On 4/1/10 6:01 AM, abdullah ahmed wrote: > I wanted to asked if there is a way to restrain the side-chain dihedrals > to angles of my choosing. If so could you please provide a brief sample > code of how to do it?

Yes, of course - you can add a custom dihedral restraint, e.g. to harmonically restrain chi1 in a CYS residue to 90 degrees, you could use:

a = mdl.atoms dih = features.dihedral(a['N:1'], a['CA:1'], a['CB:1'], a['SG:1']) mdl.restraints.add(forms.gaussian(group=physical.chi1_dihedral, feature=dih, mean=math.pi/2., stdev=0.01))

You might also want to look at forms.cosine which is commonly used for restraining dihedrals.

Ben Webb, Modeller Caretaker