Dear Lingbo,
Please read the JMB2012 paper on the Bayesian approach. CTF correction is
not done in some pre-processing-like step (it is theoretically impossible
to do a full pre-CTF correction before knowing what you will average
together). Therefore, you should just keep the CTF correction to yes for
all cryo-EM refinements. For negative stain we often don't bother with the
CTFs, but it can be done as well. Do use a much larger amplitude contrast
in that case (e.g. 0.25)
HTH, S
> Hi Sjors,
> In all steps (2D Classification, 3D Classification, and 3D refinement)
> there is an option to correct CTF. The defaults are all set to "Yes".
> I am confused with this. Why CTF correction needs to be done multiple
> times? Shall I just use the defaults? Could you please explain how how CTF
> correction is done in Relion.
>
> Thanks,
> Lingbo
>
--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres
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