6 Jun
2016
6 Jun
'16
5:27 a.m.
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