Hi,
> Does anyone know if I am correct in
> assuming that, rather than refining the Cs on a per-particle or
> per-micrograph basis, the Cs will be refined for the entire OpticsGroup
in
> the form of a 4th order Zernike polynomial?
You are right.
> If so, does anyone know if
> there is a way to extract from the output star file what the value of
the
> fitted Cs is?
First, find out the Z_4^0 term. It is the 7th number in rlnEvenZernike.
refined_Cs = nominal_Cs + (12 * 10^(-7) * Z_4^0) / (pi * lambda^3)
nominal_Cs is what you used in CTFFIND (e.g. 2.7 mm for Titan and Talos).
lambda is 0.0196 A for 300 kV and 0.0251 A for 200 kV.
Note that the Cs is usually stable. If the refined value is very
different from what you expect, most likely it is the pixel size
(or acceleration voltage) that is actually wrong.
See also
https://www3.mrc-lmb.cam.ac.uk/relion/index.php?title=Pixel_size_issues.
If you know the true, physical Cs, you can calibrate the pixel size as:
true_pixel_size = (true_Cs * nominal_pixel_size^4 / refined_Cs)^(1/4)
After CtfRefine, everything is consistent at the nominal Cs and nominal pixel
size. DO NOT change the pixel size and Cs value in the STAR file.
Proceed with it and only use the true pixel size in the PostProcess to
scale the
X-axis of the FSC table and the header of the output MRC file.
Best regards,
Takanori Nakane
> Thanks,
> Dr. T.J. Ragan
> Senior Research Computation Officer
> Leicester Institute of Structural and Chemical Biology
> University of Leicester, University Road, Leicester LE1 7RH, UK
> t: +44 (0)116 223 1287
> e: [log in to unmask]<mailto:[log in to unmask]>
> w: www.le.ac.uk/liscb<http://www.le.ac.uk/liscb>
> [University of Leicester Logo][Athena Swan Silver Award]
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