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CCP4BB Home

CCP4BB  June 2018

CCP4BB June 2018

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Subject:

Re: Table 1 successor in 3D?

From:

Gerard Bricogne <[log in to unmask]>

Reply-To:

Gerard Bricogne <[log in to unmask]>

Date:

Tue, 5 Jun 2018 16:10:11 +0100

Content-Type:

text/plain

Parts/Attachments:

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text/plain (232 lines)

Dear John,

     Further to my reply below: Claus Flensburg pointed out to me that
there is an incorrect statement in your message:
     
> The anisotropy figure of Staraniso is indeed very useful and could
> complement Table 1, and clearly can only be made with unmerged data.

If you look at http://staraniso.globalphasing.org/staraniso_about.html
you will see that STARANISO can take unmerged intensity data as input
(points 1 to 10 in the list); however the program also accepts merged
intensity data (points 11 to 19), with best effect if no resolution
cut-off has yet been applied to them.

     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* aaociated with that entry. Your
statement therefore has no factual basis. 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 informative
value of 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.


     With best wishes,
     
          Gerard.

--
On Tue, Jun 05, 2018 at 02:02:53PM +0100, Gerard Bricogne wrote:
> Dear John,
> 
>      Thank you for your interesting comments. As far as the deposition
> of raw images is concerned, you are preaching to the converted in my
> case (I would even, if I may blow my own trumpet for a second, claim
> to have been one of the earliest proponents and most persistently
> vociferous defenders of the idea, long before it gained general
> acceptance). 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, so I would be surprised if one could read
> such a message in what we have implemented and what Bernhard has
> written about. At any given stage in this evolution, however, the
> (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.
> 
>      Thank you also for the list of what STARANISO doesn't yet do, but
> be assured that most of these items already figure prominently on our
> long to-do list for the rapidly expanding set of functionalities of
> the program. My colleague Clemens Vonrhein likes to occasionally refer
> in our discussions to the universal wish for all-singing all-dancing
> software as the yearning for an "eierlegende Wollmilchsau", for which
> I am told that an approximate English transation would be "egg-laying
> Wool-Milk-Pig". It is on its way, but it will take a bit longer ;-) ,
> one step at a time.
> 
> 
>      With best wishes,
>      
>           Gerard.
> 
> --
> On Tue, Jun 05, 2018 at 11:09:42AM +0100, John R Helliwell wrote:
> > Dear Colleagues
> > Thankyou to Gerard for the prompt of last Friday on CCP4bb to read in
> > detail Bernhard's perspective in Structure on “Table 1”.
> > 
> > The anisotropy figure of Staraniso is indeed very useful and could
> > complement Table 1, and clearly can only be made with unmerged data.
> > 
> > However, the Perspective does not address some of the problems that
> > could exist with the data that are not evident from a Table I
> > 
> > summary, nor from the Staraniso figures, as they are the result of
> > data processing. Some aspects of reciprocal space could have been
> > 
> > completely missed or ignored: pseudo-merohedral twinning or multiple
> > lattices, incommensurate modulation and diffuse streaks.
> > 
> > These can be visualized by reciprocal space reconstructions from the
> > detector images, such as available in EVAL.
> > 
> > Furthermore without these special features in the raw diffraction
> > image*s* the raw data allow for reprocessing by readers of
> > 
> > article*s* by their preferred software as well as at different
> > resolutions to evaluate optimal model quality (aka Deiderichs and
> > 
> > Karplus). Overall this means that we can work towards methods that
> > provide us with quality indicators for how well the data
> > 
> > processing step actually explains the diffraction patterns in detector
> > or reciprocal space.
> > 
> > Therefore, we reiterate that raw diffraction data should be stored and
> > the dois cited in publications and the PDB depositions.
> > 
> > 
> > 
> > Best wishes,
> > Loes and John
> > See Kroon Batenburg et al 2017 IUCrJ and Helliwell et al IUCrJ 2017.
> > 
> > 
> > 
> > On Mon, Jun 4, 2018 at 10:39 AM, Bernhard Rupp <[log in to unmask]> wrote:
> > 
> > > The point is that **once you have a 3D representation of the RL**, you
> > >
> > > can map whatever RS metric you like on that presentation and articulate
> > >
> > > its effect on real space. In case of resolution measures this is straight
> > > forward;
> > >
> > > where it becomes interesting is at other atrocities and mutilations of the
> > >
> > > data, some of which Gerard has already mentioned.
> > >
> > >
> > >
> > > Ultimately, once you have classified and ranked the defects of data
> > >
> > > collection, you can look for them proactively and take corrective measures
> > >
> > > already in the data collection process. To some degree the automated
> > >
> > > collection and processing programs do that (e.g. exposure) but there are
> > >
> > > significant deficiencies that are stated posterior but not addressed in
> > > the process
> > >
> > > (e.g. optimal detector positions, orientations).
> > >
> > >
> > >
> > > Best, BR
> > >
> > >
> > >
> > > *From:* Alexandre Ourjoumtsev <[log in to unmask]>
> > > *Sent:* Monday, June 4, 2018 10:07
> > > *To:* Gerard Bricogne <[log in to unmask]>; [log in to unmask]
> > > *Cc:* [log in to unmask]
> > > *Subject:* Re: [ccp4bb] Table 1 successor in 3D?
> > >
> > >
> > >
> > > Dear Bernhard and Gerard,
> > >
> > >
> > >
> > > congratulations for nice results that both you (and Gerard team) have been
> > > contributed and published !
> > >
> > >
> > >
> > > Just a nice occasion to remind (and slightly correct Bernhard's message in
> > > that article) that the 'efficient resolution' that we suggested (2013) is
> > > NOT a single global number but exactly what Bernhard is saying : this
> > > number may vary, and sometimes drastically, from one direction to another,
> > > and our program gives the minimal - maximal - mean values as well as a
> > > histogram of its distribution and a list of major outliers (see some
> > > examples in Urzhumtseva et al., 2013, Acta Cryst *D69**,* 1921-1934, and
> > > especially in *J. Appl.**Cryst., **48*, 589-597 ). Obviously, full
> > > 3D-STARANISO-views of various data quality metrics are much more
> > > spectacular !
> > >
> > >
> > >
> > > Best regards,
> > >
> > >
> > >
> > > Sacha Urzhumtsev
> > >
> > >
> > >
> > > ----- Le 1 Juin 18, à 18:30, Gerard Bricogne <[log in to unmask]> a
> > > écrit :
> > >
> > > 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/     .
> > >
> > >
> > > ------------------------------
> > >
> > > To unsubscribe from the CCP4BB list, click the following link:
> > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> > >
> > 
> > 
> > 
> > -- 
> > Professor John R Helliwell DSc
> > 
> > ########################################################################
> > 
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> --
> 
>      ===============================================================
>      *                                                             *
>      * Gerard Bricogne                     [log in to unmask]  *
>      *                                                             *
>      * Global Phasing Ltd.                                         *
>      * Sheraton House, Castle Park         Tel: +44-(0)1223-353033 *
>      * Cambridge CB3 0AX, UK               Fax: +44-(0)1223-366889 *
>      *                                                             *
>      ===============================================================

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