FAQs

Mail-in samples must be sent to the beamline in our bar-coded sample holders. To obtain holders for your experiment please fill out and send a mail-in form. 

The sample holders have space for 8 x 200 μl PCR tubes in a strip plus a 1.5 ml tube that is typically used to contain a matching buffer for batch mode experiments. 

Our mail-in spreadsheet contains all of the information that beamline staff need to measure your samples in the way that is appropriate, please fill out all of the relevant fields to avoid delays on the day of your beamtime. Please print off the shipping label from the Shipping Label workbook of this document and attach it to your package or copy the information from there to your own label or courier shipping docket. 

When samples arrive on site and before they are taken to the beamline for data collection you can choose for your samples to be stored at: -80°C, 4°C or room temperature (~21°C). 

If you are a collaborator in the European Union, then your access to B21 should be via the iNext project. If you submitted your proposal via iNext it will have been added to our Diamond UAS system. If you applied directly via UAS then while we have approved it and can proceed with scheduling etc, it is important that you now also submit your proposal via iNext. If you have any questions about this, please contact Nicola Harrington ([email protected]). 

The procedure is as follows:

1. Let your local contact and [email protected] know how many samples you have and a mailing address. We will then send you out the right number of bar-coded sample holders for you to send your samples back in. 

2. At this time, we will allocate a visit (in multiples of 8 hours) that is long enough to measure the samples you are sending. 

3. Upon receiving the holders, you will use them, send us your samples and complete and email us our mail-in spreadsheet that contains all the information we need to measure your samples in the way that you want them measured. The spreadsheet contains instructions for sample prep and a return mailing address. Please read and fill out all of the sheet to avoid confusion when we come to measure your samples. 

4. You will need to go into your allocated session in UAS and fill out the ERA part. Note that there is ERA information associated with the proposal, but that information is needed on the session too. This takes care of the safety side of the experiment and is an important step. 

5. Upon receiving your samples, we will collect and store them as instructed on your spreadsheet. Please provide a printed copy of the spreadsheet with the samples as well as emailing the spreadsheet to your local contact. 

6. We will email you when the data collection is complete and give instructions on how to access your data. 

You can find instructions on accessing your data here: https://www.diamond.ac.uk/Users/Experiment-at-Diamond/IT-User-Guide/Not-at-DLS/Retrieve-data.html. 

The structure of your experiment folder is as follows: 

<proposal-id> 

|_ nxs, h5 files are your raw data

|_scanlist.csv is useful for linking the file names with the descriptive titles 

|_processed 

        |_dat files in subfolders with names matching the image names 

|_processing 

        |_calibration, mask, pipeline nxs files used by Dawn to reduce images to dat files 

        |_scatterIV.jar latest scatter software you will need for looking at dat files and reducing SEC data 

        |_beamline_parameters.pdf has all the beamline calibration and characteristics you might need for a paper etc 
 

        |_pyplin 

                |_raw_dat copies of the dat files with descriptive names 

                |_av_dat batch mode files averaged with outlier rejection 

                |_sub_dat subtracted batch mode files 

While we attempt to automatically average and subtract batch mode data, we do not do this for the SEC-SAXS data, as for this kind of experiment it is important to carefully assess the whole elution profile and use judgement to choose an appropriate selection of data to use as a blank and as a sample. The SEC-SAXS analysis tab in Scatter makes this very easy and so you will need to do this for each of your SEC-SAXS experiments. There are instructions on how to do this in the YouTube links below. Note also that sets of dat files from batch mode experiments sometimes contain air shots where the liquid has moved past the beam and can also have radiation damage. These are automatically removed in the av_dat and sub_dat files in the pypline folder but this does not always work, and you may need to do this manually. There are some tutorials here on using scatter: https://www.youtube.com/channel/UCvFatdC5HcZOLv6OSjblfeA and https://www.youtube.com/playlist?list=PLay9wcqjiU5SJecfoJTU925LMTTP4mJk_. 
 

In batch mode (loading samples direct to the SAXS cell via the biosaxs robot) the robot platform can hold up to 8x 8-well PCR strips (200 μl tubes) and 24x 1.5 ml tubes and 1x 96 well plate (200 μl per well). The minimum sample volume is approximately 30 μl. We move the sample at 1 μl/sec during the exposure, where collection is only possible while the leading and trailing meniscus' are clear of the beam. This is a dead volume of about 15 μl so with 30 μl of sample you will get about 15 seconds worth of data. This is fine but sending more sample volume will get you longer exposure times and more quality data.

In HPLC mode we have 1x 96 well plate for loading samples and prefer 50 μl sample volumes, although it is possible to go as low as 30 μl. We ask for a 5x or 10x stock of buffer in a 50 ml Falcon tube so that we can make 250-500 ml of the running buffer. This gives plenty for pump washing and column equilibration. If there are buffer components that are very expensive or you have a limited amount of them then we can do 1-2 column runs from a single 50 mls of a 1x buffer but this means staff have to be watching it carefully so it is not very high throughput and we couldn't staff a high number of this type of experiment over night. 

Please contact [email protected] 

All samples are spun at 15,000rpm for 5 minutes in a centrifuge. Samples that are not spun risk damaging our collumns but please tell us beforehand if samples are not to be centrifuged.

We are able to keep samples on hold at -80 to run if other visits are cancelled or finish earlier than expected.

*This does not guarantee that your samples will run before your scheduled beamtime.*

If you are interested in our cancellation option, please contact [email protected] or [email protected]