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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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cite="mid:E1fwPPC-000sEh-2B@mail.lmb.internal">
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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>
<div><br>
</div>
<div>Hth,</div>
<div>Sjors</div>
<div><br>
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<div style="font-size:85%;color:#575757">Sent from my phone.</div>
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<div>-------- Original message --------</div>
<div>From: Marin van Heel <a class="moz-txt-link-rfc2396E" href="mailto:marin.vanheel@googlemail.com"><marin.vanheel@googlemail.com></a> </div>
<div>Date: 01/09/2018 19:43 (GMT+01:00) </div>
<div>To: Natesh Ramanathan <a class="moz-txt-link-rfc2396E" href="mailto:natesh@iisertvm.ac.in"><natesh@iisertvm.ac.in></a>,
<a class="moz-txt-link-abbreviated" href="mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a> </div>
<div>Subject: Re: [3dem] GroEL best resolution map. (FSC
RESOLUTION ??) </div>
<div><br>
</div>
</div>
<div class="moz-cite-prefix"><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 class="moz-txt-link-freetext"
href="https://www.biorxiv.org/content/early/2017/11/24/224402"
moz-do-not-send="true">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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cite="mid:CAFT3tKskDTkbXBT8Qc3rJV=te7LjhRZEZjBfFwfWHLSV=65Bhw@mail.gmail.com">
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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>
<div>
<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>
</div>
<div> </div>
<div> If you have one, is it possible to share the
map with me? </div>
<div><br>
</div>
<div>Many thanks.</div>
<div>Best regards,<br>
Natesh</div>
-- <br>
<div dir="ltr" class="gmail_signature"
data-smartmail="gmail_signature">
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<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"
target="_blank" moz-do-not-send="true">natesh@iisertvm.ac.in</a><br>
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href="http://www.researcherid.com/rid/C-4488-2008"
target="_blank" moz-do-not-send="true">http://www.researcherid.com/rid/C-4488-2008</a></div>
<div>ORCID: <a
href="http://orcid.org/0000-0002-1145-5962"
alt="Go to my personal page at
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href="https://publons.com/author/1520837/ramanathan-natesh#profile"
target="_blank" moz-do-not-send="true">https://publons.com/author/1520837/ramanathan-natesh#profile</a></div>
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href="http://faculty.iisertvm.ac.in/natesh"
target="_blank" moz-do-not-send="true">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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<pre wrap="">_______________________________________________
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</pre>
</blockquote>
<p><br>
</p>
<pre class="moz-signature" cols="72">--
==============================================================
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>
</blockquote>
<p><br>
</p>
<pre class="moz-signature" cols="72">--
==============================================================
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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