modeller_usage June 2016

modeller_usage@salilab.org

5 participants
11 discussions

[Fwd: How to optimize & refine the conformation of the mutant side chain along with the backbone by using modeller (mutate_model.py ) ?]
by Mahesh Velusamy 06 Jun '16

06 Jun '16

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

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modeller_usage June 2016