On 3/2/12 9:31 AM, albert wrote: > I've got a 20 aa loop and I am wondering will the Loop refinement > protocol in Modeller can handle such big loop? Is there any parameters > can be refined to get more reliable model for such big loop?

Modeller will model a loop of any length, but the longer the loop, the larger the conformational space that needs to be explored and so the less likely you are to sample the global minimum. As a general rule of thumb, the longer your loop, the more models you need to build to sample the space. For example, the ModLoop web server builds 300 models and works reasonably well for short loops (maybe up to 8 or 12 residues). For 20 aa loop, you'd have to build many more models.

Ben Webb, Modeller Caretaker