International Tables for Crystallography (2006). Vol. F, ch. 16.1, pp. 333-345   | 1 | 2 |
doi: 10.1107/97809553602060000689

Chapter 16.1. Ab initio phasing

Contents

  • 16.1. Ab initio phasing  (pp. 333-345) | html | pdf | chapter contents |
    • 16.1.1. Introduction  (p. 333) | html | pdf |
    • 16.1.2. Normalized structure-factor magnitudes  (pp. 333-334) | html | pdf |
      • 16.1.2.1. SIR differences  (p. 334) | html | pdf |
      • 16.1.2.2. SAS differences  (p. 334) | html | pdf |
    • 16.1.3. Starting the phasing process  (pp. 334-335) | html | pdf |
      • 16.1.3.1. Structure invariants  (p. 334) | html | pdf |
      • 16.1.3.2. `Multisolution' methods and trial structures  (pp. 334-335) | html | pdf |
    • 16.1.4. Reciprocal-space phase refinement or expansion ( shaking )  (pp. 335-336) | html | pdf |
      • 16.1.4.1. The tangent formula  (p. 335) | html | pdf |
      • 16.1.4.2. The minimal function  (p. 335) | html | pdf |
      • 16.1.4.3. Parameter shift  (pp. 335-336) | html | pdf |
    • 16.1.5. Real-space constraints ( baking )  (p. 336) | html | pdf |
      • 16.1.5.1. Simple peak picking  (p. 336) | html | pdf |
      • 16.1.5.2. Iterative peaklist optimization  (p. 336) | html | pdf |
      • 16.1.5.3. Random omit maps  (p. 336) | html | pdf |
    • 16.1.6. Fourier refinement ( twice baking )  (pp. 336-337) | html | pdf |
    • 16.1.7. Computer programs for dual-space phasing  (pp. 337-339) | html | pdf |
      • 16.1.7.1. Flowchart and program comparison  (p. 337) | html | pdf |
      • 16.1.7.2. Parameters and procedures  (pp. 337-338) | html | pdf |
      • 16.1.7.3. Recognizing solutions  (pp. 338-339) | html | pdf |
    • 16.1.8. Applying dual-space programs successfully  (pp. 339-344) | html | pdf |
      • 16.1.8.1. Utilizing Pattersons for better starts  (p. 340) | html | pdf |
      • 16.1.8.2. Avoiding false minima  (pp. 340-341) | html | pdf |
      • 16.1.8.3. Data resolution and completeness  (p. 341) | html | pdf |
      • 16.1.8.4. Choosing a refinement strategy  (pp. 342-343) | html | pdf |
      • 16.1.8.5. Expansion to P 1  (p. 343) | html | pdf |
      • 16.1.8.6. Substructure applications  (pp. 343-344) | html | pdf |
    • 16.1.9. Extending the power of direct methods  (pp. 344-345) | html | pdf |
      • 16.1.9.1. Integration with isomorphous replacement  (p. 344) | html | pdf |
      • 16.1.9.2. Integration with anomalous dispersion  (pp. 344-345) | html | pdf |
      • 16.1.9.3. Integration with multiple-beam diffraction  (p. 345) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 16.1.3.1. The conditional probability distribution of the three-phase structure invariants  (p. 334) | html | pdf |
      • Fig. 16.1.7.1. A flowchart for the Shake-and-Bake procedure, which is implemented in both SnB and SHELXD   (p. 337) | html | pdf |
      • Fig. 16.1.7.2. A histogram of figure-of-merit values (minimal function) for 378 scorpion toxin II trials  (p. 338) | html | pdf |
      • Fig. 16.1.7.3. Tracing the history of a solution and a nonsolution trial for scorpion toxin II as a function of Shake-and-Bake cycle  (p. 338) | html | pdf |
      • Fig. 16.1.8.1. Success rates for triclinic lysozyme are strongly influenced by the size of the parameter-shift angle  (p. 341) | html | pdf |
      • Fig. 16.1.8.2. ( a ) Mean phase error as a function of resolution for the two independent ab initio SHELXD solutions of the previously unsolved protein hirustasin  (p. 341) | html | pdf |
      • Fig. 16.1.8.3. ( a ) Success rates and ( b ) cost effectiveness for several dual-space strategies as applied to a 148-atom P 1 structure  (p. 342) | html | pdf |
      • Fig. 16.1.8.4. Success rates for the 317-atom [P2_{1}2_{1}2_{1}] structure of gramicidin A  (p. 343) | html | pdf |
    • Tables
      • Table 16.1.2.1. Theoretical values pertaining to [|E|]'s  (p. 334) | html | pdf |
      • Table 16.1.7.1. Recommended parameter values for the SnB  program  (p. 338) | html | pdf |
      • Table 16.1.8.1. Some large structures solved by the Shake-and-Bake method  (p. 339) | html | pdf |
      • Table 16.1.8.2. Overall success rates for full structure solution for hirustasin using different two-atom search vectors chosen from the Patterson peak list  (p. 340) | html | pdf |
      • Table 16.1.8.3. Success rates for three P 1 structures illustrate the importance of using complete data to the highest possible resolution  (p. 342) | html | pdf |
      • Table 16.1.8.4. Improving success rates by `completing' the vancomycin data  (p. 342) | html | pdf |