Dany Naranjo Feliciano wrote: > When I use this script some parts of my protein appears streched. > Should I put water molecule for better refinment? Why I obtein worse > models with refine option?
Poor models are usually a consequence of a poor alignment - they will only get worse with more refinement if your scoring function is bad, unless you simply have insufficient sampling. Refinement does not make your models worse otherwise, since it's using the same scoring function as any other optimization of the models.
In comparative modeling solvation is usually implicit, in that the solvation of the template is transfered to the target, so introduction of water molecules probably won't help you. If you have crystal waters, however, there may be some benefit in introducing them with appropriate distance restraints.
Ben Webb, Modeller Caretaker