[modeller_usage] Is it possible to do single residue optimization for automodels ?

["Mahesh Velusamy" <>]

Dear All,

Since, My main objective is to get a better conformational sample for a
particular single point mutation, I have generated a 100 number of SPM
models through automodel but Since, Automodel uses the distance restraints
from the template target structure alignment there is not much variations
when comparing with the original structure.  So I thought to relax the
restrains by doing additional optimization on mutated position alone like
we see in mutate_model.py http://salilab.org/modeller/wiki/Mutate%20model.


Then, I try to modified the automodel script as same like mutate_model.py
but I endup in lot of confusions that

1.what shoud I keep for :
    #conjugate gradient
    for step in sched:
        step.optimize(atmsel, max_iterations=200, min_atom_shift=0.001

2.Whether should I include make restraints function ?

3. Is it Ok If I do only optimize and refine step ?

def optimize(atmsel, sched):
    #conjugate gradient
    for step in sched:
        step.optimize(atmsel, max_iterations=200, min_atom_shift=0.001)
    #md
    refine(atmsel)
    cg = conjugate_gradients()
    cg.optimize(atmsel, max_iterations=200, min_atom_shift=0.001)


#molecular dynamics
def refine(atmsel):
    # at T=1000, max_atom_shift for 4fs is cca 0.15 A.
    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


#use homologs and dihedral library for dihedral angle restraints
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)

a = MyModel(env, alnfile=current_file, knowns='3O26', sequence='R1Y',
assess_methods=(assess.DOPE, assess.GA341))
a.starting_model = 1
a.ending_model = 1
a.make()

So , Could you guide me on single residue optimization on automodel
structures ?

Thanking you in advance