Data Collection Xray

Hooray, you've got crystals! Now it's time to check whether they diffract and hopefully solve that structure.
We can have access to ESRF (France, through our BAG), MASSIF (automated data collection) or SLS (Switzerland).

Automated data collection (MASSIF)

At beamline ID30A-1[1] (also known as MASSIF-1) Matthew Bowler et. al.[2] set up the beam for automated data collection. This is very convenient as you don't have to go there, you don't have to stay up all night and the crystal centering method outcompetes you probably on accuracy, but definitely on time. It is being paid from our available BAG beam time: 50 crystals will cost us 1 shift.
It therefore is a pretty good option if you would like to check crystals for diffraction or if you're expecting pretty straightforward data collection.

Schedule beamtime

• Choose your preferred date for data collection

Take time into account for you (and maybe others) fishing the crystals, and sending the dewars. When they arrive at ESRF, the dear will be refilled with N2, but keep in mind that FedEx doesn't deliver in the weekends: you don't want your crystals to heat up at the sunny French storage location. All-in-all I would plan this at least one week in advance.

• Ask Tassos to put it in the calendar

Tassos has access to the beamline calendar where data collection are being scheduled. He will put in your request if you tell him our current BAG number (format mx####) and the amount of crystals. When this is done, the beamtime is, in principle, booked.

• Sort out things in SMIS

Log in onto the ESRF User portal [3] using the account of our BAG coordinator. Check whether your scheduled beamtime has an A-form available (usually after 2-3 working days of Tassos booking). Download the added Invitation Letter, it contains shipping instructions! In this letter it usually states to add the BAG responsible onto the A-form: do this via Edit A-form.
Furthermore, add your protein samples onto the A-form. If necessary, add your protein onto the list: the protein crystals you're about to send should be on there and should have green clearance for automated data collection!
Now you can submit the A-form: the BAG responsible will get a confirmation link that he/she should/will click.

• Send your crystals

Continue as if you would for any other ESRF trip Data_Collection_Xray#Sending_crystals_to_ESRF

Organise ESRF trip

Through our BAG group we have regular access to the ESRF Synchrotron facility. Our group leaders should mail schedule - keep your eyes on the mailbox or annoy them for the schedule.
Alternatively you can log on to the SMIS[4] and check yourself.

Schedule visit

• Find beamtime

If you've found an interesting slot contact the BAG responsible and let him/her know you're interested to use that particular beamtime. Also specifiy the amount of crystals and whether you are planning to go down to Grenoble or planning a remote session. Keep in mind that somebody actually has to physically be there to put in the pucks!
The BAG responsible will let you know how many others are interested in this beamtime and trusts you to sort it out among eachother. When you've got some time allocated you can start preparing your trip (if you're going there) and your crystal shipment.

• Sort out things in SMIS

For this you should have a personal SMIS account - make one!
Log in onto the ESRF User portal [5] using the account of our BAG coordinator. Find the correct A-form and add yourself onto the list via ' Edit'. Specify your date of arrival, whether you're a remote user etc. and save the A-form. Furthermore, specify the experimental setup and add your protein samples onto the A-form. If necessary, add your protein onto the list: the protein crystals you're about to send should be on there and should have green or yellow clearance. You can submit the A-form once everybody for this beamtime is registered on the form: they will get a confirmation link that he/she/you should/will click.
You will get an email for confirmation; click it and perform the required tasks. Possibly you'll get asked to do the safety training. Once this is done you can send your crystals!

Sending crystals to ESRF

Send samples

After having booked your timeslot, you can go ahead and send your crystals. So, fish, freeze and fill (the dewar)!

• Note down the puck numbers and what crystal is in what slot

You will need this information to fill out the Excel sheet required for automated data collection and/or to make sense of all the datasets you collect.

• Make a shipment with your samples

Log in at the ISpyB website[6] using the current BAG proposal number and password. Go to 'Shipment - Create Shipment'. Here fill out the details: label 'NKI_##'; amount of dewars and extra tools; select the appropriate beamtime. If your beamtime does not show up, contact the local contact that is on the A-form.
Add the lab contact details - it is easiest to select my lab contact card from the list - and tick the box of the return address. All the fields below should be filled out now. If that failed ask the secretary for details.

• Fill out sample information - obligatory for MASSIF data collection

Now that the shipment has been made you can add your sample details. It is recommended to use the Excel-file that is made available by the creation of the shipment - click 'View Samples'. Add your crystal details (puck number, slot, protein, SG) and collection strategy (for MASSIF[7]) to the file. Reupload the file and see all your samples magically appear.

• Prepare FedEx documents

Ask the secretary to prepare a FedEx shipment. The FedEx software has an option 'Biological samples - Frozen crystals' that should be used. Other data: shipping container dimensions are 30x30x50 (or measure this yourself and update this wiki), we usually claim a value of 10 EUR. Use the following address:
Name of the local contact (taken from the A-form)

ESRF Magasin
6 Rue Jules Horowitz
38043, Grenoble Cedex 9
France
Tel: +33(0)476882733

Ask the secretary to add your email for shipping notifications, so you can track the shipment yourself. Print the FedEx forms four times; no invoice is needed.

• Prepare ESRF shipping documents

Log in at the ISpyB website[8] using the current BAG proposal number and password. Make sure the shipment has been filled out completely, see above:Data_Collection_Xray#Sending_crystals_to_ESRF
If that is the case, print the shipment forms by clicking the printer icon below 'Comp. labels'. It will ask you a tracking number, take this from the FedEx forms earlier printed. Print the three ESRF forms.

• Make the dewar ready for shipping

You now should have a precooled dewar and five pucks (all *N if sending more than 50 crystals). Make sure that the dewar is fully devoid of N2 to save border control problems and load your five pucks. Close the dewar with a piece of styrofoam and the cap: do NOT use a tie-wrap to close it off. People at ESRF will NOT refill the dewar with N2 if they can't open it. It can then go into the shipping container, ready to be shipped.
On the dewar, paste the first form from the ESRF. Put the dewar in the container and close it. If it isn't there yet, paste a 'biological substance' and a 'priority alert' sticker on the container. Add two paste-on bags on the container as well: one has the FedEx forms; the other has the other two ESRF forms - put the right one (#2) in front of the other (#3)!

• Ship it

Bring the container down (with the little NKI-form) before 14:30 so FedEx can pick it up.

Follow data collection

Automated data collection can be followed through ISpyB [9] or, preferably, through [10].
These websites can also be used when your at the beam, or if you want to spy on your colleagues at the beam.

Make sure you retrieve the data afterwards Data_Collection_Xray#Recover data

Remote data collection

For remote data collection, you'll have to do it all yourself. First of all, make sure you've got the password and username (mx####). Then - know which beamline you've been granted access to. This is indicated on the A-form. Other useful info is the beamline scientist: this is also on the form. Currently BM14, ID23-1, ID23-2, ID29, ID30-3 are available for remote.

Set up the centre computer in the terminal room:

• Open NXclient NoMachine.
• Connect to firewall.esrf.fr

You will be requested username and password - fill in the details (duh).

• You should now be connected - ask to create a new virtual Desktop
• WAIT, be patient!!! (Andrea, Tassos, other mediterranean types!)
• You now should have a Desktop-like screen
• Connect to your beamline

At this point you probably should have (had) contact with either the beamline scientist (also on the A-form), or other BAG members that should put in your pucks. It is usually advisable to have already contacted them PRIOR to the actual beam time!

• In the opened terminal you will be asked the password for the beam. If the known password fails - you'll have to contact the beamline scientist (call!)

You should now be in the computer. Occasionally MxCube2 has already been started (depending on who was before you). Otherwise, start MxCube2 (doh) with the command "mxcube2".

• MxCube is now open!
• Log in with our proposal number and password
• Ask the people at the beam in which order your pucks are loaded.

This can be overcome by putting proper names etc. into ISpyB (Data_Collection_Xray#Send samples), then the machine will scan (and recognize) the puck and thus which samples are loaded into which place. On the other hand - lots of work and NOT fool-proof

• Start MEASURING!!

WAIT, be patient!!! (Andrea, Tassos, other mediterranean types!)

• Be sure to dump all the data in an NKI folder. This makes for easier synching afterwards

If RSYNCing (Data_Collection_Xray#Recover data), you can start the sync - this will save some time!

• In another screen (or pc) start the webinterface of ISpyB. Useful to see what is happening!
• Also have your email open for contact with the people at ESRF!

At the end of the beam time, you may want to get your data ASAP! Data will be kept for 50 days (as they say) at ESRF, but I don't want to test this (AND NEITHER DO YOU!) You can download everything at the end through SSH *OR You can set up an rsync:

Recover data

• Find where you want to put the data: Usually /images/YYYY-MM-DD_BEAMLINE/

Check if there is enough space and Chmod the folder.

• Find the data: connect to esrf "ssh PROPOSAL##@firewall.esrf.fr -p5122"

Usually it's located ./BEAM/DATE YYYYMMDD/RAW_DATA/your folder

• Then start another terminal for the rsync and do

rsync -avztu -e "ssh -p5122" PROPOSAL##@firewall.esrf.fr:/data_directory_found_in_previous_step directory_you_want_to_put_it

MAKE SURE TO INCLUDE THE FULL PATH.

• Let it run

References

Here could be a list of references, but we need to have the Cite extension installed!!!! Template:Reflist