Dear Dale,
On Thu, Mar 12, 2009 at 11:07:05AM -0700, Dale Tronrud wrote:
> This thread has evolved into two different topics. Just to
> clarify:
>
> 1) There is a need for additional validation of structure factor
> depositions.
>
> My recollection is that the output of SF Check is available to
> the depositor via ADIT on the RCSB site. I have found that report
> to be quite helpful in checking for gross errors in my structure
> factor files.
>
> The Electron Density Server performs similar checks. It shows
> that the R value for 3ftt is 6.4% with a correlation coefficient
> between Fo and Fc of 0.996.
>
> The EDS flags entries as "interesting" if the calculated R value
> is more than 5% higher than the reported R value. Maybe it should
> also note when the R value is more than 5% lower.
>
> The tools for validating structure factors exist but perhaps could
> be put more "in the face" of the depositor to more strongly encourage
> that they be looked at.
>
> 2) It would be useful to have a central repository of raw diffraction
> images.
>
> Most of the discussion on this point is the technical difficulty of
> storing this quantity of data. What has not been mentioned is the
> much greater difficulty of validating these images. You may think
> the images for an entry have been deposited only to find out that
> the investigator's wedding photos were accidentally deposited instead.
>
My suggestion would be to give the images to (say) XDS: it would run
successfully on wedding photographs only in rare cases where the group
photograph was taken from a helicopter and the guests were arranged in very
peculiar ways ... .
> Validating that the images correspond to the claimed structure
> will be an enormous task; probably more difficult than coming up
> with enough hard drives to store them all.
>
Not necessarily, unless the crystalline specimen is very poor. In
ordinary cases, instead of comparing structure factor amplitudes or
intensities calculated from the deposited model to those in a file of
deposited values, one would run an integration program (or several of them)
on the images, check that cell parameters and space group agree, then run
TRUNCATE if amplitudes are desired, to get those observed values (up to some
re-indexing). For this to be possible automatically one would have to be
much stricter with the completeness and accuracy of the information in image
headers produced by various detectors, a step that I think many people would
welcome.
With best wishes,
Gerard.
> Dale Tronrud
>
> Frank von Delft wrote:
> > Gerard Bricogne wrote:
> >> Looking forward to the archiving of the REAL data ... i.e. the
> >> images.
> >> Using any other form of "data" is like having to eat out of someone
> >> else's
> >> dirty plate!
> >>
> > That may be so -- but if I'm hungry now, I just pop it in the sink -- I
> > don't publish a call for tenders on an industrial-scale dish-washer,
> > call up the architects and engineers to redesign the room, re-lay the
> > plumbing, vamp up my electricity transformer and install a new drainage
> > system.
> >
> > Which doesn't mean the industrial-scale washer isn't necessary; but
> > honestly, can't we start by just washing the plate??
> >
> > phx.
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