Hi Modellers,
I need to obtain loop conformation distributions in a tetramer structure. So I used loopmodel() to redefine the 4 loops in each subunit. I found that the 4 loops in each tetramer is not symmetrical. I therefore applied model_symmetry_define() in order to fix them the same during the optimisation.
Here I have a question. The code I have used is at http://salilab.org/modeller/manual/node160.html
However, in define_symmetry-3.atm file, the structure looks very bizarre. It has lost its secondary structure elements and 4 loops are not symmetrical at all.
So I tried to add the sequence alignment between the loop model and the template. I cannot work out the python code. Could some one kindly have a look what I have done wrongly please.
Here is the code:
# Example for: model.symmetry.define()
# This will force two copies of RCK4 to have similar mainchain # conformation.
log.level(1, 1, 1, 1, 0) env = environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib')
#env.io.atom_files_directory = 'xxx' env.io.atom_files_directory = '.'
def defsym(lop, aln, seg1, seg2): for (set, seg) in [(2, seg1), (3, seg2)]: lop.pick_atoms(aln, pick_atoms_set=set, selection_segment=seg, atom_types='All', selection_status='INITIALIZE', selection_search='SEGMENT') lop.symmetry.define(symmetry_weight=1.0, add_symmetry=(True, False))
# Generate two copies of a segment: lop = model(env, file='model-nam', model_segment=('1:A', '110:D')) aln = alignment(env) aln.append_model(lop, align_codes='model-nam', atom_files='tmp-nam') aln.append_model(lop, align_codes='model-nam'+'_ini', atom_files='tmp-nam'+'_ini') lop.generate_topology(aln, sequence='model-nam'+'_ini') lop.transfer_xyz(aln) lop.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES') #lop.rename_segments(segment_ids=('A', 'B')) #, renumber_residues=(1, 1))
myedat = energy_data(dynamic_sphere = False) lop.energy(edat=myedat) lop.randomize_xyz(deviation=6.0) # Define the two segments (chains in this case) to be identical: defsym(lop, aln, seg1=('39:A', '49:A'), seg2=('39:B', '49:B'))
# Make them identical by optimizing the initial randomized structure # without any other restraints: lop.energy(edat=myedat) lop.write(file='define_symmetry-1.atm') lop.optimize(max_iterations=300, edat=myedat) lop.write(file='define_symmetry-2.atm') lop.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 lop.restraints.make(aln, restraint_type='stereo', spline_on_site=False, edat=myedat) lop.randomize_xyz(deviation=3.0) for method in (1, 3, 1): # 1 = conjugate gradients, 3 = molecular dynamics lop.optimize(max_iterations=300, md_return='FINAL', edat=myedat, optimization_method=method, output='REPORT') lop.write(file='define_symmetry-3.atm') lop.energy(edat=myedat)
# Create a blank alignment so that superpose uses its 1:1 default aln = alignment(env)
lop = model(env, file='define_symmetry-3.atm', model_segment=('39:A', '49:A')) lop2 = model(env, file='define_symmetry-3.atm', model_segment=('39:B', '49:B')) lop.pick_atoms(aln, atom_types='All') lop.superpose(lop2, aln)
Also, what does aln.append_model(lop, align_codes='model-nam'+'_ini', atom_files='tmp-nam'+'_ini') mean?
The erro message by executing the above .py file is: "_modeller.error: transfe_682E> Structural information is not available for all sequences in the alignment. Aborting."
Thank you very much.
Binbin