PyTom: Files

Big data

Big data such as raw projections from the microscope, tomograms and subtomograms is stored in binary on disk. PyTom currently supports three filetypes:

In general, all files stored in these filetypes can be read into memory by the function if you write your own code or use PyTom in the terminal. If you however want to convert filetypes from EM to say MRC, you can use the conversion scipts in pytom/bin like, to do this job. We provide all combinations.

PDB to electron density conversion

You can use our script to convert PDB files to electron densities.

    Compile a electron density from PDB file
    -p, --pdbFile    A PDB file (Is optional: No; Requires arguments: Yes)
    -c, --chain    A Chain (Is optional: Yes; Requires arguments: Yes)
    -s, --pixelSize    Pixel size of output volume (Is optional: Yes; Requires arguments: Yes)
    -v, --volumeSize    Volume length (size) in all dimensions (Is optional: Yes; Requires arguments: Yes)
    -o, --outputVolumePath    Path to output volume  (Is optional: No; Requires arguments: Yes)
    -h, --help    Help. (Is optional: Yes; Requires arguments: No)

XML Files

We use PyTom XML files to store metadata of binaries files like projections and tomograms. Furthermore, XML is a good tool to store information about processing jobs as well. Hence, XML files are used like a databank which remains open and, more importantly, readable to the user all time. It can be adjusted to the current requirements of the project using a standard text editor.