International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

© International Union of Crystallography 2006
International Tables for Crystallography (2006). Vol. F. ch. 25.2, pp. 707-708   | 1 | 2 |

Section 25.2.2.4.2. Phase-combination modes

K. D. Cowtan,b* K. Y. J. Zhangc and P. Maind

25.2.2.4.2. Phase-combination modes

| top | pdf |

Density-modification calculations are somewhat prone to producing grossly overestimated figures of merit (Cowtan & Main, 1996[link]). Users should be aware of this. In general the phases and figures of merit produced by density-modification calculations should only be used for the calculation of weighted [F_{o}] maps. They should not be used for the calculation of difference maps or used in refinement or other calculations (the REFMAC program is an exception, containing a mechanism to deal with this form of bias). The use of [2F_{o} - F_{c}]-type maps should be avoided when the calculated phases are from density modification, since they are dependent on two assumptions, neither of which hold for density modification: that the current phases are very close to being correct and that the calculated amplitudes may only approach the observed values as the phase error approaches zero.

To limit the problems of overestimation, three phase-combination modes are provided (controlled by the COMBINE keyword):

  • (1) Free-Sim weighting: This is the simplest mode to use. Although convergence is weaker than the reflection-omit mode, the calculation never overshoots the best map. If there is averaging information, then convergence is much stronger and the phase-combination scheme is much less important. In addition, phase relationships in reciprocal space limit the effectiveness of the reflection-omit scheme. Therefore, the free-Sim weighting scheme should usually be used when there is averaging.

  • (2) Reflection-omit: The combination of a reciprocal-space omit procedure with SIGMAA phase combination (Read, 1986[link]) leads to much better maps when applying solvent flattening and histogram matching. However, the omit calculation is computationally costly and introduces a small amount of noise into the maps, thus the phases can get worse if the calculation is run for too many cycles. A real-space free-R indicator (Abrahams & Leslie, 1996[link]) is therefore used to stop the calculation at an appropriate point.

  • (3) Perturbation-γ correction: This new approach is an extension of the γ correction of Abrahams (1997)[link] to arbitrary density-modification methods. The results are a good approximation to a perfect reflection-omit scheme and required considerably less computation. This is therefore the preferred mode for all calculations.

In the case of a molecular-replacement calculation or high noncrystallographic symmetry, it may be desirable only to weight the modified phases and not to recombine them back with the initial phases so that any initial bias may be overcome. In the case of high noncrystallographic symmetry, it may also be possible to restore missing reflections in both amplitude and phase. Options are available for both these situations.

References

First citation Abrahams, J. P. (1997). Bias reduction in phase refinement by modified interference functions: introducing the γ correction. Acta Cryst. D53, 371–376.Google Scholar
 First citation Abrahams, J. P. & Leslie, A. G. W. (1996). Methods used in the structure determination of bovine mitochondrial F2 ATPase. Acta Cryst. D52, 30–42.Google Scholar
 First citation Cowtan, K. D. & Main, P. (1996). Phase combination and cross validation in iterated density-modification calculations. Acta Cryst. D52, 43–48.Google Scholar
 First citation Read, R. J. (1986). Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Cryst. A42, 140–149.Google Scholar








































to end of page
to top of page