This sample script can be found in the sample_scripts directory and will be used as the template for the next sections describing how to use relax.
# Script for calculating NOEs. # Create the data pipe. pipe.create('NOE', 'noe') # Load the sequence from a PDB file. structure.read_pdb('Ap4Aase_new_3.pdb') structure.load_spins(spin_id='@N') structure.load_spins(spin_id='@NE1') # Load the reference spectrum and saturated spectrum peak intensities. spectrum.read_intensities(file='ref.list', spectrum_id='ref_ave') spectrum.read_intensities(file='sat.list', spectrum_id='sat_ave') # Set the spectrum types. noe.spectrum_type('ref', 'ref_ave') noe.spectrum_type('sat', 'sat_ave') # Set the errors. spectrum.baseplane_rmsd(error=3600, spectrum_id='ref_ave') spectrum.baseplane_rmsd(error=3000, spectrum_id='sat_ave') # Individual residue errors. spectrum.baseplane_rmsd(error=122000, spectrum_type='ref', res_num=114) spectrum.baseplane_rmsd(error=8500, spectrum_type='sat', res_num=114) # Peak intensity error analysis. spectrum.error_analysis() # Deselect unresolved spins. deselect.read(file='unresolved', res_num_col=1, spin_name_col=2) # Calculate the NOEs. minimise.calculate() # Save the NOEs. value.write(param='noe', file='noe.out', force=True) # Create Grace files. grace.write(y_data_type='peak_intensity', file='intensities.agr', force=True) grace.write(y_data_type='noe', file='noe.agr', force=True) # View the Grace files. grace.view(file='intensities.agr') grace.view(file='noe.agr') # Write the results. results.write(file='results', dir=None, force=True) # Save the program state. state.save('save', force=True)