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:

# 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:

# 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:

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:

# 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).

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.

The relax user manual (PDF), created 2020-08-26.