To be honest, the best way to use complex molecules in ATK 11.2 is to import them (as xyz files). There are several other builders you can use which can export xyz, or of course you can still use the Molecular Builder in 2008.10 and export the Python script - ATK 11.2 can understand it. In future editions of ATK there will again be a molecular builder, although we cannot say precisely in which version it will appear.
