XRD2 Info for Users

Before coming to Elettra

All the participants coming to Elettra have to:

1) Register on Elettra VUO (https://vuo.elettra.trieste.it/pls/vuo/guest.startup, "If you are a new user select this link")

2) Solve an online quiz, as a radioprotection training, accessible from your VUO account in the "Radiation Protection and Safety training for users" section


3) An "access request" is compulsory to be allowed on-site: fill the form available at the "Access requests to the laboratory (ONLY FOR USERS)" link

***** this is mandatory to obtain a Invitation letter from Elettra (for user needing a visa)! *****


4) Be listed on the active proposal and corresponding investigation (on site). This can be done by the person that created the project. After login in VUO and selecting the project an active link will allow to "add investigators" in the "Virtual Laboratory --> My investigations" section.

***** this will also allow you to access your data remotely! *****

Please note that we do not have a guesthouse  - User Office (through Travel Office) can help:

http://www.elettra.eu/userarea/users-office.html


While filing out the proposal, you will need to know the rules if you request financial support. Financial support info:
Elettra will support the cost of shipping (dewar) for the Italian community but not the cost for travel. Please contact Users' Office or the beamline scientists to have more info.

http://www.elettra.eu/userarea/eu-rules.html

 

Quick Links


Samples for XRD2 experiments

In order to maximize the survival of your samples, please take into account these instructions.

  1. If you are using caps with barcodes,  we recommend to use the ones with a white background as they don't rust, last longer and are easier to read (see figure)
  2. Unipucks are compatible with our sample changer.
  3. If you bring ESRF pucks (samples in vials), we will help you transfer your samples into Unipucks. Please let us know in advance so we make sure we have enough unipucks available for you. Our dewar can accommodate 12 pucks at the time. We recommend that you use the barcode (number) to identify your puck which enable us to quickly locate the right one with your samples.
  4. Pin length should be 22 mm total height (from the bottom of the base to the tip of the loop). All the transfer parameters and auto-alignment procedures are set for this length. Having longer or shorter pins might result in your sample being out of the field of view or worse, out of the cryostream.
  5. Pins: our double-gripper perform best with the spine pins.
Even thought we expect most of our experiments to be performed at 100K, we can accommodate capillaries for room temperature measurements. We do not support tray screening yet.

Quick Links


 

               

    

 

ESRF Spine-Style
(Must be moved to Unipucks on-site)

  • 10 sample positions

  • Barcode found on top and side

  • name found near barcode CS-118A

    

Unipuck-Style

  • 16 sample positions

  • Barcode might be on cover

  • name on cover CPS-3312

  

Form for samples: upload samples list to SynchWeb!
You need to provide us with a  form describing your samples and their location in the containers (pucks). This step is done at your home institution via a web interface, SynchWeb


Sending samples

***NEW You might be eligible to have the cost of the shipment covered by Elettra. Please contact us to have more information.

***NEW You don't have a dewar? You can contact directly any of the beamline scientists to inquire about getting a loaner dewar with pucks for you to send your samples.



Your beamtime is allocated on XRD2 and you want to send us a dewar, loaded with frozen samples:

- I'm sending my samples from a European country
- I'm sending my samples from a country, outside Europe

 

You have completed your beamtime on XRD2 and you want to retrieve your dewar from Elettra:

- I want my samples back and I live in a European country
- I want my samples back and I live outside Europe

 

Before the beamtime: Sending your samples to Elettra

  1. It is possible to send samples associated to your proposal once approved for beamtime and booked on the Elettra's calendar (you should have received an email about this). Before sending your samples, login VUO and make sure you have or are listed on a project (check “Already submitted proposals” under “Your Proposals” section).
  2. Prepare your samples and create a dewar content description, describing them according to the instructions page.
  3. Make sure your dewar is cold but dry (no liquid nitrogen). If you ship cryovials in canes, do not forget to put each cane in a plastic sleeve and make sure each pin and vial is pushed under a tab or held in place by another vial on top of them.
Depending on where you are sending the dewar, there might be some extra forms to fill and delays due to Customs requirements.
 
The procedure is greatly simplified. You will not need to fill the Customs papers.
  1. Fill the form for your express courier using the receiver/consignee info (see below). If your express courier requires a value, we recommend to use "10 Euro". Usually the express courier will have an option to add people on the tracking option: add the beamline scientist email (nicola.demitri@elettra.eu). Please report also associated proposal ID (202xxxxx) in the notes.
  2. Use this reference as "Consignee":
    Elettra-Sincrotrone Trieste S.C.p.A.
    Strada Statale 14 - km 163,5 in AREA Science Park
    34149 Basovizza (TS) Italy.
    To the attention of
    Nicola Demitri / XRD2 Beamline
    Proposal #             (ex.: 20200551)
    phone: (+39) 040 375 8861 (ESP4 1P28),
    (+39) 040 375 8435 (XRD2 Beamline),
    (+39) 3351272670 (Mobile)
  3. In your VUO account, under “Already submitted proposals” in the “Your Proposals” section, select the proposal related to the samples to be sent from the list and find the “Add shipment” link (almost at the end of the page). Provide us with information such as: Express Courier name, tracking number, dewar code (a unique product-code printed usually at the top or at the bottom of the dewar), expected dispatch date. Please if you changed any of the informations suggested in point "A" above (e.g. commercial value) let us know using the Notes box.
  4. It's strongly recommended to upload a copy of the proforma invoice you added to the shipment (if present) and a copy of any other declaration you added (if present) in the “Add shipment” VUO page. Full description of your samples and their location in the containers (pucks) can be done in any moment, at your home institution via a web interface, Synchweb

 

From Outside the Schengen Area

 

  1. Fill out the form for your express courier and Provide the dewar shipment forms for Custom using the following informations:

  • Do NOT organize the shipment as “temporary exportation”
  • Purpose/Description of contents: "Dry-shipper containing frozen organic molecules for scientific experiments at Elettra Synchrotron (Trieste, Italy) – EU harmonized tariff number: TARIC 29420000. Pure research purposes. Not dangerous. Not restricted, as per IATA special provision A152"
  • Terms of export: DDP [“Delivery Duty Paid” – this is the so called 'Incoterms']
  • Consignee:
    Elettra-Sincrotrone Trieste S.C.p.A.
    Strada Statale 14 - km 163,5 in AREA Science Park
    34149 Basovizza (TS) Italy.
    To the attention of
    Nicola Demitri / XRD2 Beamline
    Proposal #            (ex.: 20200551)
    phone: (+39) 040 375 8861 (ESP4 1P28),
    (+39) 040 375 8435 (XRD2 Beamline),
    (+39) 3351272670 (Mobile)
  • Commercial value: "Value declared for customs purpose: 10 Euro" [You are free to change it. This value was fine for other users. Avoid to declare zero as a value: it can not be accepted by the customs]
  • Duties and taxes: "Payable by exporter"
  • If required specify "Non-flammable gas 2" as hazard class
  • For administrative issues (e.g. customs problems) contact suppliers@elettra.eu - NB: Shipping from EXTRA EU countries can be subject to expensive custom fees. please, check carefully your courier policy! Contact us for doubts and suggestions.
  • We suggest to organize the shipment pick-up at the beginning of the week to avoid delays at custom due to the weekend.
  • Add the associated proposal ID (202xxxxx) to the proforma invoice, in the "Description of goods" field.
  1. In your VUO account, under “Already submitted proposals” in the “Your Proposals” section, select the proposal related to the samples to be sent from the list and find the “Add shipment” link (almost at the end of the page). Provide us with information such as : Courier name, tracking number, dewar code (a unique product-code printed usually at the top or at the bottom of the dewar), expected dispatch date. Please if you changed any of the informations suggested in point "A" above (e.g. commercial value) let us know using the Notes box.
  2. It's strongly recommended to upload a copy of the proforma invoice you added to the shipment (if present) and a copy of any other declaration you added (if present) in the “Add shipment” VUO page. Full description of your samples and their location in the containers (pucks) can be done in any moment, at your home institution via a web interface, Synchweb

 

After the beamtime: Returning your dewar back to home Institution

As soon as a beamtime ends, the person who submitted the proposal receives a notification via email to proceed with the dewar(s) pickup at Elettra.  We do not have the space or the manpower to keep your dewar(s) much longer after the experiments: the proposer is strongly invited to promptly contact an express courier for samples recovery.

Return - Within the Schengen Area (European countries that have abolished border controls)

 

  1. Schedule the pick-up on your courier account and be sure you get the the waybill document (pdf file) that we must attach to the dewars. The information you provide to your express courier (i.e. description of goods, value, weight, size) should match the informations provided upon delivery to Elettra; if you change them (e.g. commercial value) let us know using the Notes box. If you provide us with you express courier account and the address, we can take care of the shipment for you.
  2. Pick-up point, Sender's address:

    Elettra-Sincrotrone Trieste S.C.p.A.
    Strada Statale 14 - km 163,5 in AREA Science Park
    34149 Basovizza (TS) Italy.
    Warehouse
    phone: (+39) 040 375 8251/8470 (Warehouse),
    (+39) 3351272670 (Responsible – mobile)

    Goods can be picked-up at the warehouse from Monday to Friday from 09:00 to 12:30 and from 14:00 to 16:30. We suggest to organize the pick-up, directly with your courier, at the beginning of the week to avoid delays at custom due to the weekend

  3. As soon as you get the shipment data from your express courier, log-in your VUO account and under “Already submitted proposals” in the “Your Proposals” section, select the proposal related to the samples. From the list of dewars, select the dewar(s) to be returned, and fill the required “Dewar Return” data (dewar status is “Data collection concluded“).
  4. Upload required information on VUO form: waybill (pdf) document and tracking number are compulsory. Lack of these data prevents us to complete the pick-up! The form is also asking you the chosen express courier name and scheduled pick-up date.

 

 

Return - Outside the Schengen Area

 

  1. Organize the dewar pick-up shipment using the following informations:
  • Do NOT organize the shipment as “temporary exportation”
  • Purpose/Description of contents: "Dry-shipper containing frozen organic molecules for scientific experiments at Elettra Synchrotron (Trieste, Italy) – EU harmonized tariff number: TARIC 29420000. Pure research purposes. Not dangerous. Not restricted, as per IATA special provision A152".
  • Terms of import: FCA [“Free Carrier” – this is the so called 'Incoterms']
  • Consignee: Please put the address of Your home Institution first, followed by   “To the attention of“ Your name and contacts (do not forget a mobile).
  • Example:

    International Research Centre
    Albert Einstein 45,
    South Pole City, Nation.
    To the attention of
    John Smith / Structural Biology Lab3
    phone: (+99) 123 456 7890 (Room 12),
    (+99) 123 456 9865 (Lab3),
    (+99) 123 656 9866 (Mobile)
  • Commercial value: "Value declared for customs purpose: 10 Euro" [you are free to change it. This value was fine for other users. Avoid to declare zero as a value: it can not be accepted by the customs]
  • Duties and taxes: "Payable by importer" or “Payable by consignee”
  • If required specify "Non-flammable gas 2" as hazard class
  • For administrative issues (e.g. customs problems) contact suppliers@elettra.eu - NB: Shipping from EXTRA EU countries can be subject to expensive custom fees. please, check carefully your courier policy! Contact us for doubts and suggestions.
  • Pick-up point:

    Elettra-Sincrotrone Trieste S.C.p.A.
    Strada Statale 14 - km 163,5 in AREA Science Park
    34149 Basovizza (TS) Italy.
    Warehouse
    phone: (+39) 040 375 8251/8470 (Warehouse),
    (+39) 3351272670 (Responsible – mobile)

    Goods can be picked-up at the warehouse from Monday to Friday from 09:00 to 12:30 and from 14:00 to 16:30. We suggest to organize the pick-up at the beginning of the week to avoid delays at custom due to the weekend

  1. Schedule the pick-up on your courier account and be sure you get the the waybill document (pdf file) that we must attach to the dewars. The information you provide to your express courier (i.e. description of goods, value, weight, size) should match the informations provided upon delivery to Elettra; if you change them (e.g. commercial value) let us know using the Notes box. If you provide us with you express courier account and the address, we can take care of the shipment for you.
  2. As soon as you get the shipment data from your express courier, log-in your VUO account and under “Already submitted proposals” in the “Your Proposals” section, select the proposal related to the samples. From the list of dewars, select the dewar(s) to be returned and fill the required “Dewar Return“ data (dewar status is “Data collection concluded“).
  3. Upload required information on VUO form: waybill (pdf) document and tracking number are compulsory. Lack of these data prevents us to complete the pick-up! The form is also asking you the chosen express courier name and scheduled pick-up date.
  4. Please note: based on the above information we will prepare a proforma invoice for the custom. Take care to the information you give to the express courier: any inconsistency or misformed information could end up in a delay at the customs.<
  5. You can follow the status of the dewar in Elettra (arrived, returned) using your VUO account (“Your Proposals”-->“Already submitted proposals”--> -->”Shipments”).
 

Raw data folder structure (i.e. where are ".cbf" Pilatus 6M files?)

From the computer where you collect data, you can only visualise your raw data by starting  Albula by clicking on the icon on the desktop or via "Diffraction Images Monitoring" in the XRD2 launcher.

This will load automatically all the images collected so you can follow you data collection *live*. You can also go back and load previous images.


To access data collection for processing, on the beamline computers (chive and chili) or the cluster (yellow) the path will have this pattern.

/net/online4xrd2/store/ProposalNumber-visit/SampleName/run#/rawdata/*cbf    *** read only directory ***
/net/online4xrd2/store/ProposalNumber-visit/SampleName/run#/work/                 *** writable directory ***
ex.:

/net/online4xrd2/store/2022063-1/MFg/1/work/


The ProposalNumber is automatically defined when you log in MxCube (you selected it). You can not modify this. The rest is defined by you or rather will correspond to the name you gave your sample in the container description in SynchWeb

At Elettra, the protein acronym field that you might see when you create a "manual" mount is is ignored in the path. Sample name should be unique mut-A, delta_23 etc... otherwise you will add a new run to the sample previous sample. Data will not be overwriten but rather just harder to locate.

Every time you collect on a sample, a new run number will be automatically generated. We have decided to separate these directories to facilitate downloading (see below).
If you characterize manually, We suggest to proceed as followed

Run "1":    Screening on a first crystal point (3 frames at 0° + 3 frames at 90°) - screening covers a couple of degrees; it is in fact a small data collection
Run "2":    Screening on a second crystal point (3 frames at 0° + 3 frames at 90°) - default is "1°/sec": 1.5 deg. in 1.5 sec, splitted on 3 frames (0.5° each)
Run "3":    "Real" data collection
Run "4":    ...additional data collection and/or characterization?

NOTE: if you use CHARACTERIZATION in the data collection menu, the frames will be in run1 but the frame will have a "ref-" appended to the names (not overwriting any frames present in that run)

An example:
/net/online4xrd2/store/idtest000/sample1/2/rawdata/sample1_1_0001.cbf               **** data collection
/net/online4xrd2/store/idtest000/sample1/1/rawdata/ref-sample1_0_1_0001.cbf      **** first set of frames for characterization
/net/online4xrd2/store/idtest000/sample1/1/rawdata/ref-sample1_1_1_0001.cbf      **** second set of frames for characterization - 90 degrees away



Browse rawdata from home (i.e. check single detector frames)


You can look at rawdata from your home web browser through https://braggy.elettra.eu



File access from home (i.e. downloading raw, auto and manually processed files)


You can download single datasets (Rawdata & Auto Processing) from the Synchweb Summary page of your visit of interest:



...OR: the whole set of folders is accessible from your Elettra's account:
  1. From your home institution, log in VUO, with your account:
  2. Virtual Laboratory section, access "My investigations". If you don't see the proposal you want, ask the person that submitted the proposal to add you as an investigator.




From the list of projects, "[Select]" the project for which you want to access the data, in the following examples you see "idtest000" or "20190037" or "20185476".
You can see all the proteins associated with the project and also who else has access to that data.

To access the data select the "[Access online storage]" link (bottom of the screen).



Follow the instructions on the website: a custom link will be created to let you access your resource (it expires after 24 hours!):
  • If you are downloading to a Linux system, you can have access using these graphical File Manager tools (Nautilus, Caja, Konqueror, Dolphin, etc..):
  • Command line alternatives: from terminal two resumable options are easily available; create a folder (mkdir MyXRD2Backup ; cd MyXRD2Backup) and then: 

wget -m https://download2.grid.elettra.trieste.it/prox_abcde123456

Or from an account with administrative powers the folder can be accessed with this mount command syntax:

(sudo) mount -t davfs "The_link_you_generate_on_VUO (i.e. https://download2.grid.elettra.trieste.it/prox_abcde123456)" "Your_local_mount_point_folder_name"
(sudo) rsync -varz "Your_local_mount_point_folder_name" "Destination_folder_name"

NB: If this command fails, you need to install davfs support (on Ubuntu: sudo apt install davfs2)
  • On a Microsoft Windows machine use the glass magnifier (a.k.a. "Search") and paste the link below. You will be able to drag and drop every folder 


  • Mac or Windows users can try Cyberduck - the duck icon contains a link to your folder of interest. Use the File-->Synchronize option to restart a stalled download.

If you have any issues please contact us!

 

 

SynchWeb logbook - Data collection diagnostics and Autoproc output!


Data collections log and relevant files (e.g. ready to use .MTZ files) are directly accessible from the proposal "View All Data" page in Synchweb.
XRD2 data collections are automatically processed using Global Phasing data reduction pipeline "Autoproc".

The "View All Data" page gives you precious information about average diffraction limit of your crystals within each data acquisition. You can use the embedded raw diffraction image viewer or get fast and useful hints from the "Spots(Y)-Bragg(B)-Res(R) Vs Frame" plot (i.e. the graph shown on the right)

Pathological signs of radiation damage or crystal mis-centring can be easily spotted out from unstable trends in this graph!
This graph is populated on the fly while you collect data - keep an eye on it before you decide to trash your crystal!!!


Real data collections can be easily filtered using the "Full Collections" toggle (i.e. to exclude characterizations):

Summary of autoprocessing output can be expanded clicking on the "Auto Processing" grey bar.

The "Logs & Files" button allows to quickly download relevant "ready for electron density maps" files:

  • summary.html ...contains summary of relevant autoproc output statistics from core pipeline steps
  • truncate-unique.mtz ...contains merged and scaled intensities plus amplitudes, isotropic resolution cut, complete data to highest resolution
  • truncate-unique.table1 ...contains standard "Table 1" pubblication statistics
  • truncate-unique.stats ...contains complete statistics by resolution shells
  • staraniso_alldata.mtz ...contains merged and scaled intensities plus amplitudes, anisotropic resolution cut
  • staraniso_alldata-unique.mtz ...contains merged and scaled intensities plus amplitudes, anisotropic resolution cut, complete data to highest resolution
  • XDS_ASCII.HKL(.zip) ...is the final "raw XDS" output, available for rescaling through CCP4 Pointless+Aimless (using XDSIN card)
NB: "alldata" = up to the highest resolution collected (i.e. up to the detector corners), "unique" = mtz including Rfree test-set column

 


Get a quick summary of data collections out of SynchWeb

A compact summary table of data collections parameters and Autoproc results is available from the "Summary" button:



NB: A handy printable report of data collected during each visit can be downloaded from the "mx202xxxx" --> "Visits" --> "Download PDF Report" button:


 

SynchWeb - "Downstream Processing" section: automated phasing attempts!


Automated phasing pipelines are launched as soon as data are collected: you can have a free quick Molecular Replacement (Dimple) run if you upload proteins details in the "Proteins" section of your experiment:

Protein acronim is the bare minimum information needed upon protein creation and this is enough to associate samples to Unipucks in the "Add container" section:
Molecular Replacement (Dimple) pipeline needs a model that will be fetched from the latest PDB code or the latest custom model (pdb format) uploaded:
An example of a succesful run looks like this - maps, model and output files are available from the corresponding buttons:

The "Map / Model Viewer" button gives you access to an interactive viewer (based on Uglymol). Interface shortcuts are summarized here:

Software used at the beamline

XRD2 data collection, management and analysis systems use code from: MXCuBE3, Braggy, CCP4 Suite, Phenix Suite, SHELX Suite, PLATON, Coot, ADXV, XDS, autoPROC, Fast DP, SynchWeb, ISPyB.
Please refer to the specific software web pages for licensing issues.
Ultima modifica il Venerdì, 19 Aprile 2024 08:46