Sure they will
There is no irony in what I say
Dr Felix Frolow
Professor of Structural Biology and Biotechnology
Department of Molecular Microbiology
Tel Aviv University 69978, Israel
Acta Crystallographica F, co-editor
e-mail: [log in to unmask]
Cellular: 0547 459 608
On Oct 18, 2011, at 20:01 , Phoebe Rice wrote:
> One more consideration:
> Since organization is not one of my greatest talents, I would be absolutely delighted if a databank took over the burden of archiving my raw data for me.
> Phoebe A. Rice
> Dept. of Biochemistry & Molecular Biology
> The University of Chicago
> phone 773 834 1723
> ---- Original message ----
>> Date: Tue, 18 Oct 2011 18:17:14 +0100
>> From: CCP4 bulletin board <[log in to unmask]> (on behalf of Gerard Bricogne <[log in to unmask]>)
>> Subject: Re: [ccp4bb] IUCr committees, depositing images
>> To: [log in to unmask]
>> Dear Enrico, Frank and colleagues,
>> I am glad to have suggested that everyone's views on this issue should
>> be aired out on this BB rather than sent off-list to an IUCr committee
>> member: this is much more interactive and thought-provoking.
>> There would seem to be clear biases in some of the positions - for
>> instance, the statement that we overvalue individual structures and that
>> there is value only in their ensemble has to be seen to be coming from
>> someone in a structural genomics centre ;-) . However, as Wladek pointed
>> out, when an investigator's project is crucially dependent on a result
>> embodied in a deposited structure, it would be of the greatest value to that
>> investigator to be able to double-check how reliable some features of that
>> structure (especially its ligands) actually are.
>> On the other hand Enrico, as a specialist of crystallisation and
>> modelling, sees value only in improving those contributors to the task of
>> structure determination. This is forgetting (1) an essential capability of
>> crystallography: that, through experimental phasing, it can show you what a
>> protein looks like even if you have never seen nor modelled one before,
>> through the wondrous process of producing model-free electron-density maps;
>> and (2) an essential aspect of the task of structure determination: that it
>> doesn't aim at producing a model with perfect geometry, but one that best
>> explains the measured data and neither under- nor over-interprets them (I
>> realise, though, that Enrico's statement "Data just introduces experimental
>> errors into what would otherwise be a perfect structure" is likely to be
>> tongue-in-cheek ...).
>> When it comes to making explicit the advantages of archiving at least
>> the raw images that yielded the data against which a deposited PDB entry was
>> refined, many good reasons have been given, but I feel that
>> (1) there is an over-emphasis on the preservation of diffuse scattering
>> that has a tendency to give this archiving a nuance of "blue-skies" research
>> and thus to detract from its practical urgency; time will come for diffuse
>> scattering to be fully appreciated, but at the moment its mention acts as a
>> bit of a distraction, if not a turn-off in this context for people who not
>> not love it already;
>> (2) as far as I see it, the highest future benefit of having archived
>> raw images will result from being able to reprocess datasets from samples
>> containing multiple lattices ("non-merohedral twinning"). Numerous
>> structures are determined and refined against data obtained by integrating
>> only the spots from the major lattice, without rejecting those that are
>> corrupted by overlap by a spot from a minor lattice. This leads to
>> systematic errors in these data that may only be incompletely taken out by
>> outlier rejection at the merging stage, and will create noise or confusing
>> residual features in difference maps, if not false features in the main map
>> and therefore its interpretation by the model. In my opinion it will be the
>> development of methods for dealing with overlapped lattices and for the
>> proper treatment of such data in scaling and refinement (as is already
>> possible with small molecules) that will bring about the major possibility
>> of substantially improving deposited results by reprocessing the raw images
>> co-deposited with them;
>> (3) there is also the more immediate possibility of better removing ice
>> rings, or ligand powder rings, from images, than by having to throw away
>> certain thin shells of merged data in the structure factor file.
>> I see the case for raw image deposition as absolutely compelling,
>> especially in view of the auto-catalytic process through which their
>> availability will speed up the development of precisely the new methods and
>> software to extract better data from them and better refine models against
>> them. The impact of structure factor deposition on the development of better
>> refinement programs is there to prove that this paradigm of a chain reaction
>> makes total sense.
>> Various arguments tend to be fired off as decoys - "get better
>> crystals", why not "get a better post-doc"? - but they are unhelpful in the
>> way they prolong procrastination when what we need is to bite the bullet.
>> The IUCr Forum that John Helliwell pointed at already contains draft plans
>> for a pilot run of a reasonable scheme.
>> With best wishes,
>> On Tue, Oct 18, 2011 at 06:19:27PM +0200, Enrico Stura wrote:
>>> Dear Peter,
>>> How many crystallographers does it take to transform bad data into good
>>> None, you need a modeller. Only a modeller can give you a structure with
>>> geometry. Data just introduces experimental errors into what would
>>> otherwise be a perfect
>>> If you have good data do you need crystallographers?
>>> Of course there all the cases in between. That ... you are right, is the
>>> other half of the story.
>>> From a biological point of view, only borderline cases make "cents" ($+€)
>>> to store.
>>> The experimenter in consultation with a beamline scientist at an SR
>>> facility is the best
>>> small commitee suitable to evaluate what is worth keeping. I am sure that
>>> the images
>>> that are worth storing for a long long time would fit on a few Tb at a
>>> reasonable cost.
>>> Storing everything would make it harder to find something worth improving
>>> in the future.
>>> On Tue, 18 Oct 2011 17:12:42 +0200, Peter Keller
>>> <[log in to unmask]> wrote:
>>>> Dear Enrico,
>>>> Please don't get me wrong: what you are saying is not incorrect, but it
>>>> is only half the story.
>>>> On Tue, 2011-10-18 at 15:13 +0200, Enrico Stura wrote:
>>>>> With improving techniques, we should always be making progress!
>>>> Yes, of course!
>>>>> If we are trying to answer a biological question that is really
>>>>> we would be better off
>>>>> improving the purification, the crystallization, the cryo-conditions
>>>> You have left X-ray crystallography out of this list. It is a technique
>>>> like the others, and can also be improved :-)
>>>> It may be true that the number of crystallographers that are working on
>>>> improving instrumental methodology and software is small compared to the
>>>> number working on improving wet-lab techniques, but that number is not
>>>> zero, and the contribution is significant. The rest of you benefit from
>>>> that work!
>>>>> instead of having to rely on
>>>>> processing old images with new software.
>>>>> I have 10 years worth of images. I have reprocessed very few of them and
>>>>> never made any
>>>>> sensational progress using the new software. Poor diffraction is poor
>>>> Maybe so, but certain types of datasets are useful for methods and
>>>> software development, even if no new biological insights could be gained
>>>> by reprocessing them. These datasets are often hard to get hold of in
>>>> practice, especially when they are in someone's lab on a tape that
>>>> no-one has a reader for any more.
>>>> Obtaining protein, growing crystals and collecting new data in such a
>>>> way that the interesting features of those datasets are reproduced can
>>>> be much much harder than curating the images would be. This is
>>>> especially true for software-oriented people like us who don't have
>>>> regular access to wet-lab facilities.
>>>>> Money can be better spent buying a wine cellar, storage works for wine.
>>>> Images have already been lost that ought to have been kept. The
>>>> questions are: how to select the datasets that are potentially of value,
>>>> and how to make sure that they don't disappear.
>>> Enrico A. Stura D.Phil. (Oxon) , Tel: 33 (0)1 69 08 4302 Office
>>> Room 19, Bat.152, Tel: 33 (0)1 69 08 9449 Lab
>>> LTMB, SIMOPRO, IBiTec-S, CE Saclay, 91191 Gif-sur-Yvette, FRANCE
>>> e-mail: [log in to unmask] Fax: 33 (0)1 69 08 90 71
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>> * Gerard Bricogne [log in to unmask] *
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