Jayden: "==This note is based on Linux Mint 21.3==, it should be also"

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@jaydentseng

Jayden·6 months ago

==This note is based on Linux Mint 21.3==, it should be also useful if you running a Ubuntu.

XDS Related Software

Reference：https://wiki.uni-konstanz.de/xds/index.php/Installation

XDS package:

wget https://xds.mr.mpg.de/XDS-INTEL64_Linux_x86_64.tar.gz --no-check-certificate
# For some reason, wget cannot verify the server's SSL Certificates, add the --no-check-certificate parameter to igonre it

tar -xzvf XDS-INTEL64_Linux_x86_64.tar.gz
mv XDS-INTEL64_Linux_x86_64 /usr/local/bin/
ln -sf /usr/local/bin/XDS-INTEL64_Linux_x86_64/* /usr/local/bin/

Other programs: XDS-Viewer, XDSSTAT, XDSCC12, XDSGUI, XSCALE_ISOCLUSTER, spot2pdb, generate_XDS.INP

mkdir -p $HOME/xds-dep && cd $_
wget -N https://wiki.uni-konstanz.de/pub/linux_bin/get_folder.sh
chmod +x get_folder.sh
sudo ./get_folder.sh
rm -rf $HOME/xds-dep

#As root, programs will be installed into /usr/local/bin/linux_bin, and links them to /usr/local/bin.
#As a normal user, programs will be installed to HOME/bin/linux_bin, and linked to your $HOME/bin.

sudo apt install -y libxcb-xinerama0 xxdiff libqt5gui5 libqt5printsupport5 libqt5opengl5

Option: check the installation(you may encounter the graphics packages error):

ldd `which xdsgui` | grep found
# The command should show you the libraries it didn't find.
# Then you can install the libraries with commands:

sudo apt update
sudo apt upgrade
sudo apt install -y <PackageName>

XDS plugin that reads hdf5 files:

sudo apt update
sudo apt install -y build-essential libssl-dev libreadline-dev zlib1g-dev cmake git libgtk-3-dev qt5-default
git clone https://github.com/dectris/neggia && cd neggia
mkdir build && cd $_
cmake .. -DCMAKE_BUILD_TYPE=Release
cmake --build .
sudo cp src/dectris/neggia/plugin/dectris-neggia.so /usr/local/bin/linux_bin
echo export NEGGIA_PATH=/usr/local/bin/linux_bin/dectris-neggia.so >> $HOME/.bashrc
source $HOME/.bashrc

CCP4

Reference: https://www.ccp4.ac.uk/download/installation.html

Download Package Manager on this website, then:

cd /path/to/download/folder
tar -xvzf linux-x86_64_ccp4-8.0-setup.tar.gz
./ccp4-8.0-setup

Follow the instructions in Setup Manager's pages, and remember check "modify command line environment" in 2nd page.

Phenix

Reference: https://phenix-online.org/documentation/install-setup-run.html

Request a license on this website.
Download software on this website.

Install

tar xvf phenix-installer-<version>-<platform>.tar
cd phenix-installer-<version>

# will make <directory>/phenix-<version> and install there
./install --prefix=<directory>  
echo . /usr/local/phenix-<version>/phenix_env.sh >> $HOME/.bashrc
source $HOME/.bashrc

Then you can run phenix with phenix &

autoPROC

Reference: https://www.globalphasing.com/autoproc/download/academic/snapshot/Ubuntu1804_64bit/index.html

Request a license on this website, the user and password used to download and a .licence file will be sent to your email.
Installed CCP4 and XDS and set the environment as above.
Pre-requirement:
```
sudo apt-get install imagemagick
```

Download

mkdir -p $HOME/GPhL/autoPROC_snapshot_20240123 && cd$_
wget --http-user=user --http-password=password https://www.globalphasing.com/autoproc/download/academic/snapshot/GPhL_autoPROC_snapshot_20240123_install.sh
wget --http-user=user --http-password=password https://www.globalphasing.com/autoproc/download/academic/snapshot/GPhL_autoPROC_snapshot_20240123.linux64.tar
# Put .license file into this directory
# There should be three files in this directory: .tar, .sh, .licence

Install

chmod +x GPhL_autoPROC_snapshot_20240123_install.sh
./GPhL_autoPROC_snapshot_20240123_install.sh

cd $HOME/GPhL
rm -f autoPROC_latest
ln -s autoPROC_snapshot_20240123 autoPROC_latest
echo source $HOME/GPhL/autoPROC_latest/setup.sh >> $HOME/.bashrc
source $HOME/.bashrc

autoPX2

You need to enter the QQ group to get more information, I provide a copy to download for convenience:

cd $HOME
wget https://pan.xxu.do/d/guest/local/autoPX2-beta3-Linux.tar.gz
tar -xzvf autoPX2-beta3-Linux.tar.gz && cd $HOME/autoPX2-beta3-Linux
echo export PATH=$HOME/autoPX2-beta3-Linux:$PATH >> $HOME/.bashrc
source $HOME/.bashrc
# You can choose the name of command to start the program, here is autopx
ln -s autoPXgui.sh autopx