Package: scipion-em-relion
This plugin provides wrappers for several programs ofRELIONsoftware suite.IMPORTANT NOTES!If you have imported movies with a gain file inDM4format, you need toflip the gain reference upside-downin the motion correction protocol! (bug details)If you have provided a gain reference or defects file during movie import or motion correction and plan to run bayesian polishing, pleasemake sure to run first “assign optics groups” protocol for aligned movies, specifying the gain file etc. Currently, Scipion has no other way of knowing if you have e.g. rotated the gain during motion correction. Output movies then can be used in the polishing protocol.When importing EER movies, you should specify dose per single EER frame during import step. Pixel size should be the physical pixel size unless you plan to render EER on 8K grid. In the Motioncor protocol choose binning, EER fractionation and upsampling (default=1 is for 4K grid).InstallationYou will need to use 3.0+ version of Scipion to be able to run these protocols. To install the plugin, you have two options:Stable versionscipion installp -p scipion-em-relionDeveloper’s versiondownload repositorygit clone -b devel https://github.com/scipion-em/scipion-em-relion.gitinstallscipion installp -p /path/to/scipion-em-relion --develRELION sources will be downloaded and compiled automatically with the plugin, but you can also link an existing installation. Default installation path assumed issoftware/em/relion-4.0, if you want to change it, setRELION_HOMEinscipion.conffile to the folder where the RELION is installed.If you need to use CUDA different from the one used during Scipion installation (defined byCUDA_LIB), you can addRELION_CUDA_LIBvariable to the config file. Optionally, you can also specifyRELION_CUDA_BINpath for nvcc.If you have to use a MPI for Relion different from Scipion MPI, you can setRELION_MPI_BINandRELION_MPI_LIBvariables in the config file.If you want to use2D class rankerprotocol, you need to setRELION_ENV_ACTIVATIONthat points to a conda environment which includes torch and numpy modules. Default =conda activaterelion-pythonIf you want to use SIDESPLITTER, you need thesidesplitterplugin installed andSIDESPLITTER_HOMEset properly. After that, you only need to add–external_reconstructinto Additional arguments field of a 3D auto-refine or multi-body job.To check the installation, simply run one of the tests. A complete list of tests can be displayed by executingscipion test--show--greprelionSupported versions3.1, 4.0Protocols2D class ranker2D classification3D auto-refine3D classification3D initial model3D multi-bodyassign optics groupsauto-picking (reference-based)auto-picking LoGbayesian polishingcalculate fsccenter averagesclean projectcompress moviescreate 3d maskcrop / resize volumesctf refinementestimate gain to compressexpand symmetryexport coordinatesexport ctfexport particlesimport coordinateslocal resolutionmotion correctionparticles extractionpost-processingpreprocess particlesreconstructremove preferential viewssubtract projectionsymmetrize volumeReferencesScheres et al., JMB, 2012Scheres et al., JSB, 2012Kimanius et al., eLife, 2016Zivanov et al., eLife, 2018Kimanius et al., Biochemical Journal, 2021