ipcs.m
3D reconstruction of paramagnetic centre probability density from PCS data using the Kuprov-Charnock equation (http://dx.doi.org/10.1039/C4CP03106G); the user supplies atomic coordinates and pseudocontact shifts, the algorithm uses Tikhonov regularisation, and in the parameter descriptions below "source" denotes the paramagnetic-centre probability density that generates the pseudocontact shift, while "solution" denotes the pseudocontact shift itself.
Syntax
[source_cube,ranges,pred_pcs,err_ls,reg_a,reg_b]=ipcs(parameters,npoints,lambda)
Parameters
parameters.xyz - nuclear coordinates as [x y z] with multiple rows
at which PCS has been measured, in Angstrom.
parameters.xyz_all - atomic coordinates as [x y z] with multiple rows
for all atoms in the structure, in Angstrom.
parameters.expt_pcs - pseudocontact shift in ppm at each nucleus.
parameters.chi - effective magnetic susceptibility tensor, in units
of Angstrom^3.
parameters.margins - a six-element vector specifying margins to take
around the bounding box of the nuclear coordina-
tes supplied, to eliminate the effects of the
periodic boundary conditions.
parameters.box_cent - Cartesian coordinates of the centre of the source
box, in Angstrom
parameters.box_size - size of the source box in X, Y, and Z directions,
in Angstrom
parameters.plot - a cell array of strings specifying the plotting
options at each iteration:
'diagnostics' - diagnostic output
'density' - probability density
'molecule' - molecular structure
'tightzoom' - zooms the plot to the
molecular bounding box
'box' - source box
parameters.confine - source confinement radii (a two-element vector
in Angstrom). The density would only be varied
in points that are no closer than the first ra-
dius to any atom and no further away than the
second radius from the nearest atom.
parameters.sharpen - source contrast control; leave at zero unless
you know what you are doing.
parameters.guess - optional initial guess for the source density.
If this is supplied on a different grid from
the current one, it will be resampled by cubic
interpolation
parameters.equation - 'poisson' to recover the right hand side of the
Poisson's equation, 'kuprov' to recover the
probability density.
parameters.gpu - set to 1 of you have an NVidia GPU, otherwise
set to 0.
npoints - number of grid points in each dimension of the
solution cube, a positive integer; at least 64
is recommended.
lambda - Tikhonov regularization parameter; start with 1,
then use lcurve.m function to determine it
more precisely
Returns
source_cube - source term cube with dimensions ordered as
[X Y Z].
ranges - Cartesian axis extents for the source cube as
[xmin xmax ymin ymax zmin zmax] in Angstroms.
pred_pcs - pseudocontact shifts produced by the source
cube returned in the first parameter.
err_ls - least squares penalty of the final source cube
reg_a - contrast penalty of the final source cube
reg_b - Tikhonov penalty of the final source cube
Examples
See the pseudocontact shift analysis tutorial and the examples in nmr_paramag directory of the standard example set supplied with Spinach.
Notes
For further information on the equations and algorithms used in this function see http://dx.doi.org/10.1039/C4CP03106G
See also
ppcs.m, kpcs.m, ippcs.m, ilpcs.m, lpcs.m, lcurve.m, centroid.m, csa2racs.m, eqmag.m, fieldscan_enlev.m, fieldscan_magn.m, geffect.m, hfc2pcs.m, hfc2pms.m, pcs2chi.m, pcs_combi_fit.m, pms2chi.m, probmax.m, Built-in_experiments, Hyperfine_shift_module
Version 1.9, authors: Elizaveta Suturina, Gareth Charnock, Ilya Kuprov
