2-3 Troubleshooting

1. There’s no beam
  1. Are the shutters open?​

    • If no, then open the shutters silly billy.

    • If yes then move to #2.​​

  2. Has there been a beam dump?​

    • If yes, then wait until beam comes back.

    • If no:

      • Is there signal in I0? If no then:​

        • Is the energy in microscan correct? You may not have updated the scan parameters to the right energy and the mono has moved so that beam is now not aligned.

        • Make sure the TABLE motor is in the correct position, i.e., do a TABLEV vs I0 scan and set the peak position. Do a -1 to 1 scan in 0.1 steps. If there is no signal in the scan, contact the beam line scientists on Slack.

        • Check beam tuning, i.e., do a TUNE vs I1 scan.

        • Make sure tuning/Burleigh is not over limit (see below).

      • If yes:​

        • The optic has gotten misaligned somehow. Contact the beam line scientists on Slack.​

2.  Microscan is unresponsive/Sample stage will not move
  • First, try simply closing Microscan.

  • When you have done that, check the Windows task bar and look for the command prompt icon. Hover the cursor over that and investigate the names of all open command prompt windows. There may still be a Microscan command prompt window, maybe more than one.

  • Close all of the Microscan command prompts.

  • Try opening Microscan again.

If Microscan opens and is still not responsive or doesn't open, this could be due to a few things including:

  1. The system still thinks there is an active scan still running and won't let you move the stages. This is by design.

  2. One or more of the sample stage axes have disabled. Sometimes they just do that, or more likely they have been driven out of range past 12 or −12.

  3. The XPS (stage controller) has decided to take a break and needs a reboot. A way to double check this is that you close and try to restart Data Collect (Master Data queue) and that doesn't start either.

Solution to 1:
Check the Master Data Queue window. What is the data collection status light showing? If the color is green or orange it means Master Data Queue is still doing something and hasn't released control back to Microscan. Also check the bottom left of the window to see of there is a message like "Data queue active". If you see these:

a) Try hitting the "Abort Scan" button.

b) If hitting abort scan doesn't work, try closing Master Data Queue program with the tranditional red X. If it won't close, find the corresponding Command Prompt window called "DataCollect" and close that via the tradition red X to force quit the program. To reopen, use the desktop icon called "Data Queue".

Solution to 2:
READ THIS PROCESS IN FULL BEFORE ATTEMPTING!!!! There is an extreme likelihood of the wheel hitting either the optics or the detector. If you have the single rock sample holder on or thick samples you should remove the wheel.

First you will check the status of the stage motors:

  1. Double click the "XPS-D" shortcut on the desktop. If you cannot find the shortcut use a browser such as internet explorer and in the URL field enter the IP address:

  2. Login with:

Username: Administrator

Password: Administrator

Permission: Administrator (

  1. If you get no response from this window then consult Solution to 3 below.

  2. On the command bar, click FRONT PANEL (red arrow below left). Then click MOVE (red arrow below right).

  3. This should bring up the Newport status for each axis of motion which is shown below in the fully functioning state. The functioning state of the buttons under the “Action” column reads “Disable” for Y and Z and “Disable slave” for the X axis, meaning that the axis is enabled. If an axis has failed the button will read "Enable" or “Initialize”.

  4. If a single axis reads as "Enable" click that button. Things should work again now. If one or more axes read "Initialize" then....

  5. In uXAS GUI, click “Move Motor”.

  6. Scroll down to “DETECTOR” and click it. It should show the current position. Make note of it.

  7. In the “Move To” box type in a LARGER number than in the current position. Say 15.

  8. Click “Move” button and the detector should move away from the wheel. You can confirm this in the webcam.​

  9. Click those “Initialize” buttons. The buttons should change to “Home”.

  10. Click the “Home” button on the X AXIS FIRST!!!!. If you do Y first the wheel will drive with force towards the optics. The axis should return to the zero home position and the status should now read “Disable”.

  11. Click the “Home” button on the Y, Z and Phi axes.The axes should return to the zero home position and the status should now read “Disable”. Note the sample wheel will return so S0.

  12. Now find a command prompt window that has a last line ending "..../newportStages". Hit the up arrow on your keyboard and you should see a command appear "python initializeXPS_MA". Hit enter.

  13. Go back to the Newport browser page and you should see that all motors should now show "Disable" and the X axis should now read “Disable slave”.

  14. Remember this moves your focus point so you will need to refocus using the red arrow buttons. If you have already taken a map your points may no longer be precise and you will probable want to take new maps before performing XAS.

Solution to 3:

First try and get a hold of the beam line scientists to verify that the XPS does indeed need to be power cycled. If it is late and you can't get hold of us, the there are 2 potential solutions.

Double click the Newport shortcut on the desktop. A browser window will open. If you cannot find the shortcut use a browser such as internet Edge and in the URL field enter this IP address: You will probably get the login page.

Try logging in with:

Username: Administrator

Password: Administrator

Permission: Administrator

If you successfully log in then:

  1. Select "IPManagement" from the top menu.

  2. There is a red "Reboot" button at the bottom of this page. Click that and wait a few minutes for the unit to reboot.

  3. Try refreshing the page. Once the login page appears, follow the steps set out in solution 2 above from step 4.

If the Newport browser page is not reachable then we need to power cycle the stage controller box in the hutch called a Newport XPS​.​

  1. The stage controller is a beige box, located on the hutch floor on the right hand side

  2. Find the power switch next to where the power cable is plugged in. Turn the switch off and back on again after a few seconds.

  3. Refer to the steps in "Solution to 2" above from step 1.​

3. I cannot see my XAS data or my data looks really crappy

This is usually due to:

1. Having the wrong display parameters selected for the data you are collecting.

2. The plotter window having the zoom function or the vertical cursor still activated somewhere.


Solution to 1:

  • For fluorescence data being collected in SCA1, you need FF/I0 selected in the Std Plots tab.

  • For fluorescence data being collected in SCA2, 3 or 4, you need to select Custom in the Std Plots tab. Then in the Custom tab select Requested Energy as the numerator, and 1 as the denominator. Then you would select the appropriate SCA channel as the numerator (e.g. SCA2.1), and I0 as the denominator in the Y-axis group area.

  • For transmission data you should have the appropriate ion chambers selected, usually I1, either in Std Plots or in the Custom tabs.

  • You may have the first derivative selected. Go to the Math tab and just click the "None"radio button.

Solution to 2:
The display control buttons under the main plotter panel act as toggle switches i.e. one click to turn them on, one click to turn them off. As such they can be inadvertently left on causing the default auto scaling function of the plotter window to be overridden.


When the zoom rectangle or the pan scan buttons (highlight by the red box below) are activated the words “zoom rect” or “pan scan” will be displayed to the right of the icons (green box below). If this is the case, click the buttons again to turn them off. Your spectra should now appear and be auto scaling (if a spectrum is currently being collected).

If this doesn’t work then the vertical cursor may be still active somewhere. In the bottom left corner of the XASplotter window (purple box below) there is some small blue text that will either say “Marker at Nonee” (then it is already off) or “Marker at energy”. If it says a number then it is active somewhere so click just off the plot axes to deactivate it. This area should now read “Marker at Nonee” (yes it’s a typo).

5.  I cannot see my data in my T drive!

This is a problem since the “upgrade” to Windows 10. The data backup program can get interrupted. Solution:
1. Go to the Data Backup program (look in the task bar).
2. Click the “Stop” button.
3. Click the “Start” button.
4. Check your T Drive. Data should be there now