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" <[log in to unmask]> 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" <[log in to unmask]> 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:[log in to unmask]] On Behalf Of [log in to unmask]
>>>> Sent: 19 April 2012 13:54
>>>> To: [log in to unmask]
>>>> 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:[log in to unmask]] On Behalf Of
>>>> Jobichen Chacko
>>>> Sent: Thursday, April 19, 2012 2:12 PM
>>>> To: [log in to unmask]
>>>> 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
>>>> <[log in to unmask]> 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: [log in to unmask] |
>>>>>
>>>>
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>>>
>>> --
>>> Prof. George M. Sheldrick FRS
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>
> ------
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research Tel: + 44 1223 336500
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>
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