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Adrian Quintana edited this page Dec 11, 2017 · 1 revision

ctf_estimate_from_psd

Purpose

This program allows you to adjust a parametric CTF model and the underlying noise at the same time. 23 parameters corresponding to the model and noise need to be adjusted. Common use starts from a power spectrum estimation (either ARMA or Periodogram averaging) estimation. If the experimental transfer function is called <fn_root>.psd, then the following results are written:

  • [fn_root].ctfparam for the 23 parameters. This file must be used as the CTF of the piece corresponding PSD
  • [fn_root].ctfmodel_quadrant and[fn_root].ctfmodel_halfplane Images that allow to see at the same time the PSD and the CTF model (without the background noise). These two images must be seen with the-ctf option ofShow

This program is seldom called by the user. To compute the CTF of a micrograph, particles, etc. normallyAssign_CTF is used.

Usage


$ ctf_estimate_from_psd -i [CTF initial file]

Parameters

  • `` CTF initial file. It may have any of the CTF and CTFnoise parameters (seeFourierFilter) (most important are the microscope voltage, the sampling rate and the spherical aberration) plus any of the following. Since Xmipp 1.2, if Q0 is provided by the user, it is not estimated.
  • psd[power_spectrum.psd] = Power spectrum density with the transfer function to mimic
  • similar_model[similar_model.ctfparam] = Model of a similar CTF (.ctfparam)
  • defocus_range[range=8000] = If the image is tilted there might be a high defocus change between different parts of the micrograph. Use this option to indicate the maximum difference expected in Angstroms
  • min_freq[wmin=0.05] = Minimum frequency considered for adjustment. The cost function is evaluated only for those digital frequencies(<0.5) whose module is above this value
  • max_freq[wmin=0.35] = Maximum frequency considered for adjustment. The cost function is evaluated only for those digital frequencies (<0.5) whose module is below this value
  • show_optimizationyes = Show optimization. Numbers and images about the optimization process are written. All of them start asstep01_...,step02_... and correspond to the different stages of the adjustment process
  • radial_noiseyes = Allow to use radial noise. By default, it is astigmatic
  • ctfmodelSize[dim=128] = This parameter controls the size of the ctfmodel_quadrant and ctfmodel_halfplane images. By default, it takes the value 128.
  • initialCa[Ca=2] = Initial value of the chromatic aberration. This value is refined in the optimization process.
  • enhance_min_freq[w] = Normalized frequency (max. value 0.5) of the low end of the bandpass filter used for the PSD enhancement. If max_freq>0.35, then the default value of enhance_min_freq is 0.01; else, the default value is 0.02.
  • enhance_max_freq[w] = Normalized frequency (max. value 0.5) of the high end of the bandpass filter used for the PSD enhancement. If max_freq>0.35, then the default value of enhance_max_freq is 0.08; else, the default value is 0.15.
  • enhance_weight[Weight=5] = Weight of the enhancement term within the optimization problem. Increase this weight to reinforce the similarity to the enhanced PSD.

Examples and notes

In the following example the power spectrum of an image is to be fitted. First, an ARMA model is computed for the image, once you have this, the 23 parameters model is fitted to the ARMA result.


$ xmipp_ctf_estimate_from_psd -i adjust.param

whereadjust.param contains:


psd=ARMA_model.psd

sampling_rate=3.2
voltage=200
spherical_aberration=2

The resulting model is shown in the following figure (.ctfmodel):

/ARMA-fitting.gif

--Main.AlfredoSolano - 17 Jan 2007

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