Very interesting
"Response to Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen"
doi:10.1107/S1744309112008433
a quote from the response:
"Author Schwarzenbacher admits to the allegations of data fabrication and deeply apologizes to the co-authors and the scientific community for all the problems this has caused
.....
Note added in proof: subsequent to the acceptance of this article for publication, author Schwarzenbacher withdrew his admission of the allegations.
"
________________________________________
From: CCP4 bulletin board [[log in to unmask]] On Behalf Of Bernhard Rupp (Hofkristallrat a.D.) [[log in to unmask]]
Sent: Saturday, March 31, 2012 12:42 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication
This is an unresolved problem, and no real satisfactory solution exists, because the underlying reasons for zero occupancy can be different.
For people who understand this and look at electron density, it is not a problem. For users who rely on some graphics program
displaying only atom coordinates, it can be. The same holds for manipulation of B-factors, ‘trading’ high B-factors against reduced occupancy,
and other (almost always purely cosmetic but still confusing or inconsistent) practices.
Best, BR
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Nian Huang
Sent: Saturday, March 31, 2012 11:29 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication
I don't model zero occupancy in my model. But can't the refinement programs just treat those atoms with zero occupancy as missing atoms?
Nian Huang
On Sat, Mar 31, 2012 at 10:26 AM, Bosch, Juergen <[log in to unmask]<mailto:[log in to unmask]>> wrote:
really fascinating, bringing back the discussion for a repository for your collected frames.
Jürgen
Acta Cryst. (2012). F68, 366-376
doi:10.1107/S1744309112008421<http://dx.doi.org/10.1107/S1744309112008421>
Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen
B. Rupp<http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Rupp,%20B.>
Abstract: Physically improbable features in the model of the birch pollen structure Bet v 1d (PDB entry 3k78<http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78>) are faithfully reproduced in electron density generated with the deposited structure factors, but these structure factors themselves exhibit properties that are characteristic of data calculated from a simple model and are inconsistent with the data and error model obtained through experimental measurements. The refinement of the 3k78<http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78>model against these structure factors leads to an isomorphous structure different from the deposited model with an implausibly small R value (0.019). The abnormal refinement is compared with normal refinement of an isomorphous variant structure of Bet v 1l (PDB entry 1fm4<http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?1fm4>). A variety of analytical tools, including the application of Diederichs plots, R plots and bulk-solvent analysis are discussed as promising aids in validation. The examination of the Bet v 1d structure also cautions against the practice of indicating poorly defined protein chain residues through zero occupancies. The recommendation to preserve diffraction images is amplified.
......................
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742<tel:%2B1-410-614-4742>
Lab: +1-410-614-4894<tel:%2B1-410-614-4894>
Fax: +1-410-955-2926<tel:%2B1-410-955-2926>
http://web.mac.com/bosch_lab/
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