I vote for Z's idea
On Wed, May 14, 2014 at 12:32 PM, Zachary Wood <z...@bmb.uga.edu> wrote: > Hello All, > > Instead of placing the additional burden of policing on the good people at > the PDB, perhaps the entry page for each structure could contain a comments > section. Then the community could point out serious concerns for the less > informed users. At least that will give users some warning in the case of > particularly worrisome structures. The authors of course could still reply > to defend their structure, and it may encourage some people to even correct > their errors. > > Best regards, > > Z > > > *********************************************** > Zachary A. Wood, Ph.D. > Associate Professor > Department of Biochemistry & Molecular Biology > University of Georgia > Life Sciences Building, Rm A426B > 120 Green Street > Athens, GA 30602-7229 > Office: 706-583-0304 > Lab: 706-583-0303 > FAX: 706-542-1738 > *********************************************** > > > > > > > > On May 14, 2014, at 12:47 PM, Mark Wilson <mwilso...@unl.edu> 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 > > > >
