Re: [phenixbb] Table 1 successor in 3D?

Dear Gerard, Thankyou for your detailed and informative reply to our message to Phenixbb in reply to yours. The inadequacies of detector setting will not be improved by saving unmerged intensities, we agree. The raw diffraction images contain more information nevertheless, even at an imperfect detector setting. The role of the crystallographic associations and the facilities in professional training through their courses is important. There is much enthusiasm in the earlier literature about preserving raw diffraction images, as Bernhard has also referred to (1913). We appreciate the usefulness of Staraniso and the fact that it is more informative than Table 1. Not least we greatly appreciate your work for the IUCr on these matters as consultant to dddwg and now CommDat. All best wishes, Loes and John On Tue, Jun 12, 2018 at 5:24 PM, Gerard Bricogne wrote:

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

http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi

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,

Gerard.

-- 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 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: [email protected], [email protected]

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 -----

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

-- Professor John R Helliwell DSc

-- Professor John R Helliwell DSc