TF - Transfer Function - Defocus dependent

PURPOSE

Generates a transfer function, squared transfer function, or envelope function within a specified defocus range and for specified electron optical parameters.

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

.OUTPUT FILE: TRA001
[Enter the name of the file where the transfer function is to be stored.]

.CS: 3.5
[Enter the spherical aberration coefficient in mm.]

.LAMBDA: 0.037
[Enter the wavelength of the electrons. The value used in this example corresponds to 100kV. Other values are listed in the glossary under lambda.]

.LOWER DEFOCUS LIMIT: -1800.
[Enter the lower defocus limit in Angstroems.]

.UPPER DEFOCUS LIMIT: 3000.
[Enter the upper defocus limit in Angstroems.]

.NUMBER OF SP. FREQ. PTS./DEF. POINTS: 120,300
[Enter the number of spatial frequency grid points and the number of defocus grid points.]

.MAXIMUM SPATIAL FREQUENCY [A**-1]: 0.5
[Enter the spatial frequency limit in 1./Angstroems.]

.SOURCE SIZE: .005
[Enter the source size in spatial frequency units, 1./Angstroems.]

.DEFOCUS SPREAD [A]: 200.
[Enter the 1/e halfwidth of the defocus distribution in Angstroems.]

.AMPLITUDE CONTRAST RATIO [0-1], GAUSSIAN ENVELOPE PARAMETER: 0.2,100
[Enter ACR and GEP; see below for definition.]

.(D)IFFRACTOGRAM/(E)NVELOPE/(S)TRAIGHT: D
[Either the transfer function is put into the array directly as computed (option 'S'), or its square (option 'D') is stored, or else the envelope function describing the attenuation of the transfer function due to partial coherence effects (option 'E').]

.FRAME? (Y/N): Y
[The specified function will then be generated, and stored in TRA001.]

NOTES

1. Theory and all definitions of electron optical parameters are according to: 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, and an ad hoc Gaussian falloff function has been added as discussed in Stewart et al. (1993) EMBO J. 12:2589-2599. The complete expression is:
   TF(K) = [(1-ACR)*sin(GAMMA) - ACR*cos(GAMMA)]*ENV(K)*exp[-GEP*K^2]

3. 10/01/96 - The equation was corrected; dependence on the defocus spread was changed; see the 'TF' and 'TFD' subroutines.

SUBROUTINES

TF, TRAF

CALLER

UTIL1