d'Auvergne protocol script mode - relaxation interactions

The next step is to fully specify all of the relaxation interactions active on the spins of interest. Firstly the magnetic dipole-dipole interaction is defined between directly bonded nitrogens and protons:

# Define the magnetic dipole-dipole relaxation interaction.
interatom.define(spin_id1='@N', spin_id2='@H', direct_bond=True)
interatom.define(spin_id1='@NE1', spin_id2='@HE1', direct_bond=True)
interatom.set_dist(spin_id1='@N*', spin_id2='@H*', ave_dist=1.02 * 1e-10)

The regular expression `@N*' and `@H*' cannot be used with the dipole_pair. define user function as otherwise @N spins will be connected to @HE1 spins of the same tryptophan residue and @H spins to @NE1 spins. The average interatomic distance is set to 1.02 Ã…ngstrom (though the dipole_pair.set_dist user function expects the units of meters). The dipole_pair.unit_vectors is used to calculate the averaged unit vector between the two atoms.

Secondly the chemical shift anisotropy (CSA) relaxation mechanism is defined via the single command:

# Define the chemical shift relaxation interaction.
value.set(-172 * 1e-6, 'csa', spin_id='@N*')

If your system does not experience CSA relaxation, the value can be set to zero.

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