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Figure 5
Illustration of PDB format for an exchanged amide H atom in an arginine residue (residue 38 of chain A). All three possibilities describe the same configuration: one H atom with occupancy qH = 0.77 and a D atom with complementary occupancy qD = 1 − qH = 0.23. Top, method (i), using double conformation and different atom names. Middle, method (ii), implying the D atom with qD = 1 − qH. Bottom, method (iii), using an apparent occupancy. The occupancy mimics the total scattering contributions of the H and D atoms, which are of different signs, and varies from −0.56 (H fully occupied) to 1 (D fully occupied).

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