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How to use CTF in SPARX
In SPARX, the EMAN CTF object are used to store and apply all CTF parameters.
To generate a CTF object, use function [:generate_ctf:generate_ctf(p)], here p is a list of parameters [defocus, cs, voltage, apix, bfactor, ampcont]. Their descriptions are:
- defocus value of the lens in [nm].
- spherical aberration constant of the electron microscope [mm].
- electron accelerating voltage [kV].
pixel size of digitized micrograph [Å].
B-factor defines the exponentially decaying rate of Fourier amplitudes [1/Å^2].
- amplitude contrast ratio.
Notice: In some other software packages, the defocus value is in `Å` and amplitude contrast ratio is in the range of (0, 1). This function will automatically determine whether these two CTF parameters are in this convention and convert them into our convention.
To apply CTF object to an image, use [:filt_ctf:filt_ctf(img, ctf)], where ctf is a CTF object.
- To put a CTF object into the header of an image, it can be done in two ways:
use function set_ctf(img, p), whether p is a list of parameters [defocus, cs, voltage, apix, bfactor, ampcont].
if the CTF object already exists, one can use img.set_attr("ctf", ctf) directly.
To get a CTF object from an image, use function get_ctf(img).