jo hanna wrote: > In the advancde tutorial a model is built and refined and then the > ligands added, is this the way the modelling should be done? or it is > possible to build the model straight away around the ligands?

That is not what is done in the advanced tutorial; the modeling is done with the ligand included. A previous example is shown without the ligand included, for comparison.

Ben Webb, Modeller Caretaker