Documentation by Vikram K. Mulligan, Baker laboratory ( Created 14 March 2014. Updated 20 Feb 2019.

Short summary

Although nearly all of the residue types that are present in the Rosetta database are loaded by default, a few are not. Moreover, when designing, Rosetta does not by default allow design with all loaded residue types. This page documents how to load new residue types into Rosetta, and how to design with them.

Usage cases

Typically, a user would have three usage cases:

  • The user wishes to work with canonical amino acid residues, common inorganic ions, or conventional nucleic acids. In this case, Rosetta should work "out of the box" -- i.e. the user should be able to load a PDB containing these things and have Rosetta interpret it properly.
  • The user wishes to work with one or two noncanonical residues or ligands in addition to the usual set. In this case, it is simplest to specify a path to a params file using the -extra_res or -extra_res_fa flags. (The latter is for full-atom params files.)
  • The user wishes to work with a set of noncanonical residues, and wants these to be loaded by default. In this case, he or she should edit the file database/chemical/residue_type_sets/fa_standard/residue_types.txt, and uncomment lines for params files defining the residue types that he or she wants to use.

To design with anything beyond the 20 canonical amino acid residues, please see the documentation for PackerPalettes.

See also