Re: [modeller_usage] side-chain torsion angles

On Wed, Mar 24, 2004 at 11:56:16AM +0000, Binbin Liu wrote: > I got one hunderd models. The side-chain torsion angles of the interesting > residues are vary. Does anybody know why. Does MODELLER calculate the torsion > based on some rules or it is by chance.

The torsion angles are determined by the restraints acting on the corresponding atoms. These are in turn taken from the defined dihedral angles in the topology and parameter files - e.g. modlib/top_heav.lib and modlib/par.lib. See also http://salilab.org/modeller/FAQ.html#17

The angles are different in the different models because the starting conditions for each model are different, and there are many local minima in this sort of optimization problem.

Ben Webb, Modeller Caretaker