Determine the PCS error due to structural noise via simulation.
align_id: The optional alignment ID string.
rmsd: The atomic position RMSD, in Å, to randomise the spin positions with for the simulations.
sim_num: The number of simulations, N, to perform to determine the structural noise component of the PCS errors.
file: The optional name of the Grace file to plot the structural errors verses the paramagnetic centre to spin distances.
dir: The directory name to place the Grace file into.
force: A flag which if True will cause the file to be overwritten.
The analysis of the pseudo-contact shift is influenced by two significant sources of noise - that of the NMR experiment and structural noise from the 3D molecular structure used. The closer the spin to the paramagnetic centre, the greater the influence of structural noise. This distance dependence is governed by the equation:
sqrt(3) * abs(delta) * RMSD sigma_dist = --------------------------- , r
where sigma_dist is the distance component of the structural noise as a standard deviation, delta is the PCS value, RMSD is the atomic position root-mean-square deviation, and r is the paramagnetic centre to spin distance. When close to the paramagnetic centre, this error source can exceed that of the NMR experiment. The equation for the angular component of the structural noise is more complicated. The PCS error is influenced by distance, angle in the alignment frame, and the magnetic susceptibility tensor.
For the simulation the following must already be set up in the current data pipe:
The protocol for the simulation is as follows:
The standard deviation will both be stored in the spin container data structure in the relax data store as well as being added to the already present PCS error (using variance addition). This will then be used in any optimisations involving the PCS.
If the alignment ID string is not supplied, the procedure will be applied to the PCS data from all alignments.