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In recent years, several methods for determining ab initio three-dimensional shape from solution scattering have been reported. In order to clarify the common and unique features of these programs, we verified the stability and convergence of three major programs, 'dammin', 'saxs3d' and 'dalai_ga', for experimental data. Two different types of samples were prepared: troponin-C and denatured apomyoglobin. With all of the three programs, the stability of the models and fitting among different runs increased as the diameters of the packing spheres were reduced in the region larger than 4Å. In the case of troponin-C, the models obtained always bore a striking resemblance irrespective of different runs of three algorithms. The averaged model coincided with the averaged structure of multiple nuclear magnetic reasonance models. In the case of denatured apomyoglobin, the best models from different algorithms also have similar features. These results suggest that if the molecule contains highly mobile portions, the resulting model corresponds to the averaged structure.

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