Dear Jacob This is an interesting prospect - in effect you are suggesting (not unreasonably, perhaps?) that PDB-REDO is more reliable as a reviewer than the reviewers, under some circumstances.
Possibly the approach I would take with this one would be to highlight that PDB-REDO or other software tools found results which are inconsistent with the model as published, and highlight these (rather than the "red flag" which would suggest that these results are *wrong*) and perhaps post the result to the wiki which is under discussion - to make it easy for any user of that structure to check. Clearly what would be *really* nice would be to be able to rerun the processing from the original data, rerun the refinement with PDB-REDO and verify that the given answer is consistent with the claims made by the authors, and if not try to work out why. It's much easier to check and answer is right than it is to discover the answer in the first place... however I appreciate that there are many problems with this suggestion... Cheerio Graeme -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keller, Jacob Sent: 21 January 2016 21:57 To: ccp4bb Subject: Re: [ccp4bb] questionable structures Maybe there could be a red flag in the pdb when PDB-REDO says something dramatically different? I.e., when you go to a structure with something strange about it, and PDB-REDO has identified it, there could be a link or pop-up describing the nature of the issue. Could be a lot of things, including perhaps cases in which the Rfree in PDB-REDO is significantly better than the deposited structure, or in which a ligand has been cast into doubt, or in which the bulk solvent seems really really strange, etc. JPK -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kay Diederichs Sent: Thursday, January 21, 2016 4:39 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] questionable structures Emily, I think the community should just start to use what's available - new journals are not needed. People can accumulate the knowledge e.g. in Proteopedia which is a Wiki that collects information about PDB entries - see e.g. http://www.proteopedia.org/wiki/index.php/2hr0 . The PDB could link there. Second, I think that PDB_REDO could take an extended role as a repository of re-refined structures, with those wrong/dubious parts (e.g. ligands) removed and appropriately flagged. Processing of entries could be enhanced by leaving out each ligand in turn and only add it back if the density supports it. Needs some work, of course - but we are in the lucky situation that our data are so information-rich that they would support such an endeavor. Just my 2 cents. Kay On Thu, 21 Jan 2016 13:44:58 -0500, Emilia C. Arturo (Emily) <ecgart...@gmail.com> wrote: >It seems to me that there needs to be a centralized agency (that is, an >agency unaffiliated with any one publisher) that collects and vets >reports of questionable structures, rather than relegate these reports >to the hard-to-stumble-upon discussions (like the ones linked in this >thread) that are managed exclusively by the journal involved, and >involve a likely already over-taxed individual who plays the >moonlighting role of journal editor. > >What if, for example, it was the wwPDB itself that served as a >repository for these complaints? The wwPDB would collect and vet the >populace's reports of questionable structures, and make this collection >available online. Over time, there may emerge an infrastructure (easier >done because it is the wwPDB) whereby the report filed therein becomes >dynamically, digitally linked with not only the PDB id of the flagged >model, but also the publication that is associated with that PDB id. > >This sort of setup would not deal directly with what publishers >ultimately do with the original publication of the bad/incorrect model, >but it will do precisely what all these whistle-blowers ultimately >intend, which is to help keep a poor/wrong model of a protein's >structure from informing future scientific and medical endeavors; >viewers of the flagged PDB models could make a much more informed >decision based on the model and its publication. > >This sounds like the proposal of a whole new journal, which isn't >trivial, I realize. Has this ever been proposed? Is it too idealistic >or otherwise impractical? > >Emily. > >On Thu, Jan 21, 2016 at 11:56 AM, Patrick Loll <pat.l...@drexel.edu> wrote: >> Bernhard is absolutely right. The urge is definitely noble, but also >> quixotic, and reality has a way of bashing the quixotic. We once stumbled on >> a purported protein-ligand structure, for which the evidence for ligand >> binding was simply nonexistent. I spent many, many hours over the course of >> several years going back and forth with the authors, and then the editors >> (the journal, which will remain nameless, is part of the high-profile stable >> of journals beginning with the word N****e). At first, everyone paid lip >> service to idea of fixing the problem, but eventually it became evident that >> no one was incentivized (as they say) to actually do so. In the end, nothing >> changed (except perhaps my disposition, which used to be all sweetness and >> light. Really). >> >> Pat >> >>> On 21 Jan 2016, at 11:15 AM, Bernhard Rupp (Hofkristallrat a.D.) >>> <hofkristall...@gmail.com> wrote: >>> >>> Ø The overall improvement of the public resource that is the PDB >>> takes precedence over anything else…. I might be moved to write this >>> up in a letter to the editor of the journal >>> >>> This is an exceptionally noble thought that gets routinely clobbered by >>> reality. Recent example: >>> >>> http://www.jimmunol.org/content/196/2/530.2.short >>> >>> Follow the comments, replies, and final editorial perception of this >>> disaster as a ‘lively debate’ >>> >>> No retraction, no PDB update, no consequences for peptide models >>> whose geometry precludes their existence, and which are not supported by >>> density. >>> >>> Paul Feyerabend was right, after all. Anything goes. >>> >>> Cheers, BR >> >> >> >> --------------------------------------------------------------------- >> ------------------ >> Patrick J. Loll, Ph. D. >> Professor of Biochemistry & Molecular Biology Director, Biochemistry >> Graduate Program Drexel University College of Medicine Room 10-102 >> New College Building >> 245 N. 15th St., Mailstop 497 >> Philadelphia, PA 19102-1192 USA >> >> (215) 762-7706 >> pat.l...@drexelmed.edu > > > >-- >"Study as if you were going to live forever; live as if you were going >to die tomorrow." - Maria Mitchell > >"Success is going from failure to failure without losing your >enthusiasm." - Anon. > >“We are the people we have been waiting for.” >- A tag line from MIT's Vehicle Design Summit website >(http://vds.mit.edu) -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. 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