Coordinate uncertainty

Cruickshank, D. W. J.

doi:10.1107/97809553602060000697

International Tables for Crystallography (2006). Vol. F. ch. 18.5, pp. 403-418 | 1 | 2 |
https://doi.org/10.1107/97809553602060000697

Chapter 18.5. Coordinate uncertainty

18.5. Coordinate uncertainty (pp. 403-418) | html | pdf | chapter contents |
D. W. J. Cruickshank
- 18.5.1. Introduction (p. 403) | html | pdf |
  - 18.5.1.1. Background (p. 403) | html | pdf |
  - 18.5.1.2. Accuracy and precision (p. 403) | html | pdf |
  - 18.5.1.3. Effect of atomic displacement parameters (or `temperature factors') (p. 403) | html | pdf |
- 18.5.2. The least-squares method (pp. 404-405) | html | pdf |
  - 18.5.2.1. The normal equations (p. 404) | html | pdf |
  - 18.5.2.2. Weights (p. 404) | html | pdf |
  - 18.5.2.3. Statistical descriptors and goodness of fit (pp. 404-405) | html | pdf |
- 18.5.3. Restrained refinement (pp. 405-406) | html | pdf |
  - 18.5.3.1. Residual function (p. 405) | html | pdf |
  - 18.5.3.2. A very simple protein model (pp. 405-406) | html | pdf |
  - 18.5.3.3. Relative weighting of diffraction and restraint terms (p. 406) | html | pdf |
- 18.5.4. Two examples of full-matrix inversion (pp. 406-409) | html | pdf |
  - 18.5.4.1. Unrestrained and restrained inversions for concanavalin A (pp. 406-408) | html | pdf |
  - 18.5.4.2. Unrestrained inversion for an immunoglobulin (p. 408) | html | pdf |
  - 18.5.4.3. Comments on restrained refinement (p. 408) | html | pdf |
  - 18.5.4.4. Full-matrix estimates of precision (pp. 408-409) | html | pdf |
- 18.5.5. Approximate methods (p. 409) | html | pdf |
  - 18.5.5.1. Block calculations (p. 409) | html | pdf |
  - 18.5.5.2. The modified Fourier method (p. 409) | html | pdf |
  - 18.5.5.3. Application of the modified Fourier method (p. 409) | html | pdf |
- 18.5.6. The diffraction-component precision index (p. 410) | html | pdf |
  - 18.5.6.1. Statistical expectation of error dependence (p. 410) | html | pdf |
  - 18.5.6.2. A simple error formula (p. 410) | html | pdf |
  - 18.5.6.3. Extension for low-resolution structures and use of R_free (p. 410) | html | pdf |
  - 18.5.6.4. Position error (p. 410) | html | pdf |
- 18.5.7. Examples of the diffraction-component precision index (pp. 411-412) | html | pdf |
  - 18.5.7.1. Full-matrix comparison with the diffraction-component precision index (p. 411) | html | pdf |
  - 18.5.7.2. Further examples of the DPI using R (p. 411) | html | pdf |
  - 18.5.7.3. Examples of the DPI using R_free (pp. 411-412) | html | pdf |
  - 18.5.7.4. Comments on the diffraction-component precision index (p. 412) | html | pdf |
- 18.5.8. Luzzati plots (pp. 412-414) | html | pdf |
  - 18.5.8.1. Luzzati's theory (pp. 412-413) | html | pdf |
  - 18.5.8.2. Statistical reinterpretation of Luzzati plots (pp. 413-414) | html | pdf |
  - 18.5.8.3. Comments on Luzzati plots (p. 414) | html | pdf |
- References | html | pdf |
- Figures
  - Fig. 18.5.4.1. Plots of $[\sigma (r)]$ versus $[B_{\rm eq}]$ for concanavalin A with 0.94 Å data, (a) restrained full-matrix $[\sigma_{\rm res}(r)]$ , (b) unrestrained full-matrix $[\sigma_{\rm diff}(r)]$ (p. 407) | html | pdf |
  - Fig. 18.5.4.2. Plots of $[\sigma (l)]$ versus average $[B_{\rm eq}]$ for concanavalin A with 0.94 Å data, (a) restrained full-matrix $[\sigma_{\rm res}(l)]$ , (b) unrestrained full-matrix $[\sigma_{\rm diff}(l)]$ (p. 407) | html | pdf |
  - Fig. 18.5.4.3. Plot of $[\sigma_{\rm diff}(r)]$ versus $[B_{\rm eq}]$ from an unrestrained full matrix for immunoglobulin mutant (T39K) with 1.70 Å data (p. 408) | html | pdf |
  - Fig. 18.5.4.4. Plot of $[\sigma_{\rm diff}(l)]$ versus average $[B_{\rm eq}]$ from an unrestrained full matrix for immunoglobulin mutant (T39K) with 1.70 Å data (p. 408) | html | pdf |
  - Fig. 18.5.8.1. Luzzati plots showing the refined R factor as a function of resolution for 1TGI (solid squares) and 1TGF (open squares) (Daopin et al., 1994) (p. 413) | html | pdf |
- Tables
  - Table 18.5.7.1. Comparison of full-matrix $[\sigma (r, B_{\rm avg})]$ with the diffraction-component precision index (DPI) (p. 411) | html | pdf |
  - Table 18.5.7.2. Examples of diffraction-component precision indices (DPIs) (p. 411) | html | pdf |
  - Table 18.5.7.3. Comparison of DPIs using R and R_free (p. 412) | html | pdf |
  - Table 18.5.8.1. $[R = \langle |\Delta F|\rangle / \langle |F|\rangle]$ as a function of $[s\langle \Delta r\rangle]$ in the Luzzati model for three-dimensional noncentrosymmetric structures $[(s=2\sin\theta/\lambda)]$ (p. 413) | html | pdf |

Chapter 18.5. Coordinate uncertainty

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