• protein crystallography;
  • computer programs;
  • unrestrained refinement;
  • alternative conformations

Increased mobility of poorly ordered atoms compared to well ordered ones in unrestrained refinement was adopted as the basis for the development of a method for predicting alternative conformations. Two programs for the analysis of atomic mobility are presented. Shift_plot may be useful for visual analysis of magnitudes of atomic shifts in refinement. AC_prediction implements automatic decision-making procedures based on atomic shift magnitudes in unrestrained refinement to highlight the specific residues that are likely to harbour alternative conformations and that hence require checking via electron density maps.