This plugin provides wrappers for several programs of RELION software suite.
IMPORTANT NOTES!
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)
If you have provided a gain reference or defects file during movie import or motion correction and plan to run bayesian polishing, please make 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).
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:
Stable version
scipion installp -p scipion-em-relionDeveloper’s version
download repository
git clone -b devel https://github.com/scipion-em/scipion-em-relion.gitinstall
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-5.0, 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. Optionally, you can also specify RELION_CUDA_BIN path for nvcc.
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 add support for Python modules (e.g. Blush, ModelAngelo and DynaMight) you will have to setup a Python environment with dependencies. You need to set RELION_ENV_ACTIVATION that points to a conda environment. Default = conda activate relion-5.0
You might want to set TORCH_HOME pointing to the path with downloaded models. Default = software/em/modelangelomodels-1.0 (shared with ModelAngelo plugin).
If you want to use SIDESPLITTER, you need the sidesplitter plugin installed and SIDESPLITTER_HOME set properly. After that, you only need to add –external_reconstruct into Additional arguments field of a 3D auto-refine or multi-body job.
To use a scratch folder (i.e. on SSD), you can either input a custom path (e.g. /ssd) or variable name (e.g. $RELION_SCRATCH_DIR) or use Scipion’s scratch directory defined by SCIPION_SCRATCH in the scipion.conf.
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
4.0, 5.0
Protocols
2D class ranker
2D classification
3D auto-refine
3D classification
3D initial model
3D multi-body
assign optics groups
auto-picking (reference-based)
auto-picking LoG
bayesian polishing
calculate fsc
center averages
clean project
compress movies
create 3d mask
crop / resize volumes
ctf refinement
DynaMight flexibility
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
Scheres et al., JMB, 2012
Scheres et al., JSB, 2012
Kimanius et al., eLife, 2016
Zivanov et al., eLife, 2018
Kimanius et al., Biochemical Journal, 2021
2 maintainers
Metadata
2 maintainers
Release files for scipion-em-relion 5.0.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| scipion_em_relion-5.0.2.tar.gz | 271.9 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| scipion_em_relion-5.0.2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 600.7 kB
Release files / scipion_em_relion-5.0.2.tar.gz
| Download URL | scipion_em_relion-5.0.2.tar.gz |
|---|---|
| Size | 271.9 kB |
| Tags | Source |
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Release files / scipion_em_relion-5.0.2-py3-none-any.whl
| Download URL | scipion_em_relion-5.0.2-py3-none-any.whl |
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| Size | 328.8 kB |
| Tags | Python 3 |
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