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

[John R Helliwell]

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) 
>  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  
> Sent: 17 February 2020 16:36
> To: Nave, Colin (DLSLtd,RAL,LSCI) 
> Cc: CCP4BB@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) 
>  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  
> Sent: 17 February 2020 12:09
> To: Nave, Colin (DLSLtd,RAL,LSCI) 
> 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.n...@diamond.ac.uk" 
>  
> 
>  
> 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 

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

[Marin van Heel]

Dear Colin

Great that you mention the Rose equation and its consequences for cryo-EM!
I have actually written a paper on that topic some 40 years ago [Marin van
Heel: Detection of object in quantum-noise limited images. Ultramicroscopy
8 (1982) 331-342].  I honestly have not thought about it for a long time
but I have recently been thinking about revisiting the topic. It remains
one of the very first particle-picking papers ever, and certainly still one
of the very best (and reference free) ones [Afanasyev 2017].

I remember I was very pleased when I realised one could calculate local
variances rapidly using fast convolutions! I remember the very moment in
December 1979, while visiting my parents in their house in Spain and
catching a bit of winter sunshine, leaning against the wall of their house
with my eyes half closed, that the “Aha-Erlebnis” struck.  Thank you for
reminding me to go back to that issue!

Cheers

Marin

On Mon, Feb 17, 2020 at 2:36 PM colin.n...@diamond.ac.uk <
colin.n...@diamond.ac.uk> wrote:

>
>
> Dear Marin
>
> For electron microscopy, the Rose criterion (a measure of contrast/noise)
> is sometime used to distinguish low contrast features within polymers (see
> for example Libera, M. & Egerton, R. (2010). *Polymer Reviews*. *50*,
> 321-339.). A particular value of the Rose criterion implies a particular
> information content.
>
> I think this can be directly related to a particular threshold for FSC or
> FRC. If you can comment on this in your *Why-o-Why didactical crusade, I
> might even register for a twitter account!*
>
> *Regards*
>
> *Colin*
>
>
>
> *From:* CCP4 bulletin board  *On Behalf Of *Marin
> van Heel
> *Sent:* 17 February 2020 13:29
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] [3dem] Which resolution?
>
>
>
>
>
>
>
> Dear Petrus Zwart (and all other X-ray crystallographers and EM-ers)
>
>
>
> Resolution in the sense of the Abbe Diffraction Limit or the Rayleigh 
> *Criterion
> are part of what we would now call the theory of linear systems, and are
> described by a “transfer function”. “Fourier Optics” covers the theory of
> linear systems in Optics. These two (essentially identical) resolution
> criteria state that the smallest details (let us call that “A(r)” for
> “Airy”) you can possible observe in real-space is inversely proportional to
> the size of the maximum aperture in Fourier space, i.e., the extent of the
> transfer function in Fourier space “T(f)”. This defines what “Instrumental
> Resolution” one could possibly achieve in an experiment, “instrumental” to
> differentiate it from the “Results Resolution” you actually managed achieve
> in your data collection/processing experiment [#Why-o-Why #10].  What a
> linear imaging system will do the image of the object (under the best of
> circumstances) is described by a (Fourier-space) multiplication of the
> Fourier transform of the object O(r) [= O(f)] with the (Fourier-space)
> transfer function T(f) of the instrument, yielding O’(f), which you need to
> transfer back to real space to obtain the exit wave in the image plane;
> that is: {O’(f)=T(f)·O(f)}. *
>
>
>
> *Note, however, that the properties of the sample, that is, of O(r), does
> nowhere appear in the transfer function T(f) or in its real-space version
> A(r)!   The very concept of (instrumental) resolution is exactly that it
> does NOT depend on the object O(r)! The “results resolution” [#Why-o-Why
> #10], on the other hand, obviously depends on the sample; the illumination;
> on the radiation dose; the pH of the solvent; the air humidity; and the
> mood of the person doing the work on the day of preparation… *
>
>
>
> *The FRC/FSC “results resolution” measures we introduced in 1982/1986, fit
> perfectly in the abstract framework of linear systems and Fourier optics.
> The X-ray metrics like R-factor and phase-residuals and FOMs do NOT fit
> into that clean mathematical framework. Unfortunately, my EM colleagues
> started using X-ray metrics like “Differential Phase Residual” and “FOMs”
> in EM based on some gut feeling that the X-ray scientists know it better
> because they achieve a higher resolution than us EM blobologists. How wrong
> my EM colleagues were: the quality of the resolution metric is totally
> unrelated to the numerical resolution levels we operate at! Seeing 3mm
> kidney stones in a patient’s tomogram can be equally important as seeing *some
> hydrogen bond length in a cryo-EM density. The FRC/FSC actually make more
> sense than the indirect and hybrid X-ray ones.  *This misconception has
> introduced a very tainted – and still ongoing – discussion in cryo-EM. Now
> that the fields of X-ray crystallography and cryo-EM are merging it is time
> to get things right! *
>
>
>
> *I guess I cannot yet terminate my #Why-o-Why didactical crusade:  I will
> need at least one more on just this linear-transfer theory issue alone…*
>
>
>
> *Marin van Heel, CNPEM/LNNano, Campinas, Brazil  *
>
>
>
>
>
> On Sun, Feb 16, 2020 at 6:51 

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

[Nave, Colin (DLSLtd,RAL,LSCI)]

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 
Sent: 17 February 2020 16:36
To: Nave, Colin (DLSLtd,RAL,LSCI) 
Cc: CCP4BB@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) 
mailto:colin.n...@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 mailto:jrhelliw...@gmail.com>>
Sent: 17 February 2020 12:09
To: Nave, Colin (DLSLtd,RAL,LSCI) 
mailto:colin.n...@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.n...@diamond.ac.uk" 
mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Petrus Zwart
Sent: 16 February 2020 21:50
To: CCP4BB@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 
<057a89ab08a1-dmarc-requ...@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) 

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

[colin.n...@diamond.ac.uk]

Dear Marin

For electron microscopy, the Rose criterion (a measure of contrast/noise) is 
sometime used to distinguish low contrast features within polymers (see for 
example Libera, M. & Egerton, R. (2010). Polymer Reviews. 50, 321-339.). A 
particular value of the Rose criterion implies a particular information content.

I think this can be directly related to a particular threshold for FSC or FRC. 
If you can comment on this in your Why-o-Why didactical crusade, I might even 
register for a twitter account!

Regards

Colin

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Marin van Heel
Sent: 17 February 2020 13:29
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [3dem] Which resolution?



Dear Petrus Zwart (and all other X-ray crystallographers and EM-ers)

Resolution in the sense of the Abbe Diffraction Limit or the Rayleigh Criterion 
are part of what we would now call the theory of linear systems, and are 
described by a “transfer function”. “Fourier Optics” covers the theory of 
linear systems in Optics. These two (essentially identical) resolution criteria 
state that the smallest details (let us call that “A(r)” for “Airy”) you can 
possible observe in real-space is inversely proportional to the size of the 
maximum aperture in Fourier space, i.e., the extent of the transfer function in 
Fourier space “T(f)”. This defines what “Instrumental Resolution” one could 
possibly achieve in an experiment, “instrumental” to differentiate it from the 
“Results Resolution” you actually managed achieve in your data 
collection/processing experiment [#Why-o-Why #10].  What a linear imaging 
system will do the image of the object (under the best of circumstances) is 
described by a (Fourier-space) multiplication of the Fourier transform of the 
object O(r) [= O(f)] with the (Fourier-space) transfer function T(f) of the 
instrument, yielding O’(f), which you need to transfer back to real space to 
obtain the exit wave in the image plane; that is: {O’(f)=T(f)·O(f)}.

Note, however, that the properties of the sample, that is, of O(r), does 
nowhere appear in the transfer function T(f) or in its real-space version A(r)! 
  The very concept of (instrumental) resolution is exactly that it does NOT 
depend on the object O(r)! The “results resolution” [#Why-o-Why #10], on the 
other hand, obviously depends on the sample; the illumination; on the radiation 
dose; the pH of the solvent; the air humidity; and the mood of the person doing 
the work on the day of preparation…

The FRC/FSC “results resolution” measures we introduced in 1982/1986, fit 
perfectly in the abstract framework of linear systems and Fourier optics. The 
X-ray metrics like R-factor and phase-residuals and FOMs do NOT fit into that 
clean mathematical framework. Unfortunately, my EM colleagues started using 
X-ray metrics like “Differential Phase Residual” and “FOMs” in EM based on some 
gut feeling that the X-ray scientists know it better because they achieve a 
higher resolution than us EM blobologists. How wrong my EM colleagues were: the 
quality of the resolution metric is totally unrelated to the numerical 
resolution levels we operate at! Seeing 3mm kidney stones in a patient’s 
tomogram can be equally important as seeing some hydrogen bond length in a 
cryo-EM density. The FRC/FSC actually make more sense than the indirect and 
hybrid X-ray ones.  This misconception has introduced a very tainted – and 
still ongoing – discussion in cryo-EM. Now that the fields of X-ray 
crystallography and cryo-EM are merging it is time to get things right!

I guess I cannot yet terminate my #Why-o-Why didactical crusade:  I will need 
at least one more on just this linear-transfer theory issue alone…

Marin van Heel, CNPEM/LNNano, Campinas, Brazil


On Sun, Feb 16, 2020 at 6:51 PM Petrus Zwart 
mailto:phzw...@lbl.gov>> wrote:
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 
<057a89ab08a1-dmarc-requ...@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 

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

[John R Helliwell]

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) 
>  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  
> Sent: 17 February 2020 12:09
> To: Nave, Colin (DLSLtd,RAL,LSCI) 
> 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.n...@diamond.ac.uk" 
>  
> 
>  
> 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  On Behalf Of Petrus Zwart
> Sent: 16 February 2020 21:50
> To: CCP4BB@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 
> <057a89ab08a1-dmarc-requ...@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 

[ccp4bb] EMBO meeting on “Molecular Neurobiology” 8-12 May 2020, deadline registration 29 Feb.

[Janssen, B.J.C. (Bert)]

Dear all,

a gentle reminder of the upcoming EMBO workshop on Molecular Neurobiology on 
the beautiful island of Crete. The extended deadline for registration, 29 Feb., 
is approaching fast. Last chance to sign up!

Please see https://meetings.embo.org/event/20-molneuro for further details.

Best wishes

Bert


Bert Janssen

Bijvoet Center for biomolecular research

Utrecht University

Padualaan 8, 3584 CH, Utrecht



From: CCP4 bulletin board  on behalf of Janssen, B.J.C. 
(Bert) 
Sent: 28 November 2019 21:57
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] EMBO meeting on “Molecular Neurobiology” 8-12 May 2020


Dear all,



We would like to draw your attention to the EMBO workshop on "Molecular 
Neurobiology", taking place on the beautiful island of Crete on 8-12 May 2020.



The meeting brings together world leading scientists, group leaders and young 
researchers with a keen interest in the latest science occurring at the 
interfaces of structural biology, biophysics, molecular & cellular imaging and 
neuroscience. Given its cross-disciplinary nature, the meeting presents a broad 
overview of molecular neurobiology, ample opportunities for discussions and a 
sneak peek into the latest developments.



See http://meetings.embo.org/event/20-molneuro for more information and 
application guidelines.



Best wishes

Bert





Bert Janssen

Bijvoet Center for biomolecular research

Utrecht University

Padualaan 8, 3584 CH, Utrecht



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

[colin.n...@diamond.ac.uk]

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 
Sent: 17 February 2020 12:09
To: Nave, Colin (DLSLtd,RAL,LSCI) 
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.n...@diamond.ac.uk" 
mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Petrus Zwart
Sent: 16 February 2020 21:50
To: CCP4BB@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 
<057a89ab08a1-dmarc-requ...@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 
mailto:pawel.a.penc...@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
CAMERA: http://camera.lbl.gov/
-



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[ccp4bb] PhD position available

[Tobias Beck]

Dear all,

There is an opening for a PhD position in my group. The Beck group recently
moved to Hamburg, where we have labs well-equipped for chemistry,
biochemistry and molecular biology. Moreover, state-of-the-art facilities
for structural characterizations such as PETRA III are close by.

The project involves protein redesign, protein chemistry and
characterization and more. The post is available immediately / upon
arrangement. Full details of the post and the applications process are
available here:
https://www.uni-hamburg.de/uhh/stellenangebote/wissenschaftliches-personal/exzellenzcluster-cui/15-03-20-70-en.pdf

The group homepage can be found here:
https://www.chemie.uni-hamburg.de/institute/pc/arbeitsgruppen/beck.html

Deadline for applications is March 15 2020.

Please contact me for further information or informal inquiries: tobias.beck
@chemie.uni-hamburg.de

Best, Tobias.


Prof. Dr. Tobias Beck
University of Hamburg
Department of Chemistry
Institute of Physical Chemistry
Grindelallee 117
D-20146 Hamburg
Germany

phone:   +49 4042838 8210
fax:   +49 4042838 3462
web:   www.chemie.uni-hamburg.de/institute/pc/arbeitsgruppen/beck/




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

[Marin van Heel]

Dear Petrus Zwart (and all other X-ray crystallographers and EM-ers)



Resolution in the sense of the Abbe Diffraction Limit or the Rayleigh
*Criterion
are part of what we would now call the theory of linear systems, and are
described by a “transfer function”. “Fourier Optics” covers the theory of
linear systems in Optics. These two (essentially identical) resolution
criteria state that the smallest details (let us call that “A(r)” for
“Airy”) you can possible observe in real-space is inversely proportional to
the size of the maximum aperture in Fourier space, i.e., the extent of the
transfer function in Fourier space “T(f)”. This defines what “Instrumental
Resolution” one could possibly achieve in an experiment, “instrumental” to
differentiate it from the “Results Resolution” you actually managed achieve
in your data collection/processing experiment [#Why-o-Why #10].  What a
linear imaging system will do the image of the object (under the best of
circumstances) is described by a (Fourier-space) multiplication of the
Fourier transform of the object O(r) [= O(f)] with the (Fourier-space)
transfer function T(f) of the instrument, yielding O’(f), which you need to
transfer back to real space to obtain the exit wave in the image plane;
that is: {O’(f)=T(f)**·**O(f)}. *



*Note, however, that the properties of the sample, that is, of O(r), does
nowhere appear in the transfer function T(f) or in its real-space version
A(r)!   The very concept of (instrumental) resolution is exactly that it
does NOT depend on the object O(r)! The “results resolution” [#Why-o-Why
#10], on the other hand, obviously depends on the sample; the illumination;
on the radiation dose; the pH of the solvent; the air humidity; and the
mood of the person doing the work on the day of preparation… *



*The FRC/FSC “results resolution” measures we introduced in 1982/1986, fit
perfectly in the abstract framework of linear systems and Fourier optics.
The X-ray metrics like R-factor and phase-residuals and FOMs do NOT fit
into that clean mathematical framework. Unfortunately, my EM colleagues
started using X-ray metrics like “Differential Phase Residual” and “FOMs”
in EM based on some gut feeling that the X-ray scientists know it better
because they achieve a higher resolution than us EM blobologists. How wrong
my EM colleagues were: the quality of the resolution metric is totally
unrelated to the numerical resolution levels we operate at! Seeing 3mm
kidney stones in a patient’s tomogram can be equally important as seeing *some
hydrogen bond length in a cryo-EM density. The FRC/FSC actually make more
sense than the indirect and hybrid X-ray ones.  *This misconception has
introduced a very tainted – and still ongoing – discussion in cryo-EM. Now
that the fields of X-ray crystallography and cryo-EM are merging it is time
to get things right! *



*I guess I cannot yet terminate my #Why-o-Why didactical crusade:  I will
need at least one more on just this linear-transfer theory issue alone…*



*Marin van Heel, CNPEM/LNNano, Campinas, Brazil  *



On Sun, Feb 16, 2020 at 6:51 PM Petrus Zwart  wrote:

> 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 <
> 057a89ab08a1-dmarc-requ...@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.penc...@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.
>>>
>>> 

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

[colin.n...@diamond.ac.uk]

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  On Behalf Of Petrus Zwart
Sent: 16 February 2020 21:50
To: CCP4BB@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 
<057a89ab08a1-dmarc-requ...@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 
mailto:pawel.a.penc...@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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3...@ncmir.ucsd.edu
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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
CAMERA: http://camera.lbl.gov/
-



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