International Tables for Crystallography (2012). Vol. F, ch. 15.1, pp. 385-400   | 1 | 2 |
doi: 10.1107/97809553602060000847

Chapter 15.1. Phase improvement by iterative density modification

Contents

  • 15.1. Phase improvement by iterative density modification  (pp. 385-400) | html | pdf | chapter contents |
    • 15.1.1. Introduction  (p. 385) | html | pdf |
    • 15.1.2. Density-modification methods  (pp. 385-393) | html | pdf |
      • 15.1.2.1. Solvent flattening  (pp. 385-388) | html | pdf |
        • 15.1.2.1.1. Introduction  (pp. 386-387) | html | pdf |
        • 15.1.2.1.2. The automated convolution method for molecular-boundary identification  (p. 387) | html | pdf |
        • 15.1.2.1.3. The solvent-flattening procedure  (p. 388) | html | pdf |
      • 15.1.2.2. Histogram matching  (pp. 388-390) | html | pdf |
        • 15.1.2.2.1. Introduction  (p. 388) | html | pdf |
        • 15.1.2.2.2. The prediction of the ideal histogram  (pp. 388-389) | html | pdf |
        • 15.1.2.2.3. The process of histogram matching  (pp. 389-390) | html | pdf |
        • 15.1.2.2.4. Scaling the observed structure-factor amplitudes according to the ideal density histogram  (p. 390) | html | pdf |
      • 15.1.2.3. Averaging  (pp. 390-392) | html | pdf |
        • 15.1.2.3.1. Introduction  (p. 390) | html | pdf |
        • 15.1.2.3.2. The determination of noncrystallographic symmetry  (pp. 390-391) | html | pdf |
        • 15.1.2.3.3. The refinement of noncrystallographic symmetry  (p. 391) | html | pdf |
        • 15.1.2.3.4. The averaging of NCS-related molecules  (pp. 391-392) | html | pdf |
      • 15.1.2.4. Skeletonization  (p. 392) | html | pdf |
      • 15.1.2.5. Sayre's equation  (p. 392) | html | pdf |
        • 15.1.2.5.1. Sayre's equation in real and reciprocal space  (p. 392) | html | pdf |
        • 15.1.2.5.2. The application of Sayre's equation to macro­molecules at non-atomic resolution – the θ([{\bf h}]) curve  (p. 392) | html | pdf |
      • 15.1.2.6. Atomization  (pp. 392-393) | html | pdf |
    • 15.1.3. Reciprocal-space interpretation of density modification  (pp. 393-394) | html | pdf |
    • 15.1.4. Phase combination  (pp. 394-396) | html | pdf |
      • 15.1.4.1. Sim and [\sigma_{a}] weighting  (pp. 394-395) | html | pdf |
      • 15.1.4.2. Reflection omit  (p. 395) | html | pdf |
      • 15.1.4.3. The γ correction and solvent flipping  (p. 395) | html | pdf |
      • 15.1.4.4. Resolution extrapolation  (pp. 395-396) | html | pdf |
    • 15.1.5. Combining constraints for phase improvement  (pp. 396-398) | html | pdf |
      • 15.1.5.1. The system of nonlinear constraint equations  (p. 396) | html | pdf |
      • 15.1.5.2. Least-squares solution to the system of nonlinear constraint equations  (pp. 396-398) | html | pdf |
        • 15.1.5.2.1. The conjugate-gradient method  (p. 397) | html | pdf |
        • 15.1.5.2.2. The full-matrix solution  (p. 397) | html | pdf |
        • 15.1.5.2.3. The diagonal approximation  (pp. 397-398) | html | pdf |
    • 15.1.6. Statistical density-modification methods  (p. 398) | html | pdf |
    • 15.1.7. Example  (pp. 398-399) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 15.1.2.1. Density-modification calculation showing iterative application of real-space and reciprocal-space constraints  (p. 385) | html | pdf |
      • Fig. 15.1.2.2. Solvent mask determined from a map by Wang's method  (p. 387) | html | pdf |
      • Fig. 15.1.2.3. Transformation of density ρ to [\rho'_{\rm mod}] by histogram matching  (p. 389) | html | pdf |
      • Fig. 15.1.2.4. Types of noncrystallographic symmetry and averaging calculation  (p. 391) | html | pdf |
      • Fig. 15.1.3.1. The functions [g({\bf x})] and [G({\bf h})] for solvent flattening, histogram matching and averaging  (p. 393) | html | pdf |
      • Fig. 15.1.7.1. Phase correlations after different combinations of density modifications  (p. 398) | html | pdf |
    • Tables
      • Table 15.1.2.1. Constraints used in density modification  (p. 386) | html | pdf |