This will have to be automated, and not subjectively flagged by the
editors - something just like EDS ("review-EDS"?), where the data
submitted gets sent automatically by the journal to an EDS type server,
and the results are available only to the reviewers.
The reviewers should be able to log in as needed and look at the EDS
summary as well as the maps/structure interactively (in the java Astex
viewer), but not download the coordinates/SFs. Once the review is done,
the data gets deleted (or better still, archived).
EDS, PDBsum, MSD and other similar sites are invaluable, but this is all
retrospective - the time that we really need such analysis is during the
review phase of a paper/structure.
Arun Malhotra
[log in to unmask] wrote:
> Hi Arun,
> I think you have a higher opinion of journal editors than many of us?
> Unless you run the same refinement software exactly the same way (i.e.
> same bulk solvent & anisotropy corrections, TLS, etc) you won't get
> exactly the same R factors. A crystallographer would know what is and
> isn't a significant difference, hopefully, but an editor would be
> likely to flag all the wrong things.
> Phoebe
>
> At 10:52 AM 8/17/2007, you wrote:
>> The proper choice of reviewers is important, but perhaps some of the
>> burden for fact checking should be shifted to the journal. Some
>> journals are already doing image analysis to check gels/microscopy
>> images, and there is no reason why this cannot be extended for
>> structures.
>>
>> In practical terms, when you submit a paper, apart from uploading the
>> text and image files, coordinate file(s) and structure factors will
>> also have to be submitted. The journal would then run some scripts
>> (developed by CCP4?) on the coordinate/SF data and make a basic
>> analysis file available to the reviewers. This could be an extended
>> version of the table seen in crystallography papers, but with
>> outlying values highlighted, some fact-checking, and perhaps a
>> summary for non-crystallographer reviewers.
>> The journal could even make a more sophisticated "EDS"-type server
>> (perhaps contracted out to EDS?), where the electron density for any
>> region could be checked easily online by the reviewers, without
>> having to reveal the full structure factors and coordinates. This
>> would keep the burden for keeping the coordinates/structure factors
>> confidential on the journal rather than an anonymous reviewer.
>>
>> The archiving/submission of raw data are important, but it is
>> difficult to see how even competent reviewers can be convinced to do
>> detailed analysis - even for something as easy to check as gels, I
>> have never gone beyond just zooming/squinting when reviewing papers.
>>
>> Arun Malhotra
>>
>>
>>
>>
>> Bernhard Rupp wrote:
>>> Nature DOES require availability of structure factors and
>>> coordinates as
>>> a matter of policy, and also to make them available for review on
>>> demand.
>>> If the reviewer does not want them, the editor can't do anything about.
>>>
>>> One also cannot demand of a biologist reviewer to reconstruct
>>> maps, but others long ago and I recently have suggested in nature to
>>> make at least the RSCC mandatory reading for to reviewers - a picture
>>> says more than words...
>>> One way would be to carefully pair reviewers for crystallographic
>>> papers - a competent biologist and a competent crystallographer.
>>> Being not a famous biologist I am generally unimpressed by the
>>> story, and unemotional about the crystallography. The biology
>>> reviewer on the other hand could make the point how relevant and
>>> exciting the structure and its biological implications are. The
>>> proper pairing is something where I would lay the responsibility
>>> heavy on the journal editors. That is just a matter of due diligence.
>>> br
>>>
>>> -----Original Message-----
>>> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
>>> [log in to unmask]
>>> Sent: Thursday, August 16, 2007 5:10 PM
>>> To: [log in to unmask]
>>> Subject: Re: [ccp4bb] nature cb3 response
>>>
>>> A comment from my collaborator's student suggests a partial answer.
>>> This
>>> afternoon he happened to say "but of course the reviewers will look
>>> at the
>>> model, I just deposited it!". He was shocked to find that "hold for
>>> pub"
>>> means that even reviewers can't access the data. Can that be
>>> changed? It
>>> would take a bit of coordination between journals and the PDB, but I
>>> think
>>> the student is right - it is rather shocking that the data is
>>> sitting there
>>> nicely deposited but the reviewers can't review it.
>>> Phoebe Rice
>>>
>>>
>>
>>
>> --
>> Arun Malhotra Phone: (305) 243-2826
>> Associate Professor Lab: (305) 243-2890
>> Dept. of Biochemistry & Molecular Biology Fax: (305) 243-3955
>> University of Miami School of Medicine
>> PO Box 016129 E-Mail: [log in to unmask]
>> Miami, FL 33101 Web: http://structure.med.miami.edu
>
> ---------------------------------------------------------------------------------------------------------------------------
>
> Phoebe A. Rice
> Assoc. Prof., Dept. of Biochemistry & Molecular Biology
> The University of Chicago
> phone 773 834 1723
> fax 773 702 0439
> http://bmb.bsd.uchicago.edu/index.html
> http://www.nasa.gov/mission_pages/cassini/multimedia/pia06064.html
>
--
Arun Malhotra Phone: (305) 243-2826
Associate Professor Lab: (305) 243-2890
Dept. of Biochemistry & Molecular Biology Fax: (305) 243-3955
University of Miami School of Medicine
PO Box 016129 E-Mail: [log in to unmask]
Miami, FL 33101 Web: http://structure.med.miami.edu
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