I'm using Modeller 9.24 to induce a couple of mutations into a PDB. 

I noticed that when I execute model.mutate() and export the PDB, the residue indexes are completely different from the original file... ebery residue looses its original position in the sequence and gets renumbered to therever it lands.

Is there a way I can force modeller to stick to the original numbering?

Best
Pedro