Download the data

The five tilt series subset of EMPIAR-10164 used for this guide should first be downloaded from EMPIAR.

For this purpose, we provide a simple shell script (download.sh).

Note

Downloading the data may take a few hours. Start this early!

download.sh organises files according to the directory structure expected by the rest of the guide.

shell script

echo "Downloading the raw data. This may take a couple of hours!"
echo
echo
for i in 01 03 43 45 54;
do
    echo "===================================================="
    echo "================= Downloading TS_${i} ================"
    wget --show-progress -m -q -nd -P ./mdoc ftp://ftp.ebi.ac.uk/empiar/world_availability/10164/data/mdoc-files/TS_${i}.mrc.mdoc;
    wget --show-progress -m -q -nd -P ./frames ftp://ftp.ebi.ac.uk/empiar/world_availability/10164/data/frames/TS_${i}_*.mrc;
done

directory structure

.
├── frames
│   ├── TS_01_000_0.0.mrc
│   ├── TS_01_001_3.0.mrc
│   └── ...
└── mdoc
    ├── TS_01.mrc.mdoc
    ├── TS_02.mrc.mdoc
    └── ...

file extensions

Files with the .mrc extension are multi-frame micrographs for each tilt angle in a tilt series.

They are in the MRC2014 file format.

Files with the .mdoc extension are SerialEM metadata files, we have one per tilt-series.

They are plain text files containing metadata about images in a tilt-series.