EXI allows to provide information about the samples in a shipment uploading one or more CSV files. This document contains information about the format and contents of the CSV file. Since 2024, the CSV sample list can also be used to supply data collection parameters for automated exporiments (for eligible projects only).
A CSV file is a plain text format mainly used to store tabular data. CSV means Comma-Separated Values then each value is separated with a comma. Example:
Dewar1,MX001,Unipuck,1,HEWL,xtal101,,P43212,77.4,77.4,37.2,90,90,90,,,,,,,,,Lysozyme test crystal
This line describes a Hen Egg White Lysozyme crystal, located in the position 1 of a Unipuck labeled ‘MX001’ included in a parcel called ‘Dewar1’. Optional or unused columns can be left empty, although the separating commas must be present.
Using a file like this makes it easier to edit, update or correct the sample information; the CSV file also acts as a backup. The advantage of using a CSV file and not a Excel file is that CSV is a standard format that can be handled in all different operating systems and it does not depend on any program.
Note: All the fields in the CSV file are case-sensitive
| Value | Description | Example |
|---|---|---|
| Parcel (compulsory) | Identifier of the parcel. If it does not exist, it will be created automatically | Dewar1 |
| Container name (compulsory) | It must match the value engraved in the puck | MX001 |
| Container type (compulsory) | Only Unipucks are accepted at MAX IV | Unipuck |
| Container position (compulsory) | Sample position in the container | 1 |
| Protein acronym (compulsory) | Case sensitive. Must have been saved previously to the sample database | HEWL |
| Crystal name (compulsory) | Name of the sample. Must be unique for the protein | xtal101 |
| Pin barcode (not used) | For the user’s records | |
| Crystal form (optional) | If present, used for strategy calculation and autoprocessing. | P43212,77.4,77.4,37.2,90,90,90 |
| Experimental parameters in rows 9-21 | Used only to enter a data collection plan for automated experiments. See below | |
| Comment (not used) | For the user’s records | Lysozyme test crystal |
Some of the fields in the CSV file can be used to define a “diffraction plan” or data collection parameters which can be read in MXCuBE for fully automated data collection for all the samples with valid entries in these columns. Since an invalid parameter will cause MXCuBE to stop, we recommend to download and use our provided Excel template with input validation.
Once the sample list is filled up, the file can be saved in CSV format prior to importing to EXI. Note: Make sure that the comma is used as the separator when saving the Excel file to CSV format. OpenOffice prompts for the separator before saving, but Word may use a semicolon by default depending on your language settings.
The following columns must be provided for a valid diffraction plan:
| Value | Description | Example |
|---|---|---|
| experimentType | The value “Default” indicates that a diffraction plan is present for the sample | Default |
| aimed resolution | Maximum resolution (A) at the edge of the detector (fully inscribed circle). Refer to the BioMAX User Information page for the resolution limit at different energies | 1.5 |
| beam diameter | Beam size (microns). It should match as closely as possible the crystal size. Accepted values are: 100, 50 and 20 | 50 |
| total rot. angle | Full rotation in degrees | 360 |
| energy | X-ray beam energy in keV. 17 keV is recommended for collection with the new Eiger2 detector, except when collecting anomalous signal or atomic resolution data | 17.0 |
| transmission | Percentage (%) of the full beam. Most crystals can tolerate 360 deg. collection at BioMAX with 100 % transmission and 0.02 s/deg exposure | 100 |
| exposure time | Exposure per image in seconds for rotation data collection. We recommend 0.002 seconds with 0.1 degree frames | 0.002 |
| oscillation range | Rotation per frame (degrees). We recommend 0.1 degrees. | 0.1 |