The separation of the effects of atomic displacement and local resolution in crystallographic and cryo-electron microscopy maps

Uncertainties in atomic coordinates and finite resolution blur the image of an atom's density present in the observed map. A resolution cutoff leads to an additional effect, known as Fourier ripples. Ignoring these ripples when calculating an atomic model map makes it difficult to deconvolute these two sources of image blurring. However, it is possible to separate the effects of the atomic displacement and local resolution cutoff in the course of real-space refinement if an advanced method for calculating the image of the atom in the observed map is used, which includes modeling of ripples.