Welcome to choppa’s documentation!

Choppa is a package for visualizing fitness data (e.g. deep mutational scanning or phylogenetics data) on 3D protein structures. It has been built as an end-to-end CLI tool that ingests a PDB file (protein structure) and a CSV file (fitness data) and produces two files:

• A HTML file with interactive features such as logoplot pop-ups when residues are hovered over.

• A PyMOL session file with the same coloring as the HTML file. This view can be ray-traced with PyMOL and used for publication-style figures.