SWING

Your own setup is welcome on the beamline. Please contact us before submitting a project, as we need to be sure that your setup can be installed on the beamline.

It is possible to insert the control of your setup in the data collection workflow

• Remote control of your monitoring laptop
• Send to or receive a trig from your setup
  • This allow synchronization with the data collection workflow

Under one of the two specific conditions:

• A tango device (software) has already been developed for that apparatus. Unlikely.
• That apparatus includes a connection for external triggering (in/out, BNC preferred), that we can connect to one of our signal generating or reading electronic cards . Likely . (mainly 5V; 0 to 24 v possible; with BNC type cables).

This apparatus requires your capillaries to be 1.4 mm in diameter maximum. As the Linkam “oven” part is really small and its environment crowded, those capillaries need to be cut-off and sealed-off. For small diameter capillaries, we recommend to center them on the incoming beam  aperture by inserting a (homemade) shim.

To fit in the Linkam oven, it is mandatory to cut your capillaries to a maximum length of 35 mm. In order to obtain a clean cut, quartz capillaries are preferred to borosilicate.

You can either cut your capillaries in your lab or at SWING. We can show you how to do it.

After the sample is loaded in the cut capillary, you have to seal it in order to avoid evaporation of solvent or spillage in the Linkam stage. Two techniques can be used:

• Flame sealing if you have borosilicate capillaries. If you have a glassware lab you still can seal quartz capillaries with your glassmaker.
• Glue sealing for Quartz capillaries
  • In this case, we cannot firmly recommend any glue as it is sample and temperature dependent… but epoxy glues are of good use.
  • If glue sealing does not suit your requirement, you can give it a try with modeling clay (if you don’t heat over 120 °C)

SWING is equipped with:

• A MFCS-EZ system (Fluigent) with 3 pumps installed. The maximum pressure each pump can give is 345 mBar.
• A flowrate platform, consisting of 3 flow unit models and the flowboard.

Please find the flow unit characteristics:

This setup can use either three 5 mL Eppendorf and or one 15 and/or three 50mL Falcon and or one for classic chemistry glass bottles (GL45 screw cap).

This system is controlled via Maesflow, the proprietary software. It allows:

• Direct control on the pump pressure = no active control on the flow rate. But flowrate value readable.
• Direct control on the flow rate = active control of the flow, keeping each flow stable vs the other flow.

There is no feedback from the software or microfluidics controller to the beamline control system.  So you will have to control both systems from the control room.

As microfluidic chips are designed for a specific experiment, SWING staff does not provide chips. Nevertheless, if you need to make your chips at SOLEIL, we will be pleased to welcome you to the Microfluidics Lab. Furthermore, we will be happy to help designing your chips: choice of materials, size of channels for saxs measurement…

Please contact us in advance as the sample environment may be crowded and thus your chips, tubbing and other device may not fit easily in the beam path.

Installation of the microfocus setup requires more time than for a usual sample environment. Thus it is mainly installed for a whole week.

SWING Microfocused beam is obtained using a linear H-CRL for horizontal focusing and the standard VFM (vertical focusing mirror) for vertical focusing. The resulting beam size is of 20 x 20 µm² on the sample.

With this setup, the sample environment is much more crowded than for a “classic SAXS” experiment. The TX4/TZ4 table can be used to move samples holders. If you want to use your own holder please contact us to know if it will fit.

As the beam is strongly focused on the sample, the sample to detector distance is limited from 0.670 to 2.5 m and a larger beamstop than the usual one is positioned. Moreover, the number of selectable H-CRLs limits the working energy to any of four fixed values: 8, 10, 12, and 15 keV. The resulting q-ranges are shown in the following table.

Continuous 2D imaging is called “Flyscan” at SOLEIL, by opposition to step-by-step scan. It consists of a 2D cartography whose first dimension is associated with a continuously moving motor and the second dimension is a standard step movement.

Flyscan is mainly used with the combination of the Microfocused beam. Yet it is still possible to use Flyscan with a more standard beam.

In Flyscan mode, the data from the sensors (detectors, diodes, thermocouple…) and motor positions are all collected synchronously and merged in the same HDF5 file. This allows reconstructing maps from each of the scalar sensors or from an operation made on the images.

For a map of 200 by 200 pixels, with a typical exposure time of 200 ms (plus dead time of 5ms), motor steps of 25 µm, the scan will last about 1 hour and a half, about 6 times faster than the equivalent step-mode scan. (voir presentation sur le overhead)

As any for any session at SWING a specific data collection Passerelle GUI and a specific workflow visualization COOX GUI are available.

At the moment, the generation of maps using Foxtrot is under development, it will be available on the beamline in September 2020.

Don’t hesitate to contact one of the beamline scientists, for any information about:

• The Beamline
• The available sample environments describe above
• Bringing your own sample environment
• Your project feasibility
• How many shift your project requires

Aurelien Thureau (aurelien.thureau@synchrotron-soleil.fr) and Javier Pérez (javier.perez@synchrotron-soleil.fr) deal with Biosaxs

Thomas Bizien (thomas.bizien@synchroton-soleil.fr) and Javier Pérez (javier.perez@synchrotron-soleil.fr) deal with “everything else”

Access to SWING beamline is possible through

• a single proposal, peer-reviewed by a committee (PRC) every 6 months,
• a Block Allocation Group proposal which can be combined with macromolecular crystallography, reviewed every year for 2 years
• a Rapid access proposal reviewed on the fly by the Scientific Directors for hot projects.

For all these types of access, the unique portal is the Soleil Users portal.

• Industrial access is also possible, without the need to submit a peer-reviewed proposal (https://www.synchrotron-soleil.fr/en/industry).

Useful links:

• Application for beamtime:

https://www.synchrotron-soleil.fr/en/users/application-beamtime

• Project submission on the sunset:

https://www.synchrotron-soleil.fr/en/users/application-beamtime/how-prepare-proposal

• Participant declarations and sample declarations:

https://www.synchrotron-soleil.fr/en/users/preparing-your-experiment-administrative

https://www.synchrotron-soleil.fr/en/users/preparing-your-experiment-scientific/safety-requirements#SamplesSubstances

Tip: Be careful, don’t submit before your sample and participants lists are complete. Bear in mind that after selecting samples and participants on the sunset interface, you can “save only” rather than “save and submit”. Thus if your selection is incomplete, you can still edit your previous list and submit it in time when you have your final list ready, as it is requested here: https://www.synchrotron-soleil.fr/en/users/preparing-your-experiment-scientific/safety-requirements#SamplesSubstances

Support labs:

https://www.synchrotron-soleil.fr/en/know-how/supports

Tip: Biolab1 and Chemistry 1 are close to the SWING beamline.

• For any complementary information,

Please contact the User Office:

+33 1 69 35 96 51

Working hours are (from Monday to Friday):

8:30 - 17:30

Office A1.0.06, Main Building

useroffice@synchrotron-soleil.fr

Your session generally includes some time needed for set up installation. It is strongly recommended to discuss with your local contact before coming to the beamline to save time during installation. In particular, don’t hesitate to ask for help in the optimization of your own sample environment.

Support and training of users is at the center of our beamline policy. At the beginning of a beamtime session, the local contact trains the users for the time necessary to ensure their autonomy in conducting and analyzing their experiences. He remains directly reachable during the rest of the day. Outside working hours, Soleil hall coordinators can be contacted (24 hours a day) in case of problem. They are trained to identify errors and contact the appropriate support group (IT, electronics, vacuum...) or the local contact if they are unable to solve the problem by themselves. The local contact may answer 24 hours a day, in case of need, though it’s rare.

Please bring an external drive to back up your data from SOLEIL mainframe (at least 1 TB). It has to be compatible with Windows format (FAT32, exFAT or NTFS). Your local contact will run a macro for live synchronization between data on SOLEIL mainframe and data on your hard drive. However, even if we do not advise to do so, you can still download your data files a posteriori, via the sunset [Experiment Data][Soleil Data Retreaval]

Wi-Fi is available on SOLEIL site using your sunset login and password or using Eduroam network.

Accommodation and meals are available on site. The restaurant is open for breakfast, lunch and dinner.

What you have to bring

We use Agilent standard vials and inserts for the HPLC device and the Auto Sampler. We lend you the vials and the caps but you have to buy your own inserts (Agilent reference: 5181-1270). In case you forgot, we can provide you with used inserts that you can wash and dry.

The minimum quantity of buffer is 40ml for one SEC-SAXS experiment (10mL of system purge + 20 mL of column equilibration + 10mL of elution). We recommend you to bring much more (100mL to 500mL) to obtain a better equilibration of the column and to reduce stress in case of trouble.

What we can lend

The biochemistry preparation laboratory provides support to users for the preparation of their experiments. For any question, please ask the laboratory staff.

You are free to bring your own analytical columns for SEC-SAXS. We have also a wide selection of columns that we can lend to our users. All these columns have been calibrated:

What you have to bring

You have to bring your own capillaries  (Ø 1.5 mm preferred) and specifics tools if required for your own setup, or for preparing your samples. We use Agilent standard vials and inserts for the ChemSaxs Liquid AutoSampler. We lend the vials but you have to buy your own inserts (Agilent reference: 5181-1270). In case you forgot, we can provide you with used inserts that you can wash and dry.

Mail-in services are only proposed for accepted and planified proposals, in the case where users are not able to come onsite.

A discussion between the user and the local contact must be conducted beforehands to agree on the experiment conditions.

Mail-in experiments are conducted by staff member and a few restrictions apply :

• The sample preparation onsite should be as simple as possible, if any.
• Experiments will be carried out only during working hours (8h00 to 20h00)
  • An acquisition sequence might be launched outside working hours but without monitoring of the local contact
  • Users are strongly suggested to follow the experiment using the remote access tools offered by SOLEIL
• For mail-in, the document biosaxs mail-in document for users. need to be followed. A BioSAXS sample sheet (xlsx - 13.79 KB) must be filled and sent as soon as possible before the experiment date.

Keep in mind that your session can include beamline setup and sample environment installation.

The local contact will take the necessary time to make you completely autonomous on the beamline.

Data Collection sequences

All data collection sequences appear to the user as a simplified GUI with a list of parameter fields to fill (based on Passerelle workflow language). For most of the sample environments and “classical” data collections, a sequence is already written.

If necessary, a new collection strategy can be written just before your experiment, with a new GUI automatically generated. To do so, don’t hesitate to ask your local contact.

It is possible to include an action on an external apparatus (that you bring to SOLEIL) to the data collection workflow under one of the two specific conditions:

A tango device (software) has already been developed for that apparatus. Unlikely

That apparatus includes a connection for external triggering (in/out, BNC preferred), that we can connect to one of our signal generating or reading electronic cards.

Monitoring

Specific GUIs (based on COOX platform) give the possibility to monitor the beamline state (vacuum, valves, motors positions and states…) and the acquisition progress (live images from detector, live values from diodes, direct visualization of the sample,…) as well.

Simple actions like changing sample to detector distance, closing/opening the safety shutter, realigning the monochromator rocking curve, changing the working energy, …, can be done directly from the COOX GUI by clicking on active buttons.

Data Reduction

All data produced on the Swing beamline are stored in HDF5 files. Those files contain detector images, diode values, sample pictures, and a lot of beamline metadata. The files can be processed by the Java based self-installing software Foxtrot. It allows, among other functions: Data visualization (2D images from detectors, Transmission curves, …), data reduction (from 2D images to 1D curves, normalization included, gives intensity scale in cm-1, …), mathematical operations (curves averaging, curves subtraction, curves merging, useful if you recorded data at 2 or 3 sample to detector distances, other basic functions :scaling, linear function, division, summation, …), fits (Guinier, Gaussian and  Lorentzian peaks,  polynomial).

You will be trained by your local contact to use Foxtrot. You will be provided with a copy of the software as a zip file, including your masks and reduction macros.

For SEC-SAXS and BioSaxs AutoSampler, an automatic workflow for data analysis is available. This workflow takes raw images as input files and sends all results curves into the IspyB database. All intermediates files are available to users and can be reloaded into the Foxtrot application.  

Living Area

We have a living area with a self service although not free ;-), coffee machine,a sofa a fridge for food and beverages, a micro wave and a table.

This area is sample freee, Please clean it after your session.

After your session

• Sign the Safety Authorization Sheet (SAS).
• Please clean the living area and the experimental hutch. If you used support labs, please leave them  clean.
• Please don’t forget to fill the end- of- run report in the sunset webpage.
  • It takes 5 minutes ! That is the best way to specify your remarks.
  • These reports are read by many people at Soleil, including sometimes the management.

Foxtrot Software (Data reduction and treatment) can be downloaded here.

 Denfert Software (Ab initio shape determination, including hydration layer)
version 2.0 (June 2015)

Denfert : F.A.Q.
A zip archive containing executables for Mac, Linux and Windows together with a test example may be downloaded by clicking here.

... a program for the ab initio “dummy-atom” structural modeling of Biological Macromolecules including the contribution of their inherent hydration layer.

Developed by Alexandros Koutsioubas and Javier Pérez

If you use DENFERT, please cite :

A. Koutsioubas & J. Pérez, Journal of Applied Crystallography (2013) 46, 1884 and A. Koutsioubas, S. Jaksch & J.Pérez, J. (2016). J. Appl. Cryst. 49  (doi:10.1107/S1600576716003393)

Brief Description

DENFERT is implementing a simulated annealing algorithm similar to DAMMIN program by D. Svergun (Biophys. J. 76, 2879-2886) for the restoration of low-resolution structural info of bio-molecules from SAXS and SANS data. The major advantage of DENFERT is that the hydration layer around bio-molecules is taken into account by introducing a second type of beads (hydration beads) in the model.

In the top figure, we see an example of the shape restoration of Lysozyme from SAXS data using DENFERT. A cartoon representation of the crystallographic structure is also presented for comparison. The bottom figure depicts additionally the hydration layer around the reconstructed protein shape

manual (126.1 KB)

Memprot Software (Coarse grain modeling of detergent corona around a membrane protein)

Dadimodo web server

DADIMODO is a program for refining atomic models of multidomain proteins or complexes against small-angle X-ray scattering data. Domain structures are mainly kept rigid and can be user defined. Stepwise generic conformational changes are applied cyclically in a stochastic optimization algorithm that performs a search in the protein conformation space. The algorithmic structure guarantees that a physically acceptable full atomic model of the structure is present at all stages of the optimization.

A manual can be dowload : Dadimodo Manual

To prepare your complete pdb files, you can use our pre dadimodo script (3.71 KB)(remove the _.txt extension).