scipion-em-relion 1.0.5

Plugin to use Relion programs within the Scipion framework

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

Installation

You will need to use 2.0 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-3.0, 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 your shell environment - they will be recognized by Scipion.

To check the installation, simply run one of the following Scipion tests:

scipion test pyworkflow.tests.em.workflows.test_workflow_streaming.TestRelionPickStreaming
scipion test pyworkflow.tests.em.workflows.test_workflow_streaming.TestRelionExtractStreaming
scipion test pyworkflow.tests.em.workflows.test_workflow_mixed_large.TestMixedRelionTutorial
scipion test relion.tests.test_workflow_relion3.TestWorkflowRelion3Betagal
scipion test relion.tests.test_convert_relion.TestReconstruct
scipion test relion.tests.test_convert_relion.TestConvertBinaryFiles
scipion test relion.tests.test_convert_relion.TestConversions
scipion test relion.tests.test_convert_relion.TestAlignment
scipion test relion.tests.test_protocols_relion.TestRelionSubtract
scipion test relion.tests.test_protocols_relion.TestRelionSortParticles
scipion test relion.tests.test_protocols_relion.TestRelionRefine
scipion test relion.tests.test_protocols_relion.TestRelionPreprocess
scipion test relion.tests.test_protocols_relion.TestRelionPostprocess
scipion test relion.tests.test_protocols_relion.TestRelionLocalRes
scipion test relion.tests.test_protocols_relion.TestRelionInitialModel
scipion test relion.tests.test_protocols_relion.TestRelionExtractParticles
scipion test relion.tests.test_protocols_relion.TestRelionExtractMovieParticles
scipion test relion.tests.test_protocols_relion.TestRelionExportParticles
scipion test relion.tests.test_protocols_relion.TestRelionExpandSymmetry
scipion test relion.tests.test_protocols_relion.TestRelionCreate3dMask
scipion test relion.tests.test_protocols_relion.TestRelionClassify3D
scipion test relion.tests.test_protocols_relion.TestRelionClassify2D
scipion test relion.tests.test_protocols_relion.TestRelionCenterAverages
scipion test relion.tests.test_workflow_relion.TestWorkflowRelionPick
scipion test relion.tests.test_workflow_relion.TestWorkflowRelionExtract

A complete list of tests can also be seen by executing scipion test --show --grep relion

Supported versions

2.0.4, 2.1, 3.0

In 2018 the plugin was updated to support the latest (at that moment) RELION: 3.0. This required a lot of code refactoring and the support of old RELION versions (1.x) had to be discontinued. Many new protocols specific to new RELION release we added. You are welcome to check them out and give us your feedback. We are still fixing few issues related to RELION 3 support, please do let us know if something does not work as expected.

Protocols

• 2D classification

• 3D auto-refine

• 3D classification

• 3D initial model

• 3D multi-body

• auto-picking

• auto-picking LoG

• bayesian polishing

• center averages

• create 3d mask

• ctf refinement

• expand symmetry

• export ctf

• export particles

• local resolution

• motioncor

• movie particles extraction

• particle polishing

• particles extraction

• post-processing

• preprocess particles

• reconstruct

• sort particles

• 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