ShakErr is a macromolecular crystal structure precision calculator. It estimates standard uncertainties of inherent and derivative model parameters.

The companion application, ProteinRanger, analyzes distributions of atomic shifts between structural homologues and calculates the percentile based spread, which is described in the following paper (please cite if you use the p.b.s. to compare structural models):

Pozharski. (2010) Percentile-based spread: a more accurate way to compare crystallographic models, Acta Cryst. D, 66:970-978. http://dx.doi.org/10.1107/S0907444910027927

Command-line version of the p.b.s. calculation is available and described here.