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Figure 2
Confidence maps separate signal from noise for molecular-density interpretation. (a) Left: confidence map with a longitudinal section through the TMV coat protein displayed, indicating the α-helical pitch of the LR helix. The lower half shows the chosen contour at 1% FDR in blue with 5.7% of voxels detected. Right, the corresponding histogram of the confidence map with signal separated above 0.99 PPV (1% FDR). (b) Left: the same section as in (a) from cryo-EM density and the recommended threshold contoured at 1.2σ in gray with 3.7% of voxels detected. Right: the corresponding histogram of the cryo-EM density with thresholded values displayed in gray. (c) Isosurface-rendered thresholded confidence maps at 0.01%, 1% and 10% FDR (left, center left and center right, respectively) shown in blue and sharpened cryo-EM density with a 1.2σ threshold (right) in gray from TMV (EMD-2842). Shown are helix Ala86–Asp77 (top), a quarter cross-section (bottom left) and a side view (bottom right) of the TMV map.

IUCrJ
Volume 6| Part 1| January 2019| Pages 18-33
ISSN: 2052-2525
https://doi.org/10.1107/S2052252518014434