Atoms Plot Parameters
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Dialog Box: Atoms Plot Parameters [Control Window; Setting menu; Atoms Window Dialog Bar]

This specifies aspects of the Atoms graphics window (see Operation - Windows, Menus), showing the atoms and their displacements in the chosen mode.

This plot is rather rudimentary, with little attempt to give a "three-dimensional" appearance. A more sophisticated plot may be made with the program ATOMS - for this it is necessary to save a.MOT file (Control Window). See below for more on the nature of the motion vectors.

Atoms are drawn as filled circles with the specified Radius. Note that all atoms have the same radius and that the radii specified in the Atom Types dialog are use only for discriminating among bond lengths in the Coordination option, not in the Atoms Window. Only the bonds specified in the Bonds dialog (Forces menu) are drawn - angles are not drawn. The atomic displacements in the current mode are shown as lines or vectors. The relative magnitude of the displacement is shown by the distance along the vector from the atom surface to the end of the vector.

Secondary atoms are atoms outside the primitive unit cell which are needed to show all bonds and angles (i.e., those bonds and angles which cross unit-cell boundaries) in crystals and polymers. Secondary atoms are not used in molecules. If present, they may be marked with a triangle, or omitted entirely.

The Title is written along the bottom of the windows and gives information about the current mode selected.

Atom labels. Either the name, or input atom label, or the atom number, as in the final generated atoms list, may be shown. Adjust the size with the Font button.

Show unit cell. For crystals and polymers the primitive unit cell is shown as a box, drawn in front of all the atoms. This is the primitive unit cell, not the Bravais cell, so the edges are not necessarily parallel to the crystal axes. The unit cell is not shown if there are no lattice translations (Title/Axes dialog).

Scale to fraction of window. The image is scaled by making the largest dimension of the structure (furthest distance of any atom from the center, doubled) equal to the specified fraction of the shortest dimension of the graphics area (window, frame or page). This scaling applies to atomic centers and does not include the atomic radius or the displacement vectors

Arrowhead on Vectors. Why don't the motion vectors in VIBRATZ have arrowheads on the ends? Drawings of atomic motions in vibrational modes usually have arrowheads on the ends - but only if the vectors are close to being in the plane of the drawing. If the motion is nearly perpendicular to the plane of the drawing, "+" and "-" symbols are typically used instead. Using an arrowhead in this case might wrongly indicate motion in the plane. These symbols may be placed on the atoms or next to them, depending on where open space is available. Making a finished drawing, choosing when to use arrowheads and when to use symbols and where to place the symbols, is something that a human can do much more easily than a computer program - the computer results would in fact be unsatisfactory in many cases. Thus the VIBRATZ drawings can be used unchanged, if a simple line is adequate to represent motion, or as the basis for slightly more elaborate drawings with arrowheads and/or symbols.

The program ATOMS can read the .mot file written by VIBRATZ and draw motion vectors with arrowheads in a much more "3-dimensional" way - that is as cylinders and cones, even when in the 2-dimensional or "Standard" (non-OpenGL) drawing mode. These vectors are much more likely to be satisfactory without modification than simple lines and arrowheads.