[modeller_usage] Issue in selected atoms optimization

["Mahesh Velusamy" <>]

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