Polder maps [electronic resource] : Improving OMIT maps by excluding bulk solvent
- Published
- Bethesda, Md. : National Institutes of Health (U.S.), 2017.
Oak Ridge, Tenn. : Distributed by the Office of Scientific and Technical Information, U.S. Dept. of Energy - Physical Description
- pages 148-157 : digital, PDF file
- Additional Creators
- Los Alamos National Laboratory, National Institutes of Health (U.S.), United States. Department of Energy, and United States. Department of Energy. Office of Scientific and Technical Information
Access Online
- Restrictions on Access
- Free-to-read Unrestricted online access
- Summary
The crystallographic maps that are routinely used during the structure-solution workflow are almost always model-biased because model information is used for their calculation. As these maps are also used to validate the atomic models that result from model building and refinement, this constitutes an immediate problem: anything added to the model will manifest itself in the map and thus hinder the validation. OMIT maps are a common tool to verify the presence of atoms in the model. The simplest way to compute an OMIT map is to exclude the atoms in question from the structure, update the corresponding structure factors and compute a residual map. It is then expected that if these atoms are present in the crystal structure, the electron density for the omitted atoms will be seen as positive features in this map. This, however, is complicated by the flat bulk-solvent model which is almost universally used in modern crystallographic refinement programs. This model postulates constant electron density at any voxel of the unit-cell volume that is not occupied by the atomic model. Consequently, if the density arising from the omitted atoms is weak then the bulk-solvent model may obscure it further. A possible solution to this problem is to prevent bulk solvent from entering the selected OMIT regions, which may improve the interpretative power of residual maps. This approach is called a polder (OMIT) map. Polder OMIT maps can be particularly useful for displaying weak densities of ligands, solvent molecules, side chains, alternative conformations and residues both in terminal regions and in loops. As a result, the tools described in this manuscript have been implemented and are available in PHENIX.
- Report Numbers
- E 1.99:la-ur--16-24457
la-ur--16-24457 - Subject(s)
- Other Subject(s)
- Note
- Published through SciTech Connect.
02/01/2017.
"la-ur--16-24457"
Acta Crystallographica. Section D. Structural Biology 73 2 ISSN 2059-7983; ACSDAD AM
Dorothee Liebschner; Pavel V. Afonine; Nigel W. Moriarty; Billy K. Poon; Oleg V. Sobolev; Thomas Charles Terwilliger; Paul D. Adams. - Funding Information
- AC52-06NA25396