[3dem] 3dem Digest, Vol 133, Issue 4

Benjamin Himes himes.benjamin at gmail.com
Sun Sep 2 14:09:17 PDT 2018


*strikes match*

Dithering  is used in astronomy to increase the sampling rate beyond
physical Nyquist of detector. This works by moving the detector between
successive images, by fractional amounts of the pixel dimension.

*pours petrol*

So really, we're not strictly limited to even Nyquist sampling. A
sufficient but not necessary condition on achievable resolution.

*room explodes*

Thanks to Jason K for pointing this out!

Ben H.






Ben
On Sun, Sep 2, 2018, 11:57 AM <3dem-request at ncmir.ucsd.edu> wrote:

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> Today's Topics:
>
>    1. Re: GroEL best resolution map. (FSC RESOLUTION ??)
>       (Marin van Heel)
>    2. Re: GroEL best resolution map. (FSC RESOLUTION ??)
>       (Vojtech Prazak)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 2 Sep 2018 10:05:53 -0300
> From: Marin van Heel <marin.vanheel at googlemail.com>
> To: Sjors Scheres <scheres at mrc-lmb.cam.ac.uk>, Natesh Ramanathan
>         <natesh at iisertvm.ac.in>, 3dem at ncmir.ucsd.edu
> Cc: "CCPEM at JISCMAIL.AC.UK" <CCPEM at JISCMAIL.AC.UK>
> Subject: Re: [3dem] GroEL best resolution map. (FSC RESOLUTION ??)
> Message-ID: <eb904df8-d5f6-2454-52c3-a13f2a6d24cd at googlemail.com>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>
>
> Dear Sjors,
>
> It is not a matter of software implementation but it is a fundamental
> theoretical basis of signal processing and the Fourier transform!
> You seem to have misunderstood the discussion on the issue here on
> 3DEM/CCPEM mailers a while ago (June 2016?). It is NOT about "routinely
> achieve resolutions very close to Nyquist" but rather about "to which
> level you are ALLOWED to claim/interpret the significant resolution"
> based on an FSC curve.
> Maybe I need to write a separate paper about the matter to better
> explain the fundamental principles behind it.
>
> This "under-sampling problem" is an important matter because -
> especially in combination with erroneous resolution thresholds like the
> "gold standard FSC 0.143" (based on "sloppy statistics" see our bioRxiv
> paper)" - it makes it impossible to objectively compare the resolution
> levels achieved in independent experiments.? That makes efforts to
> perform projects like "resolution challenges" futile and not worth
> wasting your time on.
>
> Cheers,
> Marin
>
> ===============
>
> On 02/09/2018 07:14, Sjors Scheres wrote:
> > Dear Natesh,
> > The limitation of 3x the pixel size of the maximum reachable
> > resolution might be true for software written by Marin, but it is
> > definitely not true for many other programs, including relion. We
> > routinely achieve resolutions very close to Nyquist, which is only 2x
> > the pixel size.
> >
> > Hth,
> > Sjors
> >
> > Sent from my phone.
> >
> > -------- Original message --------
> > From: Marin van Heel <marin.vanheel at googlemail.com>
> > Date: 01/09/2018 19:43 (GMT+01:00)
> > To: Natesh Ramanathan <natesh at iisertvm.ac.in>, 3dem at ncmir.ucsd.edu
> > Subject: Re: [3dem] GroEL best resolution map. (FSC RESOLUTION ??)
> >
> >
> > Dear Natesh,
> >
> > I just checked the technical data of the EMD-3407 dataset and I saw
> > that its pixel size is 1.05A . That means that no resolution levels
> > better than 3 x 1.05A = 3.15A? may be claimed for processing results
> > based on that data set, following the standards we set in the past
> > (for the younger generation: I am the main inventor of the FSC ;) ).
> > Going beyond a resolution claim of 3.15A would mean that the dataset
> > is undersampled, and would thus require a new data collection with a
> > smaller pixel size. For a possible resolution claim of, say, 2A? you
> > need a maximum pixel size of 0.66A !? Moreover, the 0.143 threshold
> > FSC threshold used in this EMD-3407 case is itself wrong, while based
> > on sloppy statistics.
> > (https://www.biorxiv.org/content/early/2017/11/24/224402).Bottom
> > line:? to compare the results of different cryo-EM experiments you
> > need correct resolution criteria applied to sufficiently fine sampled
> > cryo-EM data.
> >
> > Cheers
> >
> > Marin
> >
> > On 01/09/2018 12:57, Natesh Ramanathan wrote:
> >> Dear All,
> >>
> >> ? ? ? Does anyone know/have a GroEL cryoEM map with resolution? 2.5 ?
> >> or better?
> >> I see that the best resolution in EMDataBank is 3.26 ??- EMD-3407 and
> >> EMD-3415.
> >> ? ? ? If you have one, is it possible to share the map with me?
> >>
> >> Many thanks.
> >> Best regards,
> >> Natesh
> >> --
> >> ----------------------------------------------------------
> >> "Live Simply and do Serious Things .. "
> >> - Dorothy Mary Crowfoot Hodgkin OM, FRS
> >>
> >> "In Science truth always wins"
> >> - Max Ferdinand Perutz OM FRS
> >> ----------------------------------------------------------
> >> Dr. Ramanathan Natesh
> >> Assistant Professor,
> >> School of Biology,
> >> Indian Institute of Science Education and Research Thiruvananthapuram
> >> (IISER-TVM),
> >> Maruthamala P.O., Vithura,
> >> Thiruvananthapuram,? 695551, Kerala, India
> >>
> >> natesh at iisertvm.ac.in <mailto:natesh at iisertvm.ac.in>
> >> http://www.researcherid.com/rid/C-4488-2008
> >> ORCID: http://orcid.org/0000-0002-1145-5962
> >> https://publons.com/author/1520837/ramanathan-natesh#profile
> >> http://faculty.iisertvm.ac.in/natesh
> >>
> >> Office Ph. 0091- 471-2778087
> >>
> >>
> >> _______________________________________________
> >> 3dem mailing list
> >> 3dem at ncmir.ucsd.edu
> >> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
> >
> >
> > --
> > ==============================================================
> >
> >      Prof Dr Ir Marin van Heel
> >
> >      Laborat?rio Nacional de Nanotecnologia - LNNano
> >      CNPEM/LNNano, Campinas, Brazil
> >
> >      tel:    +55-19-3518-2316
> >      mobile  +55-19-983455450 (current)
> >      mobile  +55-19-981809332
> >                   (041-19-981809332 TIM)
> >      Skype:  Marin.van.Heel
> >      email:  marin.vanheel(A_T)gmail.com
> >              marin.vanheel(A_T)lnnano.cnpem.br
> >      and:    mvh.office(A_T)gmail.com
> >
> > --------------------------------------------------
> >      Emeritus Professor of Cryo-EM Data Processing
> >      Leiden University
> >      Mobile NL: +31(0)652736618 (ALWAYS ACTIVE SMS)
> > --------------------------------------------------
> >      Emeritus Professor of Structural Biology
> >      Imperial College London
> >      Faculty of Natural Sciences
> >      email: m.vanheel(A_T)imperial.ac.uk
> > --------------------------------------------------
> >
> > I receive many emails per day and, although I try,
> > there is no guarantee that I will actually read each incoming email.
>
>
> --
> ==============================================================
>
>      Prof Dr Ir Marin van Heel
>
>      Laborat?rio Nacional de Nanotecnologia - LNNano
>      CNPEM/LNNano, Campinas, Brazil
>
>      tel:    +55-19-3518-2316
>      mobile  +55-19-983455450 (current)
>      mobile  +55-19-981809332
>                   (041-19-981809332 TIM)
>      Skype:  Marin.van.Heel
>      email:  marin.vanheel(A_T)gmail.com
>              marin.vanheel(A_T)lnnano.cnpem.br
>      and:    mvh.office(A_T)gmail.com
>
> --------------------------------------------------
>      Emeritus Professor of Cryo-EM Data Processing
>      Leiden University
>      Mobile NL: +31(0)652736618 (ALWAYS ACTIVE SMS)
> --------------------------------------------------
>      Emeritus Professor of Structural Biology
>      Imperial College London
>      Faculty of Natural Sciences
>      email: m.vanheel(A_T)imperial.ac.uk
> --------------------------------------------------
>
> I receive many emails per day and, although I try,
> there is no guarantee that I will actually read each incoming email.
>
> -------------- next part --------------
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> http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20180902/b4c7d63f/attachment-0001.html
> >
>
> ------------------------------
>
> Message: 2
> Date: Sun, 02 Sep 2018 16:56:41 +0100
> From: "Vojtech Prazak" <vojta at strubi.ox.ac.uk>
> To: 3dem at ncmir.ucsd.edu, "Natesh Ramanathan" <natesh at iisertvm.ac.in>,
>         "Sjors Scheres" <scheres at mrc-lmb.cam.ac.uk>,  "Marin van Heel"
>         <marin.vanheel at googlemail.com>
> Cc: ccpem at jiscmail.ac.uk
> Subject: Re: [3dem] GroEL best resolution map. (FSC RESOLUTION ??)
> Message-ID: <2f313702c62808321b3a318c44e71347 at strubi.ox.ac.uk>
> Content-Type: text/plain; charset="utf-8"
>
>
> Dear Marin,
>
> This topic is clearly important for you but I think you will find it has
> nothing to do with Natesh's original question.? I'm sure Sjors will be
> thrilled to continue this discussion in a private thread.
>
> Best,
>
> Vojta
>
>
>
> Vojt?ch Pra??k
> Graduate Student
> Department of Structural Biology
> The Wellcome Trust Centre for Human Genetics
> Roosevelt Drive, Oxford, OX3 7BN UK
> University of Oxford
>
> Email: vojta at strubi.ox.ac.uk
> Web: https://www.strubi.ox.ac.uk/research/kay-grunewald
> ?
>
> -----Original Message-----
> From: "Marin van Heel" <marin.vanheel at googlemail.com>
> To: "Sjors Scheres" <scheres at mrc-lmb.cam.ac.uk>, "Natesh Ramanathan" <
> natesh at iisertvm.ac.in>, 3dem at ncmir.ucsd.edu
> Cc: CCPEM at JISCMAIL.AC.UK
> Date: 09/02/18 14:07
> Subject: Re: [3dem] GroEL best resolution map. (FSC RESOLUTION ??)
>
>
> Dear Sjors,
>
> It is not a matter of software implementation but it is a fundamental
> theoretical basis of signal processing and the Fourier transform!
> You seem to have misunderstood the discussion on the issue here on
> 3DEM/CCPEM mailers a while ago (June 2016?). It is NOT about "routinely
> achieve resolutions very close to Nyquist" but rather about "to which level
> you are ALLOWED to claim/interpret the significant resolution" based on an
> FSC curve.
> Maybe I need to write a separate paper about the matter to better explain
> the fundamental principles behind it.
>
> This "under-sampling problem" is an important matter because - especially
> in combination with erroneous resolution thresholds like the "gold standard
> FSC 0.143" (based on "sloppy statistics" see our bioRxiv paper)" - it makes
> it impossible to objectively compare the resolution levels achieved in
> independent experiments.  That makes efforts to perform projects like
> "resolution challenges" futile and not worth wasting your time on.
>
> Cheers,
> Marin
>
> ===============
>
> On 02/09/2018 07:14, Sjors Scheres wrote:
>
>
> Dear Natesh,
> The limitation of 3x the pixel size of the maximum reachable resolution
> might be true for software written by Marin, but it is definitely not true
> for many other programs, including relion. We routinely achieve resolutions
> very close to Nyquist, which is only 2x the pixel size.
>
> Hth,
> Sjors
> Sent from my phone.
>
>
> -------- Original message --------
> From: Marin van Heel <marin.vanheel at googlemail.com>
> Date: 01/09/2018 19:43 (GMT+01:00)
> To: Natesh Ramanathan <natesh at iisertvm.ac.in>, 3dem at ncmir.ucsd.edu
> Subject: Re: [3dem] GroEL best resolution map. (FSC RESOLUTION ??)
>
>
> Dear Natesh,
>
> I just checked the technical data of the EMD-3407 dataset and I saw that
> its pixel size is 1.05A . That means that no resolution levels better than
> 3 x 1.05A = 3.15A  may be claimed for processing results based on that data
> set, following the standards we set in the past (for the younger
> generation: I am the main inventor of the FSC ;) ). Going beyond a
> resolution claim of 3.15A would mean that the dataset is undersampled, and
> would thus require a new data collection with a smaller pixel size. For a
> possible resolution claim of, say, 2A  you need a maximum pixel size of
> 0.66A !  Moreover, the 0.143 threshold FSC threshold used in this EMD-3407
> case is itself wrong, while based on sloppy statistics. (
> https://www.biorxiv.org/content/early/2017/11/24/224402).Bottom line:  to
> compare the results of different cryo-EM experiments you need correct
> resolution criteria applied to sufficiently
> fine sampled cryo-EM data.
>
> Cheers
>
> Marin
>
> On 01/09/2018 12:57, Natesh Ramanathan wrote:
>
> Dear All,
>
>       Does anyone know/have a GroEL cryoEM map with resolution  2.5 ?   or
> better?
> I see that the best resolution in EMDataBank is 3.26 ? - EMD-3407 and
> EMD-3415.
>
>
>       If you have one, is it possible to share the map with me?
>
> Many thanks.
> Best regards,
> Natesh
> --
>
> ----------------------------------------------------------
> "Live Simply and do Serious Things .. "
> - Dorothy Mary Crowfoot Hodgkin OM, FRS
>
> "In Science truth always wins"
> - Max Ferdinand Perutz OM FRS
> ----------------------------------------------------------
> Dr. Ramanathan Natesh
> Assistant Professor,
> School of Biology,
> Indian Institute of Science Education and Research Thiruvananthapuram
> (IISER-TVM),
>
> Maruthamala P.O., Vithura,
>
> Thiruvananthapuram,  695551, Kerala, India
>
> natesh at iisertvm.ac.in
> http://www.researcherid.com/rid/C-4488-2008
> ORCID: http://orcid.org/0000-0002-1145-5962
> https://publons.com/author/1520837/ramanathan-natesh#profile
> http://faculty.iisertvm.ac.in/natesh
>
> Office Ph. 0091- 471-2778087
>
>
>
>
> _______________________________________________ 3dem mailing list3dem
> @ncmir.ucsd.eduhttps://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>
>
> -- ==============================================================     Prof
> Dr Ir Marin van Heel     Laborat?rio Nacional de Nanotecnologia - LNNano
>  CNPEM/LNNano, Campinas, Brazil     tel:    +55-19-3518-2316     mobile
> +55-19-983455450 (current)     mobile  +55-19-981809332
>  (041-19-981809332 TIM)     Skype:  Marin.van.Heel     email:
> marin.vanheel(A_T)gmail.com             marin.vanheel(A_T)lnnano.cnpem.br
>    and:    mvh.office(A_T)gmail.com
> --------------------------------------------------     Emeritus Professor
> of Cryo-EM Data Processing     Leiden University     Mobile NL:
> +31(0)652736618 (ALWAYS ACTIVE SMS)
> --------------------------------------------------     Emeritus Professor
> of Structural Biology     Imperial College London     Faculty of Natural
> Sciences     email: m.vanheel(A_T)imperial.ac.uk
> -------------------------------------------------- I
> receive many emails per day and, although I try, there is no guarantee
> that I will actually read each incoming email.
>
>
> -- ==============================================================     Prof
> Dr Ir Marin van Heel     Laborat?rio Nacional de Nanotecnologia - LNNano
>  CNPEM/LNNano, Campinas, Brazil     tel:    +55-19-3518-2316     mobile
> +55-19-983455450 (current)     mobile  +55-19-981809332
>  (041-19-981809332 TIM)     Skype:  Marin.van.Heel     email:
> marin.vanheel(A_T)gmail.com             marin.vanheel(A_T)lnnano.cnpem.br
>    and:    mvh.office(A_T)gmail.com
> --------------------------------------------------     Emeritus Professor
> of Cryo-EM Data Processing     Leiden University     Mobile NL:
> +31(0)652736618 (ALWAYS ACTIVE SMS)
> --------------------------------------------------     Emeritus Professor
> of Structural Biology     Imperial College London     Faculty of Natural
> Sciences     email: m.vanheel(A_T)imperial.ac.uk
> -------------------------------------------------- I
> receive many emails per day and, although I try, there is no guarantee
> that I will actually read each incoming email.
>
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu
> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>
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