Instruments by Science Group

I03 Contact

Beamline Phone Number:
+44 (0) 1235 778707
 

Principal Beamline Scientist:
Katherine McAuley
 
Tel: +44 (0) 1235 778405 
E-mail: Katherine.McAuley@diamond.ac.uk

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Introduction

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.

Specifications

Detector     Eiger2 X 16M   Eiger2 X 4M
Beamline I03, I04 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) 133 560

 

File format

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 use 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):

  • thermolysin_xtal1_1.nxs
  • thermolysin_xtal1_1_header.cbf (header only - to be loaded in adxv before the h5 frame files) 
  • thermolysin_xtal1_1_master.h5
  • thermolysin_xtal1_1_000001.h5 (contains frames 1 - 1000)
  • thermolysin_xtal1_1_000002.h5 (contains frames 1001 - 2000)
  • thermolysin_xtal1_1_000003.h5 (contains frames 2001 - 3000)
  • thermolysin_xtal1_1_000004.h5 (contains frames 3001 - 3600)
  • thermolysin_xtal1_1_meta.h5

Data collection

The Pilatus3 6M detector on I03 was replaced by an Eiger 2X 16M detector in April 2019. The table below highlights the main differences between the 2 detectors.

Parameters Eiger2X 16M Pilatus3 6M Effects

Active area

(w x h, mm)

311.2 x 327.8 423.6 x 434.6 The Eiger is smaller than the Pilatus and the sample to detector distance will need to be reduced to achieve the same resolution. If you need better than 1.4 Å data, you will need to increase beamline energy. Use the MX Calculators to determine required energy

Pixels (w x h)

4148 x 4362 2463 x 2527  
Pixel size (µm2) 75 x 75 172 x 172  
Max Frame Rate (Hz) 133 100 Faster data collections. N.B. if you have weakly diffracting crystals and you previously needed to use long exposure times with 100% transmission with the Pilatus then you should use the same exposure times with the Eiger.
Data Format HDF5/NeXus CBF Image viewing and processing has changed. See details below.

 

Currently all data collection options are available (grid scans and rotation for MR, SAD and MAD, including line scans) with the exception of inverse beam SAD and wedge MAD.

We highly recommend fine slicing (omega 0.1o) with careful attention paid to speed and transmission (this is sample dependent - diffraction quality and radiation sensitivity and beamline dependent). On I03:

  • For strongly diffracting crystals 25% transmission at 12.7 keV with 0.008 s exposure for 360o.
  • For weakly diffracting crystals increase the transmission to the point where indexing is successful before increasing exposure times, paying careful attention to radiation sensitivity of your samples. You may need to combine data from more than 1 crystal.

These suggestions for data collection settings only apply to the default beamline energy of 12.7 keV, or very close by. Transmission should be reduced substantially at lower energies and increased at higher to reflect the varying interaction of photons with the sample. The settings were derived with the 100 micron aperture. If you have a smaller crystal and are using the 50 or 20 micron apertures, then you should increase the transmission, and reduce the total exposure time accordingly, if you have issues with insufficient spots found for indexing. A smaller aperture does not reduce radiation damage to the illuminated volume, so consider using multiple 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 1/4, 1/2, 1 X your usual transmission for 3 x 360o sweeps of a randomly reorientated crystal (chi=0/10/20) can be a useful strategy for a wide variety of use cases.

A typical example of this might be:

  • 360o sweep at 0.1o, 0.008s, 6% transmission chi=0
  • 360osweep at 0.1o, 0.008s, 12.5% transmission chi=10
  • 360o sweep at 0.1o, 0.008s, 25% transmission chi=20

Examine the 3 datasets for signs of radiation damage and truncate as appropriate. You can calculate the transmission to use for a single sweep once you have done this and use that for future collections. For more information on this approach, please see How best to use photons

Screening

Using the 'Data Collection/Screening' tab in GDA, collect three images 45 deg apart in omega with the following default settings:

  • oscillation angle = 0.5o
  • delta = 45.0o
  • exposure time = 0.01 s
  • number of images = 3
  • transmission = 100%
  • detector distance = 200 mm (or select a resolution you expect your crystal to diffract to)

Results of strategies from EDNA and mosflm will be available in ISPyB and can be applied via the strategies button in the Data Collection tab of the Data Collection view. The XOalign results are also displayed in the case where a crystal alignment along a symmetry axis is possible with the SmarGon multiaxis goniometer.

Image viewing

Images can be viewed when at or connected to Diamond via NX with the following software. We do not recommend you make decisions for data collections from viewing the compressed jpeg images you find in ISPyB. Please make use of available strategy information or by using the full image viewers below when making plans for data collections:

DIALS image viewer

From the DLS_Launchers folder on your desktop double click the Dials Image Viewer icon to open the last collected data set.

Alternatively to look at specific data sets use the Load File option from an already open viewer or, on the command line:

> module load dials
> dials.image_viewer /path/to/image_master.h5

See DIALS image viewer manual here

ADXV Autoload

The ADXV Autoload icon in the DLS Launchers has changed for the Eiger. It now launches a control window, through which you can cycle through your images, pause and unpause, and turn on/off features like resolution rings. It will automatically load image headers correctly, which won't happen through the normal adxv program (see below).

The commands are listed in the Control window, make sure the Control window is selected before pressing a key. By default, it will go to your latest data collection, and scroll through up to 30 images, at 3s intervals, with rings and weak data mode on. It will only find the latest dataset after it has finished collecting, so be patient.

ADXV

On the command line:

> module load adxv
> adxv

Browse to image folder and open the e.g. image_header.cbf file (in the figure below Thau_4_1_header.cbf) and then the image_000001.h5 file you wish to view (see figure), not the image_master.h5:

Zooming in to 50% or 100% shows the image with good contrast settings automatically.

With adxv as well as viewing individual frames, you can combine frames together using the slab fields. See figure below or page 29 of the adxv manual.

 

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

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.

Data processing

Autoprocessing 

Autoprocessing with fast_dp, xia2 DIALS and xia2 XDS and autoPROC 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 (do not currently use generate_XDS - this needs updating with this new detector):

> module load dials
> module load hdf5/1.10
> eiger2xds path/to/master.h5

If you wish to process with XDS at home then use the eiger2xds command as outlined above at Diamond and then copy home the generated XDS.INP file and update 

NAME_TEMPLATE_OF_DATA_FRAMES= /my/data/is/here/at/home

and you will need to locally install the durin-plugin - see https://github.com/DiamondLightSource/durin and adjust LIB path appropriately in your XDS.INP

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

Example XDS.INP for 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

 

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