d'Auvergne protocol script mode - setting up the spin systems

To see how to set up the spin system data in all possible situations, please see Chapter 4 for a thorough description. Here two different methods are presented. The first is by extracting the spins from a PDB file which is first loaded with:

[firstnumber=161]
# Load the PDB file.
structure.read_pdb('1f3y.pdb', set_mol_name='Ap4Aase', read_model=3)

This will read the 3 model from the 1F3Y PDB file and name the single molecule as `Ap4Aase'. The ¹⁵N and ¹H spins for the backbone and tryptophan indole sidechain are extracted from the structure with the user functions:

[firstnumber=164]
# Set up the 15N and 1H spins (both backbone and Trp indole sidechains).
structure.load_spins('@N', ave_pos=True)
structure.load_spins('@NE1', ave_pos=True)
structure.load_spins('@H', ave_pos=True)
structure.load_spins('@HE1', ave_pos=True)

As the PDB file does not contain isotope information, this is set with the user functions:

[firstnumber=169]
spin.isotope('15N', spin_id='@N*')
spin.isotope('1H', spin_id='@H*')

The spin ID `@N*' uses regular expression and will match both the `N' and `NE1' spins.

The alternative approach is if a structure is missing. This is the commented out code:

[firstnumber=172]
# Set up the 15N spins (alternative to the structure-based approach).
sequence.read(file='noe.500.out', dir=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5)
spin.element(element='N', spin_id='@N*')
spin.isotope('15N', spin_id='@N*')

# Generate the 1H spins for the magnetic dipole-dipole relaxation interaction (alternative to the structure-based approach).
sequence.attach_protons()

To use this, you will need to place comments (the # character) in front of the previous structure.read_pdb, structure.load_spins and spin.isotope user functions. Then uncomment the sequence.read, spin.element, spin.isotope and sequence.attach_protons user functions. The ¹⁵N spins will be extracted from the noe.500.out file. The spin.element and spin.isotope user functions set the information required for relax to understand which relaxation mechanisms are active. Finally the sequence.attach_protons user function will automatically attach protons to all nitrogen spin systems. As this method is devoid of atomic positional information, the N-H bonds are absent and the diffusion models requiring structural information (the spheroids and ellipsoid) must be skipped.