[modeller_usage] How to optimize & refine the conformation of the mutant side chain along with the backbone by using modeller (mutate_model.py ) ?

Dear All,

I want to know how to generate a mutant models with optimization and refinement on sidechain of mutated residue including backbone/near the residues by mutate_model.py.

Kindly , Let me know how to modify this and I hope this modification needs on the following lines (139 to 153)

#only optimize the selected residue (in first pass, just atoms in selected #residue, in second pass, include nonbonded neighboring atoms) #set up the mutate residue selection segment #s = selection(mdl1.chains[chain].residues[respos]) s = selection(mdl1.chains[chain].residues[respos])

mdl1.restraints.unpick_all() mdl1.restraints.pick(s)

s.energy()

s.randomize_xyz(deviation=4.0)

mdl1.env.edat.nonbonded_sel_atoms=2 optimize(s,sched)

Thanking you in advance