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For [[Eiger]] data processing, a h5dump binary (version 1.10 req'd for HDF5 data from DLS) and <code>H5ToXDS</code> is installed by the <code>get_folder.sh</code> script into /usr/local/bin. If the script is not used, <code>H5ToXDS</code> should be installed as [[Eiger|explained]], and <code>h5dump</code> should be installed by e.g. <code>yum -y install hdf5</code> (Ubuntu: <code>apt install hdf5-tools</code>) - but make sure that h5dump is version 1.10 or higher when processing HDF5 data from DLS. | For [[Eiger]] data processing, a h5dump binary (version 1.10 req'd for HDF5 data from DLS) and <code>H5ToXDS</code> is installed by the <code>get_folder.sh</code> script into /usr/local/bin. If the script is not used, <code>H5ToXDS</code> should be installed as [[Eiger|explained]], and <code>h5dump</code> should be installed by e.g. <code>yum -y install hdf5</code> (Ubuntu: <code>apt install hdf5-tools</code>) - but make sure that h5dump is version 1.10 or higher when processing HDF5 data from DLS. | ||
The LIB= feature for HDF5 files requires either the [https://www.dectris.com/company/news/newsroom/news-details/process-eiger-data-with-xds-fast Neggia] library (does not work for HDF5 data from DLS) or the [https://github.com/DiamondLightSource/durin Durin plugin]. These may be installed through the <code>get_folder.sh</code> script, in <code>/usr/local/lib64</code>. For using LIB= with .gz files, there is the xds-zcbf plugin. All plugins can also be found in [https://strucbio.biologie.uni-konstanz.de/pub/linux_bin the Linux installation directory.] | |||
== macOS == | == macOS == | ||
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Then make sure that the binaries are in the search path for executables, as explained in https://xds.mr.mpg.de/html_doc/downloading.html . | Then make sure that the binaries are in the search path for executables, as explained in https://xds.mr.mpg.de/html_doc/downloading.html . | ||
==== considerations for a macOS machine with Apple M1 processor ==== | If you want to process .h5 files written by Eiger detectors on a Mac with Intel CPU, use the [https://strucbio.biologie.uni-konstanz.de/pub/mac_bin/durin-plugin.so Durin plugin for Intel Mac processors] (source code [https://github.com/DiamondLightSource/durin available]) or the [https://strucbio.biologie.uni-konstanz.de/pub/mac_bin/dectris-neggia.so Dectris-Neggia plugin for Intel Mac processors] (source code [https://github.com/dectris/neggia available]). The latter may be faster, but does not work on data collected at Diamond Light Source. The former should in principle work for all HDF5 data. | ||
If you want to process *.cbf.gz files on a Mac with Intel CPU, you may get faster processing with the [https://strucbio.biologie.uni-konstanz.de/pub/mac_bin/xds-zcbf.so xds-zcbf plugin for Intel Mac processors] ([https://git.embl.de/nikolova/xds-zcbf source code]). | |||
==== considerations for a macOS machine with Apple M1 or M2 processor ==== | |||
Change the above <code>curl</code> and <code>ln</code> commands to | Change the above <code>curl</code> and <code>ln</code> commands to | ||
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A message like "Note: The following floating-point exceptions are signalling: IEEE_DIVIDE_BY_ZERO IEEE_UNDERFLOW_FLAG" may be printed after running XDS or XSCALE. This is harmless. | A message like "Note: The following floating-point exceptions are signalling: IEEE_DIVIDE_BY_ZERO IEEE_UNDERFLOW_FLAG" may be printed after running XDS or XSCALE. This is harmless. | ||
If you want to process .h5 files written by Eiger detectors, use the [https://strucbio.biologie.uni-konstanz.de/pub/mac_bin/durin-plugin-Apple-arm64.so Durin plugin for Apple ARM64 processors] ([https://github.com/DiamondLightSource/durin | If you want to process .h5 files written by Eiger detectors, use the [https://strucbio.biologie.uni-konstanz.de/pub/mac_bin/durin-plugin-Apple-arm64.so Durin plugin for Apple ARM64 processors] (source code [https://github.com/DiamondLightSource/durin available]) or the [https://strucbio.biologie.uni-konstanz.de/pub/mac_bin/dectris-neggia-Apple-arm64.so Dectris-Neggia plugin for Apple ARM64 processors] (source code [https://github.com/dectris/neggia available]). The latter may be faster, but does not work on data collected at Diamond Light Source. The former should in principle work for all HDF5 data. | ||
If you want to process *.cbf.gz files, | If you want to process *.cbf.gz files, you may get faster processing with the [https://strucbio.biologie.uni-konstanz.de/pub/mac_bin/xds-zcbf-Apple-arm64.so xds-zcbf plugin for Apple ARM64 processors] ([https://git.embl.de/nikolova/xds-zcbf source code]). | ||
=== Prerequisites (Xcode, CCP4) for [[generate_XDS.INP]], [[XDSGUI]] and other programs === | === Prerequisites (Xcode, CCP4) for [[generate_XDS.INP]], [[XDSGUI]] and other programs === | ||