16. Software Installation

Tomography pipeline in Doppio is built on top of several software packages. To get the most of the pipeline you need following software packages installed on your PATH

16.1. Relion 5.0

Relion 5.0 Installation is covered https://relion.readthedocs.io/en/latest/Installation.html.

16.2. IMOD

IMOD Installation is covered https://bio3d.colorado.edu/imod/doc/guide.html.

These are some quick steps to install IMOD on Ubuntu 20.04 into the default location in the system.

wget https://bio3d.colorado.edu/imod/AMD64-RHEL5/imod_5.1.1_RHEL8-64_CUDA12.0.sh
sh imod_5.1.1_RHEL8_CUDA12.0.sh

The above script will install Imod in /usr/local and copy /usr/local/IMOD/IMOD-linux.sh to /etc/profile.d, which will be called on startup to import appropriate paths (i.e. IMOD_DIR). For whatever reason, if the above script fails to load IMOD, you can set variables as below:

export IMOD_DIR='/usr/local/IMOD'
export PATH="/usr/local/IMOD/bin:$PATH"
export LD_LIBRARY_PATH="/usr/local/IMOD/lib:$LD_LIBRARY_PATH"

16.3. AreTomo

AreTomo Installation is covered

16.4. CTFFind4.1

CTFFind4 can be downloaded from https://grigoriefflab.umassmed.edu/ctf_estimation_ctffind_ctftilt. To install, unpack the tarball and add the path to the binary to your PATH.

tar -xvf ctffind4.1.14-linux64.tar.gz
export PATH="/path/to/ctffind:$PATH"

16.5. MotionCor2

RELION has its own implementation of MotionCor2 for CPUs. We recommend using it because that allows to take the full advantage of the Bayesian polishing. However, if you want to use the GPU version of MotionCor2, you can download it from https://emcore.ucsf.edu/ucsf-software. To install. unpack the zip file and add the path to the binary to your PATH.

mkdir -p ~/MotionCor2
cd ~/MotionCor2
mv ~/Downloads/MotionCor2_1.6.4_Mar31_2023.zip .
unzip MotionCor2_1.6.4_Mar31_2023.zip
ln -s MotionCor2_1.6.4_Cuda121_Mar312023 MotionCor2
export PATH="${HOME}/MotionCor2:$PATH"

16.6. CryoCARE

cryoCARE Installation is covered https://pypi.org/project/cryoCARE/.