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