TF LM4 - Transfer Function - Determine CTF envelope B-factor and noise parameters

(09/29/06)

PURPOSE

Apply nonlinear regression to estimate EM image CTF envelope B-factor and noise parameters. Outputs to operation line registers and doc file. Operation rarely used, may be buggy. Further info on CTF related operations in SPIDER.   Example.

SEE ALSO

CTF FIND [Contrast Transfer Function - Estimation of CTF parameters]
RO SD [Rotational average - single line output, doc file]
TF DNS [Transfer Function - Delete noise background]

USAGE

.OPERATION: TF LM4 [b],[c],[b1],[b2]
[The operation line can specify up to four optional register variables:

Variable Example Receives
First [b] B-factor of envelope function
Second [c] B-factor of CTF related Noise
Third [b1] Base-line noise
Fourth [b2] Base-line noise

.PIXEL SIZE [A], SPHERICAL ABERATION 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.]

.ESTIMATED DEFOCUS [A]: 27000
[Enter the defocus in Angstroms of image. The defocus can be estimated using 'CTF FIND' ]

.1-D POWER SPECTRUM OF MICROGRAPH: pow001
[Enter name of the rotationally averaged 1-D power spectrum file.]

.DOCUMENT FILE: tflm4_doc_001
[Enter name for the output doc file.]

NOTES

  1. The image formation is: PW(f) = CTF(f)**2*ENV(f)**2 * NOISE1**2 + NOISE2**2.

  2. CTF parameters are pre-estimated using linear constrained and uncontrained method.

  3. ENV(f) = EXP(-.5*(f/B-factor)**2).

  4. NOISE1 = Constant.

  5. NOISE2 = EXP(Af+B).

  6. Implemented by: Zhong Huang

SUBROUTINES

TFLM4

CALLER

UTIL1

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