Volume 1 Chapter 14 Introduction to GSTAT

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15.1 Introduction

PLUTO was first written in the early 1970's as a tool for visualising crystal structures. It can operate both at the individual molecule level and at the packing diagram level showing intermolecular interactions. The main function of PLUTO continues to be for elucidation of structural features of entries selected from the database by QUEST or QUEST3D. Although QUEST3D contains graphical output features for display of 3D coordinates, PLUTO has extra options for preparation of ball-and-spoke diagrams, or space filling diagrams suitable for publication and teaching purposes. PLUTO also provides an interactive method for exploration of intermolecular packing in detail, particularly H-bonded networks.

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.

15.2 Styles of diagrams and Style Defaults

The program produces three basic styles of illustration:

(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.

15.3 Plotting instructions

A wide range of instructions is available for modifying the 'basic' diagram. These may be grouped under the following headings:

(a) Style

(b) Content These instructions may be entered one at a time interactively, or as a command file. Each instruction is defined by a leading keyword, which has sub-keywords and parameters following, which are fully described in the PLUTO documentation.

15.4 Easy use of PLUTO

It is possible to use PLUTO with very few commands, and without detailed study of the documentation! The following example may help:

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

N
for next diagram.

and repeats one at a time to the end of data set

(b) To examine entry 5 in detail.

P 5 
move to entry 5 and plot stick diagram
X 90  
rotate image 90 degrees about Xp (horizontal axis)
Y 30 
rotate image 30 degrees about Yp (vertical axis)
SOLID
select solid style of drawing
P 
plot this image in solid style, (for dumping to hard copy)

(c) To produce a batch plot of all diagrams

PLOT ALL 
will plot all entries in default style without pausing

The default style is to plot all atoms, labelled, in a minimum overlap projection.

15.5 Interactive versus Batch use

PLUTO originated in the days when batch production of diagrams was the only option, and this is perhaps reflected in the nature of the instructions. It is still possible to process a file of data entries with a single set of instructions, given separately in a command file. Indeed, it is still often useful to provide a hard copy listing of a selected set of molecules, in a reasonable orientation, for general reference when working on a problem. The given instruction set will be applied to each member of an input data set. Generally this approach uses the basic default option of stick drawings, fully labelled. Solid style drawings may consume much more computer time and paper than is really necessary at this stage.

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.

15.6 Free format input data

PLUTO has retained its original feature of accepting data typed in a fairly free format, for crystal structures not in the CSD. A file of data entries may be typed in and items selected by entry number just as for an FDAT file. Each data entry begins with a TITLE line and finishes with an END line. The Overall layout is as in this example:
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.

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