Dear Remy,
You are right, and I was about to send a message confessing that I had
been rash in my response to Fred's. Another person e-mailed me off-list to
point out that sometimes a structure can be quickly solved, but that doing
all the rest of the work involved in wrapping that structure into a good
biological story for publication can take a very long time, and that it
would be wrong for a SR source's forced disclosure policy to start imposing
deadlines on that process. I entirely agree with both of you and admit that
I reacted too quickly and with insufficient thought to Fred's message.
However, as you point out yourself, this issue is related to a
different question (SR sources' disclosure policy towards all data collected
on their beamlines) from the original one that started this thread
(deposition of raw images with the pdb entries they led to). The two topics
became entangled through the idea of prototyping an approach to the latter
by tweaking the storage and access features involved in the former.
Many thanks to you and to the other correspondent for picking up and
correcting my error. This however leaves the main topic of this thread
untouched.
With best wishes,
Gerard.
--
On Fri, Oct 28, 2011 at 01:38:29PM +0200, Remy Loris wrote:
> Dear Gerard,
>
> I cannot agree. Last year my group published a paper in Cell which
> contained a structure for which the native data were collected at a
> synchrotron around 1997. Various reasons contributed to the long lag period
> for solving this structure, but basically it all came down to money needed
> to do the work. Equally I am sure there are other cases for which a first
> good native data set is a breakthrough you wish to protect rather than hand
> it out to anyone who might potentially scoop you after you have put lots of
> money and effort into the project.
>
> Therefore: Images corresponding to structures I deposit in the PDB: No
> problem. That is what we do with processed data as well. But images of
> unsolved structures, I don't see why that should be enforced or done
> automatically by synchrotrons. Nobody deposits processed data without an
> accompanying structure either.
>
> I do agree that one could be given the option to deposit interesting data
> with which he/se will not continue for whatever reason. But this should be
> optional, and a clear consensus should emerge within the community as how
> the original producers of the data have to be acknowledged if these data
> are used and the results published by another team, especially if the use
> of that particular dataset is crucial for the publication.
>
> Remy Loris
> Vrije Universiteit Brussel and VIB
>
>
> Op 28/10/2011 11:54, Gerard Bricogne schreef:
>> Dear Fred,
>>
>> Frankly, with respect, this sounds to me like fanciful and rather
>> non-sensical paranoia. The time frame for public disclosure of all SR data
>> has been quoted at 5 years, or something of that order. If someone has
>> been
>> unable to solve a structure 5 years after having collected data on it,
>> then
>> it does make perfect sense that he/she be "rescued" in one way or another.
>> Any responsible scientist in that situation would have called for
>> specialist
>> help long before then, and having failed to do so would indicate a loss of
>> interest in the project anyway.
>>
>> This is again the type of argument that strays away from a serious
>> question by throwing decoys around the place. Of course such views must be
>> heard, but so should the counter-arguments of those who disagree with
>> them.
>>
>>
>> With best wishes,
>>
>> Gerard.
>>
>> --
>> On Fri, Oct 28, 2011 at 10:42:25AM +0200, Vellieux Frederic wrote:
>>> D Bonsor wrote:
>>>> and allow someone else to have ago at solving the structure.
>>>>
>>> I'd be careful there if there was a motion to try to implement a policy
>>> at
>>> SR sources (for academic research projects) to make it compulsory to
>>> publically release all data frames after a period (1 year ? 2 years ? 4
>>> years) during which you are supposed to solve the structures you have
>>> collected the data for, so that others can have a go at it (and solve the
>>> structures "for you"):
>>>
>>> you may find yourself for example in between grants and need to spend all
>>> of your time looking for funding for a couple of years, with little or no
>>> staff working with you. With the trend we see of ever diminishing
>>> resources, this would mean that the very large and well funded labs and
>>> groups would solve their own structures, and solve those of smaller
>>> groups
>>> as well (and publish the latter). This would then mean (after a while)
>>> the
>>> concentration of macromolecular crystallography to only the "lucky few"
>>> who
>>> have managed to secure large grants and will therefore go-on securing
>>> such
>>> grants. You could call that "evolution" I suppose.
>>>
>>> We are already in a situation where the crystallographers who solved the
>>> structures are not necessarily authors on the publications reporting the
>>> structures... so is it time to go back to home sources (X-ray generators)
>>> for data collection ?
>>>
>>> Fred.
--
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