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Figure 2
Stepwise illustration of the Loopwhole algorithm, applied to three missing glycines (PDB entry 1dmn; Kim et al., 2000BB23). All 2mFo − DFc and mFo − DFc electron-density maps are shown at 0.7σ and 3.0σ, respectively. (a) The PDB structure has no apparent gap: two residues are wrongly bound to one another (highlighted in brown). The gap is detected from the sequence. (b) The two residues immediately adjacent to the missing loop are removed, as these are often in the wrong conformation. (c) All homologous chains with the loop present are structurally aligned to the target structure model (only four homologs shown). (d) If the surrounding residues align well, the loop is grafted into the target structure model. By default, the top ten alignments are kept (only one shown). (e) After real-space optimization, the loop with the best density fit is kept provided the density fit and geometrical quality pass the filter criteria.

IUCrJ
Volume 5| Part 5| September 2018| Pages 585-594
ISSN: 2052-2525
https://doi.org/10.1107/S2052252518010552