I think for questionable structures and those representing retracted paper, PDB should be able to ask the depositors for raw data and leave it for the community to decide if they still want to use the structure for science. If the depositors can't or would not submit the data, it should be clearly marked.
Debasish
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Mark Wilson
Sent: Wednesday, May 14, 2014 12:27 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone
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
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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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