2D Drawing Modes. In the Standard and Ellipsoid drawing modes of atoms, all objects in the atomic structure itself, namely atoms, bond and polyhedra, are sorted with respect to distance from the eye (perspective projection) or height in the x -coordinate (orthogonal projection). Then the objects are drawn in order from back to front. Instead of constructing three-dimensional objects and then projecting onto the plane of the drawing, it is possible in many cases to use simplified two-dimensional objects (e.g. circle instead of sphere). When objects are actually in bonding relationship the interpenetrations are solved analytically, but this is done only for certain cases where the geometry is very restricted; atom-atom, bond-atom where the bond connects that atom with another; and atom-polyhedron in the case where the atom is a ligand of the polyhedron. For the atomic structure itself, there is no need to solve for interpenetration of, for example, a bond with atoms which are not connected by that bond, or a polyhedron with bonds other than those to its ligands, because such geometries do not exist.
However, for the lines or cylinders which are used to represent the edges of the boundary polyhedron, or the edges of the unit cell, there are no such restrictions on interpenetration geometry; such lines or cylinders may interpenetrate with atoms, bond and polyhedra in any way.
For pen plots and pen-plot files, which use strictly vector methods of drawing, it is not possible to superimpose objects while drawing from back to front, and it is necessary to solve analytically for overlay relationships as well as the same limited interpenetration relationships mentioned in the first paragraph. However, this process is made much faster by the process of sorting and drawing from back to front.
For these reasons, the drawing of lines representing the boundary or other crystal shape (Crystal Forms for Display) in 2D Drawing modes assumes that there is no interpenetration between these lines and atoms, bond or polyhedra. The lines representing edges which would be hidden if the crystal shape were opaque ("back" edges) are drawn before the structure; and the lines representing visible edges ("front" edges) are all drawn after the structure.
Since it is normally necessary to show a volume of a crystal greater than one unit cell, similar assumptions cannot be made for the special drawing in the Unit-Cell option in the Input2 menu. The unit-cell edges in this option are thus all drawn after the structure. They are intended to show the translational relationships of the structure, not to delimit some particular volume.
These simplifications are primarily intended to cut down on plotting time; they may be removed in the future as processors become faster.
3D Modes. The 3D Drawing Modes use a completely different drawing method. Fully three-dimensional objects are drawn in any order, but the height (x-coordinate in the system used by ATOMS) of each pixel is compared with the value in a depth buffer and the color which is already in that pixel is replaced by the color belonging to the new object only if the new object is closer to the eye at that point (i.e. if the new object overlies all other objects at that point). In this drawing mode there is absolutely no restriction on interpenetration relations - they are drawn correctly as a matter of course. Thus unit cells are drawn in correct 3-dimensional position, not in front of the structure. Crystal edges are also always drawn in correct position, and interpenetrations are exact.
Crystal and unit-cell faces, that is actual surfaces, may also be drawn in 3D modes. Usually this is most useful if the faces are transparent or translucent. However, full transparency may not be supported by the system software and/or hardware. Absolutely correct transparency would require drawing from back to front, and would again encounter some of the problems discussed above for 2D drawing modes.