vidhya ganesh wrote: > I am new to modeller. I am using mod9v4. I have quite few doubts. I > performed homology modeling of particular protein , done all steps and > got a model. But i have to know, how to build ions in my model??

Ions are built in the same way as any other HETATM residue - just use the '.' residue type in your alignment file and set env.io.hetatm to True, and Modeller will copy the ion residue from the template to the target. See http://salilab.org/modeller/9v5/manual/node18.html

Ben Webb, Modeller Caretaker