Installation of Relion 3 on our MacOS!

The software of Scheres, Relion 3 (, we have it on our cluster and on the iMACs! For the iMacs, code can be found below, thanks to our scientific consultant and external collaborator, Koen M. Visscher:

First install the developer tools (, xquartz ( and brew (, and then you just copy/paste the following commands on the terminal, where you will be installing Relion 3:

###How we install Relion in the 
###Kastritis Laboratory on our Macs
###Install the necessary dependencies 
###for Relion 3.0 on your MacOS
brew install cmake
brew install gcc
brew install openmpi
brew install fltk
brew install fftw
###Set the correct compilers
export CXX=g++-9
export CC=gcc-9
export OMPI_CXX=g++-9
export OMPI_CC=gcc-9
export PATH="/usr/local/opt/openmpi/bin:${PATH}"
export CXXFLAGS="-I/usr/local/opt/openmpi/include"
export LDFLAGS="-L/usr/local/opt/openmpi/lib"
###Now download, compile and install relion
git clone
cd relion
git checkout 3.0.6
mkdir -p build
cd build
cmake ..
make -j 6
make install


39 Replies to “Installation of Relion 3 on our MacOS!”

  1. Thank you for sharing a lucid way to install Relion 3 in a MacOS system.

    I have a quick question (and maybe a navie one):
    Did you successfully get “ctffind4″ to run with Apple M1 or M2 system?

    For this moment (2/2/2024), installation of CCP-EM 1.6 (comes with relion 3) indeed works on both Intel-based and M1/2 MacBooks.

    The problem we encountered was that ctffind4 (up to 4.1.14) can be compiled and run well under Intel-based MacBooks, but not in M1/M2 MacBooks…

    (Parameters I adopted when compling ctffind:
    >../configure CXXFLAGS=”-I/usr/local/include -L/usr/local/lib”
    > sudo make && make install )

    * Download ctffind 4 for Mac (binary) from my NTU links:


    • Hello! No, we have done it in previous macos chips… We have not tried to compile it on M chips

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