RELION 4.0.0

RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer
program for Maximum A Posteriori refinement of (multiple) 3D reconstructions
or 2D class averages in cryo-electron microscopy. It is developed in the
research group of Sjors Scheres at the MRC Laboratory of Molecular Biology.

The underlying theory of MAP refinement is given in a scientific publication.
If RELION is useful in your work, please cite this paper.

The more comprehensive documentation of RELION is stored here.

Installation

More extensive options and configurations are available here,
but the outlines to clone and install relion for typical use are made easy through cmake.

On Debian or Ubuntu machines, installing cmake, the compiler, and additional dependencies (mpi, fftw) is as easy as:

sudo apt install cmake git build-essential mpi-default-bin mpi-default-dev libfftw3-dev libtiff-dev libpng-dev ghostscript libxft-dev

RedHat-like systems (CentOS, RHEL, Scientific Linux etc) use yum package manager:

sudo yum install cmake git gcc gcc-c++ openmpi-devel fftw-devel libtiff-devel libpng-devel ghostscript libXft-devel libX11-devel

Once git and cmake are installed, relion can be easily installed through:

git clone https://github.com/3dem/relion.git
cd relion
git checkout master # or ver4.0; see below
mkdir build
cd build
cmake ..
make

By performing git checkout ver4.0 instead of git checkout master, you can access the latest
(developmental) updates for RELION 4.0.x. The code there is not tested as throughfully as that in
the master branch and not generally recommended.

The binaries will be produced in the build/bin directory. If you want to copy binaries
into somewhere else, run cmake with -DCMAKE_INSTALL_PREFIX=/where/to/install/ and
perform make install as the final step. Do not specify the build directory itself
as CMAKE_INSTALL_PREFIX! This will not work.

Also note that the MPI library used for compilation must be the one you intend to use RELION with.
Compiling RELION with one version of MPI and running the resulting binary with mpirun from another
version can cause crash. See our wiki below for details.

In any case, you have to make sure your PATH environmental variable points to the directory
containing relion binaries. Launching RELION as /path/to/relion is NOT a right way; this
starts the right GUI, but the GUI might invoke other versions of RELION in the PATH.

If FLTK related errors are reported, please add -DFORCE_OWN_FLTK=ON to
cmake. For FFTW related errors, try -DFORCE_OWN_FFTW=ON.

RELION also requires libtiff. Most Linux distributions have packages like libtiff-dev or libtiff-devel.
Note that you need a developer package. You need version 4.0.x to read BigTIFF files. If you installed
libtiff in a non-standard location, specify the location by
-DTIFF_INCLUDE_DIR=/path/to/include -DTIFF_LIBRARY=/path/to/libtiff.so.5.

Updating

RELION is intermittently updated, with both minor and major features.
To update an existing installation, simply use the following commands

cd relion
git pull
cd build
make
make install # Only when you have specified CMAKE_INSTALL_PREFIX in the cmake step

If something went wrong, remove the build directory and try again from cmake.

Class Ranker

The default model for the class ranker has been trained and tested in Python 3.9.12 with Pytorch 1.10.0 and Numpy 1.20.0.
If you wish to retrain the class ranker model with your own data, please refer to this repo.