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
Modify the argument of the "selection" method:
https://salilab.org/modeller/9v8/manual/node221.html
Many more thanks Martin Klvana and I have one more query that :
do you know How to generate a model with double mutant/combination of mutants by using mutate_model.py ?
I hope its modifying the (mutate_model.py) script to call mutate() twice but I got stuck in between.
Also Is it ok ? if I follow this way https://salilab.org/archives/modeller_usage/2010/msg00402.html
Thanking you in advance
Yes, you can mutate multiple amino acid residues. For each mutation, select the amino acid residue to be substituted using "pick_atoms" method, and then apply "mutate(residue_type=)" method to the selection:
https://salilab.org/modeller/8v0/manual/node125.html
Dear Martin,
Thank you somuch and You are correct If our objective is to mutate multiple residue into particular(single) residue with the following line :
# Mutate the selected residues into HIS residues (neutral HIS):
mdl.mutate(residue_type='HIS')
But I want to mutate every single residue (large in number) into particular residue.
For example my interest residues to mutate:
275A,104A
276A,276H
270I
So , I have modified the script for both to do mutation of multiple residue and their optimization.
https://www.researchgate.net/post/How_to_generate_a_model_with_double_mutant_combination_of_mutants_by_using_mutate_modelpy
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