Dear CCP4BBers, The PDB_REDO entry Bernhard referred to in his interesting and very thorough article was automatically deleted because the original PDB entry was obsoleted. Since access to the 'experimental' data of any study is important, we have made a compressed copy of the PDB_REDO entry available at http://www.cmbi.ru.nl/pdb_redo/others/3k78.tar.bz2 Our apologies to those who have looked for this entry in vain.
Best wishes, Robbie Joosten (on behalf of the PDB_REDO team) Biochemistry Netherlands Cancer Institute P.S. The whole fraud thing seems to have interfered with the annual April fools' post on CCP4BB. Let's hope this will not happen again. > -----Original Message----- > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of > Michel Fodje > Sent: Saturday, March 31, 2012 21:55 > To: [email protected] > Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication > > 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 [[email protected]] On Behalf Of > Bernhard Rupp (Hofkristallrat a.D.) [[email protected]] > Sent: Saturday, March 31, 2012 12:42 PM > To: [email protected] > 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:[email protected]] On Behalf Of > Nian Huang > Sent: Saturday, March 31, 2012 11:29 AM > To: [email protected] > 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 > <[email protected]<mailto:[email protected]>> 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/S17443091120084 > 21> > > 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/
