For those of you who are in touch with these data, would deposition of unmerged intensities in P1 in the whole detector range instead of complete dataset be good enough to „correctly“ re-evaluete the structure? Or is there a doubt that even this approach would not lead to optimal structure?
My personal opinion is that storage of raw data is not a green way of science. I believe that in 50 years (not my bussines in these time), the storage and maintaining of the data we acquire in these times may take a whole capacity of one powerplant. Not talking about the material consumption. In some cases, re-doing of the complete thing may after all be less damaging the environment than storage of whole bunch of data that are irrelevant because of the perfect work that has been done previously and does not need re-evaluation. Is there a way to improve the (diffraction data vs. structure) validation tools? I know, science cannot be a green technology. But some limitations should be considered, at least. Of course, I may be absolutely wrong. A good question now could be, is there something else that the community could do for accelerating the research of SARS-CoV-2? May be, some people could offer their spare time to help the others with someting? Best regards, Petr From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Andreas Förster Sent: Thursday, March 19, 2020 7:07 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures 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<http://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<mailto: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<http://data.sbgrid.org>, zenodo.org<http://zenodo.org>, proteindiffraction.org<http://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 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
