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]> 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 <http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Rupp,%20 B.> B. Rupp Abstract: Physically improbable features in the model of the birch pollen structure Bet v 1d (PDB entry <http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78> 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 <http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78> 3k78model 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 <http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?1fm4> 1fm4). A variety of analytical tools, including the application of Diederichs plots, R[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 <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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