There are a variety of sophisticated tools currently available for displaying electron density maps derived from x-ray crystallography and for building, displaying, manipulating, and refining protein models within those maps. Similar tools are not currently available for modeling RNA molecules. This is a critical shortcoming for crystallographers who are attacking the structure of the ribosome, because it is an RNA/protein complex that is far larger than any asymmetric macromolecular assembly whose structure has been determine to date. Whereas the natural internal coordinates for described protein conformation are backbone and side- chain torsion angles, the base-paired and helical nature of RNAs dictates the use of internal coordinates involving a mixture """"""""helicoidal""""""""parameters and some torsions. JUMNA is the only modeling program that uses these coordinates, and the goal of the proposed research is to incorporate JUMNA into an RNA modeling package for x-ray crystallography.
