Code for structure determination from low-resolution data is available as part of the Rosetta molecular modeling package (https://www.rosettacommons.org/). Documentation and demos are included in the release.
Code for molecular replacement and crystallographic refinement has also been implemented in Phenix (http://www.phenix-online.org/). See the incuded documentation for more details.
ACMI, a software package using probabilistic inference to infer protein backbones de novo is available at http://pages.cs.wisc.edu/~dimaio/acmi/get_acmi.htm.