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 <jrhelliw...@gmail.com> Sent: 17 February 2020 16:36 To: Nave, Colin (DLSLtd,RAL,LSCI) <colin.n...@diamond.ac.uk> 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) <colin.n...@diamond.ac.uk<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 <jrhelliw...@gmail.com<mailto:jrhelliw...@gmail.com>> Sent: 17 February 2020 12:09 To: Nave, Colin (DLSLtd,RAL,LSCI) <colin.n...@diamond.ac.uk<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:colin.n...@diamond.ac.uk>" <colin.n...@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@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of Petrus Zwart Sent: 16 February 2020 21:50 To: CCP4BB@JISCMAIL.AC.UK<mailto: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 <0000057a89ab08a1-dmarc-requ...@jiscmail.ac.uk<mailto:0000057a89ab08a1-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<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 _______________________________________________ 3dem mailing list 3...@ncmir.ucsd.edu<mailto:3...@ncmir.ucsd.edu> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- ------------------------------------------------------------------------ P.H. 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