On 06/24/2013 02:20 PM, Ramin Ekhteiari wrote: > I am predicting a protein by homology method, this protein has a long > loop (i.e., 40 resides) and there is no any residues in template for > modeling, I don't want modeler to model this loop site by energy > minimizing method and leave it. So how can I arrange this in build script.

Just remove those residues from your target sequence (you may want to add a chain break character, '/', so that Modeller doesn't try to link the residues either side of the loop).

Alternatively, if you're happy with the initial structure (and simply don't want to minimize it) see http://salilab.org/modeller/9.12/manual/node23.html

Ben Webb, Modeller Caretaker