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 > diffractio n 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/pubme d/321558 91]. > > 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 th e > > or iginal 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 > > ------------------------------------------------------------------------------------- > > > > > >> 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
struc tures 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 dr awn from
HI
This is great news.
Can you let us at the PDB know the DOI's for each dataset so that we can associate the raw images with the PDB entry. We will be able to then show links to the raw images from PDB entry pages so that everyone can find them.
Many thanks
John
John Berrisford
PDBe
+44 1223 492529 (tel:+44%201223%20492529)
European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK (https://maps.google.com/?q=European%20Bioinformatics%20Institute%20(EMBL-EBI...)
https://www.pdbe.org
On Mar 27 2020, at 7:26 pm, Gerard Bricogne
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. > >> > >> ######################################################################## > >> > >> To unsubscribe from the CCP4BB list, click the following link: > >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > >> > >> To unsubscribe from the CCP4BB list, click the following link: > >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > > > > To unsubscribe from the CCP4BB list, click the following l ink: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1