If a structure contains disorder then the minor occupancy sites must be suppressed to leave a single representative atomic position that will then be matched against the chemical diagram. Suppressed atoms are not deleted; they simply take no further part in the establishment of the crystallographic connectivity and therefore will not be used in ConQuest 3D searches. In the majority of cases, the initial CIF file conversion will have dealt with any disorder in the structure. If there are atoms in the 3D structure that have not been dealt with correctly then these atoms can be suppressed and unsuppressed manually using either the Manual Edit dialogue or the More Info dialogue in the Visualiser pane. It is advisable to check that in the top menu, colour is set to by Element or Suppression.