[modeller_usage] How to write a dope score for selected region of optimized atoms along with whole model?

["Mahesh Velusamy" <>]

Dear All,

I have tried generate a models for single point mutation along with
own optimization and refinement criteria on the selected region of atoms
around the mutated residue which works fine but the problem is in dope
score.

I thing modeler generate DOPE score only for selected region of optimized
atoms but I want to write the dope score for optimized region of atoms
along with whole structure. Is it possible to do the same?

Here is my script used for select part of region from model and perform
optimization:


class MyModel(automodel):
     def select_atoms(self):
        s =
selection(self.atoms['CA:'+"275"+':'+"A"].select_sphere(5)).by_residue()
        self.restraints.unpick_all()
        self.restraints.pick(s)
        s.energy()
        s.randomize_xyz(deviation=4)
        return s

    def optimize(s, sched):
        for step in sched:
            step.optimize(s, max_iterations=200, min_atom_shift=0.001)
        refine(s)
        cg = conjugate_gradients()
        cg.optimize(s, max_iterations=200, min_atom_shift=0.001)

    def refine(self,s,actions):
        md = molecular_dynamics(cap_atom_shift=0.39, md_time_step=4.0,
                                md_return='FINAL')
        init_vel = True
        for (its, equil, temps) in ((200, 20, (150.0, 250.0, 400.0, 700.0,
1000.0)),
                                    (200, 600,
                                     (1000.0, 800.0, 600.0, 500.0, 400.0,
300.0))):
            for temp in temps:
                md.optimize(s, init_velocities=init_vel, temperature=temp,
                             max_iterations=its, equilibrate=equil)
                init_vel = False

Thanking you in advance

With Regards
Mahesh V