Dear Pete,
Thank you for your comments on this topic. I think, however, that no
amount of format extension or sanity checking will ever replace the ultimate
sanity of depositing the images themselves. This would eliminate the many
error-prone steps in the current deposition of "structure factors" (itself a
misnomer, to start with!), as well as the loss of information that takes
place in data reduction through the limitations of the current software and
concepts involved in it. This topic has cropped up a number of times already
and the arguments in favour of it were again spelled out e.g. in the recent
paper by Joosten, Womack et al. (Acta Cryst. D65, 176-185). My feeling is
that it is this radical solution to diffraction data deposition that should
be given top priority. Any half-way house that would pin its hopes on more
massaging of reduced data would seem to me pure procrastination, as what is
accepted as "reduced" today will be seen as "massacred" tomorrow.
With best wishes,
Gerard.
--
On Fri, Mar 06, 2009 at 06:15:33PM -0600, Pete Meyer wrote:
> Well, either there haven't been any replies yet or my institution's
> email server is unhappy with me (if it's email problems, sorry if I'm
> duplicating other responses).
>
> > This instance leaves room for some concern about the verification of
> > deposited structure factors: what happened here is consistent with the
> > hypothesis that the standard-deviation field is ignored entirely, or at
> > least that no plausibility check is carried out on the values deposited in
> > it.
>
> My experience with re-calculating maps from deposited models and
> amplitudes, although non-systematic, leads me to believe that little or
> no checking is done on deposited amplitudes. In one instance, the
> listed resolution was off by a factor of 10 (listed as ~20 Angstroms for
> a ~2 Angstrom structure). In another, the data listed as amplitudes
> were actually intensities (at least, treating the data as intensities
> allowed me to reproduce the reported R-factor).
>
> My supposition is that part of the reason for the lack of checks on
> amplitude data is the lack of crystallography software that deals
> natively with cif formatted data. It would seem to make more sense to
> me to make changes on the PDB end (allowing deposition of data in mtz or
> cns format, converting to cif internally as needed for archiving) rather
> than on the data processing side; since this might allow for easier
> sanity checking.
>
> Pete
--
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