[phenixbb] Table 1 successor in 3D?

Gerard Bricogne gb10 at globalphasing.com
Tue Jun 12 09:24:07 PDT 2018

Dear John and Loes,

     Thank you for reiterating on this BB your point about depositing
raw diffraction images. I will never disagree with any promotion of
that deposition, or praise of its benefits, given that I was one of
the earliest proponents and most persistently vociferous defenders of
the idea, long before it gained general acceptance (see Acta D65, 2009
176-185). There has never been any statement on our part that the
analysis done by STARANISO disposes of the need to store the original
images and to revisit them regularly with improved processing and/or
troubleshooting software. At any given stage in this evolution, 
however, (re)processing results will need to be displayed, and it is
with the matter of what information about data quality is conveyed (or
not) by various modes of presentation of such results that Bernhard's
argument and (part of) our work on STARANISO are concerned.

     Furthermore we have made available the PDBpeep server at

that takes as input a 4-character PDB entry code and generates figures
from the deposited *merged amplitudes* associated with that entry. The
numbers coming out of a PDBpeep run may well have questionable
quantitative value (this is pointed out in the home page for that
server) but the 3D WebGL picture it produces has informative value
independently from that. Take a look, for instance, at 4zc9, 5f6m or
6c79: it is quite plain that these high-resolution datasets have
significant systematic incompleteness issues, a conclusion that would
not necessarily jump out of a Table 1 page, even after reprocessing
the original raw images, without that 3D display.

     The truly pertinent point about this work in relation to keeping
raw images is that the STARANISO display very often suggests that the
merged data have been subjected to too drastic a resolution cut-off,
and that it would therefore be worth going back to the raw images and
to let autoPROC+STARANISO apply a more judicious cut-off. Sometimes,
however, as in the example given in Bernhard's paper, significant data
fail to be recorded because the detector was positioned too far from
the crystal, in which case the raw images would only confirm that
infelicity and would provide no means of remediating it.

     With best wishes,

On Wed, Jun 06, 2018 at 09:35:38AM +0100, John R Helliwell wrote:
> Dear Colleagues
> Given that this message is now also placed on Phenixbb, we reiterate our
> key point that deposition of raw diffraction images offers flexibility to
> readers of our science results for their reuse and at no cost to the user.
> As with all fields our underpinning data should be FAIR (Findable,
> Accessible, Interoperable and Reusable). Possibilities for free storage of
> data are Zenodo, SBGrid and proteindiffraction.org (IRRMC).
> With respect to graphic displays of anisotropy of data Gerard's three
> figures are very informative, we agree.
> Best wishes
> Loes and John
> Kroon-Batenburg et al (2017) IUCrJ  and Helliwell et al (2017) IUCrJ
> On Tue, Jun 5, 2018 at 4:49 PM, Gerard Bricogne <gb10 at globalphasing.com>
> wrote:
> > Dear phenixbb subscribers,
> >
> >      I sent the message below to the CCP4BB and phenixbb at the same
> > time last Friday. It went straight through to the CCP4BB subscribers
> > but was caught by the phenixbb Mailman because its size exceeded 40K.
> >
> >      Nigel, as moderator of this list, did his best to rescue it, but
> > all his attempts failed. He therefore asked me to resubmit it, now
> > that he has increased the upper size limit.
> >
> >      Apologies to those of you who are also CCP4BB subscribers, who
> > will already have received this message and the follow-up discussion
> > it has given rise to.
> >
> >
> >      With best wishes,
> >
> >           Gerard.
> >
> > ----- Forwarded message from Gerard Bricogne <gb10> -----
> >
> > Date: Fri, 1 Jun 2018 17:30:48 +0100
> > From: Gerard Bricogne <gb10>
> > Subject: Table 1 successor in 3D?
> > To: CCP4BB at JISCMAIL.AC.UK, phenixbb at phenix-online.org
> >
> > Dear all,
> >
> >      Bernhard Rupp has just published a "Perspective" article in
> > Structure, accessible in electronic form at
> >
> >  https://www.cell.com/structure/fulltext/S0969-2126(18)30138-2
> >
> > in which part of his general argument revolves around an example
> > (given as Figure 1) that he produced by means of the STARANISO server
> > at
> >             http://staraniso.globalphasing.org/     .
> >
> > The complete results of his submission to the server have been saved
> > and may be accessed at
> >
> >     http://staraniso.globalphasing.org/Gallery/Perspective01.html
> >
> > and it is to these results that I would like to add some annotations
> > and comments. To help with this, I invite the reader to connect to
> > this URL, type "+" a couple of times to make the dots bigger, and
> > press/toggle "h" whenever detailed information on the display, or
> > selection of some elements, or the thresholds used for colour coding
> > the displays, needs to be consulted.
> >
> >      The main comment is that the WebGL interactive 3D display does
> > give information that makes visible characteristics that could hardly
> > be inferred from the very condensed information given in Table 1, and
> > the annotations will be in the form of a walk through the main
> > elements of this display.
> >
> >      For instance the left-most graphical object (a static view of
> > which is attached as "Redundancy.png") shows the 3D distribution of
> > the redundancy (or multiplicity) of measurements. The view chosen for
> > the attached picture shows a strong non-uniformity in this redundancy,
> > with the region dominated by cyan/magenta/white having about twice the
> > redundancy (in the 6/7/8 range) of that which prevails in the region
> > dominated by green/yellow (in the 3/5 range). Clear concentric gashes
> > in both regions, with decreased redundancy, show the effects of the
> > inter-module gaps on the Pilatus 2M detector of the MASSIF-1 beamline.
> > The blue spherical cap along the a* axis corresponds to HKLs for which
> > no measurement is available: it is clearly created by the detector
> > being too far from the crystal.
> >
> >      The second (central) graphical object, of which a view is given
> > in Figure 1 of Bernhard's article and another in the attached picture
> > "Local_I_over_sigI.png") shows vividly the blue cap of measurements
> > that were missed but would probably have been significant (had they
> > been measured) cutting into the green region, where the local average
> > of I/sig(I) ranges between 16 and 29! If the detector had been placed
> > closer, significant data extending to perhaps 3.0A resolution would
> > arguably have been measured from this sample.
> >
> >      The right-most graphical object (of which a static view is
> > attached as "Debye-Waller.png") depicts the distribution of the
> > anisotropic Debye-Waller factor (an anisotropic generalisation of the
> > Wilson B) of the dataset, giving yet another visual hint that good
> > data were truncated by the edges of a detector placed too far.
> >
> >      Apologies for such a long "STARANISO 101" tutorial but Bernhard's
> > invitation to lift our eyes from the terse numbers in Table 1 towards
> > 3D illustrations of data quality criteria was irresistible ;-) . His
> > viewpoint also agrees with one of the main purposes of our STARANISO
> > developments (beyond the analysis and remediation of anisotropy, about
> > which one can - and probably will - argue endlessly) namely contribute
> > to facilitating a more direct and vivid perception by users of the
> > quality of their data (or lack of it) and to nurturing evidence-based
> > motivation to make whatever extra effort it takes to improve that
> > quality. In this case, the undeniable evidence of non-uniformity of
> > redundancy and of a detector placed too far would give immediate
> > practical guidance towards doing a better experiment, while statistics
> > in Table 1 for the same dataset would probably not ... .
> >
> >      Thank you Bernhard!
> >
> >
> >      With best wishes,
> >
> >           Gerard,
> > for and on behalf of the STARANISO developers
> >
> >
> > ----- End forwarded message -----
> >
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> >
> -- 
> Professor John R Helliwell DSc

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