raw data deposition (off-list)

Dear Petr,

    I agree that we need tools to validate processing methods, but these
tools will not come from pure thought alone: they will need vast amount of
raw data with a full range of problematic features so that the ideas of new
approaches and the algorithms to implement them can be developed and tested.
The main tools for validating methods are data!

    Also, validation is nice, but catching a problem by means of a
validation procedure does not mean being able to correct it. It is only by
retaining the original data that one can be certain not to have lost any of
the information the experiment gave through an inappropriate processing
method.

    In other words, quality of outcome does not materialise without a huge
amount of challenging data to guide and test the underlying developments,
i.e. without a large amount of storage - so I don't think the two can be
decoupled in the way you suggest.

    As I and many have said often, once you have used those stored raw data
to improve processing methods, you can go back to those same raw data and
reprocess them, to get better reduced data and hence better structural
results from them: that would not happen if you hadn't stored them in the
first place.


    With best wishes,

         Gerard.

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On Fri, Oct 28, 2011 at 08:33:53AM +0200, Petr Kolenko wrote:
> Dear colleagues,
>
> my opinion is that we should develop methods or approaches to validate
> !processing! of raw data. If this is possible. We have many validation
> tools for structure refinement, but no tool to validate data
> processing. In case we have this tools, there is no need to deposit
> diffraction images (2-5GB instead of 10 MB). I think.
> Of course, how to validate this? This might be topic for a new
> discussion. I am sure, that in the very beginning of crystallography,
> there were no tools to validate the structures as well. I am also sure
> that some opinions may arise today. (Online server, where one can
> upload the images with log files from processing?)
> We should concentrate more on quality of our outcome, than on storage
> of these data.
>
> Petr
>
>
> 2011/10/28 Katherine Sippel <>:
> > Generally during these rigorous bb debates I prefer to stay silent and
> > absorb all the information possible so that I can make an informed decision
> > later on. I fear that I am compelled to contribute in this instance. In
> > regards to the "does this make a difference in the biological interpretation
> > stage" issue, I can state that it does. In my comparatively miniscule career
> > I have run into this issue three times. The first two address Adrian's
> > point...
> >
> >> And (b) even if they do, is this continual improvement even worthwhile?  I
> >>  am always depressed at how little a model changes from an initial build to
> >> the final one, even when the rfree drops from 35 to 23. All that work! - and
> >> my biological interpretation would have been almost the same at the
> >> beginning as at the end.
> >
> >
> > In one instance I adopted an orphaned structure and ran it through a
> > slightly more advanced refinement protocol (on the same structure factors)
> > and ended up with a completely different story than the one I started with
> > [1]. Another researcher in my grad lab identified mis-oriented catalytic
> > residues in an existing structure from EDS server maps which affects the
> > biochemistry of the catalytic mechanism [2].
> >
> > In another case I decided that I would reprocess some images that I had
> > originally indexed and scaled in my "Ooo buttons clicky clicky" stage of
> > learning crystallography and the improved structure factors revealed a
> > alternate conformations for both a critical loop and ligand orientation [3].
> >
> > And this was all in the last 4 years. So I would posit that the answer is
> > yes there are significant biological insights to be had with the capacity to
> > reassess data in any form.
> >
> > Katherine
> >
> > [1] J Phys Chem Lett. 2010 Oct 7;1(19):2898-2902
> > [2] Acta Crystallogr D Biol Crystallogr. 2009 Mar;65(Pt 3):294-6.
> > [3] Manuscript in progress
> >
> > ------------
> > Katherine Sippel, PhD
> > Postdoctoral Associate
> > Baylor College of Medicine
> >
>
>
>
> --
> Petr Kolenko


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