On 05/24/2013 10:35 AM, HERBERT MAX VENTHUR PE¥A wrote: > I've read papers where the amount of models generated are not indicated, > however, indicate that more than 1 model was obtained. The script of the > tutorial of modeller provides 5 models. My question is, Is there any > effect in the quality of the model if I generate several models? for > example, 200 models versus 5 models?
Of course. The more models you generate, the more you sample the conformational space. (Obviously you have to cluster or pick the "best" model(s) from that sample.) This is particularly important for loop modeling, where the space to sample increases rapidly with loop length (the ModLoop web server builds 300 models, which is probably good for loops of up to 8-12 residues or so, but for longer loops, you'd want more models).
Ben Webb, Modeller Caretaker