Hi, thank you very much for the information, and I apologize for not being so detailed about my question/problem. With the information provided I was able to superimpose my two proteins but still not in the way I want to. I was given a photo of how it should look and my structure just does not seem to orientate the same way using the default method. I hope it is not too much trouble and are able to help me out. I attached my two proteins and a copy of the picture I was given to replicate. this with the objective to be able to duplicate the work with more complex proteins. 

ps. I am sorry for the quality of the photo, this was the best I could sharpen since they only have this one copy and are unable to duplicate the work. 

As you can see I am still left with some part of the protein not overlapped and my question and inquiry is how can I modify the structure so both proteins overlap or if the program can make the torshions or necessary turns so they fit.