In order to apply the simulated annealing (SA) algorithm, a separation-based coding procedure for complex columns sequence synthesis is presented in this paper. After the recall of the combinatorial aspect of separation sequence synthesis, the main steps of SA procedure are proposed. Then we have focused our attention on the definition of a local solution, that is an acceptable sequence structure, and on the evolution of this one to another acceptable solution. Due to the necessary feasible aspect of a reachable structure solution, we chose a structure-based coding for sequences. It consists in defining, for each structure, a list of elements describing it in a depth first manner and in transforming it by three elementary rules : creation of a complex separator, removal of a complex separator and transformation without changing the type or the number of separators. Many examples are explained, and the implementation into SA procedure is studied in detail.