iMODFIT is an efficient tool for flexible fitting of atomic structures into EM maps based on Normal Mode Analysis in Internal Coordinates.
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Flexible fitting in internal coordinates with a reduced number of normal modes provides a natural way to alleviate overfitting distortions, such as poor resolution, map defects (e.g., scale inaccuracies, missing densities, resolution anisotropy), or even partial correspondence between the map and the atomic structure.

As a proof of iMODFIT’s usefulness, different groups have already obtained impressive flexible fittings with:

Human TFIID (Lauder et al., Nature 2016)
RavA ATPase (Kandiah et al., Sci Rep. 2016)
DnaKNBD-GrpE complex (Melero et al., JBC. 2015)
Human parechovirus capsid (Shakeel et al., J Virol. 2015)
Mature HIV-1 capsid (Zhao et al., Nature. 2013, see Supplementary)
Coxsackievirus (Shakeel et al., J Virol. 2013)
ATP synthase (Lau and Rubinstein, Nature 2012)
Yeast vacuolar ATPase (Oot et al., Structure 2012)

References


iMODFIT: efficient and robust flexible fitting based on vibrational analysis in internal coordinates (2013). López-Blanco J.R. and Chacón P. JSB 184(2):261–270