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Installation: Difference between revisions
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=== [[XDS]] package === | === [[XDS]] package === | ||
If you are an academic user, | If you are an academic user, | ||
echo you may have to "sudo su" first, to obtain administrator permissions! | echo you may have to "sudo su" first, to obtain administrator permissions! | ||
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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"). | ||
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 ==== | |||
Change the above <code>curl</code> and <code>ln</code> commands to | |||
curl -L -o - https://xds.mr.mpg.de/XDS-Apple_M1.tar.gz | tar xzvf - | curl -L -o - https://xds.mr.mpg.de/XDS-Apple_M1.tar.gz | tar xzvf - | ||
ln -sf XDS-Apple_M1/* . | ln -sf XDS-Apple_M1/* . | ||
If you want to process .h5 files written by Dectris' detectors, use the [https://strucbio.biologie.uni-konstanz.de/pub/mac_bin/dectris-neggia-Apple-arm64.so Neggia plugin for Apple ARM64 processors]. | If you want to process .h5 files written by Dectris' Eiger detectors, use the [https://strucbio.biologie.uni-konstanz.de/pub/mac_bin/dectris-neggia-Apple-arm64.so Neggia plugin for Apple ARM64 processors] in the LIB= line of [[XDS.INP]]. However, for data from Diamond Light Source 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]). | ||
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 === | ||
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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] . | ||
CCP4 | 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 | ||