Information Needed to Draw a Structure
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The first three categories of information listed below are intrinsic to a given structure, and do not change in the course of a calculation. These categories require very specific data from some source, if the structure is not theoretical or imaginary. Some sources of structural information are listed at the end. Categories 4 and 5 are somewhat arbitrary, but are generally fixed by chemical or geometric considerations. Categories 6 and 7 describe not so much intrinsic information about the structure, as attributes which are assigned for display purposes.

1. Reference Axes/Coordinate System/Unit-Cell Parameters.  
The natural coordinate system for crystals is the crystal axes, which give the length and direction of the lattice translations. These are specified by as many as three axis lengths and three interaxial angles (a fourth redundant axis which is frequently used in hexagonal and trigonal crystals is ignored in ATOMS). The axis types fall into seven different crystal systems, depending on the constraints of symmetry on the equality in length of the axes and the interaxial angles. The coordinates of atoms and indices of face (if present) in the crystal system are eventually converted to coordinates in a Cartesian system with a standard orientation (z = c, x = a*; see section IV-6), but space-group symmetry operations (reproduction of atoms within the unit cell) are most easily carried out on the original crystal coordinates.  
 
Coordinates of atoms in molecules are usually given in a Cartesian axial system. If the molecule has one 3-fold or 6-fold axis of symmetry, i.e. has trigonal or hexagonal symmetry ATOMS can either use reference axes which also have this symmetry, that is trigonal or hexagonal "crystal" axes (a1 and a2 axes at 120 degrees, c axis at 90 degrees to a1 and a2), or use unit Cartesian axes. The symmetry matrices for the standard point groups are actually stored in the form appropriate to hexagonal axes, and then converted to the Cartesian form during calculation if the structure axes are unit Cartesian.  
 
2. Atom Coordinates.  
Any structure must be specified by the locations of the atoms. In the case of crystals, this is normally done in terms of fractional coordinates on the structure axes. If symmetry is used, only one atom of each equivalent set need be entered. Atoms may be grouped by types (e.g. all Si atoms, all C atoms, etc.) to facilitate location of bonds and polyhedra.  
When drawing magnetic or other vector structures, the coordinates or indices of the vector on each input atom is required.  
 
3. Space- or Point-Group Symmetry.  
This describes the way the atoms are repeated by the symmetry operators. The combinations of symmetry operators fall into a limited number of groups called space groups for crystals, and point groups for molecules. At a minimum, it is necessary to know which of these groups the crystal or molecule belongs to. The standard reference for space groups is the International Tables for X-ray Crystallography, published by Kluwer (4th edition). All of the 230 space groups are listed by number in Volume A, or Volume I in older editions (all references to the Tables will assume Volume I or A), and it is only necessary to give this number, or the standard Hermann-Maughin (International) or Hall symbol of the space group.  
 
For molecules, ATOMS can also use the data from the Tables to provide the point-group symmetry given the standard symbol for the group (either the International symbol or the Schoenflies symbol), subject to some orientation restrictions, and to the limitation that the point group is crystallographic, that is that it belongs to one of the seven crystal systems.  
If a structure is described in a crystallographic space- or point group in which the orientation or choice of origin is non-standard, it is still possible to enter the symmetry by essentially copying the information in the Tables or other source, provided the symmetry is described in the standard format.  
 
Point groups containing n-fold axes with n equal to 5 or larger than 6 are theoretically possible for molecules or one-dimensional polymers but not crystals. For such cases, the symmetry must be entered in the form of Cartesian matrices; these matrices, for any point group, can be prepared with the auxilliary program SYMGRP.  
 
4. Boundaries of the Structure.  
For a molecule, it may be presumed that all atoms entered, and usually all those generated by symmetry, are to be shown in the drawing, although selected individual atoms can be hidden or "deleted" after generation of the structure (see Deleting Atoms). Crystals and polymers, however, are ideally infinite structures, in which the unit cell is repeated by translation in as many as three directions, and some limitations must be placed on the extent of this repetition by translation. In some crystals it may be desirable to isolate molecules or other units. There are several different ways that such limitations can be imposed in ATOMS — see Boundary Options.  
 
5. Definitions of Bonds and Coordination Polyhedra.  
To specify bonds, you only need to give the types of the two atoms involved, and minimum and maximum bond distances between the two atoms; all bonds with these specifications are automatically located. These bond specifications can also be derived automatically from a set of atomic radii. To specify polyhedra, you need to give the type of the central atom, the coordination number, the types of the coordinating atoms or ligands, and the maximum distance between central atom and ligands. Normally, all polyhedra will be identified except incomplete polyhedra, i.e. those in which some of the atoms are not within the specified structure boundaries. If the coordination number and/or bond distances are not known, they can be determined with preliminary runs in which incomplete polyhedra are also accepted.  
 
6. Sizes and Colors of Atoms, Bonds and Polyhedra.  
In the Standard Model mode, atoms are shown as spheres if they are shown at all; the radius (in Angstroms) must be specified. Bonds can be represented as single lines, or as "sticks" or cylinders with a given radius. If atoms interpenetrate, there is no size parameter, but a bond between the two atoms must be identified (item I-3.5 above) if the junction is to be handled properly in 2D Drawing modes (this is not necessary for the 3D modes). If a color screen display is used, colors may be assigned to the atoms and bonds according to several schemes. For the dot-matrix plot (including laser printer) and black-and-white screen displays, different shades of gray, normally represented by dot-patterns, may be specified for atom or bond colors. For pen plots, different pen numbers or colors may be specified for different atoms, bond, and polyhedra.  
 
For drawing in the thermal ellipsoid mode, temperature factors are required for each atom, although default isotropic values are used if the temperature factors are not available for a given atom.  
 
7. Orientation, Projection, Scaling.  
These things all have defaults, but can be changed after initial input, and it may require some thought and experimentation to find the best settings. See Coordinate Systems. The projection may be orthographic (straight down the x-axis) or perspective. Perspective generally gives the most realistic appearance, while orthographic retains strict geometric relations and scaling. The drawing may be on some fixed scale (in inches or centimeters per Angstrom) or expanded automatically to fill the plotting area.  

Sources of Structure Information
. The two principal journals for crystal and molecular structure information are Acta Crystallographica and Zeitschrift fur Kristallographie, although many other chemical, biological and mineralogical journals publish structure determinations. Structure information is periodically summarized in Structure Reports. Most of the important structures are described by R.G. Wyckoff, in Crystal Structures (7 Volumes).
There are many sources of structure data in the form of computer files. See the Import Files option in the File menu for details on the formats supported by ATOMS.