Respected Sir, I am interested in knowing more about modeller. So, I request you to help me for the same. The following are the questions: 1) what is the protocol for starting with the top scripts, i.e, starting with alignment that what..? 2)is transfer_xyz.top to be carried out first before model-default or the other way? 3) will not modeller(model-default.top) itself build the loop. Then why is the loop top script for? if i want to bulit the loop separately using loop top script, is it that i have to carry out loop topscript first before model-default top script or the other way? 4)During model-default. top, if for certain residues co-ordinates are not assigned then what is the solution for that? 5)In one of the article, i have read, after building the model it is to compare the Z score for both the template and the target. where will be the Z score given, will it be given in the log file of model-default. 6)will modeller show any error if the target and the template sequences differ in lenght? 7)After building a model for the target, how will i be able to improve the structure? if i iterate the same procedure will it improve the structure? I would be grateful to you if you could help me in finding answers for the above questions. Thanking you and waiting for your reply. Sincerely, Sameer. H