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The statistical effects of translational noncrystallographic symmetry can be characterized by maximizing parameters describing the noncrystallographic symmetry in a likelihood function, thereby unmasking the competing statistical effects of twinning.

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A genetic algorithm has been developed to optimize the phases of the strongest reflections in SIR/SAD data. This is shown to facilitate density modification and model building in several test cases.

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A function for estimating the effective root-mean-square deviation in coordinates between two proteins has been developed that depends on both the sequence identity and the size of the protein and is optimized for use with molecular replacement in Phaser. A top peak translation-function Z-score of over 8 is found to be a reliable metric of when molecular replacement has succeeded.

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A procedure for model building is described that combines morphing a model to match a density map, trimming the morphed model and aligning the model to a sequence.

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The functionality of the molecular-replacement pipeline phaser.MRage is introduced and illustrated with examples.
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