The (Crystallographic Object)-Oriented Toolkit
Displays maps and models and allows certain model manipulations: idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots, model validation and other stuff.
Coot is part of the CCP4 Molecular Graphics Project. The Molecular Graphics Project has a wide remit and crystallographic map fitting is a part of that. The Coot functions have their own interface and some of them will be integrated into CCP4mg in due course.
To run this software interactively in a Linux 0.5 environment run the commands:
module load coot coot