On 2/8/13 12:29 AM, Anirban wrote: > I am trying to model a protein for which there is a gap (resi 65 - resi > 75; a loop)between two helices. I do not wish to add the missing 10 > residues and want to leave the helices unjoined . But MODELLER always > automatically joins the two helices (resi 64 with resi 76). How can I > tell MODELLER not to join the helices? Please suggest.

Add a chain break ('/' character) to your alignment between the two residues. Modeller will then treat the two parts of the sequence independently. You might want to add a weak distance restraint between the two residues though to stop them drifting too far apart.

Ben Webb, Modeller Caretaker