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
Giovanni Grazioso wrote: > 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'
Your script is incorrect. You should look at some of the examples in the manual, tutorial, wiki, and mailing list archives, or check out the Python tutorial at www.python.org.
> a = automodel(env, > alnfile = '*.pir', > knowns = 'xxx', > sequence = 'vvv')
You have to put a real filename in for your alignment, not "*.pir". "knowns" and "sequence" must also be real align codes.
> a.starting_model= 1 > a.endind_model = 1
ending_model.
> 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))
You only need to define the subroutine once - I don't know why you have it in here four times.
> 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))
I'm not sure what you're trying to do here, but what will happen is that you call the first two chains 'A' and 'B', then you call them 'B' and 'C', and so on. I think what you might actually want is mdl.rename_segments(segment_ids=('A', 'B', 'C', 'D', 'E'), renumber_residues=(1, 1, 1, 1, 1))
> # 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'))
Here you probably want defsym(mdl, aln, seg1=('1:A', '211:A'), seg2=('1:B', '211:B')) defsym(mdl, aln, seg1=('1:A', '211:A'), seg2=('1:C', '211:C')) defsym(mdl, aln, seg1=('1:A', '211:A'), seg2=('1:D', '211:D')) defsym(mdl, aln, seg1=('1:A', '211:A'), seg2=('1:E', '211:E'))
> 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)
superpose only works on one model at a time, so you could write this as: for m in (mdl2, mdl3, mdl4, mdl5): mdl.superpose(m, aln)
Ben Webb, Modeller Caretaker
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Giovanni Grazioso -
Modeller Caretaker