Table 3:

CTFFIND3 and CTFFIND4 find very similar defocus parameter values for CTF challenge micrographs. Nine sets of micrographs (described in Marabini et al., 2015) were processed with CTFFIND4, using the same parameters as had been used in one of the authors’ (N.G.) submission to the CTF challenge using CTFFIND3. Those parameters were: N_d = 256, $g_{min}^{-1}=200$Å, $g_{max}^{-1}=8$Å, $\mathrm{\Delta }{f}_{min}=1000$Å, $\mathrm{\Delta }{f}_{max}=90000$Å, $\mathrm{\Delta }{f}_{step}=200$Å, $\mathrm{\Delta }\mathrm{\Delta }{f}_{res}=200$Å. For set #9, CTF parameters were also estimated with adjusted parameters N_d = 512 and $\mathrm{\Delta }\mathrm{\Delta }{f}_{res}=-100$ Å (which inactivates the astigmatism restraint) and the results are shown in line 9*. For each set, the mean (µ) and standard deviation (σ) of the difference є between CTFFIND 4 and CTFFIND3’s estimates of each of the defocus parameters $\left(\mathrm{\Delta }{f}_1,\mathrm{\Delta }{f}_2,{\alpha }_{ast}\right)$ are shown as percentages or degrees, as are measures of the amount of astigmatism $\left(\mathrm{\Delta }\mathrm{\Delta }f/\mathrm{\Delta }{f}_1\right)$ and estimates of the highest resolution (in Å) at which Thon rings are reliably fit, as given by the CC_fit = 0.75 criterion.

Set #	$\%\in \left(\mathrm{\Delta }{f}_1\right)$		$\%\in \left(\mathrm{\Delta }{f}_2\right)$		$\%\mathrm{\Delta }\mathrm{\Delta }f/\mathrm{\Delta }{f}_1$		є(αast)(°)		CCfit = 0.75 (Å)
	µ	σ	µ	σ	µ	σ	µ	σ	µ	σ
1	−0.1	0.8	−0.8	1.1	−2.5	1.5	3.0	42.7	8.1	2.4
2	−0.1	1.0	−0.1	1.0	−2.6	1.9	28.2	53.2	8.1	1.5
3	0.0	0.2	−0.1	0.2	−2.1	0.6	21.5	79.9	6.2	1.7
4	0.2	0.5	−0.2	0.5	−2.3	1.1	9.1	77.6	7.4	1.9
5	0.2	0.8	0.2	0.7	−1.1	1.0	−14.5	42.5	11.3	8.6
6	0.3	1.2	−0.6	0.9	−1.1	0.9	−5.5	23.4	10.1	3.6
7	−0.1	1.0	−0.4	1.0	−1.8	1.6	−3.5	18.1	9.6	3.0
8	1.6	6.9	1.2	5.4	−3.2	2.8	−7.2	38.6	8.5	3.2
9	0.2	0.4	0.1	0.7	−4.3	3.7	−0.2	10.2	7.4	4.8
9*	1.5	0.6	−4.0	4.6	−7.6	3.6	−1.5	3.3	3.4	0.9