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
[EMAIL PROTECTED] 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:[EMAIL PROTECTED] On Behalf Of
[EMAIL PROTECTED]
Sent: Thursday, August 16, 2007 5:10 PM
To: CCP4BB@JISCMAIL.AC.UK
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: [EMAIL PROTECTED]
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: [EMAIL PROTECTED]
Miami, FL 33101 Web: http://structure.med.miami.edu
