[3dem] [ccp4bb] FW: [ccp4bb] Which resolution?

Tue Feb 18 02:59:41 PST 2020

Dear John,

I really like your lecture notes! My Imperial/Leiden lecture notes –
currently being updated – look a lot like yours. The earlier version:

(https://www.single-particles.org/methodology/MvH_Phase_Contrast.pdf)

And you are fully correct: “resolution of cryoEM imaging varies locally”!

That is exactly the point!

The existing cryo-EM dogmas, however,  PREVENT you from doing things right,
which seriously hampers progress (see our BioRxiv paper:
https://www.biorxiv.org/content/10.1101/224402v1 ).

Cheers,

Marin

On Tue, Feb 18, 2020 at 4:36 AM John R Helliwell <jrhelliwell at gmail.com>
wrote:

> Hi Colin,
> Yes I agree, see eg page 7 of
> https://www2.physics.ox.ac.uk/sites/default/files/2011-06-08/optics_notes_and_slides_part_5_pdf_63907.pdf (and
> there maybe better weblinks).
>
> The resolution of cryoEM imaging varies locally and so the “local scaling
> in a complex way” is what we have to get into in practice......
>
> Greetings,
> John
>
> Emeritus Professor John R Helliwell DSc
>
>
>
> On 17 Feb 2020, at 21:57, Nave, Colin (DLSLtd,RAL,LSCI) <
> colin.nave at diamond.ac.uk> wrote:
>
> 
>
> Hi John
>
> I agree that neutrons have a role to increase the contrast for certain
> atoms. The “water window” for x-ray imaging also fulfils a similar role.
> The “locally scaled in a complex way” is a bit beyond me.
>
>
>
> The relationship between “ diffraction” errors and “imaging” errors is
>  based on Parseval’s theorem applied to the errors for electron densities
> and structure factors.  See for example
> https://www-structmed.cimr.cam.ac.uk/Course/Fourier/Fourier.html and
> scroll down to Parseval’s theorem. Admittedly not a primary reference but I
> think Randy (and Parseval, not to be confused with Wagner’s opera), are
> unlikely to have got it wrong.
>
>
>
> Imaging (with both electrons and x-rays) can be lensless (as in MX, CDI
> and variants) or with an objective lens (electron microscopes have nice
> objective lenses). The physical processes are the same up to any lens but
> MX, CDI etc. use a computer to replace the lens. The computer algorithm
> might be imperfect resulting in visible termination errors. With a decent
> lens, one can also see diffraction ripples (round bright stars in a
> telescope image) due to the restricted lens aperture.
>
>
>
> Good debate though.
>
>
>
> Colin
>
> *From:* John R Helliwell <jrhelliwell at gmail.com>
> *Sent:* 17 February 2020 16:36
> *To:* Nave, Colin (DLSLtd,RAL,LSCI) <colin.nave at diamond.ac.uk>
> *Cc:* CCP4BB at JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] FW: [ccp4bb] [3dem] Which resolution?
>
>
>
> Hi Colin,
>
> Neutrons are applied to the uranyl hydrides so as to make their scattering
> lengths much more equal than with X-rays, and so side step ripple effects
> of the uranium in the Xray case, which obscures those nearby hydrogens.
>
> In terms of feature resolvability the email exchange (and there may be
> better ones):-
> http://www.phenix-online.org/pipermail/phenixbb/2017-March/023326.html
>
> refers to “locally scaled in a complex way”. So, is the physics of the
> visibility of features really comparable between the two methods of cryoEM
> and crystal structure analysis?
>
> Greetings,
>
> John
>
> Emeritus Professor John R Helliwell DSc
>
>
>
>
>
>
>
> On 17 Feb 2020, at 13:59, Nave, Colin (DLSLtd,RAL,LSCI) <
> colin.nave at diamond.ac.uk> wrote:
>
> 
>
> Hi John
>
> I agree that if I truncate the data at a high information content
> threshold (e.g. 2 bits)  series termination errors might hide the lighter
> atoms (e.g. the hydrogens in uranium hydride crystal structures). However,
> I think this is purely a limitation of producing electron density maps via
> Fourier transforms (i.e. not the physics). A variety of techniques are
> available for handling series termination including ones which are
> maximally non-committal with respect to the missing data. The issue is
> still there in some fields (see
> https://onlinelibrary.wiley.com/iucr/itc/Ha/ch4o8v0001/ ). For protein
> crystallography perhaps series termination errors have become less
> important as people are discouraged from applying some I/sigI type cut off.
>
>
>
> Cheers
>
> Colin
>
>
>
>
>
>
>
> *From:* John R Helliwell <jrhelliwell at gmail.com>
> *Sent:* 17 February 2020 12:09
> *To:* Nave, Colin (DLSLtd,RAL,LSCI) <colin.nave at diamond.ac.uk>
> *Subject:* Re: [ccp4bb] FW: [ccp4bb] [3dem] Which resolution?
>
>
>
> Hi Colin,
>
> I think the physics of the imaging and the crystal structure analysis,
> respectively without and with Fourier termination ripples, are different.
> For the MX re Fourier series for two types of difference map see our
> contribution:-
>
>
>
> http://scripts.iucr.org/cgi-bin/paper?S0907444903004219
>
>
>
> Greetings,
>
> John
>
>
>
> Emeritus Professor John R Helliwell DSc
>
>
> https://www.crcpress.com/The-Whats-of-a-Scientific-Life/Helliwell/p/book/9780367233020
>
>
>
>
>
>
>
>
> On 17 Feb 2020, at 11:26, "colin.nave at diamond.ac.uk" <
> colin.nave at diamond.ac.uk wrote:
>
> 
>
>
>
> Dear all.
>
> Would it help to separate out the issue of the FSC from the value of the
> threshold? My understanding is that the FSC addresses the spatial
> frequency at which there is a reliable information content in the image.
> This concept should apply to a wide variety of types of image. The issue is
> then what value of the threshold to use. For interpretation of protein
> structures (whether by x-ray or electron microscopy), a half bit threshold
> appears to be appropriate. However, for imaging the human brain (one of
> Marin’s examples) a higher threshold might be adopted as a range of
> contrasts might be present (axons for example have a similar density to the
> surroundings). For crystallography, if one wants to see lighter atoms
> (hydrogens in the presence of uranium or in proteins) a higher threshold
> might also be appropriate. I am not sure about this to be honest as a 2 bit
> threshold (for example) would mean that there is information to higher
> resolution at a threshold of a half bit (unless one is at a diffraction or
> instrument limited resolution).
>
>
>
> Most CCP4BBers will understand that a single number is not good enough.
> However, many users of the protein structure databases will simply search
> for the structure with the highest named resolution. It might be difficult
> to send these users to re-education camps.
>
>
>
> Regards
>
> Colin
>
>
>
> *From:* CCP4 bulletin board <CCP4BB at JISCMAIL.AC.UK> *On Behalf Of *Petrus
> Zwart
> *Sent:* 16 February 2020 21:50
> *To:* CCP4BB at JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] [3dem] Which resolution?
>
>
>
> Hi All,
>
>
>
> How is the 'correct' resolution estimation related to the estimated error
> on some observed hydrogen bond length of interest, or an error on the
> estimated occupancy of a ligand or conformation or anything else that has
> structural significance?
>
>
>
> In crystallography, it isn't really (only in some very approximate
> fashion), and I doubt that in EM there is something to that effect. If you
> want to use the resolution to get a gut feeling on how your maps look and
> how your data behaves, it doesn't really matter what standard you use, as
> long as you are consistent in the use of the metric you use. If you want to
> use this estimate to get to uncertainties of model parameters, you better
> try something else.
>
>
>
> Regards
>
> Peter Zwart
>
>
>
>
>
>
>
> On Sun, Feb 16, 2020 at 8:38 AM Marin van Heel <
> 0000057a89ab08a1-dmarc-request at jiscmail.ac.uk> wrote:
>
> 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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>
> --
>
> ------------------------------------------------------------------------
> P.H. Zwart
> Staff Scientist
>
> Molecular Biophysics and Integrated Bioimaging &
>
> Center for Advanced Mathematics for Energy Research Applications
>
> Lawrence Berkeley National Laboratories
> 1 Cyclotron Road, Berkeley, CA-94703, USA
> Cell: 510 289 9246
>
>
>
> PHENIX:   http://www.phenix-online.org
>
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