Overview of Output Files

CHAP will generally produce four different output files each time it is run. By default, these are called output.json, output.pdb, output.obj, and output.mtl, but the base name (i.e. the part before the respective file extension) can be changed using the -out-filename flag. The JSON file contains all information you need to plot profiles of the permeation pathway (e.g. its radius along the centre line) and their evolution over time in a machine-readable format. The other three files contain the information that is needed to visualise the pathway in a molecular visualisation system such as PyMOL or VMD.

The next few sections document the contents of the output files and are intended as a comprehensive reference. If you are mainly interested in quickly visualising your CHAP results, take a look at the menu on the left, where you may find practical examples of how to plot CHAP results in Python and R and how to create molecular visualisations of the permeation pathway in PyMOL and VMD.