Situs is a package for fitting high-resolution protein structures to low-resolution maps from electron microscopy or small angle X-ray scattering. The package was originally developed by Willy Wriggers in collaboration with Ronald A. Milligan and J. Andrew McCammon.

NMFF is a package for flexibly fitting atomic level structures into electron density maps using normal mode directions as flexible degrees of freedom. Utilizing normal modes constructed from multi-resolution elastic network models, very large structures can be explored and refined into electron density maps. While this package is still under development for distribution, several successful applications of the NMFF methodology have been obtained through collaborative and service projects within the MMTSB. NMFF was developed by Florence Tama and Osamu Miyashita working in collaboration with Charles L. Brooks III.