[modeller_usage] help at first script

Hi, I am a new user of modeller9v3 and I can't write the first script with which I will search for sequences similar to the target one. I also consult the manual of modeller6v2, will I confuse? If I have understood well, the appropriate command is sequence_search which has many options. I must use all the options? I can't understand the syntax of the command, i.e I must type mod9v3 before the command, but I read that the syntax is mod9v3 script_ .top. This script what does it contain? (I can't understand anything becose I start now to deal with bioinformatics). Please help me. Thank you very much, Maria.