I agree with Mark. The PDB should, at the very least, attach a warning label to entries like 2HR0, where the scientific community has overwhelmingly determined that the structure is invalid. In this case, I believe the author never admitted any wrongdoing, and perhaps PDB policy prevents removal of the entry without the depositing author's consent. I note that the PDB labels some structures associated with retracted papers as "obsoleted and superseded by NONE". For example, see 2qns and 2hlb.
Jack On May 14, 2014, at 12:06 PM, Tim Gruene wrote: > Hi Mark, > > I understand the discussion, yet as far as I understand the PDB does not > claim to be the authority to decide about the integrity of an entry (or > maybe better said, the PDB claims not to be this authority), and I find > it very honorable that the PDB have not abused their power. I don't mean > such an authority should not exist, but I think it is a good think it is > not the PDB. It is a form of separation of powers. > > Best, > Tim > > On 05/14/2014 06:47 PM, Mark Wilson wrote: >> Hi Tim, >> I agree with everything you've said about the importance of validation, >> but aren't we really talking about something different here? Users of >> structural information should of course be keeping a careful eye on >> validation reports. On the other hand, what possible reason is there for >> the PDB to continue to archive and offer for public use models whose >> fundamental integrity (rather than quality or reliability) are highly >> suspect? I hope that I'm not the only one who is frustrated that the page >> for 2HR0 is still available and unblemished by warnings. >> Best regards, >> Mark >> >> Mark A. Wilson >> Associate Professor >> Department of Biochemistry/Redox Biology Center >> University of Nebraska >> N118 Beadle Center >> 1901 Vine Street >> Lincoln, NE 68588 >> (402) 472-3626 >> mwilso...@unl.edu >> >> >> >> >> >> >> On 5/14/14 11:35 AM, "Tim Gruene" <t...@shelx.uni-ac.gwdg.de> wrote: >> >>> Dear Eric, >>> >>> On 05/14/2014 06:05 PM, Eric Williams wrote: >>>> [...] >>>> We seem to be at an impasse. The PDB won't evict highly suspect >>>> structure >>>> models unless journals retract them, and the journals in question have >>>> shown no indication of desiring to retract them. Is there anything that >>>> can >>>> be done? [...] >>>> >>>> What's the appropriate course of action for conscientious consumers of >>>> PDB >>>> data? Is there a way to petition journals to issue retractions? I wonder >>>> what the gents at Retraction Watch (http://retractionwatch.com) would >>>> recommend. >>>> >>>> Eric >>>> >>> >>> you can teach the consumers how to help themselves - you are welcome to >>> join my session MS-84 at the IUCr 2014 :-) because I believe that one of >>> the New Paradigms in Crystallography is the requirement to how to >>> correctly interpret crystallographic models, and validation is becoming >>> more and more important as subject. >>> >>> Best, >>> Tim >>> >>>> >>>> On Wed, May 14, 2014 at 10:04 AM, Bernhard Rupp >>>> >>>> <hofkristall...@gmail.com<https://mail.google.com/mail/?view=cm&fs=1&tf=1 >>>> &to=hofkristall...@gmail.com> >>>>> wrote: >>>> >>>>>> which structure ended up as number 100.000? >>>>> I guess that depends if we still count the Murthy corpses like 2a01 >>>>> This >>>>> 3-armed Swastika for example still does not come with a single warning >>>>> short of a poor quality report >>>>> http://www.ebi.ac.uk/pdbe-srv/view/entry/2a01/summary_details.html So, >>>>> sorry, 99990 (or lessŠ.) valid entries only at the time of >>>>> announcement. >>>>> >>>>> Cheers, BR >>>>> >>>>> >>>>> >>>>> Supplemental material: >>>>> >>>>> >>>>> >>>>> ³The PDB says it will remove the other ten structures only when >>>>> editors at >>>>> the journals in which they were originally published or the authors >>>>> themselves retract them² >>>>> >>>>> *http://www.nature.com/news/2009/091222/full/462970a.html >>>>> <http://www.nature.com/news/2009/091222/full/462970a.html>* >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> ³With the support of the structural-biology community, the mission of >>>>> the >>>>> wwPDB is to safeguard the integrity and improve the quality of the PDB >>>>> archive.² >>>>> >>>>> http://www.nature.com/nature/journal/v463/n7280/full/463425c.html >>>>> >>>>> >>>>> >>>>> Not to be overly cynical, but >>>>> >>>>> >>>>> >>>>> http://tinyurl.com/pmupalt >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> *From:* CCP4 bulletin board >>>>> [mailto:CCP4BB@JISCMAIL.AC.UK<https://mail.google.com/mail/?view=cm&fs=1 >>>>> &tf=1&to=CCP4BB@JISCMAIL.AC.UK>] >>>>> *On Behalf Of *mesters >>>>> *Sent:* Mittwoch, 14. Mai 2014 14:42 >>>>> *To:* >>>>> CCP4BB@JISCMAIL.AC.UK<https://mail.google.com/mail/?view=cm&fs=1&tf=1&to >>>>> =CCP4BB@JISCMAIL.AC.UK> >>>>> >>>>> *Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone >>>>> >>>>> >>>>> >>>>> Amazing, great! >>>>> >>>>> And, which structure ended up as number 100.000? >>>>> >>>>> - J. - >>>>> >>>>> >>>>> Am 14.05.14 10:42, schrieb battle: >>>>> >>>>> The Worldwide Protein Data Bank (wwPDB) organization is proud to >>>>> announce >>>>> that the Protein Data Bank archive now contains more than 100,000 >>>>> entries. >>>>> >>>>> Established in 1971, this central, public archive of >>>>> experimentally-determined protein and nucleic acid structures has >>>>> reached a >>>>> critical milestone thanks to the efforts of structural biologists >>>>> throughout the world. >>>>> >>>>> Read the full story at: >>>>> http://www.wwpdb.org/news/news_2014.html#13-May-2014 >>>>> >>>>> -- >>>>> Gary Battle >>>>> on behalf on the wwPDB >>>>> >>>>> >>>>> >>>>> -- >>>>> Dr. Jeroen R. Mesters >>>>> Deputy, Senior Researcher & Lecturer >>>>> >>>>> Institute of Biochemistry, University of Lübeck >>>>> Ratzeburger Allee 160, 23538 Lübeck, Germany >>>>> >>>>> phone: +49-451-5004065 (secretariate 5004061) >>>>> fax: +49-451-5004068 >>>>> >>>>> http://www.biochem.uni-luebeck.de <Http://www.biochem.uni-luebeck.de> >>>>> http://www.iobcr.org <Http://www.iobcr.org> >>>>> >>>>> >>>>> -- >>>>> If you can look into the seeds of time and tell which grain will grow >>>>> and >>>>> which will not, speak then to me who neither beg nor fear >>>>> (Shakespeare's >>>>> Macbeth, Act I, Scene 3) >>>>> -- >>>>> >>>>> >>>>> >>>>> >>>>> *Disclaimer * This message contains confidential information and is >>>>> intended only for the individual named. If you are not the named >>>>> addressee >>>>> you should not disseminate, distribute or copy this e-mail. Please >>>>> notify >>>>> the sender immediately by e-mail if you have received this e-mail by >>>>> mistake and delete this e-mail from your system. * E-mail transmission >>>>> cannot be guaranteed to be secure or error-free as information could be >>>>> intercepted, corrupted, lost, destroyed, arrive late or incomplete, or >>>>> contain viruses. The sender therefore does not accept liability for any >>>>> errors or omissions in the contents of this message, which arise as a >>>>> result of e-mail transmission. If verification is required please >>>>> request a >>>>> hard-copy version. Please send us by fax any message containing >>>>> deadlines >>>>> as incoming e-mails are not screened for response deadlines. * >>>>> Employees of >>>>> the Institute are expressly required not to make defamatory statements >>>>> and >>>>> not to infringe or authorize any infringement of copyright or any other >>>>> legal right by email communications. Any such communication is >>>>> contrary to >>>>> Institute policy and outside the scope of the employment of the >>>>> individual >>>>> concerned. The Institute will not accept any liability in respect of >>>>> such >>>>> communication, and the employee responsible will be personally liable >>>>> for >>>>> any damages or other liability arising. Employees who receive such an >>>>> email >>>>> must notify their supervisor immediately. *-- >>>>> >>>> >>> >>> -- >>> Dr Tim Gruene >>> Institut fuer anorganische Chemie >>> Tammannstr. 4 >>> D-37077 Goettingen >>> >>> GPG Key ID = A46BEE1A >>> >> > > -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A >
