Stéphane Téletchéa wrote: > I'm using modeller to model in two or three steps my system. > > I'm first modelling conserved residues (10 models), and then use the > best model (from modeller's objective function) to produce the loops. > > From this first to the second step, i'm using a script, but i was > figuring if there was a built-in function to do this automatically > (so i could merge the two steps into one script). I would think of > best_model.py or something like this, but i'm not sure if this exists > (i think i saw something like this once but i've not been able to > find it again).

Sure, there are various ways you could do this. One way is to use a script similar to that at http://salilab.org/modeller/9v4/manual/node29.html to build your first 10 models. By querying a.outputs you can find the best model. You can then do the loop refinement on that model in the same script by creating a loopmodel object and then proceeding as in a regular loopmodel run.

Ben Webb, Modeller Caretaker