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Macromolecular Crystallography (MX) Fragment Screening - XChem Crystallisation Facilities Cryo-Electron Microscopy at eBIC for Industry Protein SAXS (bioSAXS) Cryo-soft X-ray tomography (cryo-SXT)

User Guide for cryo Soft X-ray Tomography (cryo-SXT)

Please find below a guide to help you understand the steps required to conduct a cryo-SXT experiment at Diamond.

New users need to contact the Diamond User Office to request access to the User Administration System (UAS). After registration, you will be issued with a Fed ID and password for access to all Diamond IT systems.

Everyone who wants access to Diamond, on-site or remotely, needs to be registered in the User Administration System (UAS). If you have used Diamond previously but have since changed your affiliation (place of work), you will need to register again.

PLEASE NOTE! Do not register in the UAS yourself. Registration of industrial users is handled by the User Office.

Please email the Diamond User Office (useroffice@diamond.ac.uk) to register as a new user. You will need to provide the following details in the email:

  • Title
  • Family Name
  • Given Name
  • Gender
  • Date of birth (dd/mm/yyyy)
  • Organisation
  • Address
  • Telephone
  • E-mail

Following registration, you will be issued with a Fed ID and password. Make sure you keep a note of these, as you will need them to access all IT systems at Diamond.

In order to perform data collection and access collected data, registered users need to be added as investigators to a new proposal in the UAS. Experimental risk assessments (ERAs) for samples need to be submitted and validated before shipping them to Diamond.

Log in to the UAS (http://uas.diamond.ac.uk) with your Fed ID and password. If you have signed a new contract with Diamond or have recently renewed your existing contract, you will find your new proposal number in the UAS.

A Principal Investigator (PI) will be added to the proposal when it is created. The PI is responsible for adding additional investigators to the proposal in the UAS. Go to the proposal “Investigators” tab and click “Add investigator”. An investigator whose role is defined as Alternate Contact can also edit the proposal and add investigators. Please see the UAS for a complete list of investigator roles. Further information

You will need to prepare and submit an Experimental Risk Assessment (ERA) for each sample and experimental method used at Diamond. This can be done in the “ERA” section of your proposal in the UAS. It is the responsibility of the PI to ensure that each ERA is fully and accurately completed at least 2-3 weeks prior to the planned experiment, giving enough time for it to be validated by Diamond’s Safety Health and Environment (SHE) group before shipping samples to Diamond. Further information

If you plan to continue working on samples with ERAs that have already been submitted and validated within a previous proposal, you can copy these into your new proposal. To do this, go to “ERA/Samples” and select “Copy Samples from a previous Proposal”. You can also copy the Experimental Methods from a previous proposal - for this, go to “ERA/Experimental Methods” and select “Copy Experimental Methods from a previous Proposal”.

When an experimental session (visit) has been created, investigators and validated sample ERAs need to be added to the session in the UAS.

Log in to the UAS (http://uas.diamond.ac.uk) using your Fed ID and password. Once a new session (visit) has been scheduled you can access it under the “Sessions” tab in your current proposal.

The Principal Investigator or Alternate Contact needs to add all investigators that require access to the session. To do this, go to the session, and under the “Investigators” tab click “Add investigator”. Select an appropriate team role for the added investigator:

  • Investigators with “leader” and “member” roles refer to those people taking an active part in the experiment, either on-site or remotely. Make sure to tick the “remote” box for remote access.
  • Investigators with “data access only” roles refer to those people not taking an active part in the experiment but who will have access to the data collected.
  • For mail-in sessions, where data is collected for you, please add your Industrial Liaison Contact as a member, along with members of your organisation assigned with “data access only” roles.

When all investigators have been added, click “Submit Investigators”.

For on-site visits, you can only submit investigators when all investigators listed as on-site users have passed their safety tests, available under the “Home” tab in UAS.

Your already validated sample and experimental method ERAs now need to be added to the session. To do this, go to the session “ERA” tab and select “Samples” or “Experimental methods”. The relevant ERAs can be added from your proposal using the “Add from proposal” or “Add all from proposal” buttons. You also need to indicate whether you require lab access for your session. This is done by selecting an option from the drop-down menu under “Lab access”. If you have specific needs for lab access, please contact the  Industrial Liaison Contact. When all relevant ERAs have been added you should click “Submit session ERA”.

Preparing your samples ahead of your experiment at Diamond

Once you have completed the relevant steps on UAS, please speak to your Industrial Liaison contact at Diamond to ensure your samples are shipped and prepared in the optimal way for your experiment.

Your Diamond contact will advise you on sample preparation and shipping requirements for your experiment so please liaise with them prior to arranging a shipment. Please note that a validated experimental risk assessment (ERA) must be in place before shipping samples to Diamond.

Arranging shipment with your courier ahead of your experiment

Once your samples have been prepared, you can arrange shipment with your courier. The exact procedures for shipment and document requirements depend on your samples, courier, and country of origin. Please include a printed copy of the return airway bill in the shipment case.

Shipping Address:

Diamond Light Source
Goods Handling
Synchrotron Zone 8
Harwell Science & Innovation Campus
Didcot
OX11 0DE

Specify Diamond contact details as: goodshandling@diamond.ac.uk and +44 1235 395381.

Diamond Goods Handling is open Monday to Thursday 8am - 4pm, and Friday 8am - 3pm, to receive shipments.

Please arrange for all samples shipped on dry ice to arrive at the start of the week before your experiment (i.e. a Monday or Tuesday), to avoid thawing or sample damage if shipping delays occur. Please note that we cannot accept shipments over a weekend.

For interactive visits where users will be collecting data themselves or with the industrial liaison contact on-site users will collect data using Diamonds GDA (Generic Data Acquisition) software.

 Prior to a scheduled visit, you should receive an email notification with contact information for your local contact at Diamond. The local contact is your point of contact regarding any questions you may have before or after your visit, or if you need support during your visit. The local contact will also provide training about how to operate the beamline and run your experiment.  If you need support during a visit scheduled outside our office hours (weekdays 9am – 5pm) you should contact the Experimental Hall Coordinator (EHC) on tel. +44 (0)1235 778787.

To ensure long-term data storage, it is your responsibility to back up experimental data after your session. Your experimental data will be stored in the Diamond file system for a limited amount of time. It is therefore important that you back up your data after your session. The recommended way to back up data is by remote download from the Diamond file system. Further information

PLEASE NOTE! Data collected under IN type of proposal will be deleted 2 weeks after collection.

In special circumstances, when a remote backup is not possible (e.g. due to limitations in remote access to Diamond file systems), you can request to back up your data on a hard drive. Diamond does not recommend the use of hard drives for this purpose, as we do not consider them to provide an appropriate level of security for your data. If you still need to use this backup option, please inform the Industrial Liaison Contact in advance and provide a hard drive with sufficient free space in your shipment.

After your session, you will need to take your samples with you or arrange for their return shipment with your courier.

It is the customer's responsibility for the removal of any samples and equipment at the end of the scheduled beamtime. If these are not removed personally on completion of the experiment, users can arrange return shipping using a courier, at their own cost, If the samples are not returned within 30 days, they will be disposed of or returned to the customer without further notice.

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