The input atomic coordinates (X, Y, Z) are with reference to user-defined axes (a, b, c), which will usually be either crystallographic unit cell axes or an arbitrary orthogonal set; these coordinates are input as fractions of the unit cell edges or as Angstrom units (in the latter case they are converted and stored as fractions of dummy cell edges). A second, orthogonal system (A, B, C) with coordinates (XO, YO, ZO) in Angstroms is set up internally, see J.D. Dunitz 1979 : A is a unit vector along a, B is a unit vector normal to a in the ab-plane, and C is normal to A and B. B will coincide with b in monoclinic cells in the b-setting. If the input axes are orthogonal, the two sets of axes a,b,c and A,B,C are coincident. The third system is the plotting coordinate system in cm: XP across the picture from left to right, YP up the picture from bottom to top and ZP out of the paper. All these axial sets are right-handed and absolute configuration is preserved in all rotations.
As atoms are input to the program, they are stored in the X,Y,Z and XO,YO,ZO axes systems. Each atom also has additional information stored for it such as estimated standard deviations, thermal motion parameters, a name (the embedded element name is used by default to set various radii to be used during the subsequent calculations) and various bit flags such as the inclusion bit. Coordinate data are checked for duplications on input. Atom labels not conforming to the required format are renamed.
A CALC instruction generally initiates a distance search on the basis of the previously set or supplied radii. In the INTRA mode this results in the setup of an array that stores per atom all connections that are found. This list is used subsequently by a geometry listing routine that generates all unique bond distances, bond angles and torsion angles. Simultaneously with the setup of the connectivity array all atoms are transformed (when necessary) to obtain a connected set. In addition, in the case that the molecule lies on a special position, the primary coordinate list is expanded with additional symmetry generated atoms in order to handle the geometry of the complete molecule.