Differences between revisions 21 and 22
Revision 21 as of 2009-08-03 01:51:09
Size: 1503
Editor: adsl-68-92-212-30
Comment:
Revision 22 as of 2009-08-03 01:53:02
Size: 1501
Editor: adsl-68-92-212-30
Comment:
Deletions are marked like this. Additions are marked like this.
Line 9: Line 9:
  bfactor:: B-factor defines the exponentially decaying rate of Fourier amplitudes [{{{`1/Å^2`}}}].   bfactor:: B-factor defines the exponentially decaying rate of Fourier amplitudes [1/{{{Å^2}}}].

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
    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.

    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).

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