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CCPEM  September 2018

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Subject:

Re: [3dem] GroEL best resolution map. (FSC RESOLUTION ??)

From:

Sjors Scheres <[log in to unmask]>

Reply-To:

Sjors Scheres <[log in to unmask]>

Date:

Mon, 3 Sep 2018 13:28:34 +0100

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Hi Marin,

EMD-0144 is ours, so I hope you consider that friends, not foes. :-) Not
sure why the authors are not shown in the EMDB, probably because we still
need to finish the corresponding paper.

The pixels size is 0.81A, and we got what we estimate to be a 1.65A
resolution map, just two shells below the Nyquist frequency. Features in
the map, like holes in 5-membered rings and the appearance of sulfur
atoms, do suggest the resolution estimate is reasonable. The EMDB entry
links to EMPIAR-10200. It contains 1255 movies in compressed TIFF (only
occupying 191.5 GB), which were collected by Wim Hagen at EMBL,
Heidelberg. Hopefully the availability of these data helps the discussion.

Best wishes,
Sjors


> 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
>
>      tel:    +55-19-3518-2316
>      mobile  +55-19-983455450 (current)
>      mobile  +55-19-981809332
>                   (041-19-981809332 TIM)
>      Skype:  Marin.van.Heel
>      email:  marin.vanheel(A_T)gmail.com
>              marin.vanheel(A_T)lnnano.cnpem.br
>      and:    mvh.office(A_T)gmail.com
>
> --------------------------------------------------
>      Emeritus Professor of Cryo-EM Data Processing
>      Leiden University
>      Mobile NL: +31(0)652736618 (ALWAYS ACTIVE SMS)
> --------------------------------------------------
>      Emeritus Professor of Structural Biology
>      Imperial College London
>      Faculty of Natural Sciences
>      email: m.vanheel(A_T)imperial.ac.uk
> --------------------------------------------------
>
> I receive many emails per day and, although I try,
> there is no guarantee that I will actually read each incoming email.
>
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>


-- 
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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