SAXS Manual for Basic Operation
Contents
1. frame filename means the current file carpal Jie Smooth Unwearp wotri U that is displayed in the SAXS software will Calibrate R be unwarpped while the null in the Options for Process Spatial Unwarp First input frame filename SFRAME frames to process 1 First output frame filename Snull Suppress unwarping beam ctr Y N V Check for yes Max display counts 1 cm First output frame filename means that the unwarpped file will not be saved and you can choose to save the file afterwards It is also important to note that if add is used to collect data the file will not be automatically saved into the folder that is created at the new project so the user will need to save it manually afterwards To save the file go to file and save as shown in Fig 19 11 Scan Single Run Scan provides another way of data collection It can be achieved by collect gt scan gt single scan Fig 20 The options for collect scan single run window Fig 21 will pop up This function is mainly designed for producing a series of scans over O SAXS Small Angle X ray Scattering System 4 1 45 Copyright 1997 2012 Bruker AXS Allri Project File Edit Collect Process Analyze Peaks Special User Help Display gt Load Ctrl 0 30 Display Logfile Enabled Scriptfile Enabled Print Ctrl P 1 SAXS Small Angle2. Shutter SingleRun MultiRun EditRuns Ctrl ShFt 4 Ctrl ShFt 5 Nanography AcceptTargets EditTargets Multfargets SCAN MultiTargets List 512 lines Runt Frame Xx vg Time Ctrl ShFt F 1 Ctrl Shft F2 Ctrl ShFt F3 Ctrl ShFt F9 Ctrl ShFt F10 Ctrl ShFft F 11 Ctrl ShFt F12 TO 001 35 000 84 400 is the intrinsic name for the file For example according to the setting at Fig 25 the name for the GFRM file will be test_1_001 as shown in Fig 26 If multiple run are taken then the files will be stored with the filename Job name_Sample number with of number an extension sequence If you open the raw Ctrl ShFt 4 Ctrl ShFt 5 Goniometer Shutter Ctrl ShFt F 1 Ctrl ShFt F2 Ctrl ShFt F3 SingleRun MultiRun EditRuns Ctrl Shft F9 Ctrl Shft F10 Ctrl Shft F11 Ctrl Shft F12 Nanography AcceptTargets EditTargets MultiTargets data through file and load the file name will be shown at the right upper corner the red rectangle as shown in Fig 27 And the intrinsic file name 1s shown above the file xl Job name test 25 E Title testi Sample name bfi Sample number 1 Max display counts 16 Realtime display Y N V Check for yes Pre clear Y N M Check for yes Sequence of starting run 1 Sequence of ending run 512 Cancel testl test_1_001 gfrm Uiyusyis ir fie Created Mag Quad Theta Wid
3. The center of the drawn circle in red is set at the calibrated beam center You may adjust the radius of the circle by dragging the cursor to match the circle of the beam stop The offset of the two centers reveals the misalignment of the beam stop For example Fig 37 indicates that the center of the beam stop shadow is lower than the drawn circle suggesting that the beam stop should be moved upwards d Adjust the beam stop location using the micrometers for XY translation stage in front of the detector as shown in Fig 39 Iterate the vertical adjustmen of the beam stop 39 steps from a to d until the center the of beam stop Sa coincide with the beam center Please write down the X Y coordinates from the readouts of the micrometers in the instrument log book Once finishing the calibration and the adjustment of the beam stop then it is ready to start your experiment Apply the aforementioned data acquisition procedure for the 2D data collection of the samples Ear ii aa i Horizontal adjustment for the beam stop 5 Data analysis The raw 2D data files are in the GFRM format stored in the folder that has been set up in the directory created at the beginning of the project To reduce the 2D raw data to 1D go to the tab file gt load to import the file Then go to the tab Peaks gt Integrate gt chi as shown in Fig 40 A window Options for Peaks Integrate C
4. PRESS the enter KEY again NOTE THAT do not move the cursor around during the calibration as it may result in changing the right sample to detector distance and beam center Then a window SAXS for XP 2000 V4 1 45 will pop up to update the SDD and beam center l1 SAXS Small Angle X ray Scattering System 4 1 45 Copyright 1997 2017 Bruker AxS All Project File Edit Collect Process Analyze Peaks Special User Help 30 Flood Spatial Corr LPA Smooth d Options for Process Calibrate Minimum relative intensity 5 Sample to detector distance fioa Delta distance Detector angle ooo Delta angle Detector center fio29 00 Detector center 1017 00 Delta XY movement 0 1 L cc E ka a h e M e e a e aal ystem 4 1 45 Copyright 1997 2012 Bruker AXS All inalyze Peaks Special User Help Fig 33 Click yes You should keep iterating the calibration process until no pop up window to ask for update During the updating process the user can check the updated distance and beam center at the right side of the software as shown in Fig 33 After finishing the calibration go to the tab project gt load and load the configuration file saxs sc containing the information of SDD and beam center information which has been updated in your own folder click Ok Fig 35 The updated distance will be shown at the right lower corner as Fig 9 and be set as the correct SDD
5. Please also record the SDD beam center X Y in the red rectangle in Fig 33 and the Counts circled by the green ellipsoid in Fig 33 of the 60 s measurement of AgBeh received by the detector in the log book To obtain reliable scattering intensity at the lowest RE Tir s1ilverB_O_O0 11 29 14 01 50 04 Created 04 15 14 attainable angle it is important to align the position of x d 0000 800000 beam stop with the incident X ray beam This can be achieved by the following steps a Take a 5 s Distance e 1 measurement on the AgBeh standard unwarp the file K cantar Y center 1007 70 and zoom in by using ctrl and z at the center of the 1 54X 5 Small Angle X ray Scattering Syste Options for Pro Jea Project File Edit Collect Process Analyze F i Configuration Filename ar Switch Cancel Hew Copy Edit Backup Remove Delete Exit configuration file 2D image as shown in Fig 36 The image can be magnified by various factors 2 to 16 around rocess Analyze Peaks Special User Help Box F5 Graph Circle F6 Transmission Pixel FF Background Vector RBox the cursor which should be approximately at the center of the beam Fig 37 shows the magnified result where the inner circle arises from the shadow of the beam stop b A circle can be drawn by either using F9 or Analyze gt cursors gt conic Fig 38
6. data using the data acquisition software Here we list several most common modes Options for Collect Add Maximum seconds k Pre clear i ADD Test pattern The simplest method to collect the data is to use eee aaa S fooooco000 7 z collect gt Add Fig 15 In the options for z collect add window Fig 16 set the data eG oleate plsy Reset interval fo collection time at the maximum seconds The 7 Open amp close shutter max display counts is used to adjust the false Auto script file Snull z l color view of the 2 D image and doesn t affect the Cancel real data Make sure the open amp close shutter is checked otherwise the user needs to manually control the shutter Click OK to start the data acquisition A typical SAXS 2D pattern of the AgBeh standard is found in Fig 12 It should be noted that the data collected using ADD needs to be unwarpped to correct the spatial distortion of the detector This can be achieved by going through process gt spatial gt unwarp as shown in Fig 17 The options for process spatial unwarp window will pop up Fig 18 Load the file that you need to unwarp through the first input frame filename and save the unwarpped file through the first output frame SCIENTIST SESE filename SFRAME in the First Input Project File Edit Collect Process Analyze Peaks Special User Help Load
7. the alarm sign starts flashing Press the Alarm CY open door button once you hear the click open the chamber door by turning the door knob counter clockwise Fig b Please note that the door will be automatically locked again and another click will sound after a period of waiting time without action You may press open door button again in order to open the chamber door Please note that the X ray will be shut down automatically if the procedure is not correctly followed c To close the sample chamber 1 To close the sample chamber first close the chamber door by turning the door knob clockwise and make sure the metal piece on the door switch is completely in the groove of the door please the instructions posted on the chamber door of the instrument You should hear a click after the door is properly closed 2 Close the air values by turning them clock wise 3 Turn on the vacuum valves counterclockwise 3 Common Sample Stages There are different sample stages that are built up to meet different research purposes 1 e ambient multi slot temperature controlled 7 controlled GI SAXS tensile and shear stages The most commonly used stages are ambient and 7 controlled stages Therefore we will explain how to install the samples on these two components For further information about other stages users should inquire a special training from Jack Please remember to record in the lo
8. the heater and then circle button to turn off the whole unit 2 Close all the water valves 3 Disconnect the four cables 4 Gently detach the temperature stage and store it in the cabinet PLEASE REMEMBER TO RECORD IN THE INSTRUMENT LOG BOOK ALL SAMPLE STAGES USED IN THE EXPERIMENT 4 Start with the Software Controlling System 4 1 Ramping or tuning the x ray power The X ray light orange above the sample chamber should be on before starting ramping the X ray power up if not please inform Jack or the AP KJ p8tools Startt la xi x D Fie wew Window Hep lgj xi nesas ele saa o Sels 2191 2 Online Status mo Open STATUS File en 2 2 is 2 Open ERRORLOG File a Ben 82 GBA Je SB E sw smatarae xray PH Deroois start L xrar msntennee ESNIARUGO asoan Turn on the computer connected with the SAXS and open the D8tools on the desktop Open the D8tools it should look like as Fig 1 Click on the online status and a window like Fig 2 should pop up Click on the online refresh on button on the left corner a window like Fig 3 will pop up First check if there are any warnings alarms or abnormal signs please inform Jack E Dtools Instrument Status1 and the AP if so Click the x ray generator T File Edit View Window Utilities Help aes e sala wel a tab on the left the arrow in Fig 3 Then a window like Fig 4 will p
9. values in X and Y as well as intervals Fig 13 Usually one second frame is enough For example the setting in Fig 13 represents that a scan will take place by driving the sample stage from X 32 mm to X 35 mm with a step size of 0 5 mm as well as from Y 57 5 mm to Y 61 mm with a step size of 0 5 mm That means 56 7 along X asis x 8 along Y axis scans will be performed The total count rate will be displayed O SAXS Small Angle X ray Scattering System 4 1 49 Copyright 1997 2014 Bruker AXS All Options for Collect Scan Nanography i x gt ProJect File Edit Collect Process Analyze Peaks Special User Help o Detector Jobname saxs Sc aes Goniometer Scan SingleRun Ctrl ShFt F 1 l 3 Add Ctrl Shft 4 MultiRun Ctrl Shft F2 Shutter Ctrl ShFt S EditRuns Ctrl ShFt F3 t Nanography 3 anopraphy Ctrl ShFt F9 p vee Ctrl ShFt F10 X begin 32 mm Xx end 35 mm X increment 0 5 mm EditTargets Ctrl Shft F 11 MultiTargets Ctrl shft F12 Y begin 57 5 mm Y end 61 mm Y increment 0 5 mm Seconds frame fi sec Background Title background frame x 0 0 mm Y 0 0 mm Seconds frame fi 0 sec RSW 0 000 deg cme 3 graphically in a picture for a more detailed O SAXS Small Angle X ray Scattering System 4 1 49 Copyright 1997 2014 Bruke AXS Allrig ae oe Z Project File Edit Collect Process Analyze Peaks Special User Help sey description of using nanography please refer to the
10. Add Cuesta Update NANOSTAR SAXS System User s Manual Vol 1 7 Shutter Ctrl ShFt 5 Attenuator Ctrl ShFt N Shutter Ctrl ShFt 5 erase e s 9 For weak scattering samples it might be easier to Temperature Ctrl Shft T 1 find the center of the sample by manually moving the Options for Collect Goniometey Drive ve stage to visualize the 2D images at different positions x position mm 35 000 oe than using nanography Y position mm 80 200 ReisampWheel 0 000 To move the sample stage manually click the menu Omega Phi 360 000 tab collect gt Goniometer gt Drive Fig 14 In 360 000 the options for collect Goniometer drive window OK C 0K Cancel you may drive X Y of the sample stage to the desired position The position of RefSampWheel is 0 when empty for taking sample measurements and 40 when the glassy carbon for reducing the flux of direct beam and monitoring the flux is rotated in the beam Again Omega and Phi are only for GI SAXS stage The approximate position of AgBeh standard on the trapezoid rack for the normal stage is at X 35 and Y 60 5 O SAXS Small Angle X ray Scattering System 4 1 49 Copyright 1997 2014 Bruker AXS 4 2 3 C O ll ec t S A XS d at a ProJect File Edit Collect Process Analyze Peaks Special User Help Detector Goniometer Scan There are many different ways to collect SAXS ae ake
11. P 4 2 1 Create the directory Special User Help First go to the tab project on the x Sample Name 32 X chars MEATA C COS a a s a a rwWWOOC the dr opdown menus At the Sample Number up to 4 digit 0 tte options for project new window EO ATEST Working Directory PROJECT Sample Information menu Fig 6 and click new in fill out the sample name sample number and title of your experiments which can also be changed after data acquisition Reset to defaults Y Most importantly copy the link of the folder that you want your data Directory Information to be automatically saved in in the Frames Mu Ping Nieh Group Yan x ray maintenance 201 41127 ls working directly Fig 7 This Samate information step is to make sure that your data will be saved in your own folder instead of the previous user s SAX5 for P 2000 4 1 49 Project Wor Dew 2 Save the current configuration before changing projects Yes Mo 9 K 35 0900 Ome Y 80 700 Ph RSW 0 000 Shutter CLOSED Distance 106 550 FloodFld 2048_107 Spatial 2048_107 0486x 70465 PxC Shortcut to Saxs EXE EA Zl D tools exe 4 2 2 Find the sample position 0 000 0 000 folder Then click Ok to save the new project Click yes to save the current configuration Fig 8 At the lower right corner
12. SAXS Manual for Basic Operation 1 ed drafted by Yan Xia finalized by Mu Ping Nieh Jan 2015 e Before any user can operate on the SAXS you have to accomplish the EHS online x ray safety training and receive operation training from Dr Jack Gromek e Note that misuse of the SAXS instrument may lead to safety issues and malfunction of the instrument which may result in damage of the components and long term shutdown e The bench top should always be kept clean and neat All signed out components should be returned after experiment e Please remember to fill out the log book by the instrument Record as much detailed information as possible on the log book e Those who constantly fail to follow the rules are subject to lose their access to the instrument 1 SAXS Beamtime Reservation SAXS experiments can be scheduled through an online booking system http calendar ims uconn edu X Ray Diffraction Web Once the user finishes the safety and operation training an account will be set up by Jack No more than 48 hours week of SAXS beamtime can be requested by each user 2 Sample Chamber a Sample chamber should be under vacuum at all times when the door is closed even when it is not in use Daad b To open the sample chamber Close both of the vacuum valves Fig a and open both of the air valves counter clockwise Wait until the pressure has we _ equilibrated with the ambient pressure and open doa ty
13. X ray Scattering System 4 1 45 Copyright 1997 2012 Bruker AXS ProJect File Edit Collect Process Scan Add Ctrl ShFt 4 Shutter Ctrl ShFt 5 Analyze Peaks Special User Help Ctrl Shft F 1 trl ShFt F2 Ctrl ShFt F3 5 Ctrl ShFt Fo ets Ctrl Shft F10 MultiTargets Options for Collect Scan SingleRun Ctrl Sht F11 Ctrl Shft F12 20 x Scan parameters A I Frames f2 Seconds frame 5 Start position 58 6 mm Fixed axis 35 mm RSW 0 000 deg Step size fio mm Scan axis Y N Title Po Sample name 85_3_30mins Sample number oOo Filename parameters Job name Junknown0 Punt Frame Ch Junknown0 1 001 gfm sss several sample positions 1 e X and Y as the other axis fixed For example Fig 21 indicates that the scan axis is Y meaning the X is fixed at 35 mm The first frame of the scan starts at Y 58 6 mm Since the step size is set to be 10 mm the next scanning position is at Y 68 6 mm According to the scan parameters two frames will be taken at 35 Max display counts 5 M Realtime display Y N Iv Pre clear Y N 58 6 and 35 68 6 with 5 seconds of measurement Cance for each frame The value of Frames represents the number of scans you would like to take every 10 mm in this case along the Y axis In the filename parameters setting the Job name will be the gfrm raw data name For example the setting ba
14. g book the sample stages you are going to use 3 1 Ambient stage Fig c shows a trapezoid sample mount for the ambient stage which is loaded with a silver behenate AgBeh standard that is used for the calibration of the instrument In order to save time to find the location of AgBeh standard for the calibration please DO NOT take off the AgBeh from the sample mount as the center position has been pre calibrated to be around x 35 and y 60 5 You may use the other two trapezoid mounts You may simply fix the samples on the mount by using scotch tape Liquid samples should be sealed in the capillaries and powder samples can be adhered on scotch tapes or sandwiched between two Kapton films Note that scattering background from and transmission of capillary scotch tape or Kapton film should be measured before the sample is loaded 3 2 Temperature stage Fig d shows the 7 controlled stage installed in the chamber that requires different sample holders a For the liquid sample that can be easily cleaned there are two Bruker cells with an embedded capillary as shown in Fig e and f Since Bruker capillary cell is expensive gt 1 500 cell and fragile for liquid samples which are strongly scattered high viscous or hard to clean you should NOT use the Bruker capillary cells but use the disposable quartz or glass capillary instead The capillary can be inserted in the Al sample holder made by IMS machine sho
15. hi will pop up as shown in Fig 41 Set the 2theta scattering angle and Chi the fan angle to be integrated around the beam center ranges corresponding to the radial range and sweeping range on the 2D image You may choose 5 Bin normalized a general option as the normalization method for the intensity Step size 1s the interval angle integrated for each data point Different step size can be Options for Peaks Integrate Chi 2theta Chi _ S po c Start 0 10 de Start 0 00 de different number of data points of 20 I Click OK to ae a oe o i chosen through the drop down menu and will result in start the integration A window will pop up like Fig 42 Normalize intensity 5 Bin normalized gt which illustrates the integrating range of the above Stepsize 005 gt setting and allows you to finalize the desired range The ical radii of inner and outer circles perdmlipo i j 1 dmlipolSc2 gf are determined by the input 14 29 14 02 33 25 reate 1 0 values of 2theta i e Start and Et 1403479 10800 0 End respectively The range Distance 106 550 Size 2048 can be adjusted manually using 2th bagi 0 1000 chi 1 0 00000 keyboard as the instruction listed chi 360 000 at the bottom of the SAXS 2D image For example to change the starting 2theta value you may press 1 and then move the Distance 106 550 mouse cursor to enlarge and Fl
16. ker AXS Allri ProJect File Edit Collect Process Analyze Peaks Special User Help samples from the chamber close the chamber Switch Load door and apply the vacuum again Please pa Copy Edit remember to sign out on the log book If Backup Remove Delete Bruker capillary cells are used please clean and return them to Jack or the AP
17. llowing the same procedure as described in 1 to 3 6 Finally tighten the two metal caps simultaneously to finger tight To seal a disposable capillary cell a torch is provided at the x ray lab Please consult with Jack before operate it Controlling temperature of the stage 1 Fasten the 7 controlling sample mount on the sample stage 2 Connect the four cables as labelled in Fig j Cable 3 and 4 are for the electronics of the 7 controlling stage and Tubing 1 and 2 are for the cooling water circulation 3 Open the two water valves on the floor located at the back of the instrument Fig k 4 Turn on the a unit by pressing the circle button Fig 1 5 Wait for 10 to 15 minutes to allow water circulation through the temperature Stage 6 The heater can be turned on by pressing the green button on the TCPU unit 7 In the red rectangle shown in Fig 1 the 7 readouts at the top and bottom are the T probed at the stage and set 7 respectively The set 7 can be adjusted by pressing the up and down arrow as shown in the red ellipsoid in Fig 1 The temperature can also be set through SAXS software under collect gt goniometer gt temperature If 7 controlling stage is not in use NEVER leave the temperature stage in the chamber You should detach the 7 controlling stage following the steps below 1 Turn off the TCPU unit through pressing the red off botton to turn off
18. of the SAXS software there are some important parameters that the user should know Fig 9 X and Y are the sample stage position RSW means the position of the reference sample wheel which is the rotating wheel after the sample in the chamber Ome Phi and Aux are the tilting angle positions when the GI SAXS stage is in use Shutter is located in front of the generator During data acquisition the shutter 1s open and the indicating red light will be on When the shutter is closed the indicating green light turns on see the red circle in Fig 10 The distance in Fig 9 means the sample to detector distance SDD Two sample to detector distances can be chosen 2 tubes resulting in a distance around 107 cm and 1 tube leading to around 67 cm For each distance there are corresponding flood and spatial files that need to be used i e the file of 2048 107 is for the distance of 107 cm KV and mA are the voltage and current There are two SAXS software online and offline Fig 11 Only online one can be used to set up the measurement while the offline can be used to perform the data analysis First the sample needs to be moved to the center of the beam before taking the measurement To find the position of the sample click the menu tab collect gt scan gt nanography in the droplist Fig 12 Enter starting and ending
19. oodFld 2048_107 Spatial 2048_107 2048x2048 DEMO Shrink the inner circle The final 2 3 4 Select edge M Move ENTER L button Integrate ESC O buttons Quit information will be revealed on screen as shown in the red rectangle in Fig 42 Note that the inner circle should be always larger than the shadow of the beam stop and the full outer circle should be always within the detector range for the integration The Chi range can also be chosen to integrate either the full annulus i e from 0 to 360 or a sector of the circle as required in different scenarios For anisotropic scattering patterns sector integration may be needed After adjusting the integration range press Enter key on the keyboard to start the integration After integration an 1 D intensity curve will be produced as a function of 2theta as shown in the background of Fig 43 An Integrate Options window will also pop up for you to set the file name and sample title The reduced 1 D scattering data will be saved in a file of ATSAS format and contains three columns with first second and third columns being the scattering vector g q4 sin 9 20 being the scattering x angle the scatting intensity and the error Title SampID P zl bars of intensity respectively File name CAFrames Mu Ping Nieh Group Yan lipid exch Pama JATSAS B For weak scatterers correction of the W Append Y N Scale factor fi 0 background e g water scat
20. op up When SAXS is not in use the voltage HV and current Cur should maintain at 20kV and 6 mA respectively with the boxes being green If the boxes are gray it means that voltage and current are not stable or the x ray generator is down Make sure there are no warnings File Edit view Window Utilities Help Cyl saa o Sele e ae ellr olla Instrument 20w 3 shown at the lower part of the page Click on the utilities Fig 4 a Instrument Status MJINSTRUMENT XRAY B Omega 0 000000 Luew w S a and select x ray in the drop saage na re E ak M EOMER n E down list There are a few options B Tube Window x ray OPEN under x ray choose set HV and generator X RAY Generator HV 50 Cur 50 Cur and set up the HV and Cur to gs 50 and 50 Fig 5 and click ee OK The square boxes by the X RAY Generator will turn gray during the voltage and D amp tools Instrument Status T File Edit view Window Utilities Help oleaj Ba _ Postionma rve 9Pos SampleHandler fe AEE oS SampleRoboter current ramping process As soon as the HV and El Instrument E E Instrument Status Measuring Channel Cur reaches the set values Positioning Drives ey ae ne Tube Window i a Gee Y RAY Generator x RAY Switch off circuit OFF the square boxes should Restart Instrument H Con
21. p which mimics the appearance of Bruker capillary cell as shown in Fig g and h The Bruker capillary cells need to be signed out through Jack or the authorized personnel represented by AP hereafter After finishing the experiment users should carefully clean the Bruker capillary cells return them to and checked by Jack or the AP Users will be responsible for replacing the damaged Bruker capillary cells All the parts of a Bruker capillary cell are shown in Fig e including a metal holder with the capillary two caps two rubber o rings and two disk like metal pieces Since the SAXS experiment is conducted under vacuum the cell has to be properly sealed The procedure of sealing the Bruker cell is described below Sa 1 Place the disk like metal piece in the cap followed by f l 4 se oa ps the o ring sia 2 Gently tap the cap on the table to ensure that the metal pe z piece and o ring are centered as shown in the inset at Fig f 3 Then gently screw the cap onto the capillary holder at one end without fully tightening it yet Fig P 4 Use a 1 200 uL pipette as shown in Fig i with a and possibly break it The required RE ia a aa a NC sample volume should be less than 60 uL Tip Gently insert the tip into the capillary slowly pull the tip out during ejecting the liquid sample 5 After filling the sample seal the other end of the capillary holder with the second metal cap fo
22. sed on Fig 21 will result in a gfrm file with the name of unknownO 1 001 in which the frame number 001 is the first frame of the multiple runs After set the file name click Ok to start the data acquisition The data collected using scan is unwarpped data and will be saved automatically to the folder If you open the file that you have acquired through single scan you will see the title as the intrinsic file name shown at the upper right corner at the SAXS software please refer to Fig 27 for detailed information 11 Scan MultiTargets For data collection on multiple samples at different positions the most convenient way is to use multi targets function Select collect gt scan gt edit targets Fig 22 The scan multitargets list window Fig 23 will pop up and the user can set up multiple measurements at different positions with different durations for each run After finishing the list click Ok to save the targets Then follow Collect gt Scan gt MultiTargets Fig 24 and then the options for collect scan multitargets window Fig 25 will pop up where the Job name will be the leading file name for the raw GERM file and the title O SAXS Small Angle X ray Scattering System 4 1 49 Copyright 1997 2014 Bruker 4XS f ProJect File Edit Collect Process Analyze Peaks Special User Help Detector Goniometer Scan Add
23. tering in aqueous solutions can be important In this case the SAXS data of both samples and background are needed To subtract the background from the sample 2D file go to the menu tab file gt load The options for file load window will pop up as shown in Fig 44 Load the sample file Options for File Load Frame amp display information 44 in the Input filename box and then load Input filename C Frames Mu Ping Nieh Group Yan lipid exchange 201 41123 1 perdmlipol5c Ven ees wet the background file in the Background 2nd frame for combining with 1st filename box The N in the scale Background filename Doo O oo Offset 0 0 factor box means N times of background Special features will be subtracted from the sample file Merge CONFIG into header 1 e mathematically it follows sample N background The scale factor N can CG 66 be changed by simply typing the value but the sign should remain 6 End session After finishing the experiments go to the menu tab project gt exit to exit the SAXS software as shown in Fig 45 Then open D8tools and reset the HV and Cur to 20V and 6 Amp respectively to lower down the power for detailed operation please refer to the Sec 4 1 Ramping X Ray power Take out all the O SAXS Small Angle X ray Scattering System 4 1 45 Copyright 1997 2012 Bru
24. th Counts Time s Distance SIze test _1_001 gfrm GFRM File 4 104 KE 26 39 01 05715 1 0 0 00000 0 00000 1005 5 0070 107 400 046 name the orange rectangle at Fig 27 The data collected through multi targets are unwarpped and will be automatically save into your folder iv Scripts You can also use scripts to set up the more complicated experimental runs Please contact Jack or AP if you would like to learn how to set up the SAXS measurements with scripts 4 3 Calibration Prior to any sample measurement the instrument should be calibrated using AgBeh standards to calibrate the SDD and the beam center Fig 28 and 29 show the two AgBeh standards used for ambient and 7 controlling stages respectively Place either of the AgBeh standards depending on the stage used in the sample chamber After the vacuum gauge goes to or below 0 1 start the data acquisition To obtain a decent statistics it is recommended to take the measurement on the standard at least for 60 s followed by unwarpping the file Then click the menu tab Process gt Calibrate Fig 30 As the options for process calibrate window Fig 31 pops up BE SURE the standard file ag behen std is used and the auto mode is checked shown in red rectangles in Fig 31 Then USE enter KEY on the keyboard to start the calibration After the auto calibration stops as shown in Fig 32
25. trol Boards eE H Miscellaneous k wn turn green again Then CL TxSx Control L VACUUMS Control gt close the D8tools by Slime Primary Optics Ghange RAY Status Tube Conditioning ON OFF clicking the close button Cooling Water Devi Reset Rat Hardware Gapture Register Hard aFry Cooling Water Devi Vacuum ON permit Vacuum OFF permitted feserved _ mae el at the upper right corner Reset e Bay Software Safety Circuit Capture Register of the window Set HY and Cur of the X RAY mD x 4 2 Launch SAXS After closing the D8tools J SAXS Small Angle X ray Scattering System 4 1 49 Copyright 1997 2014 Bruker AXS All rights reserved ProJect File Edit Collect Process Analyze Peaks Special User Help please find the SAXS software on the desktop Note that when SAXS software Is in use D8tools 1S automatically AG Elta WorkDir 0141112 disabled Open the online SAXS software and click yes after the window pops up x 35 000 Ome 0 000 then you should see an Y 80 200 Phi 0 000 RSW 0 000 Shutter CLOSED f Distance 106 800 operation window as Fig 6 Flood Id 2048 107 Spatial 2048_107 2048x2048 PXC The online SAXS software 1S reate a new project from scratch to control the instrument setup for the data acquisition Here we are only going to introduce the basic steps of how to conduct the measurement If the user has special requirements please ask Jack or the A
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