Hi Mahesh,

I’m not an expert in modeler. But, I have carried out some modeling in the past with modeller. You can give different random seed number to get different conformation of your point mutation using the mutate_model.py

for example: env = environ(rand_seed=-49837) to env = environ(rand_seed=200)

By the way, I dont follow your logic when you say "there is not much variations”. For example, when you make changes to a surface residue you may get different side chain orientation, but if you have a buried residue surround by side chains, I believe you won’t get much changes as well as the size and charge will play a factor here.

All the best, David

> On Jun 27, 2016, at 8:08 AM, Mahesh Velusamy vmahesh@ibab.ac.in wrote: > > 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 > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage