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

Sun Sep 2 08:56:41 PDT 2018

Dear Marin,

This topic is clearly important for you but I think you will find it has nothing to do with Natesh's original question.  I'm sure Sjors will be thrilled to continue this discussion in a private thread.

Best,

Vojta

Vojtěch Pražák
Graduate Student
Department of Structural Biology
The Wellcome Trust Centre for Human Genetics 
Roosevelt Drive, Oxford, OX3 7BN UK 
University of Oxford

Email: vojta at strubi.ox.ac.uk
Web: https://www.strubi.ox.ac.uk/research/kay-grunewald

-----Original Message-----
From: "Marin van Heel" <marin.vanheel at googlemail.com>
To: "Sjors Scheres" <scheres at mrc-lmb.cam.ac.uk>, "Natesh Ramanathan" <natesh at iisertvm.ac.in>, 3dem at ncmir.ucsd.edu
Cc: CCPEM at JISCMAIL.AC.UK
Date: 09/02/18 14:07
Subject: Re: [3dem] GroEL best resolution map. (FSC RESOLUTION ??)

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
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

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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
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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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