Lattice matching (3D)[edit]

Lattice parameters of unknown crystal phases can be obtained from X-ray, neutron, or electron

diffraction data. Single-crystal diffraction experiments supply orientation matrices, from which lattice
parameters can be deduced. Alternatively, lattice parameters can be obtained from powder
or polycrystal diffraction data via profile fitting without structural model (so-called 'Le Bail method').
Arbitrarily defined unit cells can be transformed to a standard setting and, from there, further
reduced to a primitive smallest cell. Sophisticated algorithms compare such reduced cells with
corresponding database entries. More powerful algorithms also consider derivative super- and
subcells. The lattice-matching process can be further sped up by precalculating and storing reduced
cells for all entries. The algorithm searches for matches within a certain range of the lattice
parameters. More accurate lattice parameters allow a narrower range and, thus, a better match. [31]
Lattice matching is useful in identifying crystal phases in the early stages of single-crystal diffraction
experiments and, thus, avoiding unnecessary full data collection and structure determination
procedures for already known crystal structures. The method is particularly important for single-
crystalline samples that need to be preserved. If, on the other hand, some or all of the crystalline
sample material can be ground, powder diffraction fingerprinting is usually the better option for
crystal phase identification, provided that the peak resolution is good enough. However, lattice
matching algorithms are still better at treating derivative super- and subcells.

Visualization[edit]
Newer versions of crystal structure databases integrate the visualization of crystal and molecular
structures. Specialized or integrative crystallographic databases may provide morphology
or tensor visualization output.

Crystal structures[edit]
The crystal structure describes the three-dimensional periodic arrangement of atoms, ions,
or molecules in a crystal. The unit cell represents the simplest repeating unit of the crystal structure.
It is a parallelepiped containing a certain spatial arrangement of atoms, ions, molecules, or
molecular fragments. From the unit cell the crystal structure can be fully reconstructed
via translations.
The visualization of a crystal structure can be reduced to the arrangement of atoms, ions, or
molecules in the unit cell, with or without cell outlines. Structure elements extending beyond single
unit cells, such as isolated molecular or polyhedral units as well as chain, net, or framework
structures, can often be better understood by extending the structure representation into adjacent
cells.
The space group of a crystal is a mathematical description of the symmetry inherent in the structure.
The motif of the crystal structure is given by the asymmetric unit, a minimal subset of the unit cell
contents. The unit cell contents can be fully reconstructed via the symmetry operations of the space
group on the asymmetric unit. Visualization interfaces usually allow for switching between
asymmetric unit and full structure representations.
Bonds between atoms or ions can be identified by characteristic short distances between them.
They can be classified as covalent, ionic, hydrogen, or other bonds including hybrid forms. Bond
angles can be deduced from the bond vectors in groups of atoms or ions. Bond distances and
angles can be made available to the user in tabular form or interactively, by selecting pairs or groups
of atoms or ions. In ball-and-stick models of crystal structures, balls represent atoms and sticks
represent bonds.
Since organic chemists are particularly interested in molecular structures, it might be useful to be
able to single out individual molecular units interactively from the drawing. Organic molecular units
need to be given both as 2D structural formulae and full 3D molecular structures.[32] Molecules on
special-symmetry positions need to be reconstructed from the asymmetric unit. Protein
crystallographers are interested in molecular structures of biological macromolecules, so that
provisions need to be made to be able to represent molecular subunits as helices, sheets, or coils,
respectively.
Crystal structure visualization can be integrated into a crystallographic database. Alternatively, the
crystal structure data are exchanged between the database and the visualization software,
preferably using the CIF format.[33] Web-based crystallographic databases can integrate crystal
structure visualization capability.[34] Depending on the complexity of the structure, lighting, and 3D
effects, crystal structure visualization can require a significant amount of processing power, which is
why the actual visualization is typically run on the client.
Currently, web-integrated crystal structure visualization is based on Java applets from open-
source projects such as Jmol.[35] Web-integrated crystal structure visualization is tailored for
examining crystal structures in web browsers, often supporting wide color spectra (up to 32 bit) and
window size adaptation. However, web-generated crystal structure images are not always suitable
for publishing due to issues such as resolution depth, color choice, grayscale contrast, or labeling
(positioning, font type, font size).[36]

Morphology and physical properties[edit]

Mineralogists, in particular, are interested in morphological appearances of individual crystals, as
defined by the actually formed crystal faces (tracht) and their relative sizes (habit). More advanced
visualization capabilities allow for displaying surface characteristics, imperfections inside the crystal,
lighting (reflection, shadow, and translucency), and 3D effects (interactive rotatability, perspective,
and stereo viewing).[37][38]
Crystal physicists, in particular, are interested in anisotropic physical properties of crystals. The
directional dependence of a crystal's physical property is described by a 3D tensor and depends on
the orientation of the crystal. Tensor shapes are more palpable by adding lighting effects (reflection
and shadow). 2D sections of interest are selected for display by rotating the tensor interactively
around one or more axes.[39]
Crystal morphology or physical property data can be stored in specialized databases or added to
more comprehensive crystal structure databases. The Crystal Morphology Database (CMD) is an
example for a web-based crystal morphology database with integrated visualization capabilities.