I want to use modeller to mutate the selected residues and obtain multiply models. But modeller usually give just one model.

Then would you tell me how to redesign the python to generate multiply models? Here is the script that I have used to generate the mutant.

# Example for: selection.mutate()

from modeller import *

env = environ()

env.libs.topology.read(file='$(LIB)/top_heav.lib')

env.libs.parameters.read(file='$(LIB)/par.lib')

code = "t_str.pdb"

aln = alignment(env)

mdl = model(env, file=code)

aln.append_model(mdl, atom_files=code, align_codes=code)

sel_1 = selection(mdl.residues["40:A"])

sel_1.mutate(residue_type="SER")

aln.append_model(mdl, align_codes="1fas-1")

mdl.clear_topology()

mdl.generate_topology(aln['1fas-1'])

mdl.transfer_xyz(aln)

mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES')

mdl.write(file="4lyzT40S_S91V.pdb")