{ "info": { "author": "Grigory Sharov, J.M. De la Rosa Trevin, Josue Gomez Blanco", "author_email": "gsharov@mrc-lmb.cam.ac.uk, delarosatrevin@scilifelab.se, josue.gomez-blanco@mcgill.ca", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", "Programming Language :: Python :: 2.7" ], "description": "=============\nRelion plugin\n=============\n\nThis plugin provide wrappers around several programs of `RELION `_ software suite.\n\n.. figure:: http://scipion-test.cnb.csic.es:9980/badges/relion_devel.svg\n :align: left\n :alt: build status\n\nInstallation\n------------\n\nYou will need to use `2.0 `_ version of Scipion to be able to run these protocols. To install the plugin, you have two options:\n\na) Stable version\n\n .. code-block::\n\n scipion installp -p scipion-em-relion\n\nb) Developer's version\n\n * download repository\n\n .. code-block::\n\n git clone https://github.com/scipion-em/scipion-em-relion.git\n\n * install\n\n .. code-block::\n\n scipion installp -p path_to_scipion-em-relion --devel\n\nRELION 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.\n\nTo check the installation, simply run one of the following Scipion tests:\n\n.. code-block::\n\n scipion test pyworkflow.tests.em.workflows.test_workflow_streaming.TestRelionPickStreaming\n scipion test pyworkflow.tests.em.workflows.test_workflow_streaming.TestRelionExtractStreaming\n scipion test pyworkflow.tests.em.workflows.test_workflow_mixed_large.TestMixedRelionTutorial\n scipion test relion.tests.test_workflow_relion3.TestWorkflowRelion3Betagal\n scipion test relion.tests.test_convert_relion.TestReconstruct\n scipion test relion.tests.test_convert_relion.TestConvertBinaryFiles\n scipion test relion.tests.test_convert_relion.TestConversions\n scipion test relion.tests.test_convert_relion.TestAlignment\n scipion test relion.tests.test_protocols_relion.TestRelionSubtract\n scipion test relion.tests.test_protocols_relion.TestRelionSortParticles\n scipion test relion.tests.test_protocols_relion.TestRelionRefine\n scipion test relion.tests.test_protocols_relion.TestRelionPreprocess\n scipion test relion.tests.test_protocols_relion.TestRelionPostprocess\n scipion test relion.tests.test_protocols_relion.TestRelionLocalRes\n scipion test relion.tests.test_protocols_relion.TestRelionInitialModel\n scipion test relion.tests.test_protocols_relion.TestRelionExtractParticles\n scipion test relion.tests.test_protocols_relion.TestRelionExtractMovieParticles\n scipion test relion.tests.test_protocols_relion.TestRelionExportParticles\n scipion test relion.tests.test_protocols_relion.TestRelionExpandSymmetry\n scipion test relion.tests.test_protocols_relion.TestRelionCreate3dMask\n scipion test relion.tests.test_protocols_relion.TestRelionClassify3D\n scipion test relion.tests.test_protocols_relion.TestRelionClassify2D\n scipion test relion.tests.test_protocols_relion.TestRelionCenterAverages\n scipion test relion.tests.test_workflow_relion.TestWorkflowRelionPick\n scipion test relion.tests.test_workflow_relion.TestWorkflowRelionExtract\n\nA complete list of tests can also be seen by executing ``scipion test --show --grep relion``\n\nSupported versions\n------------------\n\n2.0.4, 2.1, 3.0\n\nIn 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.\n\nProtocols\n---------\n\n* 2D classification \n* 3D auto-refine \n* 3D classification \n* 3D initial model \n* 3D multi-body \n* auto-picking \n* auto-picking LoG \n* bayesian polishing \n* center averages \n* create 3d mask \n* ctf refinement \n* expand symmetry \n* export ctf \n* export particles \n* local resolution \n* motioncor \n* movie particles extraction\n* particle polishing \n* particles extraction \n* post-processing \n* preprocess particles \n* reconstruct \n* sort particles \n* subtract projection \n* symmetrize volume\n\nReferences\n----------\n\n1. Scheres et al., JMB, 2012 \n2. Scheres et al., JSB, 2012 \n3. Kimanius et al., eLife, 2016 \n4. 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