Installation: Difference between revisions
→Troubleshooting: check for coot |
m remove the --no-check-certificate option from wget, since the MPG server xds.mr.mpg.de 's certificate was fixed on July 31, 2025. |
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=== [[XDS]] package === | === [[XDS]] package === | ||
If you are an academic user, as root (on Ubuntu, use "sudo -i" to become root) | If you are an academic user, as root (on Ubuntu, use "sudo -i" as a separate command, to become root): | ||
<pre> | <pre> | ||
cd /usr/local/bin | cd /usr/local/bin | ||
wget | wget -O- https://xds.mr.mpg.de/XDS-gfortran_Linux_x86_64.tar.gz | tar xzvf - | ||
ln -sf XDS-gfortran_Linux_x86_64/* . | ln -sf XDS-gfortran_Linux_x86_64/* . | ||
# until 2025-05-02 the XDS tarfile for Linux had a different name: | # until 2025-05-02 the XDS tarfile for Linux had a different name: | ||
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=== other programs: [[XDS-Viewer]], [[XDSSTAT]], [[XDSCC12]], [[XDSGUI]], [[XSCALE_ISOCLUSTER]], [[spot2pdb]], [[generate_XDS.INP]] === | === other programs: [[XDS-Viewer]], [[XDSSTAT]], [[XDSCC12]], [[XDSGUI]], [[XSCALE_ISOCLUSTER]], [[spot2pdb]], [[generate_XDS.INP]] === | ||
... can be downloaded from https://{{SERVERNAME}}/pub/linux_bin/ . A simple way to obtain them is to create an empty folder, "cd" to that folder and then | ... can be downloaded from https://{{SERVERNAME}}/pub/linux_bin/ . A simple way to obtain them is to create an empty folder, "cd" to that folder and then | ||
wget | wget -N https://{{SERVERNAME}}/pub/linux_bin/get_folder.sh | ||
chmod +x get_folder.sh | chmod +x get_folder.sh | ||
./get_folder.sh | ./get_folder.sh | ||
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sudo mkdir /usr/local/bin | sudo mkdir /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. Also, this requires modification of the $PATH, by a one-time | '''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. Also, this requires modification of the $PATH, by a one-time | ||
mkdir $HOME/bin | mkdir $HOME/bin | ||
echo 'export PATH=$PATH:$HOME/bin' >> ~/.zprofile | echo 'export PATH=$PATH:$HOME/bin' >> ~/.zprofile | ||
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if [ ! -e /usr/local/bin ]; then mkdir /usr/local/bin; fi | if [ ! -e /usr/local/bin ]; then mkdir /usr/local/bin; fi | ||
cd /usr/local/bin | cd /usr/local/bin | ||
# if the next command produces an error message, use the --insecure option | |||
curl -L -o - https://xds.mr.mpg.de/XDS-OSX_64.tar.gz | tar xzvf - | curl -L -o - https://xds.mr.mpg.de/XDS-OSX_64.tar.gz | tar xzvf - | ||
ln -sf XDS-OSX_64/* . | ln -sf XDS-OSX_64/* . | ||
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now enter the password, and then | now enter the password, and then | ||
if [ ! -e /usr/local/bin ]; then mkdir /usr/local/bin; fi | if [ ! -e /usr/local/bin ]; then mkdir /usr/local/bin; fi | ||
cd /usr/local/bin | cd /usr/local/bin | ||
curl -L -o - https://xds.mr.mpg.de/XDS-Apple_M1.tar.gz | tar xzvf - | # if the next command produces an error message, use the --insecure option | ||
ln -sf XDS-Apple_M1/* . | curl -L -o - https://xds.mr.mpg.de/XDS-Apple_M1.tar.gz | tar xzvf - | ||
ln -sf XDS-Apple_M1/* . | |||
exit | exit | ||
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source $HOME/.profile | source $HOME/.profile | ||
# Added by CCP4 package manager: | # Added by CCP4 package manager: | ||
source '/Applications/ccp4-8.0/bin/ccp4.setup-sh' | |||
# or | # or | ||
source '/Applications/ccp4-9/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 | echo source /Applications/ccp4-8.0/bin/ccp4.setup-sh >> $HOME/.zprofile | ||
# or | # or | ||
echo | echo source /Applications/ccp4-9/bin/ccp4.setup-sh >> $HOME/.zprofile | ||
# depending on which CCP4 version you have installed | # depending on which CCP4 version you have installed | ||
</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. | ||
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mkdir -p /usr/local/bin/mac_bin | mkdir -p /usr/local/bin/mac_bin | ||
cd /usr/local/bin/mac_bin | cd /usr/local/bin/mac_bin | ||
# if the next command produces an error message, use the --insecure option | |||
curl -O -R https://{{SERVERNAME}}/pub/mac_bin/get_folder.sh | curl -O -R https://{{SERVERNAME}}/pub/mac_bin/get_folder.sh | ||
chmod +x get_folder.sh | chmod +x get_folder.sh | ||
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mkdir -p /usr/local/bin/mac_bin | mkdir -p /usr/local/bin/mac_bin | ||
cd /usr/local/bin/mac_bin | cd /usr/local/bin/mac_bin | ||
# if the next command produces an error message, use the --insecure option | |||
curl -O -R https://{{SERVERNAME}}/pub/mac_bin/get_folder_silicon.sh | curl -O -R https://{{SERVERNAME}}/pub/mac_bin/get_folder_silicon.sh | ||
chmod +x get_folder_silicon.sh | chmod +x get_folder_silicon.sh | ||
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In order to enable [[Eiger]] data processing, the <code>get_folder.sh</code> (or <code>get_folder_silicon.sh</code>) script | In order to enable [[Eiger]] data processing, the <code>get_folder.sh</code> (or <code>get_folder_silicon.sh</code>) script | ||
# copies Dectris' Neggia library and DLS's Durin library into <code>/usr/local/lib64</code> . NOTE that the names of the native libraries for the Apple Silicon Macs ends with *-Apple-arm64.so | # copies Dectris' Neggia library and DLS's Durin library into <code>/usr/local/lib64</code> . NOTE that the names of the native libraries for the Apple Silicon Macs ends with *-Apple-arm64.so . | ||
# 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> | ||
For XDSGUI, you have a choice between the version for Intel Macs and that for Silicon Macs. Both do work on Silicon Macs, except for the plugin libraries - for these, the correct version (ending with -Apple-arm64.so) must be used together with xdsgui_mac_silicon. | For XDSGUI, you have a choice between the version for Intel Macs and that for Silicon Macs. Both do work on Silicon Macs, except for the plugin libraries - for these, the correct version (ending with -Apple-arm64.so) must be used together with xdsgui_mac_silicon. | ||