TF ED - Transfer Function - Estimation of CTF parameters

PURPOSE

Estimates the defocus, astigmatism, and cutoff frequency of high frequencies based on 2-D power spectrum. Outputs to doc. file and to operation line registers.

SEE ALSO

TF LM4

[Transfer Function - Estimate image formation parameters]

USAGE

.OPERATION: TF ED [ang],[mag],[astdef],[overdef],[cutoff]

[On output, [ang], [mag] are the angle and magnitude of astigmatism. [astdef] is the astigmatism corrected defocus value. [overdef] is the overall defocus without taking astigmatism into account. [cutoff] is the cutoff frequency in 1/A]

.INPUT FILE: PW_AV001
[Enter name of the 2-D power spectrum file.]

.PIXEL SIZE [A], SPHERICAL ABBERATION CS [MM]: 2.8, 2

.WAVELENGTH LAMBDA [ANGSTROMS]: 0.037
[Enter the wavelength of the electrons. 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

.OUTPUT DOCUMENT FILE: CTF001

NOTES

1. The output document file contains following four 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 model of the power spectrum 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. When the power spectrum has quite weak CTF imprint, the operation will not give astigmatism estimation, and only will give an estimation of the overall defocus and the cutoff frequency.

5. The amplitude contrast is set by default to 0.1.

6. Implemented by: Zhong Huang.

7. 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.

SUBROUTINES

TFED, GETDEFOCUS

CALLER

UTIL1