MX Responsive Beamtime Guide
Diamond MX Open to Users
Beamlines are open for
- Rapid access for SARS-CoV-2 research.
- Existing BAGs.
- New projects and users via rapid access request.
With an approved proposal the current available options are:
|Run 1 (Jan-Mar)||Run 2 (Mar 2021)|
|Remote Access||Send samples from 5th January and to arrive no later than 5th March||Send samples from 5th April and to arrive no later than 14th May|
|Automated unattended data collection||Send samples from 5th January and to arrive no later than 5th March||Send samples from 5th April and to arrive no later than 14th May|
Proprietary access (Remote/ Automated/ Mail In)
|Discuss with industrial liaison office|
|Mail-in for I23 long wavelength||Discuss with Armin Wagner|
|In situ data collection on VMXi||See VMXi webpage and discuss with beamline team.|
Read all of the below carefully on how to access the beamlines.
There are no pre-scheduled visits as you may have been used to in the past. You can ship us samples following the dates in the table above, and when the dewar arrives at Diamond we will then schedule a visit for the appropriate duration.
Shipping for EU/NI based users
Due to the recent end of the UK transition period, we are improving Shipping via https://ispyb.diamond.ac.uk/, for ALL EU and NI users please contact firstname.lastname@example.org or email@example.com prior to shipping. In the initial period the shipping via DHL will work as follows:
- Setup shipment via ISPyB: https://ispyb.diamond.ac.uk/shipments/add
- Add ALL dewars to the shipment
- Add ALL samples to the shipment
- Email firstname.lastname@example.org / email@example.com respectively to generate the airway bill
- Please provide us your Economic Operators Registration and Identification number (EORI), if you do not know this directly, a contact at your institution that normally deals with international shipping should know with this.
- Download the Airway bill from ISPyB
- Attach airwaybill and dispatch to Diamond Light Source Limited
Responsive Beamtime Access
For Run 1 of 2021, Diamond's MX beamlines are running from Tuesday 9:00am to Saturday 9:00am.
As we continue to prioritise work on COVID-19, we are now operating a responsive access mode. Sessions for shipments on-site will be scheduled on a weekly basis, prioritising COVID-19 related work and taking into account user requests and beamline availability.
Experiments can only run without Users present on site, so remote access only. See the User guide.
All users requiring training or information should get in touch with the local contact associated to their visit. Please write to firstname.lastname@example.org if no local contact has been assigned yet.
Industrial users (proprietary access) should liaise with email@example.com as normal.
Accessing Diamond MX Beamlines
For the forthcoming period we will be able to offer access to MX beamlines for Diamond users. Access will either be via responsive remote access to beamlines I03, I04, I04-1 and I24, an automated unattended data collection service (UDC) using I03, or supported mail-in service (industry or for access to I23 and VMXi).
The guidance below applies to both COVID-19 and non-COVID-19 MX proposals.
For any work that is COVID-19 related we request that you apply for time through our COVID-19 call so we can provide you with priority access. Please complete the short application for "Rapid Access Call for Proposals: SARS-CoV-2" here.
Which access route should you choose?
Remote interactive data collection (academic/industrial)
Standard (responsive) remote access to all beamlines. If you have a challenging problem (for example, new crystals to test where diffraction quality is unknown, difficult phasing problems or require microfocus beam) then an interactive remote access visit is likely appropriate. For these visits we will schedule your visit once we have received your samples at Diamond.
Automated unattended data collection (academic/industrial)
If you have a crystal system that meets straightforward requirements then the automated unattended data collection service is for you.
- Single crystal >15 µm in size
- Ability to set a target resolution, either through prior knowledge or experimental requirements
You simply provide us with some limited information when creating your shipment and samples in ISPyB and we handle the rest, with data collected as soon as reasonably possible. This is the most flexible way for us to schedule beamtime currently and places no constraints on your time to be available for collection.
Currently, unattended data collection offers a choice of 4 recipes:
|Prioritises completeness/resolution and collects 2 x 360° sweeps, 1st at chi=0 and 2nd at chi=30. Each sweep uses half the expected lifetime dose.||20|
|Phasing||Multiple sweeps are collected using different chi/phi values at your chosen energy, using a lower transmission to maximise anomalous multiplicity and completeness. The total dose used is half the expected lifetime.||20|
|Ligand||Prioritises speed of data collection and collects a single sweep, 360° dataset. This single sweep uses the full expected dose and is a good choice for weakly diffracting crystals.||25|
|Stepped||Prioritises resolution and conducts a stepped transmission scan. Each 360° scan increases transmission by a factor of 4.||10|
Mail-in service (industrial only)
For industrial mail-in service please discuss your needs with the industrial liaison team.
Long wavelength beamline I23
How to ship samples
All samples must have been added to your proposal in UAS and been approved by Diamond SHE prior to shipping - do this well in advance of wanting to send samples to allow time for review and approval by Diamond.
It is now mandatory to link approved proteins in UAS when creating samples in ISPyB. Please see brief notes about Protein Acronym in "Section 3 Add container" on the UDC pages here. If you wish to use different Protein Acronyms than those specified in UAS for your folder/file names in data collections you can clone an approved protein. Go to https://ispyb.diamond.ac.uk/protein, click on the approved protein and then use the clone button to create a new instance with the Acronym of your choice. This will then be available in the Protein Acronym drop down in container creation.
A Dewar must only contain samples for UDC or responsive remote session or mail-in currently. We cannot accept Dewars with samples for mixed experiment types.
You must complete the necessary shipment details in ISPyB including all container and sample information before sending any samples to Diamond.
Specific requirements when creating shipments during this period are:
- If using the UDC route, tick the box for Automated on the First Experiment field, then complete all necessary fields for data collection preferences when creating containers/samples.
- If you wish to have an interactive remote or industrial mail-in session, tick the box for Responsive Remote on the First Experiment field, then please complete the brief questionnaire in the Shipment Comments field before shipping.
Sample mounts and shipments for I23 beamtime should be coordinated with Armin Wagner.
Please ensure ISPyB tracking labels are attached and return labels are enclosed with the Dewar.
What do we need to know from you?
For all routes we need all container and sample information completed before shipment to Diamond.
For automated unattended data collection, we simply need the information required for data collection parameters for all samples to be provided in UAS and ISPyB as outlined in the webpages here.
For a responsive remote access or industrial mail-in visits we need you to complete the short questionnaire in the Shipment Comments field when shipping your samples to help us configure the beamtime schedule.
On ticking the Responsive Remote / Mail-in session option (see image below) the questionnaire in the shipment comments requests the following information (please answer after each question as appropriate):
- INDUSTRIAL USERS ONLY is this for remote data collection or mail-in service work? [remote/mail-in]
- Requested beamline session length [hours]
- Energy or wavelength requirements [eV/A]
- Do you need microfocus beam (provide further information in additional comments)? [y/n]
- Are there times in the two weeks after delivery when the people collecting data are unavailable?
- Additional comments:
This information will be reviewed at point of scheduling and adjusted as appropriate to maximise the use of the available beamtime.
Please note until relevant information is provided and containers and samples are created, shipped and have arrived at Diamond we will not be able to schedule your beamtime.
How will scheduling work?
The normal modes of scheduling will not apply during this period.
We will be scheduling by the hour for remote access and mail-in sessions based on the information provided by yourselves at the shipment stage. Samples for automated unattended data collection will be collected at the earliest possible available slot. To make maximal use of the limited available beamtime and to be able to prioritise COVID-19 projects we will only be scheduling samples that are on-site, and have information completed on samples in ISPyB.
Scheduled users will receive notification of time automatically from UAS. Please contact us immediately if there are any issues with the allocated time. We will have limited opportunities to adjust the schedule and your time may need to be deferred to a later slot if you cannot use the offered time.
Where feasible we may be able to make slots available the same week and we will contact you to set these up.
Equally if demand is high at any time we may need to contact you to allocate the earliest available slot outside of the period you have provided with your shipment for your availability.
What do after your remote visit is scheduled
As with any scheduled beamtime, in UAS you will need to add team members who wish to collect data and complete the ERA including samples for this session. You will have only shipped samples to us that have already been approved at the proposal level (see above) and consequently if samples you add to the visit are green your visit should automatically be approved and we can load your pucks. New unapproved samples should not be added at this stage.
Who to contact?
For enquiries (except for I23, VMXi and industry) prior to any beamtime please contact firstname.lastname@example.org who will coordinate a response to your questions.
- For I23 queries please liaise with Armin Wagner (email@example.com).
- For VMXi please contact via VMXI@diamond.ac.uk.
- For industry queries please liaise with firstname.lastname@example.org.
Once a visit has been scheduled and a local contact has been assigned please liaise with them first (see UAS for your local contact).