Table of Contents

On-site experiments

  • Please make sure that you complete all required training on-line before arriving at SSRL to expedite check-in and badging. If you have a valid user badge, you can proceed straight to SSRL.

  • If you shipped frozen samples, the dewar should be at the beamline. If it is not present, check the dewar receiving area downstairs in building 120.

  • Incubators with adjustable temperature are available at each beamline to store samples; there are also cold rooms (4 C) in the sample preparation lab. You can store pre-frozen samples in the storage dewar provided at the beamline.

    Note: The sample storage facilities at the beamline are meant to be used only for the duration of the experiment; if you require longer term storage facilities please contact the user support staff. Samples left at the beamlines may be accidentally destroyed or disposed of.

  • When you arrive at the beamline call your assigned support scientist. The name and contact information will be written on the beamline white board. After you have contacted the support person, you may call the duty operator: Either call the extension number 4040 or dial 161 to access the intercom system and ask the duty operator to call the beamline extension number (written on the beamline phone). Repeat the message twice.

  • When you arrive, the hutch door will usually be open. Do not enter the hutch if the door is closed without first contacting support staff.

  • Log in to one of the terminals at the beamline using your SSRL Unix account and password. If the terminal is locked by another user, you can switch to your account or log out the previous one by simultaneously typing the keys ``Ctrl-Shift-Backspace''. You may not be able to start Blu-Ice until staff enables you to use the beamline.

    Note: The terminals at the beamline are used primarily to run the beamline control software. Although you have access to the data disks where your images are stored, you will only be able to run data processing software by logging in to the servers dedicated to that purpose from the terminal. Read about data processing.

  • Contact your support person if you experience difficulties logging in. For information on the beamline computer environment consult the document at

  • Read the beamline policy documents, paying particular attention to the safety procedures that apply to your experiment.

  • You can find additional documentation about the available user facilities at:

On-site safety protocols

As per beamline policy, it is your responsibility to know and follow all safety protocols applicable to your experiment, samples and equipment you bring to the SSRL. Please note the SSRL has policies concerning the use and disposal of propane and ethane,liquid nitrogen, heavy metals and compressed gases. Please follow all the applicable rules.

Safety in the experimental hutch

To minimize the possibility of accidents while working inside the hutch, there are restrictions on the motors that can be moved from certain locations.

  • When the hutch door is open, you must use the computer monitor in the hutch to move the detector or other motors.

  • Once the hutch is searched and locked, motors can be moved from the consoles outside the hutch.

  • Motor movements can be immediately stopped by pressing any of the large yellow emergency buttons. The motor reset button must be pushed to reactivate the motors.

    Figure 1: Emergency buttons
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    Figure 2: Motor reset button, located in the hutch near the door
    Image reset-button

    Note: If the Blu-Ice status window displays the messages ''MOTOR STOP BUTTON LATCHED'', an emergency stop has been activated. Press the green reset button to re-enable motor moves.

The hutches are equipped with oxygen deficiency sensors. An alarm will go off if the oxygen content in the hutch falls below 19.5%. This may happen while the nitrogen dewar is being refilled. Do not enter the hutch or open the door if the oxygen alarm is sounding!. If the duty operator arrives to investigate the oxygen alarm, explain that the alarm will be automatically reset once the dewar has been filled. If the alarm does not subside within a few minutes after the nitrogen filling is finished, call support staff.

Mounting samples

The following instructions describe how to mount samples manually. For automated sample mounting, please refer to the SAM robot use instructions.

Making room to safely mount samples

  • An X-terminal monitor is available inside the hutch. You can log in at this terminal and start Blu-Ice (see the Blu-Ice documentation). To be able to mount samples comfortably, the detector should be moved to about 400-500 mm and the beamstop to 40 mm.

  • On BL12-2, make sure that you retract the backlight screen for the On-Axis camera (from the Sample Video interface in Blu-Ice)

Mounting samples in the cryostream.

  • The 4LD filling dewar can be used for dispensing liquid nitrogen. It can be filled up at a filling station. The main filling station is located in building 120 near beamline 9; other filling dewars are available in different locations of the experimental floor.

    Figure 3: Dewars available at the beamline. The two white Nalgene dewars can be used for short term cassette, pucks or samples storage and transport; the 4LD dewar can be used for dispensing liquid nitrogen.

  • Cryo-tools are available on the tool board.

  • A microscope is available for mounting crystals and flash-cooling directly in the cold stream. The microscope can be placed on a small table on top of the dewar inside the hutch. The table (usually located inside the experiment hutch) can be installed as shown below. Use the plastic step stored inside the experiment hutch to reach the microscope table.

    Figure 4: Beamline microscope

    Figure 5: Mounting the microscope table in the experiment hutch
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  • Roughly align the goniometer for your samples by mounting an empty pin of the same length on the goniometer head and centering it as described in the Blu-Ice documentation.

  • Verify that you can easily insert the tongs to mount or remove the sample pin.

  • Check that the centered loop is in the center of the cryostream. If it is not, contact staff.

  • Check that the temperature of the cryo-cooler, displayed on the cryo-controller, is about 100 K. Occasionally the temperature may be a few degrees higher. This means that the unit will soon need maintenance, but it should not affect the sample. Do not try to adjust the flow rates as this can cause icing.

    Figure 6: Cryo-controller

  • If the crystal has snow flakes, it can be cleaned by pouring a small amount of liquid nitrogen (use a cryo-vial) over it. Protect the sample camera by covering it with a clean light object (for example, the light blue foam covers for the small dewars).

    Figure 7: The sample camera

Mounting crystals at room temperature

The Oxford cryostream can be used to collect data at temperatures other than 100 K. The temperature can be changed at the cryostream controller outside the hutch ( you need to ask the support staff to enable manual control of the cryojet before being able to do this):

  • On the left hand side of the controller, under the temperature display, there is a black button labeled "set". Pressing this button will display the set temperature. Pressing the "raise" red button to the right of the display while pressing the "set" button will increase the set temperature.

  • Once the set temperature has reached the desired value, release the buttons. Monitor the temperature display to find out when the system reaches the new set temperature.

  • In some cases you might have to adjust the translation of the cold stream nozzle to accommodate the capillary or plastic sleeve. Please contact staff in this case.

Sample illumination

In the case that the overhead lamp does not provide adequate illumination, the side light source can be used to better view the sample. Use the Blu-Ice interface to turn the light on and adjust the intensity of the light until you obtain a clear view of the sample. When using automated centering of the loop, the software will temporarily turn off the side light source. The software will also turn off the light if the software has been idle for some time.

On BL12-2, make sure to insert the backlight screen to be able to see small samples using the on-axis camera.

On some beamlines, a Visex microscope is available to detect the crystal. The alternative, is to use low dose X-ray rastering to find the sample.

Checking out

  • Make sure that all data are backed up or transfered to your home computer. Read the instructions for using the available backup facilities.

  • Return all the items you have borrowed to the toolboard; if the small open dewars still contain liquid nitrogen you may leave them to empty and dry off on the table (as far away from the edge as possible).

  • Throw away all garbage. Recycle white paper and printouts in the blue recycling bins near the beamline printer. Put used sharps and glass in the sharps boxes provided. Disposal of hazardous material should be arranged with the safety officer (Matt Padilla, ext. 3861).

  • Log in to the User Research Administration Database and fill out the end of run summary. Be as specific as possible when reporting problems at the beamline. For problems requiring prompt attention, you can also send an e-mail to your support staff contact person.

  • If you finish, or know in advance that you will finish your experiment more than two hours early, call your contact person on the beamline phone or, outside normal working hours, send them an e-mail.

  • Users may leave an experiment running at the end of their run, as long as it finishes before 11 am. Leave a note or e-mail support staff and leave a phone number where you can be reached. Experiments running unattended after 11 am may be stopped, unless previously arranged with support staff.