Generate XDS.INP: Difference between revisions

== The script ==

<pre>

#!/bin/bash

# purpose: generate XDS.INP

# revision 1.17 . JMK 31/05/2023 fix sed error for Mac, where \| is not supported

# revision 1.18 . JMK 19/08/2023 Pilatus 12M support, give help msg if $5 defined (i.e. unquoted frame pattern)

#

       # Known detectors for reversed-phi at SSRF BL18U1 (S/N 60-0123) and BL19U1 (S/N XX-XXX) (!; 2019-10-19: staff will fix this)

       DET_SN=`grep "Detector:" tmp2 | sed "s/^.*Detector: *//"`

       REVERSEPHI_SNs="

PILATUS3 6M, S/N 60-0125

PILATUS3 6M, S/N 60-0127

PILATUS3 6M, S/N 60-0123

"

       if echo "${DET_SN}${REVERSEPHI_SNs}" | sort | uniq -d | grep [0-9] > /dev/null; then

     if [ -e $durin_path ]; then

       LIB="LIB=$durin_path"

     else

       LIB="!LIB=/usr/local/lib64/durin-plugin.so"

     fi

   fi

# end of generate_XDS.INP

</pre>

== System-wide or personal installation ==

Ask your system adminstrator to cut-and-paste the script into e.g. /usr/local/bin/generate_XDS.INP, and to make it "executable".

  chmod +x ~/generate_XDS.INP

After that, you can just run it in a similar way as if it were installed in your $PATH:

  wget http://wiki.uni-konstanz.de/xds/index.php/generate_XDS.INP -O - | \

   sed -e s/\&nbsp\;/\ /g -e s/\&gt\;/\>/g -e s/\&lt\;/\</g -e s/amp\;//g -e s/\&quot\;/\"/g -e s/\&\#\1\6\0\;/\ /g | \

  chmod +x generate_XDS.INP

</pre>

  curl -L -o - http://wiki.uni-konstanz.de/xds/index.php/generate_XDS.INP | \

   sed -e s/\&nbsp\;/\ /g -e s/\&gt\;/\>/g -e s/\&lt\;/\</g -e s/amp\;//g -e s/\&quot\;/\"/g -e s/\&\#\1\6\0\;/\ /g | \

  chmod +x generate_XDS.INP

</pre>

If you do use cut-and-paste from the webpage, be aware of the following problem report: On the Mac, after loading frames, by clicking “generate XDS.INP”, the program gives some strange symbol “” in XDS.INP. And the more you click “save” button, the more “” appear. This looks like e.g. <br>SPACE_GROUP_NUMBER=0  ! 0 if unknown <br>UNIT_CELL_CONSTANTS= 70 80 90 90 90 90  <br> ''The problem is due to the “Rich text” format in TextEdit when saving "generate_XDS.INP". It is solved by re-downloading the script, and changing format to Plain - everything should work then.''

== Calling generate_XDS.INP from a Python script ==

== Dependencies ==

The script makes use of many GNU commands, like <code>ls, grep, egrep, awk, cut, cat, echo, wc, bc, head, sed, tail, cp, od, python</code>. Some of them (like <code>od</code> and <code>python</code>) are only used in case of specific detectors (MarCCD and RAXIS, respectively).  

For Eiger data processing, the <code>h5dump</code> program must be installed. This is part of <code>hdf5-tools</code> (Ubuntu) or <code>hdf5</code> (RHEL). The .h5 files collected at Diamond Light Source require a very new version of h5dump (namely h5dump 1.10) to extract the OVERLOAD parameter from the .h5 file; this version is available by default in Ubuntu 20.04 and RHEL/CentOS 8.

See also [[Installation]].

== 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 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.

* 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 .