Good morning everyone!

I am using the Mutate_model.py in Modeller to put mutations to my protein. However, when I generate the .pdb file of the mutated protein, the crystal water, that was in the initial pdb, does not appear. I expected mutate two amino acid residues.

Also, the number of atoms has been reduced for amino acids. For example, for amino acid ILE 15, the original pdb has 18 atoms, but the mutated pdb (after running in modeller), has 8 atoms and so on.