User Guide

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 directly (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. Once you have been issued a Fed ID and password you will have to set up and enable your UAS profile before you can be added to any experiments.

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. Initially a member of the eBIC for Industry team will be the PI, this will be handed over to you once you are comfortable with the system. 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 (protein/RNA/DNA/chemical compounds/drugs/inhibitors/ligands ...) 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 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. For EM experiments we use this system to track the shipment and location of Dewars containing pre prepared samples on grids.

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 to your proposal. This needs to be done so you can add these to a shipment in ISPyB. Please contact the eBIC for Industry team to register new dewars, or to migrate existing ones from an old proposal. You will need to provide a list of 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 eBIC for Industry. Team. Further information

PLEASE NOTE! Registration of dewars is essential for our internal sample tracking. You cannot send dewars to Diamond if they are not registered in ISPyB.

You can now contact the eBIC for Industryi Team to schedule an experiment at Diamond. Please visit our web pages regarding access modes and how to request beamtime for further detail.

Prepare samples using standard cryo EM grids, clipping can be performed
at the beginning of your session.

PLEASE NOTE! If your grids are unclipped, you will need to let your local contact know in advance of the session.

If you will be shipping your grids in something other than a standard puck, please discuss the alternative container with the eBIC for Industry team before shipping.

All  samples must be validated in the UAS and all shipment information needs to be added in ISPyB beforeshipping your samples to Diamond.

Diamond uses the Information System for Protein Crystallography Beamlines (ISPyB) and its web interface SynchWeb to manage Dewar 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 eBIC for Industry Team, and tick the relevant box in the “First experiment / Scheduling” field. Further information

•  “Responsive Remote / Mail-in” and “Automated / Imager” options are not relevant for cryo-EM experiments.

Print your Diamond shipment labels, attach these to your dewar and shipping container, and arrange the shipment with your courier.
 
PLEASE NOTE! All shipment information must be added into ISPyB before shipping samples to Diamond and samples must be validated in the UAS. 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. 
 
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.
 
Shipping Address:
Diamond Light Source Ltd
DLS Goods Handling, Zone 8
Synchrotron Stores
Harwell Science and Innovation Campus
Didcot
Oxfordshire
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 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.
 

When an experimental session (visit) has been created, investigators and validated sample ERAs need to be added to the session and Submit 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.
 
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), and have up-to-date contact details.
 
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 require lab access please get in touch with the eBIC4i team to obtain instructions for filling in the lab form. 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 EPU software. Collected data and results from our autoprocessing pipelines can be monitored inebic-pato.
 
Prior to a scheduled visit, you should receive an email notification from UserOffice 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.

You will also receive a 'Loading Template' prior to your scheduled session. This is used to specify the locations of your sample grids to postitions within the microscope autoloader. A maximum of 11 grids can be loaded at a time. If you are intending to collect data, please ensure you have designated one autoloader positon as empty for a carbon grid. This carbon grid is used for alignments and will be provided if you haven't shipped any sample grids with a carbon film. This is not required for a screening session.
 
Remote users need to download and set up the latest version of the software “NoMachine” in order to connect to Diamond and the microscope workstations. In order to connect to the microscope, please use “nx-cloud.diamond.ac.uk, port 4000” and your FedID@fed.cclrc.ac.uk and password. To manually analyse and process data during and after your visit please use “nx.diamond.ac.uk, port 4000” and your FedID and password. Further information
 
PLEASE NOTE! The remote connection should be set up and tested before the scheduled visit to leave enough time to fix any connection issues.
 
You can connect to the microscope remote computer shortly before your scheduled visit is about to start (please remember the visit start time will be in UK time). If you have been added as a remote investigator to the session (see previous section Prepare your experimental session in the UAS) the remote workstation for the microscope you are scheduled on should be available for you If you want to access your home directory to manually analyse and process data already collected, connect to nx.diamond.ac.uk and use the “Automatically select a node” option.

Once connected to the microscope remote computer you should use TeamViewer to connect to the microscope. The ID is TEM, please get in touch with your local contact for the password. 

For remote users the display quality can be improved with the following steps. Once connected to the beamline through no-machine your computer cursor to just below the X sign at the top right corner of the no-machine window. It will show a small fold with a grey area, click on the grey area. Select display icon > change settings > and move the quality cursor to maximum. Also, please select the ‘Disable client side image post-procesing’ on the same page in the ‘Options’ section. Finally, if you are connecting for a laptop we recommend using viewport mode (display icon > Enable viewport mode). 
 
PLEASE NOTE! You need to familiarise yourself with EPU and data collection procedures at Diamond before your visit. Please contact eBIC4i team if you require training as a new or returning user. 
 
We recommend that you monitor your data collections, the incoming results from our autoprocessing pipelines if running,  in ebic-pato. 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 ebic-pato (https://ebic-pato.diamond.ac.uk/)using your Fed ID and password. 

For data collection session, the session LC starts the transfer of raw moives to the session folder in the Diamond file system soon after your start your data collection. Please inform your LC after startign the EPU data collection session. The data transfer script moves raw data from microscope detector to diamond network file system so that the data is available for copying to your site and for starting data (pre-)processing immediately at your end or if you want to initiate an autoprocessing job in ebic-PATO. 

Finishing your experimental session

Please send your unloading details of grids loaded for the session an hour before the session finishes. Please remember to sign-out from Diamond remote workstations you have logged-in during the session.

At the end of screening session, all acquired data are transferred to the session processing folder in the diamond file system by the session LC.

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 theeBIC4i Team in advance and provide a hard drive with sufficiently free space in your shipment. The hard drive must be clearly labelled and registered as an item in your shipment in ISPyB.

After your session, you will need to arrange for the return shipment of your samples with your courier and submit a despatch form to Diamond Goods Handling.
 
When your experiment is finished, and your  local contact has confirmed the microscope has been unloaded you can arrange the return shipment of samples with your courier. When the shipment pick-up has been scheduled, you will also need to submit a Dewar despatch form  to inform Diamond Goods Handling when they should prepare your dewar for despatch. A mininum of a day/24hrs required for Diamond Goods Handling to keep the dewar ready at the stores for pick-up by the courier . The despatch form can be accessed through the shipment page in ISPyB. Further information
 
PLEASE NOTE! Do not arrange the return shipment or submit the despatch form before you have been notified that your microscope has been unloaded.
 
 Diamond Goods Handling is open to despatch shipments Monday to Thursday 8am - 4pm and Friday 8am- 3pm. 
 

Provide your samples in an appropriate format  

Please contact the eBIC4i Team to discuss sample container and buffer requirements before shipping.

Obtain permission to send you samples and arrange the shipment with your courier.

PLEASE NOTE! All shipment information must be added into ISPyB before shipping samples to Diamond and samples must be validated in the UAS. 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. 

Once your samples have been validated in the UAS and your eBIC4i contact has agreed an appropriate timeline 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.
 
Shipping Address:
Contacts name c/o Goods Handling
Diamond Light Source
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 NOTE! Samples must be shipped to site by a courier service. We cannot accept samples delivered by users in person.
 
•    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.
 

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.
 
 
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), and have up to date contact details.
 
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 require lab access please get in touch with the eBIC4i team to obtain instructions for filling in the lab form. 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 EPU software. Collected data and results from our autoprocessing pipelines can be monitored in ebic-pato.
 
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.
 
Any remote users need to download and set up the latest version of the software “NoMachine” in order to connect to Diamond and the microscope workstations. In order to connect to the microscope, please use “nx-cloud.diamond.ac.uk, port 4000” and your FedID@fed.cclrc.ac.uk and password. To manually analyse and process data during and after your visit please use “nx.diamond.ac.uk, port 4000” and your FedID and password. Further information
 
 
PLEASE NOTE! You need to familiarise yourself with EPU and data collection procedures at Diamond before your visit. Please contact eBIC4i team if you require training as a new or returning user. 
 
We recommend that you monitor your data collections, the incoming results from our autoprocessing pipelines, and the beamline webcams in ebic-pato. 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 ebic-pato (https://ebic-pato.diamond.ac.uk/)using your Fed ID and password. 
 

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 theeBIC4i Team in advance and provide a hard drive with sufficiently free space in your shipment. The hard drive must be clearly labelled and registered as an item in your shipment in ISPyB.