Asymmetric unit
The smallest set of atoms from which the whole crystal can be built, exactly as listed in the file's _atom_site loop. It is often a whole molecule, but a molecule sitting on a symmetry element (benzene and urea, for example) appears as a fraction of a molecule, and a salt shows one of each ion.
Molecule
The asymmetric unit completed by symmetry, so each molecule is whole. For an extended network (a metal, salt or covalent solid such as NaCl, diamond or quartz) there are no separate molecules, so each unique atom is shown with the atoms bonded to it, which shows its coordination.
Unit cell and packing
Every symmetry operator of the space group is applied to the asymmetric unit to fill the cell; Packing repeats the cell by translation along a, b and c. With Whole molecules, each molecule whose centre lies in the chosen cells is drawn complete, the usual way to show molecular packing. With Atoms in cell, only atoms inside the cell boundaries are drawn, including copies on the faces, edges and corners, the usual way to show ionic and network solids. Colour by symmetry gives each symmetry-related copy its own colour.
Z and Z′
Z is the number of formula units per unit cell. Z′ is the number per asymmetric unit (Z divided by the number of symmetry operators); Z′ = ½ means the molecule sits on a symmetry element.
Bonds and hydrogen bonds
Two atoms are bonded when they are closer than the sum of their covalent radii plus 0.42 Å, checking every periodic image, so bonds across cell edges are found. Metal–metal contacts are not drawn as bonds. A hydrogen bond is drawn from an H on N, O or F to another N, O or F when H···A is 1.4–2.6 Å and the D–H···A angle is at least 120°. If the file has no hydrogen atoms, N/O/F pairs between different molecules within 2.4–3.15 Å are shown instead. In space-fill mode, ions in salts and oxides use ionic radii, and all other atoms use van der Waals radii.
Bond lengths and angles
The table lists every bond and bond angle around each atom of the asymmetric unit; symmetry-equivalent values are listed once, with ×n showing how many copies there are (six identical Na–Cl bonds in rock salt, for example). A superscript code marks an atom generated by symmetry. Values come from the file's cell and coordinates; the file's own _geom tables (with standard uncertainties) may differ in the last digit.
Reading CIF files
The viewer reads cell parameters, symmetry operators (_space_group_symop_operation_xyz or _symmetry_equiv_pos_as_xyz), atom sites and, where present, occupancies, disorder groups, temperature, R-factor and the literature reference. If the operators are missing, they are generated from the space-group name for common groups. Disordered structures show the main part, with an option to show all parts. Files with several structures (data blocks) offer a choice of block. Macromolecular mmCIF files are only partly supported.
Example structures
The ionic and network examples use textbook cell parameters with atoms on their exact symmetry positions. The molecular examples (urea, benzene and hexamethylenetetramine) are teaching models built on published cells and space groups and checked for realistic bond lengths and contacts. For coursework or research, download the deposited CIF from one of the databases listed above.
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