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new paper on confidence intervals
Acta Crystallogr D Biol Crystallogr. 2009 Jul;65(Pt 7):679-89. Epub 2009 Jun 20. Click here to read 

Confidence intervals for fitting of atomic models into low-resolution densities.

N. Volkmann

Burnham Institute for Medical Research, La Jolla, California, USA.

The fitting of high-resolution structures into low-resolution densities obtained from techniques such as electron microscopy or small-angle X-ray scattering can yield powerful new insights. While several algorithms for achieving optimal fits have recently been developed, relatively little effort has been devoted to developing objective measures for judging the quality of the resulting fits, in particular with regard to the danger of overfitting. Here, a general method is presented for obtaining confidence intervals for atomic coordinates resulting from fitting of atomic resolution domain structures into low-resolution densities using well established statistical tools. It is demonstrated that the resulting confidence intervals are sufficiently accurate to allow meaningful statistical tests and to provide tools for detecting potential overfitting.