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Info for XRD1 Users

Some useful information and links for users of the XRD1 beamline. Here you can find the main differences with the general procedures at Elettra, which can be found following the User Area link in the Quick Links. In case of doubts, please contact .

Transnational EU users

CERIC-ERIC

CERIC-ERIC (http://www.ceric-eric.eu/) , the European Distributed Research Infrastructure offers access to more than 40 different and complementary state of the art techniques, distributed in 7 countries. A detailed description of the facilities available in CERIC can be found here. CERIC allows to combine a wide range of methods for sample preparation and analysis in a flexible and project oriented way, through the submission of multi-technique proposals through a single entry point.
The first deadline for proposals submission, with pre-evaluation and possibility of improvement is on Friday, September 1st at 17:00hs CET. (recommended)
The second deadline for proposals submission for expert users is on Friday, September 29th at 17:00hs CET
 

CALIPSOPLUS

CALIPSOplus is a EUR 10 million project funded by the European Union through its Horizon 2020 Framework Program.
It includes all free synchrotrons and electronic lasers in the vast European area, i.e. from Elettra in Italy to MAXIV in Sweden, ALBA in Spain and SESAME in Jordan. The project started on 1 May 2017 and lasts for 4 years.
Funded proposals are provided by travel and accommodation support for a maximum of two user per experiment. Please keep in mind these two considerations: 1) if you don't flag the support as crucial, a partial support (1 partecipant) will be considered; 2) due to the limited level of funding, if  you flag the support as crucial, but the fundings are already completely used, you will not get beamtime.
 Researchers from institutes in the following countries may be supported: Austria, Belgium, Bulgaria, Croatia, Cyprus, Czech Republic, Denmark, Estonia, Finland, France, Greece, Hungary, Ireland, Italy, Latvia, Lithuania, Luxemburg, Malta, The Netherlands, Poland, Portugal, Romania, Slovakia, Slovenia, Spain, Sweden, United Kingdom. EU associated countries (H2020): Albania, Bosnia and Herzegovina,Faroe Islands, FYR of Macedonia , Georgia, Iceland, Israel, Moldova, Montenegro, Norway, Serbia, Tunisia, Turkey, Switzerland, Ukraine

As recipient of financial support by the EU Commission via Elettra Sincrotrone Trieste you are obliged to meet the EU reporting requirements:

  • Please submit an experimental report via the VUO as soon as possible after the end of the experiment.

  • Please take a few minutes to fill in the EC online questionnaire. Please select the respective program (e.g. CALIPSOplus (730872) as EC contract number.

  • Acknowledge Elettra and the European Community in all publications (articles, posters, talks etc.) involving activities at Elettra if a reimbursement has been granted. Please include the following statements:"The research leading to this result has been supported by the project CALIPSOplus under the Grant Agreement 730872 from the EU Framework Programme for Research and Innovation HORIZON 2020"

Register all your publications based on the results obtained in the frame of the supported project in the Elettra Publications Database (accessible via VUO).
For more information:
https://www.helmholtz-berlin.de/pubbin/news_seite?nid=14684&sprache=en&typoid=1
http://www.wayforlight.eu/eng/home.aspx

National Users

Parallel to the CalipsoPlus initiative, National Users will be provided by travel and accommodation support for a maximum of two user per experiment. Please keep in mind these two considerations: 1) if you don't flag the support, as crucial a partial support (1 partecipant) will be considered; 2) due to the limited level of funding, if  you flag the support as crucial, but the fundings are already completely used, you will not get beamtime.
Refer to Elettra User Office for more informations.




A new allocation mechanism – dedicated to macromolecular crystallography experiments – has been introduced for beamline X-ray diffraction (XRD1) starting from May 1st 2011. In respect with the standard proposal for experiments at Elettra, the following improvements have been implemented:
  •     no deadline: it is now possible to submit a proposal at any time;
  •     proposal evaluation on a monthly basis;
  •     reduced dead-time between proposal submission and allocation (1 to 3 months);
  •     automatic re-submission in cases of overbooking.
We strongly encourage MX users to take advantage of this new procedure.  It will be still possible to apply on a six-month basis only if the experiment requires a particular setup in order to be performed or extended time is required for bureaucratic purposes such as visa applications.

Description


The new mechanism is dedicated to the macromolecular crystallography experiments, having a well-defined experimental setup and samples suffering of a rapid decay in terms of quality since formed. The new proposal submission system reduces significantly the time period  between proposal submission and allocation and supposes the crystalline samples be ready in the moment of proposal submission.

If the experiment requires a particular setup in order to be performed or extended times is required for bureaucratic purposes such as visa applications (e.g. more than 1 month), the usual procedure (based on 6-months period) should be used.

It is possible to submit a proposal at any time during the year, so no deadlines are present. At  the beginning of every month the proposals submitted in the previous one are evaluated by an appropriate Proposal Review Panel (M). The beamtime allocation is made by the beamline scientist in the following month, according to the score assigned on the basis of scientific relevance. The whole procedure is accessible via VUO following the link "Submit a proposal for macromolecular crystallography".

In case of overbooking the proposals not allocated are automatically re-submitted for the following month, (keeping the assigned rating value) for a maximum of six times.


In case of questions


For enquiries, please contact: mx@elettra.eu





For experiments different from Macromolecular Crystallography, please refer to the usual six-months based proposal submission. You can find more informations about how to became an Elettra user and submit a proposal in the User Area (follow the Quick Links)





Sending your samples to Elettra

  1. It is possible to send samples related to a specific proposal once approved for beamtime and booked on the Elettra's calendar (you should have received an email about this). Before sending your samples, log-in VUO and make sure you have or are listed on a project (check “Already submitted proposals” under “Your Proposals” section).
  2. Prepare your samples according to the instructions page.
  3. If you are going to send samples in cryogenic conditions, 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 tabbed in properly and/or held in place by another vial on top of them.
  4. If you are sending not dangerous samples from outside European Union:
    • Do NOT organize the shipment as “temporary exportation”
    • Purpose/Description of contents: Describe kind of specimen and add "for scientific experiments at Elettra Synchrotron (Trieste, Italy)”. Put the EU harmonized tariff number which better describes your samples (find it in https://www.tariffnumber.com/) and eventually add “Not dangerous”.

      Example1: Protein crystals in cryogenic dewar: Dry-shipper containing frozen protein crystals for scientific experiments at Elettra Synchrotron (Trieste, Italy) – EU harmonized tariff number: TARIC 35079090. Pure research purposes. Not dangerous. Not restricted, as per IATA speciExample1: Protein crystals in cryogenic dewar: Dry-shipper containing frozen protein crystals for scientific experiments at Elettra Synchrotron (Trieste, Italy) – EU harmoal provision A152

      Example2: Triazole-based crystals in cryogenic dewar: Molecular crystals for scientific experiments at Elettra Synchrotron (Trieste, Italy) – EU harmonized tariff number: TARIC 2933XXX. Pure research purposes.  Not dangerous, not restricted, as per IATA special provision A152

      Example3: Triazole-based crystals within glass containers in dry box: Molecular crystals for scientific experiments at Elettra Synchrotron (Trieste, Italy) – EU harmonized tariff number: TARIC 2933XXX. Pure research purposes.  Not dangerous.

    • 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
      Maurizio Polentarutti / XRD1 Beamline
      phone: (+39) 040 375 8084 (ESP4 1P27),
      (+39) 040 375 8355 (XRD1 Beamline)
      (+39) 3346715503 (Mobile)
    • Commercial value: "Value declared for customs purpose: 10 Euro" [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 Marco Palci (marco.palci@elettra.eu, (+39) 040 375 8969)).
    • We suggest to organize the shipment pick-up at the beginning of the week to avoid delays at custom due to the weekend
  1. If your samples are dangerous, do NOT send them without a written permission from the beamline responsible.

  2. In your VUO account, under “Already submitted proposals” in the “Your Proposals” section, select the proposal relative to the samples to be sent from the list and find the “Add dewar/container” link.
  3. Fill the form adding the information you got from your express courier. 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 4 above (e.g. commercial value) let us know using the Notes box.
    Once saved the information above, it is possible to update the dewar description file you have prepared according to point 2. You can upload here also a copy of the proforma invoice you added to the shipment (if present) and  a copy of any other declaration you added (if present).

Recovering your samples back to home Institution

  1. As soon as a beamtime ends, the proposer receives a notification vie email in order to download the data and organize the dewar(s)/sample caontainer 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.
  2. If you are sending back not dangerous samples outside European Uninon, organize the pick-up shipment using the following informations:
  • Do NOT organize the shipment as “temporary exportation”
  • Purpose/Description of contents: Describe kind of specimen and add "for scientific experiments at Elettra Synchrotron (Trieste, Italy)”. Put the EU harmonized tariff number which better describes your samples (find it in https://www.tariffnumber.com/) and eventually add “Not dangerous”.

    Example1: Protein crystals in cryogenic dewar: Dry-shipper containing frozen protein crystals for scientific experiments at Elettra Synchrotron (Trieste, Italy) – EU harmonized tariff number: TARIC 35079090. Pure research purposes. Not dangerous. Not restricted, as per IATA special provision A152

    Example2: Triazole-based crystals in cryogenic dewar: Molecular crystals for scientific experiments at Elettra Synchrotron (Trieste, Italy) – EU harmonized tariff number: TARIC 2933XXX. Pure research purposes.  Not dangerous, not restricted, as per IATA special provision A152

    Example3: Triazole-based crystals within glass containers in dry box: Molecular crystals for scientific experiments at Elettra Synchrotron (Trieste, Italy) – EU harmonized tariff number: TARIC 2933XXX. Pure research purposes.  Not dangerous.

  • 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" [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 Marco Palci (marco.palci@elettra.eu, (+39) 040 375 8969)).
  • 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 8251/8068 (Warehouse)
    (+39) 3346715503 (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. 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 relative to the samples to be recovered. Select the dewar to be recovered from the list of the dewars relative to the proposal and find the link “Recover dewar”.
  2. Fill the form adding the information you got from your express courier. Courier name, tracking number, pick-up date, value. Please if you changed any of the informations suggested in point 2 above (e.g. commercial value) let us know using the Notes box.
    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.
    It is possible to follow the status of the dewar in Elettra using your VUO account.

 





Sample Holders

In order to speed up measures, bring your samples already mounted on specific holders. Hereafter we list some of the common holders adopted according to the sample size and nature. Special attention has to be taken to the chemical nature of the sample support in case of fluorescence (link) analysis. In case of doubts, do not hesitate to contact the beamline staff.

  • Single crystals – for structure determination (small molecules, MOF, proteins, ..): we strongly suggest to use SPINE standardized holders and exploit the sample changer for sample manipulation in cryogenic conditions. Pin type and relative holders are described in detail hereafter. We can send you some holders and relative containers if needed. (contact the  beamline staff).
  • Powder samples in capillary: use borosilicate, kapton or quartz capillaries according to your needs. It is possible to use the classical pin support (fig.1) – mounting manually each sample – or a standardized SPINE base and use the sample changer for automatic sample manipulation and alignment to the photon beam.  In this case we recommand to keep the capillary length from 20 to 30 mm in order to allow the use of plastic vial caps (see "Single Crystal" samples section)  
  • Grazing incidence diffraction experiments: TBD
  • Bulky samples: voluminous or heavy (up to 500 grams) can be fixed directly on the goniometer head using the interface described in figure 3. In designing the sample support, goniometer linear and angular ranges as well as distances to X-ray nozzle, detector surface, and beam stopper have to be taken into account.

 

Sample Changer

The sample changer has a capacity of 50 samples mounted on SPINE standard bases. The sample changer can work in cryogenic conditions (e.g. single crystals for structure determination) as well as at room temperature (e.g. loose powders in capillaries). The sample changer uses ESRF SPINE style pucks and can accommodate 5 pucks at the time. We recommend that you use the pucks barcode to identify them and enable us to quickly locate your samples.

  • Cryogenic samples are expected to arrive at Elettra in dedicated dewars. In these cases (small molecules, MOF, proteins, etc.) we suggest to use SPINE bases with datamatrix 2D barcode printed on white background (they don't rust, last longer and are easier to read – see figures).  The sample-supporting pin should be 22 mm in length from the base to the start of the loop (this is default for the beamline: contact the beamline staff for different dimensions!). Samples on the relative bases have to be closed in the relative SPINE plastic vial (avoid screw-able and old-style vials!). Samples can be transferred to the relative containers (pucks, see figures below ) at the beamline if necessary.
  • Room temperature samples (like lose powders in capillaries or other small samples) are expected to be mounted on SPINE bases (we suggest to use bases with datamatrix 2D barcode printed on white background as are easier to read – see figures). Samples (in particular capillaries) must extend between 20 and 30 mm and have to allow the use of the SPINE plastic vial to encapsulate the sample. Please note that to be used for capillaries larger than 500 microns in diameter, the SPINE base have to be adapted, expanding opening to an appropriate size. Capillaries need to be glued at the base.
If needed, appropriate supports (bases, caps and pucks) are available at the beamline and can be borrowed. Supports can also be sent to your home institution to be prepared and sent back for remote or deputed data collection. Ask the beamline staff for availabilities.

 











Retrieving data

Data colected with the Pilatus 2M detector is firstly stored in the controller server (pilatus.blcs, accessible also from pesca.blcs at /net/pilatus/home/det/p2_det/images/projects/) and then moved to a remote server (memory4xrd1.esce), from where users can access data with their linux account created during the user login (login is the first part before the "@" of the mail registered in the VUO and password is the same of VUO account).
From pesca.blcs, it is possible to synchronize the data from the pilatus.blcs using rsync. From a terminal use the command:
rsync -urvv /net/pilatus/home/det/p2_det/images/projects/"project_name"/* "login"@memory4xdr1.esce:/store/projects/"project_name"/
using the user login, password and project_name used for the data collection. Please be careful with the "*" and the "/".

From pomodoro and paprika

The remote server can be accessed at /net/memory4xrd1/store/projects/"project_name" .
From the desktop main menu, it is possible to execute the "Elettra XRD Backup" utility (under Education) to create a link on the desktop: "browse" the folders to /net/memory4xrd1/store/projects/ , double-click on your project folder and then click the large button "Let me access ..." ; a link will  be created on the desktop in the ElettraProjects folder.

From laptop

It is possible to connect with a personal laptop to the memory4xrd1 server through a wired connection.
Near the monitors of the data collection workstation there is an ethernet plug that can be used: the ethernet connection should be set to DHCP (automatic) setting, eventually switching off other wifi connections, VPN connections or firewall restrictions.
You should see a connection as "undefined network" without internet connection: that is correct because the link is meant only for data transfer.
Check the connection using ping from a terminal/command prompt: ping memory4xrd1.esce.elettra.triete.it.
If the host is responding, you should be able to use ssh, scp, sftp, rsync or samba using the credentials used for the data collection project.
Under linux/mac all the different protocols should be available: from the file manager (es. Nautilus) it should be possible to find "Connect to server ..." and use smb://"user"@memory4xrd1.esce.elettra.trieste.it/store/projects/"project_name" or similar for sftp://, ssh://, rsync://, scp://.
Under Windows machines, samba should be used as it is already available, otherwise you need to install third party software (winscp, puttysftp, ...). If one of the "Netwok"/"My Computer"/"This PC" icon is present on the desktop (otherwise open a file manager and you should see a "Netwok"/"My Computer"/"This PC" icon on the left column) right click on that and select "Map a Network drive ..."; insert \\memory4xrd1.esce.elettra.trieste.it\store\projects\"project_name" in the resource field; check the "Connect using different credentials"; click finish and, if everything is ok, insert login and password when asked. A File manager should open and show you your files.

From home

At the moment the only possibility is to ask a beamline scientist to create a link for retrieving the data (with drive.elettra, a service similar to Dropbox).


 

Ultima modifica il Martedì, 17 Novembre 2020 11:15