Please find below a guide to help you understand the steps required to conduct an MX experiment at Diamond.
In order to use Diamond for experiments, industrial clients first need to have a contract in place. Please contact the Industrial Liaison Office at industry@diamond.ac.uk and let us know which services you are interested in. Once the contract is in place, there are several mandatory steps to complete before experiments can be scheduled.
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 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:
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.
New users who have registered with the User Office and returning users with new contracts need to complete these mandatory steps before they can request to schedule experiments 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 (the samples are defined in UAS as proteins or DNA that are crystallised; each sample ERA can represent many different single crystals) 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”.
Lab contact information and registration of dewars and containers in ISPyB needs to be done before you can use these for shipments to Diamond
Diamond uses the Information System for Protein Crystallography Beamlines (ISPyB) and its web interface SynchWeb to manage sample information, experimental data, and shipments. You can log in to ISPyB (https://ispyb.diamond.ac.uk/) using your Fed ID and password.
If you have signed a new contract with Diamond or have recently renewed your existing contract and been issued with a new proposal number, you will need to add your lab contact information into ISPyB. To add a new lab contact, go to “Lab Contacts” in the proposal drop-down menu, and click “Add Home Lab Contacts”. Lab contacts can also be migrated from an old proposal using the “Migrate” page, also accessed from the proposal drop-down menu. Further information
The next step is to register your dewars and containers (pucks) to your proposal. This needs to be done so you can add these to a shipment in ISPyB. Please contact the Industrial Liaison MX Team to register new dewars and containers, or to migrate existing ones from an old proposal. You will need to provide a list of container codes (as printed on the container) and dewar facility codes (printed on the Diamond barcode sticker attached to your dewar). If your dewar does not have a Diamond barcode sticker you will need to request one from the Industrial Liaison MX Team. Further information
PLEASE NOTE! Registration of dewars and containers is essential for our internal sample tracking. You cannot send dewars or containers to Diamond if they are not registered in ISPyB.
You can now contact the Industrial Liaison MX Team to schedule an experiment at Diamond. Please visit the next section of this guide to view further details of our access modes.
Before and after your experiment at Diamond there are several mandatory steps to complete. These steps need to be completed every time you have an experiment scheduled at Diamond.
You can now contact the Industrial Liaison MX Team regarding your experiment at Diamond. The available modes of access for MX data collection are:
Unattended Data Collection (UDC):
Provides a well-established, fast, and flexible method for automating data collection.
Logistics:
You do not need to reserve beamtime. Once your samples are ready and their ERA is validated, prepare and send your UDC shipment. If you have a large shipment (two or more dewars), please let us know in advance. Data are normally collected within a week of arrival, often sooner.
For details about user beamtime, please see the Operations calendar at www.diamond.ac.uk.
To note:
The first week of each run is reserved for Start Up and has no user beamtime. Samples arriving that week will be collected as soon as possible in the following week.
Allows you to collect your data directly via an interactive remote connection to the beamline.
You send us the sample(s), and our experienced staff will collect the data for you and provide the data and experimental details for your analysis.
Prepare and mount samples using Diamond compatible pins and containers (pucks)
Samples sent for cryo experiments at Diamond must be mounted on SPINE standard pins placed in Unipucks and shipped in a Shelved Puck Shipping Cane, or a supported crystallisation plate type for in-situ experiments. This is to ensure compatibility with the sample changers on Diamond MX beamlines. Further information
PLEASE NOTE! Samples in pins, pucks or crystallisation plates that do not conform to our standards will not be accepted for data collection at Diamond.
If you have specific requirements for sample holders or shipping containers, please discuss these with the Industrial Liaison MX Team before shipping.
All shipment and sample information needs to be added in ISPyB before
shipping your samples to Diamond.
Diamond uses the Information System for Protein Crystallography Beamlines (ISPyB) and its web interface SynchWeb to manage sample information, experimental data, and shipments. Log in to ISPyB (https://ispyb.diamond.ac.uk/) using your Fed ID and password.
Create a new shipment and complete the necessary shipment details. Go to “Shipments” in the proposal drop-down menu and click “Add Shipment”. On the new shipment page, you will need to name the shipment, select the facility dewar code of the dewar you are sending (if you do not see your dewar facility code in the drop-down menu, please contact the Industrial Liaison MX Team), and tick the relevant box in the “First experiment / Scheduling” field. Further information
Depending on your mode of access, select the relevant option in the Scheduling table:
PLEASE NOTE! A shipment can only contain samples for either a remote, mail-in or UDC visit. We cannot currently accept samples for different access modes within the same shipment.
You can now add your containers (pucks), with sample information, to your shipment. To add a container, go to your new shipment page and click "Add Container”. On the “Add New Container” page you will need to specify the container type and select a “Registered Container” from the drop-down menu. Please make sure that the “Container Name” matches the registered container code exactly, as differing container names could cause issues with the automatic assignment in the beamline sample changer. If you do not see your container in the drop-down menu, please contact the Industrial Liaison Team. Further information.
An alternative to manually creating shipments and adding sample information is to assemble all the information in a csv file and use a Diamond script to upload the data to ISPyB. This is particularly useful if you are shipping a lot of samples and want to save time compared to manually adding them in ISPyB. It could also be used to integrate with your laboratory information management system. Further information
Print your Diamond shipment labels, attach these to your dewar and shipping container, and arrange the shipment with your courier.
PLEASE NOTE! All shipment and sample information must be added into ISPyB before shipping samples to Diamond. This is to ensure that samples without validated ERAs are not delivered to Diamond, since handling these would be in breach of our safety protocols. Dewars delivered to Diamond with no sample information in ISPyB will not be accepted.
When your shipment has been created, and all sample information has been added in ISPyB, you must then print the Diamond shipping labels by clicking “Print Shipment Labels” at the top of the new shipment page in ISPyB. Please follow the instructions on the first page of the shipment labels for how to attach them to the dewar and shipment case. The Diamond shipping labels are essential for our internal sample tracking system and if not correctly attached will result in shipment and data collection delays.
Please include a printed copy of the return airway bill in the shipment case.
You can now arrange the shipment with your courier. The exact procedures for shipment and document requirements depend on your courier and country of origin.
Contact details:
goodshandling@diamond.ac.uk and +44 1235 395381.
Shipping Address:
Goods Handling, Synchrotron Zone 8
Diamond Light Source
Harwell Science & Innovation Campus
Didcot
OX11 0DE
+44 (0)1235 395381
Diamond Goods Handling is open Monday to Thursday 8am - 4pm, and Friday 8am - 3pm, to receive shipments.
PLEASE NOTE! Samples must be shipped to site by a courier service. We cannot accept samples delivered by users in person.
Here are some additional instructions regarding shipments. These are general advice and should be confirmed with your courier.
The carriage of Dewars is likely subject to dangerous good provisions. Typically, road and air transport require these declarations:
• Not restricted ADR A346 as per packing instruction 203.
• Dry shipper - not restricted as per IATA special provision A152.
Shipments from abroad should be arranged under Delivered Duty Paid Incoterms, subject to VAT and duty tax. Please include the printed customs invoice for the return shipment in the shipment case.
EORI: GB287461957003
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.
PLEASE NOTE! This is only required for remote, on-site and mail-in visits. Unattended data collection (UDC) visits are created, and session ERAs submitted automatically, when the samples are loaded on the beamline.
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:
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 MX Team. When all relevant ERAs have been added you should click “Submit session ERA”.
For interactive visits where users will be collecting data themselves, remote users need to connect to the beamline workstation using the software NoMachine. Both remote and on-site users will collect data using Diamonds GDA (Generic Data Acquisition) software. Collected data and results from our autoprocessing pipelines can be monitored in SynchWeb/ISPyB.
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. 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.
Remote users need to download and set up the latest version of the software “NoMachine” in order to connect to Diamond and the MX beamline workstations. To connect, please use “nx.diamond.ac.uk, port 4000” and your FedID and password. This remote connection can also be used to manually analyse and process data after your visit. Further information
PLEASE NOTE:
The remote connection must be set up and tested in advance of your scheduled visit to allow enough time to resolve any connection issues. For testing, please connect using the “Automatically select a node” option.
On the day of your scheduled visit, you can access the beamline workstation shortly before your allocated start time (remember: visit times are in UK time). If you have been added as a remote investigator for the session (see the previous section Prepare your experimental session in the UAS), the two workstations for your assigned beamline will be available to you.
Experiments at Diamond are controlled through the software “GDA” (Generic Data Acquisition). Once you have connected to the beamline workstation, start GDA through the icon in the system tray (top right screen corner), or through the link in the “[beamline]_launchers” folder on the Desktop. You can also open a terminal window and use the command “gdaclient” to start GDA.
PLEASE NOTE! You need to familiarise yourself with GDA and data collection procedures at Diamond before your visit. Please read the GDA manual and contact the Industrial Liaison MX team to schedule a test visit (a training session for new and returning users) if needed. This is a free‑of‑charge service during which users can test their remote connection. We then spend about one hour guiding the user through our data acquisition software (GDA). The visit will be arranged during the shutdown period or during a machine day.
We recommend that you monitor your data collections, the incoming results from our autoprocessing pipelines, and the beamline webcams in SynchWeb/ISPyB. This should be done in a local browser, and not on the remote beamline workstation, to reduce the data transfer load, which might slow down your remote connection. Log in to ISPyB (https://ispyb.diamond.ac.uk/) using your Fed ID and password. Go to “Visits” in the proposal drop-down menu and select your current visit. Webcams can be viewed by clicking the “[Beamline] Webcams & Beamline Status” banner on the top of the page. Further information.
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 need to use this backup option, please contact the Industrial Liaison MX Team in advance to arrange this.
After your session, you will need to (i) arrange for the return shipment of your samples with your courier and (ii) submit a despatch form to Diamond Goods Handling.
(i) After your session, the lab contact listed in ISPyB receives an automated email notification that dewar is ready for despatch, and you can then arrange the return shipment of samples with your courier.
(ii) When the return shipment pick‑up has been scheduled, you will also need to submit a Dewar despatch form. This form notifies Diamond Goods Handling to prepare your dewar for despatch. The despatch form can be accessed through the shipment page in ISPyB or through a link in the email notification. Further information
PLEASE NOTE! Do not arrange the return shipment or submit the despatch form before you have been notified that your dewar is ready for despatch.
If your courier is either Fedex or DHL, Diamond Goods Handling can schedule the return shipment on your behalf. You will still need to submit the despatch form after you get notified that dewar is ready for despatch. In the form, you will need to indicate “please arrange the dewar return with my courier” in the comments field and provide your courier account number.
Diamond Goods Handling is open to despatch shipments Monday to Thursday 8am - 4pm and Friday 8am- 3pm.
