To install WSL, you will need administrative access.
Start by launching a new Command Prompt with administraive access. This can be done by using the "Run as Adminstrator" option when right-clicking the Command Prompt icon.
Type
wsl --install -d ubuntu-22.04
This will install Ubuntu 22.04 as an available linux distribution. You will be prompted for a username and password. After the process completes, you should be inside a bash shell.
This is the only step that requires administraive access. You can open other Command Prompts normally and enter the linux environment with
wsl -d ubuntu-22.04
Additional linux dependencies are required for running Phenix and Coot. The sudo command is used since installing dependencies requires administrative rights in linux. The password will be the password you created when installing WSL. To install these dependencies type
sudo apt-get update
sudo apt-get install \
build-essential \
freeglut3-dev \
libglu1-mesa-dev \
libgtk2.0-0 \
libxxf86vm1 \
mesa-common-dev \
mesa-utils \
openssl \
x11-apps
For Coot, there is a build for Ubuntu 20.04 and for that build to work on Ubuntu 22.04, an older version of libssl needs to be installed. To do this, type
echo "deb http://security.ubuntu.com/ubuntu focal-security main" | sudo tee /etc/apt/sources.list.d/focal-security.list
sudo apt-get update
sudo apt-get install libssl1.1
sudo rm /etc/apt/sources.list.d/focal-security.list
sudo apt-get update
On Ubuntu, both en_US and en_GB are required. To install these locales, type
sudo locale-gen en_US.utf8 en_GB.utf8
If you on Windows 11, this step should not be needed. However, if you are on Windows 10, you will need to install an X11 server for Coot to work. These steps are for Windows, not Ubuntu. You can use the one from
https://sourceforge.net/projects/vcxsrv/
After installing the software, follow the directions here to set up the X11 server.
https://gist.github.com/Mluckydwyer/8df7782b1a6a040e5d01305222149f3c#2-window-server
Download the linux installer from the Phenix website. You can download the installer from a Windows browser. The Ubuntu installation will have access to C:\ in /mnt/c. You can go to your Windows download page by typing
cd /mnt/c/Users/<Windows username>/Downloads
The installer should be in that directory if you use your default folder for downloads.
The installer must be extracted on the linux filesystem. You can go to your linux home directory by typing
cd
This should go to /home/<linux username>. You can check with the
pwd
command.
To extract the linux installer, type
cd
tar -xf /mnt/c/Users/<Windows username>/Downloads/<Phenix installer file>
This will create a new directory in your linux home directory that will look like phenix-installer-<version>-<platform>. You can then run the installer by typing
cd phenix-installer-<version>-<platform>
./install --prefix ${HOME}
This will install Phenix into your linux home directory. The installation must be in the linux filesystem.
Download the Ubuntu 20.04 build of Coot 0.9.8 with this link
Like with the Phenix installer, extract it with
cd
tar -xf /mnt/c/Users/<Windows username>/Downloads/coot-0.9.8-binary-Linux-x86_64-ubuntu-20.04.4-python-gtk2.tar.gz
For the model viewer in Phenix to work, one of the files needed to be changed. You can do this by typing
ln -s -f /usr/lib/x86_64-linux-gnu/libstdc++.so.6 <Phenix directory>/conda_base/lib/libstdc++.so.6
To set up your linux environment to run Phenix, type
export LIBGL_ALWAYS_INDIRECT=0
source <Phenix directory>/phenix_env.sh
To simplify this, you can add these lines to your .bashrc file. Then, whenever a new linux shell is started, the Phenix environment will already be set up.
To start the Phenix GUI, type
phenix
Once you are in the main GUI, you can point Phenix to the location of Coot by opening the "Preferences", then go to "Graphics". You should see a field for "Coot path". In that field, type
/home/<linux username>/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/bin/coot