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XRD2 Info for Users

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

From the computer where you collect data (cumin), you can only visualise your raw data by starting DECTRIS Albula 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 (badger) the path will have this pattern.

/net/online4xrd2/store/projectNumber/SampleName/run#/rawdata/*cbf    *** read only directory ***
/net/online4xrd2/store/projectNumber/SampleName/run#/work/                 *** writable directory ***

The projectNumber  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 that 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 be 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

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

  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..):

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

mount -t davfs "The_link_you_generate_on_VUO (i.e. download2.grid.elettra.trieste.it/prox_abcde123456)" "Your_local_mount_point_folder_name"
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

If you have any issues please contact the beamline scientists,


Last Updated on Tuesday, 04 August 2020 11:38