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. Author manuscript; available in PMC: 2019 Sep 25.

Published in final edited form as: J Struct Biol. 2015 Aug 13;192(2):216–221. doi: 10.1016/j.jsb.2015.08.008

Figure 4: — Output diagnostic plots describing the experimental amplitudes ( $A_{d}^{1 D}$ , green), the fit CTF ( ${|{CTF}_{fit}|}^{1 D}$ , orange) and goodness of fit (CC_fit, blue) for micrograph #1 of set #7 of the CTF challenge. For this micrograph, the final estimates were $Δ f_{1} = 29070$ Å, $Δ f_{2} = 28313$ Å and α_ast = 56.5°. The highest resolution at which Thon rings were deemed to be modeled correctly was 6.5 Å. The experimental amplitude profile (green) is normalized such that: the minima of the oscillations are set to 0.0; the second peak of the power spectrum (in this case at around 0.04) is 0.95; the maxima of oscillations are further normalized to 0.1 if their maxima would be <0.1 otherwise. Because of aliasing, one does not observe zeroes in ${|{CTF}_{fit}|}^{1 D}$ . One would normally solve this by increasing N_d, but we restricted ourselves to previously-used parameter values for this experiment (see caption to Table 3 for more details).