Generate XDS.INP: Difference between revisions

== The script ==

<pre>

# revision 1.01 . KD 07/12/2020 ROTATION_AXIS=0 -1 0 for Pilatus3 2M, S/N 24-0118 at ID23-2 (http://www.globalphasing.com/autoproc/wiki/index.cgi?BeamlineSettings)

# revision 1.02 . KD 11/01/2021 recognize mar555 detector as mar345 (thanks to Thomas Hauß, HZB)  

#                                                                                                             

SEPMIN=7.0

CLUSTER_RADIUS=3.5

dname=`echo "$1" | xargs dirname`

  grep -q BRUKER tmp2 && grep -q CBF tmp2  && DET=Bruker-cbf   

  grep -q CMOS1 tmp2 && DET=adsc-CMOS1   

else

  h5dump -d "/entry/instrument/detector/description" $FIRSTFRAME | grep -i Eiger > /dev/null && DET=eiger

   DETECTOR_DISTANCE=`grep ^DISTANCE tmp2 | sed s/DISTANCE=/-/`                                                                     

   OSCILLATION_RANGE=`grep OMEGA_DELTA tmp2 | sed s/OMEGA_DELTA=//`   

elif [ "$DET" == "pilatus" ]; then

   # STARTING_ANGLE:  the \- was introduced in version 0.91 to allow negative values :

     STARTING_ANGLE=`h5dump -d "/entry/sample/goniometer/omega_start" $FIRSTFRAME | awk '/\(0\): [\-0-9]/{print $2}'`

   # If rotation vector set (NeXus)

     rotation_axis=`h5dump -a "/entry/sample/transformations/omega/vector" $FIRSTFRAME 2>/dev/null | grep "(0):" | sed -e "s/^.*://; s/,//g"`

     SN=`h5dump -d "/entry/instrument/detector/detector_number" $FIRSTFRAME | awk '/\(0\): /{print $2}' | sed s/\"//g`

       rotation_axis="-1 0 0"

   fi

   DETECTOR="EIGER MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD= $OVERLOAD"

! however, if the spots from COLSPOT extend to 2A then POSITION could, and if 1.5A POSITION should be refined

REFINE(IDXREF)=CELL BEAM ORIENTATION AXIS  ! add POSITION if high resolution, or DETECTOR_DISTANCE inaccurate

! parameters specifically for this detector and beamline:

DETECTOR= $DETECTOR

echo BKGPIX.cbf, and the agreement of predicted and observed spots in FRAME.cbf!

rm -f tmp1 tmp2

</pre>

* The script tries to interpret the header of the frames, so is currently limited to Dectris (Pilatus, Eiger), ADSC (Quantum), Rigaku (several types), MAR (CCD and image plate) detectors, and one Bruker detector. Other detectors need some values to be manually filled into XDS.INP - the relevant places are marked with XXX. These are detector properties (type, pixel size and number, min and max counts in a pixel), and experimental parameters like ROTATION_AXIS, OSCILLATION_RANGE, X-RAY_WAVELENGTH, DETECTOR_DISTANCE, and XORG, YORG. For fine-tuning of detector parameters, see the [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_prepare.html detector-specific templates].

* The authors have made a "best effort" to provide a XDS.INP that results in the correct sign of the anomalous signal. In the case of one detector type (internally called Rigaku SMV) this requires reversal of one detector axis, and a negative DETECTOR_DISTANCE, as is found in some of the [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_prepare.html detector-specific templates]. '''For an unusual or unknown detector setup, the correct sign of the anomalous signal needs to be established and verified e.g. with a good dataset from a test crystal that has an anomalous signal.''' The authors do not take any responsibility for problems arising from incorrect sign of the anomalous signal, nor - obviously! - for any other mischief arising in or from data processing.

* Sometimes, the x- and y- values of the primary beam position recorded in the header should be used for ORGY and ORGX (i.e reversed) instead of as ORGX and ORGY. For ADSC, this has been implemented in the script for a number of beamlines.

== See also ==