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Furthermore, you want 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>.
 
Furthermore, you want 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>.
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== Mac OSX ==
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== macOS ==
    
=== [[XDS]] package ===
 
=== [[XDS]] package ===
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  xattr -dr XDS-OSX_64/*
 
  xattr -dr XDS-OSX_64/*
 
if you get a security error popup (google "xattr com.apple.quarantine catalina").
 
if you get a security error popup (google "xattr com.apple.quarantine catalina").
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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 .
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==== considerations for a macOS machine with Apple M1 processor ====
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Change the above <code>curl</code> and <code>ln</code> commands to
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curl -L -o - https://xds.mr.mpg.de/XDS-Apple_M1.tar.gz | tar xzvf -
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ln -sf XDS-Apple_M1/* .
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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 source code]).
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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.
    
=== Prerequisites (Xcode, CCP4) for [[generate_XDS.INP]], [[XDSGUI]] and other programs ===
 
=== Prerequisites (Xcode, CCP4) for [[generate_XDS.INP]], [[XDSGUI]] and other programs ===
[[generate_XDS.INP]] requires the [https://developer.apple.com/download/more/ Xcode command line tools] to be installed (free of charge): open a Terminal window, and enter <code>sudo xcode-select --install</code> (for Big Sur, the download has a size of about half a GB; the downloader is much too pessimistic about the time it takes).
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[[generate_XDS.INP]] requires the [https://developer.apple.com/download/more/ Xcode command line tools] to be installed (free of charge): open a Terminal window, and enter <code>sudo xcode-select --install</code> (the download has a size of about 750MB; the downloader is much too pessimistic about the time it takes).
    
Although CCP4 is not required by XDS itself, some of the programs (XDSSTAT, and MTZ file creation in XDSCONV, POINTLESS and COOT) use CCP4 tools or libraries. Therefore, CCP4 should be installed. Open a Terminal and check the existence of the file .zprofile , and its content:<pre>
 
Although CCP4 is not required by XDS itself, some of the programs (XDSSTAT, and MTZ file creation in XDSCONV, POINTLESS and COOT) use CCP4 tools or libraries. Therefore, CCP4 should be installed. Open a Terminal and check the existence of the file .zprofile , and its content:<pre>
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-rw-r--r--  1 kay  staff  107  7 Mär 09:41 .zprofile
 
-rw-r--r--  1 kay  staff  107  7 Mär 09:41 .zprofile
 
kay@Kays-MacBook-Air-2018 ~ % cat .zprofile
 
kay@Kays-MacBook-Air-2018 ~ % cat .zprofile
source /Users/kay/.profile
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source $HOME/.profile
 
# Added by CCP4 package manager:
 
# Added by CCP4 package manager:
 
. '/Applications/ccp4-7.1/bin/ccp4.setup-sh'
 
. '/Applications/ccp4-7.1/bin/ccp4.setup-sh'
 
</pre>If the file does not exist, create it - the easiest way is:
 
</pre>If the file does not exist, create it - the easiest way is:
 
<pre>
 
<pre>
echo . /Applications/ccp4-7.1/bin/ccp4.setup-sh > $HOME/.zprofile
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echo . /Applications/ccp4-7.1/bin/ccp4.setup-sh >> $HOME/.zprofile
 
</pre>The <code>get_folder.sh</code> script (below) checks the CCP4 setup, and creates the necessary files if needed.
 
</pre>The <code>get_folder.sh</code> script (below) checks the CCP4 setup, and creates the necessary files if needed.
    
Only Terminal windows that are opened afterwards will have access to the CCP4 programs!
 
Only Terminal windows that are opened afterwards will have access to the CCP4 programs!
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Become familiar with the concept and ways to run commands as "root" - google "mac osx become root". All the installation tasks that are run in a Terminal window require root privileges, since some of the programs and their links are written to /usr/local/bin. (As an alternative that does not require root for installation, one may create a directory $HOME/bin and use that for the programs and links. That would also require modification of the $PATH, by a one-time <code>echo 'export PATH=$PATH:$HOME/bin' >> ~/.profile</code>)
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Become familiar with the concept and ways to run commands as "root" - google "mac osx become root". All the installation tasks that are run in a Terminal window require root privileges, since some of the programs and their links are written to /usr/local/bin. (As an alternative that does not require root for installation, one may create a directory $HOME/bin and use that for the programs and links. That would also require modification of the $PATH, by a one-time <code>echo 'export PATH=$PATH:$HOME/bin' >> ~/.profile; echo 'export PATH=$PATH:$HOME/bin' >> ~/.zprofile</code>)
    
So, prepare the following steps by opening the Terminal window, and then
 
So, prepare the following steps by opening the Terminal window, and then
  sudo su                   # this will make you root, and ask for your password
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  sudo su               # this will make you root, and ask for your password
 
  mkdir /usr/local/bin  # only if /usr/local/bin was not created before
 
  mkdir /usr/local/bin  # only if /usr/local/bin was not created before
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In order to enable [[Eiger]] data processing, the <code>get_folder.sh</code> script  
 
In order to enable [[Eiger]] data processing, the <code>get_folder.sh</code> script  
# copies Dectris' Neggia library and DLS's Durin library into <code>/usr/local/lib64</code>
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# copies Dectris' Neggia library and DLS's Durin library into <code>/usr/local/lib64</code> (see above for Neggia and Durin on M1 Macs; the script does not yet handle this automatically)
 
# copies [https://www.globalphasing.com GlobalPhasing's] <code>hdf2mini-cbf</code> into <code>/usr/local/bin</code>, but under the name <code>H5ToXds</code> (consider getting a [https://www.globalphasing.com/autoproc/ autoPROC] license!)
 
# copies [https://www.globalphasing.com GlobalPhasing's] <code>hdf2mini-cbf</code> into <code>/usr/local/bin</code>, but under the name <code>H5ToXds</code> (consider getting a [https://www.globalphasing.com/autoproc/ autoPROC] license!)
 
# copies <code>h5dump</code> [https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.1/bin/unix/hdf5-1.12.1-Std-macos11_64-clang.tar.gz] into <code>/usr/local/bin</code>
 
# copies <code>h5dump</code> [https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.1/bin/unix/hdf5-1.12.1-Std-macos11_64-clang.tar.gz] into <code>/usr/local/bin</code>
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A [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-macOS10.13.dmg 10.13] Qt5 version of XDS-viewer (compiled by T. Hauß) works on macOS Catalina, and is installed by <code>get_folder.sh</code>. Older Macs need [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-0.6 this version]; newer macOS should install [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-macOS10.15.dmg 10.15]. For XDSGUI, the [https://{{SERVERNAME}}/pub/mac_bin/xdsgui_qt4.dmg Qt4 version] is still the default, but a [https://{{SERVERNAME}}/pub/mac_bin/xdsgui_qt5.dmg Qt5 version] is available (but needs Qt5 libraries!).
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A [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-macOS10.13.dmg 10.13] Qt5 version of XDS-viewer (compiled by T. Hauß) works on macOS Catalina, and is installed by <code>get_folder.sh</code>. Older Macs need [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-0.6.dmg this version]; newer macOS should install [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-macOS10.15.dmg 10.15]. For XDSGUI, the [https://{{SERVERNAME}}/pub/mac_bin/xdsgui_qt4.dmg Qt4 version] is still the default, but a [https://{{SERVERNAME}}/pub/mac_bin/xdsgui_qt5.dmg Qt5 version] is available (but needs Qt5 libraries!).
    
Lastly, it is useful (for e.g. XDSGUI) to install <code>xxdiff</code> from http://furius.ca/downloads/xxdiff/releases/macosx/ . I had to go to System Preferences > Security & Privacy > Privacy and add <code>xxdiff</code> to the programs with full disk access.
 
Lastly, it is useful (for e.g. XDSGUI) to install <code>xxdiff</code> from http://furius.ca/downloads/xxdiff/releases/macosx/ . I had to go to System Preferences > Security & Privacy > Privacy and add <code>xxdiff</code> to the programs with full disk access.
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A lot of technical detail is at [https://docs.microsoft.com/en-us/windows/wsl/compare-versions] .
 
A lot of technical detail is at [https://docs.microsoft.com/en-us/windows/wsl/compare-versions] .
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CCP4 supports WSL-1 ; see info at http://www.ccp4.ac.uk/download/#os=wsl .
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CCP4 documents use of WSL-1 ; see info at http://www.ccp4.ac.uk/download/#os=wsl .
    
Graphical Linux programs require installation of a X server like [https://sourceforge.net/projects/xming/files/latest/download Xming] or [https://sourceforge.net/projects/vcxsrv VcXsvr] or [https://mobaxterm.mobatek.net/ Mobaxterm] on the Windows host. There are helpful writeups (e.g. [https://wiki.ubuntu.com/WSL#Running_Graphical_Applications] and [http://wsl-guide.org/en/latest/]). VcXsrc seems to have a problem with coot for some people (see [https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=COOT;6ef4a967.2011 WSL2 installation] and responses). To use the X server with WSL, one has to say in the shell window
 
Graphical Linux programs require installation of a X server like [https://sourceforge.net/projects/xming/files/latest/download Xming] or [https://sourceforge.net/projects/vcxsrv VcXsvr] or [https://mobaxterm.mobatek.net/ Mobaxterm] on the Windows host. There are helpful writeups (e.g. [https://wiki.ubuntu.com/WSL#Running_Graphical_Applications] and [http://wsl-guide.org/en/latest/]). VcXsrc seems to have a problem with coot for some people (see [https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=COOT;6ef4a967.2011 WSL2 installation] and responses). To use the X server with WSL, one has to say in the shell window
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