Ellipsoid Parameters
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Dialog Box - called from: Input2 Menu

This dialog controls plotting parameters for the Thermal Ellipsoid Model mode, set in the Model Mode sub-menu in the Display menu or in the Dialog Bar - Left

The following parameters are those which are in the various instruction series of ORTEP.

NPLANE - drawing of ellipses
= 0, no ellipsoid components
= 1, boundary ellipse only
= 3, principal ellipses only
= 4, boundary + principal ellipses

NDOT - back side of principal ellipses
< 0, solid line back side
= 0, back side omitted
= 3, 4 dots on back side
= 4, 8 dots on back side
= 5, 16 dots on back side
= 6, 32 dots on back side

NLINE - forward principal axes and shading (cut-out octant)
= 0, no forward axes or shading
= 1, forward principal axes only
= N, forward axes + (N-1) line shading

NDASH - dashed reverse principal axes
= 0, no reverse axes
= N, dashed reverse axes with N dashes

NBOND - bond type for stick bonds
= 0, no bonds
= 1, 2, 3, 4, 5 give lines at 180, 90, 45, 22.5 or 11.25 degrees apart, bonds ending at ellipsoids
= -1 to -5, same, bonds ending at atom centers

TAPER - bond taper. The bond radius is

R = R0 +- TAPER * ABS( COS(THETA) )

where theta is the angle between the bond and the view direction. The bond radius R0 is set in the Bond Data dialog (Input1 menu).

SCAL2 - ellipsoid probability scaling factor.

This controls the size of ellipsoids. A value of 0.76 gives 10% probability, 1.54 gives 50% probability, 3.36 gives 99% probability, etc. See the table below for sample values - for more complete values, consult the table in the original ORTEP instructions.

DISP - retrace resolution.

When lines are retraced to emphasize certain ellipsoids or make the width a function of depth, this is the separation.

A0 and A1 - depth function parameters.

Lines may be retraced to give wider lines for closer ellipsoids.

dR(x) = AO + A1 * x

where dR is the width of the line and x is the height in Angstroms.

Use b/w shades. If this box is checked, ellipsoids in black-and-white display and output will be filled with the b/w shade or color specified in the Input Atom Data dialog (Input1 menu). If it is not checked, they are filled with white before drawing ellipsoid components.

Show iso as spheres. If this box is checked, isotropic atoms are shown as spheres (i.e. circles in 2D display) without the principal planes which can give a false impression of anisotropy.

Default radius. This is the mu value which is given to atoms with no valid entered temperature factors; it is 0.1 by default.

If DISP is 0.0, lines are not retraced. For one-dot lines on typical screens, DISP should be about 0.01 inch, but it can be much smaller for printed output. Note that x is measured from the zero of coordinates, not the rear-most atom

Line widths for atoms are set independently in the Line Widths dialog (Input2 menu), and the value of DISP should take account of these settings if wide lines are used.

For color display and output, depth is probably best shown by front-back fading of color (Shading dialog, Input2 menu) rather than line retracing.

3D Drawing Modes. If temperature factor data have been entered, atoms will be shown as ellipsoids in the 3D Drawing Modes (including 3D Quad Stereo). If NLINE is greater than 0, the "forward axes" or cutout octant is shown as in ORTEP (except in 3D files - see below). If NPLANE is greater than 1, the trace of the principal planes will be shown as stripes or three-dimensional bands just outside the ellipsoids. The Width of principal- plane stripes gives the width of these bands. The Radius Factor for stripes gives the height or extent to which the curves for the principal planes are outside the ellipsoid itself; this should always be larger than 1.0. By increasing this factor and decreasing SCAL2, the principal planes can be made to dominate the representation, as elliptical disks.

For direct screen and print rendering, the bonds between ellipsoids are the same size as shape as in ORTEP drawing, and the TAPER parameter is applicable. In 3D files (VRML and POV-Ray), bonds are always strictly cylindrical. Also in these files, the ellipsoids are always complete and do not have the cutout octant as possible in ORTEP drawing. When Polyhedra are present, and ligand atoms are not shown at the corners, bonds to these corners are always cylindrical, not tapered. Note that the option to show corner atoms as spheres of constant size is not applicable to the 3D mode - such atoms are either absent, or shown as thermal ellipsoids. Of course, the atoms could be converted to isotropic temperature factors of appropriate size.

The SCAL2 parameter above determines the size of the ellipsoids as in the Ellipsoid drawing mode. Apart from SCAL2, TAPER, NLINE and NPLANE the ORTEP parameters above are not applicable to 3D drawings.

The 3D Material parameters used for both the cutout octant and the principal-plane bands are those for polyhedra - this is to avoid distracting specular reflections from large flat surfaces (although polyhedra may be assigned large specular reflection components as well).

Polyhedra in Ellipsoid mode (2D) group. In the Ellipsoid Model mode, you can either show polyhedra with flat, opaque faces (last option), or you can show the ligand-ligand "bonds" which are the edges of polyhedra, and also the central-ligand bonds. Both of these types of "bonds" are as defined in the Polyhedra input in the Input1 menu, not the Bonds input. The ligand-ligand "bonds" or edges will have the fill and edge colors which are specified for the given polyhedron in the Polyhedron Data dialog, and the central-ligand "bonds" will have the edge and fill colors of the central atom (Input Atom Data dialog). Both these bond types will have a uniform radius, as specified in the edit box.

The intersections of the solid polyhedra with the corner ellipsoids are not solved exactly, but approximated assuming the corner atoms are spheres. The size of these spheres is determined by the settings in the Polyhedra dialog (Input1 menu). This approximation will be less acceptable as the ellipsoids deviate further from sphericity.

All the atoms involved in polyhedra, except for the central atom in the case of solid polyhedra, will be shown as elllipsoids.

The central-ligand and ligand-ligand "bonds", if used, must be added to the bond list during calculation, so changes in this option may require Recalculation, rather than just replot.

Partial Table of Probability and SCAL2 values

Probability
SCAL2
0.1
0.7644
0.2
1.0026
0.3
1.1932
0.4
1.3672
0.5
1.5382
0.6
1.7164
0.7
1.9144
0.8
2.1544
0.9
2.5003
0.95
2.7955
0.99
3.3682
0.999
4.0331
0.9999
4.5943