Dear Phoebe,
As it happens, validation through the PDB is exactly what the X-ray Validation Task Force proposed (to be honest, it was a suggestion made by George Sheldrick the last time there was a debate like this on the CCP4-BB!), and the wwPDB is currently implementing the pipeline needed to automatically produce a good validation report. A preliminary version of such a report is already available when you deposit a structure now, the IUCr journals already require this for papers describing structures, and there seems to be interest from some other journals. In the meantime, if you're refereeing a paper from a journal that doesn't require the validation report to be submitted with the paper, you can always ask them to get it from the author.
Best wishes,
Randy
-----
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills Road E-mail: [log in to unmask]
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
On 2 Apr 2012, at 20:01, Phoebe Rice wrote:
> That's very sad, but a good point. I may be a bit naive because I haven't had to worry mas uch about direct competition.
>
> However, I do find it very frustrating as a reviewer to try to pass judgement on a crystal structure based only on the standard table 1. Sometimes I'm tempted to write "based on the information presented, darned if I know!"
>
> Maybe 3rd-party validation through the pdb (with a report sent to the reviewers) is more appropriate?
>
> Phoebe
>
> =====================================
> Phoebe A. Rice
> Dept. of Biochemistry & Molecular Biology
> The University of Chicago
> phone 773 834 1723
> http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
> http://www.rsc.org/shop/books/2008/9780854042722.asp
>
>
> ---- Original message ----
>> Date: Mon, 2 Apr 2012 20:00:48 +0200
>> From: Maria Sola i Vilarrubias <[log in to unmask]>
>> Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication
>> To: [log in to unmask]
>> Cc: [log in to unmask]
>>
>> Dear Phoebe,
>>
>> I cannot imagine myself delivering maps and
>> coordinates (after years of work... I insist: after
>> years of work) to a reviewer that could be, for
>> whatever chance, my best competitor (even if I
>> suggested to the editor not to include him/her as a
>> reviewer... but decisions from editors are of all
>> kind).
>>
>> I simply prefer not imagine this after two
>> publications fuelled by clear, direct and strong
>> competition. That was stressful enough, already. If
>> I have to add to this stress the thought that my
>> coordinates can go to the "wrong" hands, then I
>> think I would just give up or, alternatively, send
>> the work to a lower impact, fast-publishing journal
>> and make my life easier while sending my scientific
>> future to the low-impact bin, killing future
>> opportunities.
>>
>> Competition is there. I see that data to be
>> deposited is strictly confidential. I support the
>> PDB to make the quality check work at the level you
>> mention, but not a reviewer: People are nice but
>> the world is big and competition is crazy… at
>> least enough to make fraud or copy other's work. The
>> latter is less difficult; by copying ("simply copy
>> and paste to my computer this nice structure that I
>> was looking for!"), there is no need to invent
>> anything.
>>
>> About a wrongly fit compound, the reviewer can ask
>> images about the model in a map calculated at a
>> specific sigma and in different orientations.
>>
>> Maria
>>
>> On 2 April 2012 18:43, Phoebe Rice
>> <[log in to unmask]> wrote:
>>
>> Can we leverage this to push journals to routinely
>> allow reviewers access coordinates and maps?
>>
>> Outright fraud is outrageous, but I'm actually
>> more worried about ligands fit to marginal density
>> and other issues of under-supervised model
>> building.
>>
>> =====================================
>> Phoebe A. Rice
>> Dept. of Biochemistry & Molecular Biology
>> The University of Chicago
>> phone 773 834 1723
>> http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
>> http://www.rsc.org/shop/books/2008/9780854042722.asp
>>
>> ---- Original message ----
>>> Date: Mon, 2 Apr 2012 08:41:02 -0700
>>> From: CCP4 bulletin board <[log in to unmask]>
>> (on behalf of "Bernhard Rupp (Hofkristallrat
>> a.D.)" <[log in to unmask]>)
>>> Subject: Re: [ccp4bb] very informative - Trends
>> in Data Fabrication
>>> To: [log in to unmask]
>>>
>>> Robbie has restored the PDB_REDO of 3k78
>>>
>>>
>>>
>>> It is at
>> www.cmbi.ru.nl/pdb_redo/others/3k78.tar.bz2
>>>
>>>
>>>
>>> and Louise Jones form the IUCr office has
>> kindly
>>> made the article open access.
>>>
>>>
>>>
>>>
>> http://journals.iucr.org/f/issues/2012/04/00/issconts.html
>>>
>>>
>>>
>>> BR
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> From: CCP4 bulletin board
>>> [mailto:[log in to unmask]] On Behalf Of
>> Bernhard
>>> Rupp (Hofkristallrat a.D.)
>>> Sent: Sunday, April 01, 2012 06:06
>>> To: [log in to unmask]
>>> Subject: Re: [ccp4bb] very informative -
>> Trends in
>>> Data Fabrication
>>>
>>>
>>>
>>> >Hofkristallrat auA*er Dienst, is
>> written as
>>> Bernhard - unless you are referring to some
>> other
>>> guy with a french name Bernard.
>>>
>>>
>>>
>>> As one may extrapolate given my recent paper,
>> I have
>>> been called names a lot worse....
>>>
>>>
>>>
>>> A* And the book indeed is a bible of
>> xtallography.
>>>
>>>
>>>
>>> Enough of this - it is becoming embarrassing.
>> I wish
>>> I had done a more careful job proofing, as
>> over 500
>>> errata attest to,
>>>
>>> and we all are only seeing further because we
>> are
>>> standing on the shoulders of giants. So once
>> again
>>> thanks
>>>
>>> to all the contributors I have pestered with
>> my
>>> questions on BB and then some, and to all
>> those who
>>> actually read BMC and
>>>
>>> submitted errata.
>>>
>>>
>>>
>>> Best regards, BR
>>>
>>>
>> -----------------------------------------------------------------
>>> Bernhard Hieronimus Rupp, Hofkristallrat a.D.
>>> 001 (925) 209-7429
>>> +43 (676) 571-0536
>>> [log in to unmask]
>>> [log in to unmask]
>>> http://www.ruppweb.org/
>>>
>> ------------------------------------------------------------------
>>> Once the sun of science is standing low, even
>> dwarfs
>>> cast tall shadows
>>>
>> ------------------------------------------------------------------
>>>
>>>
>>>
>>>
>>
>> --
>> Maria Solà
>> Dep. Structural Biology
>> IBMB-CSIC
>> Baldiri Reixach 10-12
>> 08028 BARCELONA
>> Spain
>> Tel: (+34) 93 403 4950
>> Fax: (+34) 93 403 4979
>> e-mail: [log in to unmask]
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