[modeller_usage] set sequence

I am new to Modeller and am running it under Windows XP. I have little experience with computer programming, but I was able to get the model-default example using 5fd1 and 1fdx in the examples\tutorial-model directory to run OK. Now as a test of my system, I want to try to model a short 25 amino acid stretch from a test protein on the crystal structure of a related protein that is about 400 residues long. I am trying to write a top script based on the 5fd1 and 1fdx example but I do not have a pdb name for my test protein in the SET SEQUENCE line of the program since it has not been crystallized. Can someone tell me what this command does, and how I might get around this problem? Thanks for your help.

RAF