On 4/2/14, 2:47 PM, Manoj Singh wrote: > I am using mutate_model.py for making mutations. I have two questions. > > 1. How can I read the original pdb from different directory and put > output structure in current directory.

You would have to modify the script. It's pretty elementary Python.

> 2. How can I read and print hydrogen of original pdb in mutated pdb > structure (except of mutated residue)

I'm not sure what you mean by "print hydogren" but you set env.io.hydrogen=True to have Modeller read hydrogens in from PDB files, and use top_allh.lib rather than top_heav.lib.

Ben Webb, Modeller Caretaker