An example fragment showing the positioned and refined search model 1ogk_E_CHNSAW (coral) compared with the final deposited structure (PDB code 1w2y
, green) for dUTPase from C. jejuni (§4.1). The map was generated using phases generated by ACORN density modification, starting from the search-model coordinates. At the top of the figure are two regions where the search model matches the final coordinates well. At the bottom of the figure is part of a loop which differs substantially between the search model and the final coordinates. The ACORN density clearly follows the correct coordinates rather than being biased to the search model. The map is atomic in nature, as it uses coefficients from the phase-extension procedure. It also noticeable that ACORN picks out O and N atoms better than C atoms. The figure was prepared using CCP4mg (Potterton et al., 2004).