Hi Dimitry
I will try to be patient in my explanation... You have deleted the
discussion history in your response but do read our bioRxiv 2017 paper
and trace back the FSC literature from that.
I know from our own private email exchanges that you do understand the
basic principles. The EMD-0144 that you are referring to has a
pixel/voxel size of 0.81A. (I have no idea who the authors are but,
friends or foes, that is entirely irrelevant to this discussion). The
resolution claim in that paper is 1,62A , that is, exactly the Niquist
frequency or twice the pixel size of 0.81A! I have already mentioned in
this thread that the FSC 0.143 is itself wrong while based on sloppy
statistics (bioRxiv 2017 and trace back the literature, you may also
want to listen to my lecture at the Wiley 2017 award ceremony which is
available on line). I will not repeat that argumentation here.
Here I will just give you one theoretical argument why you cannot claim
the Nyquist frequency as the reproducible resolution. The sampling
theorem
(https://en.wikipedia.org/wiki/Nyquist%E2%80%93Shannon_sampling_theorem)
requires that that signal you are digitizing is band limited, implying
that the power of the signal in Fourier space at the Nyquist frequency
must have dropped to zero. If the power in the signal's FT is zero in
every measurement there is no point in correlating two independent
measurement as needed for an FSC measurement. If, on the other hand, if
the power is NOT zero at Nyquist, the data is under-sampled, thus
violating the sampling theorem. This is one reason why you will find
the 3 pixel rule in all of our FSC related papers (for example: Orlova
et al J. Mol. Biol. (1997) 271, 417-437). The safety margin we defined
in the past is 2/3 Nyquist, stick to it (Referees take heed).
Cheers,
Marin
On 02/09/2018 14:43, Dimitry Tegunov wrote:
> Dear Marin,
>
> could you please provide us with a reference for this fundamental basis in existing literature? Surely I'm not the only one who would love to learn why the seemingly correct features of e. g. EMD-0144 (http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-0144) are illegally resolved.
>
> Cheers,
> Dimitry
>
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Prof Dr Ir Marin van Heel
Laboratório Nacional de Nanotecnologia - LNNano
CNPEM/LNNano, Campinas, Brazil
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Emeritus Professor of Cryo-EM Data Processing
Leiden University
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Imperial College London
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