Bulk-solvent and overall scaling revisited: faster calculations, improved results
| Autor: | Ralf W. Grosse-Kunstleve, Pavel V. Afonine, Alexandre Urzhumtsev, Paul D. Adams |
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| Rok vydání: | 2013 |
| Předmět: |
Models
Molecular Time Factors Scale (ratio) Macromolecular Substances structure refinement Normal Distribution Structure (category theory) Bioengineering anisotropy Crystallography X-Ray Normal distribution 03 medical and health sciences 0302 clinical medicine X-Ray Diffraction bulk solvent Structural Biology Computational chemistry Physics::Chemical Physics Anisotropy Scaling 030304 developmental biology Mathematics 0303 health sciences scaling Computational Biology General Medicine Function (mathematics) PHENIX Research Papers Exponential function Solvents Algorithm Algorithms 030217 neurology & neurosurgery Order of magnitude |
| Zdroj: | Acta Crystallographica Section D: Biological Crystallography |
| ISSN: | 1399-0047 0907-4449 |
| Popis: | A fast analytical method for calculating mask-based bulk-solvent scale factors and overall anisotropic correction factors is introduced. A fast and robust method for determining the parameters for a flat (mask-based) bulk-solvent model and overall scaling in macromolecular crystallographic structure refinement and other related calculations is described. This method uses analytical expressions for the determination of optimal values for various scale factors. The new approach was tested using nearly all entries in the PDB for which experimental structure factors are available. In general, the resulting R factors are improved compared with previously implemented approaches. In addition, the new procedure is two orders of magnitude faster, which has a significant impact on the overall runtime of refinement and other applications. An alternative function is also proposed for scaling the bulk-solvent model and it is shown that it outperforms the conventional exponential function. Similarly, alternative methods are presented for anisotropic scaling and their performance is analyzed. All methods are implemented in the Computational Crystallography Toolbox (cctbx) and are used in PHENIX programs. |
| Databáze: | OpenAIRE |
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