Marco wrote: > I still have a question on the Tutorial. In the Advanced example some > news structures are used to improve the model using multiple > alignment. But some of this, like 1b8p, are already present in the > Basic example and discarded...This is not very clear, at least for > me.... :-)

There is no "best template" for comparative modeling in most cases - each PDB file gives you some information. The basic tutorial, as the name suggests, covers only very simple modeling where a single template is chosen based on the quality of the X-ray structure, sequence identity, etc. But in more advanced cases you may need to bring in information from other templates.

Ben Webb, Modeller Caretaker