Cst display.m

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Ellipsoid plots of chemical shielding tensors and their eigensystems.

Syntax

    cst_display(props,atoms,scaling_factor,conmatrix)

Description

This function takes the information loaded from quantum chemistry packages by the various parser functions (gparse, oparse, etc.) and uses it to create ellipsoid plots of chemical shielding tensors. Every ellipsoid is drawn in the following way:

  1. A unit sphere in a Cartesian space is scaled by abs(Axx) in the x direction, abs(Ayy) in the y direction and abs(Azz) in the z direction, where Axx, Ayy, Azz are the eigenvalues of the chemical shielding tensor in units of ppm.
  2. A set of axes is drawn inside the sphere with red axis for positive eigenvalues and blue for negative ones.
  3. The sphere is translated to the point of corresponding atom and rotated into the molecular frame.

Arguments

                   props -  output of the quantum chemistry package output parser function
                   atoms -  a cell array of element symbols, indicating the atoms for which
                            the shielding tensors should be visualized, e.g. {'C','H'}
          scaling_factor -  scaling factor, connecting the ppm scale to the length units in 
                            Angstrom that are used in the molecule plot, usually of the order of 0.01
               conmatrix -  optional binary connectivity matrix, with 1 if a pair of atoms should be
                            connected by a bond in the resulting plot and zero otherwise. If you are 
                            happy with the default bond drawing threshold of 1.6 Angstrom, specify an
                            empty matrix here.

Returns

The function creates a figure.

Examples

The following figure is produced by /examples/visualisation/cst_strychnine.m

Cst strychnine.png

Notes

  1. Software OpenGL is forced internally because hardware OpenGL works badly with transparency in Matlab.
  2. Antisymmetric components of the shielding tensors are ignored. Shielding values returned by quantum chemistry packages are computed relative to the bare nucleus in vacuum.
  3. Only Gaussian quantum chemistry package is supported at the moment - send an email to Ilya Kuprov if you are using somethng else.


Revision 3284, authors: Ilya Kuprov