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In a typical scenario the user selects data entries using QUEST or QUEST3D, saving them in the FDAT format in a small private file. This file may then be explored entry at a time using PLUTO to examine conformation, or packing arrangements, using a Tektronix terminal to interactively choose views and content. Finally certain selected diagrams may be prepared for hard-copy, in a solid ball-and-spoke style.
It is worth noting that PLUTO also accepts data independent of the CSD database, which the user may type in directly in a simple free-format style. This may be useful in comparing current work with examples from the database.
The operation of the PLUTO program is fully described in Chapters 10 to 14 of Volume 4 of the CSD System Documentation Set. A central feature of the PLUTO documentation is Chapter 12 which presents an alphabetic Glossary of PLUTO keywords. Chapter 11 summarises the operation of the program, Chapter 13 provides notes for programmers and Chapter 14 presents examples of the use of PLUTO.
(1) Stick diagrams
(2) Solid ball-and-spoke diagrams
(3) Space-filling models
These styles may be plotted either for a single molecule or for an assembly of molecules (i.e. a packing diagram). The user controls the constitution of such an assembly. Because stick diagrams are very much quicker to plot than the other styles, the usual progression is to find the orientation and selection of molecules required working in stick style, and then finally prepare the hard copy in solid style.
The 'basic' or default style of drawing is in stick mode with all atoms labelled.
A user has selected a set of 30 structures that contain a certain functional group of interest, say an amide group. This has been saved by QUEST or QUEST3D as an FDAT format file, named AMIDES.DAT, say. The user then proceeds in the following stages.
(a) To examine stick drawings of the items in the default style, the user types
(b) To examine entry 5 in detail.
Interactive use of PLUTO enables the user to specify the input data file, and then enter the commands from the Tektronix terminal. Most of the original commands are supported, but a number of new short commands have been introduced to enable a limited degree of interaction, while making no assumption of graphic input facilities on the Tektronix terminal. In future versions of the program these interactive commands will be extended.
The interactive commands enable the user to move to any given entry in the set of data, and then examine this entry in as much detail as required. These simple commands enable view rotation about the plot axes with minimum keystrokes, and the study of various intermolecular bonded networks, such as H-bonds. The interactive commands cause immediate action, and re-drawing of the diagram, as this is appropriate, for example X 90 means rotate the image +90 degrees and plot immediately. The older batch commands generally cause no action until the special command PLOT is given, indicating that the new image is to be drawn.
TITLE New steroid complex from Fred's Lab. CELL 12.341 7.501 25.23 90 105.3 90 SYMM x,y,z * 1/2-x, 1/2+y, 1/2-z C1 0.1234 0.5678 -.6543 . . . END
It is possible to plot non-crystallographic sets of data. If the CELL card and SYMM commands are omitted, the program assumes orthogonal data in Ångströms. This is especially useful for plotting fragments with respect to molecular axes.