Plugin to use Relion programs within the Scipion framework
Project description
This plugin provide wrappers around several programs of RELION software suite.
prod: |
devel: |
support: |
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-relion
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-3.1.0, 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 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
We are still working towards stable plugin release, so some things might not work yet. Handling optics groups needs more testing, you are welcome to be a volunteer.
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
Scheres et al., JMB, 2012
Scheres et al., JSB, 2012
Kimanius et al., eLife, 2016
Zivanov et al., eLife, 2018
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Hashes for scipion-em-relion-3.0.0b4.tar.gz
Algorithm | Hash digest | |
---|---|---|
SHA256 | 7e8014598a9374e2e99f0a5f2a1ab4a87653574a0a21f2b5f6c2fd75f04ca47c |
|
MD5 | c1b8c937f98b16ac32854dc1b56e1563 |
|
BLAKE2b-256 | dfba0113da861be1055f4a6d7df17e007c150c6e59971bc965e80a2f6913cfe7 |