Rosetta represents proteins as a polymer of residues. The chemical definiton of residues is called ResidueType and is defined in params files in the database or in your local directory. The standard amino-acids are of course predefined in the database. Additional to the possibility to define new ResidueType s one can also define residue type patch es. The latter are particular useful to define small modifications of residues (e.g., the extra atoms on terminal residues, phoshporylation and other post-translational modifications, but also the addition of virtual atoms, e.g., to allow the computation of chainbreak energies)