Xmipp

xmipp_ctf_estimate_from_micrograph (v3.0)

Usage

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

Parameters

--micrograph <file>
File with the micrograph
--oroot <rootname=>
Rootname for output If not given, the micrograph without extensions is taken rootname.psd or .psdstk contains the PSD or PSDs

PSD estimation

--psd_estimator <method=periodogram>
Method for estimating the PSD
where <method> can be:
  • periodogram
  • ARMA
--pieceDim <d=512>
Size of the piece
--overlap <o=0.5>
Overlap (0=no overlap, 1=full overlap)
--Nsubpiece <N=1>
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 <mode=micrograph>
How many PSDs are to be estimated
where <mode> can be:
  • micrograph Single PSD for the whole micrograph
  • regions <file> The micrograph is divided into a region grid and a PSD is computed for each one. The file is metadata with the position of each particle within the micrograph
  • particles <file> One PSD per particle. The file is metadata with the position of each particle within the micrograph

CTF fit

--dont_estimate_ctf
Do not fit a CTF to PSDs

ARMA models

--N_AR <N=24>
N order of the AR model
--M_AR <N=24>
M order of the AR model
--N_MA <N=20>
N order of the MA model
--M_MA <N=20>
M order of the MA model

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

Examples and notes

Estimate PSD
xmipp_ctf_estimate_from_micrograph --micrograph micrograph.mrc --dont_estimate_ctf
Estimate a single CTF for the whole micrograph
xmipp_ctf_estimate_from_micrograph --micrograph micrograph.mrc --sampling_rate 1.4 --voltage 200 --spherical_aberration 2.5
Estimate 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 -15000
Estimate 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 -15000
Estimate 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

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