[3dem] [EXTERNAL] Re: [ccpem] Differences EM CP maps vs Xray ED Maps

Wed Nov 15 10:57:07 PST 2023

Dear Joachim

I have never mentioned any "element-specific spectral distribution of the
amplitude contrast" in my 1978 work. Please don't put words in my mouth.
My 1978 paper was on the real and the imaginary part of the complex
transmission function of the object in partially coherent illumination and
applies to optical microscopy as much as it does to electron microscopy.
Any "element-specific spectral distribution" is primarily relevant in
electron microscopy. My 1978 paper is based on a convolution with the size
of the source in the back focal plane, and not on an envelope function
(Frank 1973), which is an incorrect approach.

Two more cents,

Marin

On Wed, Oct 18, 2023 at 1:11 PM Frank, Joachim <jf2192 at cumc.columbia.edu>
wrote:

>
>
> Hi Rasmus,
>
>
>
> I’m in agreement with Marin about the necessity of using a correct
> element-specific spectral distribution of the amplitude contrast.  But
> blaming a single paper is as you say unfair; the problem is rather the
> uncritical adoption of an initial oversimplification by the users.  There
> have been plenty of misjudgments like that.
>
>
>
> Related to amplitude contrast, see my proof-of-concept paper on
> heavy/light atom discrimination using Peter Schiske’s method in Biophys. J.
> (1972), and a later paper with Pawel Penczek (Frank and Penczek, Optik
> 1995) where we tried to use Schiske’s algorithm on the cryo-EM ribosome
> dataset collected in Heidelberg.  The funny thing was, the L1 stalk lit up
> in the amplitude contrast image, so we thought something must have gone
> wrong since, to our knowledge then, the L1 stalk was all protein and not,
> as we know now, part protein and part RNA.
>
>
>
> my 1c,
>
>
>
> --Joachim
>
>
>
> Dr. Joachim Frank
>
> Professor, Biochemistry and Molecular Biophysics & Biological Sciences,
>
> Columbia University Irving Medical Center,
>
> Hammer Health Sciences Center, Room 616,
>
> 701 West 168th Street, New York, NY 10032 -- jf2192 at cumc.columbia.edu
>
> *2017 Nobel Prize in Chemistry*
>
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>
>
>
>
>
>
> *From: *3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Schroeder, Rasmus
> <rasmus.schroeder at bioquant.uni-heidelberg.de>
> *Date: *Wednesday, October 18, 2023 at 5:02 AM
> *To: *Marin van Heel <marin.vanheel at googlemail.com>
> *Cc: *3dem <3dem at ncmir.ucsd.edu>, CCPEM at jiscmail.ac.uk <
> CCPEM at jiscmail.ac.uk>
> *Subject: *[EXTERNAL] Re: [3dem] [ccpem] Differences EM CP maps vs Xray
> ED Maps
>
> Dear Marin - and all others here,
>
>
>
> I would not be so harsh with that paper from 1971, there is always a
> certain level of experimental data, and - as far as I understand it - at
> that time and resolution level obtainable it looked as if amplitude and
> phase potentials could be identical.
>
>
>
> As you point out correctly, this is not the case, and I may add a study we
> did many, many years ago looking into the CTF for an energy filtered TEM
>
> (Angert et al., Ultramicroscopy 81 (2000) 203-222).
>
> Here a correct CTF needs to include yet another cos-term ….. and the zeros
> in the experimental and theoretical CTF only fit, if an additional
> cos-contrast (amplitude contrast produced by the energy filter) is added …
>
> (And yes, I apologize for the quality of the data, but it was the best we
> managed to get with that very old hardware at that time …)
>
>
>
> And I may add a bit of relief to all here: Do not get too excited that
> nobody uses this additional cos-term at present. The explanation is simple:
> Nobody cares for the extra bit of very low resolution data when fitting a
> CTF going out to better than a few Angstroms ….. But the problem with the
> density and the phase at “zero” remains ….
>
>
>
> My 2 cent ….
>
>
>
> Best,
>
>
>
> Rasmus
>
>
>
>
>
> On 15. Oct 2023, at 22:22, Marin van Heel <marin.vanheel at googlemail.com>
> wrote:
>
>
>
>
>
> Dear All,
>
> Unfortunately, a fundamental mistake has been made in the much-cited
> paper by Erickson and Klug [Erickson & Klug 1971] more than 50 years ago.
> They assumed that the EM *amplitude contrast* of the (stained )
> biological object to be *proportional* to the *phase contrast* of the
> same object over all spatial frequencies. If that were indeed the case, one
> single transfer function would suffice to describe how the linear imaging
> device would generate an output image. In reality, however, the *amplitude
> contrast* and *phase contrast* two *separate properties* of the *complex
> transmission function* of the object, and these are associated with
> different physical properties [Van Heel 1978] . The problem is that that
> proportionality error has crept into almost all popular CTF determination
> programs where, say, 10% or 15% amplitude contrast is suggested ab initio.
> Any percentage of amplitude contrast erroneously causes the average density
> of the cryo-EM 3D reconstruction to deviate from *zero*. Any
> phase-contrast image must yield a *zero average* as it should be for any
> phase contrast image where what is measured is the *difference* in *phase*
> between any point in the back focal plane of the system with respect to the
> *phase* at the origin!  That thus means that the *phase* at the origin
> must be *zero*.  (*Zero* being the average density over the image around
> which the phase information is modulated) . Adding a *cosine* component
> to  the CTF (a *sine*) will shift the zeroes of the CTF and therewith
> shift the defocus values found in most programs (no longer the real
> defocus!). That makes such results no longer comparable  to each other and
> will also complicate any comparison with zero-average density maps in X-ray
> crystallography.
>
> Two more cents added!
>
> Marin
>
> Erickson HP, Klug A (1971). Measurement and Compensation of Defocusing and
> Aberrations by Fourier Processing of Electron Micrographs. Phil. Trans. R.
> Soc. Lond. B. 261; 105-118.
>
> van Heel, M. (1978). On the imaging of relatively strong objects in
> partially coherent illumination in optics and electron optics. Optik. 49,
> 389–408.
>
> https://mail.ncmir.ucsd.edu/pipermail/3dem/2014-July/003454.html
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>
>
>
>
>
> On Sun, Oct 15, 2023 at 10:01 AM Guillaume Gaullier <
> guillaume.gaullier at kemi.uu.se> wrote:
>
> Hello Bernhard,
>
>
>
> According to PDB/EMDB validation reports, this spike in the voxel values
> histogram is caused by masking. One validation report I have says "A spike
> in this graph at zero usually indicates that the volume has been masked".
> You can probably also find this note in validation reports of released
> PDB/EMDB entries.
>
>
>
> Opening a map from 3D refinement and one of the two half-maps from the
> same job seems to confirm this. The map’s histogram shows this spike at
> zero, but the half-map’s histogram doesn’t. Half-maps are never filtered
> nor masked, whereas the main map is masked (in cryoSPARC this is done by
> default, unless one turns off automatic masking and doesn’t provide any
> mask). See the attached histograms.
>
>
>
> The fact that there is no absolute scale for contour level in cryoEM maps
> is indeed annoying (I would like to compare maps without worrying that
> maybe I chose inadequate contour levels). My understanding is that it is
> caused at least in part by the fact that the size of the box enclosing the
> particle is arbitrary. Different amounts of low-value voxels between
> different maps give them different voxel value histograms, therefore
> choosing a contour level in terms of a certain number of standard
> deviations above the mean produces different results with different maps.
> Electron density maps from crystallography don’t have this variability
> because the box always spans a full unit cell, without this variable
> padding around the region of high density.
>
> At least this is how I understand Tom Goddard’s explanation in this
> discussion from last month on the chimerax-users list:
> https://urldefense.com/v3/__https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/thread/3RNL6ODNP6QAL3BTHIPPQS2VE2B2YSVO/__;!!Mih3wA!HHQNmN65Wk1V15ioEFSz5o00Os_T-tUFkcd-dpCrdS1aw1A5xCH30H9W4LY0mmAgJmXV2PB9Bm7ykfFaDAT7ucM8HoAsIA$ 
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>
> Maybe there are other reasons adding to this.
>
>
>
> I hope this helps.
>
> Cheers,
>
>
> Guillaume
>
>
>
>
>
> On 15 Oct 2023, at 13:05, <Nonameavailable> <br at RUPPWEB.ORG> wrote:
>
>
>
> Dear EM Experts,
>
>
>
> Some of my crystallographer colleagues and I wonder about the
> fundamentally different appearance of density histograms in EM Coulomb
> potential maps vs the X-ray Electron density maps. Here is the question:
>
>
>
> “What I've noticed is that they are on different scales. That is
> understandable, a e/A^3 is different than V. But there are papers showing
> that these values are somewhat proportional to each other for lower
> resolutions. But the other thing that I have noticed is that electron
> density maps have close to normally distributed value distributions,
> whereas cryoEM maps have a sharp spike and a very long tail. As a result,
> an electron density blob in an X-ray map looks nice somewhere around
> 3sigma, whereas for cryoEM it's sometime 10sigma, 17sigma, 20sigma, all
> over the place. I'm thinking of using thresholds based on percentiles
> rather than sigmas, but my main question is: shouldn't the values on cryoEM
> maps be also approximately normally distributed? what is the cause of this
> non-normality? sharpening? the raw experimental data themselves?”
>
>
>
> And here a potential partial answer:
>
>
>
> “In cryo-EM, there is no absolute scaling, which means that density values
> can vary significantly. This variability can explain why you consistently
> encounter different sigma values. I can confirm that the density value
> distribution behaves as you described, and I have also observed this.
> However, I cannot provide a definitive answer as to why this occurs. My
> best guess is that it may be related to B factor weighting in motion
> correction, but I cannot provide a conclusive explanation, I'm afraid.”
>
>
>
> What are we missing here?
>
>
>
> Thx, BR
>
>
>
> -----------------------------------------------------------------
>
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>
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>
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>
> Rasmus R. Schroeder
>
> Cryo Electron Microscopy
> Heidelberg University / Medical Faculty
> BioQuant, Im Neuenheimer Feld 267
> 69120 Heidelberg, Germany
>
> Tel. +49-(0)6221-5451350
> e-mail  rasmus.schroeder at bioquant.uni-heidelberg.de
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