Relax-fit script mode - setting up the spin systems

The first thing which needs to be completed prior to any spin specific command is to generate the molecule, residue and spin data structures for storing the spin specific data. In the sample script above this is generated from a PDB file, however a plain text file with the sequence information can be used instead (see the sequence.read user function on page [*] for more details). In the case of the sample script, the command

[firstnumber=6]
# Load the backbone amide 15N spins from a PDB file.
structure.read_pdb(name, 'Ap4Aase_new_3.pdb')

will load the PDB file Ap4Aase_new_3.pdb into relax. Then

[firstnumber=8]
structure.load_spins(spin_id='@N')
structure.load_spins(spin_id='@NE1')

will generate the molecule, residue, and spin sequence for the current data pipe. In this situation there will be a single spin system per residue generated corresponding to the backbone amide nitrogens as well as 15N spins set up for the tryptophan indole nitrogens. Although the 3D coordinates have been loaded into the program from the PDB file, this structural information serves no purpose when calculating R1 and R2 values.

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