Dear All,
I hope you all know that there is script available in modeller
"mutate_model.py". To generate a mutant models and then optimize the
mutated residue following refinement in sidechain alone but I want to make
this process (optimization/refinement) including the backbone/near
residues instead of restricting only with sidechain.
So, Does anyone know how to modify the default script
I hope the 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