On 2/7/11 7:22 AM, albert wrote: > I just find that Modeller could build model containing a small molecular > within it. And I am wondering how to building model including a peptide > from template?

It depends what you mean by "include", but if you want to treat it like any other ligand, just use the '.' residue type in your alignment and Modeller will copy it from template to target, and model it rigidly.

Ben Webb, Modeller Caretaker