Brandon Mills wrote: > I am generating models for a strained protein chimera using weakened > restraints on one of the two domains, to see if Modeller will unfold the > domain to relax the mechanical strain. I have weakened all Ca-Ca and N-O > distance restraints (roughly 3,800 out of 16,500 total restraints) by a > factor of 100, but it had nearly no effect on my output models. Is there > something fundamentally flawed with this approach? Are there other > specific restraints that might be recommended for weakening, or would it > be best to simply weaken all restraints associated with the targeted > domain?
This may just be a sampling issue. Remember that the starting structure for comparative modeling is the target sequence threaded onto the template structure, so if you want to deviate from the template you may have to overcome local minima first. Longer simulations and/or different starting conditions may help you here.
Ben Webb, Modeller Caretaker