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, non-crystallographic symmetry and more.

WWW: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/