Frankly this is a great idea for datasets on any projects. I've been so busy the last 3-4 years that I have been unable to do it for my projects, but now I should be able to get it done. Not to mention trying to solve a couple of those pesky structures that have proven tough nuts to crack.
Diana ************************************************** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816 diana.tomch...@utsouthwestern.edu (214) 645-6383 (phone) (214) 645-6353 (fax) ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Eleanor Dodson <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> Sent: Wednesday, March 18, 2020 5:33 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures EXTERNAL MAIL What a great idea? Have you approached the depositors? Eleanor On Wed, 18 Mar 2020 at 22:31, 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 CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying. ________________________________ UT Southwestern Medical Center The future of medicine, today. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
