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Ctf_estimate_from_micrograph_v31
Estimate the CTF from a micrograph. The PSD of the micrograph is first estimated using periodogram averaging or ARMA models (See article). Then, the PSD is enhanced (See article). And finally, the CTF is fitted to the PSD, being guided by the enhanced PSD (See article).
See also Ctf_enhance_psd_v3
Parameters
--oroot <rootname>
PSD estimation $--psd_estimator <methodperiodogram> where <method> can be:
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--pieceDim <d512> $--overlap <o0.5> $--skipBorders <s2> $--Nsubpiece <N1> =: Each piece is further subdivided into NxN subpieces. This option is useful for small micrographs in which not many pieces of size pieceDim x pieceDim can be defined. Note that this is not the same as defining a smaller pieceDim. Defining a smaller pieceDim, would result in a small PSD, while subdividing the piece results in a large PSD, although smoother. $--mode <modemicrograph> where <mode> can be:
CTF fit $``: Do not fit a CTF to PSDs
ARMA models $--N_AR <N24> $--M_AR <N24> $--N_MA <N20> $--M_MA <N20>
Downsampling $--downSamplingPerformed <F1>
CTF fit: Optimization constraints $--min_freq <fmin0.03> $--max_freq <fmax0.35> $--fastDefocus <lambda2> <size=10> $--defocus_range <D8000> $: Show optimization process $: By default, noise is astigmatic $--enhance_weight <w1> $--model_simplification <s0> $--bootstrapFit <N-1>
CTF fit: Output CTF models $--ctfmodelSize <size256>
PSD enhancement $: Bandpass cutoff. Normalized to 0.5 If fmax>0.35, f1 default=0.01 If fmax<0.35, f1 default=0.02 $: Bandpass cutoff. Normalized to 0.5. If fmax>0.35, f2 default=0.08 If fmax<0.35, f2 default=0.15
CTF description $: ctfparam file Parameters from this file are overriden by the parameters in the command line $: Angstroms/pixel. Ex: 1.4 This parameter is compulsory if a CTF is needed. $: Accelerating voltage (kV). Ex: 200 This parameter is compulsory if a CTF is needed. $: Milimiters. Ex: 5.6 This parameter is compulsory if a CTF is needed. $: Defocus in Angstroms (Ex: 2000) $: If astigmatic $--azimuthal_angle <ang0> $--chromatic_aberration <Ca0> $--energy_loss <espr0> $--lens_stability <ispr0> $--convergence_cone <alpha0> $--longitudinal_displace <DeltaF0> $--transversal_displace <DeltaR0> $--Q0 <Q00> $--K <K1>
Estimate PSD
xmipp_ctf_estimate_from_micrograph --micrograph micrograph.mrc --dont_estimate_ctfEstimate a single CTF for the whole micrograph
xmipp_ctf_estimate_from_micrograph --micrograph micrograph.mrc --sampling_rate 1.4 --voltage 200 --spherical_aberration 2.5Estimate a single CTF for the whole micrograph providing a starting point for the defocus
xmipp_ctf_estimate_from_micrograph --micrograph micrograph.mrc --sampling_rate 1.4 --voltage 200 --spherical_aberration 2.5 --defocusU -15000Estimate a CTF per region
xmipp_ctf_estimate_from_micrograph --micrograph micrograph.mrc --mode regions micrograph.pos --sampling_rate 1.4 --voltage 200 --spherical_aberration 2.5 --defocusU -15000Estimate a CTF per particle
xmipp_ctf_estimate_from_micrograph --micrograph micrograph.mrc --mode particles micrograph.pos --sampling_rate 1.4 --voltage 200 --spherical_aberration 2.5 --defocusU -15000