Dear Modellers, I'm building a pentamer with assial symmetry, I'm new on modeller 8v1 and my input doesn't work. Mod8v1 builds the pentamer but when starts the refinement this error occurred:
defsym(mdl, aln, seg1=('1:A', '211:A'), seg2=('1:B', '211:B')) TypeError: defsym() got an unexpected keyword argument 'seg2'
My input is:
from modeller.automodel import * log.verbose() log.level(1, 1, 1, 1, 0) env = environ() env.io.atom_files_directory = './:../atom_files'
a = automodel(env, alnfile = '*.pir', knowns = 'xxx', sequence = 'vvv')
a.starting_model= 1 a.endind_model = 1 a.make()
def defsym(mdl, aln, seg1, seg2): for (set, seg) in [(2, seg1), (3, seg2)]: mdl.pick_atoms(aln, pick_atoms_set=set, selection_segment=seg, atom_types='ALL', selection_status='INITIALIZE', selection_search='SEGMENT') mdl.symmetry.define(symmetry_weight=1.0, add_symmetry=(True, False))
def defsym(mdl, aln, seg1, seg3): for (set, seg) in [(2, seg1), (4, seg3)]: mdl.pick_atoms(aln, pick_atoms_set=set, selection_segment=seg, atom_types='ALL', selection_status='INITIALIZE', selection_search='SEGMENT') mdl.symmetry.define(symmetry_weight=1.0, add_symmetry=(True, False))
def defsym(mdl, aln, seg1, seg4): for (set, seg) in [(2, seg1), (5,seg4)]: mdl.pick_atoms(aln, pick_atoms_set=set, selection_segment=seg, atom_types='ALL', selection_status='INITIALIZE', selection_search='SEGMENT') mdl.symmetry.define(symmetry_weight=1.0, add_symmetry=(True, False))
def defsym(mdl, aln, seg1, seg5): for (set, seg) in [(2, seg1), (6, seg5)]: mdl.pick_atoms(aln, pick_atoms_set=set, selection_segment=seg, atom_types='ALL', selection_status='INITIALIZE', selection_search='SEGMENT') mdl.symmetry.define(symmetry_weight=1.0, add_symmetry=(True, False))
# Generate five copies of a segment: code = 'xxx' mdl = model(env, file=code, model_segment=('1:A', '211:E')) aln = alignment(env) aln.append_model(mdl, align_codes=code, atom_files=code) aln.append_model(mdl, align_codes=code+'_ini', atom_files=code+'_ini') mdl.generate_topology(aln, sequence=code+'_ini') mdl.transfer_xyz(aln) mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES') mdl.rename_segments(segment_ids=('A', 'B'), renumber_residues=(1, 1)) mdl.rename_segments(segment_ids=('B', 'C'), renumber_residues=(1, 1)) mdl.rename_segments(segment_ids=('C', 'D'), renumber_residues=(1, 1)) mdl.rename_segments(segment_ids=('D', 'E'), renumber_residues=(1, 1))
myedat = energy_data(dynamic_sphere = False) mdl.energy(edat=myedat) mdl.randomize_xyz(deviation=6.0)
# Define the two segments (chains in this case) to be identical: defsym(mdl, aln, seg1=('1:A', '211:A'), seg2=('1:B', '211:B')) defsym(mdl, aln, seg1=('1:A', '211:A'), seg3=('1:C', '211:C')) defsym(mdl, aln, seg1=('1:A', '211:A'), seg4=('1:D', '211:D')) defsym(mdl, aln, seg1=('1:A', '211:A'), seg5=('1:E', '211:E'))
# Make them identical by optimizing the initial randomized structure # without any other restraints: mdl.energy(edat=myedat) mdl.write(file='define_symmetry-1.atm') mdl.optimize(max_iterations=300, edat=myedat) mdl.write(file='define_symmetry-2.atm') mdl.energy(edat=myedat)
# Now optimize with stereochemical restraints so that the # result is not so distorted a structure (still distorted # because optimization is not thorough): myedat.dynamic_sphere = True mdl.restraints.make(aln, restraint_type='stereo', spline_on_site=False, edat=myedat) mdl.randomize_xyz(deviation=3.0) for method in (1, 3, 1): # 1 = conjugate gradients, 3 = molecular dynamics mdl.optimize(max_iterations=300, md_return='FINAL', edat=myedat, optimization_method=method, output='REPORT') mdl.write(file='define_symmetry-3.atm') mdl.energy(edat=myedat)
# Create a blank alignment so that superpose uses its 1:1 default aln = alignment(env)
mdl = model(env, file='define_symmetry-3.atm', model_segment=('1:A', '211:A')) mdl2 = model(env, file='define_symmetry-3.atm', model_segment=('1:B', '211:B')) mdl3 = model(env, file='define_symmetry-3.atm', model_segment=('1:C', '211:C')) mdl4 = model(env, file='define_symmetry-3.atm', model_segment=('1:D', '211:D')) mdl5 = model(env, file='define_symmetry-3.atm', model_segment=('1:E', '211:E')) mdl.pick_atoms(aln, atom_types='MNCH') mdl.superpose(mdl2, mdl3, mdl4, mdl5, aln)
Please, someone could help me telling where are the problems? Thank you very much.
Giovanni