Example HDF5 / NeXus data set from Diamond Light Source I04 with Eiger 2 16M detector
- 1. Diamond Light Source
Description
Updated version with fixed master NeXus file - with the correct depends-on hierarchy added:
+ . + /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
Sample depends on phi not omega (only important if > 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:
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
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:
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
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.
Files
Screen Shot 2018-12-19 at 08.09.08.png
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