Xmipp

xmipp_ctf_estimate_from_psd (v3.0)

Usage

Adjust a parametric model to a PSD file. 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_estimate_from_micrograph ctf_enhance_psd

Parameters

--psd <PSDfile>
PSD file

CTF fit: Optimization constraints

--min_freq <fmin=0.03>
Minimum digital frequency (<0.5) to use in adjust. Its value should be a little lower than the dig. freq. of the first CTF zero.
--max_freq <fmax=0.35>
Maximum digital frequency (<0.5) to use in adjust. It should be higher than the last zero of the CTF.
--defocus_range <D=8000>
Defocus range in Angstroms
--show_optimization
Show optimization process
--radial_noise
By default, noise is astigmatic
--enhance_weight <w=1>
Weight of the enhanced term
--model_simplification <s=0>
0 (no simplification) 1 (simplified envelope) 2 (last Gaussian removal) 3 (symmetric intermediate Gaussian)
--bootstrapFit <N=-1>
Perform bootstrap fit (Fourier pixels are randomly chosen) This is used to test the variability of the fit N defines the number of times the fit is repeated

CTF fit: Output CTF models

--ctfmodelSize <size=256>
Size for the ctfmodel thumbnails

PSD enhancement

--enhance_min_freq <f1>
Bandpass cutoff. Normalized to 0.5 If fmax>0.35, f1 default=0.01 If fmax<0.35, f1 default=0.02
--enhance_max_freq <f2>
Bandpass cutoff. Normalized to 0.5. If fmax>0.35, f2 default=0.08 If fmax<0.35, f2 default=0.15

CTF description

--ctf_similar_to <ctfFile>
ctfparam file Parameters from this file are overriden by the parameters in the command line
--sampling_rate <Tm>
Angstroms/pixel. Ex: 1.4 This parameter is compulsory if a CTF is needed.
--voltage, --kV <kV>
Accelerating voltage (kV). Ex: 200 This parameter is compulsory if a CTF is needed.
--spherical_aberration, --Cs <Cs>
Milimiters. Ex: 5.6 This parameter is compulsory if a CTF is needed.
--defocusU <DeltafU>
Defocus in Angstroms (Ex: 2000)
--defocusV <DeltafV>
If astigmatic
--azimuthal_angle <ang=0>
Angle between X and U (degrees)
--chromatic_aberration <Ca=0>
Milimiters. Ex: 2
--energy_loss <espr=0>
eV. Ex: 1
--lens_stability <ispr=0>
ppm. Ex: 1
--convergence_cone <alpha=0>
mrad. Ex: 0.5
--longitudinal_displace <DeltaF=0>
Angstrom. Ex: 100
--transversal_displace <DeltaR=0>
Angstrom. Ex: 3
--Q0 <Q0=0>
Percentage of cosine (Q0>0)
--K <K=1>
Global gain

User's comments

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