[3dem] Which resolution?

[Jose Maria Carazo]

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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