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Crystal Clear Manual

1. Refine 21x Crystal r Statistics 4 All ee RMS Residuals v All Cell IF All Lengths Y AllAngles 7 All Rotations nm so 3 4 4 4 lv Vv lv Vv lv Vv r Reflections B Rott Rot2 Rot3 Mosaicity Start pros pa pa NN E EE E ET oso taa Accepte ts AAA AAA A Al EJ cr o e Me Result r Resolution o Min 100 0000 m 2 0000 Set i oe 126 l 10 0000 Cycles 100 M All Detector p Rejection Limits 5 RE o Bees a All pS a 1 0000 2 1 0000 e 2 0000 Tran TransY Uh es Roiz BEN Rot Wavelength Rott Rot2 Swina Single Step Refine y x Start 0272 0419 0328 0009 Start isas fost 0 0227 ee Single Step il Refine on Reflection list EZ Last 3 Ez SS Reflection List dtfind ref y Result m m _ m L Result e TEME A a o Ato F Test Mosaic ie when retining on images ony L State Additional Arguments 23 Index Rn Close Save Defaults Advanced 2 Select the desired Macro to use for refinement Macro is initially set to Single Step Refine The user may use an alternate Macro however this setting returns to the default Single Step Refine following each Run To create custom macros click Advanced button See Section 8 Additional Processing on page 119 for information on creating your own macros 3 Consider adjusting the resolution in the Resolution Min and Max fields Adjusting the value in the peak i
2. cccsccssccccsscccsscccsscccscsccsssccssscoees 27 STARTING CRYSTALCLEAR AND LOGGING IN c cceccceccsccesccusceusceeccesceueceuscesccesccesccesceeseusseusceseees 27 CREATING YOUR FIRST PROJECT AND SAMPLE cscccseccssccscccccssccusccusceusceusceuccusceusceusceuccesccesceuscs 28 Sereen Collect and Procesan a e Mlaaivedack 29 Collect and A a KOS E A GS EAS oe oN el A eae NE SR ae eh Bs Ca 29 Coll cti A on Saal ae dd 29 PS ed o 29 Combine Reflections cccccccceecceeccesccecccsccssccscccsccesccesccuscesceusceeseueceueceuecesecescceceesseussesceuseens 29 5 COMMON CRYSTALCLEAR TASKG cccssscssscccsssccscscccesccscssccsscccsssccesscccescceeesccssccosescoees 31 COLEECT IMAGES A A 31 IPROGESSSIMAGES ssdestai cus tiae Ne ttl at Blt aca AN Ao AER do AA UR Ad DE ath 32 O O O 32 AASSen Unit Cell onsena AROS igtaaa a e N ate eae 34 FInd Spots E A EEA EAA E EEE e do N EA EE E EAE A 34 MEX Spoils O A A a E AE ES 37 CrystalClear User Manual Page 7 Table of Contents Reme dls io rd Lo E do ae A o dd ei db dos NID e A ONE 38 Predict Spots ii A A A A A A A E E AA E 40 STRATEGY Aen a A E ETEN OOA TAARE EE O en io ID ek 41 INTEGRATE REFLECTIONS si a A A det 42 ANALYZING THE DATA e a a A lbs 43 Lau Sy MMe trys iei e a a e e a a Ie aa ELE so aa a SAE ASE a Ri 43 Centric iyo eosi e Ri id la bens EA 44 SPACCSTOUP seene rr E E EE E RE vhs EDE eE E E E olaaa ENE ENNE EEE S 45 Scale and Avera geohe tossen RAN 46 6 DATA COLLECT
3. aa a Dist 28 sind Axis End ae oe Exp Total Schedule Scheg Sched 10 A Tages Ness lime Images Collected Collection Start End Time estimate Required disk space Total disk space Scan 0 Scan OMB 0 Available 87 MB Schedule D Schedule 0MB Remaining 87 MB m Completeness TES Preferences Run Close _ save Import Dezingered Exposure Check this option if desired See the Mercury or Jupiter CCD manual for more information on the Dezinger Exposure feature Bin Mode Select the Bin Mode See your Mercury or Jupiter CCD manual for more information on the Bin Mode feature Collect Schedules right click down arrow Assign a schedule in the Collect Schedules edit box Scan Table User may Add Scan or Remove Scan on the Scan Table then make changes to scan settings as desired For assistance in manipulating the Scan Table columns headings or other settings see Using the Scan Table on page 103 of Section 7 Tool Reference Right click on any column heading for All Columns menu This allows the user to select or de select individual columns to be displayed or hidden Column headings are as follows Scan ID Scan identification number Template Base name of the image Page 60 CrystalClear User Manual Data Collection and Processing Detector Distance mm Crystal to Detector distance 2 Theta deg Max Resolution Wavelength A Omega 0 Ph
4. 230 61 PARAS A AAA em 59 h k 4n 9476 SSeS D Saoser 233 SSS555 o ETERS oSSsses 60 S137 S sssS asas EOG A AA San 61 T662 99 a a ZOU 90 CA ES MARS 62 h k 4n S165 prsia TY ETE RRA AS 63 A o erro a 64 A 6i E 269 86 AAA RE AA AR 65 Sending tcl command 66 Systematic Absences lt I sig I gt lt 10 00 67 Refln Type hkl Ok1 hol hko hoo 0kO 001 68 Total Reflns 12641 1460 406 312 8 374 37 69 Condition gt gt Jaen k 2n 1 2n 70 Num Reflns z Fiep TRS Heg 18 19 71 Num Observed BERE gt FcH gt T 2 72 lt I sig I gt Se Sac Stns el 0 20 50 3 01 43 Sending tcl command 74 Spacegroups found BS Number Name Presentation Centricity Likelihood 76 18 P21212 P2212 1 Acentric 1 00 TT Space groups whose Presentation field differs 78 from the Name field were found ina 79 non standard presentation 80 Re indexing will be required to convert to a 81 standard presentation 82 Options 83 T Print Texsan Output 84 S Print Selected Spacegroups 85 A Print Table of absences used to selected spacegroups 86 B Print Table of all absences applicable to laue group 87 Q Quit 88 Type spacegroup number 89 Enter Select spacegroup 18 90 Choice Q 91 Terminating 92 No reindexing done 93 Reflection file not updated 94 Header output head written Scale and Average Log Page 184 CrystalClear User Manual Appendix C dtscalemerge Copyright c 1996 Molecula
5. m Resolution A Padding Images Per Batch Minimum Maximum az 2 0 00 0 00 Set Peak Radus Batch Prefix ox i Min jo 1 Width Height _ pO bp Max o Close Save Defaults 2 The Integrate Reflections dialog allows the user to select images Image numbers may be entered manually or selected from a list When entering image numbers manually be sure to use a dash to separate consecutive image entries or use a comma to separate non consecutive images entries For example you can enter images such as 2 5 7 9 12 Before clicking the Run button to Integrate Reflections de select un highlight the To Use entry field to verify the selected image entries Right click the To Use field for further menu options as follows View Images List Displays a list of image files Select Scan Allows user to select images of a scan Clear Scan Clears selected images of a scan In the View Images List all images available are listed with a selection box in front of the image name and the type of rotation oscillation with its beginning and end angles following Click on the box to select deselect the image The sequence field dynamically changes with the selections Page 42 CrystalClear User Manual Common CrystalClear Tasks 3 Make other adjustments to desired settings such as Box Width and Height 6 to 10 times the spots size without overlapping onto adjacent spots more than half way Images
6. O OTT n a S A N ol o 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 Appendix C Sample Log Files dtintegrate Summary of results for scan rotation from 24 000 to 29 000 with image sequence numbers from 1 to 20 Total reflections predicted 2714 Total reflections with no errors 1687 Total reflections with bad errors 64 Total reflections partial in scan 886 Total reflections unprocessed at end 0 Total reflection profiles written 1764 Reflection integration status codes Status Num reflns No Errors 1687 Processed special 158 Not processed as strong but otherwise OK On edge 0 2 Some intensity on edge of box in 1st dim On edge 1 O Some intensity on edge of box in 2nd dim On edge 2 78 Some intensity on edge of box in 3rd dim Too far 0 O Obs centroid too far from calc in 1st dim Too far 1 O Obs centroid too far from calc in 2nd dim Too far 2 O Obs centroid too far from calc in 3rd dim Too big 0 O Obs size too large in lst dim Too big 1 O Obs size too large in 2nd dim Too big 2 O Obs size too large in 3rd dim Overlap 0 0 Obs peak overlapped in lst dim Overlap 1 0 Obs peak overlapped in 2nd dim Overlap 2 0 Obs peak overlapped in 3rd dim Too dark 64 Some peak pixels saturated Too low 0 Some peak pixels too low may be shadowed B
7. 3 Select Collect and Process from the Task drop down list then click OK Open Sample x Project Myoglobin y New Project Sample Myo2 C New Sample Image Directory DAD ocumentation CrystalClear data Myoglobin Myo2simages Browse Cancel Browse Import The Open Sample dialog allows the user to begin a New Project or a New Sample by clicking the appropriate buttons CrystalClear User Manual Page 31 Common CrystalClear Tasks The Setup dialog will appear Main Crystalt Crystal2 Detector Ray Source Notes Project M yoglobin Sample Myo2 Crystal ID Temperature C User defined ID string 20 00 X Crystal To Detector Distance mm Detector 28 0 00 Close Save Defaults 4 Check the values on each tab of the Setup dialog box adjusting any values as desired then click OK 5 When prompted to Initialize the device click OK 6 Mount your crystal At the Mount Crystal prompt click OK when ready 7 If you are using the Mercury CCD the shape program will open Draw the faces of the crystal to be used in the Numerical Absorption Correction 8 When the Collect Images dialog box appears choose a collection schedule and then click Run To watch the progress of the collection click the Show Instrument State Display button on the toolbar Process mages Once images have been collected you can use CrystalClear to process them If
8. Select All Clear All m Resolution 4 Padding Images Per Batch Minimum Maximum 1 2 foco 0 00 Set Peak Radius Batch Prefix B a Height ae pp jo jo Max o Close Save Defaults 2 Specify the images to be integrated To specify a sequence of images Then select the desired images in the To Use entry field The Integrate Reflections dialog allows the user to enter image numbers manually or select images numbers from a list Right click on the To Use entry field to view menu options To enter image numbers manually in the To Use entry field be sure to use a dash to separate consecutive image entries and use a comma to separate non consecutive images entries For example you can enter images such as 2 5 7 9 12 Before clicking the Run button to Integrate CrystalClear User Manual Page 83 Data Collection and Processing Reflections de select un highlight the To Use entry field to verify the selected image entries Right click an entry field for further menu options as follows View Images List Displays a list of image files Allows user to select images of a scan Clears selected images of a scan 3 Set the desired Resolution If you wish to change the default resolution click Set If you specify 0 0 for both the minimum and maximum values all reflections on the detector are predicted and integrated See Set Resolution on page 1190f Section 8 Additional Processing for
9. h00 Total Observed lt I sig gt 0k0 Total Observed lt I sig gt e 4 4 914 1 e 19 19 744 1 o 4 4 LOGO o 18 1 ice o e S 0 1 o e a 00 001 Total Observed lt I sig gt e 18 ES 2836 o 19 2 LOA o e 0 0 Zone a b 4n atb not equal 4n Total Observed lt I sig gt Total Observed lt I sig gt Ok1l 366 287 214 7 1094 841 208 4 hol 101 TO 230 6 305 La 206 9 hko T9 60 269 9 233 168 29139 Zone a 4n a not equal 4n Total Observed lt I sig gt Total Observed lt I sig gt OkO 10 10 STAS 2 27 10 SS 001 9 7 Oo deed 28 10 1 398 hoo 1 1 75 4 7 Y 5530 zone 2h 1 4n 2h 1 not equal 4n Total Observed lt I sig gt Total Observed lt I sig gt hhl 96 87 288 7 289 253 419 9 h 1 3n 1 odd h 1 3n h 1 not equal 3n Total Obsvd lt I sig gt Total Obsvd lt I sig gt Total Obsvd lt I sig gt h hol 76 60 240 0 154 131 239 8 303 259 246 1 A ee ae Meena oe ee ee h hOl 77 60 231 2 149 125 238 2 308 265 246 8 Se a yw in 4 Total Observed lt I sig gt Total Observed lt I sig gt A 212 5 r 24 11 175 0 A id AN ool E ea Ba ee END Texsan Output ALL Systematic Absences CrystalClear User Manual Appendix C Sample Log Files 93 Refln Type 94 Total Reflns 95 h 2n 96 97 98 h 2n 99 00 01 k 2n 02 03 04 k 2n 05 06 07 l 2n 08 09 0 1 2n 2 k 1 2n 13 14 5 k 1 2n 16 17 18 h 1 2n 19 20 21 h 1 2n 22 23 24 h k 2n 25 26 27 h k 2n 28 29 30 h 4n 31 32 33 h 4n 34 35 36 k 4n 37 38 39 k 4n 40 41 1
10. 0 1 0 1 82 Direction vectors 0 1 1 O 83 RX_ Goniometer listing 84 Description UNKNOWN 85 Number of values 6 86 Name Datum Current Units Vector 87 RotAboutBeam 0 169 Unknown deg 0 000 0 000 1 000 88 2Theta 0 079 Unknown deg 1 000 0 000 0 000 89 Rot Y 0 214 Unknown deg 0 000 1 000 0 000 90 XShift 0 054 Unknown mm 1 000 0 000 0 000 91 YShift 0 120 Unknown mm 0 000 1 000 0 000 92 Distance 119 478 Unknown mm 0 000 0 000 1 000 93 DetResolution min 154180 94 DetResolution max 1 51956 95 DetResolution edge 1 76436 96 Rotation list 97 Start 184 500 CrystalClear User Manual Page 169 Appendix C Sample Log Files 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 13 114 End 185 000 Increment 0 500 Time 180 000 Oscillations 0 Axis vector 1 0 O Axis name Dark start 0 Dark update 0 Dark change limit 0 DCoffset start 0 DCoffset update 0 Predict resol min 9 Predict resol max 0 Component 1 crystal mosaicity 0 6 dtpredict Number of reflections written 1339 There were 1339 reflections predicted dtpredict Reflections written to dtpredict ref Strategy Log lscale 0 30 out 1 dtstrategy Copyright c 1997 Molecular Structure Corporation 2 d TREK version 6 1SSI Oct 6 2000 3 Command line 4 dtstrategy input head cmin 99 00 rangemax 360 00 5 output head 6 Header of file input head successfully r
11. 2 i1 myo2_screen osc i 12 TT myo2 0sc 1 60 Select Scan Clear Scan Sigma Select Screen Clear All 3 00 Close Save Defaults View Images List menu option right click on entry field allows selection of image files Before clicking the Run button de select un highlight the To Use entry field to verify the selected image entries Page 64 CrystalClear User Manual Data Collection and Processing Scan Scanzo myo2 osc 1 60 myo2005 myo2006 myo2007 myo2008 myo2009 myo2010 myo2011 myo2012 myo2013 0 70 00 0700 0000 70 00 ij Sequence 25 00 Select All Clear oros Column 1 Image identification Check in box denotes image selected Column 2 Axis of Rotation P phi C chi O omega Column 3 Start angle of the image Column 4 End angle of the image The sequence field changes with the selections CrystalClear User Manual Page 65 Data Collection and Processing 2 Specify a Sigma level above the average background for a pixel to be considered a peak If Sigma is O Find Spots processes faster because it does not calculate average background and its standard deviation 3 Click the Advanced tab to set display options Find Spots x Main Advanced Minimum Pixel Value Peak Filter e ofs 2D 3D Box 3 Width Height Padding F o jo r Resolution Minimum Maximum 100 00 2 00 Set Close Sav
12. Crystal Current Pos Move to IP Positioning Detector C Dist C 26 100 00 0 00 Current Pos Move to Move P1 Unknown C P2 Unknown CIS CIP Current Pos MOJE Move to M Shutter Conttol gt Erase lamps Open Until Manually Closed C Timed U Seconds Open On 20 Seconds Manual IP Read Pixel size 100 v Starting line jo In C Dut ttenuator gt Move Ending line 1 0 Read Lines to read Beam Stop In C Dut Move Read Head Position Current Pos Move to x g99 CrystalClear User Manual m Initialize Page 109 Tool Reference If the If Mercury CCD is the Image Collection Device Type the following window will appear ll Manual Instrument Control Biel x Goniometer Positioning Expose and Read Crystal Detector Exposure Time min Current Pos Move to Current Pos Move to 10 e Dist EN r Dezingering C20 T Dezingered Exposure Multiplier 1 fave Move m Bin Mode Shutter Control _ Attenuator 1x1 Open In C 2x2 Until Manually Closed C Out C Timed Move Expose and Read a Seconds ae gt r Beam Stop m Initialize Open Cn C Out Glose Move 2 Select the desired setting and Move 3 Click Initia
13. During integration 3 dimensional data should lead to better determinations of crystal parameters and the RMS values should drop The RMS for mm should be about 1 10 to 1 5 the spot width the RMS on phi depends on the image width and mosaicity in general being between 1 2 the image width and 1 2 the true mosaicity With 3 dimensional data RMS degree should be 1 10 to 1 5 the spot size in phi 5 If the refinement does not use most of the spots found in the Find step it is usually because too many peaks are excluded the resolution limits are too restrictive or the sigma cutoff is too high rejecting criteria are too strict x and y max difference too low phi too small or there is an incorrect unit cell Split crystals should have rejected spots not matching the predicted positions Prediction of spot positions should confirm or deny the choice of unit cell 6 By default any parameters turned on during refinement at the refine step will be used in the refinement during integration Itis possible and likely that the mosaicity is turned on during the refinement of the cell after indexing but it is not refined this is because you may not have enough rocking curves determined from contiguous images to do a proper calculation of the mosaicity not necessary but may be conducted at this step 7 Look in the find log file for the average peaks size and calculate 6 to 10 times this size as a good starting integration box size Then confirm t
14. E Instrument State Display lolx Detector Image Requested settings Start XRay Source M Shutter Status End Width Time sec Slit Size p 000000 Collimation Type p 5double Image Scan m fi 00 000000 Focus 500000 Element Copper E Expected finish time This Image This scan Source Type Optic Type Rotating Anode ror alignment crystal Goniometer Crystal Detector type m CCD Status Status Detector position Distance 28 Elapsed Manually Control the Detector The instrument can be controlled from within CrystalClear with the Manual Instrument Control feature Items that can be controlled include e Goniometer and detector positioning e Shutter control e Imaging plate positioning and reading Page 108 CrystalClear User Manual e Complete instrument initialization e Erase lamps illumination R Axis only To view the Manual Instrument Control window 1 Click the Show Manual Instrument Control button on the Tool Bar ca Tool Reference e Alternately you can click View gt Manual Instrument Control on the menu The Manual Instrument Control dialog will appear The options on the dialog will vary depending on the detector that is currently selected If the R Axis is the Image Collect Device Type the following window will appear hal Manual Instrument Control M Goniometer Positioning
15. Remove a Group To remove a group 1 Select the group to be deleted in the group list 2 Click Remove When you delete a group any users who are currently a member of that group will lose the rights given to them by being a member of that group All other groups will remain intact and the user will still have any rights granted to them by other groups Edit Group Settings To edit a groups selected privileges 1 Select the group to be edited in the group list Page 148 CrystalClear User Manual Appendix B Administration 2 Click Edit Group Settings Xx Group OK Name MyoG roup Cancel Description Myoglobin Users Group Help elt Administrative Rights Application Rights Add Groups dd Users jEdit Curr User Edit Groups Edit Servers Edit Users Remove Groups Remove Users 4 K 3 Make the desired changes then click OK to save the changes Administration of Tools You can add software tools to CrystalClear with the Tools tab in the Administration dialog When you add a tool a menu entry for that tool will be added to the Tools menu This makes it easy to access your software tools from within CrystalClear To administer tools 1 Access the Administration dialog by clicking Tools gt Administration The Administration dialog will appear Ifyou have logged in as a user without administration privileges the Tools gt Administration op
16. 1 Start CrystalClear The Login dialog will appear CRYSTAL CLEAR Wersion 1 3b 09 Copyright o 1985 Rigaku All Rights Reserved Login Name ATA Password a Cancel 2 In the Login Name edit field Enter Administrator 3 Leave the Password edit field blank and click OK CrystalClear ships with an Administrator account automatically set up By default this Administrator acount has no password blank A new password for the Administrator account should be set by using the procedure to Edit User Settings on page 145 of Appendix B Administration 4 At the Open Sample dialog click Cancel to close the dialog General Settings The CrystalClear administrator can set general defaults within the program All settings made by the administrator become default settings for new users at their initial login CrystalClear User Manual Page 141 Appendix B Administration To set defaults access the Administration dialog 1 At the menu line click Tools gt Administration The Administration dialog will appear Administration x General Users Groups Tools Servers View Standard Tool Bar Nesosesvecseeacencuscessecseveescseseescesveccescuscecseeses Task List Flow Bar Command Line Bar y Default English ne O K K K K Cancel Help The settings include view options Select the options you wish to be displayed Standard Tools Toggle the display of the sta
17. 24 measured 0 317 0 463 0 556 0 617 0 665 0 698 0 723 0 745 0 766 0 781 25 deviation 0 069 0 118 0 137 0 138 0 145 0 137 0 126 0 116 0 109 0 098 26 measured average deviation gt 0 119 27 Centric Distribution Selected 28 No reindexing done 29 Reflection file not updated 30 Header output head written 31 Spacegroup Log dtcell Molecular Structure Corporation d TREK version 6 2SSI Dec 11 2000 Command line dtcell input head dtintegrate ref head output head lauegroup mmm Y acentric rejects 20 asigma 10 000000 Header input head opened Header of file input head successfully read Lattice oP assumed for space group 16 0 30014 0N e Page 180 CrystalClear User Manual o FPOWOAMAHTAUABWNEF O NN 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 48 50 51 92 58 59 60 Command line string gt gt head lt lt Appendix C Sample Log Files Output Header Name set to output head Command line string gt gt lauegroup lt lt Laue group set to mmm Laue check disabled Command line string gt gt acentric lt lt Space group is Acentric Centricity check disabled Command line string gt gt rejects lt lt Command line string gt gt asigma lt lt Absence I Sigma I set to 10 000000 O O E O O A Finished reading command line Input Cell 65367 Tol 25 07 90 00 90 00 90 00 J Input Sigmas 0 0003 0 0009 0 001
18. 6 57 6331 7 50 2659 8 42 3718 9 Method Direct space cosine Fourier transform 0 Out header dtindex head 1 Max cell 68 0689 2 Num diffs 50 3 Spacegroup 0 4 Verbose 1 5 Performing direct space cosine Fourier transform indexing 6 Suggested grid interval is 1 5 7 8 Suggested max cell is 112 5 Actual grid interval is Iys 9 Actual max cell is 11 25 20 Start peak minimum 0 924801 21 Used peak minimum 0 924801 22 Number of peaks found 4 23 Start peak minimum 0 647361 24 Used peak minimum 0 647361 25 Number of peaks found 5 26 Least squares fit of reduced primitive cell to 44 lattice characters CrystalClear User Manual Page 163 Appendix C Sample Log Files 27 sorted on decreasing highest to lowest symmetry 28 Only solutions with residuals lt 10 0 are listed 29 30 Soln LeastSq Spgrp Cent Bravais a b c 31 num residual num type type alpha beta gamma 32 33 4 3 789 75 P tetragonal 71 698 71 698 106 730 34 90 000 90 000 90 000 35 36 6 3 735 21 orthorhombic 100 969 101 820 106 730 37 90 000 90 000 90 000 38 39 9 3 677 5 monoclinic 100 969 101 820 106 730 40 90 000 90 335 90 000 41 42 10 1 130 16 P orthorhombic 69 244 74 070 106 730 43 90 000 90 000 90 000 44 45 11 0 638 3 P monoclinic 74 070 69 244 106 730 46 90 000 90 457 90 000 47 48 13 0 000 1 P triclinic 69 244 74 070 106 730 49 90 457 90 000 90 482 50 51 52 Suggested spacegroup
19. Absorption in Scaling Appendix E Absorption in Scaling CrystalClear provides a number of options for the modeling of absorption crystal decay and incident beam intensity drift These are all modeled within the absorption correction algorithms provided in the Scaling and Averaging step The goal of the absorption correction algorithm is to deduce an absorption surface associated with a crystal by requiring that this surface minimize the difference in intensities between symmetry related reflections In practice this is done by minimizing the weighted differences between the right and left hand sides of the equation 1 L w IAS where I s are the intensities and A s are the absorbances The right hand side represents a sum over the k symmetry related intensities in a group of equivalent reflections and the subscript i represents any member in the group One seeks to find an absorbance A to minimize this difference and A represents an initial estimate of the absorbance As implemented in the program the initial A values correspond to that of the spherical crystal when a new absorption surface is obtained these replace the original A values and the process is repeated until convergence is obtained The absorbance A consist of a product of the absorbance of the primary beam and the absorbance of the scattered beam i e z v t tts A e e p A A S 2 These absorbances could also be expanded in a Taylor series
20. Installation This section details how to install the CrystalClear software Introduction to CrystalClear This section gives an overview of CrystalClear s user interface Running CrystalClear for the First Time This section discusses how to log in to CrystalClear for the first time and how to set up your initial project and sample Common CrytalClear Tasks This section gives brief overviews of the common scenarios of collecting data and processing data Data Collection and Processing This section covers the process of collecting and processing data in more detail Command Reference This section gives information about peripheral features of CrystalClear such as managing projects and samples displaying the processing state etc Additional Processing This section covers how to create macros new collection schedules and merge reflections Images This section gives an overview of the Image window and how to use it Appendix The Appendix includes information about CrystalClear s directory structure administrative functions and log file information It also includes a troubleshooting section that lists common problems you may encounter in CrystalClear and how to correct them Notation Conventions Throughout this manual we will use consistent notation conventions e Product and program names are set in Initial Cap Italic type e Directory names and filenames are set in monospace type CrystalClear User Manual Page 11 Abo
21. Profile Windows The profile windows display a graphical profile showing you the values of the pixels that intersect the x and y axis cross hairs To display the integrated intensity of a spot click on the spot in the large image window You can also click and drag across an area to see how the values change from pixel to pixel CrystalClear User Manual Page 131 Images Large Image Window Toolbar You can manipulate the image in the large image window using the tools on the Image Window toolbar R Select Magnify Zoom Full View Pan Measure Profile Add Spots Delete Spots Measure Pixels Quad Erasure Circle Erasure Page 132 You can use the Select tool to point at a particular pixel and get information about that pixel in the Information Window With the Select tool you can also click to see a profile plot of pixel values in the Profile Window Choose the Magnify tool then click in the image window to see a magnification of an area Choose this tool to zoom in or out To zoom in on a specific area right click then drag out a box To zoom in left click then move the cursor up To zoom out left click then move the cursor down This tool returns the display back to full view after you have used the Zoom feature This tool allows you to pan across the image Choose this tool then click and drag in the direction you wish to pan This tool displays a measurement in angstroms between tw
22. Right click an entry field for further menu options as follows View Images List Displays a list of image files Select Scan Allows user to select images of a scan Clears selected images of a scan CrystalClear User Manual Page 35 Common CrystalClear Tasks In the View Images List all images available are listed with a sele ction box in front of the image name and the type of rotation oscillation with its beginning and end angles following Click on the box to select deselect the image The sequence field dynamically changes with the selections Find Spots x Main Advanced Scan Table Right click for further options Template 22 Mo i myo2_screen osc Rican View Images List myo2 0sc 1 60 Select Scan Clear Scan Select Screen Clear All Close Save Defaults View Images List menu option right click on entry field allows the user to select image files Before clicking the Run button to Find Spots de select un highlight the To Use entry field to verify the selected image entries Scan Ecan20 myo2 osc 1 60 myo2001 P P P P P P P P P P P P Fmyo2013 P 720 730 x Sequence s SelectAll Cea Cancel Page 36 CrystalClear User Manual 2 3 Common CrystalClear Tasks If desired change other parameters in the Find Spots dialog box When satisfied with the settings click Run CrystalClear finds the spots in each image file selected
23. Save Defaults Save the Setup Settings in the Setup dialog are automatically saved with the current sample Some values may change as the data is processed Setup data can also be saved to the project level data file or site level data file if you are a CrystalClear administrator To save Setup data to the project or site data files 1 Click Save The Default Manager dialog will appear e For assistance using the Default Manager see page 209 in Appendix F Defaults in CrystalClear Page 56 CrystalClear User Manual Data Collection and Processing Default Manager Ea Site Current Levels E Administrator qao dhulick SFE E 4 Myoglobin IV Project Myo2 current User T Site m nset Set All Unset All 2 Check the desired level to save 3 Click OK Note Site level defaults are saved to CrystalClearSiteDefaults ho in the IDATA directory User level defaults are saved to CrystalClearUserDefaults ho in the user directory Project level defaults are saved to CrystalClearProjectDefaults ho in the user project directory A Sample level default is saved to samplename ho in the user project sample directory Site level rights are enabled by the CrystalClear administrator only Collect I mages with an I maging Plate System R Axis IV The Collect Images dialog prepares a schedule for the collection of data with an Imaging Plate System R Axis IV To schedule a
24. The Double Check Settings dialog will appear Double Check Settings Please make sure that the Crystal to Detector Distance and Detector 2 theta Angle are correct before continuing Cancel Image Collection Rot Axis Angle Angle 16 C 100 0 Schedule Collection T Do not show this dialog in the future 5 Review the specified settings on the detector 6 Click Start Image Collection or Cancel Image Collection if an error is found In the event CrystalClear detects insufficient disk space available for the entire data collection a dialog will appear to guide you through selecting a new collection directory You may need to cancel the data collection and free up space on the hard drive If you wish to delete the images and processing from an old sample presumably with all necessary file archived see Delete Projects and Samples on page 97 of Section 7 Tool Reference CrystalClear User Manual Page 59 Data Collection and Processing Collect I mages with CCD System Mercury CCD The Collect Images dialog prepares a schedule for the collection of data with a CCD system the Mercury CCD To schedule a collection run 1 Click the Collect Images button on the Flow Bar The Collect Images dialog will appear Image Collection Ea IV Dezingered Exposure Bin Mode C 1x1 2x2 Collect Schedules Default Add Scan Remove Sean Scan Scan Det Max Start
25. attached to a flexible stainless steel belt When each IP is placed in the expose position the IPs are not placed in exactly the same position there is generally a 1 to 4 pixel difference in the position effectively resulting in a two 2 detector system Failure to correct for this effect can cause problems during processing due to drastic changes in the direct beam position between successive images The instrument server uses the direct beam position information to shift the images read from one of the IPs when they are written to disk so that the direct beam position on images from both IPs coincide effectively reducing the system back to a single detector system Warning In order to protect the detector the direct beam shall always be attenuated during direct beam shots To take a direct beam shot 1 Start CrystalClear and log in as the administrator 2 Close the sample by clicking Cancel or OK in the Open Sample dialog 3 Click Utilities gt Administrator Utilities The Administrator Utilities dialog will appear 4 Remove the beam stop Remember to return the beam stop when direct beam shots are complete 5 Specify the settings for Direct beam shots a Set the Number of shots to at least 5 for the R Axis detector For the CCD only one 1 direct beam shot will be taken regardless of the value entered b For R AXIS detectors the detector should generally be initialized so that the IPs are erased before taking direct
26. drive and updates the Scan State Display This is a valuable option if more images are available than when the sample was initially created If the R Axis is the Image Collect Device Type the following window will appear Page 102 CrystalClear User Manual Tool Reference El Scan State Display ode Han ad rata Sean Sean Det Wax Stat End complete San Exp Sehe ID Template Cet 20 Resh Ange Ange Width rg ress 3o o Time imes Coecded Collecbon 2 12 163 4 2 1 2 Collect Schedules Dele x Add Daae Hanaga L ar Add Scan Delete Saen Seen Scan be bas Stat Ena x Complete sten Exp Schade Resh Ange Ange eth megas ress gt Time meo Colocted Collector Cnt 26 I ce EEEO Save Syne wih Dinh If Mercury CCD is the Image Collection Device Type the following window will appear E Scan State Display olx r Screen Schedules E CrystalClear Data Myo2 MY02 Add Delete Manager Zomplete Start Exp A x Axis Angle Angle Width Step Images ness lime s Images Scan Det Max _ Rot Start Ena Template Dist 20 Resin Deg r Collect r Schedules fe CrystalClear Data Myo2 Mv02 y Delete Manager Add Sc E complet Start _Exp Scan Scan Det a Max i Rot Start End 2E D Template Dist 28 Sa A w rari ee Angle CAEN E Images ne
27. 0 6 e Accurate 1 0 e Custom Set by user 5 If desired make changes in Result Limit and or Search Rotation group boxes 6 If you wish to Use Previous Reflections check the box Select the Previous Reflection by using the down arrow 7 Ifyou with to use defaults from other projects click the Defaults button The Get Defaults dialog appears Get Defaults x Load the dialog parameters using Sample values Project level defaults _ Cancel C User level defaults Site level defaults 8 If you wish to Save click the Save button The Default Manager dialog appears e For assistance using the Default Manager see page 209 in Appendix F Defaults in CrystalClear Page 82 CrystalClear User Manual Data Collection and Processing 9 When all desired settings are selected Click Run Integration The Integrate function predicts the reflections which would appear on a range of images This process may produce several reflection files These files are merged as part of the Integrate function Integrate with d TREK RAXIS or Mercury CCD Integrated reflections are written to the file dtintegrate ref and are readily displayed within CrystalClear To integrate images 1 Click the Integrate Reflections button on the Flow Bar The Integrate Reflections dialog will appear Integrate Reflections Ea Main Advanced Scan Table Right click for further options Template Avail To Use myo2 osc 1 60
28. 11 WHAT YOU SHOULD KNO Wes das 11 HOW THIS MANUAL IS ORGANIZED cccccsccceccesccsccseccsccescccsccusceusccscesceesceescueceusceuscaecasecesceuacs 11 NOTATION CONVENTIONS A dak eee dda ea os 11 REFLECTION LISTS ul laaan a o en dea ER do aA A Ad NAL 12 CRYSTALCLEAR D TREK COORDINATE SYSTEM ccscccssccscccscccsccusccsceusceusceescueceusceuecesecesccesceuncs 13 REEATED DOCUMENTATION ss isccs2cbiocde see cbaeeasSebuee ad ae 14 2 INSTAL ATION ac cccciecsssicccsiscccsccceetecvvs secs seessesecssccceseccseocsveecoes suse ssaceseucoosbessscccesbosbessesscsccsebeess 15 SYSTEM REQUIREMENTS a daii ds 15 INSTALLING THE CRYPTO BOX DONGLE ccccccssccseccseccscccscccccusscusccscescesceescusceusceusceuecesceesceuncs 15 INSTALLING CRYSTAT CLEAR iczncsdincetonsds ccuersias dood vaactocadas oe venta dee baviet E castaeae teases deubeest deodaswectuess 15 AETERSINSTALCATION A a Nod 16 UNINSTALLING CRY STALCLEAR a A e dea titi 17 3 INTRODUCTION TO CRYSTALCLEAR cccsscccsssccssscccsscccccsccesccccesccesscccsscceecsccsccccsescoees 21 WHATIS CRYSTAL CLEAR lada a 21 OVERVIEW OF THE CRYSTALCLEAR INTERFACE ccccseccssccesceusceescesceusccusceeccesceesccesceuscenssesceuseens 21 Task DropzdOwm LIS A id es 21 CU e a a 21 Ron Moderna a ada 21 Elo WiB a A a a de ng a a El a a as Ene bl o 22 Step BUIN ea ed ee 22 Steps with SUBStEPS aa 22 TODA a a Cees a A it IN dad eda vietcces 22 4 RUNNING CRYSTALCLEAR FOR THE FIRST TIME
29. 153 0 075 0 004 0 079 0 121 0 149 0 167 0 177 0 179 measured average deviation gt 0 0462 4 Check the evaluation of centricity Select the correct centricity if it is not already selected 5 Click OK Spacegroup 1 Click Spacegroup on the Flow Bar The Spacegroup dialog will appear Spacegroup HEI Reflection List lt l Sig gt Tolerance fo Close Save Defaults 2 Select the Reflection List file to use generally dtprofit ref 3 Make other adjustments to settings including the average intensity lt I Sig gt Tolerance for the parity groups 4 Click Run 5 Evaluate the suggested space group s Crystal 2 tab of the Set Up dialog to enter the space group CrystalClear User Manual Page 45 Common CrystalClear Tasks Scale and Average Once integration is completed you should scale the reflections 1 Click Scale and Average on the flow bar The Scale and Average dialog will appear Scale and Average Main Advanced Reflection Lists dtfind ref dtintegrate ref dtintpred0001 ref dtintpredO002 ref dtintpredODO3 ref dtintpred0004 ref dtintpredO005 ref dtintpredODO6 ref dtintrefine ref Bo y T dtintrejects ref Bm h mu 14cm r Error Model Auto Weight Multiplier Auto Intelligent y r Weight Addend auto Intelligent y El Algorithms Absorption Correction I Batch Scale Method I B factor Fourier 8 3 I
30. 2 Click on the Users tab Administration x General Users Groups Tools Servers Users Administrator OK Cancel Help 3 Click the Add button The User Settings dialog will appear CrystalClear User Manual Page 143 Appendix B Administration User Name espin OK Description fi Lynn Esplin Cancel Data ft data jesplin E Help j Password Default English ba New Member of Groups Administrators rite XXXXX Confirm 4 Enter the user new name in the Name edit box For the user s convenience the name you enter in this field could be the same as the user s Windows login name By default CrystalClear displays the user s Windows login name in the initial CrystalClear Login Name field 5 Enter a meaningful description of the user in the Description edit box This description can be the person s full name their job title or any other text that is meaningful in your work environment 6 Enter the path to the user s preferred data directory in the Data filename edit box Ifyou leave this field blank CrystalClear will automatically create a subdirectory for the user and that path will be displayed in this edit window when you edit the user s settings in the future For example the default directory for the user name Jesplin would be c Program Files Rigaku MSC CrystalClear data VJesplin if fMataWesplin were not used 7 In the Password gro
31. 209 in Appendix F Defaults in CrystalClear for assistance CrystalClear User Manual Page 127 Additional Processing 1 When the Collect Images dialog Save button is clicked the Default Manager dialog will appear Default Manager x Site Current Levels E Administrator M Samol dhulick ae B Myoglobin Project Myo2 M User Myo3 current T Site Set Unset Set All Unset All ilek E Cancel 2 The Default Manager dialog allows the user to save the settings to various levels Select the Current Levels you wish to save by clicking the appropriate check box e Alternatively selections can be made by clicking the radio button beside the appropriate Site User Project or Sample names a Use the following buttons for assistance in setting defaults Set Sets a default Unset Unsets a default Set All Sets all Levels Unset All Unsets all Levels Note Only Users with Administrator privileges are authorized to set Site Defaults For most users this option is grayed out Run a Collect Schedule To run a collect schedule 1 Access the Collect Images dialog e The Collect Images dialog can be accessed by clicking the Collect Images button on the Flow Bar during a Collect task Task drop down list options Screen Collect and Process Collect Page 128 CrystalClear User Manual 2 Additional Processing and Process or Collect Use the Scan Table to alter the scan
32. 4n 42 43 44 1 4n 6295 5524 1 1335 6346 5346 167 79 6297 5439 177 22 6344 5431 161 95 6315 5471 169 97 6326 5399 169 15 6314 5378 168 25 6327 5492 170 87 6308 5427 171 94 6333 5443 167 19 6292 5399 166 00 6349 5471 t309 9912 8376 175 36 3069 2494 151 46 9469 8188 176 10 31 72 2682 150 05 9468 8175 168 43 31 73 CrystalClear User Manual 237 42 156 79 155 273 47 157 112 299 00 260 44 n00 OkO 8 37 4 i eh ka 4 Saat i a 75 91 0 4 A Tc pi i 4 at i a a as a 914 12 18 1 0 55 19 19 744 09 7 su o e ad ii F EE 554 96 al ea a ie T ai al a 75 42 27 10 311 34 10 10 gt 572 17 Appendix C Sample Log Files 45 2695 271 83 SAS ES ARS 7 46 172 94 199 04 ZU ga ARS RS PRA 351 10 47 k 1 4n 9481 1094 AR AAA AAA AAA AA 48 8124 841 SSeS sS Rare AS ASAS CARS 49 170 07 A SSeSso SSSer SS ses 50 k 1 4n 3160 cc TOSIA epee se See Sse Soe ae 51 2746 28 aasan Saeni sSSSSS8 l SESSA s5eas 52 168 02 204 60 a Spsssa lt eSsee SseRse gt Seser 53 h 1 4n 9474 305 GASDA teases a See 54 8151 22 Ses5e5 SsSesoes VSesanse gt Ses s gt 55 KOGI isa 200489 caschi paez lgeresh codsss 56 h 1 4n 3167 T01 gt o Ses O sSese yi 2119 met a esse secese Ei 58 166 43
33. 53 Main Tab 50 Notes Tab 56 X Ray Source Tab 55 Simulator Server 112 Status Bar 25 Step Button 22 Steps with Substeps 22 Stop Signs 25 Page 216 Strategy 80 System requirements 15 T Task drop down list 21 Toolbar 22 TwinSolve 23 49 76 135 138 161 199 U Updating Defaults See Defaults Updating User Preferences 110 Specify collection defaults 116 Specify directory 111 Specify other settings 115 View Settings 110 V View Settings 110 CrystalClear User Manual
34. 7 IP1 IP2 a Cycle Xx y I x y 9 20 1 504 2 1507 0 241280 506 2 1506 8 247008 21 2 506 1 1506 3 14490 1508 0 1506 7 14340 22 23 Direct Beam Utility 24 Number of cycles 5 25 Exposure time 1 0 seconds 26 Date Thu Mar 30 16 56 17 2000 27 Average direct beam position for IP1 1499 6 1509 6 28 Average direct beam position for IP2 1500 9 1509 6 29 IP1 IP2 30 Cycle xX y I Xx y 31 32 1 1499 8 1509 8 10841 500 7 1509 8 10932 33 2 1499 4 1509 6 10346 501 3 509 4 10267 34 3 1499 4 1509 4 9872 501 0 509 7 10826 35 4 1499 6 1509 7 11006 1500 9 1509 5 10846 36 5 1500 0 1509 5 10600 1500 7 1509 6 10831 Lines 1 10 Summary of direct beam shots taken on 30 September 1999 Lines 11 21 Summary of direct beam shots taken on 19 October 1999 Lines 23 36 Summary of direct beam shots taken on 30 March 2000 Important If either X beam or Y beam position differ from IP1 or IP2 this will be corrected at the time of data collection using the values from the direct beam shots If the values of either X beam position differs on the same IP between cycles the adjustments may be needed for the IP belt itself PMTCheck Log A summary of the typical log file PMTCheck 1log generated by the PMT check utility is shown below 1 PMT Check Utility Copyright c 1998 1999 Molecular Structure C
35. A A a A ANA OA dls 119 Page 8 CrystalClear User Manual Table of Contents MERGE REFLECTION LISTS WITH D TREK cccccccccccescececeeseesecseeeceeceeseeceeeeneesesseneesessuaeeseuaanes 119 GREATE AND EDIT MAGROS dida is 121 Creatina a M ACT O22 ences AE Ei 122 A Re Rea nee ct E E 124 THE COLLECT SCHEDULER retroensa ieont tido vans dra tebe E Ur did 125 Create Collect S ch dul id did 126 Import a Collect Schedule ocoocionnoncononnnonanonconocnnonocnnonoonnonoonacnnonanononnocncnnncnnonoonnonocnnnnconannnos 127 Save a Collect Schedule turca e did cand dseasdesbuvbcdertecedereobaberees 127 Ruma Collect Schedule isccocuc canada tassel beceodusencssenobueeedhonutsosht deseodasenaebenobuseedhonveees becaosugense es 128 Delete Collection Schedule miii di iia cie 129 ME A NT 131 THE IMAGE WINDOW O o die aia dec e dono de ao a e ON da e 131 A A AA EN 131 Profe AT aCe LOAI EAE la 131 Large Image Window Toolbar c scccccceceseesessenececececessessacceceeecesessesnaaececeeecesseseaeeaeeeeseeeees 132 Small Image Window Toolbar 0 0 0 0 ccceceeeessssssececececeseesesnaececceecessesesaeaeeeeeeeeeeseqnaeceeeeeeeeeeeeaas 134 Small Image WINDOW se scnceadecses ives eaaa oet aeaee OET dueggwanetage O E EERE bateas tened 134 Image Information Window 0 eeeeeessccecececeseesssenaececececesseseanaeceeeceseessnnaaececeeeeeceeseaeaeeeeeeeees 134 APPENDIX A FILES AND DIRECTORY STRUCTURE scscccccsc
36. Absorption Correction Regab Spher Diameter mm i Exclude Sigma a tw Reject OE Normal Output Th Scaled Averaged Output File F 0 00 gt ScalAveraged ref Chi 2 T No Header Max Group Chi 2 be FT Output Anomalous l m AAA FT Scale Anomalous I I Close Save Defaults 2 Select the Reflection List file to use generally dtprofit ref 2 Make any other adjustments to the settings that you desire Some items to consider are the level at which you exclude reflections from the refinement Exclude Sigma but include in R merge the level of which to reject outliers either by the standard deviation Rejection sigma or by the Chi Square deviation based on Maximum or on percentage rejected the way in which to determine the error model batch scaling absorption algorithm and hence the method of correction and output of the reflection file 3 Click Run Page 46 CrystalClear User Manual Common CrystalClear Tasks A CrystalClear message appears CrystalClear N lt is not recommended to reject reflections with chi 2 less than 2 Continue The Scale and Average Results window will appear with the results of the scaling displayed as graphs generating a log file and writing the reflection file to the sample directory CrystalClear User Manual Page 47 Data Collection and Processing 6 Data Collection and Processing There are five basic ste
37. CrystalClear See Defaults Delete Projects and Samples 97 Dialog Defaults See Defaults Dialog Display Instrument State 107 Display Processing State 98 Display Scan State 102 F Files and Directory Structure 135 Find Sp ots TwinSolve 76 Flow bar 22 I Ice Rings See Integrate Ice Rings Image window 25 Image Window 131 Index d TREK 63 Overcome perceived problems 70 TwinSolve 76 CrystalClear User Manual Index Spots 63 See Index d TREK TwinSolve 77 Indexing 37 Inherited Defaults See Defaults Inherited Installing CrystalClear 15 Integration 83 L Log File window 25 Logging in 27 Login as Administrator 141 M Macros create and edit 121 Mask Files 54 Mercury CCD 11 Merge Reflection Lists w d TREK 119 Message Window 25 N New Sample Defaults See Defaults New Sample Next Step arrows 25 O Open an Existing Sample 95 P Predict Spots d TREK 74 TwinSolve 79 PROCESS 49 135 151 161 199 Process Images 32 Processing State 98 Profile Windows 131 R R AXIS 11 Refine Cell d TREK 71 TwinSolve 78 Index Page 215 Index Resolution Set 119 Run mode 21 S Save the Current Sample 96 Saving Defaults See Defaults Saving Scaling 46 Scan Table 103 Edit 106 Manipulate 105 Selecting a processing algorithm 49 Setup 32 50 Crystall Tab 51 Crystal2 Tab 52 Detector Tab
38. CrystalClear Tasks 2 Make other adjustments to desired settings 3 Click Run to predict spots CrystalClear predicts the spots in each image file selected creating a log file called dtpredict log If the view Image Processing Updates icon is toggled on predicted spots are represented by colored circles on the image s The predicted pattern should closely match the observed pattern For more information see Index Spots on page 63 of Section 6 Data Collection and Processing Strategy For detailed help see Strategy on page 80 of Section 6 Data Collection and Processing Strategy can be used to automatically generate a collection schedule so you don t have to 1 Click Strategy on the flow bar The Strategy dialog will appear Strategy Ed Main Advanced Search Resolution Minimum Maximum Min Completeness 99 00 Close Save Defaults 2 Make changes in setting if desired 3 Click Run CrystalClear User Manual Page 41 Common CrystalClear Tasks Integrate Reflections For detailed help see Integration on page 83 of Section 6 Data Collection and Processing Once the reflections can be accurately predicted they can be integrated 1 Click Integrate Reflections on the flow bar The Integrate Reflections dialog will appear Integrate Reflections ES Main Advanced Scan Table Right click for further options Template Avail To Use myo2 osc 1 60 Select All Clear All
39. Crystallographic Troubleshooting reflections 2 Use the delete spots icon to delete spots see Tegma herer n nd Spo OO OO There are lots of spots very Increase the box size EPA esne O Indexing is incorrect based on 1 Check that the crystal to detector distance X and Y beam positions the measure tool distances wavelength and 2 theta angle are correct 2 Indexing may be correct if there is additional symmetry continue on to prediction for varification 3 If the peak shapes are poor then try raising the I sigma level to avoid the weaker peaks Additionally this will likely force the larger twin portion to index 4 If the cells are all much too large including the triclinic set the maximum cell in the indexing to a smaller value about 2x that of the closest spot separation for starters I don t see all the crystal lattices Set the maximum residual in the advanced tab of index to 100 in the table of indexed lattices The software keeps choosing Use the User Chooses Solution option in index Upon completion the wrong lattice in indexing choose the lattice from the list If all the lattices are not displayed increase the maximum residual Few of the reflections are Adjust the resolution limits I sigma and rejection limits included during refine The test mosaicity is greyed You are using Reflection List to Refine on Set this to Images and edit the To Use field A range of image
40. I sig in D TREK Find Spots 6 Click Run when satisfied with your selections Index Spots To index spots 1 Click Index Spots on the Flow Bar CrystalClear User Manual Page 77 Data Collection and Processing The Index Spots dialog will appear Index Spots x Use the first 200 available reflections Use reflections Vector Acceptable Deviation Vector Shortest Length 0 00500 foo 000 hkl Deviation 0 20000 r Known Unit Cell I Use Known Unit Cell E B Y 0 00 0 00 p 00 length tolerance eoo Anae tolerance fo 00 Defaults 2 Specify the reflections by selecting the appropriate radio button 3 If desired check the Use Known Unit Cell check box then specify the unit cell values 4 Make any desired changes in Vector and or Deviation 4 Click Run when satisfied with your settings Refine Cell The Refine Cell feature refines the crystal crystal goniometer detector goniometer and source properties in order to reduce the differences between observed and calculated reflection centroids CrystalClear can display the observed and calculated reflection centroids so the progress and validity of refinement can be judged To refine cells 1 Click Refine Cell on the Flow Bar The Refine dialog will appear Page 78 CrystalClear User Manual Data Collection and Processing Detector IV Test Cell M XCenter M Pitch M Y Center MV Roll M Distance M Yaw hkl Deviation Use Overlapp
41. Main Crystal Ciystal2 Detector X Ray Source Notes Project M yoglobin Sample M y02 Crystal ID Temperature C User defined ID string 20 00 v Crystal To Detector Distance mm Detector 28 0 00 Close Save Defaults 4 Check the values on the different tabs of the Setup dialog box change any values that are not correct and then click OK In particular pay close attention to the necessary parameters X and Y Direct Beam positions Crystal To Detector Distance Detector 20 and Source Wavelength The CrystalClear Flow Bar will automatically begin the next step Assign Unit Cell The Find Spots dialog will appear Assign Unit Cell The next step in the Flow Bar is Assign Unit Cell This step in the Process assists the CrystalClear user in procedures Find Spots Index Spots Refine Cell and Predict Spots The purpose of this section is to determine and confirm the unit cell and mis setting angles Find Spots The Find Spots dialog allows the user to select images Image numbers may be entered manually or selected from a list When entering image numbers manually be sure to use a dash to separate consecutive image entries or use a comma to separate non consecutive images entries Before clicking the Run button to Find Spots de select un highlight the To Use entry field to verify the selected image entries Page 34 CrystalClear User Manual Common CrystalClear Tasks Find Spots
42. Main Advanced m Profile Analysis C User Defined Size 1 Size 2 ps 0 20 AA PA Wait Limit sec 900 Refinement Macro Single Step Refine y Pre refinement None Close Save Defaults Ice Rings Min Resin Max Resin Add Delete 10 In the Profile Analysis group box select whether you want CrystalClear to automatically pick a profile size use no profile size None or define your own profile size If you select User Defined specify the sizes of the transformed local Kabsch 3D profile in degrees The Size 1 value is the angular spread of a reflection in directions tangent to the Ewald sphere while the Size 2 value is the angular spread of a reflection in the direction perpendicular to the reciprocal lattice vector when in the diffraction condition Good starting values are 0 5 arctan spot_size crystal_to_detector_distance and max crystal_mosaicity 3 2 image_rotation_width These are the same as the Kabsch XDS parameters DIVRAD and DIVBET For either if a value of 0 is used then an appropriate value is calculated For either if a negative value is used then profile analysis is not performed 11 Specify the maximum number of seconds to wait for a required image to appear before stopping in the Wait Limit field The value of O means do not wait so if an image cannot be found integration will finish 12 Select the Refinement Macro to be use
43. Poissonian counting statistics then the expected Rmerge for this shell would be 1 T So for the shell of highest o 1 1470 0 026 is consistent with 0 029 found In the 4 6 shell 1 2 49 0 142 is consistent with 0 117 found Number of reflections in this shell Number of rejected reflections There should be very few if any rejected reflections Any shell with a large number of rejected reflections should be investigated Perhaps there are a number of saturated reflections or unaccounted shadows on the detector Number of reflections in this shell having symmetry related mates and that contributed to the Rmerge Number of unique reflections measured multiple times in the shell The average multiplicity or redundancy for the shell is Num ovlps Num mults The average Intensity Sigmal for averaged reflections in the shell As expected there is a larger lt I sig gt for the averaged reflections than shown for unaveraged reflections in the Rmerge vs Batch table This is the normalized 7 popularized by Dr Zbyszek Otwinowski calculated as 1 N Nai 2 2 Q N ee l l where N is the number of unique reflections and N is the number of contributors to or multiplicity of averaged reflection I Values close to 1 suggest that the error model w is valid This is the Rmerge for reflections which belong to this shell This is the cumulative Rmerge for reflections which belong to this shell and all previous shell
44. TREK Processing Server Options Stand Alone Server E uleelient Serves m Configuration IP Address Port 127001 MV Auto Generate Port Number e234 Range e233 To e302 Specify Default Site level Settings After installing CrystalClear you should set the default settings for your site These settings will be inherited by all projects that are created later To set the default settings 1 Start CrystalClear and log in as the administrator 2 Close the sample by clicking Close in the Open Sample dialog 3 Click the Setup button on the Flow Bar Alternatively you can click Sample gt Setup on the menu bar Make adjustments to the settings on each tab then click Save The Default Manager dialog will appear Page 154 CrystalClear User Manual Appendix B Administration Default Manager x Site Current Levels 5 Administrator dhulick Ao Myoglobin Project Myo2 User Myo3 current Site Set Unset Set All ilele Unset All Cancel 5 Check the Site radio button then click OK If the Site radio button in the Current Levels group box is grayed out you do not have administrator privileges Exit CrystalClear and log in as an administrator then repeat these steps 6 Continue through all of the dialogs available from the flow bar repeating steps 4 and 5 for each dialog The settings will be saved to
45. The Main tab in the Setup dialog includes the basic settings that are most often adjusted during collection and processing of data A few of the items found on the Main tab are also found on the other Setup tabs along with additional settings that normally do not change Project and Sample The names of the current project and sample are listed for your reference Crystal ID The Crystal ID is a name or number you can give to your crystal for your personal reference This value is not used in collection or processing Temperature C The temperature of the crystal sample at the time of collection in Celsius Crystal to Detector Distance mm The distance from the crystal to the detector when collecting images If you are processing existing images the value specified when the images were collected will be displayed Detector 20 Swing angle of the goniometer If you are processing existing images the value specified when the images were collected will be displayed Page 50 CrystalClear User Manual Data Collection and Processing Main Crystalt Crystal2 Detector Ray Source Notes Project fu yoglobin Sample Myo2 Crystal ID Temperature C User defined ID string 20 00 X Crystal To Detector Distance mm Detector 28 0 00 Close Save Defaults Note Crystal To Detector Distance mm and Detector 20 fields show the hardware or unrefined values If per scan is displayed in
46. cycles 10 weight 9999 display go 88 Refine listing 89 90 Crystal listing 91 Page 172 CrystalClear User Manual Appendix C Sample Log Files 92 Unit cell lengths 68 7533 73 7744 107 0866 93 Unit cell angles 90 0000 90 0000 90 0000 94 Unit cell volume 543168 687 95 Orientation angles 155 9357 29 9512 102 4337 96 Mosaicity 0 480 97 Description unknown 98 99 Spacegroup number 16 00 name P222 01 Num equiv posns 4 02 03 CRYSTAL_Goniometer listing 04 05 Description Eulerian 3 circl 06 Number of values 3 07 08 Name Datum Current Units Vector 09 10 Omega 0 000 Unknown deg 1 000 0 000 0 000 11 Chi 0 000 Unknown deg 0 000 1 000 0 000 12 Phi 0 000 Unknown deg 1 000 0 000 0 000 13 14 15 Source listing 16 17 Single wavelength 1 5418 18 Polarization 0 5 1 0 O 19 Intensity 0 20 21 RX_Detector listing 22 23 Pixel dimensions 1900 1900 24 Nominal size in mm 193 23 199 5 25 Description RAXIS conversion 26 27 RX_Goniometer listing 28 29 Description UNKNOWN 30 Number of values 6 31 32 Name Datum Current Units Vector 33 34 RotZ 0 230 Unknown deg t 0 000 0 000 1 000 35 RotX Swing 0 026 Unknown deg 1 0 003 0 000 0 000 36 RotY 0 042 Unknown deg 0 000 1 000 0 000 37 TransX 0 092 Unknown mm 1 000 0 000 0 000 38 TransY 0 061 Unknown mm 0 000 1 000 0 000 39 TransZ Dist 98 0
47. dependant dependant 8 min RAXIS II Pixel resolution 100 um pixel 2x2 binned 2x2 binned Readout Integration All collection images All collection images All collection images CrystalClear User Manual Page 207 Appendix F Defaults in CrystalClear 0 0 0 user sets user sets O user sets Peak radius min max dtprofit ref Centricity Reflection file Reflection file Vsig Scale and Average Reflection file Algorithms Absorption Exclude sigma Error model mul Addend Rejection sigma Chi square Scale anomalous Optional output Dtprofit ref dtintegrate ref o Saz Apel gt e N O o SES oj gt e Nn o EE OPN a Y Reflection file dtprofitref EAN Reflection file dtprofitref USB gt AAA dtprofit ref tprofit ref dtintegrate ref tprofit ref tprofit ref tintegrate ref o Nn Ww Eh Uy dtprofit ref Batch absorption Spherical 4 3 dtprofit ref Batch absorption Spherical 4 3 dtintegrate ref Batch absorption Spherical 4 3 2 5 Auto Rmerge Auto intelligent Auto Rmerge Auto intelligent Auto Rmerge Max fraction 0 0075 No Output anomalous Max fraction 0 0075 Max fraction 0 0075 Uncorrected unaveraged F2plus dat Output anomalous Output name Resolution D Ww Page 208 CrystalClear User Manual Appendix F Defaults in CrystalClear Using the Default Manager The Default Manager dialog allows you to save at the User Level Proje
48. module which can be use to process twinned crystals Find Spots To find spots 1 Click Find Spots on the Flow Bar Page 76 CrystalClear User Manual Data Collection and Processing The Find Spots dialog will appear Find Spots xX Image List myo2_screen001 osc myo2_screen002 osc myo2001 osc myo2002 osc myo2003 o0sc myoZ2004 osc myo2005 osc myo2Z006 osc A ppend spots to myo2007 osc a current spot list mpo2008 ase zl Sequence Spot Size Pixels f 5 Pm Distances Pixels Peak Threshold 3 00 x 7 Y Z E 3 Close 2 Select the images to be used to find spots You can either select the desired images from the Image List or specify a single range of image sequence numbers in the Sequence edit box We recommend that you perform a find on all the images from the first scan of data then repeat the find step using all the images from each subsequent scan of data checking the Append spots to the current spot list box This will use all of the reflections resulting in better determination of the twin components 3 Specify the Neighbor Distances The neighbor Distance is the distance between spots in pixels Specify the distance for the X Y and Z axes The default values of 7 7 and 3 are sufficient for most samples 4 Specify the size of spot to find in the Spot Size edit box The default value of 15 is sufficient for most samples 5 Specify the Peak Threshold analogous to
49. ness ime zE Images _ Colle ae 0 4 750 47 47 24 myo2 0sc 1200 00 163 15418 00 El 63 0 En EES 7 13 25 myo2 0sc 1200 00 163 15418 00 00 660 740 10 10 7 75 0 7 13 4 Using the Scan Table The Scan Table is useful in changing various settings of scans in a Collect Schedule The Scan Table consists of a series of manageable columns and column headings The user can manipulate the Scan Table allowing columns to be viewed or hidden and columns widths can be changed The Scan Table CrystalClear User Manual Page 103 Tool Reference 1s used to edit the various settings within a scan to serve their particular needs within a Collect Schedule Using the Scan Table consists of Manipulating the Scan Table Assisting the user in viewing the Scan Table by clicking dragging and viewing columns Editing the Scan Table Assisting the user in altering the individual scan settings within the columns to achieve the desired Collect Schedule The Scan Table is accessible on the Collect Images dialog and on twice the Scan State Display e To access the Collect Images dialog Click the Collect Images button on the Flow Bar during a Collect task Task drop down list options Screen Collect and Process Collect and Process or Collect e To access the Scan State Display Click the Show Scan State Display button a on the toolbar Or click View gt Scan State Display on the CrystalClear menu The Col
50. of a new project and sample A Projectis a collection of related samples For example you may grow ten myoglobin crystals which you plan on processing as individual samples You can create a project called Myoglobin then create ten samples in that project one for each crystal A Sample is roughly equivalent to the data collected and processed from one individual crystal 1 In the Project Name field enter a name for your new project then click Next Project Name Wizard Ea As anew user you need to set up a project The project will contain all the data associated with the different samples you will create Use a descriptive name for your project example XYZ Protein Project Name Beck Cancel Help 2 In the Sample Name Wizard dialog enter a name for your new sample in the Sample Name field then click Next Sample Name Wizard x Each sample will store all the data settings and current state for a sample Sample Name New Sample lt Back Cancel Help 3 In the Task Selection Wizard dialog select a task from the Task drop down list then click Next Page 28 CrystalClear User Manual Running CrystalClear for the First Time Task Selection Wizard Select a task that you want to perform on the new lt Back Cancel Help This chart shows the tasks on the dropdown menu by clicking the Task down arrow Screen Collect This task allows you to screen crystals
51. or more images in the same scan separated by nearly 90 degrees and use difference vectors in indexing 3 If the lattice is uncertain but the detector parameters are remembered vaguely try indexing and using the triclinic cell for refinement then reindex to see if the higher symmetry cell is determined How do I change the resolution Anywhere there are Resolution Limits fields and a Set box select ranges for all steps in the box and choose the processing steps to use the resolution limits processing currently in the edit fields and press OK You have no idea what the cell In an image display window zoom in on an area where spots are lengths may be regularly spaced Turn on the measure tool by selecting the ruler icon Touch on one spot and drag to an adjacent spot The inter spot distance will be displayed as you drag The red plus sign is not in the You are collecting images with an improper direct beam position and I got the Find Spots Failed The image is not there or is corrupted Wait for the image read to message and the log file shows finish reading image lys0001 osc Error opening file lysO001 0sc Error is 2 Find only found a few spots 1 Decrease the I sigma 2 Widen the resolution range 3 Decrease the minimum pixel value 4 Decrease the peak filter Find Spots found too many 1 Slide the number of spots slide in the image information window CrystalClear User Manual Page 211 Appendix G
52. reintegrate up to that point The assumed symmetry is too high Change the putative space group CrystalClear User Manual Page 203 Appendix F Defaults in CrystalClear Appendix F Defaults in CrystalClear Site Level pwoods sgrapelli User Level Project Level Zn_13 May22a May22b Cyt_tryl Myol_3 Sample Level New Sample Defaults When a new sample is created the defaults are obtained from the project under which it is created Example When sample Zn_13 was created a copy of the defaults from project Zn was made and assigned to Zn_13 Inherited Defaults When the user saves defaults at the project level the changes are not automatically reflected in other existing samples in the project However any new samples created will reflect the changes Example If the user changes defaults in 2n_13 and then saves to the project level Zn_cub will not be modified as a result Thus 2n_13 Zn Zn_cub If the user creates a new sample Zn_1 4 its defaults will be identical to Zn Thus Zn_13 Zn_14 Zn Zn_cub When the user saves defaults at all levels the defaults are only immediately reflected in objects residing in a direct line from the sample currently open to the site level Example If the user changes defaults in May22a and then saves to all levels the defaults will be reflected in the following databases e May22a Sample e May22 Project e mdavis User e Site The new defaults are not immediatel
53. s and Remove Scan s then make changes to scan settings as desired For assistance in manipulating the Scan Table columns headings or other settings see Using the Scan Table on page 103 of Section 7 Tool Reference Calculated based on supplied values and number of images Required disk space The amount of disk space required to complete the scheduled collection request Total disk space drive The amount of disk space currently available Completeness Completeness of data in the scan Note If insufficient disk space is available to complete the scheduled image collection request a CrystalClear warning dialog will appear The collection request may be cancelled to allow the user to Page 58 CrystalClear User Manual Data Collection and Processing free more disk space on the system before continuing See Create a Collect Schedule on page 126 in Section 8 Additional Processing for more information about adding your own collection schedule 2 Use the Scan Table to alter the scans you may e Use the Add Scan button to increase the number of scans at a different crystal orientation Adjust settings as desired e Use the Remove Scan button to remove undesired scans For assistance in manipulating the Scan Table columns headings or other settings see Using the Scan Table on page 103 of Section 7 Tool Reference 3 Make adjustments to the settings as required 4 Click Run to start the scheduled collection scan
54. set to the R merge of the data Advanced 1 Absorption Correction Outlier Sigma The default value of 125 tends to suffice In the event that the absorption correction fails this number can be raised for very strong absorbers to see if it allows a successful absorption correction 2 Resolution These can be left at 0 unless you want to cut off poor data at high angles Scaling Constraints Only available when absorption is not checked The default values should suffice 4 Optional Output Uncorrected Unaveraged Reflections with Correction Factors should be selected with an output file name of f2plus dat to be imported into teXsan or CrystalStructure When an absorption correction is not applied or fails the Corrected Unaveraged Reflections should be selected with an output file name of f2 dat and the Output hkl I Sigl No Header box checked to be imported into teXsan or CrystalStructure w CrystalClear User Manual Page 6 Table of Contents Table of Contents CRYSTALCLEAR USER S MANUAL ABRIDGED cccoooooccnonnonccnonnonccnnnnonccnonnanccnnnnonccnnononccnnnonss 3 CRYSTALCLEAR USER S MANUAL ABRIDGED csssccccssssccccccssscccccssssccecssccccecssscceesees 5 TABLE OF CONTENTS iissceccccdeccesceseseScevssredvsssceeseustsacedecbovs lor In UE vue beeeSecceseeseve ccessecoeb ecbveseceSousses 7 ABOUT THIS MANDA Eisicsiscdacesciecisl sccssdesestcestescosacosscecoegocnessecSesbobbacsoosecceveacesscosessuebeccsossoosnees
55. the CrystalClear Site Default database All the settings in this database will be inherited by each project as it is created Users can modify these setting for their own projects and samples For additional information about the options in the Setup dialog see page 50 in Section6 Data Collection and Processing Set Up I mage Collection Device Type CrystalClear operates with either a Rigaku R Axis or a Rigaku Mercury or Jupiter CCD image collection device After you install the CrystalClear software you will need to select the device type in order to control the instrument Select the I mage Collection Device Type To select the correct device type 1 Start CrystalClear and log in as the administrator 2 Close the sample by clicking Cancel or OK in the Open Sample dialog CrystalClear User Manual Page 155 Appendix B Administration 3 Click Utilities gt Administrator Utilities The Administrator Utilities dialog will appear E Administrator Utilities Image Collection Device Type 3 r Direct beam shots r Continuous IP Read Indi poo Number of cycles B T Initialize R AXIS FT write images to same file I Initialize before direct beam shots IV Open X ray shutter during read Take Take Photo Multiplier Tube PMT check r Light leak check r Attenuator factor T Initialize R AXIS Take Take Take Exposure Time sec 1 0 4 From the Image Collection Device Type drop d
56. the appropriate Number or Name field Number and Name To enter a known spacegroup type either the number or the name in the appropriate field Alternately if you know the Crystal System and need to be reminded of the possible Space Groups select the Crystal System then scroll and choose the Space Group from the list under Number and Name Orientation Angles These values will be calculated later on by CrystalClear Leave them as 0 000000 when starting a new sample Molecular formula Specify the molecular formula for the crystal You may enter the formula as it appears in your compound CrystalClear will determine the empirical formula for you The Detector Tab CrystalClear User Manual Page 53 Data Collection and Processing The Direct Beam settings on the Detector tab are based on the type of X ray detector Normally the values are set as site defaults by your CrystalClear administrator The Crystal to Detector Distance may be changed on the Main tab of the Setup dialog as well as on the Detector tab The Rot2 26 can also be set on the Main tab The other Direct Beam settings on this tab are generally not changed The Non uniformity Type group box offers the user several options The user may choose to create a mask file to exclude areas of the detector from consideration in integration Mask are used due to uncertain intensities resulting from shadows bad pixels or detector flaws Although it is not necessary to use a mask d
57. the row in an Index Results Window CrystalClear User Manual Page 37 Common CrystalClear Tasks Index Results Choose a solution Soln Least Sq Spacegrp 143 trighexagonal P 90 00 120 00 9 0 07 21 orthorhombic C 92 23 160 25 46 16 682272 90 00 90 00 90 00 12 0 07 a monoclinic P 9223 4616 9245 341161 90 00 119 92 90 00 13 0 02 5 monoclinic C 92 08 160 22 46 30 682999 90 00 9016 90 00 14 0 00 1 triclinic P 4613 91 81 9208 338099 6011 89 41 89 26 4 Look over the Index Results to identify the cell in question Least Squares Residuals LSR represent the residual between the current cell and the triclinic cell lower is better Depending upon the degree of accuracy of your detector geometric parameters the LSR will vary very small is well known Select a solution if it is not already selected 5 Click OK The Processing State Display may appear It shows the current parameters for the sample For more information on the Processing State see page 98 of Section 7 Tool Reference For more information see Index Spots on page 63 of Section 6 Data Collection and Processing Refine Cell The CrystalClear Flow Bar will automatically begin the next step within Assign Unit Cell The Refine Cell dialog will appear 1 The Refine Cell dialog allows the user to refine the crystal detector and source parameters Page 38 CrystalClear User Manual Common CrystalClear Tasks
58. to appear integrates and looks for the next image or reaches the end of the wait limit completes integration with the reflections it has to that point What should I do if Laue shows Here you will need to think about what it is showing you In general that I integrated the data in the if the symmetry during integration is higher than merited by Laue then wrong crystal system you should consider reintegrating If the symmetry is higher than that for integration it is recommended that you reintegrate but you may Page 212 CrystalClear User Manual Appendix G Crystallographic Troubleshooting still have good data which is usable for a first reflection file I need to have a different format In the CCP4 suite there is a conversion program to convert to mtz for my reflection file format from the d TREK format CrystalClear User Manual Page 213 Index C Close the Current Sample 96 Collect Image 31 Collect Images Mercury CCD 60 Collect Schedule Create 125 126 Delete 129 Import 127 Run 128 Save 127 Command Bar 25 Control the Detector 108 Create a New Processing State 100 Create a New Sample 94 Creating a New Project and Sample 93 Creating Your First Project and Sample 28 Crypto Box 15 27 137 200 Crystallographic Troubleshooting See Troubleshooting Current sample 21 D d TREK 23 25 49 63 83 89 92 119 151 161 178 199 Decision Point 25 Defaults in
59. wish to change the default resolution click Set See Set Resolution on page 119 of Section 8 Additional Processing for more information on the Set Resolution function 12 Set the Scaling Constraints Batch ID Specifies the name of the batch whose scale factors will remain fixed The scale factors of all other batches will shift relative to this batch Default first batch in the input reflection list Scale Factor Specifies the scale factor of the fixed batch All shifted scale factors are rescaled so this value remains fixed Default 1 B factor These options are only available when None is selected for the Absorption Correction Method list box on the Main tab 13 If you desire Optional Output file click the appropriate option then specify a name for the output file in the Output Name edit field If set the scaled but unaveraged reflections are written to the specified file This may be useful for further scaling or for use with other averaging and rejection algorithms Reflections rejected by the scaling process will have their Sigmal values set to 0 or less CrystalClear User Manual Page 91 Data Collection and Processing Check the Output hkl I SigI No Header check box if you want the output file to include only the h k l Intensity and sigmal fields in free format with no header Rejected measurements sigmal lt 0 will be excluded from this file This format is suitable for input to many non d TREK programs
60. 0 2Theta 0 0968 0 0182 0 0433 Direct Beam at 6 0 o Crystal System x 1500 0000 Pixel Size s0 0000 30 0000 120 000 Trigonal y y fis00 0000 15000 y Number Name Roti Rot2 Rot3 87 6125 23 3212 2 9291 Salca Mos Volume E Wavelength Rott Rot2 0 50 932603 46 P3 1 5418 on 0 05 Mask File Gave lthanaes lio New State Discard changes 2 Select the state that is most like the new state you wish to create from the State History drop down list Change the desired parameters in the Processing State Display window Save Changes to New State or Discard Changes Ifyou want to go back to the original settings click the Discard Changes button Discard Changes sets all the current parameters back to the values active during the previous state Click Save Changes To New State The New State dialog will appear MoN ewState i Type a name for your new state and click OK The New State will automatically become the current state The New State will be saved with the sample along with all other states The New State will be placed in the State History list CrystalClear User Manual Page 101 Tool Reference View the Scan State Display The Scan State Display shows all image information relevant to the current sample All images and scans available for collection and processing can be viewed The Scan State Display also allows the user to modify scans To view the Scan St
61. 13 Unknown mm 0 000 0 000 1 000 40 41 DetResolution min 154180 42 DetResolution max 1 66982 43 44 Refine resol min 99999 45 Refine resol max le 05 46 I sigma cutoff 0 47 Rejection limits 1 1 2 48 Rel rot weight 9999 49 50 Refinement results 51 52 Crystal 53 aye by e 68 7510 73 7993 107 0777 54 Sigmas 0 0032 0 0025 0 0053 55 Shifts 0 0000 0 0000 0 0000 56 CrystalClear User Manual Page 173 Appendix C Sample Log Files 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 200 201 202 203 204 205 206 207 208 209 N o NODNNNNNN NN 00 0 J004s0NnNRp4 22 N N p alpha beta gamma 90 0000 90 0000 90 0000 Sigmas fixed fixed fixed Shifts fixed fixed fixed Crys Rotl Rot2 Rot3 155 988 29 965 102 437 Sigmas 0 0012 0 0011 0 0035 Shifts 0 0000 0 0000 0 0000 Mosaicity 0 442 Sigma 0 0221 Shift 0 0000 Detector 0 Transl Trans2 Trans3 0 095 0 058 98 009 Sigmas 0 0185 0 0138 0 0358 Shifts 0 0000 0 0000 0 0000 Det Rotl Rot2 Rot3 0 252 0 024 0 043 Sigmas 0 0166 0 0082 0 0085 Shifts 0 0002 0 0000 0 0000 Source Wavelength Rotl Rot2 1 5418 0 000 0 000 Sigmas fixed fixed fixed Shifts fixed fixed fixed Refinement residuals rmsResid mm 0 0724333 rmsResid Deg 0 0393826 Reflections in
62. 17 Normally when you click a step button a dialog is displayed allowing you to change parameters then you click the Run button to start the process Clicking the Execute Step button starts the process without displaying the associated dialog The current values are used for the processing When the process for a particular step is running the Execute Step button is displayed with a red X You can click this button to stop the process mse DR Page 24 CrystalClear User Manual Introduction to CrystalClear Next Step arrows a The Next Step arrows indicate the next step in the task This arrow will change to a Decision Point or Stop Sign when further action is required You can also click the Next Step arrow to change it to a Decision Point or Stop Sign You can pause the current processing by changing the Next Step arrow to a stop sign Decision Points gt Whenever you must make a decision on what direction to go next a decision point icon will appear below the current step Arrows leading from the decision point icon will point to the next step for each possible choice Click the decision point icon to open the decision dialog then select the next step Alternatively you can click one of the buttons to which the Decision arrows points Stop Signs 0 You can click the Next Step arrow until 1t becomes a Stop Sign When a Stop Sign icon appears below a step button CrystalClear is paused at that step and is awaiting the user to click
63. 2 0 Distance theta oe eae PARAR Crystal 1 unit cell Crystal size Mosaicity oe jos se Color Mount Morphology Orientation Jooo fooo foo Roas ooo jooo Doo Copper 1 5418 Copper 1 5418 Molybdenum 0 71073 Sealed Tube Optics Confocal Confocal Graphite monochromator Initial images 1 scan of 2 images at 1 scan of 2 images at 4 scans of 1 image at Page 206 CrystalClear User Manual Appendix F Defaults in CrystalClear 0 90 degrees Full frames 2 min image 100 um pixel 0 90 degrees 0 30 60 90 degrees Readout Exposure Pixel resolution 2 min image 2x2 binned 5 sec image 2x2 binned 1 4 of screen 1 100 if already collected 3 sigma Images First image of screen 1 2 of screen I sigma level Min pixel Peak filter 3 sigma sigma o gt lt J J J 2D 3D Resolution Known cell User chooses solution Reflection file Max residual Indexing method Refine Resolution limits Cycles Vsig Rejection limits Macro Unknown Yes dtfind ref yes dtfind ref dtfind ref W 9 G J oel c 3 1D FFT 1D FFT 1D FFT Images First image of first 1 10 of collected 1 10 of collected scan screen images images images unless collect images are available Mosaiciy Per cent completeness Resolution Speed Result Limit 360 360 Search Rotation 0 360 Collect Exposure time 2 min RAXISIV 10 20 sec sample 20 30 sec sample 4 min RAXIS IV
64. 3 20 Images batch 5 21 Batch prefix 22 Image padding 2 23 Window size 30 30 24 Profile size 0 5 0 4 5 25 26 CrystalClear User Manual Page 171 Appendix C Sample Log Files 27 dtintegrate 3D method used 28 RX_NONUNF_TYPE gt gt None lt lt 29 30 File user4 DATA NUCL4 nuc14001 osc successfully opened 31 32 33 34 IMAGE 1 of 20 35 Name user4 DATA NUCL4 nucl14001 osc 36 Date 25 Sep 1997 34 Time 14 53 12 38 39 40 Rotation list 41 Start 24 000 42 End 24 250 43 Increment 0 5250 44 Time 120 000 45 46 Reflection dispositions 47 48 Status New Active Full DNormal DSpecial 49 Number 340 340 0 0 0 50 51 52 Shoebox dispositions 53 54 Status Total Filling Full Freed 55 Number 1951 340 0 1611 56 57 58 59 File user4 DATA NUCL4 nuc14020 osc successfully opened 60 61 62 63 IMAGE 20 of 20 64 Name user4 DATA NUCL4 nucl14020 osc 65 Date 25 Sep 1997 66 Time 14 58 28 67 68 69 Rotation list 70 Start 28 750 71 End 29 000 72 Increment 0 250 73 Time 120 000 74 75 Reflection dispositions 76 77 Status New Active Full DNormal DSpecial 78 Number 0 338 338 648 90 J9 80 81 Shoebox dispositions 82 83 Status Total Filling Full Freed 84 Number 1951 0 738 1213 85 86 Refinement options found 87 CrysAll DetAll rej 1 0 1 0 2 0
65. 3 Vesa s gt 50 6 mmm 2310 12 4 75 0 64 51 m 3 z 3276 12 S 0 54 52 m 3m 2557 24 4 39 0 69 gt 53 mmm selected with R merge of 0 02 54 No reindexing done 55 Reflection file not updated 56 Header output head written Centricity Log 1 dtcell Molecular Structure Corporation 2 d TREK version 6 2SSI Dec 11 2000 3 Command line 4 dtcell input head dtintegrate ref head output head centricityonly 5 Header input head opened 6 Header of file input head successfully read 7 Lattice oP assumed for space group 16 8 Command line string gt gt head lt lt 9 Output Header Name set to output head 0 Command line string gt gt centricityonly lt lt O O E O O O O AS 1 Finished reading command line 2 Input Cell 6 36 15 51 25 07 90 00 90 00 90 00 J 3 Input Sigmas 0 0003 0 0009 0 0013 0 0000 0 0000 0 0000 4 Input Orientation 97 41 1 70 171 25 5 Reading Reflection file dtintegrate ref 6 Creflnlist nRead with filename dtintegrate ref Y INFO in Creflnlist nRead EOF after 12641 reflections read in 12641 total now in list 8 N Z test fraction of intensities less than Z x lt I gt 9 0 1 0 2 0 3 0 4 0 5 0 6 0 7 0 8 0 9 1 0 20 centric 248 345 419 479 520 561 597 629 657 683 21 acentric 095 181 259 330 394 451 503 wood 093 632 22 deviation 153 164 160 149 126 110 094 078 064 051 23 theoretical average deviation gt 115
66. 3 0 0000 0 0000 0 0000 Input Orientation 97 41 Li TO DIL 2 50 0 Reading Reflection file dtintegrate ref Creflnlist nRead with filename dtintegrate ref INFO in Creflnlist nRead EOF after 12641 reflections read in Checking systematic absences Outputing dtcell_rejects ref Number of reflections written 3724 BEGIN Texsan Output Odd Even parity class Class Total Observed lt I sig gt eee 1606 364 160 9 eeo 1593 325 166 6 e0e 1576 29 9 169 2 eoo 1571 362 174 5 oes 157 2 362 164 9 oeo 1573 380 155 4 ooe 1572 378 181 8 000 1578 404 18 33 hkO Total Observed lt I sig gt ee 83 68 3675 3 eo 74 44 222 4 oe 78 63 296 6 oo 77 53 Zo T Okl Total Observed lt I sig gt ee 374 287 185 4 eo S12 291 181 9 oe 354 266 21751 oo 360 284 257 4 h hl Total Observed lt I sig gt ee 114 98 236 7 eo 113 77 183 4 oe 113 107 249 9 00 ce 108 304 1 hhh Total Observed lt I sig gt 5 5 708 6 o 7 7 1008 4 CrystalClear User Manual 12641 total now in list h01 Total Observed lt I sig gt ee 102 79 258 4 eo 101 62 1 05 23 oe 103 85 276 9 o o 100 80 208 8 hhl Total Observed lt I sig gt ee 97 89 380 6 e 0 98 13 357 0 oe 96 90 38m T o o 94 88 434 2 hh0 Total Observed lt I sig gt e 5 3 496 1 o 5 5 919 9 Page 181 Appendix C Sample Log Files 61 62 64 65 66 67 68 69 70 71 de ES 74 do 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92
67. 39 TransX 0 000 Unknown mm 1 000 0 000 0 000 40 TransY 0 000 Unknown mm 0 000 1 000 0 000 41 TransZ Dist 98 000 Unknown mm 0 000 0 000 1 000 42 43 DetResolution min 154180 44 DetResolution max 1 6678 45 Refine resol min 99999 46 Refine resol max le 05 47 I sigma cutoff 0 48 Rejection limits 1 1 2 49 Rel rot weight 9999 50 Refinement results 51 52 Crystal 53 a b ci 68 6284 73 7186 106 5789 54 Sigmas 0 0170 0 0102 0 0235 55 Shifts 0 0000 0 0000 0 0000 Page 166 CrystalClear User Manual Appendix C Sample Log Files 56 alpha beta gamma 90 0000 90 0000 90 0000 57 Sigmas fixed fixed fixed 58 Shifts fixed fixed fixed 59 Crys Rotl Rot2 Rot3 TSS ATS 29 915 102 325 60 Sigmas 0 0094 0 0029 0 0084 61 Shifts 0 0000 0 0000 0 0000 62 Mosaicity 0 300 63 Sigma 0 0000 64 Shift 0 0000 65 66 Detector 0 67 Transl Trans2 Trans3 0 074 0 069 97 011 68 Sigmas 0 1201 0 1350 0 2432 69 Shifts 0 0000 0 0000 0 0000 70 Det Rotl Rot2 Rot3 0 056 0 026 0 034 71 Sigmas 0 1259 0 0640 0 0724 72 Shifts 0 0017 0 0000 0 0000 73 74 Source 75 Wavelength Rotl Rot2 1 5418 0 000 0 000 76 Sigmas fixed fixed fixed TF Shifts fixed fixed fixed 78 79 Refinement residuals 80 rmsResid mm 0 271192 81 rmsResid Deg 0 292639 82 83 Reflections in list 553 84 Reflections accepted 514 85 Reflections rejected 39 86 Reflections ignored 0 Outside I sigI or Resolution
68. 6 41 19 2000 E TN E es R A Cope E et ee ee 0 augs DRDS Nig Sys ao i DIT 2A cscs 2 234565432 3 223579497532 4 2357ADFFB85311 5 235 7AFIJNMHB6321 Direct beam for IP 1 cycle 1 6 2469DJQUINE8421 Position x y 1499 84 1509 80 7 24 7AFMUZXOG95211 Pixel Intensity 10841 8 g 247BGOV YQOG9521 Integrated Intensity sigma I 330647 895 9 246AGMTXVNF 8421 I sigma 1 369 5 20 12358DIOROKC7321 3sigma width x y 12 13 21 112469DHJJE95311 Full width at half maximum x y 5 57 6 86 22 123469BDDA7421 23 iso LLUIS 788 7537 Le DE gsc 223455532 Fieis 25 ts DAZ 3B O ta oss 26 ads ASADAS E E yee E ob E IA 32 33 Average direct beam results for IP 1 34 Position x y 1499 64 1509 61 0 262854 0 14148 35 Pixel Intensity 10533 445 806 36 Integrated Intensity sigma I 336594 893 455 4324 93 4 73774 37 I sigma I 376 732 4 30341 33 Full width at half maximum x y 5 55258 6 88398 0 0486711 0 0397825 Page 194 CrystalClear User Manual Appendix C Sample Log Files 39 Average direct beam r
69. Administration dialog by clicking Tools gt Administration The Administration dialog will appear Ifyou have logged in as a user without administration privileges the Tools gt Administration option is disabled Log in as Administrator to access this option 2 Click on the Users tab CrystalClear User Manual Page 145 Appendix B Administration Administration TT Jesplin 2 Select the user name or Administrator from the Users list then click Edit The User Settings dialog will appear User Settings 3 Make the desired changes in the settings It is recommended that the default blank Administrator password be changed to a specific password to protect against unauthorized changes in the CrystalClear settings To change a Password enter the New password Re enter the password in the Confirm field 4 Click OK to save the changes Page 146 CrystalClear User Manual Appendix B Administration The user s current data will not be moved to a new user path Administration of Groups To help manage the privileges given to different users assign users to Groups CrystalClear ships with two pre defined Groups Administrators and Users By assigning a user to the pre defined Administrators Group the user will have privileges to add edit or remove users groups tools or servers To administer groups 1 Access the Administration dialog by clicking Tools gt Administration The Admin
70. Clear predefined macros select a macro with values similar to those to be used in the New Macro then click OK 5 The Macro Editor dialog will appear with a step by step list of the selected macro Customize the macro by altering the values of the predefined macro Highlight a step and change the values to reflect those desired Continue to highlight steps and make changes as desired Use the New Step button to access the New Refine Step dialog to add a new step to the macro New Refine Step x p ox Cancel Copy Values From Cancel All Detector All Crystal Use Remove Step button to delete the macro step selected 6 When the customized New Macro is satisfactory click Close When you click Close on the Macro Editor the customized steps and values are saved with the New Macro name This New Macro is specific to the current sample 7 When the Refine dialog appears click Save The Default Manager dialog appears CrystalClear User Manual Page 123 Additional Processing Default Manager x Site A eta Administrator dhulick Y Sample Myoglobin T Project Myo2 User Myo3 current Site Set Unset Set All ilele Unset All Cancel Default Manager dialog allows the New Macro to be saved at the Site Level User Level Project Level or Sample Level Using Default Manager allows you to use the New Macro in other projects and samples 8 Choose the level o
71. Clear x When you delete a project or sample through this dialog box CrystalClear will attempt to delete the directories on the file system associated with that project and sample Therefore please back up any data in those directories that you don t want to lose The Delete Projects Samples dialog will appear CrystalClear User Manual Page 97 Tool Reference Delete Projects S amples Ea Projects Samples New Project Delete Project s Delete S ample s 2 Select highlight the project or sample you wish to delete then click the appropriate Delete Project s or Dele te Sample s button The project or sample will be removed from the CrystalClear database These files will also be removed from the actual files and directories where the project and sample files were stored WARNING Selecting a Project will delete the Project and ALL Samples within that Project Processing State View Edit and Set The processing state is a collection of crystal and instrument parameters associated with each step of processing the data A Processing State consists of default calculated or refined crystal detector and source values For example a current sample is in one state following Index Spots and in a different state following Refine Cell The Processing State of the current sample can be viewed while processing the data To view the Processing State Display window 1 Click the Show Processing State Display toolbar button
72. CrystalClear Software User s Guide for the Rigaku R AXIS and Mercury and Jupiter CCD Automated X ray Imaging Systems Version 1 3 MOLECULAR STRUCTURE CORPORATION a Rigaku company 1999 2000 2001 Copyright Molecular Structure Corporation All rights reserved Reproduction adaptation or translation without prior written permission 1s prohibited except as allowed under copyright laws CrystalClear 1 3 01 2001 Rigaku MSC SSI 491 South Orem Blvd Orem UT 84058 http www msc com CrystalClear User s Manual Abridged Or What To Do After You ve Started Your Data Collection INDEX FIND INDEX REFINE REFINE REFINE INTEGRATION REFINE REFINE INTEGRATION INTEGRATION INTEGRATION INTEGRATION CrystalClear User Manual 1 Use the reciprocal space lattice spacing ruler to see what the maximum cell length is use 1 5 2x for max Remember that this is for the primitive cell 2 Find and index off one image then find and refine off several images throughout phi space 3 Although refinement from a single image is okay sometimes better results can be obtained with one of the following strategies for indexing and refining two images 90 degrees apart a 5 to 10 degree wedge of data 2 or 3 images at three different areas of space 4 RMS values on a few images should be close to zero values around a few pixels and half the image rotation width are to be expected when the mosaicity is not well known
73. Crystallographic Troubleshooting Appendix G Crystallographic Troubleshooting This section covers a few common crystallographic problems that you may encounter in CrystalClear and how you may solve those problems Solution The crystal to detector distance In this sample there are images with different crystal to detector is not editable it states Per distances Try looking in the Scan State Display for information Scan relative to each scan I started a sample as a Process You collected the data without setting the crystal to detector distance task and the crystal to detector in the software for addition into the header If you know what the distance shows 0 distance is edit the field in the Setup dialog and continue If you do not know what the true crystal to detector distance is try 1 In an image display window turn on the arcs tool and play with the crystal to detector distance in the image information area The arcs will change size and shape relative to this and the 2 theta angle See if you can line up a ring ice salt etc Then take these numbers to the Setup dialog and edit the fields 2 Set a best guess in the crystal to detector distance field in Setup and try to index The closer you are to the read crystal to detector distance or any geometric parameter the lower the residual of the correct lattice This may be quite a bit of work If no solutions pop out after many attempts Find Peaks off 2
74. Error Model Reject Auto m Rejection Sigma r Normal Output Scaled Averaged Output File Weight Multiplier fi 0 00 z Scal veraged ref Auto Intelligent y Chi T No Header Max Group Chi 2 TF Output Anomalous I 1 Weight Addend jo Auto Intelligent ind FT Scale Anomalous I 1 Close Save Defaults 2 The Reflection Lists box displays the sample reflection list files Select a reflection file 3 In the Algorithms box select the corrections to be applied More than one may be applicable CrystalClear User Manual Page 89 Data Collection and Processing 4 In the Absorption Correction group box specify Method to use e Fourier e Spherical 4 3 e Spherical 3 2 In order to perform an Absorptive Correction the user must choose Absorption Correction from the Algorithms box see Step 2 If None is selected specify Max Cycles also to perform Fox and Holmes scaling If a method other than None is selected the REQAB program of Dr R Jacobson is used to calculate and apply scale factors The REQAB program usually gives the best results 5 Specify the number of Max Cycles This option refers to the maximum number of non linear least squares cycles to perform If the refinement converges the maximum number of cycles may not be reached No shifts are applied to the last cycle 6 In the Error Model group box spec
75. FIND SPOTS process 3 The rest can be left at the defaults values from installation 6 SCALE AND AVERAGE Main 1 Reflection list Select dtintegrate ref 2 Exclude Sigma The default value of 3 will exclude reflections which have about a 99 chance of being an outlier 3 Rejection Sigma The default value of 10 will normally suffice however it can be raised to any value if you are rejecting a large number of reflections 4 Algorithms a Batch scaling uses simple batch scaling to model all incident beam absorption decay etc b B factor applies temperature dependent scale factors to the data c Absorption correction Currently 3 methods exist Spherical 4 3 tends to apply a better correction to small molecule data the others If it fails choose another method and see if it succeeds If none work your sample may not have required an absorption correction 5 Error Model This is probably the hardest part to get down to a simple explanation There is no canned method for doing this a Weight Multiplier This multiplies the standard deviations by the value set b Weight Addend This adds a systematic value to the standard deviations The idea here is to adjust these parameters to get a relatively flat x value between 0 8 and 1 2 over all the resolution regions of data Experience has shown that the Weight Multiplier is specifically dependent on the instrument Typically between 2 and 3 The Weight Addend can normally be
76. From the Method drop down box select a method The choices are 1D FFT The DPS indexing algorithm of Steller Bolotovsky amp Rossmann is used About 7300 different directions are examined by an 1D FFT algorithm for whether a principal cell axes is parallel to that vector Three of the vectors with the most order are selected for cell reduction 3D Fourier A 3D cosine Fourier is calculated over a real unit cell volume with grid points x F cos 2n d x i l where d i is the reciprocal lattice vector for refln_i Peaks will appear in the Fourier function at the end points of the real cell axes a b c and linear combinations of these axes Reciprocal Space The reciprocal space method of Sparks is used Cell reduction used as published by Andrews amp Bernstein and Paciorek amp Bonin If indexing fails and you know the correct cell select the Use known cell check box to force the program to look at vectors that match a known unit cell Selecting this check box forces the program to look at vectors that match a known unit cell The unit cell in the header is converted to a reduced primitive cell based on the Spacegroup The program will search for this reduced primitive cell Check the Diffs check box if desired Steller Bolotovsky and Rossmann 1997 J Appl Cryst 30 1036 1040 2 Bricogne Proc EEC Cooperative Workshop on Position Sensitive Detector Software 1986 3 28 a Pflugrath J 1997 Method of Enzy
77. ION AND PROCESSING esssseescssceccsseeccsseeccesseeccsseeccsseeccosseeccsseeccsseescssseecssse 49 SELECT A PROCESSING ALGORITHM cccssccceccescececeeseececseseeeeceeseesessuseeseeeeaeesecseneesessuneesesuaneeseauanes 49 A ae en NS Ro E AEEA Ro E 50 COLLECT IMAGES WITH AN IMAGING PLATE SYSTEM R AXIS IV ooocccccccnncnooccccccnnnncnonononccccnnnncnonos 57 COLLECT IMAGES WITH CCD SYSTEM MERCURY CCD oooccccccnnnnnnnoococonnnnnnnnnnoncnnnnnonononononanacnnnnnnnnos 60 INDEXSPO LS tt IS a ai riada 63 Index with d TREK RAXIS or CCD oooocccncccnnnononococoncnononononncoccncnnnnnononnoncnnnnnnnnnnnnnnncnccnnnnnnnnnnnnos 63 Index with TwinSolve Mercury CCD cccccececccecccecececececeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeess 76 STRATEGY a aa ld irae Wu dks ai A T 80 INTEGRATION a e aaae A A eS aha E A hE net 83 Integrate with d TREK RAXIS or Mercury CCD occccccnncoconoconocccnnncnnononononccnononnnnonononanccnonanna nos 83 ANALYZING THE DATA e E RN CR O IA AN eke A CL 87 Late Symmetry svi ed cescecesstes A A NN 87 CENITI E A EE EE AAA DECI ERE 87 A A RAN 88 SCALE AND AVERAGE ii A ds aot wa da A td di ie 89 Scale with d TREK RAXIS or Mercury CCD 0 000ccceeeceeeeeeeeeeeeeeeeeeeeeeeeeeseeeeeeeeeeeeeteeeeeeeeeees 89 7 TOOL RETERENC AAA A RN 93 CREATE A NEW PROJECT AND SAMPLE orere eE A A AAAS EAS ANAE I Aan 93 EREATE A NEW SAMPLE a daa 94 OPENAN EXISTING SAMPLE AT A E SE A OEA AE OSA A TEE ATS AA E 95 C
78. If desired check the All twins check box 5 If desired check the Alpha2 spots check box 6 Click Run If you are satisfied that you have a rotationally twinned sample please contact Rigaku MSC for the latest command line version of the TwinSolve module and further instructions on integrating your sample Strategy Strategy can be used to automatically generate a collection schedule so you don t have to Results are written to the file dt strategy log and are readily displayed within CrystalClear To process Strategy 1 Click Strategy on the flow bar The Strategy dialog will appear Page 80 CrystalClear User Manual Data Collection and Processing 2 In Search Resolution group box make changes to setting by clicking Set button The Set Resolution dialog appears Set Resolution EJ SSI __Tottgectinge _ ToConerotimeoe For assistance in using the Set Resolution dialog see page 119 in Section 8 Additional Processing 3 Click the Advanced tab CrystalClear User Manual Page 81 Data Collection and Processing Strategy x Main Advanced m Speed Accuracy Result Limit Very Fast 360 00 C Fast C Accurate Search Rotation C Custom Scale Factor Begin End 0 30 fo 00 360 00 Use Previous Reflections I Output Reflections Previous Reflections fa Close Save Defaults 4 In Speed Accuracy group box make appropriate selections e Very Fast 0 3 e Fast
79. JA A A a higher order terms j j 3 If the usual approximation is made of assuming that the higher order contributions are negligible then by a least squares approach the Ap values can be calculated and the whole process repeated until convergence is obtained We assume the absorption surface is smoothly varying in reciprocal space In order to enforce this powerful constraint two sets of analytical functions are used Spherical harmonics are one convenient set of analytic functions for A The maximum order is limited to 8 four even term and four odd terms lt 8 L A 9 v ay Am Y im Q V l 1 0 4 Blessing R H 1995 Acta Cryst A51 33 38 CrystalClear User Manual Page 201 Appendix E Absorption in Scaling where am represents the coefficients to be determined by refinement and y m are the corresponding spherical harmonics and and U are the equatorial and azimuthal angles of the diffracted x ray beam respectively An alternate analytic function employs a Fourier series to represent absorbance A 9 0 0 0 Q0 Y Y P in no mv sini nd mv 0 n cos n mu cos ny m gt 5 Here the coefficients P and O are fit via a least squares procedure The maximum values of n and m are 8 and 4 respectively In this case of the Fourier method both the primary or incident and scattered beams are modeled In addition to absorption the apparent intensity of the prima
80. New Project or New Sample Alternately to open a current sample click File gt Open Sample To begin a new sample click File gt New Sample If a new sample is created when sample is current CrystalClear automatically saves and closes the existing current sample Upon exiting CrystalClear the current sample is automatically saved and closed See Section 7 Tool Reference on page 93 of this manual for more information on adding new samples Page 30 CrystalClear User Manual Common CrystalClear Tasks 5 Common CrystalClear Tasks This section gives a brief overview of several common CrystalClear tasks In later sections each task is discussed in more detail with explanations of parameters preferred procedures etc Collect I mages CrystalClear can be used to collect images of your crystals on the Rigaku R AXIS IV or Rigaku Mercury or Jupiter CCD Automated X ray Imaging Systems To collect images 1 Start CrystalClear and enter Login Name and Password When a Login Name is used for the first time the Project Wizard will lead the user through the creation of a new project and sample See Section 4 Running CrystalClear for the First Time on page 27 if you need assistance When a Login Name is repeated the Open Sample dialog allows the user to open an existing Project or begin a new Project The last project and sample used for the Login Name will be listed as default 2 At the Open Sample dialog select the Project and Sample
81. OSF THE CURRENT OGAM E e e e e cde A diced oe ond e aia 96 SAVE THE CURRENT SAMPLE Sed Mesa ea e 96 DELETE PROJECTS AND SAMPLES cccccssccsscccescccessseusccceescscuseseusceeeussseuceseuscsceessseceeeessseuessesceeees 97 PROCESSING STATE VIEW EDIT AND SET ccccccseecccccsescccensesceceaseeecsesseeeesesseecseaseeeeseaueneeseaaeneess 98 CREATE A NEW PROCESSING STATE sto eiii 100 VIEW THE SCAN STATE DISPLAY ccccccescececeeseececeuseececeeeesesseseesesseeeeseseneeseseuneesesuunecseauaneeseauanes 102 Using the Scan Table codiciosos tad voarscavene ESTEER A PELEA REESE ETERA EEEE EEEE ot 103 Mampu lating the Scan Table cremosa id peda to 105 Editing the Scan Tablero A nese tweaks 106 VIEW THE INSTRUMENT STATE ccccccsescccscccesssccscscesesscescccscsceusseesesseesessuscsecsessesssesescessesenecsees 107 MANUALLY CONTROL THE DETECTOR ccsescececsseececeeseececeuseesecueeeeseceuseeseesuaeesesauaecseauaneeeeauanes 108 SET USER PREPERENCES narena uee ct bo cok bbs At Seek SSR ORO DER GN a SERS REI NLO 110 Configure the Instrument Server Simulator ccccceccceceeeesssnecececececeesesnaaececeeecessesenneaeeeeeeeeees 113 REARS Simulator secre sso ato ota sanas 114 CED SITUA A A SN oka acca cote ec BONE NAL A is 114 VIEW LOGFILES union ido a a E E RO ia eden 117 8 ADDITIONAL PROCESSING essesssesessecsoeesessesecccsseccosssocoeeccsossecsosseseossesossesssesseesossecsossssoseesssss 119 SET RESOLUTIONS aia A A
82. Per Batch 2 to 4 times the mosaicity for macromolecules and 10 to 30 times for small molecules 5 Click Run A CrystalClear message may appear This reminds the user to create a mask file to exclude areas of the detector from consideration in integration due to uncertain intensities resulting from shadows bad pixels or detector flaws Although it is not necessary to use a mask it is advisable See Non uniformity Type on page 54 a sub section of Setup in Section 6 Data Collection and Processing CrystalClear MN You are not using a mask file Do you wish to continue CrystalClear integrates the reflections for each image file selected creating a log file called dtintegrate log The Integrate Reflections step can take considerable time depending upon 1 the number of images to be integrated 2 the number of reflections per image 3 the computer s available memory and 4 the computer s processing speed Analyzing the Data Once integration is comple ted data may be analyzed to determine Laue symmetry centricity and spacegroup See Section 6 Data Collection and Processing on page 49for detailed help Laue Symmetry 1 Click Laue on the flow bar The Laue dialog will appear Laue REI Max R merge fo 50000 y Reflection List Highest Laue Symmetry E y El Es lV Only check Laue groups compatible with current cell 2 Select the Reflection List file to use generally dtprofit ref 3 Make other adjustments to
83. Start CrystalClear and log in 2 At the Open Sample dialog select a sample CrystalClear User Manual Page 119 Additional Processing This sample should have been processed at least up through Integrate Reflections 3 At the Task drop down list select Combine Reflections 4 Click Merge on the Flow Bar The Merge Reflection Lists dialog will appear Merge Reflection Lists El E Reflection Lists Dutput Merged File merged ref dtintegrate ref dtintrejects ref Zone Type dtpredict ref a None z I Restrict Resolution Minimum Manman fi 00 00 2 00 Import Reflection File Close Save Defauits 5 Select the reflection lists to be merged in the Reflection Lists list box 6 Specify a name for the resulting output file in the Output Merged File edit field 7 Specify a Zone Type The available options are None H00 OKO 00L HKO HOL OKL 8 To restrict resolution check the Restrict Resolution check box then specify the Minimum and Maximum values 9 To Import Reflection File click the button The Select Reflection File to Import dialog appears Page 120 CrystalClear User Manual Additional Processing Lookin E Mye2 Y El dl 3 dtcell_rejects ref B dtrefinetmp ref 3 dtintegrate ref a dtintegrate1 ref a dtintrejects ref 3 dtprofit ref 3 dtprofit1 ref Fie name T Files of type Reflection Files ref y Cancel a There are several ways to select a file to
84. The Select Directory dialog will appear Select Directory 53 Documentation EE CrystalClear 6 data EE Myoglobin EE Myo2 i E THERES H Scripts QQ Manual 1 3 ALA Ratirad Varsinne 4 Navigate to the directory to use then click OK The selected directory will appear in the Preferences dialog 5 Continue to check other tabs or click OK to save changes Specify Instrument Server Simulator Page 112 CrystalClear User Manual Tool Reference It may be limiting or unfeasible to run CrystalClear only on the computer connected to an Image Collect Device detector For example it may be necessary and convenient to process collected data on a computer other than the one connected to the Image Collection Device detector or 1t may be useful to conduct in house training sessions on CrystalClear on a computer other than that connected to the Image Collection Device detector CrystalClear provides an X ray Detector Simulator The detector simulator allows the processing of data or user training on a computer other than the one connected to the Image Collection Device X ray detector To configure CrystalClear to use the detector simulator 1 Click Tools gt Preferences on the menu The Preferences dialog will appear 2 Click the Server tab Preferences x General Directories Server General Collection Run As Simulator Cancel Help 3 Inthe Run As Simulator list box check the box nex
85. This tool allows you to adjust the size of the circle drawn around each spot Note that this circle is for display purposes only and does not reflect the integration area or background peak separation This tool allows you to filter out spots that are not found in the current image For example a spot that appears in Image 10 may not intersect Image 1 This tool filters out all spots whose rotation range does not intersect the displayed image This tool displays the previous image in the series For example 1f the current image is Img004 osc clicking this tool will display Img003 osc This tool displays the next image in the series For example if the current image is Img004 osc clicking this tool will display Img005 osc Page 133 Images E Overlay Images Displays an image created from a specified series of images Each MAX pixel in the resultant image is generated by using the maximum value occurring in the images for that pixel position This is generally used to display the image that would result from a wider rotation oscillation angle Underlay Images Displays an image created from a specified series of images Each pixel in the resultant image is generated by using the minimum value occurring in the images for that pixel position This is generally used for examining the background over wide rotation oscillation angle or for examining the extent of a reflection across several images and rotation angle values MIN Aver
86. a scroll bar appears you can scroll up and down to see additional items in the control If the background for a field is white then that field is editable To enact a change to the window but not a permanent change to the state enter the desired value and press Tab Page 134 CrystalClear User Manual Appendix A Files and Directory Structure Appendix A Files and Directory Structure The CrystalClear program ships with the files in the following lists Your installation may not include all files depending on the detector type that your copy of CrystalClear came with Installed Files CrystalClear program files CrystalClear exe CoreCodel 1 dll CoreRes1 1ENG dll CoreHobjectl 1 dll gzip exe DundasUG dll system configuration xg_dll dll Compute Servers MSCServDetCCD_Simulator exe MSCServDetCCD exe MSCServDetCCD configuration MSCServDetRAXIS_Simulator exe MSCServDetRAXIS exe MSCServDetRAXIS configuration RAXIS_IV configuration RAXIS_IV configuration MSCServProcDTREK exe MSCServProcPROCESS exe MSCServProcTwinSolve exe AFC7_RCD2 configuration AFC8_RCD3 configuration MercuryDefault header Errors xer Huber xpa huhelp xhe spacegrp xsg Help Files CrystalClear chm CrystalClearDoc pdf CoreHelp chm TwinSolve chm infolist txt hh exe hhctrl ocx itircl dll CrystalClear User Manual Executable program file Shared code program library English language resource file DLL for database functions Decompression
87. ad background 0 Error in background determination Bad background sd 0 Error in background sigma determination Bad non uniformity A O Peak pixels flagged as bad Bad non uniformity B O Background pixels flagged as bad Partial at scan start 513 Reflns incomplete at start of the rotation Partial at scan end 393 Reflns incomplete at end of the rotation Rotation too wide O Reflns predicted to be on too many images Rejected from output dtintegrate There were 1764 profiles written to file reflnprofiles profit dtprofit Copyright c 1996 Molecular Structure Corporation dtprofit settings Minimum required contributors to a reference profile 50 Minimum reference profile value in peak area 0 Variance weighted profile analysis method B used Maximum number of reference profiles 72 Number of reflection profiles read in 1764 Profile Reflns Sum Pi 2 Vi Contributors 0 149 670 o 0 0 18 0 1 1 6 0 19 6 24 0 7 21 25 121 1 149 670 1 1 1 19 6 7 21 2 0 6 0 0 0 25 121 71 193 648 71 71 0 53 0 70 12 65 0 52 8 47 0 64 173 72 1764 620 Overall profile File DO001 refprof successfully opened Success writing file D0001 refprof File D0019 refprof successfully opened CrystalClear User Manual Page 175 Appendix C Sample Log Files 287 Success writing file D0019 refprof 288 File D0037 refprof successfully opened 289 Success writing file D0037 refprof 290 File D0055 refprof successf
88. again to resume processing You may want to set a stop sign after a specific sub step in the Flow Bar so that processing pauses after that step Image window In the Image window the data images will appear as they are processed See Section 9 Images on page 131 for more information about this window Command Bar The Command Bar displays the commands sent to the compute server d TREK In a future release you will be able to enter commands on the Command Bar directly allowing you to bypass the graphical user interface if you desire Message Window In the Message Window CrystalClear will display various messages informing you of the progress of the current process Status Bar As you scroll through menu items a brief description of the selected menu item is displayed on the status bar Log File window The log file window not pictured above displays the contents of a log file Log files are created with each process in CrystalClear You can display the log file by clicking the View Log File button on the tool bar or by selecting View gt Log File from the menu See Appendix C Sample Log Files on page 161 for more information on log files CrystalClear User Manual Page 25 Introduction to CrystalClear Page 26 CrystalClear User Manual Running CrystalClear for the First Time 4 Running CrystalClear for the First Time Starting CrystalClear and Logging in Once CrystalClear is installed and your administrator has cr
89. age Images Displays an image created from a specified series of images Each AVE pixel in the resultant image is generated by using the average value occurring in the images for that pixel position Tile Images Displays an image created from tiling a specified series of images ER Spots that appear with a red circle during Integration are rejected spots the spots may be saturated or otherwise invalid while those spots that appear within a red circle during refinement are spots whose difference between observed and calculated positions the exceed rejection limits in x y or 6 Spots that appear with a green circle during refinement have been excluded from refinement either because they fall outside the resolution limits or the lie too close to the rotation axis or they are below the l a 1 cutoff Small mage Window Toolbar The toolbar for the small image window includes tools similar to the Large Image Window toolbar However they act upon the small image window only Small mage Window A smaller portion of the image appears in the Small Image Window You can select the portion that will appear here by moving the cursor in the Large Image window and clicking the mouse I mage nformation Window Information about the image appears in the Image Information window Much of the data listed here is for information purposes However you can manipulate such things as the number of spots displayed with the controls listed here If
90. alClear files installed The default location is C PROGRAM FILES RIGAKU MSC CRYSTALCLEAR We suggest using the default location but if you prefer to install CrystalClear in a different location modify the path and click Next Follow the remaining prompts until the CrystalClear installation program is completed See Appendix A Files and Directory Structure on page 135 for information on the files that are installed and the directory structure that is created during the installation After installation Page 16 CrystalClear User Manual Installation After you have installed CrystalClear log on as administrator and set up the users and system configuration See Appendix B Administration on page 141 for detailed information on administrative functions You should also make sure that the Rigaku R AXIS or Rigaku Mercury or Jupiter CCD Automated X ray Imaging System that CrystalClear will be working with is set up correctly Uninstalling CrystalClear To uninstall CrystalClear 1 2 3 Click the Start button on the Windows Task Bar Select Settings gt Control Panel In the Control Panel click Add Remove Programs The Add Remove Programs Properties dialog will appear Locate Rigaku MSC CrystalClear in the list and double click CrystalClear and all its components will be removed Any image files you may have and data files that were created or processed by CrystalClear will not be removed from your system CrystalClear U
91. alues are 0 05 0 1 mm and 0 05 0 1 degrees Lines 83 86 The number of input reflections is listed along with the number used in the refinement CrystalClear User Manual Page 167 Appendix C Sample Log Files Those reflections that are rejected exceeded the rejection limits for the differences between observed and calculated centroid or were too close to the rotation axis Those reflections that are ignored did not pass the Intensity Sigmal and resolution limits Predict Log i dtpredict Copyright c 1996 Molecular Structure Corporation 2 d TREK version 6 1SSI Oct 27 2000 3 Command line 4 dtpredict input head seq 180 180 mosaicity 0 60 out output head ref 5 dtpredict ref display list 6 Header of file input head successfully read 7 Crystal listing 8 Unit cell lengths 78 9495 78 9495 36 8831 9 Unit cell angles 90 0000 90 0000 90 0000 10 Unit cell volume 229893 231 11 Orientation angles 58 4917 54 9206 90 2980 12 Mosaicity 0 600 13 Description unknown 14 RX_NONUNF_TYPE gt gt None lt lt 5 Predict listing 16 Spacegroup number 96 17 name P43212 18 um equiv posns 8 19 Equival position 1 20 1 0 0 0 21 0 Ly 0 0 22 0 0 1 0 23 Equival position 2 24 1 0 0 0 25 0 Ly 0 0 26 0 0 1 0 5 27 Equival position 3 28 0 E 0 0 5 29 I 0 0 0 5 30 0 0 1 0 75 Sul Equival position 4 32 0 0 0 5 33 Ty 0 0 0 5 34 0 0 1 0 25 35 Equ
92. and STL RAXIS image files CrystalClear will also support Bruker MAR CCD MAR IP ADSC CCD MacScience Brandeis CCD and MedOptics image files Create a New Sample Following the first Login to CrystalClear at least one project and sample had been created in the user s database To create additional samples 1 Start CrystalClear Enter your Login Name and Password The Open Sample dialog will appear The names listed in the entry fields are the Project and Sample most recently updated by the user Additional projects and samples can be viewed and or selected by clicking the appropriate down arrow Alternatively the Open Sample dialog can be accessed with the Toolbar icon O The Open Sample dialog can also be accessed from the CrystalClear menu Click File gt New Sample to create a new project sample e The Open Sample dialog can also be accessed with the shortcut Ctrl N Page 94 CrystalClear User Manual Tool Reference Open Sample Ea Project Myoglobin y New Project Sample Myo2 y C New Sample Task Collect and Pr Image Directory DAD ocumentation CrystalClear data Myoglobin Myo2 images Browse Cancel Browse Import 2 Click the New Sample radio button The existing sample name will be highlighted 3 Type the new sample name in the Sample edit field This will replace the existing text 4 Select the desired project from the Project drop down field By default the last projec
93. and cell reduction tools are available here Click Data Analysis on the Flow Bar Several buttons become available Laue Symmetry 1 Click Laue on the flow bar The Laue dialog will appear Laue Max A merge 0 150000 y Highest Laue Symmetry E lV Only check Laue groups compatible with current cell Close Save Defaults I Reflection List 2 Select the Reflection List file to use generally dtprofit ref 3 Make other adjustments to settings as follows Max R merge Highest Laue Symmetry Only check Laue groups compatible with current cell Average Bijvoets Assume 1 1 4 Click Run Centricity 1 Click Centricity on the Flow Bar The Centricity dialog will appear CrystalClear User Manual Tolerance for considering a Laue class present Limits the highest Laue class to be checked Unchecked examines all Laue classes compatible with current cell Unchecked examines Laue classes desired Page 87 Data Collection and Processing 2 Select the Reflection List file to use generally dtprofit ref 3 Click Run Centricity Results 0 248 0345 0 419 0 479 0520 0561 0 597 0629 0657 0 683 0 153 0164 0160 0 149 0126 0110 0 094 0 078 0 064 0 051 theoretical average deviation gt 115 0 061 0192 0 344 0483 0599 0682 0748 0 796 0834 0 862 0 187 0153 0 075 0 004 0 079 0 121 0149 0167 0177 0179 measured average deviation gt 0 0462 4 Check the e
94. and to better estimate the crystal mosaicity if it was not refined previously as would occur if 2D data were used for indexing Predicted reflections are written to afile dtpredict ref The Predict Spots feature creates a reflection list file with calculated reflection centroids that can be plotted and displayed To predict spots 1 Click the Predict Spots button on the Flow Bar The Predict Spots dialog will appear Page 74 CrystalClear User Manual Data Collection and Processing Predict Spots Ed Main Advanced Scan Table Right click for further options Template Avail To Use myo2_screen osc 1 2 myo2 asc 1 60 1 10 Clear All Use Sequence Pe Hise Rotation Crystal Mosaicit Use Current Displaved Imane jo 60 r Rotation Resolution Begin End Minimum Maximum Close Save Defaults 2 Specify the image or images to be processed To specify a sequence of images select Use Sequence Then select the desired images in the To Use entry field The Predict Spots dialog allows the user to enter image numbers manually or select images numbers from a list Right click on the To Use entry field to view menu options To enter image numbers manually in the To Use entry field be sure to use a dash to separate consecutive image entries and use a comma to separate non consecutive images entries For example you can enter images such as 2 5 7 9 12 Before clicking the Run b
95. ar Page 152 CrystalClear User Manual Appendix B Administration Server Settings Ea Server Path igaku MSC CrystalClear MSCServDetCCD exe Gy Cancel Arguments OE Help Description CCD Controller Software Options I Stand Alone Server To MuleGient Senet Configuration IP Address Port f 27 0 0 1 Auto Generate Port Number e055 Hange 2055 T 3 Change the desired options then click OK to save the changes Path Arguments Description Options IP Address Port Auto Generate Specify the path where the server program is located By default the servers are installed in the same directory as the CrystalClear program You can change this path if you need to move the server to another location For example c program files Rigaku MSC CrystalClear dtrek exe Specify any argument that you wish to pass to the server upon its startup By default no startup options are specified Specify a description of the server software For example CCD Controller Software Generally if the server software were running in the background all the time you would check the Stand Alone Server check box The application would then forgo an attempt to start the server software when it is needed However CrystalClear always opens and closes the servers as needed so you should leave this option unchecked By default the server software will use the local machine for processi
96. ate Display window 1 Click the Show Scan State Display button on the toolbar D The Scan State Display window will appear CrystalClear displays a window specific to the Image Collection Device Type selected namely R Axis Jupiter CCD or Mercury CCD e Alternatively click View gt Scan State Display on the CrystalClear menu The information reported on the Scan State Display is as follows Screen group box contains Schedules Use the down arrow to view additional Schedules User may Add Delete or use Manager on Screen Schedules Scan Table User may Add Scan or Delete Scan on the Scan Table then make changes to scan settings as desired For assistance in manipulating the Scan Table columns headings or other settings see Using the Scan Table on page 103 of Section 7 Tool Reference Collect group box contains Schedules Use the down arrow to view additional Schedules User may Add Delete or use Manager on Collect Schedules Scan Table User may Add Scan or Delete Scan on the Scan Table then make changes to scan settings as desired For assistance in manipulating the Scan Table columns headings or other settings see Using the Scan Table on page 103 of Section7 Tool Reference Save When Save is clicked the Default Managerappears For assistance see Using the Default Manager on page 209 of Appendix F Defaults in CrystalClear Sync with Disk In a Process task Syne with Disk updates the image directory on the
97. ator Utilities The Administrator Utilities dialog will appear 4 Specify if the instrument should be initialized before checking the PMT by either checking initialize the instrument or unchecking do not initialize the instrument the Initialize R AXIS check box in the Photo Multiplier Tube PMT check group 5 Click Take to check the PMT On CCD systems this check is not available 6 Close the Administrator Utilities by clicking the E on the upper right of the dialog box For information on how to interpret the result consult the appropriate instrument hardware manual The images generated during the PMT check is placed in the PMTCheckImages subdirectory of the Program Directory The PMT check utility generates a log file called PMTCheck 1og which contains output information concerning the average background 30 level and the number of pixels having a value of 0 in the image The PMT check utility also generates a summary file called PMTCheckSummary log which contains the summaries for all PMT checks performed on the detector A summary of the typical log file PMTCheck 1log generated by the PMT check utility can be found in in Appendix C Sample Log Files on page 161 Continuously Reading an IP On R AXIS systems the system can be set up to continuously read the IPs This is mostly used as a diagnostic tool and will normally only be performed by a Rigaku MSC service technician To put the R AXIS in continuous IP r
98. ax Cell Length field specify the maximum cell length in ngstroms to search If this is 0 then CrystalClear tries to determine a maximum cell length on its own which is subject to errors In the Max Residual field specify the maximum allowed least squares residual for a solution to be Page 68 CrystalClear User Manual 10 11 12 13 14 15 Data Collection and Processing listed The program fits the reduced primitive cell to 44 lattice characters Only those solutions with a residual less than or equal to Max Residual are displayed Typically residuals greater than 2 5 are not valid solutions The maximum residual is 100 The default of 2 5 reduces output and helps make it easier to choose the correct solution If using the Rossman method a residual of 1 or higher indicates either the wrong solution or misaligned hardware In the Max Vectors field specify the maximum number of difference vectors to use in the calculations With more difference vectors the calculations take more time and the residuals will be larger With fewer difference vectors the calculations take less time and the correct solution may be missed If 0 CrystalClear picks a suitable number In the Grid Size field specify the grid size in Angstroms for the direct space Fourier map This is not used if Use Fourier Method is not selected If 0 then the program selects an appropriate grid size In the I SigI field specify the desired value
99. beam shots and so Initialize before direct beam shots should be selected 6 Click Take to take direct beam shot s When doing direct beam shots you do not need to turn down the generator but you must place some attenuation in the X ray beam The images generated during direct beam shots are placed in the DirectBeamShots subdirectory of the Program Directory The direct beam utility generates a log file called Direct Beam log which contains output information concerning the position and shape of the direct beam for each shot taken For R AXIS detectors there also a summary at the end of the log file containing the important results from the direct beam shots The direct beam utility also generates a summary file called DirectBeamSummary log which contains the summaries for all direct beam shots taken on the detector CrystalClear User Manual Page 157 Appendix B Administration A summary of the typical log file Direct Beam log generated by the direct beam shot utility can be found in Appendix C Sample Log Files on page 161 7 Replace beam stop when finished 8 Close the Administrator Utilities by clicking the E on the upper right of the dialog box Check PMT PhotoMultiplier Tube On R AXIS systems to check the photomultiplier tube 1 Start CrystalClear and log in as the administrator 2 Close the sample by clicking Cancel or OK in the Open Sample dialog 3 Click Utilities gt Administr
100. by collecting and Process initial images decide to collect a data set on a crystal help determine a data collection strategy collect the data and process the images The software is designed to have one data set per sample Collect and This task allows you to go directly to data collection Process and process the images once they are available Collect This task allows you to only collect data This option is used when the intention is to process the images at a later time Process This task allows you to process already collected images Combine This task allows you to combine reflection files from Reflections different data sets Next the Image Files dialog appears If you are using existing image files to Process a sample you may specify one image file in the Image File path CrystalClear will include all image files in the same location for the sample If you Collect images for this sample specify the path to store images upon collection Collected images may be stored in a separate location as the Project and Sample data Note Each time a New Project or New Sample is created CrystalClear creates new folders on your system located in the assigned path For example when a New Project named Myoglobin and a New Sample named Myol is created CrystalClear creates a folder called Myo1 nested within a folder called Myoglobin project Each time a New Sample i e Myo2 Myo3 Myo4 etc is created within the Myoglobin Projec
101. cal harmonic coefficients or Fourier coefficients via singular value decomposition is very robust and in most cases will lead to a satisfactory result However there are some cases in which error messages are displayed Use the troubleshooting tips in Table 2 to guide yourself through these problem cases Walker N amp Stuart D 1983 Acta Cryst A39 158 gt Jacobson R A private communication j Press W H Flannery B P Teukolsky S A Vetterling W T Numerical Recipes in C The Art of Scientific Computing Cambridge University Press Cambridge 1991 pps 60 72 Page 202 CrystalClear User Manual Appendix E Absorption in Scaling Table 1 Absorption options Fourier This option uses Fourier coefficients to model diffracted beam absorption and simple batch scaling to model incident beam absorption decay etc 4 3D 3 2D This option uses 4 order even and odd spherical harmonics to describe the diffracted beam absorption and 3 order even and odd circular harmonics to model incident beam absorption 3 3D 2 2D This option uses 3 order even and odd spherical harmonics to describe the diffracted beam absorption and 2 order even and odd circular harmonics to model incident beam absorption Table 2 Absorption correction trouble shooting guide Number of outliers exceeds The assumed symmetry is too high Use Data analysis gt 2000 Laue Group to automatically determine the Laue group a
102. changes Finally double check that refinement has converged The shifts should be 0 on the last cycle In the tables below Rmerge is defined as Rmerge Sum Sum Ihi lt Ih gt Sum Sum lt Ih gt h i h i where Ihi is the ith used observation for unique hkl h and lt Ih gt is the mean intensity for unique hkl h Lines 221 225 A reminder of the equation for Rmerge 226 Rmerge vs Batch 227 228 Batch Average ChiSq Rmerge Rmerge 229 name counts j i j batch cumul 230 231 232 233 234 235 236 237 238 239 24 24 24 24 24 24 24 24 24 0 03004 0UN RO SiO iO DO 10 001 010 60 00 00 00 OOO OO OOO ODO SS IO 1 90 DQO O OOO O AO O NO uy HR 0000 ds 0 Y gt 000 J J00 JO PRPPPPPPEPRPENEPWANHEHEHPUN N Oo o CrystalClear User Manual Page 189 Appendix C Sample Log Files Lines 226 252 This table lists Rmerge vs Batch It is easy to recognize any batch not matching well with the other batches Average counts Num refs Num rejs Num ovlps Num singles lt I sig gt ChiSq Rmerge batch Rmerge cumul The average counts of reflections in the batch This includes reflections that overlap and those that do not If you assume Poissonian counting statistics then the expected Rmerge for this batch would be 1 V 7 So for batch L001 1 865 0 034 is consistent with 0 036 found Total number of reflections in this batch Number of rejected reflections There should be
103. collection run 1 Click the Collect Images button on the Flow Bar The Collect Images dialog will appear CrystalClear User Manual Page 57 Data Collection and Processing Collect Images xi Pixel Size Readout Area Start Line Number lines it Full ban 0 Collect Schedules Default y Add Scan Remove Scan Scan Scan Det Max Start End Complete Start Exp Schedule ID Template Dist 28 Resin Angle Angle som Lt ness Time _ Images Collected Collection 1 E osc 153 EM EN 1 360 m Time estimate Required disk space r Total disk space Scan 0 Scan OMB 0 Available 117 MB Schedule 0 Schedule OMB Remaining 117 MB m Completeness Preferences Update JE Run Close L save Import Pixel Size u Readout Area Collect Schedules right click down arrow Scan Table Time Estimate Select appropriate value Select desired entry Full Middle Bottom Half Custom Grayed out options will appear as required Start Line Number Lines Assign a schedule in the Collect Schedules edit box Several common schedules are One 0 collects one image at 6 0 Two 0 30 collects one image at 4 0 and one at 30 Four 0 30 60 90 collects images at 0 30 60 and 90 Default Screen Schedule The Scan Table contains contains information about scans in columns with headings which can be manipulated Users are able to Add Scan
104. create a custom macro 1 On the Refine dialog click the Advanced button The Macro Editor dialog will appear e The Refine dialog can be accessed by clicking the Refine Cell button on the Flow Bar during aProcessing task Task drop down list options Process or Screen Collect and Process Click the Advanced button to access the Macro Editor dialog Macro Editor Ed Step Name Min Res MaxRes Num Cycles Al Detector a Crystal Rot 100 00 3 00 10 All Crystal 100 00 3 00 10 All Detector All Crystal 100 00 3 00 10 T Ca pu al Macro Detector then all crystal y Al Cell fan Detector T AllLengths All nales P All Rotations ae CU BEBE 8B 8 8 a a bc a B y Rotl Rot2 Rot3 Mosaicity m Detector Source All Detector New Macro IV All Translations T All Rotations All Rotations New Step lv V M Dor Ww a a E Transi Trans2 Trans3 Roti Rot2 Rot3 Wavelength Rott Rot2 Remove Step Control Resolution LAO 500 Rejection Limits Min 100 00 Max 2 00 Cycles fio x 1 00 Y 1 00 Rot 2 00 Page 122 CrystalClear User Manual Additional Processing 2 Click the New Macro button The New Macro dialog will appear Name DK DO Lo Cancel Copy Values From Single Step Refine Detector then all crystal Crystal then all detector Low reso then all reso 3 Enter a unique name for the New Macro 4 From the list of Crystal
105. creating a reflection and log file called dtfind ref and dtfind log respectively Each image appears in the image window as it is p rocessed Index Spots The CrystalClear Flow Bar will show the next step of Assign Unit Cell Click Index Spots on the Flow Bar The Index Spots dialog will appear 2 3 The Index Spots dialog allows the user to index the spots from a reflection file and thus assign the unit cell This can be done either automatically with judicious setting of the parameters or interactively with the User Chooses Solution option The Index Spots dialog allows the user to index the spots from a reflection file and thus assign the unit cell This can be done either automatically with judicious setting of the parameters or interactively with the User Chooses Solution option Index Spots x Main Advanced m Spacegroup __ Reflection Lists Unknown Spacegroup r Known ar Wumber Hame Resolution Minimum Maximum 0 00 jo 00 Set IV User Chooses Solution Close Save Defaults If desired change parameters in the Index Spots dialog box When satisfied with the settings click Run CrystalClear indexes the spots from the reflection file selected updates the database for this sample and generates a log file called dtindex log If User Chooses Solution is checked the user must choose one of the crystal lattice solutions displayed by double clicking on
106. csssssssscececcccccecessscsceceees 135 INSTALLED PILES ia A Ta Sas Siete A a A a OE Taaa 135 Crystal lear program fes erd irrogate dansa adan RIA dedos an 135 O O NS 135 Help ld adn 135 OCX C mponehtS serren ieee tE lila 136 RAXWISHFilES ee egan rd 136 Crypto Box Tiles tutti a e e EAEE E 136 ea E PIES 6 59 AS NE EAN OE EET EE EA AN EAEE OAE ENOS EA A EA 137 FILES CREATED BY CRYSTALCLEAR padano E O A Ad Ae 137 DIRECTORES A ss a a E 138 APPENDIX B ADMINISTRATION ccsscsccccccccsssssscsccccccccccessssscsceccccecessssscsssceccccesessscssececes 141 ADMINISTRATOR LOGIN 235 sissies aA decidan Tribal ea iia netos ias 141 GENERAL SETTING Su ias 141 ADMINISTRATION OF USERS micos aci o ad 142 Adda Usada illo riada lleida idad iodo sfaesdeaseues 143 REMOVE a Usa tt ita 144 Edit USER SEMI AAA ia 145 ADMINISTRATION OF GROUBS ccssccccccsseececeeeececeeseeccceeeeseceuseesecuueeesseeeeeseeueneesecueneessauaneeseauanes 147 Ad As GrOUp e a E E a SE a aaae E sev iaeanageabecd usdaa soni ATETA E STIE a Tai 147 Remove a GLOUp ii a tai 148 Edit Group Setn S meore ge reen anara E EOE SEa tase EERE RETE EEEE SATA EE EOE E 148 ADMINISTRATION OF OESTE si 149 NS A tect teak abba O EEA EE O E AOE RNA 150 Remove a ol AAA A 151 Edit Tool Settings onnenn r ia e eT E EEE eta das geseah oaacenticascectbeveseebifeagecesbssoverteehecacthedese 151 ADMINISTRATION OF SBR VERS ita iii a os 151 Edit Servet Settini Sie tii EII II A Aia 152 CrystalClear Use
107. ct Level or Sample Level Using Default Manager also allows you to make information available to other samples or all projects in other projects and samples Site Level settings are inherited by all users for each project and sample as they are created Only users with administrator privileges are authorized to save at Site Levels For most users this option is grayed out e To access administrator privileges exit CrystalClear and log in as an administrator e Ifa user wishes to access the Site Level administrator privileges may be assigned in the User Settings dialog For more information see Edit User Settings on page 145 of Appendix B Administration 1 When the Default Manager dialog appears select the Current Levels you wish to save by clicking the appropriate check box e Alternatively selections can be made by clicking the radio button beside the appropriate Site User Project or Sample names on right side of dialog Default Manager x Site Current Levels 5 E Administrator dhulick Y Sample ds Project O Myo2 F User Myo3 current l Site Set Unset Set All Unset All ilele 2 Use the following buttons for assistance in setting defaults Set Sets a default Unset Unsets a default Set All Sets all Levels Unset All Unsets all Levels 3 When appropriate Levels are selected click OK CrystalClear User Manual Page 209 Appendix G
108. d CrystalClear User Manual Page 85 Data Collection and Processing The choices are 13 Select the Pre refinement to be used Crystal then all detector Detector then all crystal Low reso then all reso Single Step Refine All The choices are None First image First amp Last First Last amp Middle 1 images of 3 batches All images of 5 batches 14 In the Ice Rings box make desired entries in the Min Resin and Max Resin fields if necessary Click the Add button the Ice Ring dialog will appear prompting the user to enter the Min and Max resolutions of the Ice Ring Alternately Min and Max resolutions can be entered by clicking and dragging on the displayed image This method provides a visual representation of the Ice Ring as well as providing numerical values in the entry fields Errei resciuions of cick on mage OK Mn Mx pen pan 15 Click Run to integrate reflections Page 86 Inage Name Image Number Piefinction List SS StanAnde feud Image Widh 1 fic o Exposure Tims zec 500 Custo Det Diet mm 1200 Detector 29 1 foco us Spo Disterce Number of Spots Las Spots Hore Spaz z CrystalClear User Manual Analyzing the Data Data Collection and Processing Once integration is completed you may wish to analyze the data for purposes of evaluating and determining Laue symmetry centricity and spacegroup Additionally cell transformations
109. d A E a 2 AE Result Result UU ARRE AMES loza Ato mie Cie ishen remna on Images ony State Additional Arguments Unda 23 Index Fun Close Save Defaults Advanced 2 Specify any settings changes as desired With the new refinement algorithms it is recommended that all crystal detector and source parameters except wavelength be refined initially Itis rare that anything other than this is necessary CrystalClear User Manual Page 71 Data Collection and Processing 3 If desired click the Advanced button to go to the Macro Editor which will allow the user to create a series of refinement steps varying the parameters refined for each step This is seldom used and ifused is for extreme cases We leave it in the software for the exceptional case Macro Editor Ed Step Name Max Res Num Cycles Step Crystal M Single Step Refine v Y All Crystal acto Single Step V All Cell IV AllLenaths M AllAngles IV All Rotations Vi Ww Vr MMM Vv abe aB y Rotl Rot2 Rot3 Mosaicity r Detector M All Detector New Macro M All Translations IV All Rotations M All Rotations rarer Tew Step M M M Vw Mw L M M Trans Trans2 Trans3 Roti Rot2 Rot3 Wavelength Rot Rot2 Hemose Step r Control Resolution ooo Rejection Limits Min 100 00 Max 2 00 Cycles fron x 1 00 Y 1 00 Rot 2 00 4 Create a new macro by clicking the N
110. d or twinned crystal will give extraordinarily long lengths which is diagnostic of these conditions Lines 15 19 A direct space cosine Fourier map is calculated for a hemisphere volume with radius 112 5 A and grid size 1 5 A If the maximum cell length of the crystal is larger than the Actual max cell line 19 then it will be impossible to get an initial cell so set Max Cell Length in the dialog and re run For small cell lengths if the Actual grid interval line 18 is too large then it will be difficult to get a solution set Grid Size in the dialog and re run Line 20 An initial minimum peak height in the Fourier map is determined and listed Since the origin of the Fourier map point 0 0 0 is normalized to have a value of 1 a peak minimum of 0 9 or greater suggests that a solution to indexing will be found Initial peak minimums below 0 9 suggest a problem such as incorrect grid size incorrect spatial distortion incorrect direct beam position incorrect detector position or a split cracked or twinned crystal Line 22 Four peaks were found with a height above the minimum and at least 3 were non coplanar and define a 3 dimensional lattice If at least 3 non coplanar peaks were not found the peak minimum would have been lowered by 5 and the Fourier map searched again This will be repeated until a solution is found or the minimum peak height is 0 3 Lines 23 25 Just in case after 3 non coplanar peaks are found the peak minimum is reduced
111. dited macro on additional projects or make it available to other samples or all projects make the appropriate selections on the Default Manager dialog then click OK The Collect Schedule The Collect Images dialog is useful in working with Collect Schedules New schedules can be created existing schedule can be imported and altered to meet the various needs of each user The Collect Images dialog is used to Run and Save Collect Schedules Use the Collect Images dialog to e Create a Collect Schedule e Import a Collect Schedule e Runa Collect Schedule e Save a Collect Schedule 1 Access the Collect Images dialog e The Collect Images dialog can be accessed by clicking the Collect Images button on the Flow Bar during a Collect task Task drop down list options Screen Collect and Process Collect and Process or Collect CrystalClear User Manual Page 125 Additional Processing Collect Images x Pixel Size Readout Area Start Line Number Lines v a Full y p 3000 Collect Schedules Default y Add Scan Remove Det Max Rot Start Era Complete Start Exp Dist 28 sin D Axis Angle Angle E _ness ime s ru _Images C osc 19 3 ss gt m Time estimate Required disk space p Total disk space D Scan 0 Scan OMB 0 Available 178 MB Schedule 0 Schedule 0MB Remaining 178 MB m Completeness Preferences Update hun Clos
112. e Defaults 4 Specify a Minimum Pixel Value for a pixel to be considered a peak The Minimum Pixel Value is compared to non uniformity corrected pixel values The actual threshold used is the maximum of Minimum and Sigma above the average background 5 Specify the Peak filter The Peak size filter is specified as the number of pixels in a 3x3 area that must be above the threshold Sigma Minimum Pixel Value for a peak to be considered a reflection If spots are large you might want to make this 9 If the spots are small you might make this 4 Peak filter helps distinguish between true spots and noise in the images 6 Select 3D check box to perform a 3D search to determine peak widths for mosaicity refinement By default a 2D search is automatically performed 7 Specify the Padding to be added The padding is the number of images for 3D shoeboxes in 3D search mode only at the start and end in the rotation angle direction In order to completely contain a 3D peak with a 3D shoebox or volume pad by 2 4 images and have a Box width and height large enough to encompass the reflections If any significant peak intensity is on the edge of a shoebox CrystalClear rejects the centroid determined for Page 66 CrystalClear User Manual Data Collection and Processing that peak Thus Padding is important to ensure that the peak goes down to background in the rotation angle direction 8 Specify the Box Width and Height in pixels of t
113. e Import Note When CrystalClear is using the R Axis as the Image Collect Device Type the illustrated Collect Images dialog appears When CrystalClear is using the Mercury CCD Image Collection Device Type a slightly different Collect Images dialog appears The following instructions apply for both dialogs Create a Collect Schedule To create a new collect schedule 1 Access the Collect Images dialog e The Collect Images dialog can be accessed by clicking the Collect Images button on the Flow Bar during a Collect task Task drop down list options Screen Collect and Process Collect and Process or Collect 2 Use the Scan Table to alter the scans e Use the Add Scan button to increase the number of scans at a different crystal orientation Adjust settings as desired e Use the Remove Scan button to remove undesired scans For assistance in manipulating the Scan Table columns headings or other settings see Using the Scan Table on page 103 of Section 7 Tool Reference 3 Make adjustments to the settings as required 4 When all settings are satisfactory for the new Collect Schedule you can e Run See Run a Collect Schedule on page 128 for assistance e Save See Save a Collect Schedule on page 127 for assistance Page 126 CrystalClear User Manual Additional Processing Import a Collect Schedule To import an existing collect schedule 2 Access the Collect Images dialog e The Collect Images dialog ca
114. e female end of the dongle Installing CrystalClear To install CrystalClear CrystalClear User Manual Page 15 Installation Place the CrystalClear CD in your CDROM drive 2 Click the Start button then click Run 3 Enter d setup where d is the drive letter of your CDROM drive then press Enter The Welcome dialog will appear Welcome Welcome to the CrystalClear Setup program This program will install CrystalClear on pour computer It is strongly recommended that you exit all Windows programs before running this Setup program Click Cancel to quit Setup and then close any programs you have running Click Next to continue with the Setup program WARNING This program is protected by copyright law and international treaties Unauthorized reproduction or distribution of this program or any portion of it may result in severe civil and criminal penalties and will be prosecuted to the maximum extent possible under law Click Next to continue The license agreement will be displayed Read the license agreement and click Yes to continue with the installation 6 The INFOLIST TXT file will be displayed This document includes important information about CrystalClear including release notes for the current version and other information that may not be included in the user manual Click Next after reading the material 7 Inthe Select Destination Location dialog select the location where you want the Cryst
115. e to finish e g a 30 second simulator exposure will take 30 seconds to finish If the value is immediate then the exposures will finish immediately Specify User Preferences To customize other user preferences 1 Click Tools gt Preferences on the menu The Preferences dialog will appear 2 Click the General tab CrystalClear User Manual Page 115 Tool Reference Preferences 3 Select the Scale and Average Graphs to be displayed 4 Set the Resolution Units for the image display 5 Set the Exposure Time Units for data collection and image display 6 Continue to check other tabs or click OK to save changes Specify Collection Defaults To customize the preferences for setting up collection 1 Click Tools gt Preferences on the menu The Preferences dialog will appear 2 Click the Collection tab Page 116 CrystalClear User Manual Tool Reference Preferences 3 Make changes to the options 4 Continue to check other tabs or click OK to save changes View Log Files CrystalClear creates log files that help you see what settings were used during processing The results of the log files can help in troubleshooting problems To view a log file or another file in text mode 1 Click the View Log File button on the Tool sa Bl The Open dialog will appear e Alternatively click View gt Log File on the menu 2 Select the log file to view 3 Click Open See Appendix C Sam
116. ead 7 RX_NONUNF_TYPE gt gt None lt lt 8 Setting predict resolution to detector EDGE not corner 9 Predicting reflections 0 Component 1 crystal mosaicity 0 6 1 done 8936 reflections predicted 2 Crystal listing 3 Unit cell lengths 78 8782 78 8782 36 8650 4 Unit cell angles 90 0000 90 0000 90 0000 5 Unit cell volume 229365 567 6 Orientation angles 53 5160 71 4165 86 2778 7 Mosaicity 0 600 8 Description unknown 9 Spacegroup number 75 20 name P4 21 Num equiv posns 4 22 Reducing reflnlist to asymmetric unit and sorting 23 done 24 Searching for best rotation start and range 25 done 26 Strategy results 27 Resolution 23 66 1 76 28 Rotation start 42 00 29 Rotation end 102 00 30 Rotation range 60 00 31 Completeness vs Rotation range 32 Rotation Cumul Comp Comp 33 range range shell cumul 34 42 0 47 0 5 0 1D 51 TS 1 Page 170 CrystalClear User Manual Appendix C Sample Log Files 35 47 0 52 0 10 0 15 4 3139 36 5260050 BTL 0 15 0 6 3 45 9 ey PaO Su 625 0 200 14 4 58 4 38 62400 6070 20 3 0 19 50 69 7 39 67 0 72 0 30 0 Dub BRA 40 72 0 77 0 354 0 4 5 85 1 41 77 0 82 0 40 0 15 6 91 4 42 82 0 87 0 45 0 14 7 94 5 43 BO 19 20 50 0 5 4 97 1 44 92 Orme OO 550 3 58 98 5 45 97 0 102 0 60 0 To 0 Y AL 46 42 0 102 0 60 0 9931 DL 47 Expected Completeness vs Resolution 48 Resolution Calc Num Num Num Num Num Avg Comp Comp 49 range unique reflns rejs mults single unique mu
117. ead mode Page 158 CrystalClear User Manual Appendix B Administration 1 Start CrystalClear and log in as the administrator 2 Close the sample by clicking Cancel or OK in the Open Sample dialog 3 Click Utilities gt Administrator Utilities The Administrator Utilities dialog will appear 4 Specify the setting for the Continuous IP Read mode a Specify the number times to read the IPs in the Number of cycles field b If the R AXIS should be initialized before performing the test select the Initialize R AXIS check box c Select the Write images to same file check box if the images are to be written to the same file on disk If this check box is unselected then each image will be written to a separate file on disk Unless there is a need for saving the images read writing the images to the same file on disk is the preferred mode of operation Each image is approximately 18 Mb in size and so writing the images to separate files can quickly fill up the disk which may be the system disk d If itis desired that the X ray shutter open briefly for approximately 1 second before reading an IP select the Open X ray shutter during read option Unless there is a valid reason for selecting this option we strongly suggest that you unselect this option for safety reasons 5 Click Take to begin the continuous IP read On CCD systems this feature is not available The images generated during the continuous IP read check is placed
118. eak fills Profile size too large Peak Profile size too small Peak box but there is background at crowded into center so decrease overfills box so increase first edges and faces first Profile size value make box Profile size value make box smaller bigger Each image file shows 18 reference profiles Each reference profile is a three dimensional cube of 9 by 9 by 9 Kabsch transformed pixels The pixels are NOT in image or data space but rather in a transformed Kabsch space read his 1988 paper J Appl Cryst 21 916 924 Since images are displayed in 2D each 9 by 9 by 9 cube is displayed as a series of 9 two dimensional 9 by 9 planes Figures 19 22 Page 178 CrystalClear User Manual Appendix C Sample Log Files Stack them up in your mind to make them 3D Because of the Kabsch transformation reference profiles should look very similar throughout reciprocal space The appearance of the reference profiles is affected by the Profile size option The width of the profile in the plane of the display is determined by the first value to Profile size while the number of squares the profile fits in is determined by the second value To make the profiles appear larger in the plane decrease the first value To make them appear smaller increase the first value To make them appear on more squares decrease the second value To make them appear on fewer squares increase the second value In reality the profiles do not change physical size
119. eated a user account you can start CrystalClear and Log in to begin working on your crystal samples Before you are able to log in to CrystalClear your administrator must create a user account for you You will receive a Login Name and a Password For convenience your Login Name could be the same name used for your system login If you do not know your user name and password see your CrystalClear administrator Important CrystalClear will not run without the Crypto Box dongle installed on the parallel port of the computer Before starting CrystalClear make sure the dongle Crypto Box is installed To start CrystalClear 1 Click Start on the Windows task bar then select Programs gt Rigaku MSC gt CrystalClear The CrystalClear program will start and the Login dialog will be displayed The current system login user name will automatically be displayed in the Login Name edit field If CrystalClear is not on your Start menu see your CrystalClear administrator CRYSTAL CLEAR Yersion 1 3b 09 Copyright o 1968 Rigaku All Rights Reserved Login Name Password Cancel 2 Enter Login Name then press Tab User names and passwords are not case sensitive 3 Enter the password then click OK CrystalClear User Manual Page 27 Running CrystalClear for the First Time Creating Your First Project and Sample When you log into CrystalClear for the first time the Project Wizard will lead you through the creation
120. ed Reflections 0 20000 r Crystal Displacements IV x IV Mz Crystal Goniometer Vo My IV Orientation Matrix 3 Close Defaults 2 Click Run Save Twin 1 Click Save Twin to save the current component Return to Index Spots to index the remaining reflections and repeat the above steps until you are satisfied that you have found all of the twin components Get Twin Relationship When you are satisfied that you have found all of the twin components click the Get Twin Relationship on the Flow Bar This will print the rotation angle and the orientation matrix between all the components Predict Spots To predict spots 1 Click Predict Spots on the Flow Bar The Predict dialog will appear CrystalClear User Manual Page 79 Data Collection and Processing Image List myo2_screen001 osc myo2_screen002 osc myo2001 osc myo2002 osc myo2003 osc myo2004 osc myo2005 osc myo2006 osc TT Alpha2 spots myoZ007 osc myo2008 0sc hd Sequence peoo Expected Spot Size X pixels Y pixels Z degrees 0 90 i Close Twins All Twins Single Component 0 y Defaults 2 Select the images to be processed You can either select the desired images from the Image List or specify a single range of image sequence numbers in the Sequence edit box 3 Specify the Expected Spot Size for the Z axis in degrees 0 9 should be used as a default value 4
121. ed by CrystalClear A reflection list with spot centroids such as dtfind ref from the Find Spots procedure is also required A header file called dtrefine head with refined crystal detector and source properties is created by the Refine Cell procedure A scratch reflection list with observed and calculated reflection centroids that can be plotted by CrystalClear will also be created as well as a script file and an output log file dtrefine log To refine parameters 1 Click the Refine Cell button on the Flow Bar The Refine dialog will appear Refine 21x Crystal m Statistics M All Crystal M RMS Residuals V All Cell I All Lengths F All Angles All Rotations mm degrees lv lv lv lv Vv Vv Vv lv Vv Vv Reflections sa a b o B Yy Rott Rot2 Rot3 Mosaicity Start rss E E 46 02 fao oo 80 00 fi 20 00 F 87 6590 23 3985 93 0047 aso Total Accepted Last Rejected Excluded eS A EEEE EE E E as Min 100 0000 Max 3 0000 Set a A a A ee r Detector m Source 10 0000 Cycles 100 M All Detector ERRE IV All Translations M All Rotations M All Rotations cs v v v E 1 Y r v Y x 1 0000 Y 1 0000 Rot 2 0000 Tran Trans Transz nay Roty Wavelength Rot Rot2 Dist Macro Single Step Refine y Start 0 0272 0 0419 119 299 0 0328 aust 0 0009 Start 1 5s180 fost 0 0227 Les l Refine on Reflection list Reflection List dtfind ref b
122. ed by the user Additional projects samples can be viewed and or selected by clicking the appropriate down arrow s If the New Project Wizard appears rather than the Open Sample dialog it means CrystalClear did not find an existing project database file Follow the steps in Section 4 Running CrystalClear for the First Time on page 27 to set up the first project and sample or see your administrator CrystalClear User Manual Page 93 Tool Reference 2 To create a new project click the New Project radio button The existing project name will be highlighted Type the new project name in the Project edit field This will replace the existing text Click and highlight the existing Sample name Type the new sample name in the Sample edit field This will replace the existing text Select the task you wish to use for this sample from the Task drop down list Specify the directory with the images for this project Type the full directory name in the Image Directory field If image files already exist select using the Browse button CrystalClear can be used to process data collected previously Images collected with CrystalClear or other software should contain header information with common filename extensions Images collected with the Rigaku R Axis detector use filename extension OSC Images collected with the Rigaku Mercury or Jupiter CCD detector use filename extension IMG CrystalClear will support IMG CCD OSC RAXIS
123. ed to SessionScript bak and a new SessionScript scp file is created This file is a backup of the previous session SessionScript scp Only one previous session is saved in the SessionScript bak This is a log of the activity during a Find operation This is a log of the activity during an Index operation Additional log files are created specific to the current operation Directories A subdirectory called Data is created off the CrystalClear program directory This subdirectory will contain information about the users projects and samples that are processed with CrystalClear Program Directory Administration Data Directory User User Project User Project Sample Scripts Twinsolve RAXWish Page 138 The directory where the CrystalClear program and its peripheral files installed The Administration database is stored in this directory The directory where the data about users projects and samples is stored The data directory is a subdirectory of the Program Directory Each user has a directory where their project and sample data is stored The Administrator directory is a user directory created for the Administrator All of a user s projects have a unique directory located under the user directory A project can contain any number of samples The sample data is stored in a unique subdirectory under the Project to which it belongs A script directory is created for each user This directory is
124. er MAR CCD MAR IP ADSC CCD MacScience Brandeis CCD and MedOptics images Overview of the CrystalClear nterface The CrystalClear interface pictured above contains several elements that let you control collection and processing The items below refer to the numbers in the display above Task drop down list Current sample Run mode Flow bar Step within the selected task Substeps of a step Toolbar Image window Command Bar 10 Message Window 11 Status Bar NN 0 DU un Task Drop down List The Task drop down List displays the currently selected task Display the list by clicking the drop down button Specific tasks will be discussed in later sections of this manual Tasks include Screen Collect and Process Collect and Process Collect Process Combine Reflections Current Sample CrystalClear allows one open or current sample at a time After Login the sample most recently opened 1s automatically displayed in an Open Sample dialog The user may wish to open this sample or create a New Project or New Sample Alternately to open a current sample click File gt Open Sample To start a new sample click File gt New Sample If a new sample is created when sample is current CrystalClear automatically saves and closes the existing Upon exiting CrystalClear the current sample is automatically saved and closed Run Mode The Run Mode buttons allow you to choose whether you want to process your data in automatic mode or manua
125. ergence of the refinement algorithm is small so the starting properties should be very close before trying a refinement This is usually the case 1f indexing has given a solution If the starting crystal and detector properties are not close to the true values one might increase the Rejection Limits so more reflections are included in the refinement However there is a danger they will be increased too much and refinement will proceed to a false minimum It is sometimes better to use only low resolution reflections at first because the radius of convergence with them is larger Then use high resolution reflections to get the more accurate results With good reflection centroids it is best to use all reflections The refinement algorithm should be used to refine all parameters from the first If this is not successful it is useful to fix or not refine a property In the Refine Window a checked box means a property is refined so uncheck the check box to fix the property Some properties are not refined because of the choice of spacegroup For example in orthorhombic cells B and y are not refined With input reflections found in a single image the crystal rotation around the source and the detector rotation around the source are correlated so one of them should be fixed unchecked The same is true for the CrystalClear User Manual Page 73 Data Collection and Processing detector translation along Y and the detector rotation around X the swin
126. es with the centroids of strong reflections found in the images Reflections in the batch of images will all have the same Batch field in the dtintegrate refand dtprofit ref files The larger the value ofImages Per Batch the more memory CrystalClear will use You may wish to strive to have 100 1000 reflections per batch so for crystals with large unit cells you may set Images Per Batch to 2 or 3 while for crystals with small unit cells you may setImages Per Batch to 10 20 7 Inthe Peak Radius field specify the minimum and maximum reflection radius to use This is a measure of the minimum radius of a reflection in pixels Since spot shape is automatically determined this minimum radius should be smaller than the actual spot so that the algorithm can use itis as a seed from which to grow the spot shape The maximum radius should be larger than the biggest peak but smaller than one half the box size The shape of weak reflections is determined from nearby strong reflections 8 Specify a Batch prefix to use for batch IDs or names given to reflections in the output reflection Page 84 CrystalClear User Manual lists Data Collection and Processing Use this option to distinctly label reflections from different scans and or crystals The prefix should not be longer than 4 characters If no prefix is specified here a batch prefix may be added to any reflection list at a later time 9 Click the Advanced tab Integrate Reflections x
127. esults for IP 2 w Position x y 1500 92 1509 61 0 266244 0 175193 a1 Pixel Intensity 10740 4 268 098 a2 Integrated Intensity sigma I 336789 896 288 4495 92 3 81553 a3 I sigma I 375 777 6 19005 a4 Full width at half maximum x y 5 57419 6 89354 0 0479199 0 0299656 45 IP1 IP2 46 Cycle Xx y I x y 47 48 1 1499 8 1509 8 10841 500 7 1509 8 10932 49 2 1499 4 1509 6 10346 501 3 1509 4 10267 50 3 1499 4 1509 4 9872 501 0 1509 7 10826 51 4 1499 6 1509 7 11006 1500 9 1509 5 10846 52 5 1500 0 1509 5 10600 1500 7 1509 6 10831 Lines 5 31 ASCII text representation of the spot profile Each character represents the value of a pixel Pixel values are on a 0 35 scale 0 is represented by 10 35 are represented by A Z Pixel closest to the center of the spot is represented by a Line 15 For R AXIS systems the IP number and cycle number are listed For CCD systems a description of the type of CCD is listed Lines 16 17 The position of the center of the spot and the value of the pixel closest to the center are listed Lines 18 19 The integrated intensity I o 1 and I o 1 for the peak are listed Lines 20 21 The width of the peak at the 30 level and at half of the maximum value of the peak are listed Lines 33 38 For R AXIS systems the results for IP1 averaged over all of the cycles For CCD systems these lines do not appear
128. ew Macro button 5 Click OK when done The Refine dialog will return The Macro you created will be in the list of Macros 5 Click Run to begin the Refine step The refinement process is complete when the number of cycles are completed If the delta error further refinement is needed 2D vs 3D reflection centroids in refinement The size and pixel coordinates of reflections will change as they pass through the Ewald sphere due to crystal mosaicity source divergence and source bandwidth AA A Thus the reflection centroids will be different for 2D data and 3D data This is illustrated in Figure 1 which shows an 80 by 80 pixel portion of 3 adjacent images of 0 25 rotation width along with an overlay of these images i e 0 75 width Each image was searched for spots then ellipses were drawn centered on the observed spot Page 72 CrystalClear User Manual Data Collection and Processing positions The overlay shows the shifts in the spot centroids Thus the rms errors lines 80 81 in the output found in Appendix C Refine Spots Log from 2D data will be larger than from 3D data Also if a 2D reference profile is applied to a partial reflection while integrating with a profile fitting method the reference profile must be oriented properly Refinement strategy O a e O o a O 0 00 0 252 0 25 0 50 0 50 0 752 Overlay of above 3 images Figure 1 2D vs 3D spot considerations The radius of conv
129. g angle It is a good idea to fix one of them With input reflections from widely spaced rotation values these correlations should not be a problem The crystal to detector distance can be refined even with reflections from a single image especially with a tetragonal or higher spacegroup Sometimes refinement works better if you fix most properties and refine only a few at a time Common sense should dictate the order of properties that are fixed and refined For example if you know the unit cell parameters from previous work then a b c and Qt B y can be initially fixed If the detector has just been moved refine the detector translations first then the crystal orientation angles then the unit cell parameters then everything The detector distance should be fixed if there are reflections from a narrow rotation range and a crystal principal axis is nearly parallel to the source For any changed settings to take effect you must click RUN or SAVE The refinement scheme used is stored in an output header and is also used during integration Every few images specified by the Integrate dialog Batch option the integrated reflection centroids are used to refine the crystal and detector properties Thus the settings of the Refine window are important for integration too Predict Spots The Predict Spots feature predicts the reflections that would appear on a range of images It is typically used to confirm the results of the refinement step
130. g modules supported by CrystalClear are d TREK TwinSolve To select a processing module 1 Click the toolbar button representing the processing modules you wish to use Use d TREK ES Use TwinSolve available only when processing CCD images e Alternatively the processing module options are available on the CrystalClear menu Click Sample gt then select the processing module you wish to use TwinSolve includes only an indexing algorithm You should use the solution found in TwinSolve to index a known cell in indexing If you select TwinSolve d TREK will automatically be selected as the algorithm for Integrate and Scale CrystalClear User Manual Page 49 Data Collection and Processing Setup The first step in collecting or processing data is to set the parameters to be used in the Setup dialog Once you have selected the sample the Setup dialog will appear For processing it is necessary only to have the following five fields correct X and Y Direct Beam positions Crystal To Detector Distance Detector 20 and Source Wavelength All other parameters are kept inside CrystalClear for your use Many of the values on the Setup tabs are set as site defaults assigned by your CrystalClear administrator or by the user as Project defaults e Alternatively Setup dialog can be accessed by clicking the Setup button on the Flow Bar e The Setup dialog can also be accessed on the CrystalClear menu ClickSample gt Setup The Main Tab
131. ggling display items moving through images etc As you move your mouse cursor over each button a Tool Tip will appear that describes the button s function Note that these functions are also available on the menu Page 22 CrystalClear User Manual OSE SH 04402006014 9 Introduction to CrystalClear GH El Ed El mi New Sample Open a Sample Save Sample Use d TREK as the processing module Use TwinSolve as the processing module When you choose this option CrystalClear automatically uses a mix of processing modules TwinSolve is selected for the Index algorithm while d TREK is selected as the Integrate and Scale algorithms available only with CCD View Image Collection updates When toggled on image updates will be displayed during collection View Image Processing Updates When toggled on processing results will be displayed during processing View Image Show Processing State Display A dialog displaying the processing state will be displayed Show Scan State Display A dialog displaying the scan state will be displayed Show Instrument State Display A dialog displaying the instrument state will be displayed Show Manual Instrument Control View Log File The Open dialog appears allowing you to select the LOG file to view That file is then opened in the Log File Editor Set Resolution The RAX Shape crystal viewer will be displayed This is available for CCD instruments only Previous Window The pre
132. hat there is not any critical overlap of adjacent spots using a test prediction and changing the size of the circle By increasing decreasing the circle size using the set reflection size button see that a circle includes no more than half of an adjacent reflection maximum size The minimum size of the box cannot be smaller than including all of the area of the peak and considering all regions of the image although setting it this small is not recommended 8 Images per batch is the number of images used in obtaining a refinement and scaling batch of reflections 10 or more is typical for small molecule data sets while 2 to 4 may be used for macromolecular crystals This is to allow for enough reflections to be available for proper treatment of refinement and scaling too few will result in poor refinement or refinement crashing too many will increase memory use beyond installed resources causing swapping and slowing the calculation 9 Padding is the number of images before and after the extent of the reflection including calculated center and mosaicity in which some of the background of a Page 3 INTEGRATION INTEGRATION INTEGRATION SCALING SCALING SCALING CrystalClear User Manual particular reflection is determined In wide slice data a value of zero may be appropriate otherwise values of one or two are typical 10 At the start of integration always have the processing updates turned on and carefully obser
133. he box that appears around each spot in the display In either search mode if these are both set to 0 then CrystalClear will try to determine the box size for each spot automatically Of course this will take extra computational power and time A good box size is 6 to 10 times larger than the biggest spot but without intruding more than half way into neighboring spots 9 Specify the minimum and maximum resolution 10 When satisfied with your settings click Run to find spots The Find Spots feature will create the reflection file dt find ref which will be used in the Index Spots step and the log file dt find log Index Spots The Index Spots feature indexes reflection centroids in the selected reflection list to elucidate the crystal unit cell dimensions the crystal orientation and the Bravais Lattice type To index spots 1 Click the Index Spots button in the Flow Bar The Index Spots dialog will appear Index Spots Ea Main Advanced m Spacegroup Reflection Lists Unknown Spacegroup goreeseseesesesesepseseseeseseesoseseeseseseeseg A e erna e S f y y l t A Triclinic Y Number Hame Minimum Maximum jo oo jo 00 Set IV User Chooses Solution Close Save Defaults CrystalClear User Manual Page 67 Data Collection and Processing 2 If you know the Spacegroup select the Known Spacegroup button then select the Crystal System from the drop down li
134. hedule To delete a collection schedule Access the Scan State Display dialog CrystalClear User Manual Page 129 Additional Processing Click the Show Scan State Display button on the toolbar Del Or click View gt Scan State Display on the CrystalClear menu The Scan State Display window will appear CrystalClear displays a window specific to the Image Collection Device Type selected namely R Axis or Mercury CCD Weknpoledive RAPISAINYD2 i o Manager tt an 3 e same 8 Compete ES ms CESA EA 1 Select the schedule in the Collect Schedule drop down box of the Scan State Display dialog 2 Click Delete button CrystalClear 3 Click Yes button to permanently delete the Collect Schedule Page 130 CrystalClear User Manual Images 9 Images The Image Window CrystalClear offers a graphical view of your data in the image window E Image Displas Documentation Worstall hear data YH yo globin tipo images Vayo2_ Screen ose y a Es 4 ES 1 Cyst o Del Disi fm 12000 Detector 28 1 foo Pol Position Nunber of Spats Loss Spots Mars Sois Large Image Window Profile Windows Large Image Window Toolbar Small Image Window Toolbar Small Image Window Image Information Window Du Bu n Large Image Window The image is displayed in the large image window Cross hairs allow you to select the portion of the image that will display in the Small Image Window
135. hines if Winsock has not attempting to run CrystalClear been installed The Winsock installation file is included in this installation To install Winsock2 go to the CrystalClear directory after A OS ca t found this installation usually c Program Files Rigaku MSC CrystalClear ae and run WS295SDK EXE This will copy the Winsock setup files to your hard drive Next run the Winsock setup by going to the Winsock directory usually c ws295sdk setup and run Ws2setup exe Crypto Box Messages Crypto Box Error 8 no dongle The CrystalClear Crypto Box dongle was not found Install the found dongle and try again Crypto Box Error 30 Error the A Crypto Box was found but it was not issued by MSC The dongle attached Crypto Box did not that came with CrystalClear should be installed on the PC on which come from MSC CrystalClear is installed Crypto Box Error 31 Error Normally this is caused when CrystalClear was installed with an registration key in the registry incorrect license number In this case reinstall CrystalClear and input and registration key in the the correct license number during installation Crypto Box do not match This error can also occur if a non CrystalClear Crypto Box dongle is found on the PC but the CrystalClear dongle was not In this case install the CrystalClear Crypto Box and Crypto Serv software on the PC then click the Check Again button Page 200 CrystalClear User Manual Appendix E
136. i Rotation Axis Start Angle End Angle Width Step Number Images Completeness Start Number Exp Time Total Images 20 offset of the detector Specify maximum resolution in degrees Specify the wavelength of your X ray source The wavelength is based on the Element type When you selected an Element a valid wavelength will be selected automatically The rotation axis on an AFCS8 or 9 Specify the position of the crystal goniometer in degrees or the rotation axis on the AFC7 Specify Omega or Phi 0 Omega used for AFC8 or 9 Omega and Phi one normally used for the AFC7 The angle in degrees of the start position The angle in degrees of the ending position The width of one image in degrees The angular distance between the start angles of two consecutive images in the scan The number of images to be collected in the scan The percent completeness of the data in that scan The start number to assign to the first image of the scan Specify exposure time in minutes Specify total number of images Images Collected Images already collected if any Images Scheduled Images currently scheduled for collected during next collection run Scheduled Start Angle The angle in degrees of the start position for currently scheduled images Scheduled End Angle The angle in degrees of the ending position for currently scheduled images 1 Make adjustments to the settings as requi
137. ify a Weight Multiplier and Weight Addend 7 Specify a value for Exclude Sigma Input reflections with Intensity sigma less than Exclude sigma are excluded from contributing to the scale factor refinement However these reflections are included in the final statistics and output files 8 Specify a value for Rejection Sigma This field sets the rejection level for reflections measured more than once Reflections with scaled intensities differing by more than Rejection sigma from the weighted average intensity calculated from other symmetry related measurements are flagged as rejected by setting their observed standard deviations to be negative 9 If the user wishes selection of rejected reflections may be based on Chi 2 values reflections above set value of Chi 2 are rejected or Max Fraction values only the worst reflections up to this fraction of total number of reflections are rejected 10 In Scaled Averaged Output File specify a name for the output file Click the Advanced tab to set advanced values Page 90 CrystalClear User Manual Data Collection and Processing Scale and Average x Main Advanced m Resolution Minimum Maximum f 00 00 2 00 set m Scaling Constraints fiw Batch Batch ID Scale Factor B factor FP m Optional Output o Corrected Unaveraged Reflections ES Uncorrected Unaveraqed Betector Close Save Defaults 11 Specify the desired Resolution If you
138. import Click el to browse for a file to import Select a file to import by clicking on it Type the File name to import in the entry field Click Files of type down arrow to view files other than ref b Click Open to import the file Merge Reflection Lists El E Reflection Lists Dutput Merged File merged ref Zone Type None z FT Restrict Resolution importi dti ef Miniman Mazmun import2dtinte of 00 00 2 00 Import Reflection File Save Detaws Note When files are imported the filename is added to the Reflection List Ifthe imported file has a unique name it is placed in the list with the same name If the imported file has a duplicate filename it is augmented as importi filename Doing a second file with the same name augments that filename to import2 filename See the Merge Reflection Lists dialog above 10 When satisfied with your selections click Run Create and Edit Macros Once a group of settings has been selected it is convenient to quickly apply those settings A macro CrystalClear User Manual Page 121 Additional Processing allows you to store a group of settings for crystal refinement then select the macro to quickly apply those settings CrystalClear offers several predefined macros All Single Step refine Detector then all crystal Crystal then all detector Lo reso then all reso CrystalClear also allows you to create and edit custom macros Creating a Macro To
139. in the Cont inuousIPReadImages subdirectory of the Program Directory The continuous IP read check utility generates a log file called ContinuousIPRead log which contains output information indicating the success of failure of each of the IP reads The continuous IP read check utility also generates a summary file called Cont inuouslPReadSummary 1log which contains the summaries for all continuous IP read checks performed on the detector A summary of the typical log file ContinuousIPRead 1log generated by the PMT check utility can be found in Appendix C Sample Log Files on page 161 CrystalClear User Manual Page 159 Appendix C Sample Log Files Appendix C Sample Log Files During processing CrystalClear records information in log files You can use these log files to double check that the correct parameters were used during processing and to help you refine your settings Below is a list of the logs files that are created by the d TREK compute server For d TREK Process Find Spots Refine Spots Index Spots Predict Spots Integrate Spots Scale and Merge Merge Reflections Strategy For PROCESS Process Peak Search Index Refine Integrate Merge Scale Post Refine Average For TwinSolve Process The log files are stored in the Sample directory CrystalClear User Manual Log Filename dtfind log dtrefine log dtindex log dtpredictspots log dtintegrate log dtscalemerge log dtreflec
140. in the file Lines 39 44 For R AXIS systems the results for IP2 averaged over all of the cycles For CCD systems these lines do not appear in the file Lines 48 52 For R AXIS systems the direct beam positions and pixel value tabulated for each IP and cycle For CCD systems these lines do not appear in the file Important If either X beam or Y beam position differ from IP 1 or IP2 this will be corrected at the time of data collection using the values from the direct beam shots If the values of either X beam position differs on the same IP between cycles the adjustments may be needed for the IP belt itself A summary of the typical summary file Direct BeamSummary 1og generated by the direct beam shot utility is shown below Direct Beam Utility Number of cycles 1 Exposure time 1 0 seconds Date Thu Sep 30 17 34 19 1999 Bou N BP 5 Average direct beam position for IP1 2682 6 1505 9 6 Average direct beam position for IP2 2683 5 1505 5 7 IP1 IP2 a Cycle Xx y I x y CrystalClear User Manual Page 195 Appendix C Sample Log Files 0 1 2682 6 1505 9 7090 2683 5 1505 5 7209 1 Direct Beam Utility 2 Number of cycles 2 3 Exposure time 1 0 seconds 4 Date Tue Oct 19 11 02 31 1999 s Average direct beam position for IP1 1505 1 1506 6 6 Average direct beam position for IP2 1507 1 1506 7
141. ion about strong peaks is listed for 18 different areas of the detector The detector is divided into 6 by 3 areas fast pixel direction by slow pixel direction The columns are Num Number of strong reflections Intensity Average intensity of strong reflections Sigma Average standard deviation of intensity BackAvg Average background value BackSig Average background standard deviation SIzZO Average peak size at lo in pixels in the fast pixel direction Sizl Average peak size at 10 level in pixels in the slow pixel direction Siz2 Average peak size at lo level in images in rotation direction D1 Average spot size as a function in reciprocal space Shft0 Average shift in pixels between observed and calculated centroid in the fast pixel direction Shftl Average shift in pixels between observed and calculated centroid in the slow pixel direction Shft2 Average shift in images between observed and calculated centroid in the rotation direction The calculated centroid of non strong reflections is shifted by the above shifts The number of reflections processed in the batch is listed The end of images is reached and integration is done A summary of the number of reflections integrated along with their status is listed Reflections with bad errors and that are partial are not included in the output reflection files The status codes are self explanatory A reflection that is partial at both the scan start and scan end is counted in both places but co
142. istration dialog will appear If you have logged in as a user without administration privileges the Tools gt Administration option is disabled Log in as Administrator to access this option 2 Click on the Groups tab General Users Groups Tools Servers Groups Administrators Remove OK Cancel Help Add a Group To add a group and create groups that use combinations of Administrative and Application Rights 1 Click the Add button The Group Settings dialog will appear CrystalClear User Manual Page 147 Appendix B Administration Group Settings Ed Group Name Administrators Description User has full administrator rights to configure users Administrative Rights Application Rights Add Groups Add Users Edit Curr User Edit Groups Edit Servers Edit Users Remove Groups Remove Users Cancel Help elt 4 XI S S lt S In the Name edit field enter a name for the user group In the Description entry field enter a description for the new group In the Administrative Rights list select the rights you wish to grant to members of this group q oe In the Application Rights list if applicable select the rights you wish to grant to members of this group 6 Click OK to save the new group Once you add a new group it will appear in the Members of Groups list in the User Settings dialog
143. ith no overlaps in the entire dataset To have many of these is undesirable One observation for a data point as opposed to numerous is not recommended 194 Refined scale factors Page 188 CrystalClear User Manual Appendix C Sample Log Files 195 Se A A A A A A A e A ee See Se e A ee ee ee 196 Batch Num Scale 197 name ovlps K Shifts B Shifts A E 199 LOO1 1327 1 0138 0 0000 0 0389 0 0000 200 L002 1341 1 0000 0 0000 0 0000 0 0000 201 L003 1310 0 9911 0 0000 0 0036 0 0000 216 L018 1203 1 0519 0 0000 3011 0 0000 217 L019 1149 1 0593 0 0000 0 3365 0 0000 218 L020 1152 1 0748 0 0000 0 3388 0 0000 A AAA AAA A A A AA A A A A e A A A A A et mie e e e a E 220 shifts are for previous cycle only Lines 194 220 This table lists the refined scale factors for the batches and the number of reflections that contributed to the refinement Examine this to assure that the scale factors make sense In this example an unfrozen lysozyme crystal was used Some radiation damage is expected but not much That is the later batches will need to be scaled up and to have larger scale factors Indeed this is the case Remember that 2B sin 0 0 eit exe corr Also since the batches are from the same crystal and same experiment expect the scale factors to vary relatively smoothly Indeed this is the case However if the crystal had been a plate or larger than the beam expect larger variations due to more drastic volume
144. ival position 5 36 0 i 0 0 37 1 0 0 0 38 0 0 1 0 39 Equival position 6 40 0 i 0 0 41 1 0 0 0 42 0 0 1 0 5 43 Equival position 7 44 Sily 0 0 0 5 45 0 Ty 0 0 5 46 0 0 1 0 75 Page 168 CrystalClear User Manual Appendix C Sample Log Files 47 Equival position 8 48 Iy 0 0 0325 49 0 ziy 0 0 5 50 0 0 L 0 25 51 Crystal Orientation Matrix is 52 0 3 78606e 005 0 00727938 0 0103656 53 1 0 00666557 0 00880277 0 00620622 54 2 0 0230547 0 0117159 0 00814348 59 CRYSTAL_ Goniometer listing 56 Description Eulerian 3 circl 57 Number of values 3 58 Name Datum Current Units Vector 59 60 VirtualOmega 0 000 Unknown deg 1 000 0 000 0 000 61 VirtualChi 0 000 Unknown deg 0 000 0 000 1 000 62 Phi 0 000 Unknown deg 1 000 0 000 0 000 63 Source listing 64 Single wavelength 1 5418 65 Direction vector 0 0 1 66 Spectral Dispersion 0 0002 0 0002 67 Crossfire 0 0002 0 0002 0 68 Polarization 0 5 1 0 O 69 Size 0 0 0 O 70 Intensity 0 71 RX_Detector listing T2 Pixel dimensions 3000 3000 73 Nominal size in mm 300 300 74 Description RAXIS conversion 1D Fast pixel vector 1 0 O 76 Slow pixel vector 0 1 0 77 Spatial distortion descriptive text 78 Simple pixel scaling spatial distortion 79 Simple spatial distortion 80 Center of primary beam 1479 1529 81 Pixel size mm
145. l The Processing State Display window will appear e Alternatively access Processing State Display from the CrystalClear menu Click View gt Processing State Display Page 98 CrystalClear User Manual Tool Reference ll Processing State Display Al x Current State ai Refine Run State History a Refine Run y Set s surrent Distance fi 20 1003 o 146 0 7500 2Theta di b a gt Spacegroup 5 0 0888 0 0182 0 0433 81 8371 91 8371 46 0339 oe Direct Beam at 6 0 a Crystal System x 1500 0000 Pixel Size foso fonos fran Trigonal Y 1500 0000 15000 u Number Name Rotl Rot2 Rot3 pe P3 87 61 25 23 3212 92 9291 Source Mos Volume z Wavelength Rott Rot2 0 60 393260 3 46 P3 1 5418 on 0 05 m Detector Mask File Save Bhandes lio New State Discard henge The information in the Processing State Display is as follows Current State The current processing state is displayed State History Previous states are displayed in a drop down list If desired one may select a previous state and set it as the current state Scans Click the down arrow to view a listing of scans Crystal Settings for the crystal can be viewed and changed These are the same settings as in the Setup dialog on the Crystall and Crystal2 tabs Spacegroup Settings for the Spacegroup can be viewed and changed These are the same settings in the Setup dialog on the C
146. l raxshape ini autoexec bat raxvideo ini Initialization file for RAX Video exe Crypto Box files Version txt Win95 98 Cbn vxd Win95 98 Install bat Win95 98 Marx reg Win95 98 Readme txt Win95 98 Cbn inf Win95 98 Register bat Win95 98 Marxdev1 ini WinNT Marxdevl reg WinNT Marxdevl sys WinNT Marxdev2 ini WinNT Marxdev2 reg WinNT Marxdev2 sys WinNT Marxdev3 ini WinNT Page 136 CrystalClear User Manual Marxdev3 reg Marxdev3 sys Cbnvdd dll Install bat All_devs reg Msdos bat Readme txt Regini exe Register bat Additional Files tcl80p2 exe ws295sdk exe uninst isu MoveData dll MoveCCData exe Appendix A Files and Directory Structure WinNT WinNT WinNT WinNT WinNT WinNT WinNT WinNT WinNT Tcl installation program Windows Sockets installation required for Windows 95 Uninstallation file DLL for MoveCCData exe Moves and converts older databases to new version Files Created by CrystalClear CrystalClear creates settings and script files AdminDatabase ho InstrumentName ho SiteInfo ho CrystalClearProjects ho CrystalClearUserDefaults ho CrystalClearProjectDefaults ho CrystalClearSamples ho Samplename ho CrystalClear User Manual Administration database file This file is located in the Administration directory It stores information about groups users servers tools modules and default preferences Databases detector specific for se
147. l mode The Auto will allow CrystalClear to process the data with current settings without user intervention Click Abort to stop the Auto feature if you wish to manually process your data step by step CrystalClear User Manual Page 21 Introduction to CrystalClear Flow Bar The CrystalClear interface is designed to help the user complete the tasks of collecting and processing crystal data by following the steps displayed on the Flow Bar The Flow Bar displays the current task and all the steps required to complete that task As you move through the steps in the task the current step button will change to yellow Note that the steps in the Flow Bar change depending on the Task selected from the drop down List Step Button A button represents each step in the task When you click the button a dialog will be displayed with information pertinent to that step You can make adjustments to the settings then click the Run button on the dialog to continue Y Assign Unit Cell 17 When a step is running the button will be yellow se f Steps with Substeps Step buttons that have a small arrow to the left of the button label include substeps Click the button to display the substeps Clicking the step button again will collapse the list so the substeps are no longer displayed Mr mona meio Toolbar The Toolbar includes buttons needed to complete common activities Some of these include selecting a processing algorithm to
148. lect Images dialog and the Scan State Display window displayed in CrystalCle ar is specific to the Image Collect Device Type selected namely R Axis Jupiter CCD or Mercury CCD Even if your display is different from that illustrated in this manual the instructions are the same The following Scan Table appears on the Collect Images dialog and twice on the Scan State Display Scan Scan ex Start End i Start Exp Total _ Schedule Sched Sched ID tewes 20 lsin one E En Sir Width En _ Ness EIZ s _ Images Collected Collection Start End 19 Myo2 7 img 0 ENE O 534 450 90 0 En oO 300 0 50 Ea 5 0 481 600 481 600 30 0 300 The Scan Table contains the following column headings Scan ID Scan identification number Template Base name of the image Detector Distance mm Crystal to Detector distance 2 Theta deg 20 offset of the detector Max Resolution Specify maximum resolution in degrees Wavelength n Specify the wavelength of your X ray source The wavelength is based on the Element type When you selected an Element a valid wavelength will be selected automatically Page 104 CrystalClear User Manual Phi o Rotation Axis Start Angle End Angle Width Step Number Images Completeness Start Number Exp Time Total Images Images Collected Images Scheduled Scheduled Start Angle Scheduled End Angle Tool Reference Specify the position of the crystal g
149. lection List Write Reflection List Set Reflection Size Toggle Filtering Previous Image Next Image CrystalClear User Manual Images This tool is not yet implemented This tool will undo the last erasure This tool only allows a single undo Save an image file This tool allows for saving an image that has been modified Click this tool to save a mask file The mask file is an image file that includes any erasures you might have made See Quad Erasure and Circle Erasure or See Non uniformity Type on page54 in Section 6 Data Collection and Processing for help with Mask Files Use this tool to adjust the contrast of your image Use this tool to reverse the pixel values in your image Use this tool to toggle between gray scale and color display This tool displays the image with each pixel value being converted to 1ts square root This gives more contrast to the image truncating the strong pixels and raising the display of weak pixels This tool sets the contrast of the displayed portion of the image This 1s useful in zoomed areas where there is a smaller or greater difference in minimum and maximum pixel intensities than the current contrast values This tool loads a reflection list into memory You can then add or remove spots with the Add Spots and Delete Spots tool then use Write Reflection list to save the edited reflection list This tool saves the current reflection list with any additions or deletions
150. les a B y alpha Cell angle a beta Cell angle B gamma Cell angle y All rots Crystal orientation angles Roti Crystal orientation angle around X Rot2 Crystal orientation angle around Y Rot3 Crystal orientation angle around Z Mosaicity Crystal mosaicity Detector CrystalClear User Manual Page 13 About This Manual All detector All detector translations and rotations All trans Detector translations along X Y Z X Trans1 Detector translation along X Y Trans2 Detector translation along Y Dist Trans3 Detector translation along Z All rots Detector rotation around Z X Y Rotl Detector rotation around Z Swing Rot2 Detector rotation around X Rot3 Detector rotation around Y Source Wavelength Source wavelength All rots Source vector rotations around X amp Y Rotl Source vector rotations around X Rot2 Source vector rotations around Y Related Documentation For more information on the image collection device that you will be using with CrystalClear see the user guide that came with the device Currently CrystalClear collection tasks support the Rigaku R Axis and Rigaku Mercury and Jupiter CCD Automated X ray Imaging Systems CrystalClear processing supports the Rigaku R Axis and Rigaku Mercury and Jupiter CCD Automated X ray Imaging Systems In addition CrystalClear processing supports Bruker MAR CCD MAR IP ADSC CCD MacScience Brandeis CCD and MedOptics images You can also check the Molecular Structure Corporation
151. limits 87 dtrefin Wrote header file dtrefine head 88 DTREK_STATUS 0 Lines 4 13 The original or starting crystal properties in the input header are listed Lines 14 22 The original crystal goniometer properties are listed Lines 23 26 The original source properties are listed Lines 27 42 The original or starting detector properties and position are listed Lines 43 44 The minimum and maximum resolution in Angstroms of pixels on the detector are computed and listed Lines 45 49 The input command line options to Refine Spots are listed Lines 50 78 The refinement results refined crystal detector and source properties are listed The shifts shown are for the last cycle and should be very close to 0 0000 Any property not refined will have the word fixed in the output or possibly 0 0000 for the estimated standard deviation Lines 79 82 The root mean square residuals for the observed reflection centroids in millimeters and degrees are shown Residuals depend on spot centroid variances which depend on the size of the detector pixels whether the reflection centroids are from 2D single image or 3D multiple images data the detector calibration the spot size the crystal mosaicity the image rotation angle increment etc For 2D data the residuals will be higher than with 3D data Typical values for 2D data when the image rotation width is less than the mosaicity are 0 1 0 4 mm and 0 1 to 0 5 degrees For 3D data these v
152. list 648 Reflections accepted 645 Reflections rejected 3 Reflections ignored 0 Outside I sigI or Resolution limits Strong peak info listing Area Num Intensity Sigma BackAvg BackSig Siz0 Sizl Siz2 Dl Shft0 Shftl Shft2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 8 824481 1482 705 84 13 0 12 6 3 011 0 9 0 1 0 0 3 22 1667487 2064 831 92 12 7145 e458 12 0 1 0 0 0 0 4 21 1296592 1936 854 89 13 525 13352 ag 12 0 5 0 3 0 0 5 15 578864 1376 774 84 12 9 11 8 3 1 9 0 0 0 6 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 133 783169 1433 820 88 14 4 10 2 2 8 12 0 5 0 5 0 0 9 116 871217 1401 693 79 13 3 10 8 3 3 14 0 7 0 0 0 0 10 101 802518 1323 715 74 1343 10 7 325 13 0 3 0 3 0 0 EI 150 664956 1398 842 87 14 8 10 2 2 9 13 Oi 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 6 1027184 1709 698 83 13 0 13 2 3 8 15 0 1 0 9 0 0 1 5 22 961800 1779 767 89 12 1 13 4 4 5 14 0 9 0 45 0 0 16 22 908059 1754 806 85 12 3 4 3 2525513 0 0 0 2 0 0 17 11 655907 1430 714 182 D206 124 3 13 59 2 0 5 0 2 0 0 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 All 627 828911 1465 778 84 13 8 11 0 3 4 13 0 0 0 1 0 0 Normal 648 Special 90 Reclassified as partial 1 Integrate done Page 174 CrystalClear User Manual 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 24 24 24 24 24 24 24 24 24 24 T3
153. lize to datum the detector and goniometer Note In general one must initialize the instrument before running individual items Set User Preferences Users can set preferences for how CrystalClear will appear on their computer screen For example a user may wish to turn off the message window Command Bar and Status Bar to allow more space for the image window Users can also specify their preferred language to be used within CrystalClear where they want to store certain files whether to simulate the X ray detector and other user specific preferences Select View Settings To customize the View Settings 1 Click Tools gt Preferences on the menu The Preferences dialog will appear Page 110 CrystalClear User Manual Tool Reference Preferences 2 Check the desired options to appear on the CrystalClear interface 3 Select the language to use in CrystalClear 4 Continue to check other tabs or click OK to save changes Specify a directory for user files or scripts To customize the locations of user files and scripts 1 Click Tools gt Preferences on the menu The Preferences dialog will appear 2 Click the Directories tab CrystalClear User Manual Page 111 Tool Reference Preferences User De D Documentation CrystalCleardata Myoglabin Myo2 Ml Script D Documentation CrystalClear data Myoglobin Myo2 3 Click the Ellipses Button H to the right of the item you wish to modify
154. lt shell cumul 50 23n DO BE ZN 5666 0 2037 592 2629 2 38 94 7 94 7 51 de BOT 2592 5555 0 888 703 2591 2 42 100 0 T2 52 3601 263 2370 5370 0 925 444 2369 2 45 100 0 98 53 Zoos 2239 2481 5296 0 814 666 2480 2 40 100 0 98 5 54 LESA 222 2370 5333 0 814 555 2369 2 49 100 0 98 8 55 DEl Es S209 2666 6185 0 2222 444 2666 2 49 100 0 99 0 56 209 5 5918 2370 5148 0 814 555 2369 2 41 100 0 99 Sl Li QB 1 89 2481 5259 0 888 592 2480 2530 LOOO 99 2 58 1 89 1 82 2185 5037 0 666 518 2184 2 54 100 0 99 3 59 Tagh es Tere 2629 5259 0 777 777 2554 2 36 97 1 99 60 236165 76 24921 54108 0 18845 5846 24691 2 43 99 1 99 61 Note cell length factor was 0 30 so the results above are approximate Integrate Log An edited summary of a typical log file called dtintegrate log that is created is shown following ab dtintegrate Copyright c 1996 Molecular Structure Corporation 2 Header of file dtrefine head successfully read 3 RX_NONUNF_TYPE gt gt None lt lt 4 5 6 Command line string gt gt reso lt lt 7 Command line string gt gt window lt lt 8 Command line string gt gt pad lt lt 9 Command line string gt gt profsize lt lt 0 Command line string gt gt batch lt lt 1 Command line string gt gt display lt lt 2 Command line string gt gt seq lt lt 3 4 5 Integrate object listing 6 7 Verbose level 1 8 Scan sequence range 1 20 9 Resolution range 100
155. mology v 276 Andrews amp Bernstein 1988 Acta Cryst A44 1009 1018 Paciorek amp Bonin 1992 J Appl Cryst 25 632 637 CrystalClear User Manual Page 69 Data Collection and Processing 16 17 CrystalClear can use the vectors calculated from the reflection centroids e g d i or it can use difference vectors calculated from these vectors d i d j Difference vectors are useful if the detector position is not well established Difference vectors can be bad to use if the crystal is twinned or split If Use Known Cell is set select whether to use Percent Error or Absolute Error within the Known Cell Parameters Errors group box The Use Known Cell is set and the cell errors are specified here If these are 0 then a 3 error is used When satisfied with your settings click Run to index the reflections Overcome perceived problems If there are problems indexing try the following 1 Make sure the detector source and scan properties in the setup dialog are accurate In particular make sure the detector translations i e direct beam position on detector crystal to detector distance and the scan rotation axis are correct Make sure the calculated or input Max cell length is large enough Make sure the crystal is not outrageously split cracked or twinned Expose images 90 and 45 away from the original image to double check this Use a different image or set of images in Find to get reflection centroid
156. more information on the Set Resolution function Resolution sets the resolution range of reflections to predict and integrate Remember that low resolution reflections may be blocked by the beam stop while high resolution reflections may be limited by the detector swing or edges 4 Inthe Box Width and Height fields set the integration box size in pixels Be sure to choose a Box size that completely encloses the Bragg reflection and allows for changing spot shape and shifting spot positions due to misalignment of the hardware and or a slipping crystal A typical box size will be 6 to 10 times the spot dimensions The larger the values of Width and Height the more memory CrystalClear will use It is normal and OK if neighboring reflections intrude into this box this will be predicted and excluded but it should not intrude by more than one half through the image 5 In the Padding field specify the number of images to include in a three dimensional integration volume a shoebox both before and after the predicted rotation width of a Bragg peak Padding allows for 1 a shift of the predicted peak position 2 a change in crystal mosaicity and 3 background pixels before and after the Bragg peak that lie on the Ewald sphere The larger the value of Padding the more memory CrystalClear will use 6 Specify the Images Per Batch This value is the number of images that are treated as a batch Refinement is done after every batch of imag
157. n be accessed by clicking the Collect Images button on the Flow Bar during a Collect task Task drop down list options Screen Collect and Process Collect and Process or Collect 3 Use the Import button to use an existing Collect Schedule from Project User or Site Levels e Ifyou wish to use the defaults of different Sample you must open that Sample and Save the defaults at the Project User or Site level For assistance see Using the Default Manager on page 209 of Appendix F Defaults in CrystalClear The Import Schedule dialog will appear OATES OATES Project Defaults User Defaults Site Defaults Rename Delete 4 There are several options on the Import Schedule dialog e Use the Rename button to rename a selected schedule A Rename Schedule dialog appears e Use the Delete button to delete a selected schedule A CrystalClear warning dialog appears e Use the Import button to import a selected schedule A Name Schedule dialog appears 5 Use the Close button to close this dialog and return to the Collect Images dialog 6 Manipulate the imported schedule making changes to settings on the Scan Table as desired For assistance in manipulating the Scan Table columns headings or other settings see Using the Scan Table on page 103 of Section 7 Tool Reference Save a Collect Schedule When the Save button is used the Default Manager dialog appears For assistance using the Default Manager Dialog see page
158. nd rerun The sample is a strong absorber uR gt 2 In the Advanced Menu set outlier rejection criterion to 500 or 1000 This will ensure reflections that are strongly affected by absorption will be used in the calculation of the surface improving the overall correction The crystal is split and some reflections overlap and some do not Try to find a better crystal No convergence in SVDCMP The redundancy is low If the sample is triclinic try to collect at least one scan of 180 If the sample is of higher symmetry collect more data in a different region of f or The diffraction data are poor The algorithms significant data to calculate the absorption surface reliably and there are not enough to do this Recollect the data with longer exposure times Spherical harmonics methods Multiple scans have different exposure times You may be able do not complete to recover by repeated runs of Fourier S Del 2 gt 10 The crystal died or fell off the generator went down etc Inspect your images to determine if diffraction stopped at some definite point in time and reintegrate up to that point The assumed symmetry is too high Change the putative space group Fourier methods do not Multiple scans have different exposure times Recovery complete unlikely S Del 2 gt 10 The crystal died or fell off the generator went down etc Inspect your images to determine if diffraction stopped at some definite point in time and
159. ndard tools such as Open Save View Log file etc View Tools Toggle the display of the View tools Task List Toggle the display of the task box Flow Bar Turn display of the Flow Bar on or off initial default on Command Line Bar Turn display of the Command Line Bar on or off initial default on Message Bar Turn display of the Message Bar on or off initial default on Script Tools Toggle the display of the script tools play record pause and stop Status Bar Turn display of the Status Bar on or off initial default on A default language for CrystalClear can be selected with the Default Language option Default Language Select the default language for the application Administration of Users With the Administration dialog the Administrator can access the Users tab to add users edit user settings and remove users Note When a new Login Name is created the general settings defined by the administrator are applied Page 142 CrystalClear User Manual Appendix B Administration to the user s personal settings database Each user can modify their own settings for their Login Name once they have logged in Add a User To add a user 1 Access the Administration dialog by clicking Tools gt Administration The Administration dialog will appear Ifyou have logged in as a user without administration privileges the Tools gt Administration option is disabled Log in as Administrator to access this option
160. ng the data This is specified by the default IP address of 127 0 0 1 If you wish the server software to use a different machine for processing specify that machine s IP address here The Port options allow you to select the port to be used for communication between the application and the server software This is not referring to a port such as the serial or parallel port rather it is a software communication port By default a port value and port range have already been specified for you and in most cases you can use the default values However if you are running other software that is using the same port as one of the servers you can adjust the port ID here If you are not sure what port may be free you can select the AutoGenerate check box to allow CrystalClear to select a free port for you CrystalClear User Manual Page 153 Appendix B Administration Port Number To specify a specific unique port value you can enter a value here Generally the default port will work fine You should only change this value if you are familiar with your system and software Range If you select Auto Generate you may want to also specify a port range from which to choose a port ID You can do so in the Range edit fields Note At this time CrystalClear does not support adding or removing servers Server Settings Ea Server Nam Pe o Path gram FilestRigaku MSC CrystalClear dtrek exe w Cancel Arguments Help Description
161. ng the unit cell I recommend using this very early on if you have any questions about the crystal s quality 1 Choose about 20 images to predict on and set the mosaicity to 1 or so Run After the first image is displayed choose the overlay option on the image toolbar labeled MAX to the right of the right arrow a Atthe bottom of the pop up menu set the sequence start number to the number of the first image you used in the predict spots menu Set the number of images to equal the number of images you predicted Run A new image will be displayed that has all the images on top of each other b Set your reflection circle size the button with the bubbles to a small number so that you can see where the predicted reflection is c Adjust you mosaicity if it looks like you have too many or too few reflections and re run predict d Look very closely and make sure that the prediction matches the reflections you see If it does not there is a good chance the unit cell is wrong or there are problems with the crystal as mentioned above in the REFINE section CrystalClear User Manual Page 5 5 INTEGRATE REFLECTIONS 1 Resolution Set maximum and minimum resolution to 0 the program will automatically set the resolution to include the entire image window during integration 2 Box Box sizes should be set to a similar size as was used for FIND SPOTS if you set it to 0 it will automatically be set to 6X the size of the spots found in the
162. ntensity inclusion criterion in the I o I field will allow more reflections in the refinement or consider adjusting the rejection tolerances in the X Y and Rot fields 4 Click Run to refine with current settings When the refinement is finished the fields in the dialog will be populated with values 5 Make any desired changes in the Refine dialog Selecting boxes will include a parameter in a refinement Deselecting boxes will withdraw a parameter from the refinement Click Run to repeat the refinement if desired Remember Macro resets to the default Single Step Refine following each Run 6 If View Image Processing Updates icon is toggled on the reflection in the reflection file will be represented on each image using one of the following colors included blue circles excluded green circles and rejected red circles Adjusting Resolution Range fields and I o will include exclude reflections Adjusting the rejection limit X and Y in mm Rot in Degrees will include reject peaks Also displayed on each peak is a vector representing the difference between the peak top on the image and the center of the predicted reflection related to the current values of the orientation matrix CrystalClear User Manual Page 39 Common CrystalClear Tasks 7 Click Close when you are satisfied with the Refine results Predict Spots The CrystalClear Flow Bar will show the next step within Assign Unit Cell Click Predict Spots on the Flow Bar and
163. number until systematic absences ar xamined 53 Enter solution number of your choice 10 54 Solution number 10 selected 55 Unit cell parameters and orientation angles 56 57 Integer a b E 58 um residual alpha beta gamma Rot1 Rot2 Rot 3 59 60 1 0 044 69 241 74 081 106 637 155 782 30 261 102 479 61 89 463 90 013 89 579 62 2 0 044 69 241 74 081 106 637 155 782 30 261 77 521 63 90 537 89 987 89 579 64 3 0 044 69 241 74 081 106 637 24 218 30 261 77 521 65 90 537 90 013 90 421 66 4 0 044 69 241 74 081 106 637 24 218 30 261 102 479 67 89 463 89 987 90 421 68 69 Enter your choice 1 70 Orientation angles choice 1 selected 71 Crystal listing 72 Unit cell lengths 69 2409 74 0809 106 6370 73 Unit cell angles 90 0000 90 0000 90 0000 74 Unit cell volume 546986 750 75 Orientation angles 155 7821 30 2615 102 4790 76 Mosaicity 0 300 77 Description unknown 78 Spacegroup number 16 79 name P222 80 Num equiv posns 4 81 dtindex Wrote header file dtindex head 82 DTREK_STATUS 0 Page 164 CrystalClear User Manual Appendix C Sample Log Files Lines 3 8 The reciprocal lengths in ngstroms of the shortest reciprocal lattice difference vectors are listed These often but not always suggest the longest unit cell length Sometimes the difference vector indicating the longest cell length is not available from the input reflection list Sometimes a split cracke
164. o points Click on a point then drag to a second point Use this tool to get a profile of a cross section Unlike the Select profile which gives only right angle profiles with this tool you can get a profile of pixel values in a line connecting two points Click on a point then drag to a second point to display the profile With this tool you can click on a spot to add it to the reflection list With this tool you can remove spots from the reflection list The spot closest to where you click will be removed Use this tool to measure pixels in the Image Window This tool is used to define a four sided area to be masked out during processing This is handy to remove the beam stop shadow from an image To use click in four corners of the area to be removed See Non uniformity Type on page 34 in Section 6 Data Collection and Processing for help with Mask Files This tool is used to define a circular area to be masked out during processing To use click the center of the circular area then drag to the outside edge of the area When the mouse button is released the circular area will be defined See Non uniformity Type on page 54 in Section 6 Data Collection and Processing for help with Mask Files CrystalClear User Manual m oe U a 2450 l Free hand Erasure Undo Last Erasure Write File Write Mask File Contrast Reverse Color Toggle Square Root Display Reset Local Contrast Load Ref
165. of the first scan ADVANCED Lower peak filter to increase the number of spots found Increase the filter to find any large size spots The box size can be set to 0 x 0 if necessary which lets the program pick the best box size so do not be afraid to try this and work from there Ze INDEX You should always check the USER CHOOSES SOLUTION This allows you to choose an appropriate Laue group ADVANCED Gives some brute force options Most are self explanatory Setting the MaxResidual to 100 will cause indexing to show all Laue classes 1D FFT without difference vectors is currently the preferred method for unit cell determination 3 REFINE A typical starting point is All which refines all parameters except the wavelength and is currently the best option Resolution can be set here if you wish this can be used to eliminate outliers at high resolution etc I ocan be set to the value you used to find spots RMS Residuals should be low ie Less than 0 5 mm and 0 3 degrees You want to have most of your reflections accepted Not using a large percentage of your reflections may indicate problems with the unit cell split or twinned crystal etc ADVANCED Not too much to do here You can edit your refinement procedure and save it to your user profile Recommended only for the experienced user or the site administrator 4 PREDICT The most powerful tool in the assign unit cell menu for determining crystal quality and confirmi
166. oniometer in degrees Phi 6 Phi 0 is normally used for the R Axis The angle in degrees of the start position The angle in degrees of the ending position The width of one image in degrees The angular distance between the start angles of two consecutive images in the scan The number of images to be collected in the scan The percent completeness of the data in that scan The start number to assign to the first image of the scan Specify exposure time in minutes Specify total number of images Images already collected if any Images currently scheduled for collected during next collection run The angle in degrees of the start position for currently scheduled images The angle in degrees of the ending position for currently scheduled images Manipulating the Scan Table The Scan Table can be easily manipulated using the computer mouse Right click on the various column contents or the column headings or click and drag columns CrystalClear User Manual Right click any column heading Right click Schedule heading Click and drag heading lines All Columns menu appears This allows the user to select de select individual columns to be displayed If all column headings are selected all columns are displayed A Schedule All Clear All menu appears in addition to the All Columns menu Dragging a vertical column line allows the user to widen column widths to view a column heading Making columns narrow allo
167. ormation about the crystal unit cell dimensions and spacegroup is listed next This comes from the input_header_file which in this example is 1yso head 44 There are 20 different batches in the input reflection list CrystalClear User Manual Page 185 Appendix C Sample Log Files Line 44 20 different batch names were found in the input reflection list Observed position limits of the Batches Lines 45 70 A table lists for each batch the minimum and maximum value of the observed reflection positions found in the input reflection list file In this example the fObs_pixel0 and fObs_pixell1 fields are in millimeters and not pixels This table is a quick check that the input reflection list contains the expected range of values Intensity and Resolution limits of the Batches Intensity 11964 6 13621 4 14997 3 12513 4 Lines 71 96 The minimum and maximum intensity resolution and ld 2sin0 A for each batch is listed in this table Check that the minimum intensity of each batch is not outrageously less than zero this would indicate problems with integration Confirm that the resolution limits are what is expected 97 Sorting and reducing reflnlist to asymmetric unit 98 done sorting Lines 97 98 The reflection list was reduced to the asymmetric unit and sorted The input list need not be sorted as this step will ensure that symmetry related reflections are adjacent in the file 99 Selection string fIntensi
168. orporation 2 Date Wed Apr 05 15 52 11 2000 Page 196 CrystalClear User Manual Appendix C Sample Log Files Result of PMT Test Average 5 5770 3 Sigma 1 8184 Number of 0 pixels 0 252000 an oO B UW Line 4 The average background counts in the image Line 5 The 30 level of the background Line 6 The number of pixels in the image with a value of 0 A summary of the typical log file PMICheckSummar y log generated by the PMT check utility is shown below PMT Check Utility Date Wed Jan 05 12 21 51 2000 Result of PMT Test Average 6 354 3 Sigma 1 623 r of 0 pixels 0 252000 PMT Check Utility Date Wed Apr 05 15 52 11 2000 Result of PMT Test Average 5 5770 3 Sigma 1 8184 r of 0 pixels 0 252000 Lines 1 6 Results of the PMT check run on 05 Jan 2000 Lines 7 12 Results of the PMT check run on 05 April 2000 Continuous I P Read Log A summary of the typical log file ContinuousIPRead 1log generated by the PMT check utility is shown below 1 Continuous IP Read Utility Copyright c 1998 Molecular Structure Corporation 2 Date Thu Feb 10 12 19 01 2000 3 Continuous IP Read test 1 100 gt OK Error count 0 4 Continuous IP Read test 2 100 gt OK Error count 0 5 Continuous IP Read test 3 100 gt OK Error count 0 6 Continuous IP Read test 4 100 gt OK Error count 0 7 Continuous IP Read test 100 100 gt OK Error c
169. ount 0 s Results of Continuous IP Read test CrystalClear User Manual Page 197 Appendix C Sample Log Files 9 Number of Read Write Other Total 10 Cycles Failures Failures Failures Failures dl 100 0 0 0 0 Lines 3 7 Lines 8 11 Success Failure results of the IP reads Summary of the number of cycles performed and the number and types of errors encountered A summary of the typical log file ContinuousIPReadSummar y 1og generated by the PMT check utility is shown below Continuous IP Read Utility Date Thu Oct 07 11 51 04 1999 Results of Continuous IP Read test Number of Cycles 5 Continuous Read Write Failures Failures 1 0 Other Total Failures Failures 0 0 IP Read Utility Thu Feb 10 12 19 01 Date 2000 Results of Continuous IP Read test Number of Read Write Other Total Cycles Failures Failures Failures Failures 100 0 0 0 0 Lines 1 6 Summary of the IP reads done on 07 October 1999 Lines 7 12 Summary of the IP reads done on 10 February 2000 Page 198 CrystalClear User Manual Appendix D Troubleshooting Appendix D Troubleshooting This section covers a few common problems that you may encounter in CrystalClear how you can solve those problems General CrystalClear Problems CrystalClear does not CrystalClear uses Windows Sockets to communicate with the X ray communicate correctly with the detector and with compute server modules While Window
170. own list select the appropriate device The current choices are R AXIS IT R AXIS IV R AXIS IV AFC7 Mercury AFCS Mercury AFC9 Jupiter and AFC9 Jupiter210 5 If changes are made in Administrator Utilities the following CrystalClear dialog appears Click OK You must exit CrystalClear and restart the program in order for the new Administrator Utilities settings to be embedded CrystalClear Ed AN Please restart CrystalClear If no changes are made close the Administrator Utilities dialog by clicking the El on the upper right of the dialog box 6 If necessary exit CrystalClear by clicking the EJ on the upper right of the screen e Alternatively you can click File gt Exit on the menu bar Determine Direct Beam Position Page 156 CrystalClear User Manual Appendix B Administration In order to correctly process data that have been collected on the instrument the position of the direct X ray beam on the face of the detector at 20 equal to O must be determined This procedure must be performed after every filament change on instruments using a rotating anode source or after replacing the X ray tube on instruments using a sealed tube source Note that the procedure outlined below can also be used to align the detector to the X ray beam see the appropriate hardware manual for instructions on how to perform this procedure Note for R AXIS users On the R AXIS IV and R AXIS IV systems the imaging plates IPs are
171. ple Log Files on page 161 for more information on log files CrystalClear User Manual Page 117 Additional Processing 8 Additional Processing Set Resolution You can Set Resolution used during various data processing steps Each of the following dialogs within the processing procedure includes a Set button Find Spots Index Spots Refine Cell Predict Spots Strategy Integrate Reflections Scale and Average When this button is clicked the Set Resolution dialog appears To Set Resolution for one or more processing steps 1 Click the Set button on a displayed dialog displayed within processing procedure The Set Resolution dialog will appear Set Resolution Ea Apply to IV Find IV Index Cancel M Refine M Predict M Strategy IV Integrate M Scale And Average Minimum 4 Maximum 4 0 000000 0 000000 To Edge of Image To Comer of Image 2 Check the steps to set the default resolution 3 Specify the resolution values in the Minimum and Maximum edit windows or press To Edge of Image or To Corner of Image buttons 4 Click OK Once the resolution is set for each step the specified values will appear on the respective dialog Merge Reflection Lists with d TREK In addition to scale and average in the d TREK processing module reflection lists can be merged separately The Merge Reflections task will also merge reflection list files with different columns or fields To Merge Reflection Lists 1
172. plicity or redundancy for the shell is Num ovlps Num mults lt I sig gt The average Intensity Sigmal for averaged reflections in the shell As expected there is a larger lt I sig gt for the averaged reflections than shown for unaveraged reflections in the Rmerge vs Batch table ChiSq norm This is the normalized x popularized by Dr Zbyszek Otwinowski Values close to 1 suggest that the error model is valid Rmerge shell This is the Rmerge for reflections which belong to this shell Rmerge cumul This is the cumulative Rmerge for reflections which belong to this shell and all previous shells It shows what the Rmerge would be if the data were cut off at different resolution levels Page 192 CrystalClear User Manual Appendix C Sample Log Files Completeness vs Resolution Resolution unique 593 403 736 556 863 668 966 777 1061 833 1131 911 1226 935 1290 943 Lines 287 303 This table lists Completeness vs Resolution In order to perform subsequent crystallographic analyses you would like to have very complete data Resolution rangeThe resolution range of the shell in ngstroms Calc unique Number of calculated unique reflections in this shell This is calculated from the unit cell dimensions and the space group in an exact manner it is not an approximation Num obs Number of observations for reflections in this shell The more the better Num rejs Number of rejected reflections There should be ver
173. ps to collecting and processing data with CrystalClear The Flow Bar leads you through each of these basic steps with some variations based on the processing algorithm that is selected Setup This step allows you to set default parameters for the data collection and processing The CrystalClear administrator can specify many setup values as default values for your entire site See Appendix B Administration on page 141 for information on setting site default values Users can also override site defaults for a specific project This step is not dependent on the selected processing algorithm Collect ImagesIn this step the data is collected using CrystalClear on your R AXIS or CCD X ray detector This step is not dependent on the selected processing algorithm Index Indexing determines the unit cell parameters and orientation of the crystal Integrate This step integrates the reflections on the collected images In this step the operation required and the results are dependent on the selected processing algorithm Analysis This step helps to determine the Laue class centricity and space group Scale This step performs post processing analysis and normalization of the collected data In this step the processes required and the results are dependent on the selected processing algorithm Select a processing algorithm CrystalClear is designed with two processing modules allowing you to choose the way your data is processed The processin
174. r discarded 1 To close the current sample click File gt Close Sample The following CrystalClear dialog will appear CrystalClear AN Do you want to save changes made to Myo2 wl This dialog allows the user to save changes made to a sample or discard changes made during that session Once the sample is closed the user is free to open another sample or create a new project or sample Save the Current Sample To save an open sample click the Save Sample button on the Toolbar a If a new sample is created when another sample is current CrystalClear saves and closes the current sample Upon exiting CrystalClear the current sample is saved and closed Page 96 CrystalClear User Manual Tool Reference e Alternatively access the save feature from the CrystalCle ar menu Click File gt Save Sample to save the current sample e The save feature can also be accessed with the CrystalClear shortcut Ctri 5S Delete Projects and Samples To delete a project or sample from the CrystalClear database 1 Click File gt Delete Projects Samples If a current sample is open the following CrystalClear dialog appears If you wish to close the current sample and continue the delete procedure click Yes CrystalClear AN The current sample must be closed before continuing Close the current sample The following CrystalClear dialog appears To continue with the delete procedure read the warning and click OK Crystal
175. r Manual Appendix C Sample Log Files 17 Average peak 3sigma size in pixels 18 7 99 by 6 69 pixels 19 dtfind There were 553 spots found 20 dtfind Spots written to dtfind ref 21 DTREK_STATUS 0 If the sequence range had included multiple contiguous images and the 2D method was not specified then lines 17 18 in the output above would have also included the peak size in degrees 17 Average peak 3sigma size in pixels and degrees 18 11 82 by 9 87 pixels by 0 66 degrees If the box size is incorrectly chosen reflection centroids may not be accurate and subsequent autoindexing and refinement will fail If the crystal is slipping during data collection it will have multiple orientations and subsequent steps will fail If the crystal is twinned or cracked reflection centroids may come from different crystal fragments with different orientations and subsequent steps will fail For the lowest residuals during refinement between observed and calculated reflection centroids it is best to have spots from a narrow rotation range For a better refinement of detector position and crystal properties it is better to have spots from a wider rotation range Index Spots Log A summary of a typical log file called dt index log that is created during the Index Spots procedure is shown below 1 dtindex Copyright c 1996 Molecular Structure Corporation 2 Pens 3 Reciprocal lengths of shortest difference vectors 4 72 6744 5 60 6784
176. r Manual Page 9 Table of Contents SPECIFY DEFAULT SITE LEVEL SETTINGS c cccccceccssccusccscceeccescencceeccesccescessceusceuscesseesseeceuecenecsa 154 SET UP IMAGE COLLECTION DEVICE TYPE cccccccsscccsscccscseesccceuscscsecsescesessssesecseesceueessesceeensss 155 DETERMINE DIRECT BEAM POSITION ccccccceccsceecssceeccsceecesceecesceecusceecesseecussescusceecuseuecuseuecuscs 156 CHECK PMT PHOTOMULTIPLIER TUBE ccccccccsssssesscececeeeaeesseececeeeeeaesseesseeeeeeseseaaeseseeeeeeeeaeaaes 158 CONTINUOUSLY READING AN IP oo ec ccec ccc cccccseccseccsccceccesccusccusccusceusceescesseusceusceuscesesesceenceusseuscenseens 158 APPENDIX C SAMPLE LOG UTR 6 sscssisisccscscoveciscesecessessvesdeceseossasescovetceovscdsecevesevsesdosssscessvees 161 BIND SPOTS LOG EAEE A E EAE dde baca 162 INDEX SPOTS LOG cuado 163 REFINE SPOTS LOG a a ds dade devo ae 165 PREDICT IE OG ce illo aa 168 STRATEGY LOG IE A led eat he Sai oa ool es at coat ia an das 170 INTEGRATE oO Gio EE A ad 171 TAUB A A E Sue tala eens EA AE 179 CENTRICIRNY LOG PE ide 180 SPACEGROUBLOG ona A ee Ss see Se eed 180 SCALE AND AVERAGE LOG ccccsscessccscccsccsccusccsceuscenscescseeccusceuscesccesceesseeseusseuscensseesseeceuecensess 184 DIRECT BEAM OG vice ca e ada 194 PMT CHECK DOE a ion dida 196 CONTINUOUS IP READ LOG sean dunntanceccasadacsduves ocadosanadansdetas tuandiacseavesdeemanaacess 197 APPENDIX D TROUBLESHOOTING cscsccssccccs
177. r Structure Corporation Header of file lyso head successfully read Creflnlist nRead called Names of reflection fields H int K int L int Partial BatchIndex PackedHKL ReducedH ReducedK ReducedL nAnomFlag nCentPhase fIntensity fSigmal fO0bs_pixel0 fObs_pixell fObs_rot_mid f2STLsq fResolution sBatch w0 0 30170 4 YN EP 5 n n n n n n n n int int int int int int int int float float float float float float float Cstring INFO in Creflnlist nRead EOF after 31914 reflections read in Sample Log Files 31914 total now ip Tist Lines 1 25 The input reflection list is read in and the fieldnames in the reflection list are listed Note that for efficiency the fields normally added by dtscalemerge are present in the reflection list If not present they would be added but this would take additional time Cscalemerge listing Batch fixed Scale fixed Bvalue fixed Rej criteria Mul sig fact Add sig fact Max cycles FixB Flag Anom Flag pA o o N O0Ooororawor Lines 27 36 The option settings used by this run of dtscalemerge are listed These confirm what is set on the command line or in the Scale menu Crystal listing Unit cell lengths 38 9 Unit cell angles Unit cell volume LIZ 90 90 244006 EOD 90 96 Spacegroup number P43212 equiv name Num posns 8 Lines 37 43 Inf
178. r destination of the macro and click OK Edit a Macro To edit a macro 1 On the Refine dialog click the Advanced button The Macro Editor dialog will appear e The Refine dialog can be accessed by clicking the Refine Cell button on the Flow Bar during aProcessing task Task drop down list options Process or Screen Collect and Process Click the Advanced button to access the Macro Editor dialog 2 Select the macro you wish to edit from the macro list 3 Edit the macro by changing the values of the listed macro Highlight a step and change the values to reflect those desired Continue to highlight steps and make changes as desired Use the New Step button to access the New Refine Step dialog to add a new step to the macro Page 124 CrystalClear User Manual Additional Processing New Refine Step x Name r Cancel di Copy Values From All Detector All Crystal Use Remove Step button to delete the selected macro step 4 When all macro steps are satisfactory click Close When you click Close on the Macro Editor the customized steps and values of the edited macro are saved specific to the current sample 5 When the Refine dialog appears click Save The Default Manager dialog appears This dialog allows the edited macro to be saved at the Site Level User Level Project Level or Sample Level 6 The Default Manager allows you to use the edited macro in other projects and samples If you wish to use the e
179. r reflections That is reflections that are symmetry related need to appear in multiple batches Reflections with a multiplicity of 1 are neither used in scale factor refinement nor in the Rmerge calculations A high redundancy will improve the o in the merged and averaged results see e g the dtscalemerge documentation Eqn 10 14 Overlaps among scaling batches 15 a 16 Batch L001 L002 L003 1004 L005 L006 L007 L008 L009 L010 Li SRS ssa ses SSRs SS Shean a RSS SSSR SSR SSS RS SS RASS RS SS Sea ses 55R eo 18 LOO1 298 745 671 239 196 168 199 174 182 263 LOOL 19 L002 787 659 286 243 193 162 204 166 161 280 1002 20 L003 656 226 240 246 217 173 162 162 191 259 1003 63 LO20 137 172 TSI 166 178 166 198 169 191 134 L020 CrystalClear User Manual Page 187 Appendix C Sample Log Files 16400 o 165 Batch L011 L012 L013 L014 L015 L016 L017 L018 L0O19 L020 Lines 114 166 Overlaps among the scaling batches are listed next but only if the dtscalemerge command line option countoverlap was used The entire refinement of scale factors depends on overlaps among the different batches If a batch has no overlaps with the other batches then there is no information present in the reflection list which can be used to refine the scale factor of that batch In this case the procedure used in the non linear least squares algorithm will simply keep the scale factor for that batch unchanged Note that this table is normally NOT s
180. rce from the predefined drop down list The possible predefined choices are Chromium Copper Gold Iron Molybdenum Silver and Tungsten Wavelength Specify the wavelength of your X ray source The wavelength is based on the Element type When you select an Element a valid wavelength will automatically be selected for you Source Type Select the source type of the X ray source from the predefined drop down list The predefined choices are Rotating Anode Sealed Tube and Synchrotron Optics In this section of the tab specify the following attributes of your detector Type Select from list Mirrors Confocal Graphite Monochromator or Multilayer Focus Select from a predefined list 0 1 0 15 0 2 0 3 or 0 5 Slit Size Specify the slit size Collimation Type Specify the Collimation type Note Many of the fields contain pulldown menus Although there are several common items in each list the user can enter text strings if an option is not present for their experiment CrystalClear User Manual Page 55 Data Collection and Processing The Notes Tab The Notes tab provides a small notepad to record notes about a sample Notes can be stored as site level data if you are a CrystalClear administrator or as Project User or Sample level data Notes can be accessed at any time by opening the associated project and sample open the Setup dialog click the Notes tab Main Crystal Crystal2 Detector Ray Source Notes Close
181. red For example if you wish to scan 90 of the crystal with a 0 5 image width and scan every 0 5 your settings may be CrystalClear User Manual Page 61 Data Collection and Processing Start Complete Angle rea Width Step ios ness ato ICI O E Ta Right click on column entries to Propagate Down Up All This feature is helpful in setting the same parameter for several different scans Time Estimate Calculated based on supplied values and number of images Required disk space Amount of disk space required to complete the scheduled collection request Total disk space drive Amount of disk space currently available Completeness Completeness of data in the scan Note If insufficient disk space is available to complete the scheduled image collection request a CrystalClear warning dialog will appear The collection request may be cancelled to allow the user to free more disk space on the system before continuing See Create a Collect Schedule on page 126 of Section 8 Additional Processing for more information about adding your own collection schedule 3 Click Run to start the scheduled collection scan The Double Check Settings dialog will appear Double Check Settings Ea Please make sure that the Crystal to Detector Distance and Detector 2 theta Angle are correct before continuing Cancel Image Collection Scan Scan Rot Start End Schedule Sched Sched ID Template Axis Angle Angle Collection Star
182. ry or incident beam may be affected by decay beam in homogeneity and source instability CrystalClear provides two methods for modeling these effects simple batch scaling which is applicable to either the spherical harmonics and Fourier methods and circular harmonics which applicable to only with only the spherical harmonics In the batch scaling method the data are first scanned to find the batch with the greatest overlap This batch becomes the reference batch and the absorbances described in Equation 3 are allowed to vary with respect to the reference batch That is the derivatives 0A dp are zero unless j corresponds to a batch and the reference batch Alternatively if the azimuthal angle in equation 4 is fixed at 0 the spherical harmonics collapse into the equatorial plane becoming circular harmonics and the resulting function A f 0 can be used to model incident beam absorption CrystalClear provides nine options for scaling and absorption correction The options are found in the Scaling and Averaging Dialog and are described in Table 1 The option 4 3D 4 2D appears to be the most robust and effective for small molecule data However Fourier and batch is the best method for macromolecule data The preceding statements are generalizations If one method does not provide the results you were expecting try one of the other methods You will find this useful in special cases Fitting the absorption surface using spheri
183. rystal2 tab Detector Settings for the detector are specific for the scan Settings can be viewed and changed These settings are the same settings as in the Setup dialog Detector tab If the values in the Scans field are changed the Detector settings may change Source Settings for the X ray source can be viewed and changed These are the same settings as in the Setup dialog on the X ray Source tab The settings in the Processing State Display are the same settings in the Setup dialog The Processing CrystalClear User Manual Page 99 Tool Reference State Display presents different view This display is accessible during data processing To change the current state 1 Click the State History drop down list 2 Select the desired state 3 Check the values in all fields If correct click the Set As Current button All parameters will be set to the values that were active during the selected state Create a New Processing State You can create your own processing state as well as selecting an existing state To create a custom state 1 Click the Show Processing State Display toolbar button om The Processing State Display dialog will appear e Alternatively access Processing State Display from the CrystalClear menu Click View gt Processing State Display Page 100 CrystalClear User Manual Tool Reference Current State ai Refine Run State History ai Refine Run y Set es lonent fi 20 1003 fo 146 0 750
184. s Use reflections from more than one image as input to indexing These images could be 10 or more separated in rotation angle Generally the fewer images used the better If the rotation axis is specified incorrectly i e it has a slight tilt not specified in the input header this could lead to problems However small tilts in the rotation axis can be refined in the Refine module Use 3D reflection centroids from a single wedge a contiguous set of images or from more than one wedge Use a higher Sigma and or Minimum cutoff in Find or select reflections with the Combine Reflections task Use a different number of Max diffs Both smaller and larger numbers could be tried Use a different method of autoindexing Try Use known cell if you know the unit cell dimensions 10 Accept a triclinic cell and refine the detector position then re index Page 70 CrystalClear User Manual Data Collection and Processing Refine Cell The Refine Cell feature refines the crystal crystal goniometer detector goniometer and source properties in order to reduce the differences between observed and calculated reflection centroids CrystalClear can display the observed and calculated reflection centroids so the progress and validity of refinement can be judged A header file such as dtindex head or dtrefine head with complete information about the crystal detector source and scan properties is required in order to refine cells this is creat
185. s It shows what the Rmerge would be if the data is cut off at different J o levels Remark Use the table to determine at what resolution the crystal stopped diffracting CrystalClear User Manual Page 191 Appendix C Sample Log Files Rmerge vs Resolution Resolution Average counts Lines 270 286 This table lists Rmerge vs Resolution Resolution rangeThe resolution range of the shell in ngstroms Average counts The average counts of reflections in the shell This includes reflections that overlap and those that do not If you assume Poissonian counting statistics then the expected Rmerge for this shell would be 1 7 So for the shell of highest 1 0 1 12260 0 021 which is inconsistent with 0 042 found It was then discovered that low resolution reflections which were obscured by the asymmetric beamstop were not rejected hence the higher Rmerge for this shell In the 2 05 1 94 shell 1 4 118 0 092 is consistent with 0 090 found Num obs Number of reflections in this shell Num rejs Number of rejected reflections There should be very few if any rejected reflections Any shell with a large number of rejected reflections should be investigated Perhaps the shell contains extraneous diffraction from ice Num ovlps Number of reflections in this shell having symmetry related mates and that contributed to the Rmerge Num mults Number of unique reflections measured multiple times in the shell The average multi
186. s you may e Use the Add Scan button to increase the number of scans at a different crystal orientation Adjust settings as desired e Use the Remove Scan button to remove undesired scans For assistance in manipulating the Scan Table columns headings or other settings see Using the Scan Table on page 103 of Section 7 Tool Reference Make adjustments to the settings as required When all settings are satisfactory for the new Collect Schedule you can Click Run to start the scheduled collection The Double Check Settings dialog will appear Double Check Settings Please make sure that the Crystal to Detector Distance and Detector 2 theta Angle are correct before continuing Cancel Image Collection Rot Start End Schedule Axis Angle Angle Collection 100 0 UA T Do not show this dialog in the future 5 6 Review the specified settings on the detector Click Start Image Collection or Cancel Image Collection if an error is found In the event CrystalClear detects insufficient disk space available for the entire data collection a dialog will appear to guide you through selecting a new collection directory You may need to cancel the data collection and free up space on the hard drive If you wish to delete the images and processing from an old sample presumably with all necessary file archived see Delete Projects and Samples on page 97 of Section 7 Tool Reference Delete Collection Sc
187. s NT X ray detector on a Windows includes the Windows Sockets module Windows 95 does not Install 95 machine the Winsock module WS295SDK EXE which is located in the CrystalClear directory Make sure the detector is set up correctly When I start CrystalClear only CrystalClear was closed while it was minimized After logging into the menus are displayed I do CrystalClear and selecting the project sample right click CrystalClear not see a full CrystalClear on the task bar and select Maximize Close CrystalClear while it is window only the task bar maximized Open CrystalClear and log in Now you can reshape the CrystalClear window You attempt to select a You must have a sample open before you can select a processing processing algorithm such as algorithm Click File gt Open Sample from the menu to select a d TREK PROCESS or sample or File gt New Sample to create a new sample TwinSolve and you receive the following message You must have a sample open to set processing algorithms The TwinSolve button is grayed TwinSolve is only available with the Mercury CCD out on the Toolbar You wish to process data but You have a Collection task selected From the Task drop down select the selections on the flow bar do a task that includes processing such as the Process task not include processing options The settings shown in a dialog Your previous settings were not saved Specify the desired settings have re
188. s must be used for this refinement There is no reflection file listin You are using images to Refine on Set this to Reflection List All of the option boxes are You are using the All macro Select Single Step Refine to toggle on off individual parameters There are more less spots than In the Predict Spots dialog increase decrease the mosaicity and predict prediction circles on my again Or you may have the wrong cell and need to reindex predicted image The predictions are terribly Open the Processing State Display go to the State History press the wrong and I wish to start from down arrow scroll to the bottom select one of the earlier states like scratch with the images again 1 Setup or 2 Find Run and Set as current Refinement seems to have Try increasing the number of images per batch PA ne I don t want to refine mosaicity Return to the refine dialog set a value in the mosaicity field and un check the mosaicity box Go back to integration and restart Can I get rid of ice rings during Sure Go to the advanced tab of Integrate Reflections and Add Delete Integration keeps stopping Adjust the wait limit in the Advanced tab of Integrate Reflections If when it finishes all the images an image is not on disk when integration gets to that image it will on disk at the time and I want it query the disk every 15 seconds until it either finds the image to wait for the images
189. sccccscccsscccssscccsccccesccesscccescceeesccsscccsescoees 199 GENERAL CRYSTALCLEAR PROBLEMS ccccccescccsseseusccccsssscsecseusceceesseuucceeessseeecseusceusesseeceeeeesees 199 CRYPTO BOX MESSAGES vcsscciccccseantwecessguscasaes seesssatoadeanne E Qeemocabanseasoeaweaoodpevencoateescsaneseets 200 APPENDIX E ABSORPTION IN SCALING cccccsssccsscsccsscccscsccsccccesccesssccesccesesccssccesescoees 201 APPENDIX F DEFAULTS IN CRYSTALCLEAR cccccssccccssccssccccssccescsccescccccsccscscceescoees 205 New Sample Det it AA 205 Inherited Detalla od ti n 205 Updating Detalla dt A A da 206 Dialog Detaults ictericia EEST ees 206 Using the Default Manager io A 209 APPENDIX G CRYSTALLOGRAPHIC TROUBLESHOOTING cccscscssscccsssccsssccrsscoees 211 TIN BI DE NN RT 215 Page 10 CrystalClear User Manual About This Manual 1 About this Manual What You Should Know This manual is a user guide for CrystalClear the instrument control and processing software that is a companion to the Rigaku R AXIS and Rigaku Mercury and Jupiter CCD Automated X ray Imaging Systems To effectively use this software you should be familiar with e Your detector equipment and how it operates e Crystallography techniques and terminology e Windows NT or Windows 95 98 How This Manual Is Organized The manual includes the following sections About this Manual This is the section you are reading now It gives an overview of this manual
190. se from a drop down list of predefined mount types or enter a different mounting type name in this field The predefined choices are Loop Capillary and Fiber Morphology Specify the morphology of the crystal You can choose from a drop down list of predefined morphologies or enter another name in this field The predefined morphology types are Block Chip Chunk Platelet and Prism The Crystal2 Tab The Crystal2 tab contains additional information about the crystal as a continuation of the Crystall tab Page 52 CrystalClear User Manual Data Collection and Processing Main Crystal Crystal2 Detector X Ray Source Notes m Spacegroup C Unk 5 Number Name nknown Spacegroup pa 43 P3 Crystal System Trigonal Orientation Angles Rot 1 Rot2 Rot3 Molecular Formula variable variable variable Close Save Defaults Spacegroup Specify the spacegroup of the crystal if known Unknown vs Known Spacegroup If you know the spacegroup select Known Spacegroup If you do not know the spacegroup select Unknown Spacegroup Specifying a known spacegroup may save time later on as the crystal is processed Crystal System If you selected Known Spacegroup this option will become enabled You can select from the drop down list of predefined Crystal Systems and then scroll through the available spacegroups from the list under Number and Name or alternately type either the number or name in
191. sed as input to the next step Refine Refine Spots Log A summary of a typical log file created by Refine Spots called dt refine log is shown below dtrefine Copyright c 1996 Molecular Structure Corporation Header of file dtindex head successfully read Crystal listing CrystalClear User Manual Page 165 Appendix C Sample Log Files 5 Unit cell lengths 69 2409 74 0809 106 6370 6 Unit cell angles 90 0000 90 0000 90 0000 7 Unit cell volume 546986 812 8 Orientation angles 155 7820 30 2610 102 4790 9 Mosaicity 0 300 0 Description unknown 1 Spacegroup number 16 2 name P222 3 Num equiv posns 4 4 CRYSTAL Goniometer listing Description Eulerian 3 circl 6 Number of values 3 7 Name Datum Current Units Vector 8 9 Omega 0 000 Unknown deg 1 000 0 000 0 000 20 Chi 0 000 Unknown deg 0 000 1 000 0 000 21 Phi 0 000 Unknown deg 1 000 0 000 0 000 22 23 Source listing 24 Single wavelength 1 5418 25 Polarization 0 5 1 0 O 26 Intensity 0 27 RX_Detector listing 28 Pixel dimensions 1900 1900 29 ominal size in mm 193 23 199 5 30 Description RAXIS conversion 31 RX_Goniometer listing 32 Description UNKNOWN 33 Number of values 6 34 Name Datum Current Units Vector 35 36 RotZ 0 000 Unknown deg 0 000 0 000 1 000 37 RotX Swing 0 000 Unknown deg 1 000 0 000 0 000 38 Rot Y 0 000 Unknown deg 0 000 1 000 0 000
192. ser Manual Page 17 DC CUK MER Japie TGQ MENECUORS QUES LUUR AMO OCP Tene Pecess e Ea Arpas a Flea me H i Abort Auto DE a ES ES ate Ed BE a O a S O E m y E v Find Spots 2 o Index Spots Dos Refine Cell y Predict Spots Image Name Image Number Start Angle i F Reflection List fk F E fi o Image Width Integrate Reflections 7 Exposure Time min mm CrysTo Det Dist mm E atm 7 a v Pizel Value Numerical Abs Cor Peak Intensity T y Resolution Scale and Average 7 Intensity Sigma HKL Spot Distance j Number of Spots 911 9 Command Line SetFindParams_DTREK NumSequences 1 SeqlBeg 1 SeqlEnd 2 Seq Root lys SeqlExt osc ResoMax 0 00000 ResoMin 0 00000 Fieldwidth 3 ScanlD 5 Sigma 5 01 Messages 10 11 For Help press F1 Introduction to CrystalClear 3 Introduction to CrystalClear What is Crystal Clear CrystalClear is a software program designed to work with the Rigaku R AXIS or Rigaku Mercury or Jupiter CCD Automated X ray Imaging Systems for the collection and processing of crystal data CrystalClear interfaces with the X ray imaging system to collect data then will process that data CrystalClear can be used to process data that may have been collected previously It can support IMG CCD OSC RAXIS and STL RAXIS image files CrystalClear can also support Bruk
193. settings as follows CrystalClear User Manual Page 43 Common CrystalClear Tasks Max R merge Highest Laue Symmetry Only check Laue groups compatible with current cell Average Bijvoets Assume 1 1 4 Click Run Laue Results Tolerance for considering a Laue class present Limits the highest Laue chss to be checked Unchecked examines all Laue classes compatible with current cell Unchecked examines Laue classes desired Observed a 4 3 00 3m1 6 6 00 31m 77 6 00 im 13 6 00 G mmm 81 12 00 2 00 2 00 2 00 2 00 2 00 0 51 0 39 0 54 0 66 0 54 5 Look over the Laue groups and R merges for the Laue equivalent reflections Select the Laue class if it is not already selected 6 Click OK Centricity 1 Click Centricity on the Flow Bar The Centricity dialog will appear Centricity Reflection List LM El ES Close Save Defaults Page 44 CrystalClear User Manual Common CrystalClear Tasks 2 Select the Reflection List file to use generally dtprofit ref 3 Click Run Centricity Results N Z test fraction of intensities less than Z x lt I gt 0 345 0 419 0 520 0 561 0597 0629 0657 0 683 0 09 0481 0 259 0330 0394 0451 0503 0 551 0 593 0 632 0 153 0 164 0 160 0 149 0 126 0 110 0 094 0 078 0 064 0 051 theoretical average deviation gt 115 measured 0 061 0 192 0344 0483 0599 0682 0 746 079 0834 0 862 deviation 0 187 0
194. splay the Instrument State Display window 1 Click the Show Instrument State Display toolbar button A e Alternatively you can click View gt Instrument State Display on the menu The information reported on the Instrument State Display is as follows X ray Source group box Information about the X ray Shutter orientation Source Type and Optic Type Goniometer group box Information on the Crystal orientation and Detector position Detector group box Information on Image Requested Settings Expected finish time and Detector type The Instrument State Display window will appear CrystalClear displays a window specific to the selected Image Collection Device Type namely R Axis Jupiter CCD or Mercury CCD If the R Axis is the Image Collect Device Type the following window will appears CrystalClear User Manual Page 107 Tool Reference gt Ray Source Instrument State Display gt Shutter Status ky m Slit Size a a Element Focus Collimation Type Source Type Optic Type Detector Image Requested settings Start End Width Time sec Image Scan m Expected finish time This Image This scan Goniometer ReadHead Positio Detector type Detector position IP Status Distance Position 28 Expose Erase Read Decay Moving IP Elapsed File If Jupiter CCD or the Mercury CCD is the Image Collection Device Type the following window will appear
195. st A Spacegroup number of 0 indicates no user preference In this case the output header will have the lowest symmetry spacegroup consistent with the selected lattice type The Reflection Lists box displays the available reflection files Select the file you wish to use for the Index Spots procedure Specify the desired Resolution range If you wish to change the default resolution click Set See Set Resolution on page 119 of Section 8 Additional Processing for more information on the Set Resolution function If you wish to select a solution manually check the User Chooses Solution check box You will be prompted to select the desired solution from a list of solutions If not set the program will automatically select a solution The number of Bravais Lattices in the list will depend on the value set for Max Residual in the Advanced Tab see below If you wish to set all the values back to the defaults click the Defaults button You will be prompted to select whether you wish to use Project level defaults or Site level defaults Click the Advanced tab to set additional values Index Spots x Main Advanced Max Cell Length Max Residual Max Vectors 6 00 8 00 0 Grid Size 1 Sigl Method o o 0 00 fio FFT y Use Known Cell T Diffs r Known Cell Parameters Errors Percent Eror Absolute Error 8 E UnitCell 91 94 197 84 a 13 y 80 00 90 00 G 46 03 Close Save Defaults In the M
196. string gt gt anom lt lt 5 Laue check assumes I I 6 Command line string gt gt maxrmerge lt lt 7 Maximum R merge is 0 150000 8 Command line string gt gt spacegroup lt lt 9 Space group set to P222 16 20 Laue check disabled 21 Laue group set to mmm 22 Lattice set to oP 23 Command line string gt gt laueonly lt lt ILULA E O LLIA IIA LILLL 24 Finished reading command line 25 nput Cell 6 36 V5 5 25 07 G00 90 00 90 00 26 nput Sigmas 0 0003 0 0009 0 0013 0 0000 0 0000 0 0000 oh nput Orientation 97 44 L 70 171 25 28 Reading Reflection file dtintegrate ref 29 Creflnlist nRead with filename dtintegrate ref 30 NFO in Creflnlist nRead EOF after 12641 reflections read in 31 12641 total now in list 32 Laue Check 33 Laue Unique Num Calc Obs R Merge Pass 34 class axis unique mult mult 35 t gt 1314 1 2 01 0 02 PASS 36 2 m a 3786 2 2 25 0 02 PASS 37 2 m b 4037 2 2 29 0i 0 2 PASS 38 2 m c 1996 2 2 13 0 02 PASS CrystalClear User Manual Page 179 Appendix C Sample Log Files 39 mmm 4195 4 2 45 0 02 PASS 40 4 m a 3091 4 Ze 03 0 43 41 4 m b 2186 4 2 45 06 33 gt 42 4 m c 3504 4 2 87 0 32 43 4 mmm a 3213 8 3 40 0 44 44 4 mmm b 2532 8 2 81 0330 lt 45 4 mmm e 2732 8 4 10 0633 gt 46 3 2782 3 2 58 ORSO Herna 47 3m1 2979 6 3 50 23 0 65 2 2 48 31m E 3169 6 3 25 0 64 49 6 m 2947 6 3 44 O5
197. such as teXsan for subsequent processing 14 When you are satisfied with your settings click Run to run the Scale and Average step Page 92 CrystalClear User Manual Tool Reference 7 Tool Reference CrystalClear provides tools for the following functions Create open save and delete Projects and Samples View edit and set CrystalClear state information Create new processing state Display scan state View instrument state display Manually control X ray instrument Set user preferences View log files Create a New Project and Sample When a new Login Name and Password are used the New Project Wizard assists the user in setting up the first project and sample A complete description of this process is available in Section 4 Running CrystalClear for the First Time on page 27 Once the initial project is set up additional projects and samples are created using the following procedure 1 Start CrystalClear and log in The Open Sample dialog is displayed e Alternatively the Open Sample dialog can be accessed on the CrystalClear menu Click File gt New Sample or New Project to create a new project and sample Open Sample x Project Myoglobin y New Project Sample Myo2 C New Sample Task Collect and Pr Image Directory DAD ocumentation CrystalClear datasMyoglobin Myo2 images Browse Cancel Browse Import The project sample listed in the entry field s is the project sample most recently updat
198. t a new folder for each sample is nested within the Myoglobin folder CrystalClear User Manual Page 29 Running CrystalClear for the First Time Note CrystalClear automatically stores Project and Sample data to the default location CAProgram Files RigakuMSC CrystalClear data Login Name During user set up your administrator may assign a unique path for each user to store Project and Sample data It is not recommended that administrators use this directory for user base directories Additionally it is not recommended that the same directory be used by different users Image Files Ed If you plan to process existing image files input one of the image files in order to load the image header information Image File C Program Files Rigaku MSC Crystal Browse eae Seay 4 Click Finish The project and sample will be created Later you can add more samples to the same project or you can create additional projects as needed Each Project Name is unique for a Login Name To access a specific Project a user must use the same Login Name as was used when the Project was created 5 Now that you have logged in and created your first project and sample you can begin collecting and or processing data At your next Login the Open Sample dialog will display the most current sample CrystalClear allows only one open or current sample at a time in each CrystalClear window The user may wish to open this sample or create a
199. t End 22 y osc nta 120 0 T Do not show this dialog in the future 4 Review the specified settings on the detector 5 Click Start Image Collection In the event CC detects that the available disk space is insufficient for the entire data collection a dialog will appear to guide you through selecting a new collection directory You may need to cancel the data collection and free up space on the hard drive If you wish to delete the images and processing from an old sample presumably with all necessary file archived see Delete Projects and Samples on Page 62 CrystalClear User Manual Data Collection and Processing page 97 in Section 7 Tool Reference Index Spots During the Index phase of processing your crystal data CrystalClear will determine the unit cell parameters The settings specified in the Setup phase are used as a starting point in indexing the data Indexing consists of finding spots auto indexing and refinement Index with d TREK RAXIS or CCD Find Spots The Find Spots step finds reflection centroids in a single image or a collection of images The reflection centroids are written to a file called the dtfind ref file by default The found reflection centroids are subsequently used in an autoindexing or refinement step In order for autoindexing and refinement to function properly you should find 50 70 reflection centroids The exact number needed can vary depending on the centroid acc
200. t field labels fResolution fLPfactor fCorrelation sBatch 1 string label 22 1 163566 77 121 549 1001 actual reflection file with 3 integers 7 floats 2 shown and one string Page 12 CrystalClear User Manual About This Manual CrystalClear d TREK Coordinate System The d TREK default laboratory coordinate system shown in the next figure is defined as follows Nr The origin of the laboratory is at the crystal The X axis goes from the crystal toward the goniometer baseplate This may be horizontal vertical or neither INN KW The Z axis goes from the crystal toward the source The Y axis make a right handed system after X and Z are chosen All positive hardware rotations are right handed The crystal to detector distance is positive even though it is usually at a negative Z value The direct beam position on the detector in pixels is specified when the detector is perpendicular to the source rotations are at zero AND the detector translations in X and Y are zero In the actual experiment the detector may be rotated or translated away from this position Source Z X Goniometer baseplate The following text lists the 19 different properties that can be refined or fixed Crystal All crystal Crystal cell lengths and angles orientation and mosaicity All cell Cell lengths and angles All lengths Cell lengths a b c a Cell length a b Cell length b c Cell length c All angles Cell ang
201. t to the name of the detector that you wish to run as a simulator 4 Continue to check other tabs or click OK to save changes Configure the I nstrument Server Simulator Generally the instrument server simulators do not require changes to the configuration files However note that the default images created by the server simulator will be bogus Images created by the server simulator cannot be used for processing The instrument server simulators should be reconfigured to read previously collected images already on disk CrystalClear User Manual Page 113 Tool Reference When using the server simulator reconfigured to read previously collected images already on disk all data collection conditions must be set up consistent with the parameters originally used in collecting the images i e scan rotation range scan rotation axis image width direct beam position in order to correctly process the images R Axis Simulator The R Axis instrument server simulator MSCServDetRAXIS_Simulator exe reads the same configuration file as its non simulator counterpart namely MSCServDetRAXIS configuration The simulator interprets all options as the non simulator server plus two additional options which are ignored by the non simulator server These options are SimulatorBaseFilename and SimulatorMode SimulatorBaseFilename drive path base This option specifies the base name for the image files used by the simulator d
202. t you worked on will automatically be selected Select the task you wish to use for this sample from the Task drop down list Specify the directory with the images for this project Type the full directory name in the Image Directory field If image files already exist select using the Browse button Open an Existing Sample Following the Login procedure for CrystalClear the Open Sample dialog appears The Project and Sample listed in the entry field are those most recently opened by the user Other Projects and Samples can be accessed by clicking the down arrows Alternatively access the Open Sample dialog with the Toolbar icon The Open Sample dialog can also be accessed with the shortcut Ctrl 0 The Open Sample dialog can also be accessed from the CrystalClear menu Click File gt Open Sample to open a sample 1 Following the Login procedure the Open Sample dialog will appear CrystalClear User Manual Page 95 Tool Reference Open Sample x Project Myoglobin y New Project Sample Myo2 y C New Sample Task Collect and Pr Image Directory o Documentation CrystalClear data Myoglobin Myo2 images Browse Cancel Browse Import 2 Select the desired project from the Project drop down list 3 Select the desired sample from the Sample drop down list 4 Click OK Close the Current Sample When CrystalClear closes a sample the changes made during that work session may be saved o
203. tegy on page 80 of Section 6 Data Collection and Processing for assistance if necessary Double click in the End Angle field and specify the ending angle for the scan For example ifimages are to be collected over the first 90 degrees of the sample specify 90 0 Double click in the Image Width field and specify the width of an image in the scan Commonly the image width is 0 5 degrees Double click in the Exposure Time min field and specify the length of time for the exposure Units for the exposure time can be in minutes or seconds depending on the procedure Refer to General Settings on page 141 of Appendix B Administration Additional information about changing the unit of exposure time is in Set User Preferences on page 110 of Section 7 Tool Reference Double click in the Start field and specify the starting number for the images The Images and the Completion Time fields will be calculated automatically based on the values assigned in the various parameters Page 106 CrystalClear User Manual Tool Reference 8 Make other adjustments to the settings as required For example if you wish to scan 90 of the crystal with a 0 5 image width and scan every 0 5 your settings may be Start End Complete ra Angle Angle Width Step Es ges E 0 00 900 View the I nstrument State You can view the state of the X ray detector with the Instrument State Display window The information reported is as follows To di
204. the Crystal To Detector Distance mm field different scans will have different values In this case refer to the Scan State Display window to see the values for each scanned image The Crystall Tab The Crystall and Crystal2 tabs include information about the crystal Main Crystal Crystal2 Detector lt Ray Source Notes Unit Cell Parameters AA a b A c A 91 84 1 84 46 03 ae 7 B EI gt MS so 00 30 00 fi 20 00 z Ste Color x nom Y rom 2 mm Colorless v 0 20 0 20 0 20 Mount Fiber v Mosaicity Morphology 0 50 Prism y Close Save Defaults CrystalClear User Manual Page 51 Data Collection and Processing Unit Cell Parameters The unit cell parameters for the cell a D default 50 000000 b D default 100 000000 c D default 150 000000 a default 90 000000 B default 90 000000 y 2 default 90 000000 Size The size of the crystal in millimeters X mm default 0 2 Y mm default 0 2 Z mm default 0 2 Mosaicity Specify the starting value to use for crystal mosiacity The default starting value is 0 6 Color Specify the color of the crystal You can choose from a drop down list of predefined colors or enter a different color name in this field The predefined choices are blue colorless gray green orange red white and yellow Mount Specify the mounting type used for the crystal You can choo
205. the Predict Spots dialog will appear Predict Spots Ed Main Advanced Scan Table Right click for further options Template Avail To Use myo2_screen osc 1 2 myo2 030 1 60 1 10 Clear All Use Sequence p C Use Rotation Crystal Mosaicit Use Curent Displayed Image 0 60 Rotation Resolution 4 Begin End Minimum Maximum Close Save Defaults 1 The Predict Spots dialog allows the user to select images to predict reflections Image numbers may be entered manually or selected from a list When entering image numbers manually be sure to use a dash to separate consecutive image entries or use a comma to separate non consecutive images entries For example you can enter images such as 2 5 7 9 12 Before clicking the Run button to Predict Spots de select un highlight the To Use entry field to verify the selected image entries Right click the To Use field for further menu options as follows View Images List Displays a list of image files Select Scan Allows user to select images of a scan Clear Scan Clears selected images of a scan In the View Images List all images available are listed with a selection box in front of the image name and the type of rotation oscillation with its beginning and end angles following Click on the box to select deselect the image The sequence field dynamically changes with the selections Page 40 CrystalClear User Manual Common
206. tion is disabled Log in as Administrator to access this option 2 Click on the Tools tab CrystalClear User Manual Page 149 Appendix B Administration Administration HENMDYE Add a Tool You can add tools such as a script that you have created to automate the processing of a sample or an executable program To add a tool 1 Click the Add button The Tool Settings dialog will appear Tool Settings Page 150 CrystalClear User Manual Appendix B Administration 2 In the Name edit field enter the name of the tool This name will appear on the Tools tab and in the Tools pull down menu In the Command edit field enter the command line of the tool In the Arguments edit field enter any arguments that are required for correct operation of the tool In the Initial edit field specify the directory that should be active when the tool application starts SUR If you want to be prompted for arguments when the tool starts check the Prompt for Arguments check box 7 If you want the tool to run without having a window pop up on the screen select the Run Minimized check box 8 If the tool is a script check the Tool is a Script check box Remove a Tool To remove a tool 1 Select the tool to be deleted in the tool list 2 Click Remove The tool will be removed from the Tool list in CrystalClear only It will not be deleted from the hard drive Edit Tool Settings To edit a tool s se
207. tionmerge log dtstrategy log Log Filename psearch log index log refosc log integ log merge log scale log post log average log Log Filename Page 161 Appendix C Sample Log Files You can view the log files during processing to follow the progress of the job To view a log file during a processing step 1 Click Windows gt Log File Viewer The selected log file will be displayed on the screen If you wish to view log files from previous processing steps 1 Click View gt Log File The Open dialog appears Lookin moza e E dtfind a discaleaverage E dtindex E dtintegrate Ea dtpredict E dtrefine E dtrefInmerge Fie name EE Files of type Log Files log y Cancel 2 Select the log file to view 3 Click Open The selected log file will be displayed on the screen Find Spots Log A summary of a typical log file which is produced by Find Spots is listed below The filename is dtfind log dtfind Copyright c 1996 Molecular Structure Corporation File user4 jwp DATA NUCL4 nucl4001 osc successfully opened Find object listing Sigma 0 Minimum 2000 Circle lim 950 950 0 1343 Rect lim 19 1881 19 1881 9 Spot wind 30 30 10 Peak filt 6 11 Back tile 237 237 12 Pad 3 13 Seg num 1 1 14 Image dim 1900 1900 15 3D dump 0 16 There were 554 preliminary reflections found in a 2D search e o SS E o a B oO BWN EB Page 162 CrystalClear Use
208. tions from the current image Full reflections are those for which the 3D integration box has just filled DNormal reflections are those full reflections from this image or a previous image but within a batch which have a normal preliminary integration DSpecial reflections are those full reflections which have a special preliminary integration and which do not have an accurate centroid determination A special integration might occur if the reflection is not strong or a warning or error occurred during integration Page 176 CrystalClear User Manual Lines 52 56 Line 58 Lines 59 85 Lines 86 87 Lines 88 191 Lines 184 185 Lines 194 218 Line 219 Line 220 Lines 225 265 Line 267 Appendix C Sample Log Files The total number of allocated 3D shoeboxes a shoebox is the 3D data array of pixels for a single reflection is listed the number that are filling i e in use those that are full and those that are freed not in use are listed Full shoeboxes are buffered until the end of a batch when refinement is done and profiles are written out A big portion of the output log file was edited away The last image in the scan to integrate is read in and info about it is listed The end of batch refinement is about to take place The refinement options are listed The standard refinement output is listed For an explanation see section 4 8 Notice that the residuals are very low since 3D centroids are used in refinement Informat
209. to 70 of the original value and the Fourier map is searched again Lines 26 51 The 3 non coplanar peaks are used to determine a reduced primitive cell This reduced primitive cell is then fit with a least squares procedure Anderson amp Bernstein 1988 Paciorek amp Bonin 1992 to the 44 lattice characters Int Tables Vol A pp 746 The solutions with residuals less than or equal to 10 are listed in order of decreasing symmetry Usually residuals below 5 have been solutions Any lattice symmetry must be ultimately confirmed by examining symmetry in the diffraction intensities Line 53 Since User Chooses Solution in the menu was set the user is prompted to select a solution Solution 10 was selected Lines 55 68 The orientation angles for the selected cell and lattice are displayed sorted on an Integer residual Residuals greater than 0 10 are considered poor solutions and suggest a problem such as incorrect spatial distortion incorrect direct beam position incorrect detector position or a split cracked or twinned crystal In general orientations with the same residual are equivalent Line 69 The user was prompted to select a solution and number 1 was selected Lines 71 80 The crystal cell properties are listed Note that indexing does not determine the crystal mosaicity but nevertheless a default value is listed line 76 Line 90 The resulting unit cell properties is written to the output header file dt index head which can be u
210. torMode MSCServDetCCD SimulatorBaseFilename drive path base This option specifies the base name for the image files used by the simulator during data collection This option is only recognized by the CCD Camera server simulator MSCServDetCCDCamera_Simulator exe The files should exist on the disk in the form drive path base img where Page 114 CrystalClear User Manual Tool Reference represents a number padded on the right with Os All image numbers in a scan must have the same number of digits i e if there are 1000 images in the scan then the first image number is denoted by 0001 The previously collected images must be on a disk accessible by the framegrabber PC The minimum number of digits in the image number depends on the version of MSCServDetCCD_Simulator exe not MSCServCCDCamera_Simulator exe In versions earlier than 3 0 0 the minimum number of digits in the image number is three 3 i e image 1 is denoted by 001 unless the largest image number in the scan would require more than three 3 digits as described above In versions 3 0 0 and later the minimum number of digits in the image number is four 4 unless specified otherwise by the MinimumScanTemplate keyword in MSCServDetCCD configuration SimulatorMode realtime immediate This option indicates if the simulator will mimic real time when simulating exposures If the value is realtime then the exposures will take real tim
211. ttings 1 Select the tool to be edited in the tools list 2 Click Edit 3 Make the desired changes then click OK to save the changes Administration of Servers A server is a software package that interfaces with CrystalClear The purpose of the server is to perform complex calculations and pass the results back to CrystalClear CrystalClear ships with two compute servers d TREK and PROCESS and two instrument server CCD control and R AXIS control When you install CrystalClear the servers are installed and configured automatically You cannot remove the servers nor can you add additional servers to CrystalClear at this time The items that appear in the Servers list may vary depending on which detector you have and which servers shipped with your particular copy of CrystalClear To administer servers 1 Access the Administration dialog by clicking Tools gt Administration The Administration dialog will appear CrystalClear User Manual Page 151 Appendix B Administration Ifyou have logged in as a user without administration privileges the Tools gt Administration option is disabled Log in as Administrator to access this option 2 Click on the Servers tab Administration CCD Simulator Dtrek Process Rasis Raris Simulator Remove TwinSolve Edit Server Settings To edit the settings of a server 1 Select the server to be edited and click the Edit button The Server Settings dialog will appe
212. ttings There is a defaults database file for every detector supported by CrystalClear in DATA SiteDefaults These files contain the default settings for new users The settings stored in this file and are transferred to the CrystalClearUserDefaults ho file each time a new user is added Please refer to the document entitled Defaults in CrystalClear for more information on detector inheritance Database for detector settings This file is located in the DATA directory This file is located in each User directory It includes a list of all the projects created for that user Each user has a unique CrystalClearProjects ho file This file is located in each User directory It includes the user s own default settings This file is located in the User Project directory This file includes defaults used when a new sample is created This file is located in the User Project directory This file is included in each project directory It holds settings for each sample This file is located in the User Project Sample directory Each sample will have its own Samplename ho file Page 137 Appendix A Files and Directory Structure Images SessionScript scp SessionScript bak Dtfind log Dtindex log This file holds current settings for the sample CrystalClear records all actions that change the program state in this file throughout the CrystalClear session When a new session is started the previous SessionScript scp file is sav
213. ty fSigmal lt 3 000 100 Number of reflns which match above selection 5294 Lines 99 100 This confirms that you excluded reflections with o lt 3 from contributing to the refinement of the scale factors 5294 of the input reflections were thus excluded These reflections are included however in the final statistics 101 Last cycle no shifts 102 For cycle number 10 Page 186 CrystalClear User Manual Appendix C Sample Log Files Lines 101 102 The last cycle was reached so no shifts were applied Dtscalemerge calculates and prints out statistics on the results 103 Method 1 Expected Rmerge 0 033 104 Method 2 Expected Rmerge 0 034 105 Actual Rmerge 0 032 Lines 103 105 Two methods for approximating the Rmerge are given followed by the actual Rmerge see the equation below in the data set The actual Rmerge should be close to the expected Rmerges or something is wrong with the error model The expected Rmerges are calculated as follows Method 1 Rmerge y vie where I is the average intensity for all averaged reflections Method 2 averaged reflections N is the number of unique reflections and N is the number of overlaps YY 11 1 Actual Rmerge 4 Reflections with a multiplicity of 1 are not used in scale factor refinement nor in Rmerge calculations Lines 106 113 The multiplicity of observed reflections is listed in a table The entire process of refining scale factors requires multiple observations fo
214. ully opened 291 Success writing file D0055 refprof 292 293 Int Sigmal vs Average correlation of 294 observed to reference profiles 295 296 Sigma range Avg Corr Num Refln 297 298 Dies 3 0 169 31 299 Dios 6 0 636 52 300 6 ws 9 0 845 65 S01 A 2 0 926 142 302 2 a ES 0 954 286 30319 ui 8 0 970 279 304 18 21 0 978 245 305 21 24 0 983 219 306 24 27 0 988 149 307 Ll tros 30 0 993 296 308 os gt F 309 310 Correlation range vs 311 number of reflections 312 313 Corr range Num Refln 314 315 0 0 0 1 7 316 0 1 0 2 8 317 0 2 0 3 6 318 0 3 0 4 7 319 0 4 0 5 9 320 0 5 0 6 14 321 0 6 0 7 13 322 0 7 0 8 25 323 0 8 0 9 71 324 0 9 1 0 1604 325 326 Number of reflections written 1764 327 DTREK_STATUS 0 Lines 14 25 The command line options settings are listed Line 27 The 3D method is used rather than the 2D method The 2D method is not available at this time Line 28 The non uniformity type see section 4 5 and p 17 is None Line 30 The first image is read in Lines 34 37 The name of the image current date and time are listed Lines 40 44 The rotation start end increment and exposure time are listed Lines 46 50 The numbers of new active full done normal and done special reflections are listed New reflections are those for which the 3D integration box is newly created Active reflections includes all reflections which receive any pixel contribu
215. unted only once at the top Reflections in categories that are asterisked are rejected Reflections may fit in multiple categories The number of reflection profiles written to reflnprofiles profit is listed These profiles will be read by dtprofit and processed CrystalClear User Manual Page 177 Appendix C Sample Log Files Lines 269 270 The dtprofit module is started in order to fit profiles This performs three dimensional profile analysis with a method similar to that of Kabsch 1988 Reference profiles Line 272 At least 50 strong reflections must contribute to a reference profile If too few reflections are found in the same region nearby regions are used until sufficient strong reflections contribute Line 274 A variance weighted profile analysis method is used This is different from Kabsch 1988 but like Otwinowski amp Minor 1997 Line 275 In this scan there are up to 72 regions 18 per detector 4 batches for which reference profiles are calculated Lines 277 282 For each regional reference profile the number of strong reflections that contribute and their original region as m n pairs are listed If too few strong reflections are found all strong reflections in the input are used Line 283 A single overall reference profile is also calculated Lines 284 291 The reference profiles are written to disk in the form of a d TREK image file yt COC EE 3 PTET tt NNN Profile size just right P
216. up box enter a user password in both the New and Confirm edit fields The password is not case sensitive 8 Select the default language to be used for the user English is the default language In the future other languages may be added to CrystalClear 9 In the Member of Groups group box select the groups s to which the user should belong The user will be a member of all groups with a check in the box 10 Click OK to add the user Remove a User To remove a user 1 Access the Administration dialog by clicking Tools gt Administration The Administration dialog will appear Ifyou have logged in as a user without administration privileges the Tools gt Administration option is disabled Log in as Administrator to access this option Page 144 CrystalClear User Manual Appendix B Administration 2 Click on the Users tab 4 Select the user to be removed from the user list 5 Click Remove The following CrystalClear dialog appears CrystalClear AN Would you like to remove the user directory and all directories below it from your hard drive When you remove a user you also be given the option of deleting the user s data and data directory 6 Click the appropriate response e Yes Remove user and all directories e No Remove user but do not remove all directories Edit User Settings Use this feature to edit a user s password description data path or assigned groups To edit user settings 1 Access the
217. uracy and location in reciprocal space The prerequisite for finding reflection centroids is knowledge of the properties of the images from which you are finding reflections To find spots 1 Click the Find Spots button in the Flow Bar The Find Spots dialog will appear Select images to be processed The Find Spots dialog allows the user to enter image numbers manually or select images numbers from a list Right click on the To Use entry field to view menu options Find Spots x Main Advanced Scan Table Right click for further options Template Avail To Use myo2_screen osc 1 2 myo2 osc 1 60 Sigma Select Screen Clear All 3 00 Close Save Defaults CrystalClear User Manual Page 63 Data Collection and Processing To enter image numbers manually in the To Use entry field be sure to use a dash to separate consecutive image entries and use a comma to separate non consecutive images entries For example you can enter images such as 2 5 7 9 12 Before clicking the Run button to Find Spots de select un highlight the To Use entry field to verify the selected image entries Right click an entry field for further menu options as follows View Images List Displays a list of image files Select Scan Allows user to select images of a scan Clears selected images of a scan Find Spots x Main Advanced Scan Table Right click for further options Template Avail To Use
218. uring data collection The files should exist on the disk in the form drive path base img where represents a number padded on the right with Os All image numbers in a scan must have the same number of digits i e if there are 1000 images in the scan then the first image number is denoted by 0001 In versions 2 1 2 and earlier the minimum number of digits in the image number is three 3 i e image 1 is denoted by 001 unless the largest image number in the scan would require more than three 3 digits as described above In versions 2 1 3 and later the minimum number of digits in the image number is four 4 SimulatorMode realtime immediate This option indicates if the simulator will mimic real time when simulating exposures If the value is realtime then the exposures will take real time to finish e g a 30 second simulator exposure will take 30 seconds to finish If the value is immediate then the exposures will finish immediately CCD Simulator The CCD instrument server simulators namely MSCServDetCCD_Simulator exe and MSCServCCDCamera_Simulator exe read the same configuration files as the non simulator counterparts MSCServDetCCD configuration and MSCServCCDCamera configuration respectively The simulators interpret all options as the non simulator servers plus two additional options which are ignored by the non simulator servers These options are SimulatorBaseFilename MSCServCCDCamera and Simula
219. uring processing 1t is advisable None Simple Mask Simple Scale e Dark and Mask Dark DC and Mask Select the desired radio button then specify the mask filename and or dark filename Usually the software will set these as the occasion permits such as the creation of a simple mask for integration Main Crystal Crystal2 Detector xRay Source Notes xShift YShift Distance Direct Beam at 0 0 00 0 00 8 x fi 500 00 Pixel Size Rot bout Beam 2Theta _ Roty Y 1500 00 100 y 0 00 0 00 0 00 m Non uniformity Type None Mask Filename C Sinple Mask O Browse Simple Scale Dark Filename C Dark and Mask a E C Dark DC and Mask Meee Close Save Defaults Page 54 CrystalClear User Manual Data Collection and Processing The X Ray Source Tab The X Ray Source tab allows you to specify the X ray source that your system uses Normally this information is set as site defaults by your CrystalClear administrator Setup x Main Crystal Crystal2 Detector Ray Source Notes ky m 50 03 100 00 Element Wavelength Copper y 1 5418 Source Type Rotating Anode Optics Type Focus Yale mirrors focused at crysta y fo 30 y Slit Size Collimation Type jo 00 5 double Close Save Defaults kV Specify the kV of your X ray source mA Specify the mA of your X ray source Element Select the element type of your X ray sou
220. used by default to store the SessionScript scp and SessionScript bak files as well as any scripts that the user may record Users can change their script directory in Preferences if desired A directory called cAhuber is created to store files required by the TwinSolve module A directory called cCARAXWish is created to store files required by the RAXWish software CrystalClear User Manual DirectBeamShots ContinuousIPReadImages PMTCheckImages CrystalClear User Manual Appendix A Files and Directory Structure A directory called DirectBeamShots is created located off of the CrystalClear program directory information for storage of direct beam shot A directory called ContinuousIPReadImages is created located off of the CrystalClear program directory for storage of continuous IP Read information A directory called PMICheck1 CrystalClear program directory information mages is created located off of the for storage of PMT Check Image Page 139 Appendix B Administration Appendix B Administration CrystalClear has a built in mechanism for managing various projects and samples based on the Login Name Once Crystal Clear is installed the administrator should specify default settings for the detector and set up an account for each user In order to add accounts to CrystalClear you will need to log into CrystalClear as administrator Administrator Login To log in as Administrator
221. ut This Manual e Code listings are set in monospace type e Menu options dialog options and field names are set in bold e Instructions for choosing menu items will include a gt between items For example Choose File gt New e Keystrokes are displayed in parentheses For example Press Enter e Aplus sign between keys indicates that the keys should be pressed at the same time For example Press Ctrl C to copy the selected text e Instructions for using the mouse to select dialog buttons or toolbar buttons or to select items in a graphical display will read Click the Start button or Click and drag the mouse pointer to select the desired spot Reflection Lists CrystalClear reflections lists are saved as ASCII files The first line consists of 3 fields telling the number of integer float and string values for each reflection The next lines are the field labels as character strings for each integer float or string value the first three fields are H K and L integers the next two are intensity and sigma floats the rest are optional Field labels cannot contain white spaces spaces tabs etc and should begin with n for integer f for float or s for string After the field labels are listed the reflections one per line in free format For example the first lines of a reflection file follows 4 integers 7 floats 1 string 3 integer field labels fIntensity fSigmal fObs_rot_mid fObs_rot_width 7 floa
222. utility used to decompress image files DLL for table controls System configuration file DLL for x ray generator control CCD compute server simulator CCD compute server CCD compute server configuration file RAXIS compute server simulator RAXIS compute server RAXIS compute server configuration file RAXIS IV configuration file RAXIS IV configuration file D TREK compute server PROCESS compute server TwinSolve compute server Configuration file for AFC7 goniometer RCD2 controller Configuration file for AFC8 goniometer RCD3 controller Default header file for Mercury CCD Twinsolve errors list Twinsolve file Twinsolve help file Twinsolve spacegroup file Online help file for CrystalClear Online Manual for CrystalClear Online help file for CrystalClear Online help file for TwinSolve module Readme file containing release notes and other info HTML help engine Help engine file Help engine file Page 135 Appendix A Files and Directory Structure Images 1tss d ll Help engine file popup ocx Help engine file OCX Components FlowCtrl ocx Flow Control OCX RegFlowCtrl bat Batch file for registering FlowCtrl OCX UnRegFlowCtrl bat Batch file for un registering FlowCtrl OCX Regsvr32 exe Program that registers OCX components RAXWish Files deisl1 isu _isreg32 dll blt80b1 dll raxvideo exe raxwish exe shape dat shape ico aaa log shape001 ppm shape002 ppm shape003 ppm shape004 ppm tc180 dll tclpip80 dll tif2rax exe tk80 dll tix4180 dl
223. utton to Predict Spots de select un highlight the To Use entry field to verify the selected image entries Right click an entry field for further menu options as follows View Images List Displays a list of image files Select Scan Allows user to select images of a scan Clears selected images of a scan 3 Set the Resolution range in ngstroms If you wish to change the default resolution click Set See Set Resolution on page 119 of Section 8 Additional Processing for more information on the Set Resolution function If resolution is set to 0 0 and 0 0 the resolution is set to be the entire resolution possible on the image Only reflections that will appear on the detector are predicted but the resolution range may be restricted further with this option CrystalClear User Manual Page 75 Data Collection and Processing 4 Specify the desired Crystal mosaicity If not 0 the specified crystal mosaicity overrides the value found in the input header In addition a new header will be written with the updated value for crystal mosaicity 1 To use a mask click the Advanced tab Predict Spots 3 Click the Apply Mask check box if desired 4 Click Run to predict spots For information on masking see the erasure tools in Small Image Window Toolbar on page 134 of Section 9 Images Index with TwinSolve Mercury CCD Twinned crystals require special processing to be resolved CrystalClear includes the TwinSolve processing
224. valuation of centricity Select the correct centricity if it is not already selected 5 Click OK Spacegroup pul Click Spacegroup on the Flow Bar The Spacegroup dialog will appear Spacegroup 2 Select the Reflection List file to use 3 Select the lt I Sig gt value above which the reflections in the parity class will be considered present Page 88 CrystalClear User Manual Data Collection and Processing 4 Click Run 5 Carefully look through the table and evaluate if the lt I Sig gt should be raised or lowered Repeat the run after you have made adjustments Scale and Average The Scale and Average step calculates and applies scale factors to different batches of reflections in an input reflection list averages symmetry equivalent reflections calculates merging and completeness statistics and creates a reflection list of unique reflections Scale with d TREK RAXIS or Mercury CCD To Scale and Average your data 1 Click the Scale and Average button on the Flow Bar The Scale and Average dialog will appear Scale and Average Xx Main Advanced Reflection Lists Algorithms r Absorption Correction dtfind ref I Batch Scale Method dtintegrate ref I B factor Fourier 8 3 TT Absorption Correction Regab Sphere dtintpred0005 ref Diameter ram dtintpredO006 ref Exclude Sigma dtintrefine ref Bo y 0 dtintrejects ref x 200 gt mu 14cm
225. ve the agreement between the predicted and observed spot positions 11 During integration refinement shifts for each parameter should be zero Otherwise you may have crystal movement sliding precession mount instability etc too small a batch or a wrong cell refinement altogether 12 Check to see that the profile fitting correlations are good in the integration log file both in number and in intensity Reflections of 9 sigma and higher should have greater than 90 correlation but may show lower correlation 13 When scaling the data absorption correction should be run in the every attempt The new algorithm needs fresh information from the absorption calculation The calculation is relatively fast 14 A good subsequent approximation for the Weight Addend is the Rmerge of your current result Consider using Auto Rmerge 15 A good subsequent approximation for the Weight Multiplier is the square root of the Chi Square multiplied by the current Weight Multiplier Consider using Auto Intelligent Page 4 CrystalClear User s Manual Abridged Or What To Do After You ve Started Your Data Collection ASSIGN UNIT CELL 1 FINDS SPOTS Select the images on which you want to find spots Adjust sigma higher or lower depending on the crystal Typically the 4 screen images are enough to get a good unit cell again adjust the number of images based on the crystal For poorly diffracting crystals it is not unusual to find on all images
226. verted back to the then click the Save button on the dialog Specify the location to save defaults instead of to settings the settings to and click OK you specified in a previous session CrystalClear takes a long time If you are not actually connected to an X ray detector you should to respond then an error make sure CrystalClear is set in Simulator mode Click Tools gt message occurs saying that Preferences then click the Server tab Check the detector in the list to CrystalClear cannot get a force CrystalClear to run in Simulator mode response from the RAXIS When you attempt a step that Open system configuration which is found in the CrystalClear requires communication with directory and change the value of DaemonIP to be the IP address of the CCD Camera CrystalClear the computer on which the Rigaku Daemon is running 9 This solution CrystalClear User Manual Page 199 Appendix D Troubleshooting hangs applies if MSCServDetCCD exe or MSCServDetCCD_Simulator exe is started before the hang occurs You installed CrystalClear 1 2 Your data is not removed when you uninstall or reinstall so you can over a 1 1 version and now just recreate the users in CrystalClear making sure you use the same your user list is empty names as the previous version In the User Settings screen for each user specify the path to the user s directory in the Data field You receive an error when This error will occur on Windows 95 mac
227. very few if any rejected reflections Any batch with a large number of rejected reflections should be investigated Perhaps the batch is indexed differently from the other batches Number of overlapping reflections in this batch that have symmetry related mates and that contributed to the Rmerge Number of reflections with no overlaps in the entire dataset One observation for a data point as opposed to numerous is not recommended The average Intensity Sigmal for reflections in the batch This is for the corrected but unmerged reflections A higher lt I sig gt was expected for the averaged reflections shown in subsequent tables This is the pseudo normalized for each batch Nii 1 as ies A Ix N Lvl hi 1 This is the Rmerge of the reflections which belong to this batch where J is calculated from reflections from all batches This is the Rmerge of the reflections which belong to this batch and all previous batches in the table where 7 is calculated from reflections from all batches Rmerge vs Intensity Sigmal Int sigmal Average counts Lines 253 269 This table lists Rmerge vs Intensity Sigmal Page 190 CrystalClear User Manual Average counts Num obs Num rejs Num ovlps Num mults lt I sig gt ChiSq norm Rmerge shell Rmerge cumul Appendix C Sample Log Files The average counts of reflections in the shell This includes reflections that overlap and those that do not If you assume
228. vious window will be displayed Next Window The next window will be displayed About The About dialog will be displayed Toggle Task List The task List on the toolbar will be toggled on and off as you click this button CrystalClear User Manual Page 23 Introduction to CrystalClear Toggle Standard Tools The standard tools on the toolbar will be toggled on and off as you click this button Toggle Flow Bar The Flow Bar display will be toggled on and off as you click this button Toggle Command Bar The Command Line display will be toggled on and off as you click this button Toggle Message Bar The Message Bar display will be toggled on and off as you click this button Toggle Status Bar The Status Bar display will be toggled on and off as you click this button Toggle Script Tools The Script Tool button display will be toggled on and off as you click this button The Script tool buttons are gt Play Record Il Pause E Stop Scripting is not fully implemented in CrystalClear Shutter Status open or closed ZIUR Close the shutter and shut down the device driver or processing server immediately NE Processing and Collection Status The cube rotates when data is being collected or processed Execute Step Button F You can immediately execute a particular step by clicking its Execute Step button This is the small button on the right of the large button with the Lightening icon Y Assign Unit Cell
229. web site for product information application notes service bulletins and on line documentation Set your browser to http www msc com Page 14 CrystalClear User Manual Installation 2 Installation System requirements To run Crystal Clear you will need the following Imaging System Rigaku R AXIS IV or Rigaku Mercury or Jupiter CCD Automated X ray Imaging Systems Computer System Pentium 450 MHz or better 500 MHz recommended Minimum 256 Mb RAM 512 Mb recommended for CCD plus additional space as needed for your data storage Video System 1280 by 1024 256 color capability or better or 95 98 Parallel LPT port A parallel DB25 port to accommodate the Crypto Box dongle Installing the Crypto Box Dongle CrystalClear comes with a Crypto Box dongle This Crypto Box must be installed on the same computer where CrystalClear is installed The Crypto Box works transparently with CrystalClear to prevent unauthorized use and distribution of CrystalClear To install the dongle 1 Detach printer if any from the parallel port The parallel port is a DB 25 port that is normally located on the back of the computer It is a female connector with 25 holes that match up with pins in the male end of the dongle 2 Plug the male end of the dongle into the parallel port and tighten the screws If the computer has more than one working parallel port you may attach the dongle to either one 3 If needed reattach the printer to th
230. ws the user to fit more columns into the viewing area Dragging on horizontal lines expands depth of the table Page 105 Tool Reference e Right click column entries Depending upon the particular column entry a useful pop up menu appears o View Images Set All Unset All Propogate Down Up All o Autoset O Editing the Scan Table Editing the Scan Table allows the user to change settings in various scans in a Collect Schedule After using the Add Scan button changes in column entries values can be made 1 When the Add Scan button is used scans are added to the list Each image is named by using the Scan Template Name then adding on a numeric value The number will increment by one with each added image and is usually four digits long A filename extension such as osc for R AXIS images or mg for CCD images completes the filename For example for the Project Myoglobin and Sample My if the Root Image Name is Myo3 and the Start is 1 then the image files will be named Myo30001 0sc Myo30002 0sc Myo30003 osc and so on For Collect Sample the Scan Template name defaults to the Sample name Double click in the Start Angle field to specify the starting angle for the scan Initially this field may be set at 0 00 or set at the angle determined in the Strategy step However if a scan should be stopped for some reason the Start Angle should not be reset in order to continue the scan See Stra
231. y few if any rejected reflections Any shell with a large number of rejected reflections should be investigated Perhaps the shell contains extraneous diffraction from ice or low resolution reflections are behind the beamstop Notice that more than 10 of the observations in the lowest shell are rejected That s bad Num mults Number of unique reflections resulting from the overlaps in the shell In other words the number of unique reflections measured more than once Num single Number of unique reflections measured just once Num unique Number of unique reflections measured Num mults Num single Avg mult The average multiplicity or redundancy in the reflections in the shell Simply Num obs Num rejs Num unique Comp shell This is the percent completeness for reflections which belong to this resolution shell 100 x Num unique Calc unique Comp cumul This is the cumulative percent completeness for reflections which belong to this shell and all previous shells It shows what the completeness would be if the data were cut off at different resolution levels CrystalClear User Manual Page 193 Appendix C Sample Log Files Direct Beam Log A summary of the typical log file DirectBeam log generated by the direct beam shot utility is shown below 1 Direct Beam Utility Copyright c 1998 Molecular Structure Corporation 2 Number of cycles 5 3 Exposure time 1 seconds 4 Date Thu Mar 30 1
232. y reflected in any other object May22b Myol sgrapelli all remain the same If a new user cparker is then added it will receive its new user defaults from CrystalClear User Manual Page 205 Appendix F Defaults in CrystalClear the site level However if pwoods adds a new project Abt it will not reflect the site level changes because new projects obtain their defaults from the user level and pwoods does not yet reflect the site level changes Updating Defaults One difficulty is that the user may want changes to the site level reflected in all other users The way to do this is to have each user log in and open a sample They should then load the site level defaults and save defaults to the user level Example mdavis changes May22b and saves defaults to all levels If pwoods then logs onto CrystalClear and opens sample Zn_13 She then loads the site level defaults into the sample and then saves defaults to the project and user level Now any new project she makes will inherit the defaults she just saves at the user level In addition any new sample she creates unless it is created in some already existing project that isn t Zn will have these new defaults Note CrystalClear 1 2 x allows only the administrator to save defaults at the user and site levels CrystalClear 1 3 allows any user to save up to the user level Administrator privileges are required only for saving at the site level Dialog Defaults Crystal To Detector 1
233. ymmetric For example there are 745 reflections in batch 1001 that have at least 1 symmetry related reflection in batch 1002 But there are 787 reflections in batch 1002 that have symmetry mates in L001 There are 298 reflections in L001 which overlap with a symmetry related reflection in the same batch each reflection is counted once To make this excrutiatingly clear here is another example suppose batch X001 has 10 copies of a reflection with hk 10 1 2 and batch X002 has just 1 copy The table will then appear Batch x001 X002 x001 10 10 x002 1 0 If a batch has few overlaps you might use dtreflnmerge or an editor to combine that batch with another batch that you think will have the same scale factors 1 e a batch that is adjacent in rotation angle or time scan see section 4 13 Reflections in input file refs excluded All batches Lines 167 193 Information about reflections in the batches is listed in a table Num refs Total number of reflections in this batch Num excludedNumber of reflections excluded because of the o cutoff Num rejs Number of rejected reflections There should be very few if any rejected reflections Any batch with a large number of rejected reflections should be investigated Perhaps it is indexed differently from the other batches Num ovlps Number of reflections in this batch which overlap another reflection either in this batch or another batch Num singles Number of reflections w
234. you change the size of the box around them That is by cropping the box closer to the profile the profile will fill a larger portion of the box If you make the box larger the profile will fill a smaller portion of the box In any event do not make the second value less than 2 times the image rotation angle increment Lines 293 308 The average correlation between observed profiles and the corresponding reference profile is listed for 10 Intensity Sigmal ranges If the assumptions of profile fitting are valid then the correlations should be very high gt 0 85 for strong reflections You are reminded that the assumptions are 1 Reflection centroids are accurately predicted and 2 Reflections do have the same profiles that is the same shape and boundary and the same relative intensity distribution within the boundary Laue Log dtcell Molecular Structure Corporation d TREK version 6 2SSI Dec 11 2000 Command line dtcell input head dtintegrate ref head output head tols le6 le6 le6 le6 le6 le6 anom maxrmerge 0 150000 spacegroup 16 laueonly Header input head opened Header of file input head successfully read Lattice oP assumed for space group 16 Command line string gt gt head lt lt OoOmAAIADUOPFP UNA 0 Output Header Name set to output head 1 Command line string gt gt tols lt lt 2 Cell tolerances set to 1000000 00 1000000 00 1000000 00 1000000 00 3 1000000 00 1000000 00 4 Command line
235. you selected Screen Collect and Process or Collect and Process as your task the CrystalClear Flow Bar will automatically begin the Process steps when collection is complete If you have previously collected the images to Process continue with the following steps Setup The first step in the CrystalClear Flow Bar is Setup 1 Start CrystalClear Enter Login Name and Password Page 32 CrystalClear User Manual Common CrystalClear Tasks When a Login Name is used for the first time the Project Wizard will lead the user through the creation of a new project and sample See Section 4 Running CrystalClear for the First Time on page 27 if you need assistance When a Login Name is repeated the Open Sample dialog allows the user to open an existing Project or begin a new Project The last project and sample used for the Login Name will be listed as default 2 At the Open Sample dialog select the Project and Sample Open Sample Ea Project Myoglobin y New Project Sample Myo2 y C New Sample Task Collect and Pr Image Directory D Documentation CrystalClear data Myoglobin Myo2 images Browse Cancel Browse Import 3 Select Collect and Process from the Task dropdown menu then click OK The Open Sample dialog allows the user to begin a New Project or a New Sample by clicking the appropriate buttons The Setup dialog will appear CrystalClear User Manual Page 33 Common CrystalClear Tasks

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