Synopsis

Molecular graphics is concerned with the graphical representation of three-dimensional molecular structures and properties. Molecular structures are commonly represented using stick, space-filling, and ball-stick drawing styles and mixtures thereof. Protein and nucleic acid backbone structures can be represented by smoothly varying ribbons (or tubes). Such drawing styles help to emphasize the secondary structure elements and motifs in proteins.

Major Uses for Molecular Graphics

As part of the graphical interface of a molecular modeling program, in which the molecular structure drawing and the program's data structure are reciprocally linked. Graphical operations on the structure drawing can be used to interact with the contents of the data structure (e.g. modifications to spatial orientation or bond rotations, editing, etc.). Computations and graphical operations, such as labeling and color-coding, can be selectively applied to the data structure by picking atoms or other substructures from the molecular structure drawing.

For interactive visualization, in which high performance drawing, depth cueing, perspective, stereo imaging, clipping, color coding, and labeling are used to convey the three-dimensional sense of molecular structures.

As an aide in the analysis of crystallographic, NMR, or molecular modeling data, in which calculated spatial and structural properties are graphically represented by surfaces, contours, and vectors that can be overlayed on three-dimensional molecular structure representations. Animation can be used to represent time dependent processes.

Dot, wire-mesh, and solid rendering surface representation techniques are used to plot three-dimensional data, such as van der Waals and solvent-accessible boundaries, and three-dimensional contours of electrostatic potential, electronic wavefunctions, and electron density.

Properties, such as electrostatic potential, can also be "mapped" onto van der Waals or solvent-accessible surface drawings. Mixtures of structure and property drawing styles can be used to view three-dimensional structure and property information simultaneously (e.g. electrostatic potential in the binding site of a protein).

Applications include:

  1. Visualization of molecular dynamics trajectories - animation or superposition of structures.
  2. Comparison of conformations or shapes - graphical fitting/superposition, volume comparisons, CoMFA.
  3. Visualization of the interactions or shape complementarity between two or more molecules (e.g. ligand and binding site) - graphically controlled docking, van der Waals or solvent-accessible surfaces, clipping.
For presentation of computationally or experimentally determined molecular structures in publications and slides, or for a poster or the cover of a book ("pretty pictures"). Graphical data types used to produce hardcopy and other kinds of output include bitmaps (for printed or electronic documents) and plotting instructions (mainly for printed documents).