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Generate XDS.INP: Difference between revisions

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added section for Bruker-sfrm data format. TH
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m →The script: Pilatus3 1M
 
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# revision 1.20 . KD 13/7/2024 Comment out line STRONG_PIXEL=4 in preparation for mid-2024 version of XDS.
# revision 1.20 . KD 13/7/2024 Comment out line STRONG_PIXEL=4 in preparation for mid-2024 version of XDS.
# revision 1.21 . Thomas Hauß 12/03/2025 define for Bruker sfrm format DET= Bruker-sfrm and corresponding section
# revision 1.21 . Thomas Hauß 12/03/2025 define for Bruker sfrm format DET= Bruker-sfrm and corresponding section
REVISION="1.21 (13-Mar-2025)"
# revision 1.22 . KD 28/5/2025 UNTRUSTED_RECTANGLEs for Pilatus3 1M, S/N 10-0159
REVISION="1.22 (28-May-2025)"


#
#
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  UNTRUSTED_RECTANGLE=    0 4149  3812 3851
  UNTRUSTED_RECTANGLE=    0 4149  3812 3851
eof
eof
# PILATUS 1M, S/N 10-0159
  elif [ "$NX" == "981" -a "$NY" == "1043" ]; then
    if ! grep -q Flat_field tmp2 ; then
    echo Flat_field not found, smaller UNTRUSTED_RECTANGLEs than for bigger Pilatus
    cat >> XDS.INP << eof
! the following specifications are for a detector _without_ proper
! flat_field correction; they mask one additional pixel adjacent
! to each UNTRUSTED_RECTANGLE
!EXCLUSION OF VERTICAL DEAD AREAS OF THE PILATUS3 1M, S/N 10-0159
UNTRUSTED_RECTANGLE= 487  495    0 1044
!EXCLUSION OF HORIZONTAL DEAD AREAS OF THE PILATUS3 1M, S/N 10-0159
UNTRUSTED_RECTANGLE=  0 982  195  213
UNTRUSTED_RECTANGLE=  0 982  407  425
UNTRUSTED_RECTANGLE=  0 982  619  637
UNTRUSTED_RECTANGLE=  0 982  831  849
eof
    else
    echo Flat_field found, smaller UNTRUSTED_RECTANGLEs than for bigger Pilatus
    cat >> XDS.INP << eof
!EXCLUSION OF VERTICAL DEAD AREAS OF THE PILATUS3 1M, S/N 10-0159
UNTRUSTED_RECTANGLE= 488  494    0 1044
!EXCLUSION OF HORIZONTAL DEAD AREAS OF THE PILATUS3 1M, S/N 10-0159
UNTRUSTED_RECTANGLE=  0 982  196  212
UNTRUSTED_RECTANGLE=  0 982  408  424
UNTRUSTED_RECTANGLE=  0 982  620  636
UNTRUSTED_RECTANGLE=  0 982  832  848
eof
    fi
# Pilatus 12M
   elif [ "$NX" == "2463" -a "$NY" == "5071" ]; then
   elif [ "$NX" == "2463" -a "$NY" == "5071" ]; then
     : # handled above, before writing XDS.INP, untrusted regions come from site file
     : # handled above, before writing XDS.INP, untrusted regions come from site file
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== Limitations ==
== Limitations ==


* 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 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, and Bruker sfrm Version 18 . 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.
* 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.
* At some beamlines, the ROTATION_AXIS needs to be -1 0 0 ("backwards") instead of the usual 1 0 0 ("horizontal"), or even 0 1 0 ("vertical") like at one of the PETRA Hamburg BLs. The frame headers do not have this information, but for some beamlines the correct value has been implemented in the script. For other beamlines, the default chosen by [[generate_XDS.INP]] may be wrong and need manual correction of XDS.INP. The correct choice can be enforced by you with a [[Generate_XDS.INP#Site_Files|site file]]. Pls also see the article [[Beamline notes]].
* At some beamlines, the ROTATION_AXIS needs to be -1 0 0 ("backwards") instead of the usual 1 0 0 ("horizontal"), or even 0 1 0 ("vertical") like at one of the PETRA Hamburg BLs. The frame headers do not have this information, but for some beamlines the correct value has been implemented in the script. For other beamlines, the default chosen by [[generate_XDS.INP]] may be wrong and need manual correction of XDS.INP. The correct choice can be enforced by you with a [[Generate_XDS.INP#Site_Files|site file]]. Pls also see the article [[Beamline notes]].
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