Coot is for macromolecular model building, model completion and
validation, particularly suitable for protein modelling using X-ray
data.

Coot displays maps and models and allows model manipulations such as
idealization, real space refinement, manual rotation/translation,
rigid-body fitting, ligand search, solvation, mutations, rotamers,
Ramachandran plots, skeletonization...
Author: Paul Emsley