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

Marin van Heel marin.vanheel at googlemail.com
Sun Sep 2 06:05:53 PDT 2018


Dear Sjors,

It is not a matter of software implementation but it is a fundamental 
theoretical basis of signal processing and the Fourier transform!
You seem to have misunderstood the discussion on the issue here on 
3DEM/CCPEM mailers a while ago (June 2016?). It is NOT about "routinely 
achieve resolutions very close to Nyquist" but rather about "to which 
level you are ALLOWED to claim/interpret the significant resolution" 
based on an FSC curve.
Maybe I need to write a separate paper about the matter to better 
explain the fundamental principles behind it.

This "under-sampling problem" is an important matter because - 
especially in combination with erroneous resolution thresholds like the 
"gold standard FSC 0.143" (based on "sloppy statistics" see our bioRxiv 
paper)" - it makes it impossible to objectively compare the resolution 
levels achieved in independent experiments.  That makes efforts to 
perform projects like "resolution challenges" futile and not worth 
wasting your time on.

Cheers,
Marin

===============

On 02/09/2018 07:14, Sjors Scheres wrote:
> Dear Natesh,
> The limitation of 3x the pixel size of the maximum reachable 
> resolution might be true for software written by Marin, but it is 
> definitely not true for many other programs, including relion. We 
> routinely achieve resolutions very close to Nyquist, which is only 2x 
> the pixel size.
>
> Hth,
> Sjors
>
> Sent from my phone.
>
> -------- Original message --------
> From: Marin van Heel <marin.vanheel at googlemail.com>
> Date: 01/09/2018 19:43 (GMT+01:00)
> To: Natesh Ramanathan <natesh at iisertvm.ac.in>, 3dem at ncmir.ucsd.edu
> Subject: Re: [3dem] GroEL best resolution map. (FSC RESOLUTION ??)
>
>
> Dear Natesh,
>
> I just checked the technical data of the EMD-3407 dataset and I saw 
> that its pixel size is 1.05A . That means that no resolution levels 
> better than 3 x 1.05A = 3.15A  may be claimed for processing results 
> based on that data set, following the standards we set in the past 
> (for the younger generation: I am the main inventor of the FSC ;) ). 
> Going beyond a resolution claim of 3.15A would mean that the dataset 
> is undersampled, and would thus require a new data collection with a 
> smaller pixel size. For a possible resolution claim of, say, 2A  you 
> need a maximum pixel size of 0.66A !  Moreover, the 0.143 threshold 
> FSC threshold used in this EMD-3407 case is itself wrong, while based 
> on sloppy statistics. 
> (https://www.biorxiv.org/content/early/2017/11/24/224402).Bottom 
> line:  to compare the results of different cryo-EM experiments you 
> need correct resolution criteria applied to sufficiently fine sampled 
> cryo-EM data.
>
> Cheers
>
> Marin
>
> On 01/09/2018 12:57, Natesh Ramanathan wrote:
>> Dear All,
>>
>>       Does anyone know/have a GroEL cryoEM map with resolution  2.5 Å 
>> or better?
>> I see that the best resolution in EMDataBank is 3.26 Å - EMD-3407 and 
>> EMD-3415.
>>       If you have one, is it possible to share the map with me?
>>
>> Many thanks.
>> Best regards,
>> Natesh
>> -- 
>> ----------------------------------------------------------
>> "Live Simply and do Serious Things .. "
>> - Dorothy Mary Crowfoot Hodgkin OM, FRS
>>
>> "In Science truth always wins"
>> - Max Ferdinand Perutz OM FRS
>> ----------------------------------------------------------
>> Dr. Ramanathan Natesh
>> Assistant Professor,
>> School of Biology,
>> Indian Institute of Science Education and Research Thiruvananthapuram 
>> (IISER-TVM),
>> Maruthamala P.O., Vithura,
>> Thiruvananthapuram,  695551, Kerala, India
>>
>> natesh at iisertvm.ac.in <mailto:natesh at iisertvm.ac.in>
>> http://www.researcherid.com/rid/C-4488-2008
>> ORCID: http://orcid.org/0000-0002-1145-5962
>> https://publons.com/author/1520837/ramanathan-natesh#profile
>> http://faculty.iisertvm.ac.in/natesh
>>
>> Office Ph. 0091- 471-2778087
>>
>>
>> _______________________________________________
>> 3dem mailing list
>> 3dem at ncmir.ucsd.edu
>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>
>
> -- 
> ==============================================================
>
>      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.


-- 
==============================================================

     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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