Crystal Edges and Faces

Dialog Box: Crystal Edges and Faces [Input2 Menu]

This dialog controls the appearance of the display crystal shape. The

Crystal Forms for Display dialog in the Input1 menu controls the actual generation of the faces which make up this shape.

Display. Crystal means the edges which define the external boundary faces. Atoms means the atomic structure including bonds and polyhedra. If you are drawing a molecule or polymer, crystal edges are not normally shown, but you can nevertheless display a crystal shape if desired.

Edges Only/Faces Only/Both. In 3D display modes the actual planes of the crystal faces can be shown, instead of or in addition to the edges between faces. Set the

Opacity and color of the faces in the group at the bottom of the dialog.

Dash length and dash ratio. The dashes are used for back edges of crystals and in display of Crystal Axes and Unit Cell. Length or repeat distance is in inches/centimeters, and the length factor is the actual length of the solid part divided by the repeat distance.

Note that when using Frames in output the dash length remains the same - it may be desirable to decrease the length for very small plots.

Back edges - those not visible if the crystal is opaque - may be specified as none (not shown at all), dashed or solid.

Lines/Cylinders. In 3D display modes the edges may be shown as lines or cylinders of the specified width.

Colors, Patterns, Pen numbers. Front edges are those which are visible; back edges are not visible in an opaque crystal. Widths of lines are set in the Line Widths dialog in the

Input2 Menu). See Input Colors/Patterns/Pens for general aspects of input.

For alternate ways of drawing unit cells, and problems sometimes encountered with crystal edges, see Drawing Crystal and Unit-Cell edges.

3.2.3.2 Perspective

Dialog Box: Perspective [Input2 Menu]

If perspective is not in effect, or turned off, the drawing is simply a perpendicular or orthographic projection down the observer x axis. If perspective is on, the drawing is projected from a point (xp+xo, yo, zo), where xp is the perspective distance and xo, yo and zo are the projection offsets (below), perpendicularly onto the plane (xo, y,z ), that is a horizontal plane passing through the structure center. Scaling applies to the projection plane, but obviously fixed scaling has limited intrinsic meaning. Generally the scaling modes Universal Maximum or Each View Maximum (set in the Scaling dialog in the Input2 menu) should be used when perspective is in effect. The perspective distance is the distance xp of the projection point from the projection plane, or in other words the

distance from which the structure is viewed (distance from the center of the structure to the eye). Smaller distances will accentuate the "perspective"; larger distances will cause the plot to appear more like a straight-on projection. The perspective distance should be considerably larger than the distance of the furthest atom from the center (or the plane x=xo) in the positive x direction. If atoms come within about 1 Angstrom of the x coordinate of the eye they will be omitted, but many of such atoms would be off scale (sideways) anyway.

Projection Offsets. During calculation the midpoint of the structure is determined - this includes all atoms, but does not include crystal edges, unit cell or axes. When projecting

in Perspective viewing, the coordinates of this midpoint, xo, yo and zo are used as the coordinates of the projection point (xp+xo, yo, zo), where xp is the perspective distance.

This insures that the projection is never oblique to the projection plane. This is equivalent to the Automatic Centering option in previous versions of ATOMS. Although arbitrary specification of the offsets is no longer allowed, you can attain almost any attitude of the structure by suitable rotations. Note that the structure can be displaced in the plotting area with the Centering and Displacements dialog (Input2 menu). In effect, the

projection direction moves along with the structure. If you also have structure axes or a unit cell (Display of Axes and Unit Cell dialogs, Input2 menu) which are separated from the structure, they will be projected obliquely, according to their distance in Angstroms from the structure center; that is, if you are looking down, say, the a-axis in the structure itself, structure axes placed to the side will not have that axis exactly parallel to the view direction. You can rotate to effect a compromise between the two orientations.

3.2.3.3 Stereopairs

Dialog Box: Stereopairs [Input2 Menu]

When stereopair display is on, two images of the structure will be drawn. The upper part of this dialog pertains to non-Anaglyph display modes, in which each image centered in one half of the plot area. The left or left-eye image will be rotated by the stereopair Rotation angle clockwise from the normal orientation, and the right-eye image will be rotated the same amount counter-clockwise. If shading is active the illumination vector will be rotated along with the structure. The stereopair rotation angle is typically about 3 degrees, although the proper angle may vary depending on the perspective distance, the actual viewing method, etc.

The Stereopairs on check box applies only to separated-image stereopairs drawn in non-Anaglyph display modes.

If the hard copy of stereopairs is to be viewed directly or with a small viewer, a frame size in the dot-matrix or pen plot of 4 to 5 inches across will give a distance between the two images about equal to the normal interocular distance. If you want a pair of images larger than a single page, you can use the Stereopair Rotation in the Rotation menu to rotate the images separately, if shading is in effect; if shading is not in effect, ordinary rotation on z is sufficient..

Few people can directly view a stereo pair as shown on the full screen because the images are considerably further apart than the eyes. However, if a negative rotation angle is used, some people can view the image by crossing their eyes.

The lower half of the dialog pertains to the Anaglyph display mode, selected in the Display Mode command in the Display menu, or the Dialog Bar - Left. In this type of display, there are two skeletal images of two different colors, superimposed. Generally

red/blue with a black background works best for the screen, while red/green with a white background works best for printed output. However, depending on the color of the glasses, red/cyan may work better for either.

The stereopair Rotation Angle for anaglyphs is separate from that for separated-image stereopairs, since a smaller angle is usually better (e.g. 2 degree instead of 3). The angle for anaglyphs should always be positive, whereas that for separated-image stereopairs may be negative for cross-eyed viewing.

Windows only

----Anaglyphs in 8-bit (256-color) screen modes are not drawn correctly, because the colors are not added correctly for areas of red/green or red/blue overlap. If possible, switch Windows to a "true color" (16-, 24- or 32-bit) mode to get a correct drawing.

Macintosh only

----The Macintosh adds colors correctly even in 8-bit screen modes.

End Macintosh only

----Colors are not added or mixed correctly for labels in anaglyph mode.