Extract particles

Place the micrographs from the EMPIAR database into the Micrographs folder within Relion_refinement that you downloaded and unzipped from Data Dryad.

$ cp *.mrcs Relion_refinement/Micrographs

Rename the micrographs to have .mrc as the extension:

$ foreach file (*.mrcs)
mv $file ${file:r}
end

Run the following relion extraction command (this needs to be run from the folder above Micrographs/) using the existing .box and ctffind log files:

$ /programs/x/relion/1.3/bin/mpirun -np 22 relion_preprocess_mpi --o particles --mic_star all_micrographs_ctf.star --coord_suffix .box --extract --extract_size 240 --norm --bg_radius 98 --white_dust 5 --black_dust 5 --invert_contrast