Randy, This is somewhat of a "thought" experiment at best...but to think on whilst I commute home after a great BCA meeting...
You don't necessarily need a password-protected server - just a way of making a particularly cryptic URL - which the author is (at first) the only person to receive - and able to share a they wish. Now that you point out that you could take snapshots and reconstruct the model (something that I hadn't quite thought about! )- perhaps having an online viewer is a risk, but you'd have to go to quite a bit of effort to "steal" coordinates this way? Plus you would have to have some diffraction data yourself, in order to use the model unfairly to scoop a reviewee... I certainly appreciate and thank you (!) for the sterling work in producing the new validation reports - but as a reviewer myself, it's still not quite the same as seeing the maps and fits themselves. Tony. Sent from my iPhone On 19 Apr 2012, at 15:39, "Randy Read" <rj...@cam.ac.uk> wrote: > The idea of referees being given a link to the structure at the PDB came up > in discussions with PDB people, when we were preparing our X-ray validation > report. Among other potential issues, it would be a lot of work for them to > set up a secure password-protected system, and the growth in the PDB keeps > them pretty busy doing other things. The upcoming validation report is meant > to satisfy most of what referees would want to know about the structure and > its fit to the data. If it raises some flags, then they have a good excuse > to ask for more, through the journal. > > On the suggestion of a pre-release server: if you allow someone to rotate a > molecule and take several screenshots of it from different orientations, you > might as well give them the coordinates because that's all you need to > reconstruct them pretty precisely. For those who know how to compile Fortran > programs, Michael Rossmann wrote a program years ago that will extract > coordinates from a stereo pair, and I'm sure one could do much better with > multiple images. > > Regards, > > Randy Read > > On 19 Apr 2012, at 15:09, Antony Oliver wrote: > >> This subject raised (and keeps raising) its head above the parapet not all >> that long ago on this bulletin board. Maybe it's time to bite the bullet >> and try and do something about it? >> >> I would like to see and can imagine the following scenario... something I >> have tentatively suggested before... >> >> There is a secure web server (at the PDB?) where you can upload your >> coordinates and structure factor file - a Pre-release server if you will. >> On uploading you are then given a unique URL which can be provided to a >> journal and passed on to any selected reviewer. Crucially this does *not* >> allow the coordinates or maps to be downloaded, but visually inspected >> online - via some form of web-browser plugin; Aztex Viewer or similar. >> >> This way reviewers can see the model, and the density that the authors have >> built into, but not have any access to either the coordinate file or mtz - >> and sti make an informed judgment. >> >> With regards, from a tilting pendolino train, somewhere in the bowels of >> south -east England. >> >> Tony. >> >> On 19 Apr 2012, at 14:55, "George M. Sheldrick" >> <gshe...@shelx.uni-ac.gwdg.de> 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 > > ------ > 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 >
