Replacing a single residue in a structure

I have a structure i have been working with for a while, and I wish to replace the last residue in the sequence with a cysteine. I have tried to write a xml script that would perform the spot mutation, but I could not figure it out. Is there a specific rosetta function or way to perform spot mutations? I have also considered just manually replacing the residue with cysteine, and relaxing the structure through rosetta, but i'm not sure if the cysteine would stay in the sequence.