TF CRF - Transfer Function - Determine Defocus & ACR

PURPOSE

Estimate defocus and amplitude contrast ratio based on a cross-resolution curve between a single defocus group volume and a partial CTF-corrected volume. Outputs defocus parameters to SPIDER operation line registers. Further info on CTF related operations in SPIDER.

SEE ALSO

CTF FIND	[Contrast Transfer Function - Estimation of CTF parameters]
TF DDF	[Transfer Function - Determine Defocus & amplitude contrast]

USAGE

.OPERATION: TF CRF [ll],[cll],[ul],[cul],[err]

[The operation line can specify up to five optional register variables:
The first (called [ll] in this example) receives the lower limit of the defocus.
The second (called [cll] in this example) receives the corresponding lower limit of the amplitude contrast ratio.
The third (called [ul] in this example) receives the upper limit of the defocus.
The fourth (called [cul] in this example) receives the corresponding upper limit of the amplitude contrast ratio.
The fifth (called [err] in this example) receives the error value.]

.PIXEL SIZE [A], CS [MM]: 3.95, 2.0
[Enter pixel size in Angstroms of volumes used to calculate the cross-resolution curve and the spherical aberration constant.]

.DEFOCUS [A], WAVELENGTH LAMBDA [A]: 0,0. 037
[Enter zero for defocus value to request estimation of the defocus. If a non-zero value (in Angstroms) is entered, it will be used by the program as a default value and only the amplitude contrast ratio will be estimated.
Next, 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]: 0.2
[Enter zero to request estimation of the <a href="../glossary.html#ACR">ACR If a non-zero value is entered, it will be used by the as a default value and only the defocus will be estimated.]

.CROSS-RESOLUTION DOC FILE: docrf3
[Enter cross-resolution file, such as the output of 'RF 3'.]

NOTES

1. Theory and all definitions of electron optical parameters are according to:
   Frank, J. (1973). The envelope of electron microscopic transfer functions for partially coherent illumination.
   Optik, 38(5), 519-536.
   and
   Wade, R. H., & Frank, J. (1977). Electron microscope transfer functions for partially coherent axial illumination and chromatic defocus spread.
   Optik, 49(2), 81-92.
   Internally, the program uses the generalized coordinates defined in these papers.

2. In addition, an optional cosine term has been added with a weight. The complete expression is:
   TF(K) = [(1-ACR) * sin(GAMMA) - ACR*cos(GAMMA)]

3. Written by P.A.Penczek, UTH.

SUBROUTINES

TFCRF

CALLER

UTIL1