Single model-free model script mode - the sample script

The sample script which demonstrates the optimisation of model-free model m4 which consists of the parameters {S2, τe, Rex} is model_free/single_model.py. The text of the script is:

# Script for model-free analysis.

# Create the data pipe.
name = 'm4'
pipe.create(name, 'mf')

# Set up the 15N spins.
sequence.read('noe.500.out', res_num_col=1, res_name_col=2)
spin.name('N')
spin.element(element='N', spin_id='@N')
spin.isotope('15N', spin_id='@N')

# Load the relaxation data.
relax_data.read(ri_id='R1_600',  ri_type='R1',  frq=600.0*1e6, file='r1.600.out',  res_num_col=1, data_col=3, error_col=4)
relax_data.read(ri_id='R2_600',  ri_type='R2',  frq=600.0*1e6, file='r2.600.out',  res_num_col=1, data_col=3, error_col=4)
relax_data.read(ri_id='NOE_600', ri_type='NOE', frq=600.0*1e6, file='noe.600.out', res_num_col=1, data_col=3, error_col=4)
relax_data.read(ri_id='R1_500',  ri_type='R1',  frq=500.0*1e6, file='r1.500.out',  res_num_col=1, data_col=3, error_col=4)
relax_data.read(ri_id='R2_500',  ri_type='R2',  frq=500.0*1e6, file='r2.500.out',  res_num_col=1, data_col=3, error_col=4)
relax_data.read(ri_id='NOE_500', ri_type='NOE', frq=500.0*1e6, file='noe.500.out', res_num_col=1, data_col=3, error_col=4)

# Initialise the diffusion tensor.
diffusion_tensor.init(10e-9, fixed=True)

# Create all attached protons.
sequence.attach_protons()

# Define the magnetic dipole-dipole relaxation interaction.
interatom.define(spinid1='@N', spin_id2='@H', direct_bond=True)
interatom.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.02 * 1e-10)
#interatom.unit_vectors()

# Define the CSA relaxation interaction.
value.set(-172 * 1e-6, 'csa')

# Select the model-free model.
model_free.select_model(model=name)

# Grid search.
minimise.grid_search(inc=11)

# Minimise.
minimise.execute('newton')

# Monte Carlo simulations.
monte_carlo.setup(number=100)
monte_carlo.create_data()
monte_carlo.initial_values()
minimise.execute('newton')
eliminate()
monte_carlo.error_analysis()

# Finish.
results.write(file='results', force=True)
state.save('save', force=True)



The relax user manual (PDF), created 2016-10-28.