A drawing of a molecular structure as generated by PLUTON may be thought of in three principle aspects: the content, the style and the viewpoint. The content of the drawing requires the definition of items such as ARU's (= asymmetric residue units, vide infra) making up the list of molecules and anions to be displayed, atoms within ARU's, connections between atoms (= bonds), labels, and unit cell representation. By default, connected and possibly symmetry expanded sets of atoms constituting molecules or ions will be assembled. The style of the drawing may be like a STICK model (atoms are points and bonds are single lines joining them), a SOLID ball-and-spoke, ball-and-STRAW or ball-and-ROD model, mainly differing in the default settings of the variable radii for atoms and bonds, or a space filling model with van der Waals radii assigned to each atom (also called CPK model). The atom types may be distinguished with various patterns in the black-and-white mode or colored to differentiate between the atom types. Drawings may be made in parallel projection, perspective, or stereo-pair perspective. By default, a STICK-style drawing will be generated. The view direction may be chosen with reference to molecular features such as lines and planes defined by atoms, or with reference to the unit cell or orthogonal axial systems. The view direction may be further modified by rotations, giving flexible control of the viewpoint. By default a minimum overlap view is chosen.
All input to the program is free-format, using (sub)keywords and numerical data. The input to PLUTON is normally provided by interactive input of the instructions via the keyboard. In general, a small set of instructions in terms of global keywords with associated default parameter settings will suffice to produce a drawing for the set of atomic coordinates. Alternatively, all input may be given on the disk file or interactively from the keyboard. More than one data set, separated by an ENDS card may be present on the disk file. This is a convenient feature for browsing the structures retrieved from the Cambridge Structural Database. In that case, an interactively supplied END statement will not stop program execution but load the next data set (use the instruction STOP for premature abortion). Facilities are available (the SAVE instruction) to run the same set of instructions on a file that contains more than one data set (e.g. a series of structures extracted from the Cambridge Structural Database).
It is advised to consult the on-line manual (available with the HELP ALL feature of the program) for the most current list of instructions. An explanation of how the program operates is given, and an introductory example of a PLUTON run is provided.