Visualization of two ligands from the PDB together with electron-density maps where LLDF values provide misleading indications. (a) Example of a false positive: the map for PDB entry 1kcc at atomic resolution (1.0 Å; Shimizu et al., 2002) shows electron density for a well placed ligand GTR where each atom is individually resolved. The high RSCC value reflects the good fit. In contrast, the LLDF value is high so that the ligand is incorrectly marked as an electron-density fit outlier in the current VR. (b) Example of a false negative: the ligand FER in PDB entry 1kyz (Zubieta et al., 2002) has a poor fit to the electron density, resulting in large amounts of difference density. The LLDF value of 1.3 results in the ligand not being marked as an electron-density fit outlier in the current VR, whereas the low RSCC value suggests a problem.