Hi Tim,
Getting to Eric's point about an impasse, if the PDB will not claim the
authority to safeguard the integrity of their holdings (as per their
quoted statement in Bernhard's message below), then who can? I understand
that there are many potential complications to the PDB claiming some
plenary authority to prune out structures that they don't like for
whatever reason and agree that they should not claim such authority.
Furthermore, I sympathize with the difficult situation that the curators
must confront in the (hopefully) very rare cases of models whose integrity
is suspect. However, dealing with these in some manner surely falls
squarely within a mission "to safeguard the integrity and improve the
quality of the PDB archive." Strict neutrality on the part of the PDB in
these cases is not working well in my opinion, as evidenced by the absence
of any indication of the dark history of 2HR0 on its PDB page. There are
many possible ways of indicating something is seriously amiss with these
entries, and I wish that the community wasn't in the position of having
PDB entries that some users know are deeply suspect but that other, less
informed users do not.
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 12:06 PM, "Tim Gruene" <[log in to unmask]> 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
>> [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 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:[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)
>>>>> --
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> *Disclaimer * This message contains confidential information and is
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>>>>> Employees of
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>>>>
>>>
>>> --
>>> 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
>
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