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Ctf_estimate_from_micrograph_v3
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> $--Nsubpiece <N1> =: Each piece is further subdivided intoNxN 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>
CTF fit: Optimization constraints $--min_freq <fmin0.03> $--max_freq <fmax0.35> $--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