TF ED - Transfer Function - Estimate Defocus from image power spectrum

(11/05/15)

PURPOSE

Estimates the defocus, and cutoff frequency of high frequencies for CTF based on 2-D power spectrum. Outputs defocus to operation line register. This operation is normally used on power spectra from square 'tiles' windowed from a larger original micrograph; e.g. use the procedure: powdefocus.spi Outputs defocus parameters to SPIDER operation line registers. Note: We recommend you use the 'CTF FIND' operation instead, especially if there is any astigmatism present, as it gives poor results for astigmatic images. The astigmatism calculation was unreliable and has been removed. Further info on CTF related operations in SPIDER. This operation was never reliable and should not be used anymore. It is kept for historical reasons only. Use 'CTF FIND' instead.   Example.

SEE ALSO

TF LM4 [Transfer Function - Determine CTF envelope B-factor and noise parameters]
CTF FIND [Contrast Transfer Function - Estimation of CTF parameters]

USAGE

.OPERATION: TF ED [dum],[dum],[astdef],[def],[cutoff]
[The operation line can specify up to five optional register variables:

Variable Example Receives
First [dum] Dummy value for legacy compatibility
Second [dum] Dummy value for legacy compatibility
Third [astdef] Dummy value for legacy compatibility
Fourth [def] Overall defocus (without accounting for astigmatism)
Fifth [cutoff] Cutoff frequency in 1/A

.INPUT FILE: PW_AV001
[Enter name of existing power spectrum file (must be square).]

.PIXEL SIZE[A] and SPHERICAL ABBERATION CS [MM]: 2.8, 2
[Enter pixel size in image (in A) and spherical aberration coefficient of the objective, usually referred to as CS, (in mm).]

.WAVELENGTH LAMBDA [A]: 0.037
[Enter the wavelength of the electrons (in Angstroms) . The value used in this example corresponds to 100kV. A table of values is listed in the glossary under lambda.]

.AMPLITUDE CONTRAST RATIO [0-1]: 0.1
[Enter the amount of amplitude contrast (as a fraction). For ice images this may be about 0.1, for negative stain about 0.15. Default value is 0.1.]

.OUTPUT DOCUMENT FILE: CTF001
[Enter name for document file which will contain 4 register columns of noise information (NOT defocus values).]

NOTES

  1. The output document file contains following four register columns:
    a) - Spatial freqency (1/A).
    b) - Estimated background noise: BACKGROUND_NOISE(f)**2.
    c) - Background-subtracted power spectrum: {CTF(f) * ENV(f) * SIGNAL(f)}**2 = PW(f) - BACKGROUND_NOISE(f)**2
    d) - Estimated ENV(f)**2

  2. The power spectrum model is: PW(f) = {CTF(f) * ENV(f) * SIGNAL(f)}**2 + BACKGROUND_NOISE(f)**2

  3. For details about this algorithm and cutoff frequency see: Z. Huang, P.R. Baldwin, and P. A. Penczek. Automated determination of parameters describing power spectra of micrograph images in electron microscopy. J. Struct. Biology 144, 2003, 79-94

  4. Implemented by: Zhong Huang.

  5. If the operation is unable to determine the parameters due to a abnormal power spectrum SPIDER will not stop in procedural mode. The output file will contain zeros for all values. This allows processing a large set of images efficiently.

  6. For calculating agstigmatism use the SPIDER operation 'CTF FIND' which outputs the angle and magnitude of astigmatism as determined by: CTFFIND3

SUBROUTINES

TFED

CALLER

UTIL1

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