Name

defocus_get - Estimate defocus from 1D rotationally averaged power spectrum. This function is semi-automated, and requires the user to give correct cut_off frequency to determine the area of power spectrum for defocus estimation.

Usage

defocus = defocus_get((fnam_roo, volt=300,ps=1,cs=2,amplitude_contrast=.1,f_start=30,f_stop=8,docf="a",skip="#",round_off=100,nr1=3,nr2=6)

Input

fnam_roo

document file name of 1D rotational average of power spectrum

volt

voltage

ps

pixel size of the micrograph

cs

Sherical abberation constant

amplitude_constrast

amplitude constrast ratio

f_start

low frequency limit (in Ansgtrom) of selecting power spectrum containing strong CTF for defocus estimation. The default value is 30 Angstrom.

f_stop

high frequency limit (in Angstrom) of selecting power spectrum containing strong CTF for defocus estimation. The default value is 8 Angstrom.

docf

1D power spectrum document file format, either standard spider one "s" or arbitrary format "a"

skip

the mark of comments in the document file, such as ";", or "#"

round_off

round_off error,by default it is set as 100 Angstrom. By adjusting this number, the defocus estimation can be accurate to any digits the user expects.

nr1

the highest rank of polynomials used to fit envelop function

nr2

the highest rank of polynomials used to fit background noise

Output

defocus

the estimated defocus in Angstrom.

Options

Description

1. The function requires the user to define the area in the 1D rotationally averaged power spectrum for defocus estimation.
2. Empirically power spectrum from 1/30 Ansgtrom to 1/8 Angstrom contains discernable CTF traces, and tends to give estimation which is close to the true defocus setting.
3. The starting frequency is supposed to exclude the protein peak, and other spurious peaks caused by artifacts.
4. The stopping freqeuncy is supposed to exclude too flat area of the power spectrum in high frequency area, which tends to underestimate the defocus.
5. This function doesn't incude astigmatsm estimation.

Method

• Constrained simplex method.

Reference

.1. 1. Barrodale and F.D.K. Roberts L1 solution to linear equations subject to linear equality and inequality constraints ACM TOMS 6 (1980), 231-235.

.2. Z. Huang, P. R. Baldwin, S.Mullapudi, and P .A. Penczek, Automated determination of parameters describing power spectra of micrograph images in electron microscopy. J. Struct. Biol. 144 (2003), pp. 79–94.

Author / Maintainer

Zhong Huang

Keywords

category 1

UTILITIES

Files

utilities.py

See also

guess defocus,pw_extract

Maturity

stable

works for most people, has been tested; test cases/examples available.

Bugs

None. It is perfect.