> I wouldn't claim 99.99% are honest reviewers (that would only be one black > sheep out of 10000 crystallographers). Similarly to sexual orientation, honesty is not a two-state phenomenon, but the one that varies from 0 to 100%. So, it is likely that a higher percentage of referees (than 0.01%) would find it acceptable to hurt a competitor by giving his/her work an unfavorable review, but stealing is too much of a sin, and 99.99% of reviewers may find it unacceptable. In other words, when a reviewer asks me to provide the coordinates, I sleep easier, because if he intended to beat me, he would not leave the fingerprints...
Alex On Apr 19, 2012, at 12:34 PM, Bosch, Juergen wrote: > To pick a bit on George's point with MR & citation. > > Here's how you can read it in the paper from your favourite competitor: > > A homology model was generated using [fill in any program for ab initio > prediction] and subsequently used for molecular replacement with Molrep. The > structure was refined to an Rwork of 21% and Rfree of 24 %. > > Where was the citation to the real structure I grabbed of the PDB from my > competitor ? Did I need to cite it ? Well when we were working on this there > was no structure in the PDB (another lie) so we generated a homology model as > our SeMet and HA soaking experiments failed [add more blabla]. > > I wouldn't claim 99.99% are honest reviewers (that would only be one black > sheep out of 10000 crystallographers). > > And the problem would really be to demonstrate you were right and the person > who rejected your paper scooped you because (s)he had an advantage of you > making all the effort of writing the paper and even providing an excellent > model for MR. > > It's a though decision to make and it surely depends on your career path. One > could make a phase diagram showing career path versus likelihood of > pre-release of a structure and find the sweet spot where it doesn't matter > anymore to you if it's released or not. > > I'm definitely not at that point were I feel comfortable releasing a > structure before publication. However I deposit before submitting the paper > and as soon as the paper is accepted I tell the PDB to release the > coordinates and structure factors as soon as possible - typically 10-14 days. > > I hope by providing the key data points from the validation that reviewers > are convinced the structure is actually good. If Molprobity shows all green I > guess you did pretty well. Plus if you are in the top few percentiles for the > range of structures deposited with a comparable resolution as yours no > Ramachadran outliers, good R factors etc. > > Anyhow, just my 2 cents > > Jürgen > > > On Apr 19, 2012, at 9:55 AM, George M. Sheldrick wrote: > >> Colin, >> >> Speaking as someone who has one foot in small molecule crystallography >> and the other in macromolecular, I have to say that attitudes are >> completely different, and that there are good reasons for this. A PhD >> student or junior postdoc in a macromolecular lab may have spent the >> last three (or more) years cloning, expressing. purifying and >> crystallizing a protein, and it is very likely that three or more groups >> elsewhere in the world are working on the same target. Even if the >> organisms are different, usually only one group will be able to publish >> in a high-profile journal, so being scooped is a major worry and happens >> frequently, even when all concerned are completely honest. A single >> small molecule structure is a very much smaller part of the average >> chemical PhD which often involves dozens of structures, and a couple of >> duplicated structures will have little influence on the future career of >> the PhD student. >> >> Releasing the PDB hold on a structure just before submitting the paper >> has something to be said for it. I would like to do this more often, but >> it is usually vetoed by paranoid biological co-authors. Even if one is >> providing the competition with a good MR model, at least they will have >> to cite it. >> >> George >> >> On 04/19/2012 03:09 PM, Colin Groom wrote: >>> It has always struck me as something of a surprise that pre-publication >>> review of structures in protein-land >> differs so significantly from small molecule-land. One of the activities >> of the CCDC is to supply pre-release >> CSD structures to referees, using a simple, automated system to >> establish that the requestors are referees. >> This avoids the need for any involvement of the depositor or journal and >> allows a centralised record to be kept >> as to who saw which structures and when (although, to my knowledge, we >> have never needed to refer to this). >> In 2012, requests have averaged at about 5 a day, but the real figure >> is probably much higher, as some journals >> provide this facility themselves. The sense I get from the >> small-molecule community is that they (we) have a >> great degree of well placed trust and see real value in pre-publication >> review of structures, not just papers - >> I'm sure this is true for the overwhelming majority of the >> macromolecular world too. >>> >>> Colin >>> >>> -----Original Message----- >>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of >>> herman.schreu...@sanofi.com >>> Sent: 19 April 2012 13:54 >>> To: CCP4BB@JISCMAIL.AC.UK >>> Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers >>> >>> This is off course a valid point. A desperate graduate student faking a >>> structure risks his or hers career and reputation, while an anonymous >>> referee, "borrowing" someone else's results gets away without any risk >>> of being caught. Besides making the name of the reviewer public, I see >>> other options: >>> >>> 1) submit the coordinates and structure factors to the pdb to get a >>> priority date as has been suggested before. Many journals require >>> anyways a pdb code before acceptance of the paper. One could even >>> publish this priority date in the paper in the footnote where the pdb >>> code is mentioned. >>> 2) require from referees a conflict-of-interest-statement that they, or >>> close colleagues are not working on the same or a very similar >>> structure. If an author gets the impression that he may have been >>> scooped by a less-ethical referee, he could ask the journal to verify >>> that the referees of his rejected paper were not involved in the >>> accelerated publication. If it turns out that a referee has made a false >>> statement this would clearly constitute fraud and a reason for >>> repercussions. >>> >>> Herman >>> >>> >>> -----Original Message----- >>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of >>> Jobichen Chacko >>> Sent: Thursday, April 19, 2012 2:12 PM >>> To: CCP4BB@JISCMAIL.AC.UK >>> Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers >>> >>> Dear All, >>> Here comes the problem of blind reveiw, the authors are always at the >>> receving end to share all there data, results and now the full >>> cordinates to an unknown person, just trusting the journal editor. Why >>> don't the journals think about making the name of the reviewer also >>> public. >>> >>> Eventhough the persons advocated giving the cordinates, there were cases >>> of holding the paper for reveiw for few months and finally rejecting it, >>> while a very close article appeared as accelerated publn within few >>> weeks of rejection of the original paper. Refer to the previous >>> discussion on fake structure. >>> >>> Again it depends on how close you are towards the acceptance. Also >>> hesitation to give away your cordiantes without any guarantee of >>> publishing it in that journal cannot be considered as a big sin, >>> especially if someone's graduation is depend on a single paper. >>> >>> Jobi >>> >>> >>> >>> On Thu, Apr 19, 2012 at 6:34 AM, Marc Kvansakul >>> <m.kvansa...@latrobe.edu.au> wrote: >>>> Dear CCP4BBlers, >>>> >>>> I was wondering how common it is that reviewers request to have a copy >>> >>>> of the PDB coordinate file for the review purpose. I have just been >>>> asked to supply this by an editor after several weeks of review, after >>> >>>> one of the reviewers requested a copy. >>>> >>>> Not having ever been asked to do this before I feel just a tad >>>> uncomfortable about handing this over... >>>> >>>> Your opinions would be greatly appreciated. >>>> >>>> Best wishes >>>> >>>> Marc >>>> >>>> Dr. Marc Kvansakul >>>> Laboratory Head, NHMRC CDA Fellow >>>> Dept. of Biochemistry| La Trobe University | Bundoora Rm 218, Phys Sci >>> >>>> Bld 4, Kingsbury Drive, Melbourne, 3086, Australia >>>> T: 03 9479 2263 | F: 03 9479 2467 | E: m.kvansa...@latrobe.edu.au | >>>> >>> >>> LEGAL NOTICE >>> Unless expressly stated otherwise, information contained in this >>> message is confidential. If this message is not intended for you, >>> please inform postmas...@ccdc.cam.ac.uk and delete the message. >>> The Cambridge Crystallographic Data Centre is a company Limited >>> by Guarantee and a Registered Charity. >>> Registered in England No. 2155347 Registered Charity No. 800579 >>> Registered office 12 Union Road, Cambridge CB2 1EZ. >>> >> >> -- >> Prof. George M. Sheldrick FRS >> Dept. Structural Chemistry, >> University of Goettingen, >> Tammannstr. 4, >> D37077 Goettingen, Germany >> Tel. +49-551-39-3021 or -3068 >> Fax. +49-551-39-22582 > > ...................... > Jürgen Bosch > Johns Hopkins University > Bloomberg School of Public Health > Department of Biochemistry & Molecular Biology > Johns Hopkins Malaria Research Institute > 615 North Wolfe Street, W8708 > Baltimore, MD 21205 > Office: +1-410-614-4742 > Lab: +1-410-614-4894 > Fax: +1-410-955-2926 > http://web.mac.com/bosch_lab/ > > > >
