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
[log in to unmask]
On 5/14/14 11:35 AM, "Tim Gruene" <[log in to unmask]> 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
>>
>><[log in to unmask]<https://mail.google.com/mail/?view=cm&fs=1&tf=1
>>&[log in to unmask]>
>>> 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 less.) 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:[log in to unmask]<https://mail.google.com/mail/?view=cm&fs=1
>>>&tf=1&[log in to unmask]>]
>>> *On Behalf Of *mesters
>>> *Sent:* Mittwoch, 14. Mai 2014 14:42
>>> *To:*
>>>[log in to unmask]<https://mail.google.com/mail/?view=cm&fs=1&tf=1&to
>>>[log in to unmask]>
>>>
>>> *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)
>>> --
>>>
>>>
>>>
>>>
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>>
>
>--
>Dr Tim Gruene
>Institut fuer anorganische Chemie
>Tammannstr. 4
>D-37077 Goettingen
>
>GPG Key ID = A46BEE1A
>
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