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