| TF | [Transfer Function - Generate image showing effect of defocus on CTF] |
| TF C | [Transfer Function - Generate a straight, complex, CTF correction image] |
| TF C3 | [Transfer Function - Generate a straight, complex, CTF correction volume] |
| TF CT | [Transfer Function - Generate a binary, phase flipping, complex, CTF correction image] |
| TF CT3 | [Transfer Function - Generate a binary, phase flipping, complex, CTF correction volume] |
| TF CTS | [Transfer Function - CTF correction with SNR, image/volume] |
| TF DDF | [Transfer Function - Determine Defocus & amplitude contrast] |
| TF DEV | [Transfer Function - Determine Envelope function] |
| TF DNS | [Transfer Function - Delete noise background] |
| TF L | [Transfer Function - Generate CTF, in doc file] |
.CS [MM]: 2.0
[Enter the
spherical aberration coefficient.]
.DEFOCUS [A], ELECTRON VOLTAGE [Kev]: 20000, 300
[Enter the amount of
defocus,
in Angstroms. Positive values correspond to underfocus
(the preferred region); negative values correspond to overfocus.
Next, enter the energy of the electrons in Kev.
(Note: operation still accepts the legacy input of electron wavelength
lambda [A] instead of voltage)].
.NUMBER OF SPATIAL FREQ. POINTS: 128
[Enter the dimension of the 3D array. In our example,
each element of the array (K,I) corresponds to a
spatial frequency
Kx = (K-65) * DK
Ky = (I-65) * DK
where DK is defined by the next input.]
.MAXIMUM SPATIAL FREQUENCY [1/A]: 0.15
[Enter the
spatial frequency
radius corresponding to the
maximum radius ( = 128/2 in our example) of pixels in the
array. From this value, the spatial frequency increment
(DK = 0.15/128) is calculated.]
.SOURCE SIZE [1/A], DEFOCUS SPREAD [A]: 0.005,250
[Enter the
size of the illumination source
in reciprocal Angstroms. This is the size of the source as it appears in
the back focal plane of the objective lens. A small value
results in high coherence; a large value, low coherence.
Enter the estimated magnitude of the defocus
variations
corresponding to energy spread and lens current fluctuations.]
.ASTIGMATISM [A], AZIMUTH [DEG]: 400, 30
[Enter the defocus variation due to axial
astigmatism.
The value given indicates a defocus range of +/- 400 A around
the nominal value as the azimuth is changed. Then, enter the
angle, in degrees, that characterizes the direction of
astigmatism. The angle defines the origin direction in which
the astigmatism has no effect.]
.AMPL CONTRAST RATIO [0-1], GAUSSIAN ENVELOPE HALFWIDTH: 0.1, 0.15
[Enter the ACR and the
GEH.
The Gaussian envelope parameter specifies
the 2 sigma level of the Gaussian (see note 2 for details).]
.DIFFRACTOGRAM, ENVELOPE or STRAIGHT (D/E/S): 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') is stored.]
NOTES