Ab initio
       phasing

Sheldrick, G. M.; Gilmore, C. J.; Hauptman, H. A.; Weeks, C. M.; Miller, R.; Usón, I.

doi:10.1107/97809553602060000850

International Tables for Crystallography (2012). Vol. F. ch. 16.1, pp. 413-432 | 1 | 2 |
https://doi.org/10.1107/97809553602060000850

Chapter 16.1. Ab initio phasing

16.1. Ab initio phasing (pp. 413-432) | html | pdf | chapter contents |
G. M. Sheldrick, C. J. Gilmore, H. A. Hauptman, C. M. Weeks, R. Miller and I. Usón
- 16.1.1. Introduction (pp. 413-415) | html | pdf |
  - 16.1.1.1. Data resolution (pp. 413-414) | html | pdf |
  - 16.1.1.2. Data completeness (p. 414) | html | pdf |
  - 16.1.1.3. Summary (pp. 414-415) | html | pdf |
- 16.1.2. Normalized structure-factor magnitudes (pp. 415-416) | html | pdf |
  - 16.1.2.1. SIR differences (p. 416) | html | pdf |
  - 16.1.2.2. SAD differences (p. 416) | html | pdf |
  - 16.1.2.3. Difference intensities and direct methods (p. 416) | html | pdf |
- 16.1.3. Starting the phasing process (pp. 416-417) | html | pdf |
  - 16.1.3.1. Structure invariants (pp. 416-417) | html | pdf |
  - 16.1.3.2. `Multisolution' methods and trial structures (p. 417) | html | pdf |
- 16.1.4. Reciprocal-space phase refinement or expansion (shaking) (pp. 417-418) | html | pdf |
  - 16.1.4.1. The tangent formula (p. 417) | html | pdf |
  - 16.1.4.2. The minimal function (pp. 417-418) | html | pdf |
  - 16.1.4.3. Parameter shift (p. 418) | html | pdf |
- 16.1.5. Real-space constraints (baking) (pp. 418-419) | html | pdf |
  - 16.1.5.1. Simple peak picking (p. 418) | html | pdf |
  - 16.1.5.2. Iterative peaklist optimization (pp. 418-419) | html | pdf |
  - 16.1.5.3. Random omit maps (p. 419) | html | pdf |
- 16.1.6. Fourier refinement (p. 419) | html | pdf |
- 16.1.7. Resolution enhancement: the `free lunch' algorithm (p. 419) | html | pdf |
- 16.1.8. Utilizing Pattersons for better starts (pp. 419-420) | html | pdf |
- 16.1.9. Shake-and-Bake: an analysis of a dual-space method in action (pp. 420-422) | html | pdf |
  - 16.1.9.1. Flowchart and program comparison (pp. 420-421) | html | pdf |
  - 16.1.9.2. Parameters and procedures (p. 421) | html | pdf |
  - 16.1.9.3. Recognizing solutions (pp. 421-422) | html | pdf |
- 16.1.10. Applying dual-space programs successfully (pp. 422-425) | html | pdf |
  - 16.1.10.1. Avoiding false minima (pp. 422-423) | html | pdf |
  - 16.1.10.2. Choosing a refinement strategy (pp. 423-424) | html | pdf |
  - 16.1.10.3. Expansion to P1 (pp. 424-425) | html | pdf |
  - 16.1.10.4. Substructure applications (p. 425) | html | pdf |
- 16.1.11. Substructure solution for native sulfurs and halide soaks (pp. 425-426) | html | pdf |
- 16.1.12. Computer programs for dual-space phasing (pp. 426-429) | html | pdf |
  - 16.1.12.1. ACORN (pp. 426-427) | html | pdf |
  - 16.1.12.2. IL MILIONE (pp. 427-428) | html | pdf |
  - 16.1.12.3. SHELX (p. 428) | html | pdf |
  - 16.1.12.4. SnB and BnP (p. 428) | html | pdf |
  - 16.1.12.5. HySS (p. 428) | html | pdf |
  - 16.1.12.6. SUPERFLIP: charge flipping (pp. 428-429) | html | pdf |
  - 16.1.12.7. CRUNCH2 – Karle–Hauptman determinants (p. 429) | html | pdf |
- 16.1.13. Conclusions and the grand challenge (p. 429) | html | pdf |
- References | html | pdf |
- Figures
  - Fig. 16.1.1.1. Averaged squared normalized structure-factor amplitudes over 700 protein structures with standard deviations calculated from the population of individual |E|² profiles (from Morris & Bricogne, 2003) (p. 413) | html | pdf |
  - Fig. 16.1.1.2. (a) Mean phase error as a function of resolution for the two independent ab initio SHELXD solutions of the previously unsolved protein hirustasin (p. 414) | html | pdf |
  - Fig. 16.1.3.1. The conditional probability distribution, $[P(\Phi_{\bf HK})]$ , of the three-phase structure invariants, $[\Phi_{\bf HK}]$ , having associated parameters A_HK with values of 0, 1, 2, 4 and 6 (p. 416) | html | pdf |
  - Fig. 16.1.9.1. A flowchart for the Shake-and-Bake procedure, which is implemented in both SnB and SHELXD (p. 420) | html | pdf |
  - Fig. 16.1.9.2. A histogram of figure-of-merit values (minimal function) for 378 scorpion toxin II trials (p. 421) | html | pdf |
  - Fig. 16.1.9.3. Tracing the history of a solution and a nonsolution trial for scorpion toxin II as a function of Shake-and-Bake cycle (p. 422) | html | pdf |
  - Fig. 16.1.10.1. Success rates for triclinic lysozyme are strongly influenced by the size of the parameter-shift angle (p. 423) | html | pdf |
  - Fig. 16.1.10.2. (a) Success rates and (b) cost effectiveness for several dual-space strategies as applied to a 148-atom P1 structure (p. 424) | html | pdf |
  - Fig. 16.1.10.3. Success rates for the 317-atom $[P2_{1}2_{1}2_{1}]$ structure of gramicidin A (p. 424) | html | pdf |
  - Fig. 16.1.11.1. Relative occupancy against peak number for SHELXD substructure solutions of elastase (p. 426) | html | pdf |
- Tables
  - Table 16.1.1.1. Success rates for three P1 structures illustrate the importance of using complete data to the highest possible resolution (p. 415) | html | pdf |
  - Table 16.1.1.2. Improving success rates by `completing' the vancomycin data (p. 415) | html | pdf |
  - Table 16.1.2.1. Theoretical values pertaining to 's (p. 415) | html | pdf |
  - Table 16.1.8.1. Overall success rates for full structure solution for hirustasin using different two-atom search vectors chosen from the Patterson peak list (p. 420) | html | pdf |
  - Table 16.1.9.1. Recommended parameter values for the SnB program (p. 421) | html | pdf |
  - Table 16.1.10.1. Some large structures solved by the Shake-and-Bake method (p. 423) | html | pdf |

Chapter 16.1. Ab initio phasing

Contents