Difference between revisions of "Ipcs.m"
(→Arguments) |
|||
| Line 12: | Line 12: | ||
parameters.xyz - nuclear coordinates as [x y z] with multiple rows | parameters.xyz - nuclear coordinates as [x y z] with multiple rows | ||
at which PCS has been measured, in Angstroms. | at which PCS has been measured, in Angstroms. | ||
| − | + | ||
parameters.xyz_all - atomic coordinates as [x y z] with multiple rows | parameters.xyz_all - atomic coordinates as [x y z] with multiple rows | ||
for all atoms in the structure, in Angstroms. | for all atoms in the structure, in Angstroms. | ||
| Line 25: | Line 25: | ||
tes supplied, to eliminate the effects of the | tes supplied, to eliminate the effects of the | ||
periodic boundary conditions. | periodic boundary conditions. | ||
| − | + | ||
parameters.box_cent - Cartesian coordinates of the centre of the solu- | parameters.box_cent - Cartesian coordinates of the centre of the solu- | ||
tion box, in Angstrom | tion box, in Angstrom | ||
| − | + | ||
parameters.box_size - size of the source box in X, Y, and Z directi- | parameters.box_size - size of the source box in X, Y, and Z directi- | ||
ons, in Angstrom | ons, in Angstrom | ||
| − | + | ||
parameters.plot - a cell array of strings specifying the plotting | parameters.plot - a cell array of strings specifying the plotting | ||
options at each iteration: | options at each iteration: | ||
'diagnostics' - diagnostic output | 'diagnostics' - diagnostic output | ||
| − | + | ||
'density' - probability density | 'density' - probability density | ||
| + | |||
| + | 'molecule' - molecular structure | ||
| − | |||
| − | |||
'tightzoom' - zooms the plot to the | 'tightzoom' - zooms the plot to the | ||
molecular bounding box | molecular bounding box | ||
| − | + | ||
'box' - source box | 'box' - source box | ||
Revision as of 17:24, 1 January 2017
3D reconstruction of paramagnetic centre probability density from PCS data using Kuprov-Charnock equation (http://dx.doi.org/10.1039/C4CP03106G).
Syntax
[source_cube,ranges,pred_pcs,diag_data]=ipcs(parameters,npoints,lambda)
Description
This function implements the three-dimensional paramagnetic centre probability density algorithm described in our forthcoming paper on the subject. The user needs to supply atomic coordinates and pseudocontact shifts. The algorithm uses Tikhonov regularisation.
Arguments
parameters.xyz - nuclear coordinates as [x y z] with multiple rows
at which PCS has been measured, in Angstroms.
parameters.xyz_all - atomic coordinates as [x y z] with multiple rows
for all atoms in the structure, in Angstroms.
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 solu-
tion box, in Angstrom
parameters.box_size - size of the source box in X, Y, and Z directi-
ons, 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
npoints - number of points in each dimension of the source
cube, a positive integer greater than 10.
lambda - regularization parameters, the first element is
the coefficient in front of the maximum entropy
term and the second element is the coefficient in
front of the Tikhonov term.
Outputs:
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.
diag_data - the first element is the least squares error
in ppm^2, the second element is the entropy
penalty in the error functional, the third
element is the tikhonov penalty in the error
functional.
Note: for further information on the equations and algorithms used in this function see http://dx.doi.org/10.1039/C4CP03106G
