Standard Operating Procedure for Powder Diffraction on Rigaku MiniFlex 600


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Starting up the instrument

1.     Look and see if the orange light on top of the Miniflex is on
1.A. On means the instrument is in standby mode
1.A.i.     Proceed to step 2.B.iv.c
1.B. Off means the instrument needs to be fully powered up.
1.B.i.     Proceed to next step

2.     Switching on the instrument       
2.A. Turn on the chiller. Flip the switch to the on position and a red light should indicate the chiller is running.

Haskris instrument with top right circled to denote switch position

2.B.  Turn on the Miniflex. Press the green button
2.B.i.     The Operate button will be red then flash green quickly
2.B.ii.    The Door Lock Button will begin to blink and an alarm will sound
2.B.ii.a.   Push the Door Lock Button to lock door and stop alarm. 

Left, yellow button: Door Lock; Middle, red: Operate; Right, green: Power

2.B.iii.   Log into computer – (If you do not know this login or where to find it you should not be using this instrument)
2.B.iv.  Open Miniflex Guidance program : User = administrator, no password
2.B.iv.a.       Program will handshake with the instrument and initialize axes.
2.B.iv.b.       Control, XG Control – Turn X-rays on (wait until the process is finished and then close the window)

XG Control window; “ON” button under X-ray section circled

2.B.iv.b.1. Now at 20kV, 2mA and orange light on top of Miniflex is on.

Orange light located at top surface of Rigaku instrument

2.B.iv.c.     Control, Aging, Execute

Execute ButtonAging window with Execute button on bottom left

2.B.iv.c.1.   Wait 7.5 minutes for tube to condition and power up.
2.B.iv.c.2.  Now at 40kV, 15mA.  Click ok to close Aging window.

X-ray: On; Target: Cu(Ka); Tube voltage: 40 kV; Tube current: 15 mA

Preparing your sample

  1. Make sure the sample is flat and flush with the top of the holder.  Below are several pictures that show different prepared samples.

    Examples of various prepared samples

    1. Press a Pellet (left) – takes the largest amount of material and because it is not flush with the instrument will have a zero point offset. To accurately measure the zero point offset dope sample with known material like Si.
    2. Fill an aluminum holder (2nd image) – Takes similar amount as pressing pellet.  Put Kapton tape of the back and fill the Al holder with material. Tamp down and smooth the surface flush with the holder.
    3. Glass holder (3rd image) – Takes much less material than Al holder.  2 types a 10 and a 50 µm deep well. Fill the holder with material and tamp down and smooth the surface flush with the holder.
    4. Double stick tape over Al holder (4th image) – Takes similar amount of material as thin glass holder. Adhere a thin layer of material to the double stick tape.
    5. Use the zero background Quartz crystal holder (not shown) – needs least amount of material.  Take a small amount of material and place it in the center of the crystal. Use a drop of solvent to disperse the material.
  2. Note you may cover your sample with Kapton film to aid in the protection of the sample from moisture and air.  This will only work for short periods of time.

Taking a measurement

  1. Push Yellow Door Lock button. An alarm will sound and you can open the door.
  2. Insert the prepared sample holder into one of the six sample positions.

Insert sample holder into one of six sample positions

  1. Close the Door and push the Yellow Door Lock button and the door will lock and the alarm will stop sounding.
  2. Set up your experiment
    1. Make sure the General Measurements is highlighted at the top left and then press the big yellow General measurements button on middle left.
    2. Set up the folder, what you are calling your pattern, and where you are going to collect your data to.

      Select 'General Measurements' at top left and press yellow 'General measurements' button on middle left; Set up folder, file name, sample name; Define location of sample and check box to run line
    1. Define the location of your sample:
      i.     A checked Exec. box (purple box) tells the instrument to run that line. Unchecked boxes will be grayed out and not run.
      ii.     If you want to spin your sample during data collection to improve particle statistics and help remove preferred orientation effects, check the Spin box (pink box). NOTE: The sample will spin at 80 rpm, so samples must be very well packed if this option is used.
      iii.     Select which sample holder position (number on the wheel) contains your sample using the Sample pull down menu (teal box).
      iv.     If you are running multiple samples, fill out one line of the table for each of your samples.
    1. Design your experiment
      i.     2 theta range – you can collect from 3-120 degrees but you may only want to look at a smaller range of data.
      ii.     Continuous or Stepwise and time
      1.  A continuous experiment essentially measures the intensity of an oscillation image where the measured data is total counts over a 0.02 degree oscillation.
      a.     Decide time per measurement
      i.     10 degrees/minute = fast
      ii.     1.2  degrees/minute = slow
      2.     A stepwise experiment is a still image of the intensity every 0.02 degrees.
      a.     Decide time per measurement
      i.     1 second per 0.02˚ = fast
      ii.     1 minute per 0.02˚ = slow
      iii.     Width of step or continuous scan measurement
      1.     Default is 0.02 degrees this is the minimum step size. To speed up the time you can increase your step size, but your pattern will be less accurate.
    1. Click the set Meas. Conditions button (blue box above)

Choose set Meas. Conditions from tabs

i.      No1, No2, No3, and No4 are set as standard continuous experiments. The only thing you are permitted to
change in these experiments is the speed of the scan (blue box).
1.     No1 = 3-100˚scan
2.     No2 = 3-80˚scan
3.     No3 = 3-60˚scan
4.     No4 = 3-40˚scan
ii.     No 10 experiment is reserved for the teaching labs and should NEVER be changed.
iii.    No 5-9 can be set up according to the experiment you designed 
iv.    Click ok when you have decided.

    1. Assign the condition No of your experiment
      Choose condition No from dropdown menu
    1. Click Run
    2. A box will pop up asking you to confirm the slit configuration click OK

Confirm slit configuration by pressing 'OK'

    1. Wait for your experiment to complete. (The light next to General Measurement will blink Green during your data collection)
    2. When your collection is finished click Yellow Open Door Button and open door
    3. Remove sample
    4. Close door and click Yellow Open Door Button to lock door and the alarm will stop sounding.

Shutting down the instrument / Putting instrument in standby

You should put the instrument into standby when you are done with an experiment unless you are told to shut the instrument down.


1. Click the Shutdown button on the left side of the screen
2. On the XG set pull down and select Set to minimum

Click 'Shutdown' on left; Choose 'Set to minimum' on XG set dropdown menu

  1.  Click Execute and then you are done

If you are told to fully shut down the instrument

  1. Click the Shutdown button on the left side of the screen
  2. On the XG set pull down and select XG Off
Click 'Shutdown' on left; Choose 'XG off' on XG set dropdown menu

  1. Click Execute and wait
    1. Orange light on top of Miniflex will go out
    2. Processing window appear and it is down when the window disappears
  2. Close the Miniflex Guidance program
  3. Push the White button on the front panel of the Miniflex
Click white button on front panel (middle)
  1. Wait at least 15 minutes
  2. Shut off the water chiller

 Options for processing your data

  1. Use the .raw file directly and input it into Jade software (not available in G.L.Clark X-ray Facility)
  2. Use the .raw file in PDXL2 and convert it to something more useable.
    1. Open PDXL2 (user: Administrator, no password.
      i.     Click Load button on left hand column
      ii.    Choose the .raw file
      iii.   In PDXL2 you can manipulate the data
      1.     Change the auto background
      2.     Smooth the data
      3.     Change scale
      4.     Change 2 theta to Q or S
      5.     Phase ID with Auto Search
      iv.     To get a usable file
      1.     File
      2.     Export graph
      3.     CSV format
      4.     This file can be opened in Excel and has
      a.     Raw data
      b.     Background plot
      c.     Corrected data
      d.     Any additional manipulation you have applied
  1.  Create an xy file from the CSV in PDXL2 and do refinements in TOPAS
    1. Open the CSV file
    2. Make note of which columns contain what data
    3. Delete row 1
    4. Change the format in the columns to numerical 3 decimal places
    5. If you want the raw uncorrected data delete all columns except A and B
      i.     Note you may want the PDXL2 background corrected data so you would keep different columns.
    1. File, Save As, space delineated file format
      i.     Type “filename.xy”
    1. Open Topas import the .xy file
  1. There are also other programs, Fit2D, GSAS, JANA2006 and many more.  None of these programs will be detailed here.

Keywordssop standard operating procedure powder diffraction rigaku miniflex 600 x-ray xray   Doc ID97837
OwnerToby W.GroupSchool of Chemical Sciences
Created2020-02-11 13:45 CDTUpdated2022-11-09 17:56 CDT
SitesUniversity of Illinois School of Chemical Sciences
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