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<div>Dear Marin,</div>
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<div>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.</div>
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<div>Best,</div>
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<div>Vojta<br>
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<div class="signature">Vojtěch Pražák<br>Graduate Student<br>Department of Structural Biology<br>The Wellcome Trust Centre for Human Genetics<br>Roosevelt Drive, Oxford, OX3 7BN UK<br>University of Oxford<br><br>Email: <a href="mailto:vojta@strubi.ox.ac.uk">vojta@strubi.ox.ac.uk</a><br>Web: <a href="https://www.strubi.ox.ac.uk/research/kay-grunewald">https://www.strubi.ox.ac.uk/research/kay-grunewald</a><br> </div>
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<hr size="1">-----Original Message-----<br>From: "Marin van Heel" <<a href="mailto:marin.vanheel@googlemail.com">marin.vanheel@googlemail.com</a>><br>To: "Sjors Scheres" <<a href="mailto:scheres@mrc-lmb.cam.ac.uk">scheres@mrc-lmb.cam.ac.uk</a>>, "Natesh Ramanathan" <<a href="mailto:natesh@iisertvm.ac.in">natesh@iisertvm.ac.in</a>>, <a href="mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a><br>Cc: <a href="mailto:CCPEM@JISCMAIL.AC.UK">CCPEM@JISCMAIL.AC.UK</a><br>Date: 09/02/18 14:07<br>Subject: Re: [3dem] GroEL best resolution map. (FSC RESOLUTION ??)<br><br><div class="moz-cite-prefix">
<br>Dear Sjors,<br><br>It is not a matter of software implementation but it is a fundamental theoretical basis of signal processing and the Fourier transform!<br>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.<br>Maybe I need to write a separate paper about the matter to better explain the fundamental principles behind it.<br><br>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.<br><br>Cheers,<br>Marin<br><br>===============<br><br>On 02/09/2018 07:14, Sjors Scheres wrote:<br>
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<div>Dear Natesh,</div>
<div>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.</div>
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<div>Hth,</div>
<div>Sjors</div>
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<div id="composer_signature"><div style="font-size:85%;color:#575757">Sent from my phone.</div></div>
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<div>-------- Original message --------</div>
<div>From: Marin van Heel <a href="mailto:marin.vanheel@googlemail.com" class="moz-txt-link-rfc2396E"><marin.vanheel@googlemail.com></a>
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<div>Date: 01/09/2018 19:43 (GMT+01:00)</div>
<div>To: Natesh Ramanathan <a href="mailto:natesh@iisertvm.ac.in" class="moz-txt-link-rfc2396E"><natesh@iisertvm.ac.in></a>, <a href="mailto:3dem@ncmir.ucsd.edu" class="moz-txt-link-abbreviated">3dem@ncmir.ucsd.edu</a>
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<div>Subject: Re: [3dem] GroEL best resolution map. (FSC RESOLUTION ??)</div>
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<br>Dear Natesh,<br><br>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. (<a href="https://www.biorxiv.org/content/early/2017/11/24/224402" class="moz-txt-link-freetext">https://www.biorxiv.org/content/early/2017/11/24/224402</a>).Bottom line: to compare the results of different cryo-EM experiments you need correct resolution criteria applied to sufficiently fine sampled cryo-EM data.<br><br>Cheers<br><br>Marin<br><br>On 01/09/2018 12:57, Natesh Ramanathan wrote:<br>
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<div dir="ltr">Dear All,<div>
<br><div>Does anyone know/have a GroEL cryoEM map with resolution 2.5 <span style="color:rgb(0,0,0);font-family:verdana,DejaVu,sans-serif;font-size:12px;text-align:justify">Å</span> or better?</div>
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<div>I see that the best resolution in EMDataBank is <span style="color:rgb(0,0,0);font-family:verdana,DejaVu,sans-serif;font-size:12px;text-align:justify">3.26 Å</span> - EMD-3407 and EMD-3415.<br>
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<div>If you have one, is it possible to share the map with me?</div>
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<div>Many thanks.</div>
<div>Best regards,<br>Natesh</div>--<br><div data-smartmail="gmail_signature" class="gmail_signature" dir="ltr"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr">
<div dir="ltr">----------------------------------------------------------<br>"Live Simply and do Serious Things .. "<br>- Dorothy Mary Crowfoot Hodgkin OM, FRS<br><br>"In Science truth always wins"<br>- Max Ferdinand Perutz OM FRS<br>----------------------------------------------------------<br>Dr. Ramanathan Natesh<br>Assistant Professor,</div>
<div>School of Biology,</div>
<div dir="ltr">Indian Institute of Science Education and Research Thiruvananthapuram (IISER-TVM),<br><div>Maruthamala P.O., Vithura,<br>
</div>Thiruvananthapuram, 695551, Kerala, India<br><br><a href="mailto:natesh@iisertvm.ac.in">natesh@iisertvm.ac.in</a><br><a href="http://www.researcherid.com/rid/C-4488-2008">http://www.researcherid.com/rid/C-4488-2008</a>
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<div>ORCID: <a style="color:rgb(0,90,132);font-family:Arial,Helvetica,sans-serif;font-size:12px" title="Go to my personal page at http://orcid.org/" alt="Go to my personal page at http://orcid.org/" href="http://orcid.org/0000-0002-1145-5962">http://orcid.org/0000-0002-1145-5962</a>
</div>
<div dir="ltr"><a href="https://publons.com/author/1520837/ramanathan-natesh#profile">https://publons.com/author/1520837/ramanathan-natesh#profile</a></div>
<div dir="ltr"><a href="http://faculty.iisertvm.ac.in/natesh">http://faculty.iisertvm.ac.in/natesh</a></div>
<div dir="ltr">
<br>Office Ph. <span style="font-size:12.8px">0091- 471-2778087</span><br>
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<br><pre wrap="">_______________________________________________
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<pre cols="72" class="moz-signature">--
==============================================================
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
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Emeritus Professor of Cryo-EM Data Processing
Leiden University
Mobile NL: +31(0)652736618 (ALWAYS ACTIVE SMS)
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Emeritus Professor of Structural Biology
Imperial College London
Faculty of Natural Sciences
email: m.vanheel(A_T)imperial.ac.uk
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I receive many emails per day and, although I try,
there is no guarantee that I will actually read each incoming email. </pre>
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<pre cols="72" class="moz-signature">--
==============================================================
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. </pre>
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