On 19 Mar 2020, at 11:32, Kroon-Batenburg, L.M.J. (Loes)
<l.m.j.kroon-batenb...@uu.nl> wrote:
Dear Gerard,
This is a great idea. Of course I am very much in favour of making
available raw diffraction images, and such a virtual workshop could
demonstrate the usefulness of reprocessing raw diffraction data and
structural refinements. I am not at all afraid that archiving of raw
data that are the basis of a scientific paper will have significant
environmental effects: this is minor compared to our everyday use of
cloud services. And as Graeme mentioned: when archiving raw data
make sure to add sufficient and correct meta data.
Best wishes,
Loes
___________________________________________________________
Dr. Loes Kroon-Batenburg
Dept. of Crystal and Structural Chemistry
Bijvoet Center for Biomolecular Research
Utrecht University
Padualaan 8, 3584 CH Utrecht
The Netherlands
E-mail : l.m.j.kroon-batenb...@uu.nl
phone : +31-30-2532865
fax : +31-30-2533940
Van: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> namens Gerard
Bricogne <g...@globalphasing.com>
Verzonden: woensdag 18 maart 2020 23:30
Aan: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
Onderwerp: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures
Dear colleagues,
Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease
structures in the PDB seems to indicate that that there might be potential
to improve these if refinements could be repeated after some reprocessing
and further analysis of the raw diffraction images, rather than
against the
deposited merged data. This statement should in no way be construed
as a
criticism of the remarkable achievements of the research groups concerned,
who have been operating under tremendous time pressure, but as an exciting
opportunity to push methods to their limits on a uniquely significant class
of structures.
Another consideration is that the various logistical problems created by
COVID-19 may soon make it increasingly difficult to collect new diffraction
data on potential drug targets relevant to the fight against SARS-CoV-2,
underlining the importance of ensuring that the best results be obtained
from every dataset actually collected, and that the most useful conclusions
be drawn from the analysis of those datasets towards improving the quality
of subsequent data collections.
On this basis we would like to propose that special efforts be made
to grant
public access to the raw image data associated with any SARS-CoV-2 related
structure that is deposited into the PDB. This can be done by (1) archiving
these raw image data using resources such as data.sbgrid.org, zenodo.org,
proteindiffraction.org or any other cloud-based data-sharing service, and
(2) communicating the corresponding DOIs to the wwPDB centres. This idea
could be extended to datasets that investigators would like to offer to
interested methods developers or expert users at the pre-deposition stage.
Experts making use of those raw data would be encouraged to document,
in as
much detail as possible, how particular programs or workflows could
be used
on those structures/datasets to obtain the best results. This would
be a
kind of "virtual workshop", a particularly valuable collective
activity at
the present time when several in-person workshops (e.g. RapiData)
have been
cancelled and many meetings are in limbo for several months.
The latter activity would benefit from having a centralised facility
set up
for the experts to post their results and annotations: we could
create such
a facility, but other, larger groups might want to consider doing so.
With best wishes,
Clemens & Gerard.
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