WarpTools and MCore processing of a 5 tilt series subset of EMPIAR-10491

This dataset contains an example of cryo-electron tomography (cryo-ET) data processed using command line tools available in Warp v2.0.0dev9.

Processing a 5 tilt series subset led to a 2.92 Å reconstruction of apoferritin.

The subset processed includes

• TS_1
• TS_11
• TS_17
• TS_23
• TS_32

External packages used for processing include AreTomo2 for tilt series alignment and RELION 5 for initial 3D refinement.

The raw data is not included but can be downloaded from EMPIAR using the following code snippet on UNIX systems

wget --show-progress -N -q -nd -P ./ ftp://ftp.ebi.ac.uk/empiar/world_availability/10491/data/gain_ref.mrc;

for i in 1 11 17 23 32;
do
    echo "======================================================"
    echo "================= Downloading TS_${i} ================"
    wget --show-progress ---timestamping --quiet --no-directories --directory-prefix ./mdoc ftp://ftp.ebi.ac.uk/empiar/world_availability/10491/data/tiltseries/mdoc/TS_${i}.mrc.mdoc;
    wget --show-progress ---timestamping --quiet --no-directories --directory-prefix ./frames ftp://ftp.ebi.ac.uk/empiar/world_availability/10491/data/tiltseries/data/*-${i}_*.tif;
done

Processing is detailed in the `processing.sh` shell script. This script is not designed to be run end to end and instead should be run one command at a time.