I searched the archives and could not find how to do what seems to be a simple procedure. I have a sequence that has high homology with a published X-ray structure A. A second state of the protein is defined by the conformation of a conserved loop. A related protein B containing the conserved loop is in the second state, albeit with lower homology. I would like to model the sequence in the second state using the structure A as a template, but using structure B to model the loop only. I believe I need an alignment like this: proteinA aaaaaaaaaaaaaaaa-------------------aaaaaaaaaaaa proteinB ----------------------------bbbbbbbbbbb--------------------- sequence cccccccccccccccccccccccccccccccccccccccccccccc

I realize this is a very simple question. I've been going through the manual and searching the archives and cannot figure out how to do it. Any help will be much appreciated. Thanks. EGY