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<mailto:herman.schreu...@sanofi.com> Sent: 19 April 2012 13:54 To: CCP4BB@JISCMAIL.AC.UK<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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 ...................... 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