Hi Amer,
This is not an issue, but a direct effect of the lowest frequencies now
being weaker in the 2D class averages. No need to worry about. Often 3D
classification/refinement works OK again with full CTF correction. If
not, and you also need to ignore the lowest freqs of the CTF there, you
may need to upweight those again in your final reconstruction. There is
currently no convenient tool to do that, but many general-purpose
toolboxes should have things to do so.
HTH,
Sjors
On 02/13/2018 08:32 AM, Amer Alam wrote:
> Related to this question: While using the 'ignore ctfs till their first peak' options does yield good looking classes in these cases, I have noticed it is generally accompanied by a corresponding decrease in contrast between the classes and background, which can be more grey than black. As the classes look good I have so far ignored this and was wondering if it is an issue (I have been told the background needs to be as dark as possible).
> Thank you
> Amer
--
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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