The MX group are in the process of updating beamlines with Eiger2 X detectors. This page provides useful information on the detectors, the file format we are using here at Diamond and how to use, view and analyse the data.
| Detector | Eiger2 XE 16M | Eiger2 X 4M |
|---|---|---|
| Beamline | I04, (I03 asap) | VMXi |
| Active area (w x h, mm) | 311.2 x 327.8 | 155.2 x 162.5 |
| Pixels (w x h) | 4148 x 4362 | 2068 x 2162 |
| Pixel size (µm2) | 75 x 75 | 75 x 75 |
| Count rate capability (ph/s/pixel) | 107 | 107 |
| Point-spread function (pixel) | 1 | 1 |
| Silicon sensor thickness (µm) | 450 | 450 |
| Data format | HDF5 / NeXus | HDF5 / NeXus |
| Frame rate (Hz) | 560 | 560 |
With Eiger2 detectors the file format and handling has changed compared with Pilatus detectors. The Eiger detectors do not write individual cbf image files, instead using the HDF5 format which is well suited to handling large data sets at high data rates.
Diamond has developed it's own file structure optimised for our network to optimise detector performance here. The structure of the data is similar to that produced by the Dectris internal file writer, but is not the same. To this end you will need to follow the instructions below to view and process data.
An example of the files produced for a 3600 frame acquisition (Given the ID of thermolysin_xtal1):
Currently all data collection options are available (grid scans and rotation for MR, SAD and MAD, including line scan) with the exception of inverse beam SAD and wedge MAD.
We highly recommend fine slicing (omega 0.1o or 0.2o) with careful attention paid to speed and transmission (this is sample dependent however 25-100% transmission at 12.658 keV with 0.008 s exposure for 180-360o on I04 works well for reasonably diffracting crystals).
Collecting highly redundant, low dose data can be an effective way to collect high quality data, particularly if used in conjunction with random reorientation of the crystal using the multi-axis SmarGon goniometer. In this case using 5-20% transmission with 3 x 360o sweeps of a randomly reorientated crystal can be a useful strategy for a wide variety of use cases.
There are different approaches to screening crystals.
1) Using the 'Data Collection/Screening' tab in GDA, collect three images 45 deg apart in omega with the following settings:
Results of the mosflm strategy will be visible in ISpyB. The XOalign results are also displayed in the case where a crystal alignment along a symmetry axis is possible.
2) Collect a low dose, continuous sweep, setting the detector resolution to the expected diffraction property of your sample. Suggested parameters (defaults in the GDA screening tab):
This data set will be processed automatically by fast_dp. The results can then be analysed with BEST as below. We are working on automating this and providing results via ISPyB and GDA as soon as possible.
3) Alternatively, collect a 180 deg low dose, continuous sweep, setting the detector resolution to the expected diffraction property of your sample. Suggested parameters:
This data set will be processed automatically by fast_dp and the results might already be satisfactory. Otherwise the data collection parameters can be adjusted accordingly.
Images can be viewed when at or connected to Diamond via NX with the following software
Albula
On the command line:
> module load albula
> albula
or double click on the Albula icon in Desktop_Launchers
Open master file.
Use tools:histogram to adjust contrast (both lower and upper levels) - autocontrast currently not working. Good starting values are: Background -4.0, Foreground 4.0
DIALS image viewer
On the command line:
> module load dials
> dials.image_viewer /path/to/image_master.h5
See DIALS image viewer manual here
ADXV
On the command line:
> module load adxv
> adxv
Browse to image folder and open the eg image_000001.h5 file (or image_000002.h5 etc) you wish to view, not the image_master.h5.
Zooming in to 50% or 100% shows the image with good contrast settings automatically.
For correct display of resolution edit the detector distance, pixel size (0.075), wavelength and beam centre X and Y in Adxv Settings.
With adxv as well as viewing individual frames, you can combine frames together using the slab fields. See page 29 of the adxv manual.
GDA Image Viewer
We are working on this.
Viewing results from Grid Scans
Results of the DIALs analysis are overlaid on the crystal image in both GDA and ISPyB. To view the diffraction images click on the box in the grid scan results tab or use your preferred image viewer from the list above. We aim to have the image viewing capabilities in ISPyB as soon as possible.
Autoprocessing
Autoprocessing with fast_dp, xia2 DIALS and xia2 XDS all work and results are available in ISPyB.
Reprocessing your data via ISPyB works also. Instructions are here.
Manual Processing
DIALS
For manual processing with DIALS, xia2 is probably easiest -
> module load xia2
> xia2 pipeline=dials image=/path/to/master.h5
If you have a massive data set i.e. multiple turns it can be substantially quicker to process this in blocks i.e.
> xia2 pipeline=dials image=/path/to/master.h5:1:9600:1200
to process in 8 x 1200 image blocks (relates to how DIALS refinement works).
DIALS Regular manual processing pipeline as shown in the tutorial will work fine:
XDS
For manual processing with XDS xia2 is probably easiest:
> module load hdf5/1.10
> module load xia2
> xia2 pipeline=3dii image=/path/to/master.h5 plugin=durin-plugin.so
You can also generate an XDS.INP input file automatically using eiger2xds as follows:
>module load dials
>module load hdf5
>eiger2xds path/to/master.h5
If manually creating an XDS.INP file, the specific lines needed for the EIGER detector are:
DETECTOR=EIGER MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=65535
SENSOR_THICKNESS= 0.450
NX=4148 NY=4362 QX=0.0750 QY=0.0750
LIB=/dls_sw/apps/XDS/20180808/durin-plugin.so
If you wish to process at home with XDS, as above but you will need to locally install the durin-plugin - see https://github.com/DiamondLightSource/durin and adjust LIB path appropriately.
Example XDS.INP for I03 and I04:
DETECTOR=EIGER MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=65535
SENSOR_THICKNESS= 0.450
DIRECTION_OF_DETECTOR_X-AXIS= 1.00000 0.00000 0.00000
DIRECTION_OF_DETECTOR_Y-AXIS= 0.00000 1.00000 0.00000
NX=4148 NY=4362 QX=0.0750 QY=0.0750
DETECTOR_DISTANCE= 200.000000
ORGX= 2214.85 ORGY= 2301.00
ROTATION_AXIS= 1.00000 0.00000 0.00000
STARTING_ANGLE= 0.000
OSCILLATION_RANGE= 0.150
X-RAY_WAVELENGTH= 0.97950
INCIDENT_BEAM_DIRECTION= -0.000 -0.000 1.000
FRACTION_OF_POLARIZATION= 0.999
POLARIZATION_PLANE_NORMAL= 0.000 1.000 0.000
NAME_TEMPLATE_OF_DATA_FRAMES= /dls/i04/data/2018/cm19645-5/Thaum/thaumatin_9_1_??????.h5
TRUSTED_REGION= 0.0 1.41
DATA_RANGE= 1 3600
JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT
LIB=/dls_sw/apps/XDS/20180808/durin-plugin.so
Diamond Light Source is the UK's national synchrotron science facility, located at the Harwell Science and Innovation Campus in Oxfordshire.
Copyright © 2022 Diamond Light Source
Diamond Light Source Ltd
Diamond House
Harwell Science & Innovation Campus
Didcot
Oxfordshire
OX11 0DE
Diamond Light Source® and the Diamond logo are registered trademarks of Diamond Light Source Ltd
Registered in England and Wales at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom. Company number: 4375679. VAT number: 287 461 957. Economic Operators Registration and Identification (EORI) number: GB287461957003.
Macromolecular Crystallography
Macromolecular
Soft Condensed 
Imaging and
Biological
Magnetic
Structures and
Crystallography 
Spectroscopy