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) > <[email protected]> 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 <[email protected]> > Sent: 17 February 2020 16:36 > To: Nave, Colin (DLSLtd,RAL,LSCI) <[email protected]> > Cc: [email protected] > 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) > <[email protected]> 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 <[email protected]> > Sent: 17 February 2020 12:09 > To: Nave, Colin (DLSLtd,RAL,LSCI) <[email protected]> > 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, "[email protected]" > <[email protected] 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 <[email protected]> On Behalf Of Petrus Zwart > Sent: 16 February 2020 21:50 > To: [email protected] > 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 > <[email protected]> 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 > <[email protected]> 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 > [email protected] > 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. 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/ > ------------------------------------------------------------------------- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > > -- > > This e-mail and any attachments may contain confidential, copyright and or > privileged material, and are for the use of the intended addressee only. If > you are not the intended addressee or an authorised recipient of the > addressee please notify us of receipt by returning the e-mail and do not use, > copy, retain, distribute or disclose the information in or attached to the > e-mail. > Any opinions expressed within this e-mail are those of the individual and not > necessarily of Diamond Light Source Ltd. > Diamond Light Source Ltd. cannot guarantee that this e-mail or any > attachments are free from viruses and we cannot accept liability for any > damage which you may sustain as a result of software viruses which may be > transmitted in or with the message. > Diamond Light Source Limited (company no. 4375679). Registered in England and > Wales with its registered office at Diamond House, Harwell Science and > Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > > -- > > This e-mail and any attachments may contain confidential, copyright and or > privileged material, and are for the use of the intended addressee only. If > you are not the intended addressee or an authorised recipient of the > addressee please notify us of receipt by returning the e-mail and do not use, > copy, retain, distribute or disclose the information in or attached to the > e-mail. > Any opinions expressed within this e-mail are those of the individual and not > necessarily of Diamond Light Source Ltd. > Diamond Light Source Ltd. cannot guarantee that this e-mail or any > attachments are free from viruses and we cannot accept liability for any > damage which you may sustain as a result of software viruses which may be > transmitted in or with the message. > Diamond Light Source Limited (company no. 4375679). Registered in England and > Wales with its registered office at Diamond House, Harwell Science and > Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > > > > -- > > This e-mail and any attachments may contain confidential, copyright and or > privileged material, and are for the use of the intended addressee only. If > you are not the intended addressee or an authorised recipient of the > addressee please notify us of receipt by returning the e-mail and do not use, > copy, retain, distribute or disclose the information in or attached to the > e-mail. > Any opinions expressed within this e-mail are those of the individual and not > necessarily of Diamond Light Source Ltd. > Diamond Light Source Ltd. cannot guarantee that this e-mail or any > attachments are free from viruses and we cannot accept liability for any > damage which you may sustain as a result of software viruses which may be > transmitted in or with the message. > Diamond Light Source Limited (company no. 4375679). Registered in England and > Wales with its registered office at Diamond House, Harwell Science and > Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
