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: rj...@cam.ac.uk 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 <msv...@ibmb.csic.es> >> Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication >> To: pr...@uchicago.edu >> Cc: CCP4BB@jiscmail.ac.uk >> >> 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 >> <pr...@uchicago.edu> 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 <CCP4BB@JISCMAIL.AC.UK> >> (on behalf of "Bernhard Rupp (Hofkristallrat >> a.D.)" <hofkristall...@gmail.com>) >>> Subject: Re: [ccp4bb] very informative - Trends >> in Data Fabrication >>> To: CCP4BB@JISCMAIL.AC.UK >>> >>> 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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of >> Bernhard >>> Rupp (Hofkristallrat a.D.) >>> Sent: Sunday, April 01, 2012 06:06 >>> To: CCP4BB@JISCMAIL.AC.UK >>> 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 >>> hofkristall...@gmail.com >>> b...@hofkristallamt.org >>> 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: maria.s...@ibmb.csic.es
