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Generate XDS.INP: Difference between revisions
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* 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. 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, | * 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]]. | ||
* 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 certain beamlines. | * 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 certain beamlines. | ||
* there are apparently several flavours of HDF5 files produced at Diamond Light Source. They differ e.g. in the naming of the header items. This means that items like NX, NY, DETECTOR_DISTANCE and number of images cannot always be determined by the [[generate_XDS.INP]] script. Example: The data at /dls/i04-1/data/2021/mx28114-9/processing/Lenye_Diamini/ThiL/ThiL found during the CCP4 2021 online Cape Town workshop. A workaround is to use e.g. xia2 pipeline=3dii to process these files, and - if needed - extract those items from its output files, e.g. from DEFAULT/NATIVE/SWEEP1/index/XDS.INP . | * there are apparently several flavours of HDF5 files produced at Diamond Light Source. They differ e.g. in the naming of the header items. This means that items like NX, NY, DETECTOR_DISTANCE and number of images cannot always be determined by the [[generate_XDS.INP]] script. Example: The data at /dls/i04-1/data/2021/mx28114-9/processing/Lenye_Diamini/ThiL/ThiL found during the CCP4 2021 online Cape Town workshop. A workaround is to use e.g. xia2 pipeline=3dii to process these files, and - if needed - extract those items from its output files, e.g. from DEFAULT/NATIVE/SWEEP1/index/XDS.INP . | ||