scipion-em-aretomo 3.1

Plugin to use AreTomo program within the Scipion framework

This plugin provides a wrapper for AreTomo program.

Installation

You will need to use 3.0+ version of Scipion to be able to run these protocols. To install the plugin, you have two options:

1. Stable version

scipion installp -p scipion-em-aretomo

2. Developer’s version

   • download repository

   git clone -b devel https://github.com/scipion-em/scipion-em-aretomo.git

   • install

   scipion installp -p /path/to/scipion-em-aretomo --devel

AreTomo binaries will be installed automatically with the plugin, but you can also link an existing installation. Default installation path assumed is software/em/aretomo-1.2.5, if you want to change it, set ARETOMO_HOME in scipion.conf file to the folder where the AreTomo is installed. Depending on your CUDA version you might want to change the default binary from AreTomo_1.2.5_Cuda101_08-01-2022 to a different one by explicitly setting ARETOMO_BIN variable. If you need to use CUDA different from the one used during Scipion installation (defined by CUDA_LIB), you can add ARETOMO_CUDA_LIB variable to the config file. Various binaries can be downloaded from the official UCSF website.

To check the installation, simply run the following Scipion test:

scipion test aretomo.tests.test_protocols_aretomo.TestAreTomo

Licensing

AreTomo is free for academic use only. For commercial use, please contact David Agard or Yifan Cheng for licensing:

• [e-mail]

• [e-mail]

Supported versions

1.0.6, 1.0.8, 1.0.10, 1.0.12, 1.1.0, 1.1.1, 1.2.0, 1.2.5

Protocols

• tilt-series align and reconstruct

Detailed manual can be found in software/em/aretomo-1.2.5/bin/AreTomoManual-08-01-2022.pdf

References

• AreTomo: An integrated software package for automated marker-free, motion-corrected cryo-electron tomographic alignment and reconstruction. Shawn Zheng, Georg Wolff, Garrett Greenan, Zhen Chen, Frank G. A. Faas, Montserrat Bárcena, Abraham J. Koster, Yifan Cheng, David Agard. bioRxiv 2022.02.15.480593; doi: https://doi.org/10.1101/2022.02.15.480593