oers o e ome oss Rims oara o jc owe ame oido oara o uus mmc ass osr o o js mmc awe os
101. ed 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 Selection Grouping Tools Current Group MIA Group 5 Add To Current Group Remove From Current Group Select Visible Groups p Deletion Helpers 3 M86 E01078 APEX2 User Manual RLATT 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 E01078 A 19 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 r a LIS E 2 EL M E E E 0 E Figure A 23 Using the Measure Distance tool A 20 M86 E01078 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 bec
102. em 7 XPREP has chosen the crystal lattice P Figure 8 8 Press Enter to accept Lattice exceptions P A B C I F Obv Rev All N total o 5634 5622 5620 5623 8438 749 7501 11249 N int gt 3sigmaj D 5157 5089 5194 5096 7720 6834 6834 10243 Mean intensity 0 0 224 9 214 3 211 3 225 4 216 9 223 9 224 6 220 3 Mean int sigma 0 0 20 7 19 7 20 9 20 5 20 4 20 5 20 5 20 5 Lattice type P 4 B C I F Ofobv R rev rhomb on hex axes Select option P i Figure 8 8 Choose the lattice 8 XPREP evaluates the data and looks at the systematic absences for all possible glide planes and screw axes Figure 8 9 These are displayed across the middle of the fig ure By examining the number of reflections with 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 APEX2 User Manual 8 1 2 Reflection Statistics Mean E E 1 0 687 expected 968 centrosym and 736 non centrosym Systematic absence exceptions h c n 21 c a n 21 a h n 21 N 457 455 460 16 360 374 358 19 233 230 223 L4 N I gt 3s 388 394 386 281 282 229 o 192 203 171 o lt I gt 201 1 300 0 317 2 0 5 449 8 377 8 201 2 0 5 290 7 311 3 277 0 0 6 I s 22 1 22 6 23 6 D 4 23 9 21 5 15 9 0 6 20 8 22 7 21 7 0 6 Identical indices and Friedel opposites combined before calcu
103. er 1 connected clients Activate auto de ice feature B x rays ON 9 Aen ster Interval time n a sec Use version 12 BIS frame headers Monitor instrument Debug instrument Connections Messages received by BIS YES CID 52 Get amp xesLimits Distance 50 000000 CID 53 GETAXESLIMITS_YES CID 53 Get xesLimits Distance 51 000000 CID 54 GETAXESLIMITS_YES CID 54 Get xesLimits Distance 52 000000 CID 55 GETAXESLIMITS_YES CID 55 Get xesLimits Distance 53 000000 CID 56 Defective messages a di Messages sent by BIS Command zd poe Frames left 0 Time left IN ew client program connected to BIS Figure 3 3 BIS main window 2 000 2THETALOW 75 000 2THET4HIGH 20 000 OMEGALOW 0 000 OMEGAHIGH 0 000 PHILOW 0 000 PHIHIGH 0 000 CHILOW 52 a AXESLIMITS DISTANCE 153 000 2THETALOW 25 000 2THE TAHIGH 20 000 OMEGALOW 0 000 OMEGAHIGH 0 000 PHILOW 0 000 AXESLIMITS DISTANCE 154 000 2THETALOW 75 000 2THE TAHIGH 20 000 OMEGALOW 0 000 OMEGAHIGH 0 000 PHILOW 0 000 AXESLIMITS DISTANCE 155 000 2THE TALOW 75 000 2THETAHIGH 20 000 OMEGALOW 0 000 OMEGAHIGH 0 000 PHILOW 0 000 8XESLIMITS DISTANCE 156 000 2THE TALOW 75 000 2THE TAHIGH 20 000 OMEGALOW 0 000 OMEGAHIGH 0 000 PHILOW 0 000 AXESLIMITS DISTANCE 157 000 2THETALOW 75 000 2THE TAHIGH 20 000 OMEGALOW 0 000 OMEGAHIGH 0 000 PHILOW 0 000 8XESLIMITS DISTANCE 158 000 2THE TALOW 7
104. er Manual 1 2 Terms and Conventions Used in this User Manual Before using this User Manual it is important to understand the terms and typographical con ventions used Certain kinds of formatting in the User Manual s text are used to identify special kinds of information 1 2 1 Typographical Conventions Table 1 1 shows typographical conventions used to help you quickly locate and identify informa tion in this User Manual Convention PET Software interface elements such as icons menu items and buttons to be selected as part of the current proce dure boldface New terms and words requiring italics emphasis Information read from or entered into a monospace command prompt Navigation through a hierarchical menu For example Select Start gt Programs Bruker AXS APEX2 describes navigating Windows menus from Start to Programs to Bruker AXS to APEX2 square brackets Keyboard input Table 1 1 Typographical conventions APEX2 User Manual 1 2 2 Equivalent Terms Frame Image In this User Manual the terms frame and image are used interchangeably to describe two dimensional X ray data whether read from the CCD camera or generated within APEX2 Greek and Roman Text This User Manual uses scientific terminology that may be rendered in Greek text However this User Manual follows a convention of using Homan text to the greatest extent possible
105. ermine Unit Cell module Section 6 2 to set defaults However you can modify the suggested values 2 Check the inputs for defining the data collection 2 1 Set the data collection distance For SMART APEX ll systems this should be set to the actual detector distance For Kappa APEX II sys tems the distance is variable and will default to the shortest reason able distance For the APEX ll detector the distance in millimeters should generally be about the same as the longest cell dimension in angstroms Typically distances ranging from 35 mm to 45 mm are reasonable 6 16 APEX2 User Manual 2 2 Setthe exposure time and press Enter For normal crystals and an APEX II detector 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 with longer exposures than inner shell data 24 Setthe desired resolution 0 75A is a reasonable value 2 5 Check the other values Laue class Lattice etc 2 6 Each time a value is changed the Data Collection Strategy module recalculates the statistics for the runs The results are displayed in the column labeled Current NOTE The rescanning of runs can be inter rupted by pressing Esc No statistics will be displayed M86 E01078 APEX2 User Manual Data Collection ensed to Single Crystal App lab at Bruker AXS Data Collecti
106. ess Enter The 2d m Data Collection Strategy module will n o el 2 reload all of the possible runs amp 4 5 5 2 O 20 2 0 100 10 60 3 8 60 gt o a c 54 40 E E 2 amp 4 Time h Figure 6 16 Completeness and Redundancy charts after sorting for completeness 6 20 M86 E01078 APEX2 User Manual Data Collection 6 3 3 Looking at the Current Strategy 1 To look at the actual runs chosen select View gt Detailed Strategy This opens a window that shows the runs to be collected see Figure 6 17 bd Current Strategy Experiment 37 50 45 50 288 43 9 77 22 88 Phi 0 50 719 359 50 13 8 Experiment 37 50 7 00 158 24 27 83 99 23 Omega 0 50 64 32 00 13 8 Experiment 37 50 49 50 379 48 141 44 20 99 Omega 0 50 84 42 00 13 8 Experiment 37 50 38 00 304 81 3 54 28 52 Phi 0 50 473 236 50 13 8 5 Experiment 37 50 40 50 328 49 340 58 43 25 Phi 0 50 719 359 50 13 8 ees e Bes EM ES amp Polmele o Figure 6 17 Current Strategy window Each line in this list represents one run It is specified by e Origin e Crystal to detector distance e Angular positions of the goniometer axes e Name of the scan axis e Image width e Number of Images e Total Sweep e Exposure time overhead M86 E01078 6 21 Data Collection Each run is displayed in a color that indicates its behavior during the strategy refinement Black runs are permanent and always active during the
107. est Spots menu items APEX2 User Manual Menu Item Function D right arrow Go to the next step in the unit cell determination process Finish Finish the sequence of steps in the unit cell determination process beginning with the current step Perform any tasks that are necessary Harvest Proceed with harvesting according to the options set in the preceding menu items Cancel Leave Manual Mode and return to the initial Unit Cell Determination page performing no operations and ignoring any changes made to menu items Table 6 2 Harvest Spots menu items M86 E01078 APEX2 User Manual Data Collection Index Menu Item Function Reflections TEE Group 0 270 reflections y Opens the Reflection Group Combo Reflections Box to allow you to select a certain Go to Image C Framestguestiylid_exampleimatrix_01_0001 sfrm group of reflections for indexing M Rd SEES Select a frame filename from this drop ioc MMC CE EC EN I C Go to Image down menu to display the frame in the Resolution 4 9535 00 fo Image Display Area V Reflections must be isolated Adjust the criterion for indexing a Reflections must span images reflection based on its integrated inten Reflections must be whole sity versus its standard deviation Slide Min l sigma l the slider between More Spots and 270 Reflections selected for Indexing Fewer Spots to vary the minimum 225 954 b 9 02
108. ew Sample mounting collar Z axis lock Locking collar _ B Y axis lock Z axis adjustment screw Y axis Mie adjustment adjustment acre screw X axis lock Goniometer head collar Figure 5 4 Huber goniometer head in detail 5 4 M86 E01078 APEX2 User Manual Crystal Centering and Screening Crystal Sample mounting screw Locking collar Z axis adjustment Z axis lock collar Y axis X axis adjustment adjustment s screw Goniometer head collar Figure 5 5 Nonius goniometer head in detail M86 E01078 5 5 Crystal Centering and Screening 5 3 Center the Crystal To obtain accurate unit cell dimensions and col lect good quality data position the crystal in the center of the X ray beam and maintain this posi tion for the entire experiment Your video microscope should be aligned so that the reticle of the video microscope coincides with the center of the goniometer and the center of the X ray beam for instructions on aligning the microscope to the center of the instrument see M86 Exx024 Microscope Focus and Sam ple Alignment If the microscope is not centered you can still center the crystal A successfully centered crys tal stays in the same place in the microscope s field of view in all orientations To center the crystal on a Kappa APEX II sys tem see Section 5 3 1 To center the crystal on a SMART APEX II sys tem see Section 5 3 2 APEX2 User Manual NOTE Use the thin end
109. fitting peaks see Figure A 8 bier Files Rellechon Sine zoom Figure A 8 RLATT display looking down layers of Enni AA RR reflections Figure A 9 RLATT display looking down layers of reflections Weaker reflections i e those with smaller l sigma l are black because the Intensity Filter slider bottom left has been moved slightly to the left M86 E01078 A 5 RLATT APEX2 User Manual With additional rotations the layers of reflec 2D profiles can be organized into clusters As tions can be further oriented so that stacks of shown the 2D profiles are counting intensity reflections become visible Sometimes it is quite The counting mode can be changed to spot useful to right click on the background and count or turned off completely using the Visual choose Z rotations from the rotation options ization menu RLATT gt Visualization or by The 2D profiles on the top and to the left are a pressing the s key to cycle through the count valuable aid in this process With practice the ing modes Axis A ae a ENTES bodes nonce EAS Direct Space Laboratory None Colorization Method C By Group C By ACH S Flags C By Intensity XX vV Se 2 2 2 2 2 U V A di di AR dA da SL SR SR SS SL Light Direction and Colors 2D Projection Scale 5 By Intensity Count By Spot Count C None Intensity Filter Reflection Size Zoom Null Resolution N DISABLED Figure A 10
110. h deg Sweep deg Direction 4 Pal Omega Scan Yes 37 500 T 000 1 58 240 27 830 33 230 10 000 0 500 32 000 positive 3 OmegaScan Yes 37 500 49 500 379 480 141 440 20 990 10 000 0 500 42 000 positive 4 PhiScan Yes 37 500 36 000 304810 3540 28520 10 000 0 500 236 500 positive 15 PhiScan Yes 37 500 40 500 328 490 340 580 43 250 10 000 0 500 359 500 positive 6 No Operation Yes i Data Collection NOTE At the top of the Setup Experiment tab are controls for data collection Usually the default values are correct For data collection times of less than five sec onds correlation can usually be turned APEX2 User Manual 5 To begin the experiment click Execute APEX shifts to the Monitor Experiment tab and diffraction images begin to appear This may take a minute or two if new darks are being collected or if the generator is being ramped up from a low power state off If new dark frames are required BIS will automatically collect them Check ing Generate New Darks forces the collection of darks before every run In Figure 6 19 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 4 f you choose to enter your own
111. hat the moveable beamstop is pushed in and set the desired position typi cally 45 mm for Distance in the data window 2 2 On SMART APEX II systems with movable DX set the desired position typically 50 mm for Distance in the data window 2 3 On SMART APEX ll systems with fixed DX check that the distance displayed is the same as the actual distance in mm on the detector arm M86 E01078 Crystal Centering and Screening Click 360 Phi and set the desired expo sure time The default of 15 seconds is usu ally sufficient Click Drive Scan Since these are evalu ation scans there is no need to request correlated images or new darks The shut ter opens and the phi scan begins The resulting Phi 360 image is shown in Figure 5 33 The crystal diffracts nicely with lots of sharp spots Figure 5 37 shows a Phi 360 scan with a bad crystal Figure 5 33 A 360 Phi scan on a good quality crystal Click Wide 2 0 The phi scan range changes to 2 An exposure time of 5 to 15 seconds is usually sufficient for a wide scan Crystal Centering and Screening APEX2 User Manual 6 Click Drive Scan The resulting 2 scan 7 Click Phi 90 in the middle row of boxes is shown in Figure 5 34 The spots are sharp and clean There are no peaks that are very close together Figure 5 38 shows a 2 scan with a bad crystal Click Drive Scan The resulting 2 scan is shown in Figure 5 35 This image is mea sured 90
112. he obstruction typically the beamstop Narrow Wide Algorithm A garnthm C Use Narrow Frame Algorithm f Use Wide Frame Algorithm Figure 7 12 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 1 5 should be integrated as narrow frames Those greater than 1 5 should be integrated as wide frames M86 E01078 Data Integration and Scaling Image Queue mage Queue Active Image Queue Half wridth Images 7 4 Figure 7 13 The Image Queue tool The Image Queue sets the number of frames being used to determine profiles For crystals with high mosaic spread i e large wide reflec tions increasing the queue size can improve integration 7 1 3 Start Integration 1 Click the Start Integration button on the far right of the bottom row This starts the integration and opens the SaintChart win dow discussed in Section 7 2 for monitor ing the integration 2 Examine the output Double click any of the output entries in the Output Filename for one additional tool the Is button at the far right of the line see Figure 7 14 The Is button opens the SAINT listing file for that integration run MEG manualwork ylid manual 04 raw m 4x 1s Figure 7 14 The runs list s Is button Data Integration and Scaling APEX2 User Manual 7 2 SaintChart SaintChart is a powerful too
113. he next step in the unit cell deter E right arrow mination process Finish the sequence of steps in the unit Finish cell determination process beginning with the current step Perform any tasks that are necessary 4 D Finish Accept Cancel y eset Accept the choice of Bravais lattice type P given in the menu items above Figure 6 9 Bravais menu Leave Manual Mode and return to the initial Unit Cell Determination page Cancel performing no operations and ignoring any changes made to menu items Table 6 4 Bravais menu items M86 E01078 Data Collection APEX2 User Manual Refine V 985A Orthorhombic P Unit cell a 5 95 b 9 024 c 18 36 Unit Cell a 30 00 B 90 00 y 30 00 90 00 Parameters y 30 00 fa v 90 00 V 63 385 CO Domain translation i w mm 0 00 pee y mm 0 00 xl Reflections E Group 0 270 reflections y Go to Image C Frames quest yplid_example matrix_01_0001 sfrm More Reflections Tolerance 2 78 Fewer Reflections 258 Reflections selected for Refinement C Show selected Reflections Show predicted Reflections RMS XY mm n a Tools Refine afoj Finish Figure 6 10 Refine menu RMS angle n a Histograms Transformations Accept Cancel Menu Item Function Unit Cell Use the Unit Cell Combo Box to select a unit cell to refine Parameters Within the Parameters window several area
114. in Sort Bin Akom List lt Top of List gt Sorti Alpha Mumeric Sorki Alpha Mumeric Sorti Mumeric Alpha Figure 9 34 Carbon atoms in Sort Bin Insert Selected 4fter gt Insert All AfEer 3 After the atoms are in the Sort Bin click Sort Alpha Numeric to get them into a Figure 9 35 Sorted atoms with insert after atom O2 normal order selected 4 Highlight O2 and click Insert All After as in 5 Click OK to accept the sorting Figure 9 35 Figure 9 36 OK button The resulting list of atom information is easier to examine M86 E01078 9 19 Structure Solution and Refinement INFORMATION ON ALL ATOMS GE jel 0 0000 3 WS w10 D2 pa t B Um Wo IE JJ DOUU CI OIA p Xu 0 1 pera pen D UH poz 0 00000 a ra a EA Fa pE a e QUOS yc 0000 c E 37 2 n 1944 n 1500 sn E IRETE Cz DO oi C DL EA a 1245 D 122613 E DL STET c D ODORE C f 5 0 3 6 1313 rn 0 6447 CA 01 i hares hea 1 76 sri p HETAZ Ics D nam c f 2978 m st OITA qax n fi neues Ice 0 0000 0 1496 0 502 0 283 0 0 0549187 lc 0 0000 c 0 1798 oito 0 377 sp3 0 0 0462133 cs 0 0000 ee et ee dee 0 0 03482 co mem Ua 0 24 QW praga U DAI IG fog UJ DOUU C UEH ma Dane t U C CIA QJ ERE C UEFA wiring l menen 503 U UD US for amp rint Figure 9 37 Sorted atoms The Ueq values are reasonable if there are lower values for the sulfur atom and the five member ring highe
115. in status window 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 smb file when BIS is running on the same machine and smb if BIS is running remotely M86 E01078 D 13 Configuring APEX2 APEX2 User Manual userposl type scan default Not set User defined instrument axis position See the example on page D 2 userpos2 type scan default Not set User defined instrument axis position See the example on page D 2 userpos3 type scan default Not set User defined instrument axis position See the example on page D 2 userpos4 type scan default Not set User defined instrument axis position See the example on page D 2 calibweaklevel type integer default 10 Minimal I sigma for peaks to be used in calibration routines D 14 M86 E01078 Index A About box Absorption correction and Face Indexing in Scale module Access levels Accounts Acentric space groups and Intensity Statistics ACTA output Active Mask and Spatial Distribution plots Align Crystal Anisotropic refinement APEX II detector APEX2 modules overview required rights shutting down starting APEX2Server Append Strategy Archive function M86 E01078 3 10 B 1 7 14 4 2 4 2 7 18 9 23 7 20 3 3 9
116. ion The upper right hand corner of the Determine Unit Cell module contains two sections e Automatic Mode for fully automated unit cell determination Section 6 2 1 e Manual Mode for unit cell determination with user defined parameters Section 6 2 2 APEX2 User Manual NOTE The Determine Unit Cell module auto matically determines crystal mosaicity and provides a table of exposure time versus diffraction limit Figure 6 3 lower right hand corner This table is strictly informational and its contents are not used when determining exposure times for a data collection strategy However you can use the infor mation in the table to manually set expo sure times for your maximum desired resolution For more information on the Data Collection Strategy module refer to Sec tion 6 3 M86 E01078 APEX2 User Manual Data Collection LE ba APEX2 v2 0 2 User guest Sample ylid example Licensed to Single Crystal App lab at Bruker AXS Determine Unit Cell Sample Instrument Windows jBa He e x l ald om mA 4 ON G Automatic Mode Start at Collect Data y Q Collect Data m Stop after Refine Harvest Spots Determine Unit Cell ijs HE Bn D Indes o 240 Bravas Vy e Hetine Transform unit cell Unit cells wen b Edit f Le Delete Reciprocal Lattice Viewer Delete All eb View Images Reflections Edit Delete Delete All e Earring poco l
117. ion factor at a constant level i e gt 90 for very good crystals and gt 80 for good crystals Correlation factors below 40 indicate that the orientation matrix does not describe the diffraction pattern cor rectly Integration Progress 1 Check Integration Progress to add the new display seen in Figure 7 16 When the integration is complete the blue progress bars will be full and the remaining time will be zero e Integration Progress E vlid_example_01_0001 sfrm 64 64 2 RR n a wid example Q2 0001 sfrm 984 84 R88 n a wid example Q3 OO01 sfm 338 473 BB B 17 40 13 00 00 17 ylid example Q4 ODO1 sfrm O 719 All 486 1340 B BI 17 43 20 00 03 24 17 43 20 00 03 24 Figure 7 16 Integration Progress display Data Integration and Scaling Spot Position Overlay Check Spot Position Overlay in the Per Image Statistics category to add a window for monitoring the progress and quality of the inte gration Pull up on the Window Tool Bar for Inte grated Spots to display the entire window 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 The shape of the overlay represents the reflec tions sizes and shapes determined during the integration APEX2 User Manual Setup Y I
118. ions 1 The Integration Options window has a few values that are changed more frequently We will change the default options for inte gration in the Integration Options window Model Prodi pe Background Update FB Enable L5 Proble Fibra Blond Profiles hom AN Deteci Regem ledere piss Loewe Lara for Model Profile peste Tum Imega osos Function of Modal Pac le Maxim ioe Simple Sum Maik 050 MR Bae eee Mi j7 E leienehy Sigea Upper Lint for LS Model Profle Fit F000 pe panne Lower Resolubor Land lor LS Model Profle Fiji niam Bechground Update Scaling Factor 1 000 Enable Beam Mordor Homalkzation Pille rZ Haee a Ja fa r Figure 7 9 Integration Options window 2 Click the More Options button This results in an expanded window see Figure 7 10 and gives access to several other useful features in particular Active Mask see Fig ure 7 11 Algorithm see Figure 7 12 and Image Queue see Figure 7 13 APEX2 User Manual Hada Probes if Beckgourd Lipdans 7 Enable L5 Proin Fitting Blend Profit kom All Dielechor Regina Ietersaly Scena Lowe Land ber Maciel Prolia Update 150 SOA Quem Function af Model Profile Masimam lot Simple Sum Mask Sese ners PARIS UNE HA VN paa FPF sj IoenelyFiwa Uem Link ler LS Model Pieter 8000 ers EE Liveses Flesukiion Land lor LS Model Polis Fa A rum Background Update Scaling Factor 100 Enable Beam Mondor Homake
119. is mode Click OK APEX2 automatically connects to the user specified IP address or DNS name of a computer running BIS More infor hlLogin HE mation about the bn config py file may be found in M86 Exx087 APEX2 and ue PROTEUM2 Installation Notes and in Appendix D Password AAA You are now ready to begin using APEX2 TN Figure 4 3 Login dialog 3 Foronline operation within APEX2 select Instrument Connection In the Instru ment Connection window enter the instru ment host name The window shows the default host Click Connect 3 Instrument Connection E ES Host Name localhost Figure 4 4 Instrument connection dialog 4 4 M86 E01078 APEX2 User Manual Program Startup and Shutdown 4 4 License Considerations You need a software license to activate your pur chased software packages options and or fea tures APEX2 requires a valid license file to operate This file bn license dat must be present in the root directory of drive CA for the software to start properly If the license file is not present or has expired an error window will appear when you try to start APEX2 This window prompts you to run the License Manager application to obtain a valid license for APEX2 For more information on licenses and License Manager refer to M88 Exx099 License Man ager User Manual Error No valid license is available to run amp PEXZ Please use the License Manager to order
120. it 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 D 12 M86 E01078 APEX2 User Manual Configuring APEX2 scanrepr type integer default 1 Determines how scans are represented in text 1 scan angle from x to y length y x O scan angle length y x starting from x 1 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 smbroot type string default 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 mails statuslines type integer default 1000 Maximum number of lines displayed
121. itle Bar Table 3 1 Sample menu commands Software Overview Instrument Menu Sample instrament Windows Help Connection Status Toggle Shutter Abort Windows Menu ample Instrument windows Help 1 Describe 2 Experiment m 3 Structure Solution Help Menu istrument Windows Help About APEXZ Instrument menu Command APEX2 User Manual Description Opens a connection to a server com Connection puter running BIS If connected already select this menu to disconnect Opens a window showing a summary Status of the current status of the instrument and your connection to it Toggle Shutter Instructs BIS to send a shutter open or close command to the instrument If all interlocks and safety circuits are satis fied the shutter will open and close Abort Stops a currently running data set Table 3 2 Instrument menu commands Windows menu Command Window selection Description Displays a list of active windows Any of these windows may be brought to the front by clicking its title in the Windows menu Table 3 3 Windows menu commands Help menu Command About APEX2 Description Displays version and copyright infor mation for APEX2 Table 3 4 Help menu commands M86 E01078 APEX2 User Manual 3 4 3 Tool Icon Bar Some icons on the Tool Icon Bar provide short cuts to the options av
122. l EEEREN Fari 39 399 9999 99999 999999 Expected resolution Collect Exposure time 4 Resolution A T Posi 1 200 n a Scale Position pixels 60 0 n a Examine Data i Intensity counts 1200 n a t HKL index 600 0 n a Solve Structure Resolution A Refine Structure im 2Theta Crystal Mosaicity 0 40 Image Header A Tool Editor 4 Cursor Position Figure 6 3 Determine Unit Cell module M86 E01078 6 5 Data Collection 6 2 1 qu Automatic Mode In the Task Bar click Evaluate and then Determine Unit Cell The Determine Unit Cell module appears Figure 6 3 From the Start At pull down menu select the step at which you want APEX to begin automatic unit cell determination useful if you want to find a unit cell from frames that have already been collected From the Stop After pull down menu select the step at which you want APEX2 to stop automatic unit cell determination Click Run Automatic data collection begins and collected frames appear in the Infor mation Display Area The area containing the Automatic and Manual mode options changes to a list showing APEX2 s progress through the steps of unit cell determination B Monitor Data Collection O Harvest Spots O Index O Choose Solution Figure 6 4 Automatic Mode progress list E Harvest Spots ET Index Selected 270 reflection s for indexing FA Choose Solution H Refine 5 83 8 88 18 24 90 00 88 14 8
123. l for monitoring the progress of the integration process and for graphically presenting the results of the integra tion process bd APEX2 2 0 2 User guest Sample ylid_example Temporary license 4 days remaining Integrate Images El Sample Instrument Chart Windows jn s Mo x e UNIES Setup ntegration ieee correlation E fat Average Spot Intensity and 1 Sigma I Values Integration Finished Collect de E All Components y ntegrate 80000 00 O Progress Statistics O Integration progress O Per lmage Statistics Spot shape correlation pu Spot intensity and I Sigma l e co e c ce 60000 00 Integrate Images Spot intensity lt 2 Sigma Number of reflections harvested 40000 00 O 0 i O Spot position overlay O O coefficient e Mm ce 20000 00 i euibiS ebe1oAv A Y Z error X Y Z RMS difference Average correlation c Average spot intensity 0 00 i L X Y Z spot size FB RA A E iii O Queue extent used 0 100 200 300 400 500 0 100 200 300 400 500 L Primary beam intensity Image Image Periodic Statistics FI Profile snapshots O A axis ESD ta Spot Shape Profiles by Detector Region oO B axis ESD tL C axis ESD Correlation coefficient Intensity sigma E O LS goodness of fit O LS Residuals O x YZ crystal translation tL X Y beam center HC Distance correction O Pitch Roll Yaw correction O Anale zeros O Coverag
124. lating R sym Option Space Group No Type Axes CSD Risym N eq Syst Abs CFOM 4 P2 1 2 1 2 1 19 chiral 1 5917 0 015 3394 0 6 15 9 0 89 Select option a M Figure 8 9 Systematic absences and a suggested space group 1 XPREP returns to the general menu seen previously Figure 8 5 This time D is cho sen to evaluate the data set Press Enter to accept 2 here are multiple choices for data manipu lation Figure 8 10 S chooses a display of statistics Index Data Filename or Source of Data 1 11249 ylid hkl lt current dataset M Sort MERGE current data no scaling C Change CURRENT dataset L LEAST SQUARES scale and merge datasets W WRITE dataset to file I INCLUDE Rfree flags from another file R READ in another dataset 5 Display intensity STATISTICS D DELETE stored dataset F FACE indexed absorption corrections P PSI scan absorption corr T Copy file TRANSFORM hkl and cosines 4 MAD SAD SIR or SIRAS H Apply HIGH low resolution cutoffs N NORMALIZE scale sigmas 6 Generate simulated powder diagrams U Anisotropic scaling 2 Expand data to triclinic E EXIT to main menu X Parsons Q values and Flack x parameter 0 QUIT program Select option 3 i Figure 8 10 The data manipulation menu 3 The data can be merged in several ways Choose the Merge ALL equivalents includ ing Friedel opposites option A Figure 8 11 Press Enter to accept NOTE This merge wi
125. lculates the angle in 3D SHIFT F8 store user defined orientation 4 adjust intensity slider adjust intensity slider change axis modes change colorization method invert selection toggle Null Resolution Mode change 2D Projection Scale mode A E I M toggle distance measurement during lattice selection tool N S U toggle Unt Cell Tool Figure A 6 Shortcut keys and commands M86 E01078 A 3 RLATT APEX2 User Manual 3D Reciprocal Lattice View Iri 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 Ted and drag ta 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 E01078 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
126. lect co e e Completeness Aduepunpey Experiment Oriented Scans lez Resolution A Completeness Y Redundancy Completeness Aduepunpey Integrate Examine Data Solve Structure Refine Structure Time h Instrument Figure 3 8 Task Display area showing the Data Collection Strategy module dat foz7 2Theta 54 97 sint 1 4 0 65 Distance mm 37 50 Mosaicity 0 40 Image Width 0 33 Bijvoet Pairs merged y Laue Class 1 y Lattice Type P A Axis B Axis C Axis Alpha Beta Gamma Total Reflections Unique Runs 67 Images Reg Disk Space 7361 MB Exposure Times s Inf 1 37 M 30 0 36 0 714 0 504 0 30 0 9974 0 414 120 1 2274 0 374 150 1 36 fio zi 30 E 3o zi zo El 30 E 30 44 30 BE 0 0044 0 7074 1 4144 Same Extend Reduce Reset Target Priority ono fho hoo pam fm Custom 5 z Execute Refine Strategy gt Current Completeness 99 52 Redundancy 46 12 Time h 106 18 Strategy M86 E01078 4 Program Startup and Shutdown As discussed in Chapter 3 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 the folder containing these programs and desktop shortcuts linked directly to these programs However the Start
127. les linked to the samples table A third set of tables contains the values of standard crystallographic data such as Laue classes space groups and point groups These tables are referenced by the sample data and are not modified in any way by the user Finally there are a few miscellaneous tables dealing with audit trails version control of the database and other assorted functions M86 E01078 APEX2 User Manual Software Overview 3 4 The APEX2 GUI The APEX2 graphical user interface GUI has This window is divided into five sections one main window see Figure 3 5 e Title Bar e Menu Bar e Tool Icon Bar e Task Bar e Task Display Area Title Bar Menu Bar bg APEXZ v2 1 RC5 User quest Sample Example Licensed to Eric Amble at Bruker AXS Sample Instrument Windows Help Tool Icon Bar _ Describe Center Crystal Task Display Area Task Bar Figure 3 5 APEX2 GUI M86 E01078 3 7 Software Overview NOTE Throughout the APEX2 user interface input fields with pink backgrounds indi cate invalid entries Disabled greyed out fields indicate that a feature is not available e not supported or depen dent upon the instrument configuration 3 4 1 Title Bar The Title Bar displays the name and version of the software user name sample name license type and option currently selected in the Task Bar The right edge of the Title Bar also contains
128. les 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 blt a2 b2 a3 b3 a b 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 without an hkl file taking the lattice type found with CELL_NOW into account If necessary this conventional cell may be reinput in specified cell search mode to find the orientation matrix If CELL NOW fails to suggest a sensible cell either something is seriously wrong 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 AUN
129. lid hkl Wavelength 0 71073 Chiral Original cell 5 949 9 018 18 353 20 00 20 00 20 00 Vol 984 6 Esds 0 000 0 000 0 000 0 00 0 00 0 00 Lattice P Current cell 5 949 9 018 18 353 90 00 90 00 90 00 Vol 984 6 D Read modify or merge DATASETS C Define unit cell CONTENTS P Contour PATTERSON sections F Set up shelxtl FILES H Search for HIGHER metric symmetry R RECIPROCAL space displays 5 Determine or input SPACE GROUP U UNIT CELL transformations 4 Absorption powder SIR SAD MAD etc T Change TOLERANCES M Test for MEROHEDRAL TWINNING 0 Self rotation function L Reset LATTICE type of original cell Q QUIT program Select option 3 i Figure 8 5 Determine the space group 5 Ifthe space group is known or if the com pound is known to be chiral enter that information Figure 8 6 Generally it is suf ficient to press Enter to start the space group determination 5 Determine SPACE GROUP C Must be CHIRAL sample is optically active N NOT NECESSARILY chiral eg may be racemate I INPUT known space group E EXIT to main menu or 0 QUIT program Select option 3 i Figure 8 6 Space Group options M86 E01078 Examine Data 6 XPREP has chosen the crystal system O Figure 8 7 Press Enter to accept A Triclinic M Monoclinic O0 Orthorhombic T Tetragonal H Trigonal Hexagonal C Cubic or E EXIT Select option 0 Jj Figure 8 7 Choose the crystal syst
130. line defines a plane along the micro scope axis which should be parallel to the crystal face Use the mouse to move the line until it touches the crystal face M86 E01078 Face Indexing 4 Click to fix the face An entry appears in the Face List showing the Miller Indices of the crystal face along with the face s distance from the instrument center Figure B 7 Face normals Figure B 8 Fix the face Face Indexing APEX2 User Manual 5 Repeat all steps in this section to specify all of the crystal s visible faces If APEX2 does not suggest a face normal for a certain face you can increase the value in the Max Miller index field to show more sug gested normals 6 As you define more faces APEX2 will begin to display its geometric model of the crystal superimposed over the video images Figure B 9 Continue until all faces are defined Figure B 10 All faces defined Figure B 9 Some but not all faces defined B 6 M86 E01078 APEX2 User Manual Face Indexing B 3 3 Editing the Face List Consider Figure B 11 The face 1 3 2 does not Unit Celt appear to define a face correctly Removing this a 21 35 b 11 824 c 8 80 eer B 36 61 y 90 00 v face will give a more accurate model of the crys Marita A cda tal manra PERA ee MW o0o 200 2200 MO Oo a 4 464 4 4 o Clear list Figure B 12 Face List right click menu t Figure
131. ll not average the reflec tions in the final data file It is only for the calculation of statistics Current dataset ylid hkl R Define resolution ranges currently selected automatically P Output Ripim rather than R sigma N Do NOT merge reflections I Merge IDENTICAL indices only 5 Merge SYMMETRY equivalents but not Friedel opposites A Merge ALL equivalents including Friedel opposites E EXIT to merge datasets menu OQ QUIT program Select option A A Figure 8 11 The merge data menu 4 A table of statistics appears Figure 8 12 Examine the data presented ls the com pletion 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 reso lution data The completion should be near 100 for both the high resolution shell and the complete data set The redundancy and Rin Should be similar for the two The Mean Intensity and the Mean l sigma l will usu ally be quite different The Mean l sigma l for the high resolution data should be greater than 3 0 M86 E01078 APEX2 User Manual Resolution Data Theory Complete Redundancy Mean I Mean I s Rint 103 102 105 82 82 78 59 53 51 43 35 30 27 26 21 21 18 15 56 60 41 44 63 60 78 04 83 72 6g 32 15 73 75 51 60 58 0 0177 0 0171 0 0175 0 0191 0 0212
132. m another data set in which the Active Mask was not used during integration Consequently the reflections collected in that area are consistently weaker than expected This kind of problem may affect the final results Scan 1 detector 2 theta 12 00 Il lt L gt 1 23 00su red blue errors black 50 100 150 200 250 300 350 400 450 X gt Figure 7 28 A Spatial Distribution plot showing a problem area M86 E01078 APEX2 User Manual Data Integration and Scaling 7 3 5 Exit 1 Click Exit AXScale to close the Scale module Exit AXS cal Figure 7 29 Exit AXScale M86 E01078 7 21 Data Integration and Scaling APEX2 User Manual M86 E01078 8 Examine Data In this step the space group for the crystal is determined and optional simulated precession photographs are calculated to further evaluate the overall quality of the data APEX2 provides two tools for this Space Group Determination based on XPREP and Precession Images for looking at undistorted slices of reciprocal space This is the final step before beginning the struc ture solution and refinement process 8 1 Space Group Determination With XPREP 1 Under Examine Data in APEX2 s Task Bar click Space Group Determination 2 Check that the two files in the pop up win dow are correct see Figure 8 1 and click OK M86 E01078 hy Select Files For XPrep EE P4P file C Frames quest ylid_example work ylid_example_Om p4p gt
133. mation BrukerInstrument ini BCP Bruker Configuration Program 2 0 1 1 14 Dec 2005 File Edit View Tools Help OD SW Se a Beometry p Controllers Left C Vert Right Goniometer PHOENIX com Axes nta v 7 2theta Thetaltube Low hightemp KRYOFLEX v va y v Omega Theta2 det Generator NONE manual IBE Configuration v Phi Robot NONE Elfs 2 jv Chi Psi Kappa Barcode reader none Ae 2 Alpha oo deg Single Crystal SC Digital IO Lines Base Angles X E ha ms 2theta 3000 deg i n a Omega 3200 deg Gonio Heads xm a va Phi po deg A aE Tira ch 5474 deg a ears v Distance i eee is Knife edge F Capilla stage F Beam stop F Gther n AGH Attenuator Beam stop Present Attenuation factor n a Distance o mm m Monachromator r Microscope Lenath o mm Angle 0 00 M Present s Base gt Circle 0 0 00 Radius mm Roll Y C 2Theta r Descriptive information Angle horz 0 Cw Goniometer D85 E Angle vert 35 Gonio s n lt sn gt Stage FIXED CHI r Cold stream e Detector DEMO APEX1 X V Present Generator Generator SEALED TUBE y K780 hd Angle horz n a Cw Detector Opti i ptics Graphite Monochromator parallel Y Angle vert 30 0 Axes Security For Help press F1 Admin only Mas
134. ment type is set correctly click Relabel to number the peaks sequentially in the order they were selected starting with the number in the First Sequence field Structure Solution and Refinement 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 Pipes This makes the bonds thicker and makes it obvious that there is an incorrectly labeled atom This will be corrected when the car bon atoms are labeled Wireframe Ball And Stick Thermal Ellipsoid Select Hide Part s Show all Atoms Disassociate Atoms Unit Cell Zoom Out Toggle Pan And Rotate Restore Deleted Atoms Find Duplicate Labels Information on All Atoms Figure 9 18 Select the pipes view J NOTE If working on YLID test data look at Fig Click on the remaining peaks in the order that you want them labeled ure 9 19 and click on the peaks to give the same order as used here Right click and select Labelling Select Carbon and apply the labels APEX2 User Manual In the Labelling tool change the element type to C carbon The starting atom num ber changes to 1 the first available num ber for carbon atoms Click Relabel Click Cancel to close the window The labeled YLID molecule is now ready for refinement Figure 9 19 Correctly labeled model M86 E01078 APEX2 Use
135. n RLATT Unwarp images User Manager V Validate when preparing an experiment Variables in bn config py Video microscope Video zip stream View Images M86 E01078 3 14 0 9 2 7 3 7 3 8 6 14 3 7 9 24 3 12 3 15 B 3 C 10 8 10 C 10 1 2 7 11 7 13 6 14 A 16 3 14 3 6 6 24 D 1 2 1 2 7 5 6 B 2 3 12 View Molecule vzs file W Warnings defined Water ice resolution shells Wavelengths for K alpha What s This Help Whole reflections XPREP Preparing an Output File X ray safety issues X ray Source XS XShell changing displayed atom sizes overview Y YLID test data in this User Manual Z Z values Zoom functions Index 3 13 B 2 1 3 6 10 1 4 3 11 6 11 3 14 3 1 3 1 8 1 1 4 2 6 9 24 9 5 1 1 8 5 3 11 Index 7 Index APEX2 User Manual Index 8 M86 E01078
136. ndexing Initial View M86 E01078 a 21 35 b 11 82 c 8 80 a 90 00 B 96 61 y 90 00 W 220542 Monoclinic C H K L Distance immi Remove Invisible Faces Closed No Size mm va Face Indexing APEX2 User Manual Face Indexing Item Description Show and hide the T tool for a better Show T tool view of the crystal faces Max Miller The highest Miller index shown as face index normals in the overlay When the T tool snaps to a face normal E the plane you define may differ from the so 9 specified index by a maximum of this amount Show possible face normals APEX2 suggests face normals Snap to possi ble face normals The T tool snaps to the suggested face normals Dial or mouse wheel Use the dial to rotate around 360 of phi The right click menu lets you rotate phi by 180 to define parallel faces Crystal face information Shows the Miller indices of a given face the face s distance from the instrument center and the out of plane angle Table B 1 Fac e indexing controls Item Description Unit Cell Displays the unit cell that APEX2 uses to display faces in the overlay HKL Miller indices of the normal to the specified an face Distance The specified face s distance to the center mm of the instrument E Faces obscured by the body of the crystal Faces are removed from the Face list
137. nement Global Refinement v Enable Periodic Refinement JV Enable Global Refinement v Enable Initial Passes Frequency Images 50 Refinement Options Constrain Metric Symmetry of Unit Cell to Integration Options Orthorhombic C Crystal System Triclinic Find Runs Import Runs from Experiment O Detector Max Number of Reflections 9999 E Constrain Metric Symmetry of Unit Cell to Orthorhombic C Crystal System Triclinic Refinement Parameters Y Horizontal Beam Center REC Horizontal Beam Center pM Vertical Beam Center Y Vertical Beam Center eM Distance rM Distance A Pitch eM Pitch LA Yon LA Yaw D Unit Cell HM Axes L zi E Figure 7 7 Refinement and Integration Options buttons O Twin Component 2 Twin Component 2 O Unit Cell as Component 1 i O Unit Cell as Component 1 iO All as Component 1 O Refine separately O Twin Component 3 O Unit Cell as Component 1 O All as Component 1 9 Refine separately hd O All as Component 1 es O Refine separately O Twin Component 3 Unit Cell as Component 1 The default values are generally very good There is seldom any need to change the values in the Refinement Options window O All as Component 1 O Refine separately Figure 7 8 Refinement Options window M86 E01078 75 Data Integration and Scaling 7 1 2 Check the Integration Opt
138. ntegration b I C Frames quest ylid_example ylid_example_03_0036 sfrm E MIO Figure 7 17 Spot Position Overlay M86 E01078 APEX2 User Manual Data Integration and Scaling 7 2 2 Examine Final Results At the end of integration examine this text criti cally In particular look at the Overall Rey the Coverage Statistics and the Unconstrained Unit Cell refinement 1 View the SAINT text output At the bottom of the SaintChart window is the scrolling text window that displays text output from SAINT This window can be expanded by dragging the horizontal bar above the text 2 Examine the final results M86 E01078 7 11 Data Integration and Scaling APEX2 User Manual Overall Rey and Coverage Statistics The coverage statistics are reported by resolu tion shells e The values in the Rs ym column give the cumulative agreement of equivalent reflec tions e TheRshel1l values give agreement within a particular shell These change faster than the Rs ym values e The lt 2s column is useful for checking where the weak data becomes predominant greater than 50 or 60 e The Sigma column gives the average l sigma for each shell If that number is less than 1 5 or 2 then little significant data is being measured in that shell e The overall Reym is usually less than 8 Higher values may indicate problems with absorption twinning or poor crystal quality Overall Pairs uUniq Marg lt 2s
139. o the Index options set in the preceding menu If instead of the unit cell parameters items an entry is labeled empty this indicates an unassigned entry Choosing the Leave Manual Mode and return to the E Il apu Store Unit Cell empty entry creates a new unit ce ESSI initial Unit Cell Determination page instead of replacing the current one performing no operations and ignoring Combo Box i any changes made to menu items A color is associated with each unit cell The color is displayed in the box to Table 6 3 Index menu items the left of the unit cell The color helps in recognizing a unit cell while navigat ing through the software It is also used in the image display to color the overlay and indicate the unit cell that was used to calculate the overlay Right click to edit or clear unit cells Select corrections to detector parame ters Corrections are available from the Corrections stored parameters i e BIS configura tion file from the last harvest or from manual input Select methods employed in indexing Methods difference vectors fast fourier trans form or least squares Go to the previous step in the unit cell Al left arrow determination process iaht Go to the next step in the unit cell D right arrow determination process Table 6 3 Index menu items 6 12 M86 E01078 APEX2 User Manual Data Collection Bravais Initial Unit Cell
140. oF S 1 167 Restrained GooF 1 167 for 0 restraints Mean shift esd 0 101 Maximum 0 688 for U13 C3 at 19 05 00 Max shift 0 002 4forC5 Max dU 0 000 for C5 wR2 0 1389 before cycle 5 for 2389 data and 2 127 parameters GooF S 1 164 Restrained GooF 1 164 for Orestraints R1 0 0459 for 2262 Fo 4sig Fo and 0 0476 for all 2389 data wR2 0 1389 GooF S 1 164 Restrained GooF 1 164 for all data R1 0 0498 for 1418 unique reflections after merging for Fourier Highest peak 0 47 at 0 8147 0 9219 0 2317 0 97 4 from C10 Deepest hole 0 27 at 0 2028 0 5207 0 0249 1 27 A from C6 be He Eee bebe EEE bb EEE EAE EEE EEE EE EEE EEE A EEE EEE EEE EE ERE EEE ERR EEE EEE ERR ylid_Om finished at 19 05 00 Total elapsed time 0 6 secs dede HERE bebe e eb b EE e eb E EE Eb E EE EE bb EE ERE HER ERR Figure 9 25 Least squares refinement summary M86 E01078 Structure Solution and Refinement The value for R1 0 0459 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 47 and is 0 97A from C10 there are cer tainly some hydrogen atoms to be included 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 26 Difference peaks correspond to expect
141. omes the pivot point for a new line Moving the mouse with no buttons depressed gives angle measure ments see Figure A 24 As described the angle measurements will be done in 2D mode Pe eS LS 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 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 L a eS uu it iii Sk el it Codecs a piat cane aa or vM LR E E E FP E 23 22 51 2 21 3 25 5 55 2 05 5 23 22 21 1 5 E e r a Ld La 8 i 2 2 E E MB RM D B M NM ue LI TEP ee eee eS eS F Figure A 24 Using the Measure Angle tool M86 E01078 m i E Parra aa are i 2 1 I E E 2 B EZ 1 E ee D x 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 E01078 Appendix B Face Indexing
142. on Strategy Data Collection Strategy Driented Scans TT Hf Figure 6 11 Data Collection Strategy module M86 E01078 6 17 Data Collection 6 3 2 Refining the Strategy At this point if all of the runs available were col lected it would take 91 60 hours and the data would have a redundancy of 184 36 Of course this is not desirable 1 Below the Target and Priority columns is a pull down menu with several different strategies Choose the one that best meets the needs of the experiment for the YLID example Best in 2 hours was selected The Target column changes to reflect your choice 2 Click in the Execute field A list of options appears Click Refine Strategy The strat egy begins to refine approaching the target Completeness Redundancy and Time set in step 1 Execute Refine Strategy Refine Strategy Lo or Completeness Figure 6 12 Click Refine Strategy 3 When you are satisfied with the Complete ness Redundancy and Time displayed in the Current column whether the module is finished refining or not click Stop It is neither necessary nor advisable to wait until the refinement reaches 100 APEX2 User Manual NOTE When refining the strategy the objective is to get good completion 98 or better with high redundancy in a reasonable amount of time When the Data Collec tion Strategy module is first started it will tell you the Completeness Redun
143. or Linux type hostname at the command prompt For Windows type echo computername atthe DOS prompt fileserverz 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 D 4 M86 E01078 APEX2 User Manual Configuring APEX2 Configuration of the APEX amp PROTEUM programs The appearance and working of this suite of programs can be modified by a configuration file The programs read the a series of configuration files in following order As described below a specification in a later file overwrites a setting in an earlier file On unix these files are lm file Jusr local iliab bn contig py 2a file bn config in your home directory Please note the initial 5 character which renders this file invisible for the normal Is command 3 a file bn config in your current directory On Windows these files are bn config py in the SystemDrive folder bn config py in the USERPROFEFILE folder bn config in the current folder O N e If none of these files is present the situation when the program has just been installed all parameters are using built in defaults To change a single configuration parameter 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 if it should be the system default for
144. ow and the contents of the Main Window will then be updated You are now ready to perform the experiment using the optimum strategy M86 E01078 APEX2 User Manual 6 4 Data Collection Run Experiment 1 Under Collect in APEX2 s Task Bar select Experiment The Experiment module opens First Run 1 Ba Copy TA Paste 1 Clear Figure 6 18 Deleting the matrix runs Data Collection 2 Click Append Strategy The runs deter mined in Section 6 3 appear in the list of operations to be performed 3 APEX changes the filename to the name of the current sample in this example ylid example NOTE You can load and save your own experi ments in exp format by using the Load Table and Save Table buttons at the bottom of the Setup Experiment tab bg APEX2 v2 0 2 User guest Sample ylid example Temporary license 78 days remaining Experiment lll Sample Instrument Windows lax By Setup Experiment Monitor Experiment Collect Data Collection Strategy Experiment Figure 6 9 Experiment view with strategy appended M86 E01078 Image location C Frames guest ylid_example z v Attenuate if topped Default time 10 000 sec frame Filename or prefix vid example v Correlate Frames Default width 0 500 degrees First Run 1 a Generate new Dark Images Detector Format 512x512 v 2Theta deg Omega deg Phi dea Chi dea Widt
145. pended to each Image Location C Frames quest yplid_example i m pa E dii Pee frame s filename and is used to identify In frames by their filenames First Run 1 Choose which run number will be the Distance mm 400 First Run first run useful for adding runs without Exposure Time 100 4 sec image overwriting previous ones Image Width dea 05 ij Distance mm Detector distance Detector Format 512612 y Exposure Time Duration in seconds of each frame Conelate Frames ves 7 Distance in degrees that the scan axis mage width t th fasi al deg ravels over the course of a single exposure Detector tomat Resolution of the frames collected by the detector Two frames are taken each with half Correlate the duration of the overall Exposure Frames Time to correct for spurious events appearing on individual frames Go to the previous step in the unit cell x left arrow determination process iaht Go to the next step in the unit cell D right arrow determination process Finish the sequence of steps in the unit Finish cell determination process beginning with the current step Perform any tasks that are necessary Proceed with data collection according E LA MES TEE Collect to the options set in the preceding menu items Figure 6 6 Collect Data menu Leave Manual Mode and return to the Cancel initial Unit Cell Determination page performing no operations and ignoring any changes made to menu items
146. play refreshes with the results of the least squares calculations Figure 9 23 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 M86 E01078 APEX2 User Manual 4 Inthe refinement box click Invert Struc ture and Refine All Non H Atoms Aniso tropically as in Figure 9 24 Number of residual peaks zo Sigma Cutoff nsigma Resolution Cutoff 2 Theta M Invert structure Late stage ek options P Refine all non H atoms anisotropically Figure 9 24 Inverting and choosing anisotropic refinement 5 Click the Refine button to launch the least squares refinement program The output window opens and a summary of the results of individual cycles of refinement appears GooF S 1 487 Restrained GooF 1 487 for O restraints Mean shift esd 1 718 Maximum 13 893 for U13 51 at 19 05 00 Max shift 0 009 A for C5 Max dU 0 003 for C5 wR2 0 1407 before cycle 3for 2389 data and 127 127 parameters GooF S 1 184 Restrained GooF 1 184 for Orestraints Mean shift esd 0 422 Maximum 2 423 for U11 C6 at 19 05 00 Max shift 0 004 A for C5 Max dU 0 002 for C6 wR2 0 1391 before cycle 4for 2389 data and 127 127 parameters Go
147. position M86 E01078 517 Crystal Centering and Screening 5 4 Simple Scans APEX2Server s Simple Scans software module provides tools for rapid screening of the crystal to check crystal quality It allows you to quickly set up scans to measure a 360 phi rotation as well as thin 0 5 and thick 2 0 still images 1 Under Setup in APEX2Server s Task Bar click Simple Scans The menu shown in Figure 5 32 opens Distance mm 45 2 Hr 2Theta ha 4 L Omega 0w 4 P Zero Current Phi 0 Phi 50 User 1 User User User 4 Drive Scan Axis te Phi Omega Scan Range Image width Exposure Time 10 bd secs Image Scan Option Correlate 2 images New dark image Still 360 Phi Marrow 0 5 Wide 2 0 Drive Scan Figure 5 32 Simple Scans menu APEX2 User Manual M86 E01078 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 32 the Drive Scan button is grey and therefore inactive because no scan has been requested 1 Click Zero and then Drive 2 Set the distance 2 1 On Kappa APEX ll systems check t
148. r Manual 9 3 2 Refine the Model 1 Click the Refine button in the Tool Icon Bar the cursor is pointing to it in Figure 9 20 type Ctrl R or select Refine gt Refine in Xshell s Menu Bar This opens the Refine Box a al ME Figure 9 20 The Refine icon 2 Click Refine to launch XL the least squares refinement program using the default parameters as given in Figure 9 21 M86 E01078 Structure Solution and Refinement REFINE Least squares options v Full Matrix Conjugate Gradient Refinement Cycles la Number of residual Q peaks zo Sigma Cutoff n 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 21 The Refine menu After a few seconds a Refine window will open with output results for the calculation Structure Solution and Refinement WR2 0 2818 before cycle 3for 2445 data and 57 57 parameters GooF S 2496 Restrained GooF 2 496 for D restraints Mean shift esd 0 686 Maximum 2 456 for y C11 at 11 50 43 Max shift 0 015 A for C11 Max dU 0 001 for C2 wR2 0 2787 before cycle 4for 2445 data and 57 57 parameters GooF S 2473 Restrained Goof 2 473 for D restraints Mean shift esd 0 18
149. r back to the center position Figure 5 18 Top position The crystal is now centered on the instrument 5 12 M86 E01078 APEX2 User Manual Crystal Centering and Screening 5 3 2 For SMART APEX Il Systems NOTE If the image of the crystal is difficult to see illuminate the crystal 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 goniometer head drive to a position per pendicular to the microscope To center the crystal make adjustments to the height with the Z axis adjustment Figure 5 21 Initial mounted crystal Figure 5 20 Right position Z axis adjustment screw M86 E01078 5 13 Crystal Centering and Screening APEX2 User Manual 2 Click the Center button Move the crystal so that it is centered in the microscope reti cle by adjusting the X or Y axis translation adjustment screw that is perpendicular to the microscope axis and facing you see Figure 5 4 and Figure 5 5 Figure 5 23 Initial center position before X or Y axis adjustment Figure 5 22 Center position Y and Z adjustments Figure 5 24 Crystal after X or Y adjustments 5 14 M86 E01078 APEX2 User Manual Crystal Centering and Screening 3 Click Spin Phi 90 Remove half of the dif ference with the adjustment screw that is facing you After removing half the error crystal displaced approx 1 ti
150. r right hand corner of the module become avail able APEX2 User Manual Button Function Refresh the tabs using the absolute lat Refresh Files est contents of all the files Copies the contents of the results file OR eo HONS lai sire insiructions file Saves any changes you have made to Save Files the files Refine with XL Refines the instruction file using XL Open in XP Opens XP for editing the results file Open in XShell Opens the selected file in XShell Table 9 2 Structure Refinement module buttons M86 E01078 APEX2 User Manual 4 Click Open in XShell The XShell Main Window appears Structure Solution and Refinement XShell 6 2 C frames qguest cust work ylid 0 m res File Refine Disorder Constrain Model Render Preferences Help ES Ejea o cc SELECT ATOMS Element Name Component Include E Exclude Numeric Component Include lo to aaa Exclude to Trailer Component Include e Select Components Exclude Deselect Components Clear Current Selection OK Cancel Legend Atom Name x Y z Height Bond Length Residual Difference Fourier Q Peaks No ofQPeaks 20 Figure 9 6 Initial view of the YLID molecule M86 E01078 Structure Solution and Refinement 5 Right click in the background to open a pop up window with image display options M Wireframe Ball And Stick Thermal Ellipsoid
151. r software on the computer control ling the instrument i e the Server in a dual computer setup The steps in Chapter 6 are performed using the APEX2 program on the Client computer in a dual computer setup M86 E01078 See Chapter 5 for e Centering the crystal on the diffractometer using APEX2Server s Center Crystal mod ule e Crystal quality check using APEX2Server s Simple Scans module See Chapter 6 for e Cell determination using APEX2 s Determine Unit Cell module e Data collection setup using APEX2 s Data Collection Strategy module e Data collection using APEX2 s Experiment module 5 1 Start APEX2Server 1 If APEX2Server is not running on the com puter controlling the instrument start it by going to Start Programs Bruker AXS APEX2Server Crystal Centering and Screening 2 Ensure that APEX2Server is connected to the instrument by checking the Instrument gt Status menu 5 2 Mount the Goniometer Head on the Instrument 1 Open the enclosure doors by pushing either of the rectangular green Open Door buttons on the enclosure s side posts This releases the door locks for approximately five seconds While the door locks are released pull outward on one or both of the handles to physically open the doors Figure 5 1 D8 Enclosure Open Door button 2 Under Setup in APEX2Server s Task Bar click Center Crystal The centering buttons Figure 5 2 appear and the VIDEO p
152. r values for the terminal atoms methyls and carbonyls sensible numbers for the six member ring lower for C8 and C9 higher for C5 and C6 and in between for C4 and C7 APEX2 User Manual 9 3 5 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 refine ment or include the hydrogen atoms in fixed idealized positions riding on the atoms to which they are attached In this User Manual we will illustrate the latter fixed idealized method NOTE In some cases e g hydrogen atoms on hetero atoms or on geometrically strained carbon 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 hydrogen atom and there is difference electron density present 1 Using the slider tool remove all of the Q peaks M86 E01078 APEX2 User Manual Figure 9 38 Refined model with difference peaks removed 2 Right click on the background and click Add Hydrogen atoms gt Hybridize All Add Hydrogen atoms P Figure 9 39 Hybridize button The colors of the atom labels change to indicate the atom hybridization NOTE If the atom hybridizations are hard to see right click on the background and open the Information on All Atoms win dow 3 Right click in the background and click Add Hydrogen atoms gt Calculate Hydrogens M8
153. refinement process They are not altered during the refinement This options is intended for runs that have already been col lected and therefore definitively contribute to the data set Red runs are considered as is and unlike the permanent runs can be disabled by the refine ment algorithm However the configuration of such a run remains unchanged i e the scan range will not change Blue runs can change their scan range during the course of the refinement They are therefore called partial runs This is the default option for all runs from the basis set because it provides the refinement algorithm with the highest flexibil ity in finding a strategy that fulfills the criteria for the data set completeness its redundancy and the total data collection time Gray runs are disabled and are not taken into account at any time during the strategy refine ment APEX2 User Manual To change the behavior of a run 1 Place the Data Collection Strategy algo rithm in idle mode e make sure that it is not calculating the reflection list refining a strategy or sorting the run list 2 Select the run or runs you wish to change by clicking inside the Current Strategy win dow or by dragging the mouse while hold ing down the left mouse button 3 Right click inside the Current Strategy win dow to open the contextual menu 4 Select the desired behavior permanent as is partial or disabled The Current Strategy wind
154. 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 E01078 C 3 Using CELL_NOW Length fom Followed by 12 692 0 11 016 0 90 0 0 798 16 802 0 395 0 1340 Mitad oso Lodo Oh dvd AO TL 0 749 0 739 LADA Oi 23 4 60906 0 079 0657 2 wu 15640 6646 0 697 X559 25 428 0 LIS 950 4 0 601 00 574 1930 O Oa c I Va 9o uou C2820 di LIO UOS Quare US 14 648 O0 Soul UL USOS 3045005 components ex od TS 0 491 OG Uu DO 446 496 SO 120 0 248 14 633 Iel hits 0 1 0 2 0 3 angle correlation to previous vectors 902 30 94 493 19 999 99 999 991 20 SOS DIOS DOLUS 836 24 Poe DO DOCSIS CIS 93 9 29 POLED QO TUS IFO 91 9 0 688 741 L9 90 2349 993 692 99 599 1524 Alo 0 038 0 616 736 43 TSAI SUMSOST 974296 64 4 17 5 133 2 0620 0 645 0 569 122 45 X4 340 SORS GO 99 qd TOU A ouo 02 638 0 600 0397 0 593 688 35 2620 Seco XS Too LIS ee POS 2 MOA ee 592 9 0 556 0 544 0 480 0 484 0 487 686 4 65 465 65 465 65 465 ZO 9 WI ID56 2355 SOOO 207 0 532 0 524 0 459 0 469 0 465 0 426 684 18 TISTI 95 494 914090 De XUI GO IO E OS E db D 0 556 095539 0 47 QudTT 0 290 0 539 0 4224 iom e 14 493 S912 SALT 402 si SS o wA LO OS 692 ex 16 S de L9 ZO APE
155. rogram window opens APEX2 User Manual F Manual Y Motanzad Y spin Phi 30 Spin Phi 180 Mount Left Top Right Center Figure 5 2 Centering buttons M86 E01078 APEX2 User Manual NOTE If the VIDEO window does not stay on top of the APEX2Server window select Grab gt On top from the VIDEO program Menu Bar The bottom five buttons in Figure 5 2 Mount Left Top Right and Center drive the goniom eter to various pre defined positions that are designed to simplify crystal centering The two large square buttons rotate phi by either 90 or 180 degrees 3 Click Mount to drive the goniometer to a convenient position for mounting the goni ometer head 4 Carefully remove the goniometer head containing the crystal from its case Use extreme care when handling the goniometer head to prevent damage to the crystal on the end of the small glass fiber M86 E01078 Crystal Centering and Screening 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 3 Line up this slot with the pin on the goniometer s mounting base Figure 5 3 View of the bottom of the goniometer head 6 Screw the goniometer head collar to the base so that the head does not move Do not overtighten it finger tighten only Crystal Centering and Screening APEX2 User Manual Crystal Sample mounting scr
156. rown forest green PEkhaki mudmrirgh E lue tvrolet turquorise ugurays0t guicolor type tuple of three integers making a color default 0xd4 0xd0 0xc8 Overall background color of user interface guistyle type string default windows The style of the GUI Do not touch M86 E01078 D 9 Configuring APEX2 APEX2 User Manual hardwareprofile type file name default None The hardware profile to be used by COSMO for strategy calculations hashfilepattern type string default 44 PEE Do not touch headerdisplay type default not set If present this variable defines the name of a file containing the default image header items that should be displayed in the table underneath the image display imageextension type string default sfrm Do not touch 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 network names On Windows machines this is set automatically On unix this should represent a copy of the relevant parts of the samba configuration 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
157. rregularly shaped crystals it will probably be sinusoidal and the R int plot should not show large variations more than 2 Overall scale and Rint vanatons tor ylid_exomple Normalized Scale Factor Smocihed Ry int y Figure 7 23 Overall Scale and R int variations 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 24 An IE 1l plot should have a constant value IE 11 is a strong indicator for centric and acentric space groups The two hori zontal lines indicate the expected values for cen tric top and acentric bottom space groups This plot clearly suggests an acentric space group Intensity statistics for ylid_example Rint blue R sigma red R int or R sigma 4 0 2 1 L 6 Les b 1 0 0 9 0 8 Resolution d o o IE2 11 for general hkl E x ox go e t3 o q o N 40 24 1 6 1 3 m 1 0 0 9 0 8 Resolution d A Figure 7 24 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 The plots shown in Figure 7 25 are typical Chi squared distributions for ylid_example Chi squared Mean of N Sum l lt l gt N L Sum su D N equivalents 5 4 T B 3 zt
158. rs instead 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 dbhost typesstring detauli 127 001 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 D 8 M86 E01078 APEX2 User Manual Configuring APEX2 dbport type string default 5432 IP port to use to address the database Normally dependent on database installation dbname type string default BAXSdb 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 defaulthardwaretype 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 not touch 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 x groupcolors type tuple of color names default gray 5 red green yellow blue magenta cyan white gray2b5 b
159. runs click Validate to test the strategy for illegal movements by the goniometer If all motions are valid the All operations are valid window will appear Figure 6 20 ba Info i All operations are valid Figure 6 20 Operations valid window NOTE If resuming after a data collection inter ruption APEX2 will automatically skip images that were previously collected with matching angles and generator set tings Otherwise APEX2 will ask if you want to overwrite the images NOTE After data collection is started the Experiment window can be closed and APEX2 can be stopped The Server computer must be left on in a single computer setup BIS must be left run ning If communications are lost between the Client and the Server frames will be stored on the Server Typi cally they will be in the directory C frames They should be copied into the correct project directory before start ing integration M86 E01078 APEX2 User Manual bg APEX2 2 0 2 User guest Sample ylid_example Temporary license 78 days remaining Experiment lll Sample Instrument Windows Collect 1 Data Colles Strategy Experiment Driented Scans Integrate E 4 EFI 0 9 Cursor Position mm 30 60 Position pixels 511 Intensity counts 46 HKL index 3 01 Resolution 4 0 83 t 2Theta 1 50 63 Image Header Tool Editor FOL n EO OE HN FOL 38 383 3333 Cursor Position
160. s Background Color Choose colors and Figure 9 14 New background color click Apply Click Cancel to exit the back ground color mode Note that the selected peaks are blue in Figure 9 14 9 10 M86 E01078 APEX2 User Manual 3 Right click to view a pop up menu and select Labelling The Atom Labelling box opens Delete Atoms Hide Atoms Information Labelling Set Pivot point Sorti 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 15 Select Labelling ATOM LABELLING IN ORDER OF SELECTION Element Ic El First Sequence Ascending Suffix C Descending Relabel Cancel Figure 9 16 Atom Labelling box M86 E01078 Structure Solution and Refinement 4 The two selected atoms need to be changed to oxygen atoms Do this one of two ways e Click the Element field and type in the ele ment symbol case does not matter e Click the El button to the right of the Ele ment field to open a periodic table Click the appropriate element symbol to select it the periodic table will automatically close o efofs n v o mirelco u cul an refs y m fm re n a 60 co 4 te w J nef os a oe a Figure 9 17 The periodic table for selecting atom types 5 Once the ele
161. s F Set up shelxtl FILES H Search for HIGHER metric symmetry R RECIPROCAL space displays 5 Determine or input SPACE GROUP U UNIT CELL transformations 4 Absorption powder SIR SAD MAD etc T Change TOLERANCES M Test for MEROHEDRAL TWINNING 0 Self rotation function L Reset LATTICE type of original cell OQ QUIT program Select option H i Figure 8 3 Reduced cell 3 For the YLID no higher symmetry cell is found The program has determined that the YLID crystal has an orthorhombic prim itive lattice Figure 8 4 Press Enter to accept Determination of reduced Nigglij cell Transformation from original cell HELF matrix 1 0000 0 0000 0 0000 0 0000 1 0000 0 0000 0 0000 0 0000 1 0000 Unitcell 5 949 9 018 18 353 90 00 90 00 90 00 Niggli form a a 35 39 b b 81 32 c c 336 82 b c 0 00 a c 0 00 a b 0 00 Search for higher METRIC symmetry Identical indices and Friedel opposites combined before calculating R sym Option A FOM 0 000 deg ORTHORHOMBIC P lattice Risym 0 015 3394 cell 5 949 9 018 18 353 90 00 90 00 90 00 Volume 984 57 Matrix 1 0000 0 0000 0 0000 0 0000 1 0000 0 0000 0 0000 0 0000 1 0000 Option B retains original cell Select option A i Figure 8 4 Higher symmetry cells M86 E01078 APEX2 User Manual 4 The next logical step is to determine the space group XPREP suggests this Figure 8 5 Press Enter to determine the space group Current dataset y
162. s are available for refinement Unit Cell Domain Translation Domain Ori entation Detector Translation Beam Center Detector Orientation and Goni ometer Zeros By activating or deacti vating the checkbox on the left the parameters in this group are selected for refinement or are constrained to their current values during the refine ment Reflections Go to Image Use the Reflection Group Combo Box to the select a group of reflections for refinement Select a frame filename from this drop down menu to display the frame in the Image Display Area Tolerance Upon startup the Refine dialog deter mines a useful value for the tolerance this may take a few seconds depending on the number of reflections Show selected In the Image Display Area reflections selected for refinement are marked penecHons with circles Show predicted In the Image Display Area predicted reflections reflections are marked with circles Table 6 5 Refine menu items M86 E01078 APEX2 User Manual Menu Item Function RMS XY mm angle The root mean square of the deviation between observed and predicted spot positions in the XY image plane and along the trajectory of the spot while it passed through the Ewald sphere Tools Refine Refine the unit cell using the selected parameters Histograms Displays histograms of reflections variances in H K L detec tor X detec
163. save Intensity Filter Reflection Size Zoom Export Visible Spots to P4P Figure A 17 Selected reflections are blacked out A 14 M86 E01078 APEX2 User Manual Save the file by clicking the disk icon Figure A 18 or use File gt Save to remove the reflec tion 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 Figure A 18 Save File icon M86 E01078 RLATT RLATT APEX2 User Manual Enable the Unit Cell tool to put a colored box in Size determines the boundaries of the planes the view This allows you to see if reflections are and the number of unit cells displayed Grid actually falling on the corners of the box see Planes mode displays planes as grids with Figure A 19 and Figure A 20 There are multi spacings determined by the lattice ple options in the Unit Cell tool Select a Visible Plane displays individual planes Select Plane Unit Cell Tool 11 ENABLED A opnam n mentee ine em ee ea a a mem mm L ASS Select Unit Cell Tool Style C Planes Grid Planes C Single Box Layered Box Select amp Visible Plane along a b vs c3 along b a vs c C along c a ys b C ab c fall planes E TOO ERE isl WI Li A ae ea a Select Plane Sizes pu
164. shon Pile XYZ Haie a 4 Ja ru Activo Mask l E I Twin Dvodap Deiemingiem Generate Mask Mina Common Volume AU Fenema Lower Lint el venne inter man epu aen Factor 1000 Moyamam Hange 130 F7 Uen Pon E mitra Mik e x 1 zl Output Dusgnioitic Files j Generate Diagrasia Pol Files prha Keep Temporary Files TF Um Harea Furna digorit r Append Listing Files C Le Wide Frame Algoci m ade Leg nen EE nl E i z Robsona Conpchon huiman Detector onb 0 Verbosty of Listing Fie 2 3 E Hisar Reference Lonechon Snagakel Durguit Frequency Imsger o 2 Consi Figure 7 10 Integration Options window expanded Active Mask Active Mask amp Generate Mask Fractional Lower Limit of Average Intensity 0 000 f Use Pre Esisting Mask Active Mask File amp a Figure 7 11 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 M86 E01078 APEX2 User Manual NOTE If this option is set you 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 t
165. software an automatic system interruption device that senses when the doors and panels are open and prevents 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 The goniometer is controlled by the D8 controller APEX2 User Manual 2 1 5 Refrigerated Recirculator for the Detector To minimize dark current in the APEX II detector 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 SMART or Kappa APEX II system uses a single computer for control of the experiment storage of raw frame data integration of the data and solution and refinement of the struc ture An additional client computer can be set up to improve the performance of the system 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 M86 E01078 APEX2 User
166. ter fruesday 17 January 2006 A Figure 3 4 BCP main window Configuration screen Software Overview APEX2 User Manual 3 3 3 The Sample Database The sample database is used for the storage of data generated by the APEX2 Suite It is designed to transparently handle data from all of the APEX2 modules without intervention from the user The sample database is used internally by the APEX2 Suite and is not available for user cus tomization or manipulation It is automatically started on computer startup and it is automati cally stopped before the computer is shut down Structure of the Sample Database The tables in the database are divided into four categories First there are tables with users data such as user names passwords and contact informa tion These tables provide information about a user s working group and information about for whom the sample is scanned The administrator assigns each user to a working group or groups See M86 Exx092 User Manager User Manual for more information The second set of tables contains data about the sample These tables contain all of the sam ple data required by APEX2 s various modules Data with a single value per sample are con tained in a table called samples Preliminary information about the sample such as the name ID and color are stored in the samples table as well Data with multiple values per sam ple are contained in other tab
167. the SADABS program to put all of the measured data on the same scale This process involves five steps e Set up input files e Parameter refinement e Error model refinement e Display diagnostics e Exit 7 3 1 Set Up Input Files 1 Under Scale in the Task Bar click Scale the initial Scale window appears Figure 7 20 shows the right hand portion of the Setup tab The defaults and file names are typically correct 2 Check that the defaults are correct Gener ally the Absorption Correction Type is the only value that might be changed Numeri cal Absorption Correction requires indexed faces Face indexing is discussed in Appendix B 3 Click Next APEX2 User Manual Base vid example gt Output hkl file vi hil Diagnostic Plots File Name ylid_examplem eps Title of Diagnostic Plots plid_example Log File vlid examplem abs v Use only centrosymmetric point groups Point Group mmm X Additional Spherical Absorption Correction Mur of Equivilant Sphere JV Lambda 2 Correction Correction Factor 0 001 5 Allow for crystal decomposition Mme sj s one M by B value refinement Extra Linear Correction to be Applied Noe a to Each Reflection udi Absorption Correction Type Multiscan Absorption Correction Numerical Absorption Correction from Face Indices P4P File None eS Next Finish Figure 7 20 Initial Scale window Setup tab M86 E01078
168. the 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 M86 E01078 APEX2 User Manual 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 crystal 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 illuminating the crystal 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 Its 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 the crystal and rear near the source These pinholes help to define the size and shape of the incident X ray beam that strikes the crystal Collimators are available in a vari ety of sizes depending on your appli
169. the three buttons 011 used by Windows for minimizing restoring and closing the APEX2 main window APEX2 User Manual 3 4 2 Menu Bar The Menu Bar provides drop down menus for a variety of file operations image tools and help files An icon for the currently active window appears on the left side of the Menu Bar Clicking on this icon allows you to minimize restore resize close or move the currently active window M86 E01078 APEX2 User Manual Sample Menu 4 Sample Instrument Windows Help Mew Open mh O Save Close Archive M86 E01078 Sample menu Command Software Overview Description Opens a dialog window for logging into Login the Sample Database using your user name and password Logout Logs out of the Sample Database Lets you create a new sample in the New Sample Database Open Opens a previously saved sample Save Saves the current sample Close Closes the current sample Opens a dialog for archiving samples in the Sample Database to CD or zip Archive files Previously archived samples can also be restored using this dialog Allows you to import crystal information Import contained in a p4p or spin file into the Sample Database Allows you to export crystal data for the Export current sample as a p4p file Exits the application This menu item Exit has the same function as the but ton in the corner of the T
170. tor Y and rotation angle Transformations Opens a dialog for transforming the unit cell 4 left arrow Go to the previous step in the unit cell determination process D right arrow Go to the next step in the unit cell determination process Finish Finish the sequence of steps in the unit cell determination process beginning with the current step Perform any tasks that are necessary Accept Accept the options set in the preceding menu items and proceed with a single cycle of least squares refinement The Refine dialog has a built in safety which checks whether enough reflections are available for the refine ment If the number of reflections is critically low a warning is displayed with the option to override Cancel Leave Manual Mode and return to the initial Unit Cell Determination page performing no operations and ignoring any changes made to menu items Table 6 5 Refine menu items M86 E01078 Data Collection Data Collection 6 3 Determine the Data Collection Strategy APEX2 includes a powerful algorithm for deter mining an efficient strategy that fully utilizes the flexibility of your instrument 6 3 1 Operation and Initial Settings 1 Under Collect in APEX2 s Task Bar click Data Collection Strategy The Data Col lection Strategy module opens in the Main Window Figure 6 11 The Data Collection Strategy module uses information from the Det
171. 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 D 6 M86 E01078 APEX2 User Manual Configuring APEX2 autoconnect type boolean default 0 If this is set to 1 the connection to the 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 decide 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 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
172. us 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 DX track The camera distance is computer controlled a typical dis tance for the camera is 60 mm On SMART APEX II systems the detector is mounted on a DX dovetail track The track has a scale that is calibrated in mm to indicate the dis tance from the crystal to the detector face a typ ical distance is 60 mm The detector distance has to be changed manually An optional motorized DX track is available for the SMART APEX ll M86 E01078 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 II detector e X ray source including shielded X ray tube X ray safety shutter and graphite crystal monochromator e K780 X ray generator Timing shutter and incident beam collimator with beamstop e Video microscope Hardware Overview APEX2 User Manual Kappa APEX Il Goniometer The Kappa APEX II system uses a horizontally oriented Kappa goniometer with 2 theta omega kappa and phi drives and a motorized DX track for setting the detector distance It includes mounting points for the video micro scope
173. x 02 0007 sftm ylid example 03 fii 1 v v vlid example Utt 1 File type deselected Figure 8 18 File Selection window with matrix runs 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 resolution 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 simu lation is looking for all pixels that have 0 1 lt h lt 0 1 and any value including fractional values for k and l Planes oki h hkD hk TE hil Images from ruc guest vlid example vlid example 1127 image files in 4 runs best resolution 0 77 Thickness 0 10 Calculate Created files r Figure 8 19 Detail of the input section APEX2 User Manual A progress bar appears Figure 8 20 and after approximately 5 10 minutes depend ing on the number of sfrm files read the simulated precession image will appear on the screen Display other planes by clicking on the calculated images to the bottom right of the work area or by browsing as usual with the View module Processing 1127 image files e ex Figur
174. y click Spin Phi 180 and Spin Phi 90 to verify that the crystal stays in the same place in the microscope reticle through all motions of phi If the crystal fails to stay in the same position as phi is rotated make adjustments to the axes by repeatedly removing half the error as in step 3 7 Click the Left button The goniometer drives to place the fiber horizontal and to the left Note the height of the crystal in the video microscope reticle Figure 5 15 Crystal in left position Figure 5 14 Left position 5 10 M86 E01078 APEX2 User Manual Crystal Centering and Screening 8 Click the Right button The goniometer drives to place the fiber horizontal and to the right Figure 5 17 Crystal in right position 9 Check that the crystal height is the same as the height you noted in step 7 9 1 Ifthe height is the same proceed to step 10 9 2 Ifthe height is not in the same place adjust to remove half of the difference click Spin Phi 180 and repeat steps 7 to 9 M86 E01078 5 11 Crystal Centering and Screening APEX2 User Manual 10 Click the Top button The goniometer drives so that the phi axis is pointing directly into the microscope Figure 5 19 Crystal in top position 11 Click Spin Phi 180 a few times to verify that the crystal stays in the same position as Phi rotates If the crystal does not remain cen tered go back to step 1 12 Click Center to drive the goniomete

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