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]> wrote: > really fascinating, bringing back the discussion for a repository for your > collected frames. > > Jürgen > > > *Acta Cryst.* (2012). F*68*, 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 allergenB. > 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*[image: [sigma]] 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 > Lab: +1-410-614-4894 > Fax: +1-410-955-2926 > http://web.mac.com/bosch_lab/ > > > > >
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