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Figure 2
Comparison of different substructure determination algorithms for a protein using PDB entry 6e9c. (a) The runs of four different phase-retrieval algorithms with and without phase constraints (the π-half variant and tangent formula) across 750 Fourier iterations, all starting with the same random phase values. The red dots represent the use of the tangent formula. (b)–(d) Recovered electron-density maps of the three different RAAR algorithms superimposed with the reference heavy atoms. The standard RAAR algorithm is shown in blue [(a) and (b)], the standard RAAR algorithm incorporating π-half phase perturbation for weak reflections is shown in orange [(a) and (c)], and the standard RAAR algorithm incorporating the π-half phase perturbation and tangent formula (i.e. the modified phase-retrieval algorithm) is shown in purple [(a) and (d)]. The green balls represent 15 Se atoms in the asymmetric unit from the PDB-deposited structure and the red balls are the equivalent Se sites that are symmetry expanded according to the space-group information. The directions of the three unit-cell axes are also shown in the maps and all three electron-density maps are contoured at the same value of 5σ.

IUCrJ
Volume 11| Part 4| July 2024| Pages 587-601
ISSN: 2052-2525
https://doi.org/10.1107/S2052252524004846