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