Installation and Download

Installation

We recommend to use the conda client mamba for installation. You should use mambaforge for installation of mamba. Alternatively you can replace mamba with conda in the commands below.

There are three main steps to install TomoTwin:

1. Install TomoTwin

mamba env create -n tomotwin -f https://raw.githubusercontent.com/MPI-Dortmund/tomotwin-cryoet/main/conda_env_tomotwin.yml

2. Install Napari

Here we assume that you don’t have napari installed. Please do:

mamba env create -n napari-tomotwin -f https://raw.githubusercontent.com/MPI-Dortmund/tomotwin-cryoet/main/conda_env_napari.yml

3. Link Napari

This is an optional step, but for convenience reasons we link an adapted napari call into the tomotwin environment. With that you don’t need to switch environments when working with tomotwin. While this is optional, I assume during the tutorials that you did this step. Here is what you need to do:

conda activate tomotwin
tomotwin_dir=$(realpath $(dirname $(which tomotwin_embed.py)))
napari_link_file=${tomotwin_dir}/napari_boxmanager
conda activate napari-tomotwin
echo -e "#\!/usr/bin/bash\nexport NAPARI_EXE=$(which napari)\nnapari_exe='$(which napari_boxmanager)'\n\${napari_exe} \"\${@}\""> ${napari_link_file}
ln -rs $(which napari) ${tomotwin_dir}
chmod +x ${napari_link_file}
conda activate tomotwin

Update TomoTwin & Napari

To update an existing TomoTwin installation just do:

mamba env update -n tomotwin -f https://raw.githubusercontent.com/MPI-Dortmund/tomotwin-cryoet/main/conda_env_tomotwin.yml --prune
mamba env update -n napari-tomotwin -f https://raw.githubusercontent.com/MPI-Dortmund/tomotwin-cryoet/main/conda_env_napari.yml --prune

Download latest model

Last update

09.2023

Number of proteins

120

Link

Zenodo

System requirements

So far we run it on Ubuntu 20.04 and the following GPUs:

• NVIDIA V100

• NVIDIA RTX 2080

• NVIDIA A100