TF CRF - Transfer Function - Determine Defocus & Amplitude contrast ratio

PURPOSE

To determine defocus and amplitude contrast ratio based on a cross-resolution curve between a single defocus group volume and a partial CTF-corrected volume. For literature, see Notes.

SEE ALSO

TF C	[Transfer Function - Complex]
TF C3	[Transfer Function - Complex 3D]
TF CT	[Transfer Function - phase flipping, Complex, Binary]
TF CT3	[Transfer Function - Complex, Binary 3D]
TF CTS	[Transfer Function - 2D & 3D CTF correction]
TF D	[Transfer Function - Display]
TF DDF	[Transfer Function - Determine DeFocus & amplitude contrast]
TF DEV	[Transfer Function - Determine Envelope function]
TF DNS	[Transfer Function - Determine and delete Noise background]

USAGE

.OPERATION: TF CRF [ll],[cll],[ul],[cul],[err]
[Optional register variables on the OPERATION line will receive the output of the command:

[ll] - lower limit of the defocus
[cll] - corresponding lower limit of the amplitude contrast ratio
[ul] - upper limit of the defocus
[cul] - corresponding upper limit of the amplitude contrast ratio
[err] - error value.]

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

.DEFOCUS(ANGSTROMS), LAMBDA(ANGSTROMS): 0,0.037
[Enter zero for defocus value to request estimation of the defocus. If a non-zero value (in Angstroems) 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 ACR. If a non-zero value is entered, it will be used by the program 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 as in: J. Frank (1973) Optik 38:519, and R. Wade & J. Frank (1974) Optik 49:81. 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