scipion-em-relion 3.0.1

Plugin to use Relion programs within the Scipion framework

This plugin provide wrappers around several programs of RELION software suite.

prod:

devel:

support:

IMPORTANT!

If you have imported movies with a gain file in DM4 format, you need to flip the gain reference upside-down in the motion correction protocol! (bug details)

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-relion

2. Developer’s version

   • download repository

   git clone https://github.com/scipion-em/scipion-em-relion.git

   • install

   scipion installp -p path_to_scipion-em-relion --devel

RELION sources will be downloaded and compiled automatically with the plugin, but you can also link an existing installation. Default installation path assumed is software/em/relion-3.1.1, if you want to change it, set RELION_HOME in scipion.conf file to the folder where the RELION is installed. If you need to use CUDA different from the one used during Scipion installation (defined by CUDA_LIB), you can add RELION_CUDA_LIB variable to the config file. Moreover, if you have to use a MPI for Relion different from Scipion MPI, you can set RELION_MPI_BIN and RELION_MPI_LIB variables in the config file.

To check the installation, simply run one of the tests. A complete list of tests can be displayed by executing scipion test --show --grep relion

Supported versions

3.1.0, 3.1.1

IMPORTANT: Relion-3.0 can be used with this plugin but we do not officially support it anymore, i.e. there will be no bugfixes for it.

Protocols

• 2D classification

• 3D auto-refine

• 3D classification

• 3D initial model

• 3D multi-body

• assign optics group

• auto-picking

• auto-picking LoG

• bayesian polishing

• center averages

• compress movies

• create 3d mask

• ctf refinement

• estimate gain to compress

• expand symmetry

• export coordinates

• export ctf

• export particles

• local resolution

• motion correction

• particles extraction

• post-processing

• preprocess particles

• reconstruct

• remove preferential views

• subtract projection

• symmetrize volume

References

1. Scheres et al., JMB, 2012

2. Scheres et al., JSB, 2012

3. Kimanius et al., eLife, 2016

4. Zivanov et al., eLife, 2018