Dear Gerard
Isolating your main points:
but there would have been no PDB-REDO because the
data for running it would simply not have been available! ;-) . Or
do you
think the parallel does not apply?
...
have thought, some value. From the perspective of your message,
then, why
are the benefits of PDB-REDO so unique that PDB-REPROCESS would have
no
chance of measuring up to them?
I was thinking of the inconsistency while sending my previous
email ... ;-)
Basically, the parallel does apply. PDB-REPROCESS in a few years would
be really fantastic - speaking as a crystallographer and methods
developer.
Speaking as a structural biologist though, I did think long and hard
about
the usefulness of PDB_REDO. I obviously decided its useful since I am
now
heavily involved in it for a few reasons, like uniformity of final
model treatment,
improving refinement software, better statistics on structure quality
metrics,
and of course seeing if the new models will change our understanding of
the biology of the system.
An experiment that I would like to do as a structural biologist - is
the following:
What about adding an "increasing noise" model to the Fobs's of a few
datasets and re-refining?
How much would that noise change the final model quality metrics and
in absolute terms?
(for the changes that PDB_RE(BUILD) does have a preview at
http://www.ncbi.nlm.nih.gov/pubmed/22034521
....I tried to avoid the shamelessly self-promoting plug-in, but could
resists at the end!)
That experiment - or a better designed variant for it ? - would maybe
tell us if we should be advocating the archive of all images,
and being scientifically convinced of the importance of that beyond
methods development, we would all argue a strong case
to the funding and hosting agencies.
Tassos
PS Of course, that does not negate the all-important argument, that
when struggling with marginal
data better processing software is essential. There is a clear need
for better software
to process images, especially for low resolution and low signal/noise
cases.
Since that is dependent on having test data I am all for supporting an
initiative to collect such data,
and I would gladly spend a day digging our archives to contribute.
