New subject: Raw diffraction images for SARS-CoV-2 related structures

27 Mar 2020

      Dear all,

     It is a pleasure to be able to end the (GMT) week by calling for a huge
round of applause for the Diamond team, who this afternoon started uploading
a large collection of sets of raw diffraction images (77 as we write but the
upload is still ongoing) for PDB entries that were released two days ago.

     Special thanks to Graeme Winter who organised the upload to Zenodo. The
datasets are collectively accessible via the following link:

https://zenodo.org/search?page=1&size=20&q=keywords:%22SARS-CoV-2%20main%20protease%22

     Graeme asked that "major kudos [be given] to Zenodo developers who have
been very responsive with helping us do automated downloads".

     Happy scrutiny and reprocessing of these datasets, and re-refinement of
the associated structures, to all hard-core MX addicts!

     With best wishes,

     Clemens & Gerard.

--
On Thu, Mar 19, 2020 at 10:00:11AM +0000, John Berrisford wrote:
...
Dear all
The wwPDB OneDep system allows depositors to provide DOIs of raw
diffraction images during deposition to the PDB and once again
encourages depositors to provide a DOI for raw images when they have
submitted.
Out of the 9665 X-ray entries that were released in 2019 we have DOI's
for raw images in 205 of these entries.
We would encourage depositors to provide the DOI for their raw images
when they are available.
Regards
John
On Mar 19 2020, at 9:48 am, Joel Sussman  wrote:
...
19-Mar-2020
Dear Loes, Peter, Clemens & Gerard,
I concur that it is crucial to preserve the original diffraction data
and make it available to anyone who would like to use it.
As an example, please see the very recent paper by 
Nachon et al (2020). "A second look at the crystal structures of
Drosophila melanogaster acetylcholinesterase in complex with tacrine
derivatives provides Insights concerning catalytic intermediates and
the design of specific insecticides" Molecules 25 pii: E1198 
[https://www.ncbi.nlm.nih.gov/pubmed/32155891].
The study reexamines the original data, with modern software tools,
the original data of a paper we published in 2000 (~20 years ago) and
revealed features that had not been noticed. Specifically 
1) previously unmodeled density in the native active site can be
interpreted as stable acetylation of the catalytic serine. 
2) Similarly, a strong density in the DmAChE/ZA complex, originally
attributed to a sulfate ion, is better interpreted as a small molecule
that is covalently bound. The complex is reminiscent of the
carboxylate/BChE complexes observed in crystal structures of hBChE
[Brazzolotto et al, 2012; Nicolet et al, 2003], and demonstrates the
remarkable ability of ChEs to stabilize covalent complexes with carboxylates.
Thus, the study demonstrates that updated processing of older
diffraction images, and the re-refinement of older diffraction data,
can produce valuable information that could not be detected in the
original analysis, and strongly supports the preservation of the
diffraction images in public data banks.
Best regards
Joel
------------------------------------------------------------------------------------
Prof. Joel L. Sussman.        [email protected]   www.weizmann.ac.il/~joel
Dept. of Structural Biology   tel: +972  (8) 934 6309       proteopedia.org
Weizmann Institute of Science fax: +972  (8) 934 6312
Rehovot 76100 ISRAEL          mob: +972 (50) 510 9600
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...
On 19 Mar 2020, at 11:32, Kroon-Batenburg, L.M.J. (Loes)
 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 : [email protected]
phone  : +31-30-2532865
fax    : +31-30-2533940
Van: CCP4 bulletin board  namens Gerard
Bricogne 
Verzonden: woensdag 18 maart 2020 23:30
Aan: [email protected] 
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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Raw diffraction images for SARS-CoV-2 related structures

Gerard Bricogne

John Berrisford

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