Manual

Welcome to the beamline manual. There are many similarities between the MX beamlines so you will find parts of this manual are common to all the beamlines. 

Each beamline manual contains common elements, shared across the beamlines, and individual elements providing specific guidance on the best way to work on that particular beamline.

Please feedback to your local contact any errors in the manual or any areas that might be improved.

Quick Guide to Using the MX Beamlines

  1. Plan
  2. Prepare
  3. Beamtime
  4. Post Beamtime
Plan -

 

Reserve access well ahead of your visit either at the links in the web page or via your local contact to facilities such as

Check the Diamond MX web pages and individual beamline pages for updates, manuals and contact details prior to your experiment.

Register your shipping dewars with Diamond to use our shipping account and help with tracking.

Always purchase and use SPINE pins and Unipucks to mount and ship your samples. Non-SPINE standard pins cause robots to crash and damage to equipment: you lose beamtime, we lose sleep.

For full remote access experiments we prefer pucks to arrive in the shelved shipping cane or alternatively the puck shipping canister. Please avoid the narrow canisters where possible.

Prepare - +

 

Understand the visit timings you are scheduled for.

For experimenters coming on-site simplify your arrival by taking the Fast Track approach.

For remote experimenters read the remote access guidelines.

  • For full remote access experiments register users and contact phone numbers for the visit and email your local contact and mx-usersupport@diamond.ac.uk with your expected number of pucks five working days before experiment.
  • For mixed remote access (i.e. where a member of your team is on-site) ensure they will be available to change pucks.
  • In both cases discuss your requirements for remote access with your local contact before your experiment.

For all experiments we highly recommend preparing your shipments in advance in ISPyB, identifying your pucks by the puck identifier (e.g. CPS-0024) and assigning samples at the same time. This allows pucks to be assigned to robot positions as loaded by either you or Diamond staff making them available in GDA immediately. For remote access this is a requirement  rather than a recommendation to ensure reliable information transfer.

For UK users with Diamond registered dewars you can book your next working day shipping to us with Diamond’s DHL account. We recommend shipping your dewars three or more days before your experiment to ensure arrival in time.

Register your PDB and sequences for your proteins in ISPyB. These can then be used automatically if you use default file names in GDA for all future visits in downstream processing such as XIA2, DIMPLE and MrBUMP and avoids the need to do this for each visit.

Beamtime - +

Refer to the manual for data collection possibilities –

Read the message of the day in GDA for beamline status.

Refer to beamline specific manuals where appropriate.

Start your data back-up as soon as you can.

Load your pre-registered pucks and assign positions on the touch screen in the hutch (soon in all beamlines). Now start GDA and all your samples will be preloaded in the sample changer view (or press refresh to update if GDA was already running).

Use default file names in GDA to streamline experiments, avoiding the need to type information at each sample load, preventing mistakes and ensuring downstream processing uses the information you have provided in advance (PDB, sequence, space group).

Monitor your results from our automatic software pipelines either in Today's Jpegs webpage, ISPyB or Synchlink.

Talk with your local contact about your experiment plans – we are here to help you solve structures.

 

Post Beamtime - +

 

Unload your last sample with the sample changer with sufficient time to ensure you have removed pucks from the sample changers before the end of your shift (unless you have discussed a time extension with the local contact).

Deregister your pucks in GDA or on the touch screen in the hutch as you remove them from the sample changer.

Finalise your backup disk and unmount cleanly in the data dispenser interface.

Complete your dewar dispatch form for storage at Diamond or return of your dewars. You can use our shipping agents for dewar return.

Diamond pays for sample shipping (2 dewars per shift) but for UK users only if you use our shipping agents via our webpages. No reimbursement of UK shipping will be made after August 2014 for shipping you arrange yourself.

You can reprocess your data afterwards on our cluster.

Acknowledge beamline access.

Diamond Light Source

Diamond Light Source is the UK's national synchrotron science facility, located at the Harwell Science and Innovation Campus in Oxfordshire.

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