As someone who's done this (for one structure of minor significance), I would like to make a few comments:
- I highly encourage deposition of raw data. Why would you not? Now that many labs are shut is the time to do it for all these datasets hiding somewhere on abandoned hard disk. These disks will break. One hopes Zenodo will not. - The link to the raw data can be found inside the mmCIF file under _pdbx_related_exp_data_set.data_reference. Whether it's also shown on one of the PDB sites is up to the designers of these sides. I cannot find a link to the experimental data on rcsb.org. PDBe, in contrast, has a clearly visible box linking to "Experimental raw data" on the start page of the structure. Deposit your raw data! Andreas On Wed, Mar 18, 2020 at 11:31 PM Gerard Bricogne <g...@globalphasing.com> wrote: > 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. > > ######################################################################## > > 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
