Dear All,

I have a small issue in getting correct models after optimizing selected atoms. Instead I am getting models with distorted atoms in some residues.

Actually, what I have done is as follows: I tried to build a models for single mutant with separate optimization on neighbor residues ( residues that are located with in 15Å of mutated residue) by using mutate_model.py where I used the default optimize ,refine and restraints with random deviation equal to 4 but I didn’t get that which parameters that leads atom distortion in optimized models. So kindly give me some suggestion about the parameters that I can tune to resolve the atom distortion.

def optimize(atmsel, sched): for step in sched: step.optimize(atmsel, max_iterations=200, min_atom_shift=0.001) refine(atmsel) cg = conjugate_gradients() cg.optimize(atmsel, max_iterations=200, min_atom_shift=0.001) def refine(atmsel): 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(atmsel, init_velocities=init_vel, temperature=temp, max_iterations=its, equilibrate=equil) init_vel = False def make_restraints(mdl1, aln): rsr = mdl1.restraints rsr.clear() s = selection(mdl1) for typ in ('stereo', 'phi-psi_binormal'): rsr.make(s, restraint_type=typ, aln=aln, spline_on_site=True) for typ in ('omega', 'chi1', 'chi2', 'chi3', 'chi4'): rsr.make(s, restraint_type=typ+'_dihedral', spline_range=4.0, spline_dx=0.3, spline_min_points = 5, aln=aln, spline_on_site=True)

s.randomize_xyz(deviation=4.0)

Thanking you in advance

With Regards Mahesh V