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Eiger: Difference between revisions
→General aspects
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== General aspects == | == General aspects == | ||
# It is advisable to use the most recent 64bit version of XDS (since version Oct 15, 2015 the 32bit versions are no longer distributed anyway). The idea of the new framecache in XDS is that RAM is used to save on I/O. To this end, XDS tries to store NUMBER_OF_IMAGES_IN_CACHE=DELPHI/OSCILLATION_RANGE images in memory. Each frame is stored as (number of pixels)*(4 bytes) which means 72 MB in case of the Eiger 16M. As an example: if DELPHI=20 and OSCILLATION_RANGE=0.05 your computer has to have 400*72MB = 29GB of memory (plus some more for the program and the operating system). If it has not, the fallback is to the old behaviour of reading each frame three times. | # It is advisable to use the most recent 64bit version of XDS (since version Oct 15, 2015 the 32bit versions are no longer distributed anyway). The idea of the new framecache in XDS is that RAM is used to save on I/O. To this end, XDS tries to store NUMBER_OF_IMAGES_IN_CACHE=DELPHI/OSCILLATION_RANGE images in memory. Each frame is stored as (number of pixels)*(4 bytes) which means 72 MB in case of the Eiger 16M. As an example: if DELPHI=20 and OSCILLATION_RANGE=0.05 your computer has to have 400*72MB = 29GB of memory (plus some more for the program and the operating system). If it has not, the fallback is to the old behaviour of reading each frame three times. | ||
# Dectris provides [https://www.dectris.com/news.html?page=2 H5ToXds] (Linux only!) which is needed by XDS. As an alternative, one could use GlobalPhasing's hdf2mini-cbf program (needs autoPROC license) or, from http://www.mrc-lmb.cam.ac.uk/harry/imosflm/ver721/downloads, the eiger2cbf-osx or eiger2cbf-linux program written by T. Nakane. | # Dectris provides [https://www.dectris.com/news.html?page=2 H5ToXds] (Linux only!) which is needed by XDS. That program converts (as the name indicates) the HDF5 files to CBF files; however, it does not write the geometry and other information into the CBF header (therefore, [[generate_XDS.INP]] does not work with these files). As an alternative, one could use GlobalPhasing's hdf2mini-cbf program (needs autoPROC license) or, from http://www.mrc-lmb.cam.ac.uk/harry/imosflm/ver721/downloads, the eiger2cbf-osx or eiger2cbf-linux program written by T. Nakane. These programs do write a useful CBF header. | ||
# For faster processing (Linux only | # For faster processing (Linux only; script needs to be adapted for OSX), the [[Eiger#A_script_for_faster_XDS_processing_of_Eiger_data|shell script]] below should be copied to /usr/local/bin/H5ToXds and made executable (<code>chmod a+rx /usr/local/bin/H5ToXds*</code>). The binary H5ToXds then should be named e.g. /usr/local/bin/H5ToXds.bin - note the .bin filename extension! The script ''also'' uses RAM to speed up processing; it uses it for fast storage of the temporary file that H5ToXds/eiger2cbf/hdf2mini-cbf writes, and that each parallel thread ("processor") of XDS reads. The amount of additional RAM this requires is modest (about (number of pixels)*(number of threads) bytes). | ||
A suitable [[XDS.INP]] may have been written by the data collection (beamline) software. Latest [[generate_XDS.INP]] or the XDS_from_H5.py script (below) can be used if XDS.INP is not available. | A suitable [[XDS.INP]] may have been written by the data collection (beamline) software. Latest [[generate_XDS.INP]] (<code>generate_XDS.INP xxx_master.h5</code>) or the XDS_from_H5.py script (below) can be used if XDS.INP is not available. | ||
== Compression == | == Compression == | ||