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 * 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:: defocus value of the lens in [nm].
  cs:: spherical aberration constant of the electron microscope [mm].
  voltage:: electron accelerating voltage [kV].
  apix:: pixel size of digitized micrograph [{{{Å}}}].
  bfactor:: B-factor defines the exponentially decaying rate of Fourier amplitudes [1/{{{Å^2}}}].
  ampcont:: amplitude contrast ratio.
 * 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 definitions are:
     defocus :: defocus in {{{`µ`m}}}. Positive number means underfocus.
     voltage :: microscope voltage in kV (default 300 kV).
     apix :: pixel size in {{{`Å`}}}.
     cs :: Spherical aberration constant in mm. (Default 2.0)
     amp_contrast :: Amplitude contrast ratio, unitless, given as percentage of (0,100). (Default 10%)
     bfactor :: B-factor defining exponential decay of Fourier amplitudes decay {{{`Å^2`}}}. (Default 0.0, i.e., no decay).
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 * To access or set individual parameters in a ctf object, use:
 . bfactor = ctf.bfactor
 . ctf.bfactor = 200.0

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 definitions are:

    defocus

    defocus in `µ`m. Positive number means underfocus.

    voltage
    microscope voltage in kV (default 300 kV).
    apix

    pixel size in `Å`.

    cs
    Spherical aberration constant in mm. (Default 2.0)
    amp_contrast
    Amplitude contrast ratio, unitless, given as percentage of (0,100). (Default 10%)
    bfactor

    B-factor defining exponential decay of Fourier amplitudes decay `Å^2`. (Default 0.0, i.e., no decay).

    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:
    1. use function set_ctf(img, p), where p is a list of parameters [defocus, cs, voltage, apix, bfactor, ampcont].

    2. if the CTF object already exists, one can use img.set_attr("ctf", ctf) directly.

  • To recover the numerical values of CTF parameters from CTF object stored in the header of an image, use function p=get_ctf(img).

  • To access or set individual parameters in a ctf object, use:
  • bfactor = ctf.bfactor
  • ctf.bfactor = 200.0

CTF_info (last edited 2017-05-07 11:51:17 by penczek)