Gentle and fast all-atom model refinement to cryo-EM densities via a maximum likelihood approach
Fig 2
Similarity score determines ruggedness of the effective refinement potential energy landscape, also when balancing it with structural bias.
From top to bottom: a One-dimensional refinement of a single particle (black circle) towards a Gaussian-shaped density (gray) with inner-product (purple), cross-correlation (ochre), relative-entropy swapped (dark blue) and relative-entropy (green) as similarity scores. b Expanded model with two particles (black circles, x1 smaller and x2 larger) with two amplitude peaks in a one-dimensional density and target distribution (gray), and the resulting two-dimensional effective potential energy landscapes for inner-product, cross-correlation, swapped relative-entropy and relative-entropy similarity measures. c Combination of the similarity measure and force field contribution to the potential energy landscape, exemplified by a harmonic bond that keeps particles at half the distance between the Gaussian centers. For all relative weights of the contributions of the refinement potential and bond potential energy landscape (ratio 1:2 upper panel, 2:1 middle panel, as illustrated by the scale on the left), the relative entropy similarity score produces smooth landscapes with minima at the positions that are expected from the model input.