DOI: 10.5281/zenodo.2412269
title: Example HDF5 / NeXus data set from Diamond Light Source I04 with Eiger 2 16M detector

description: Updated version with fixed master NeXus file - with the correct depends-on hierarchy added:

<pre>+ .
  + /entry/sample/transformations/omega
    + /entry/sample/transformations/sam_z
      + /entry/sample/transformations/sam_y
        + /entry/sample/transformations/sam_x
          + /entry/sample/transformations/chi
            + /entry/sample/transformations/phi
</pre>

Sample depends on phi not omega (only important if &gt; 1 sweep under consideration or shadowing a concern.)

 

 

Thaumatin data set taken from Diamond Light Source beamline I04 with Eiger2 16M detector, taken during detector commissioning, to allow software developers to test data reduction and image viewing software. 

 

Processing with xia2 / DIALS gives:

 

<pre>For AUTOMATIC/DEFAULT/SAD                    Overall    Low     High
High resolution limit                           1.26    3.42    1.26
Low resolution limit                           54.07   54.12    1.28
Completeness                                   99.5   100.0    94.5
Multiplicity                                   20.6    23.5     5.2
I/sigma                                        11.3    60.8     0.5
Rmerge(I)                                     0.147   0.050   1.217
Rmerge(I+/-)                                  0.144   0.049   1.136
Rmeas(I)                                      0.150   0.051   1.354
Rmeas(I+/-)                                   0.150   0.051   1.363
Rpim(I)                                       0.031   0.010   0.572
Rpim(I+/-)                                    0.042   0.014   0.735
CC half                                       0.999   1.000   0.484
Wilson B factor                               8.694
Anomalous completeness                         98.7    99.6    85.2
Anomalous multiplicity                         11.0    13.7     2.8
Anomalous correlation                        -0.021  -0.004  -0.037
Anomalous slope                               0.643
dF/F                                          0.085
dI/s(dI)                                      0.583
Total observations                          1436998   90941   16809
Total unique                                  69841    3869    3236
Assuming spacegroup: P 4 2 2
</pre>

Data are in blocks of 1,000 images, with both "Dectris style" master file and NeXus master file (both point at the same underlying data). The former is to work with e.g. XDS which requires that file name; the latter is more compliant with the standard, both work with DIALS.

 

For processing with XDS needs durin plugin from https://github.com/DiamondLightSource/durin

 

XDS.INP:

 

<pre>DETECTOR=PILATUS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=65535
SENSOR_THICKNESS= 0.450
!SENSOR_MATERIAL / THICKNESS Si 0.450
!SILICON= 3.960372
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 1.021
FRACTION_OF_POLARIZATION= 0.999
POLARIZATION_PLANE_NORMAL= 0.000 1.000 0.000
NAME_TEMPLATE_OF_DATA_FRAMES= /dls/i04/data/2018/cm19645-5/20181214/gw/Eiger/Thaum/thaumatin_9/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
</pre>

Data collection parameters:


	distance 200 mm 
	oscillation 0.15 degrees
	wavelength 0.97950 angstroms
	transmission 20% / flux 4.96e10 ph/s / beam size 26 x 15 µm
	exposure time 0.008s (125 frames / s) - total collection time 19.2s


Experimental geometry shown in screen shot.