Big data such as raw projections from the microscope, tomograms and subtomograms is stored in binary on disk. PyTom currently supports three filetypes:
pytom.basic.files.readfunction 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
em2ccp4.pyto do this job. We provide all combinations.
You can use our
pdb2em.py script to convert PDB files to electron densities.
NAME pdb2em.py DESCRIPTION Compile a electron density from PDB file http://pytom.org/doc/pytom/files.html OPTIONS -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)
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.