Table of Contents

Remote experiments

Complete protein crystallography experiments can be carried out from remote locations using remote access applications. Users wishing to collect data remotely should indicate this on their beamtime request form.

Remote users have access to all experimental facilities, except when they require on-site preparation.

New remote users

New remote users who have never collected data at SSRL before should get training on the beamline control software and other users facility, unless they can get assistance or instructions from other experienced members of the group. Hands on training can be done at SSRL. Training sessions can be arranged on a need to basis by contacting user administration.

New users who are unable to get hands-on training session at SSRL or at their home institution must schedule a remote training session a few weeks or as soon as possible in advance of their beamtime. It is advised to review this guide, and, where relevant, the video tutorials.

IMPORTANT: new users must obtain an SSRL-PX Unix account by filling out a request form and submitting it to SSRL-PX computing staff.

Preparing a remote experiment

  • Determine the beamline contact person for your experiment by consulting the support staff schedule. Staff contact information is available by clicking on the name of the support person in the Support Staff list or by using the support staff web page. Contact the assigned support person before the experiment to provide your contact information during the experiment (preferably a cell phone).

  • Download and install the free NX client software as explained in the remote Unix desktop documentation. Verify that the NX client can be used to successfully access the SMB computers before the experiment. The user passwords at SSRL expire every six months. If the authentication fails, contact staff so that your password can be reset.

    Frequent users should set up e-mail notifications and change their password before it expires.

    Important: Please check the NoMachine site periodically (e.g., every few months) for updated versions of the NX client.

  • Infrequent remote users are encouraged to arrange a practice run with the beamline simulator in advance of their scheduled beam time.

  • Carefully read the instructions for preparing and shipping samples to SSRL. Pay special attention to the following:

    • Only use sample pins that are compatible with the SSRL robot (SAM).
    • Know the safety practices at SSRL for handling liquid nitrogen.
    • Replace the liquid nitrogen in the loading dewar as soon as any ice forms.

  • Download an Excel spreadsheet template for the SSRL cassette or the Unipuck from the Sample Database (New Spreadsheet tab). Fill out a separate spreadsheet for each cassette or adapter (four pucks); see the SAM documentation. Enter the cassette or puck pin number (engraved in the top of the container) in the Excel file ContainerID column for proper identification by the user support staff.

  • Once the spreadsheet is filled in, upload it into the Sample database; for help uploading the spreadsheet see the SAM documentation. When your beam time begins the excel spreadsheet information can be be assigned to a particular beamline and cassette location inside the dewar; see the SAM documentation.

  • Dewars should arrive at SSRL 1 working day in advance of beam time; e.g., if the beamtime starts on Monday, the dewar should be shipped so that it arrives on Friday the previous week. Dewars are not delivered to SLAC during the weekend or on holidays!.

    Use the Shipping Dewars to SSRL form. Make sure that you specify that you are doing a remote experiment by clicking on the corresponding check box and fill up the requested information for return of the dewar.

  • After submitting this form, a PDF file will be created that includes your shipping labels and return shipping forms. Save this file, print these forms, attach the shipping labels to each dewar container and insert the return shipping forms inside each container.

    Important: Staff will not be able to send your dewar back unless you send the return form!

Remote data collection

  • Remote experiments are scheduled to start at the normal time (12 PM). However, support staff may contact you to start earlier in the day. Please review the experiment policies that apply to remote access beamtime.

  • Support staff will mount your cassette(s), search and lock the experimental hutch, probe cassettes for jammed pins and enable access to Blu-Ice.

  • Support staff will then contact you and inform you of the following:

    • Cassette locations (left, middle or right position) in the dewar; you can then assign the excel spreadsheet(s) to the correct location in the dewar from the Sample Database or Blu-Ice as described in the SAM system documentation.
    • Pin locations that might cause a port jam (when a real port jam is detected during the probing, the corresponding cassette port is automatically disabled).
    • When you can start your experiment.

  • Data collection and data processing are carried out in exactly the same way as on-site; see the data collection and processing section.

  • The beamline can be monitored using the standard video feeds in Blu-Ice.

  • When you finish your experiment, contact the beamline support staff (use e-mail between 9 pm and 9 am); once staff have been notified, they will put your cassette(s) back into the shipping dewar, attach the return form (supplied by you) and arrange for its shipment. Note that your dewar cannot be shipped unless you provide a return shipping form.

  • Log in to the User Research Administration Database and fill out the end of run summary.

  • If you wish to store your dewar at SSRL between experiments, make sure that you inform the user support person. It is important that you also notify the support person for your next experiment, who may not be the same one as for your current experiment, even if using the same beamline. Please check the Support Schedule.

    Note: At the moment users' sample containers may only be stored in the dewar they were shipped, with accompanying paperwork. We are unable to return the dewar and provide our own storage for the cassette or Uni-Puck.

Remote experiment support

For questions or problems that develop during the experiment, please consult the online documentation or the FAQ before contacting support staff. Use the beamline cell phones or weekend phone to reach staff during call hours (see below), e-mail at any other time.

Information about the beam status is available through the SSRL Web site. You can also call the number (650) 926-4040 to contact the Duty Operator on call.

Support staff will be on call from 9AM to 9PM. If the system should stop for some reason after 9PM, please send an e-mail to the assigned user support staff and the problem will be addressed in the morning. If beam time should be lost, additional time may be assigned at the end of the normally scheduled beam time (8AM-12PM).

Currently the following are not supported:

  • Exchanging cassettes or Unipucks once the beamtime has started. However, staff will exchange the sample containers if the users receive more than one day (three shifts) of beamtime. In this case case the exchange will usually take place between 11:00 and 15:00 Pacific time or other convenient time for staff.
    The robot dewar holds up to three cassettes or Unipuck adaptors (holding 4 pucks each), therefore up to three cassettes or 12 Unipucks per day of beamtime are allowed. Additional containers may be stored at SSRL for use on future beamtime.

  • Manual sample mounting; Automated sample mounting with the SAM robot is required for remote access.

  • The use of a Kappa offset (currently incompatible with automated sample mounting).

  • Derivatizing samples with the SSRL Xe/Kr pressure cell.

  • Data backups: see options available in the computing resources documentation.

  • GL dependent graphics programs such as COOT are supported by the NX client, but the graphics applications may be slow.