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(1) Extension by resolution shell: This performs phase extension in resolution steps, starting from the low-resolution data, and extends the phase to the high-resolution limit of the data or that specified by the user. Structure factors are related by the reciprocal-space density-modification function that is dominated by low-resolution terms, as shown by equation (15.1.3.2
) and Fig. 15.1.3.1
in Chapter 15.1. This means that only structure factors in a small region of reciprocal space are related. Thus, when initial phases are only available at low resolution, phase extension is performed by inclusion of successive resolution shells. In the case of fourfold or higher NCS, this can allow extension to 2 Å starting from initial phasing at 6 Å or worse.
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(2) Extension in structure-factor amplitude steps: In this mode, those reflections with larger amplitudes are added first, gradually extending to those reflections with smaller amplitudes in many steps. The contribution of a reflection to the electron density is proportional to the square of its structure-factor amplitude according to Parseval's theorem, as shown in equation (25.2.2.2). This favours the protocol of extending the stronger reflections first so that they can be more reliably estimated. These stronger reflections will be used to phase relatively weaker subsequent reflections.
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(3) Extension in figure-of-merit step: To extend phases for those structure factors with experimentally measured, albeit less accurate, phases and figures of merit, the reflections can be added in order of their figure of merit, starting from the highest to the lowest. It is advantageous to use the more reliably estimated phases with higher figure of merit to phase those reflections with lower figure of merit. This can be useful when working with initial phasing from MAD or MR sources.
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(4) Automatic mode: This combines the previous three extension schemes. The program automatically works out the optimum combination of the above three schemes according to the density-modification mode, the phase-combination mode and the nature of the input reflection data. The automatic mode is the default and is the recommended mode of choice unless specific circumstances warrant a different choice.
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(5) All reflection mode: One advantage of the reflection-omit and perturbation-γ methods is that the strength of extrapolation of a structure-factor amplitude is a good indicator of the reliability of its corresponding phase. As a result, a phase-extension scheme is unnecessary in reflection-omit calculations; all reflections may be included from the first cycle.
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