A three-dimensional structure of reasonably high resolution is the starting point of any protein engineering project, whether intended to improve the affinity of an antibody, change the specificity of an enzyme, or to test a hypothesis regarding the role of a particular residue in determining structure or stability. The atomic coordinates determined by X-ray crystallography or, increasingly, NMR, provides the means to visualize the shape of a protein as well as the distances between atoms within a protein, or between a protein and ligand or another macromolecule. The free energy changes that determine protein structure, stability, and interaction properties ultimately arise from the distances that separate the various types of atoms involved, including proteins, ligands, and solvent molecules.