[3dem] Which resolution?

Thu Feb 20 14:46:42 PST 2020

Hi Jose-Maria,

I appreciate that you consider all our contributions to be important (“Ed,
Paul and Marin papers are very important”) and that people need to
“reconnect” to the resolution issue since that remains so very important! I
couldn’t agree more!

But then you go on to suggest that everyone who does “feel like not
sleeping at all today” read your 2017 review. The review you are promoting,
is the one we had refuted in our BioRxiv paper (see below), with very
serious criticism, which you never bothered to respond.  I feel compelled
to repeat what I have said in my earlier reaction to Pawel’s response,
above.

“What I am criticising is the very foundation you use to construct your
science, namely the flawed Frank & Al-Ali (1975) formula relating SNR and
CCC! Agreed, their errors are not of your making and not your
responsibility!  It is, however, your choice and your judgement to build
upon that flawed foundation.  At the end of the day, your construct, even
when based on shaky foundations created by others, will remain your
responsibility!”

Sorry,

Marin

Our criticism (https://www.biorxiv.org/content/10.1101/224402v1) was:
[image: image.png]

On Sun, Feb 16, 2020 at 4:08 PM Jose Maria Carazo <carazo at cnb.csic.es>
wrote:

> Dear Marin and colleagues,
>
> As Ed, I have tried to stay away from these interchanges about resolution,
> simply because they go forever and I think that most people either get fed
> up, drop the attention, or -and this is the danger- end up thinking that we
> do not know what we are doing.
>
> For all of you that have already "disconnected", please "reconnet",
> because it is an important topic, but think about it in the context of
> "validation" / "quality assessment". At the end of the day what we want to
> know is whether there are problems with a map and how much one can trust a
> structural model derived from it. Consider that if we know already that
> something is a simplification of what we really want to do, to keep going
> over it yet another time may not add too much to the discussion (perhaps
> this applies to the whole point on the FSC)
>
> Ed, Paul and Marin papers are very important because we must have sound
> theoretical and statistical bases..... but do not forget to contextualize
> the whole topic around "validation".
>
> If you want to have another quite deep view on the statistics of many
> things we do, Carlos and me we did a review a few years ago (as Ed said in
> his email, 2017 may be considered already "dated" in this fast evolving
> field). Still, it gives you an idea that statistics has been worked out a
> lot, that we know that a number of "common approaches " have intrinsic
> limitations, and that it is precisely because of that that we keep working
> on validation
>
> If you feel like not sleeping at all today, another paper to add to your
> list could be:
>
>
> A review of resolution measures and related aspects in 3D Electron
> Microscopy. <https://www.ncbi.nlm.nih.gov/pubmed/27666962>
>
> *Sorzano* CO, Vargas J, Otón J, Abrishami V, de la Rosa-Trevín JM,
> Gómez-Blanco J, Vilas JL, Marabini R, *Carazo JM*.
>
> Prog Biophys Mol Biol. 2017 Mar;124:1-30. doi:
> 10.1016/j.pbiomolbio.2016.09.005.
>
> ..... but may be you have already had your share of discussion about
> "resolution measures" ...
>
> With best regards...JM
>
> On Sun, Feb 16, 2020 at 5:59 PM Penczek, Pawel A <
> Pawel.A.Penczek at uth.tmc.edu> wrote:
>
>> Marin,
>>
>> The statistics in 2010 review is fine. You may disagree with assumptions,
>> but I can assure you the “statistics” (as you call it) is fine. Careful
>> reading of the paper would reveal to you this much.
>>
>> Regards,
>> Pawel
>>
>> On Feb 16, 2020, at 10:38 AM, Marin van Heel <
>> marin.vanheel at googlemail.com> wrote:
>>
>> 
>>
>> ***** EXTERNAL EMAIL *****
>> Dear Pawel and All others ....
>>
>> This 2010 review is - unfortunately - largely based on the flawed
>> statistics I mentioned before, namely on the a priori assumption that the
>> inner product of a signal vector and a noise vector are ZERO (an
>> orthogonality assumption).  The (Frank & Al-Ali 1975) paper we have refuted
>> on a number of occasions (for example in 2005, and most recently in our
>> BioRxiv paper) but you still take that as the correct relation between SNR
>> and FRC (and you never cite the criticism...).
>> Sorry
>> Marin
>>
>> On Thu, Feb 13, 2020 at 10:42 AM Penczek, Pawel A <
>> Pawel.A.Penczek at uth.tmc.edu> wrote:
>>
>>> Dear Teige,
>>>
>>> I am wondering whether you are familiar with
>>>
>>> Resolution measures in molecular electron microscopy.
>>> Penczek PA. Methods Enzymol. 2010.
>>> Citation
>>>
>>> Methods Enzymol. 2010;482:73-100. doi: 10.1016/S0076-6879(10)82003-8.
>>>
>>> You will find there answers to all questions you asked and much more.
>>>
>>> Regards,
>>> Pawel Penczek
>>>
>>>
>>> Regards,
>>> Pawel
>>> _______________________________________________
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>
>
> --
> Prof. Jose-Maria Carazo
> Biocomputing Unit, Head, CNB-CSIC
> Spanish National Center for Biotechnology
> Darwin 3, Universidad Autonoma de Madrid
> 28049 Madrid, Spain
>
>
> Cell: +34639197980
>
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