Frequently Asked Questions


If you feel something strange

 Check the following content when you see an error message from UGUI. If you have any questions, please contact the responsible staff (PHS 2613). Please click the following items you want to see.


Beamline control software "UGUI"

  • The Status line remains red and indicates Idle.
    Click [EMERGENCY STOP].The background color will return to blue.

  • Linux PC is freezing.
    Try to return to the login screen by "Ctrl"+"Alt"+"Backspace" or login to the PC using ssh from another PC and reboot. Please contact the responsible staff (PHS 2613) if you can not login.

  • After an action such as Snapshot or Data collection, the Status line shows Idle but the shutter remains "Open".
    1. Click [EMERGENCY STOP].
    2. Take a snapshot as a test.
    3. Reboot UGUI.
    Please contact the responsible staff (PHS 2613) even if you can solve this problem.

  • The view of Omega status is incorrect.
    Input a value (e.g. 0,90,180,270,360°) and rotate the sample. Then, check that the sample moves to the specified value.
    Please contact the responsible staff (PHS 2613) even if you can solve this problem.

  • The equipments don't move after I specified the wavelength and/or the energy.
    When changing the values from [Snapshot] and [Collect] widgets, the equipments should start moving only after clicking the [Snapshot] button. Even if you change the values in the [Advanced...] widget, or in the data collection table, the equipments will move only after starting the experiment.
    If the equipments do not move even though you are starting the experiment, please contact the responsible staff (PHS 2613).

  • UGUI is freezing.
    Try to reboot the PC and restart UGUI. Please contact the responsible staff (PHS 2613) if you can not solve the problem.

  • UGUI has stopped when I try to start the experiment.
    The following troubles have been identified.
    1. If there is a duplicate file name in the same directory, UGUI will stop.
      =>Please click [EMERGENCY STOP], and change the file name.
    2. UGUI has stopped when I create a new directory and set the directory as the working directory.
      =>Please check that there is no illegal characters in the new directory name.
    3. UGUI has stopped after the action such as Snapshot or Data collection.
      =>Please click [EMERGENCY STOP], and then click the [All restart] button on the control tab.
    If you cannot solve this problem, please contact the responsible staff (PHS 2613).

  • There are no x-rays.
    Please make sure of the following points, and contact the responsible staff (PHS 2613) if necessary.
    1. Check that the shutters are open. (PF: MBS-BBS-DSS; PF-AR: MBS-BBS)
    2. Check the value of slit size. Did you set the appropriate value?
      Standard slit size
      BL-5A NW-12A NE-3A 0.2 x 0.2 mm
      BL-1A 0.03 x 0.01 mm
      BL-17A 0.04 x 0.03 mm
    3. Check the attenuator size.
    4. Check the distance between the sample and the cryo nozzle.
    5. Close the GAP after every injection.

  • X-ray intensity is weak.
    Please make sure of the following points, and contact the responsible staff (PHS 2613) if necessary.
    1. Check the value of slit size. Did you set the appropriate value?
      Standard slit size
      BL-5A NW-12A NE-3A 0.2 x 0.2 mm
      BL-1A 0.03 x 0.01 mm
      BL-17A 0.04 x 0.03 mm
    2. Check the attenuator size.


Sample centering

  • The crystal moves while it is being centered.
    Although rarely, it sometimes happens that when mounting onto the goniometer head one crystal kept in liquid nitrogen, some ice get caught between the cryo pin and the goniometer head. The cryo pin slips once the ice is melting. Before centering the crystal, wait for a short time that all the ice melts, or warm the base of cryo pin with your hands to locally melt the ice.

  • I cannot see my loop on the screen.
    If the loop is out of the screen, please make sure of the following points.
    First of all, we recommend to use loops between 16 and 18mm of size.
    1. Click the [Zoom out] button, and check again on the centering screen.
    2. Rotate the loop from a different angle, keeping your eyes on the centering screen while rotating.
    3. Your loop might be located at the very left of the centering screen. Please click on the left edge of centering screen until the tip of loop appears.

  • I cannot adjust the brightness of the crystal light.
    Please exit and restart UGUI.

  • The screen stays dark after switching to the Crystal Centering mode.
    1. Click the [Zoom out] button and check again the screen. Try to change the brightness of the centering screen. The light control bar is located in the middle part of the program window.
      (When you set the centering views as "Zoom in", if the view is located on the cryo pin's cupper part or the base of the cryo pin, the screen appears dark.)
    2. Check that there are no obstructing objects around the goniometer head.
    3. Reboot UGUI.
    Please contact the responsible staff (PHS 2613) if you can not solve this problem.

  • The screen is not updated after you are centering the crystal or rotate it.
    (The screen remains dark after you changed the brightness.)

    On the control tab, please click the [All restart] button. Then, please reboot UGUI. Please contact the responsible staff (PHS 2613) if you can not solve this problem.

  • The crystal does not move after double-click.
    A quick and dirty solution would be to triple-click; the crystal should then move. However, the best solution would be to re-create the configuration file of GNOME. To do so, please follow the instructions below.
    1. Open the terminal, and rename the configuration file.

      [yourID@ugui (yourID)]$ cd
      [yourID@ugui ~]$ mv .gconf .gconf.bak

    2. Logout of the system and login again.
    3. A new .gconf file will be created automatically.

    Please contact the responsible staff (PHS 2613) if this can not solve the problem.


XAFS measurement

  • I want to perform an XAFS measurement with an atom not on the list.
    You need to set the x-ray wavelength manually. To do so, please perform the following steps.
    1. Check the absorption edge of the atom you would like to measure.
      The absorption edge can be checked in the [Anomalous Wizard] option in the Project menu of HKL2000.
    2. Enter a wavelength shorter than the absorption edge on the MCA tab.
      If the crystal contains the metal atom you would like to measure, and if you entered the correct wavelength, the spectrum should contain two peaks. If the spectrum only contains one peak, please enter an even shorter wavelength and start again the measurement.
    3. Set the "Range" value around the peak wavelength on the left side (lower energy side).
    4. Set a range of energy to scan in the [Advanced...] widget on MCA tab.
      Recommended range of energy while scanning:
      Rough scanning absorption edge ± 0.1 A
      Precise scanning absorption edge ± 0.002 A
    5. Start the CHOOCH analysis and get the values of peak and edge wavelengths.

  • After MCA analysis the graph has a sharp edge.


    The attenuator size that was chosen is thiner than what should be selected. Select an attenuator size thicker than the one presently set. The optimum thickness can be selected from the [Advanced...] widget on MCA tab.


Sample exchange robot

  • The robot stopped.
    1. Please check the interlock system for the robot (SafeGuard ON).
      The robot stops when the hutch is opened while the robot is working.
    2. Please use recommended cryo pin.
      We recommend the base CrystalCap Copper Magnetic 18mm and the Mounted Cryoloop sold by Hampton Research Co.
    3. The robot will stop without drying the tongs for a long time.
      Please dry tongs every two to three hours.

  • An error message appears when I added the sample list.
    1. Please make sure that all the required fields (ContainerID, Port, CrystalID, Protein) are written in the CSV file.
    2. Please make sure you are not using an older version of the CSV file. You can download the newest file here.


Diffraction image

  • The Adxv widget is not updated or does not appear on the desktop.
    Please click the "Adxv" menu, and select "Refresh Adxv".

  • I want to see the previous image on Adxv.
    Please click "Adxv" menu, and select "Standalone Adxv". Choose the image file you would like to see.

  • A shadow appears at the same place on each diffraction image (excluding the ice ring).
    The guard slit or the beam stopper might have been shifted from their original position, causing scattering. Please contact the responsible staff (PHS 2613) to fix the problem (it might take up to 1 hour for a complete fix).

  • One part of the previous diffraction image still appears on the latest diffraction image.
    1. Please click "Adxv" menu, and select "Refresh Adxv".
    2. Reboot UGUI.
    Please contact the responsible staff (PHS 2613) if you can not solve this problem.


UV-light Capturing

  • After clicking on the [Capture] button, there is an error message coming that tells me the UV controller is not accessible.


    The most probable reason is the UV controller has not been made accessible. Please contact the responsible staff (PHS 2613). If you want to perform more checks, please refer to the [Before starting centering] chapter and confirm the following points.
    1. UV-LED is installed at the beamline.
    2. UV-LED controller box is switched ON.

    After properly connecting the UV-light controller box, it is necessary to restart the Crystal client, as it should recognize the box during start. Please click the [All restart] button on the control tab of UGUI to restart all the device managers.

  • After clicking on the [Capture] button, there is an error message coming that tells me the snapshot did not work.


    Please check the intensity of the UV-light from the sliding bar in the >Crystal Image<. If the intensity is set to 0 (zero), please try to change this value to a positive value and click the [Capture] button again. If you cannot solve this problem, please contact the responsible staff (PHS 2613).

  • After clicking the [Capture] button, everything looks to be fine, the pictures are taken, but I cannot see the loop nor the crystal inside the loop.
    1. The UV-LED blob is broken.
    2. The UV-LED blob is not focused on the sample position.

    These problems will have to be fixed by the responsible staff (PHS 2613). You can check these problems by directly looking at the UV-LED blob when switched ON, remembering to wear UV-glasses (available in tne experiment hutch).

  • I can see the loop on the picture, but not the crystal. What is wrong?
    If you can still see the loop, it means that either your crystal is not a protein crystal or that somehow the surrounding of the crystal adds too much background (fluorescence not sufficient enough), or that the crystal is just too small to be seen, or even that the protein crystal has some properties that makes the UV-light not useful for visualization purpose.


Devices, Supplies

  • The field of the microscope is dark.
    The field may indeed be set as dark. Check the four knobs that control the filters and the light settings on the right side of the stage. Please then try to brighten the field using the front knob. After use, the bulb is very hot. Please be careful not to burn yourself.

  • The lamp bulb of the microscope has burned out.
    Some spare bulbs are prepared near the working bench. Please use one of them to replace the burned one. After use, the bulb is very hot. Please be careful not to burn yourself.

  • The lamp to light up the crystal on the goniometer head has burned out.
    Some spare bulbs are prepared near the working bench. Please use one of them to replace the burned one. After use, the bulb is very hot. Please be careful not to burn yourself.

  • I dropped something in the Fancybox (the box which contains the beam stopper, Guard slit etc.).
    Please contact the responsible staff (PHS 2613).

  • I want to perform capillary experiments.
    As the cryo temperature settings need to be modified, please ask directly the responsible staff (PHS 2613) for further assistance.

  • The liquid nitrogen tank near the beamline is empty.
    To replenish the tank please use the pumping liquid nitrogen room behind BL-7A (PF) or in the pumping liquid nitrogen room (PF-AR Northwest lab 1F).


Analysis PCs, User PCs

  • After logging in Linux or windows PC, I cannot do anything because of a pending certification.
    Wait a few minutes for the registry to update. Please contact the responsible staff (PHS 2613) if you can not login even after 5 minutes.

  • The Windows PC cannot recognize my USB HDD.
    1. The Windows PC cannot recognize directly USB bus-powered 2.5"HDD because it does not provide enough power supply capacity. Please use an external power supply.
    2. Compatibility issues between Windows PC and USB HDDs do happen from times to times. Please contact the responsible staff (PHS 2613) if none of the Windows PC can recognize your USB HDD.

  • I cannot access the file servers from the linux PC.
    Each beamline file server is mounted on the linux PC by autofs. The file servers being mounted automatically, you can access the file server directories using the linux "cd" command.
    [yourID@pc3.bl5 ~]$ cd /gpfs/data/(yourID)


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