Chilton::CCD::PLUTO78 Manual

PLUTO78 User's Reference Manual

G M Crisp

August 1983

GEC and CMS Version

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1.1 Introduction
1.2 Example PLUTO78 plots
2.1 Coordinate systems used within PLUTO78
2.2 Introduction to the PLOTTING COMMANDS
2.3 The LOCAL commands used for plotting
- 2.3.1 Definition of OPT KEYWORDS
- 2.3.2 Definition of QUALIFIER COMMANDS
2.4 The GLOBAL commands used for plotting
2.5 Data Entry Commands used for plotting
2.6 Data Entry Commands using FREE Format
2.7 MACRO commands
3.1 CMS use of PLUTO78
3.2 ICF GEC use of PLUTO78
4.1 Definition of Cambridge data format
4.2 Example of Cambridge data formats
5.1 Definitions of VIEW with minimum overlap
5.2 Bonding radii used by default
5.3 Hints + tips on using PLUTO78
5.4 LOCAL command summary
5.5 GLOBAL command summary

1.1 Introduction

PLUTO78 is the molecular drawing program from the Cambridge Crystallographic Data Centre in its 1978 form. It has been extensively modified at RAL for use on interactive systems, (CMS and the GEC computers connected to the SERC X25 network ), and on batch IBM central computers for high quality output to the FR80 microfilm recorder. A comprehensive HELP system is available to the interactive programs.

When working interactively the viewing position is altered by typing in simple commands at the terminal. The molecule is drawn in several formats, such as stick, ball + spoke, space filling, unit cell packing, half tone and colour. Colour is supported on both CMS (on Sigma 5660, 5680 terminals and Calcomp 81 desktop plotters), and the GEC's (on sigma 5660, 5680 terminals and Benson 1302, 1332 plotters).

The plotting commands can be submitted across the network to the batch version of PLUTO78 to produce output from the FR80 as high quality film, in black & white or colour 16/35 mm, black & white 105mm microfiche at 48 times reduction or hard copy paper. The output is posted back to your site. You may also obtain good quality stereo pairs on 35mm film which fit into the inexpensive Open University stereo viewer.

You can adjust the speed of plotting on the screen, to either take a quick, rough, look at your molecule or plot it more slowly and carefully. The latter method enables you to take a reasonable photograph from the screen, or to use one of the direct hard copy devices. The best of these does not give FR80 quality but you will have the results more quickly. On application to the Graphics section, a Dunn camera at RAL may be used to record plots directly from the screen of the colour GOC onto your 35mm film, which you take away for developing locally.

The commands are applied to the atomic coordinate data defining the molecule, which can be input from the terminal or from a file in either Cambridge database format or Free format. Free format enables you to enter coordinates quickly, for large numbers of atoms, to see the plot immediately and to save the data in a file for later use. These files are known as datasets.

Examples of the types of plot available follow. Details of the coordinate systems used by the programs, the commands, and an example of Free Format data are in section 2. Instructions for running PLUTO78 on CMS are in section 3.1, and on a GEC in section 3.2. Section 4 explains the Cambridge database format (also known as FDAT) used by PLUTO78. Section 5 contains various definitions, defaults and indexes.

1.2 Example PLUTO78 plots

All the plots in this section are of two different molecules taken from the standard set of data available on both CMS and the GEC's. Each plot is given with the command set that produced it. Details of the commands are given in section 2, with a summary in section 5. A set of commands for a continuous demonstration are held in file PLDEMO COMMAND D on CMS (a private minidisk, see section 3.2.15), or .PLDEMCOM on GEC's (see section 3.2.15). In all the examples, references to COLOUR only apply exactly to a Sigma colour terminal. Other terminals will show either white or grey shades.

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2.1 Coordinate systems used within PLUTO78

PLUTO78 uses three right handed cartesian coordinate systems in plotting a molecular or crystal structure (see figure below). Atomic coordinates are generally input in fractional units referred to the set of crystal axes XC, YC, ZC. These are transformed to an orthogonal set of axes internally, XO, YO, ZO, such that the atomic positions within the unit cell are measured in angstroms. Before a structure is plotted on the screen or an FR80 output device, the coordinates are transformed again to plot axes, XP, YP, ZP, which have units nominally in millimetres. However, on some output devices (for example, 35mm film) the units are scaled automatically for the user's convenience, to give the largest possible size of plot for that device. The XP, YP, ZP directions on the device are: XP horizontally from bottom left to bottom right, YP perpendicular to XP from bottom left to top left, and ZP normal to both and directly out of the plotting surface.

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2.2 Introduction to the PLOTTING COMMANDS

The plots produced by PLUTO78 are controlled by typing commands. These are grouped into three types, those which RESET default values of flags and variables, QUALIFY these values with new ones, and INITIATE plotting. There are two commands to reset (OPT and GOPT), many which use qualification and a single command to initiate the plot (PLOT). The simplest example has two commands:-

OPT 
PLOT

Each command MUST start in column 1 and end before column 80. Commands may not be continued onto the next line. Some should only be given once, others can be repeated. The default plot is shown as Example 1 and consists of:-

Stick diagram
Single view with no perspective
All atoms labelled
All hydrogen atoms included
View direction giving minimum overlap of the atoms
Output lines are drawn white on black for terminals and FR80 16/35 mm film and microfiche, and black on white for FR80 hard copy paper.
Bonds are drawn between atoms, i) according to the connections lists given with the Cambridge formatted data, or ii) for FREE Format, if the separation of the atoms is less than or equal to the sum of the bonding radii supplied by default. Bonds may be changed in both formats by using the commands JOIN and CALC.
Atom coordinates are NOT changed by small amounts to give a UNIQUELY bonded molecule. This is important for FREE Format data, but not so for Cambridge data as it has already been verified in this way.>
Scaled such that the molecule is centred within a box of nominal size 220 'units'. The 'units' are millimetres on devices with a large plotting area, otherwise they are scaled down to fit the device.

All the commands may have keywords, values, or keywords and associated values. These are separated from the command and each other by at least one blank. The order in which the keywords follow the command is not important, but values going with a particular keyword must follow it on the command line. As a simple example of a keyword/ value pair, consider a dataset of more than 1 structure where each is read into the program with an associated entry number (ENTNO). To plot the xx'th one, use the command:-

PLOT ENTNO xx

The commands are further subdivided into categories LOCAL and GLOBAL. GLOBAL ones (mostly RAL additions) are obeyed for many plots, while LOCAL ones affect only a single plot, unless they are reset (by GOPT or OPT) before plotting starts. Consider the following examples:-

GOPT SOLID	    GOPT SOLID
SEGMENT 50	    SEGMENT 50
PLOT ENTNO 1    PLOT ENTNO 1
GOPT SOLID	    OPT SOLID
PLOT ENTNO 12	PLOT ENTNO 12

The SEGMENT command specifies how many straight line chords are to be drawn to complete the atom circle. In the left hand set, entry 1 is plotted with 50 segments, a GLOBAL reset done and then entry 12 plotted with the default of 8 segments. In the right hand set, entry 1 is plotted with 50 segments, a LOCAL reset done, and entry 12 plotted with 50 segments. Note that the SEGMENT is still in force.

2.3 The LOCAL commands used for plotting

Cambridge commands are indicated by a 'C' in the command name column, and additional RAL commands by 'R'. A summary of the Keywords associated with the RESET command OPT follows:-

OPT   COMMAND   KEYWORD         MEANING
00C)..OPT.......................Set up default options.
01R)............ANGLE...........Calculate bond angles and print them out. 
02C)............CELLPLOT........Plot outline of unit cell.
03C)............DEBUG...........Invokes debugging facility.
04C)............NOHYD...........Omit all hydrogen atoms.
05C)............NOLABEL.........Suppress all atom labelling. 
06R)............NOTITLE.........Suppresses output of title.
07C)............PACK............Plot packing diagram.
08R)............PFRED...........Print free format data on terminal when input is from disk. 
09C)............SEPRES..........Treat each bonded residue by itself. 
10C)............SOLID...........Plot ball + spoke model.
11C)............STEREO..........Plot side-by-side  stereo pair. 
12C)............VIEWS...........View  down  shortest of XO,YO,ZO. 
13C)............VIEWX...........View along XO.
14C)............VIEWY...........View along YO.
15C)............VIEWZ...........View along ZO.

2.3.1 Definition of OPT KEYWORDS

1) ANGLE

Calculates angles between connected bonds in the asymmetric molecule. These values are written to disk. No torsion angles are calculated.

*** Note : these calculations are made only for FREE FORMAT data which have axial lengths not all equal to unity and interaxial angles not all equal to 90 degrees.

2) CELLPLOT

Plots the outlines of the unit cell, with the appropriate labelling of the origin and axes.

3) DEBUG

Lists various variable and array values at the terminal or lineprinter.

4) NOHYD

Excludes all hydrogen atoms from the plot. If NOHYD is absent then all hydrogen atoms will be plotted.

5) NOLABEL

Stops the plotting of all atom labels. If NOLABEL is absent they are labelled by default.

6) NOTITLE

Suppresses the plotting of the title on the terminal and FR80.

7) PACK

Plots a packing diagram by drawing the set of 'units' whose 'coordinate centres' lie within the range 0 - 1 on all three unit cell axes. The complete set of input coordinates constitutes a 'unit'. Other 'units' are related to the input 'unit' by symmetry operations. A 'unit' may contain more than one molecular residue. The 'coordinate centre' is the mid point of the box enclosing the 'unit'. The 'coordinate centre' of a 'unit' is given by:-

(xmin + xmax)/2, (ymin + ymax)/2, (zmin + zmax)/2

where xmin, xmax are the minimum and maximum coordinates in the X direction of the orthogonal internal axes system, and similarly for Y and Z.

8) PFRED

Allows FREE Format data to be printed at the terminal, when it is read in from a disk dataset.

9) SEPRES

Allows for the separate treatment of each residue (either a whole molecule or a molecular fragment or residue ). For example, consider the structure of a charge transfer complex compound of two molecules A and B, SEPRES causes the program to orient each molecule (or residue) so that each is plotted with minimum overlap. The true crystallographic orientation of A with respect to B is usually altered by this process. If SEPRES is absent the program treats the structure as if it were a single residue.

10) SOLID

Plots a ball and spoke model. The radius of an atom circle = (2x bonding radius of that element) in angstroms. The radius of each bond cylinder = 0.04 angstroms. Each bond is made up of 8 lines. Each entry in the Cambridge Crystallographic Database contains explicit values for the elemental bonding radii if the entry is error free. For free format data entries, the program will assign bonding radii (see section 5.2 of the manual), unless specific values are assigned. These can be given by using the qualifier command RADII. If SOLID is absent a stick molecule is plotted.

11) STEREO

Plots a side by side stereo pair. The view corresponds to that seen by an observer with eye-separation 60 mm at a distance of 600mm from the centre of the plot coordinates. If STEREO is absent a single view is plotted with no perspective.

12) - 15) VIEWS, VIEWX, VIEWY, VIEWZ

These keywords specify the view direction to be used by the program. They correspond to the 'standard' crystallographic views.

VIEWX indicates that the view direction is along XO 
VIEWY .......................................... YO
VIEWS .......................................... ZO
VIEWS .......................................... the shortest of XO, YO, ZO

If VIEWm (m = X, Y, Z or S) is absent the program will choose the view which gives the minimum overlap (see section 5.1 of the manual). These keywords may be overridden by the qualifier command VIEW.

QUALIFIER KEYWORDS MEANING
COMMANDS +VALUES
16C)..C...............TEXT......Comment record.
17C)..CALC............BOTH......Calculate 'non-standard' connectivity.
18C)..COLOUR........KEYWORDS....Specify colour of lines for plotting.
19R)..DCLEAR..........NONE......Erase current Free-format data-in-core and reset flags
and variables for next set of data.
20R)..DIRCOS........KEYWORDS....Specify a vector within the molecule and calculate
its direction cosines, or form a right-handed set of
axes, or calculate the crystal diamagnetic susceptibility.
21R)..DIST............BOTH......Specify two atoms and print out the distance between them,
or define plotting of the distance on the device.
22C)..EXCL..........KEYWORDS....Exclude the specified elements.
23R)..FR80............NONE......Send current commands/ data to file.
24R)..HELP..........KEYWORDS....Invokes the help facility.
25C)..INCL..........KEYWORDS....Include the specified elements.
26C)..JOIN..........KEYWORDS....Specify connectivities.
27C)..LABEL.........KEYWORDS....Plot specified element labels only.
28C)..MATRIX.........VALUES.....Specify rotation matrix.
29C)..MOLE...........VALUES.....Specify molecules for packing.
30C),.PERSP..........VALUES.....Plot with perspective.
31C)..PLOT............BOTH......Initiate plotting.
32C)..PRINT...........NONE......Print out geometry + connectivity.
33C)..RADII...........BOTH......Specify radii of atoms, bond cylinders, or the inclusion of
a stick plot overlaid on a space filling plot.
34C)..RANGE..........VALUES.....Specify range of unit cell for packing.
35C)..SHADE..........VALUES.....Shade atom circles.
36C)..STEREO.........COLOUR.....Specify red/ green stereo pair.
37R)..STEREO.........VIEWER.....Specify Open University stereo pair.
38C)..STOP............NONE......Closes output files + stops program.
39C)..TITLE...........TEXT......Print specified title at top of plot.
40C)..VIEW............BOTH......Specify view direction.

2.3.2 Definition of QUALIFIER COMMANDS

16) C

Any number of comment records may be inserted using this command, which starts with C followed by a blank, followed by the text of the comment which may be not more than 78 characters of text.

17) CALC

The qualifier command CALC allows the standard bonding radii and tolerance for intramolecular connectivity to be modified. It also allows intermolecular connectivity to be generated. There are 3 basic forms:-

CALC INTRA RAD EL1 r1 EL2 r2 ...
CALC INTRA TOL t
CALC INTER EL1 r1 EL2 r2 ...

where EL1, EL2 ... are specific atom types and r1, r2 ... are the associated bonding radii in angstroms.

a) CALC INTRA RAD C 0.8 H 0.5 CU 1.7

Defines the new intramolecular bonding radii in angstroms for carbon, hydrogen and copper.

b) CALC INTRA TOL 0.55

Specifies a tolerance of 0.55 angstroms in the calculation of connectivity distances.

*** Note: a) and b) can be combined into the same command line, for example:-

CALC INTRA RAD CU 1.7 TOL 0.5

c) CALC INTER N 1.6 0 1.5

This allows calculation of intermolecular distances involving nitrogen and oxygen such that N-N separations are less than 3.2 angstroms and N-O less than 3.1 angstroms.

18) COLOUR

This command takes the form:-

COLOUR keyword

The keyword can be RED or GREEN. It has no effect on non-colour devices. All the lines in the plot are drawn using the specified colour, on colour display devices.

*** Note : See also the GLOBAL colour command (section 2.4).

19) DCLEAR

This command is used only with free format data. It must be given before a new set of data is to be entered, so that the current set of data-in-core is erased and the flags and variables reset correctly.

20) DIRCOS

There are three forms:-

a) DIRCOS mylab < EL1 EL2 >
b) DIRCOS DIAMAG
c) DIRCOS ANG

where EL1, EL2 are specific atom types and mylab is a user defined label. There are three special labels, L,M,N, which form an orthogonal right handed set of axes and are used by the commands b) and c).

a-1) DIRCOS L C1 C2: The vector from atom C1 to C2 is labelled L, and the direction cosines are output on the terminal.
a-2) DIRCOS M C3 O1: The vector M is chosen at 90 degrees to L to form the basis of a right handed set of axes.
a-3) DIRCOS N: If L and M have been defined as in a-1,2), then the vector N can be found by the vector cross product. No atoms need be defined for this vector. The vectors L,M,N now form an orthogonal right handed set of axes, assuming the angle between L and M is 90 degrees.
b) DIRCOS DIAMAG: Once the L,M,N axes have been defined in the molecule, this command will prompt for the free format input of the known molecular diamagnetic susceptibilities along L,M and N. The output displayed on the screen are the calculated crystal susceptibilities. These can be compared with experimental values as a quick check on molecular orientation in the unit cell.
c) DIRCOS ANG: This outputs the non-torsion angle between the L and M vectors.

21) DIST

This command has four forms:-

a) DIST EL1 EL2 < MOL1 MOL2 < MOL3 ... MOLN > >
b) DIST EL1 EL2 EL3 EL4 ....
c) DIST PLOT
d) DIST NOPLOT

where EL1, EL2 ... are specific atom labels and MOL1, MOL2 ... are the symmetry numbers of molecules related by different symmetry operations to the asymmetric molecule. These numbers are given in the output before plotting starts and can be put on the plot using the command LABEL MOLE (see 27)).

a-1) DIST Cl 01: This calculates the distance between atoms C1 and O1 in the asymmetric molecule.
a-2) DIST H6 N2 1 2 5 6: The distances between atom H6 in the asymmetric molecule, number 1, are calculated for each of the atoms N2 in molecules numbered 2, 5 and 6.
b) DIST C1 C2 C3 N1 O1 H6: The distances between the pairs of atoms, C1 and C2, C3 and N1, O1 and H6 are found in the asymmetric molecule.
c) DIST PLOT: Up to 20 pairs of atom distances can be plotted on the device at any one time. Each distance consists of a dashed line between the atom pair and up to 6 characters for the distance value, including 3 decimal places.
d) DIST NOPLOT: No distances are plotted.

22) EXCL

This takes the form:-

EXCL EL1 EL2 EL3 etc...

It excludes from the plot atoms corresponding to the specific atom types EL1, EL2, EL3 etc.,. For example:-

EXCL H

in a compound containing H, C, O, N leaves out the hydrogen from the plot.

23) FR80

The current set of commands and free format data typed in at the terminal are to be written to disk. The data is only written out once irrespective of the number of times that different command sets are saved using FR80. The command can only be issued after the command PLOT has been obeyed by the program, following entry of the data.

24) HELP

This invokes the HELP facility of the program. Keywords correspond to those given in the menu, which is displayed on the screen after 'HELP' is typed in, for example:-

HELP SOLID

25) INCL

This includes in the plot only the specified atom types:-

INCL ELI EL2 EL3 ...

As an example:-

INCL C O N

in a compound containing H, C, O, N leaves out the hydrogen from the plot.

26) JOIN

This command allows atoms to be joined together. There are five basic forms:-

a) JOIN EL1 TO EL2 EL3 ...
b) JOIN EL1 EL2 EL3 * EL4 EL5 * EL6 ...
c) JOIN RADII EL1 r1 EL2 r2 ...
d) JOIN RADII UNIQUE EL1 r1 EL2 r2 ...
e) JOIN RADII INTER EL1 r1 EL2 r2 ...

where EL1, EL2 ... are either specific atom types or atom labels and r1, r2 are the corresponding bonding radii.

a) JOIN C1 TO C2 C3: Atom C1 is joined to atoms C2 and C3
b) JOIN C1 C2 C3 C4 C5 C6 C1 * C2 BR1 * C4 C7 C8: A benzene ring is formed by joining C1, C2, C3, C4, C6, C6 sequentially as a group. The bromine is joined to C2 and an ethyl group joined to C4. Each group is independent and separated by a '*'
c) JOIN RADII C 0.85 BR 1.35 H 0.04: A search is made for all interatomic bond distances between the atoms such that all C-C bonds are less than 1.7 angstroms, all C-BR bonds are less than 2.2 and all C-H bonds are less than 1.25 angstroms.
d) JOIN RADII UNIQUE C 0.85 BR 1.35 H 0.04: This is similar to c), except that some or all of the atoms may be moved slightly, depending on the molecular symmetry, to form a uniquely bonded molecule.
e) JOIN RADII INTER B 1.0 N 1.0: This will join atoms intermolecularly such that B-B bonds are less than 2.0 angstroms and B-N bonds are less than 2.0 angstroms.; *** Note: It is not possible to redefine the JOIN command in the current plot for free format data. The plot must be reset using OPT/GOPT.

27) LABEL

This takes the form:-

LABEL MOLE EL1 EL2 ELS etc...

The keyword MOLE causes the program to plot against the first atom of each symmetry generated molecule the number of the symmetry operator and the translation components which were used. If MOLE is absent no such annotation is produced. The keywords EL1, EL2 etc.,. are atom symbols and if they are present the program will label atoms only for those specified element types. The program tries to find a label position close to the relevant atom giving minimum overlap with other atoms, bonds and labels.

28) MATRIX

If the components of the rotation matrix are known, from earlier plots, then the rotation matrix can be input directly. This command takes the form:-

MATRIX r11 r12 r13 r21 r22 r23 r31 r32 r33

r11...r33 are the components of the matrix which will replace the current rotation matrix. The program checks that the determinant of this new matrix is equal to + 1 within a tolerance +/- 0.0001.

An example of the use of MATRIX would be:-

OPT SOLID NOHYD
MATRIX -.9881 0.0270 0.1511 0.0864 0.9117 0.4017 -.1269 0.4100 -.9032
PLOT

29) MOLE

The PACK option produces a packing diagram for all molecular residues lying within a defined box. The qualifier command MOLE allows specification of which residues should be plotted and thereby produce a diagram which concentrates on the residues of interest. The command takes the form:-

MOLE s1 tx1 ty1 tz1 s2 tx2 ty2 tz2 etc...

Each residue to be plotted is defined by two sorts of keywords, s = the serial number of the symmetry operator to be applied to the input residue, and tx, ty, tz = unit cell translations to be added to the symmetry operator. The first symmetry operator is always the identity, so if the input residue is to be plotted the command takes the form:-

MOLE 1 0 0 0 ....

The values of s are available from previous calculations and appear on the terminal before plotting takes place. For a given plot more than one record may be needed to input the list of specified residues. Each continuation record starts with the command MOLE.

30) PERSP

This command takes the form:-

PERSP d

This causes the coordinates to be projected with perspective applied from a viewpoint d mm from the molecular model. Perspective can be incorporated into both mono- and stereo- views. If this command is absent the default action is to plot a mono- view with no perspective or a stereo- view with d = 600 mm.

31) PLOT

The plot initiator command is the last command of the set and takes the form:-

PLOT TRACE a COPIES b ENTNO c

The keywords TRACE, COPIES and ENTNO are optional, but in the BATCH version care must be taken that ENTNO is specified when a single set of data is to be taken from a multiple set of data is run under a single command set. Failure to do this will result in all the sets of data being plotted until time or line limits are exceeded. TRACE causes the plot to be retraced a times, which can be useful when the plot has to be photographed. COPIES results in the production of b copies of the plot and was originally used for pen plotters. ENTNO specifies that only entry number c in the dataset is to be plotted. The 'c' associated with ENTNO can be either a number or the Cambridge format CODEN of 6 characters, e.g. 'PLOT ENTNO BAOXLM'. The CODEN is not applicable to FREE FORMAT. To get the next set of FREE FORMAT data you have to erase the current set of data using the DCLEAR command (see 19)).

32) PRINT

Gives a detailed printout of the interatomic distances and angles between atoms in molecules and also atom connection lists.

33) RADII

The RADII command is used only with the SOLID option. It specifies the radii of atom circles and bond cylinders, and the number of lines used in composing a bond. It has a very important application in the plotting of space filling models. If the command is not given, defaults are used (see section 5.2) unless radii are read in with the Cambridge format data. There are seven forms:-

a) RADII ATOMS EL1 r1 EL2 r2 ...
b) RADII BONDS ALL r m
c) RADII BONDS TO EL r m
d) RADII BONDS INTER r m
e) RADII BONDS TAPER t
f) RADII STIK
g) RADII NOSTIK

where EL1, EL2 ... are specific atom types, r1, r2 ... are the associated radii in angstroms and t is a tapering parameter.

a) RADII ATOMS C 1.2 N 1.3 H 0.7

The atom types C, N and H are assigned the radii 1.2, 1.3, 0.7 angstroms. If the structure contains other atom types then the default bonding radii will be used. Space filling models are plotted with bonding radii equal to or slightly less than the van der Waals radii.

b) RADII BONDS ALL 0.05 10

This command causes all bonds to be plotted with cylindrical radius 0.05 angstroms and 10 lines per bond. The default values are 0.04 and 8.

c) RADII BONDS TO H 0.01 4

This command causes bonds to hydrogen to be plotted with cylindrical radius 0.01 angstroms and 4 lines per bond. Suppose you wanted to distinguish the coordination around Fe by plotting bonds to Fe as single lines then you can use the command:-

RADII BONDS TO FE 0 1

d) RADII BONDS INTER 0.02 2

This command causes intermolecular bonds which have been defined by a CALC command to be plotted with cylindrical radius 0.02 angstroms and 2 lines per bond. This is useful in allowing graphical differentiation between inter- and intramolecular bonds.

e) RADII BONDS TAPER 20

When the bond between atoms i and j is plotted, bond radii RBI, RBJ are assigned to each end of the bond. RBI and RBJ have slightly different values when perspective is being applied to the coordinate projection. This perspective effect is generally not noticeable so this command is provided to exaggerate the tapering of bonds. Assuming that atom i is nearer to the viewpoint than atom j then RBI is multiplied by (1 + tcos a/10) and RBJ by (1 - tcos a/10), where a is the angle between the vector from j to i and the ZP axis, and t = 20 in this instance. A useful general value of t is 10.

f) RADII STIK

If RADII ATOMS has been used to define a Van der Waals space filling plot, then this command will allow a stick plot to be superimposed. If the space filling plot is to be coloured, the stick molecule will have coloured bonds and only a white space filling outline will be drawn.

g) RADII NOSTIK

This removes the stick plot from the space filling one and restores the previous colour command.

34) RANGE

The option PACK produces a packing diagram for a box in the range 0-1 along each of the 3 unit cell axes. It may often be convenient to specify the minimum and maximum values along XC, YC, ZC rather than accept the standard values of 0 and 1 in all directions. This is done using the qualifier command RANGE which takes the form:-

RANGE xmin xmax ymin ymax zmin zmax

In practice it is best to restrict the range to 1 cell translation on the axis closest to the view direction and to allow 2 cell translations along the other two axes. Thus for a z-axis projection the RANGE command takes the form:-

OPT NOHYD PACK VIEWZ 
RANGE -.5 1.5 -.5 1.5 0 1 
PLOT

35) SHADE

This command takes the form:-

SHADE a1 a2

This causes the drawing of shade lines representing shadow from a light source whose position is defined by the two angles a1, a2. If a1 = a2 = 0 degrees then the light comes directly towards the viewer along the ZP axis so that the whole atom is shaded. The angles a1, a2 correspond to the rotation of the light about YP and ZP respectively. Convenient values of a1, a2 for approximate half-shading are 100, -60 degrees.

36) STEREO COLOUR

This command makes the colour device.

37) STEREO VIEWER

This command makes the interactive version of the program plot a side by side stereo pair, but not a red/green pair, and makes the BATCH version plot stereo pairs on 35mm film, suitable for use in an Open University stereo viewer.

*** Note: In some cases the use of the COLOUR BONDS command AFTER the STEREO VIEWER causes only a single plot instead of a stereo pair. This can be prevented if all COLOUR commands are given before STEREO VIEWER.

38) STOP

This stops the program and closes down all relevant output streams.

39) TITLE

This takes the form:-

TITLE title

where title is any appropriate text (up to 74 characters long) to be printed at the top of the plot. All characters are converted to upper case.

40) VIEW

For each plot the program requires a view direction. For a given view direction the program calculates a (3x3) rotation matrix R, which transforms the input coordinates to the plot ones. Any directions given as keywords in the OPT command will be overridden by VIEW. This has two advantages:-

a) more basic directions
b) the ability to set up a view direction, as above, and then rotate the model with respect to the plot axes.

In the options command the view directions are either the view with minimum overlap or defined with respect to the unit cell axes. In the VIEW command a direction can be defined either with respect to the unit cell axes or the atoms of the structure.

I) Basic view directions

*** Note: the '.' between words should not be typed, instead use a space.

Command                             Meaning
a)..VIEW.XO.........................View direction is along XO.
b)..VIEW.YO.........................View direction is along YO.
c)..VIEW.Z0.....................*...View direction is along ZO.
d)..VIEW.HOR.AT1.AT2.VER.AT3.AT4....Horizontal axis XP in direction AT1 to AT2. Vertical axis YP 
                                    as near as possible to direction AT3 to AT4. 
                                    For example, 'VIEW HOR Nl Cl VER Nl N3'.
e)..VIEW.LINE.AT1.AT2.HOR.AT3.AT4...View direction is along the line from AT1 to AT2. Horizontal 
                                    axis XP in direction AT3 to AT4. For example, 
                                    'VIEW LINE N1 C1 HOR N1 P4'.
f)..VIEW.BISECT.AT1,AT2.AT3.........View direction is along the bisector of the angle AT1-AT2-AT3 
                                    towards AT2. For example, 'VIEW BISECT C1 N5 O4' .
g)..VIEW.PERP.AT1.AT2.AT3...........View direction is normal to the plane of AT1-AT2-AT3. For example, 
                                    'VIEW PERP O1 CU1 O1A'.
h)..VIEW.PLANE.ATI.AT2.AT3.AT4.etc..View direction is along normal through AT1-AT2-AT3-AT4.. For example, 
                                    'VIEW PLANE N1 C2 N3 C4 C5 C6'.

II) Rotation of Model with respect to Plot axes

In addition to the special view directions, it is possible to specify any general direction by fixing the angles of rotation with respect to the plotting axes. The convention is:-

Clockwise rotation of the model when looking along the axis from its positive end towards the origin corresponds to a positive rotation angle. Rotations about XP, YP, ZP are indicated by:-

XROT a YROT b ZROT c

where the rotation about XP is a degrees, about YP is b degrees and about ZP is c degrees. For example:-

OPT SOLID NOHYD
VIEW PERP C1 C2 C3 ZROT -30 XROT 45
PLOT

The VIEW PERP command generates a view direction normal to the plane Cl, C2, C3, The corresponding rotation matrix is stored as the current matrix. The program next rotates the model by -30 degrees around ZP and then by 45 degrees around XP. The current matrix is modified to take account of these rotations and the new rotation matrix is stored as the current matrix. The final version of the current matrix is used to plot the model.

2.4 The GLOBAL commands used for plotting

These commands remain in force over many plots unless reset by the GLOBAL options command GOPT (which has the same keywords as OPT), or changed by using the command to redefine keywords and values. In the summary below, 'C' following the command number denotes an original Cambridge command, 'R' an RAL extension.

COMMAND NAME       KEYWORDS      MEANING 
                   +VALUES           
00R)..GOPT........SAME.AS.OPT...Set up default options.
01R)..COLOUR........KEYWORDS....Specify atom/ colour pairs, or coloured bonds.
02R)..COMPLOT.......KEYWORDS....Commands are listed on the plot.
03R)..DEMO...........VALUES.....Set up a continuous demonstration with a variable 
                                amount of time between plots.
04R)..DENSITY........VALUES.....Specify the spacing of lines which shade atoms,
05R)..INTENSITY......VALUES.....Set up scaled intensities for all colours on FR80.
06R)..INTHIT..........BOTH......Set up absolute intensities + hits of colours on FR80.
07R)..JOIN............BOTH......Allows atoms to be joined within specified distances, 
                                groups of atom bonds to be coloured, and display 
                                limits defined.
08R)..MANYUP.........VALUES.....Set up the FR80 hard copy many subdivisions,
09R)..MOVE............BOTH......Allows you to move molecules within the unit cell and 
                                move the origin of the whole plot.
10R)..ROTATE..........BOTH......Specify bond rotation.
11R)..SEGMENT.........BOTH......Specify the number of segments in the atom circles.
12C)..SIZE............BOTH......Set up the size of the plot.

1) COLOUR

This command takes five forms:-

a) COLOUR OFF
b) COLOUR HT < EL1 COLR1 EL2 COLR2 ... EL20 COLR20 >
c) COLOUR ON < EL1 COLR1 ............. EL20 COLR20 >
d) COLOUR BONDS
e) COLOUR NOBONDS

where EL1, EL2 ... are the specific atom types and COLR1, COLR2 ... are the associated colours.

a) COLOUR OFF: This switches off the colours on all devices.
b-1) COLOUR HT: This turns on the 'half-tone' colouring on all devices. A default list of atom types/ colour pairs is used (see below) and the colours are black, white, light grey and dark grey and are simulated by drawing shading lines at different spacings.
b-2) COLOUR HT SI WHITE B LGREY: In this case the default colour list is extended by inclusion of silicon and boron. The defaults may be modified, for example by setting N DGREY as keywords on the command. The final list may have up to 20 atom types/ colour pairs.
c-1) COLOUR ON: This turns on the colour on devices capable of displaying colour. The default colour list is given below.
c-2) COLOUR ON SI GREEN C MAGENT H YELLOW: The default list is both modified and extended in this example. In addition to the colours given below, some devices support additional grey levels or pastel shades. These colours may be accessed by calling each colour in the form Pn, where n = 8 to 15. P8 is black and P15 is white on devices supporting grey levels. The colours P9 to P14 are then grey shades.
d) COLOUR BONDS: This allows stick molecules to be coloured in such a way that each half of the bond is coloured according to the atom to which it is attached. If COLOUR ON ... has not been used, the default colour list will be invoked.
e) COLOUR NOBONDS: This turns off the colouring of bonds but leaves the colour list intact.

The full default colour table is:-

BLACK WHITE RED BLUE GREEN YELLOW CYAN MAGENT LGREY DGREY 
 C     H     O   N    Cl    S      Br    P     O,N  Rest

Where possible, normal chemical convention is followed for atom colours, but the choice of the atoms is given according to the most frequently occuring elements in molecules.

*** Note: Magenta is input as MAGENT because the command decoder only allows a maximum of 6 characters for keywords. Any of the colours can be abbreviated to the minimum number of letters which uniquely define that colour. These are:-

BLA, W, R, BLU, G, Y, C, M, L, D

2) COMPLOT

This takes two forms:-

a) COMPLOT OFF
b) COMPLOT ON

and lets you switch 'OFF' or 'ON' the display of the current command set on the screen. The default is 'OFF' to give the largest possible plot. The commands are displayed down the right hand side of the enclosing box, with the exception of STEREO plots which never display the commands.

3) DEMO

This command must be the first in the set when running the demonstration on the terminal. It has the form:-

DEMO n

where 'n' is an integer which determines the amount of time between plots. If no value of 'n' is given, a default of 100,000 is used. Values between 50,000 and 200,000 are useful, but note that the real time between plots depends on the type of computer, its load and your connection to it.

4) DENSITY

This command takes the form:-

a) DENSITY n
b) DENSITY -n

where 'n' is an integer, excluding 0. Positive values decrease the spacing of shading lines and negative values increase it. Shading by drawing lines is used for HALF-TONE, COLOUR and SHADing on ball + spoke or space filling plots. The default value of 'n' is 1. Useful values for fast plotting/ quick look are -2 or -4 and for well filled molecules 2 or 4. To obtain shading lines which almost fill the atom circles use SEGMENT 20 or 50 for ball + spoke and 150 for space filling plots.

5) INTENSITY

This command is used only for FR80 plotting, it changes the intensity of all colours in the same way by scaling all the intensities by a given value in the range 1.0 to 5.0. Any resulting intensity above 255 is reset to 255. Since the intensities follow a log relationship, changes of contrast are noticed more at low intensity values than high ones. An example is:-

INTENSITY 0.7

6) INTHIT

This command changes the intensities and hits of individual colours on the FR80. The command name is followed by sets of three items (the colour name, intensity and hits required). It should be used with caution. The intensities are restricted to values between 0,255 and hits to 0,15. An example of the command is:-

INTHIT BLACK 200 1 RED 255 7

7) JOIN

PLUTO78 is able to draw framework structures, using the LOCAL JOIN command (see section 2.3, 26C) ). However, a more convenient method of joining particular atom types is given here. There are 7 forms:

a) JOIN ALL EL1 TO EL2 dmin dmax
b) JOIN ALL RESET
c) JOIN ALL DUMP
d) JOIN ALL COLOUR <colr1 colr2 ... colr7>
e) JOIN LIMIT xcmin xcmax ycmin ycmax zcmin zcmax
f) JOIN LIMIT RESET
g) JOIN LIMIT DUMP

The first form of ALL is to specify which atom type, EL1, will be joined to the same or a different atom type, EL2. Connections will only be made if the distance between atoms is >= dmin AND <= dmax. Both these values are in angstroms. The RESET keyword resets all occurrences of JOIN ALL... There may be from 1 to 10 defined at any time. The DUMP keyword outputs the list of atoms which are being joined. The connection list is extended after PLUTO78 has joined all possible atoms in the normal way, (see the manual, chapter 2). Each time a new JOIN ALL EL1... is specified, the connection list is recalculated using the previously stored JOIN ALL EL1... commands and the current one. The COLOUR keyword allows you to set up coloured bonds (only if the SOLID keyword is absent from the GOPT/ OPT command), for each of the JOIN ALL EL1... commands. Each set of bonds defined in this way has a different default colour in the order:-

CYAN, YELLOW, GREEN, MAGENT, BLUE, RED, WHITE

The default may be changed by adding the colour name list to the default command JOIN ALL COLOUR. Thus to colour the first set of bonds red and the second blue, and leave the other sets, if they exist, as the defaults use:-

JOIN ALL COLOUR RED BLUE

The LIMIT keyword specifies a region within which atoms are joined and outside of which connections are ignored. The limits are taken along the XC,YC,ZC crystal axes and are defined in the same way as for the RANGE command (see section 2.3, 34C) ). For example, xcmin = -2 or 1.3 are both valid. This part of the JOIN command is distinct from the RANGE command, and has the advantage that once the RANGE of the crystal lattice has been defined the JOIN LIMITs can be repeatedly changed or RESET. The LIMIT DUMP allows inspection of the current LIMITs. Examples are.-

JOIN ALL O TO O 2.0 2.5
JOIN ALL RESET
JOIN LIMIT 0 1 0 2 0 .5

8) MANYUP

This command is only used to control output from the FR80. It must be the first in the BATCH command set, and it changes the number of HARD COPY MANY subdivisions (the default is 2x2). If you want I plots across and J down the page, then the form of the command is:-

MANYUP I J

9) MOVE

This command takes two forms:-

a) MOVE ORIGIN x y z
b) MOVE MOLE x y z

a) MOVE ORIGIN 10 -20 0: The whole plot is moved such that the new origin of all the plot coordinates are the original values plus the x,y,z defined in the command. The z value has no effect. Since the command acts on the plot coordinates, the distance that the plot moves around on the screen will depend on the current scale factor. x,y,z values of between +/- 10 to 100 are useful.
b) MOVE MOLE 0.03 0.1 -0.05: This moves the asymmetric molecule such that the input fractional coordinates x/a, y/b, z/c are changed to x/a+0.03, y/b+0.1, z/c-0.05 with respect to the fixed unit cell. All symmetry related molecules are generated correctly.

10) ROTATE

This command takes five forms:-

a) ROTATE BOND n EL1 EL2 ATOMS EL3 EL4 EL5 ...
b) ROTATE BOND n EL1 EL2 ATOMS EL3 TO EL4
c) ROTATE BOND n x
d) ROTATE SAVE
e) ROTATE RESET

where EL1, EL2 ... are the specific atom labels, n is the bond identifier which may be from 1 up to 10 at any one time, and x is the absolute value of the rotation in degrees around the particular bond.

a) ROTATE BOND 1 C1 C5 ATOMS H51 H52 H53

This defines bond 1 to be directed from atom Cl1 to atom C5 with atoms H51, H52, H53 being rotated. This example is of a methyl group, but up to 400 atoms may be rotated on any of the 10 bonds. Therefore, the definition of the bond may be given on more than one ROTATE command. For example:-

ROTATE BOND 4 C1 C2 ATOMS C3 C4 C5 
ROTATE BOND 4 C1 C2 ATOMS H3 H4 H5 H6

b) ROTATE BOND 1 C1 C5 ATOMS H51 TO H53

In this case all atoms from H51 to H53 are to be rotated, assumming that the input atom list has H51, H52 and H53 arranged consecutively.

c) ROTATE BOND 1 60

This rotates bond 1 by 60 degrees in absolute terms and the rotation is clockwise about the bond directed from C1 to C5. Any suitable free format value may be given, for example 55.117 degrees.

d) ROTATE SAVE

This saves the orthogonal angstrom coordinates of the atoms on disk in a FREE FORMAT type of file.

e) ROTATE RESET

This resets all the bond definitions and rotation angles without having to use GOPT.

*** Note : The molecule MUST be plotted once before defining the bonds. This is necessary because PLUTO78 reads, and processes, commands before data. Since bond rotation depends on matching up atom labels do not use GOPT/ OPT before defining the bonds, otherwise the atom label flags set up in the previous plot will be reset and no rotation will occur. See section 1.2 for examples of the initial plot and 'ROTATE' command.

11) SEGMENT

This takes three forms:-

a) SEGMENT OFF
b) SEGMENT ON
c) SEGMENT n

It controls the number of straight line segments used to draw the circles defining the atoms. 'OFF' switches the fixed segment part of the program off and allows PLUTO78 to determine how many segments to draw for each type of atom circle,- 'ON' is the default state with 8 segments for all atom circles for fast plotting; 'n' allows you to define how many segments you want to be used for all atom circles, subject to a minimum of 4 and a maximum of 600 segments. Convenient values of 'n' for ball + spoke and space filling plots are:-

SEGMENT 20 
SEGMENT 50

There is an additional keyword 'FR80' which the interactive program ignores. It is used in the BATCH version to indicate that the SEGMENT command is to be acted on. By default all film and hard copy paper with multiple plots use SEGMENT 50 for ball + spoke and SEGMENT 150 for space filling plots. This is done to obtain an acceptable plot and to minimise the CPU time required to produce the output. The hard copy single paper output defaults to SEGMENT OFF to give the best quality. By using 'FR80' on the SEGMENT the effects of the BATCH defaults are overridden. If, for example, an interactive plot of a molecule is made in ball + spoke with 20 segments, then:-

SEGMENT 20

gives a batch hard copy multiple-type plot with 50 segments, but the use of 'FR80':-

SEGMENT 20 FR80

gives a multiple-type plot with 20 segments.

12) SIZE

The most general form of this command is:-

SIZE s1 CHAR s2 SCALE s3 XMIN x1 XMAX x2

SIZE defines the size, nominally in mm units, of the square frame enclosing the plot. Note that the mapping onto the device does not always give units as millimetres. It has the following default values of s1:-

125 units, for a side by side stereo pair. 
220 units, for a single view.

CHAR defines the character height for labels and the title and is principally of use on the FR80. On terminals, hardware generated characters are used and these are unaffected by CHAR. The default is s2 = 3, which produces characters about 2.5 mm in height. SCALE defines the scale of the plot in mm. per angstrom. If SCALE is specified with value s3, then s1 is ignored and no enclosing frame is plotted. If the scaled plot is too large for the display area, then the excess portions are lost. XMIN and XMAX define the limits, in angstroms in the internal coordinate system, of the coordinates to be plotted, which is useful when these values of the fragment are known with respect to defined molecular axes and origin. In this case no relative scaling occurs. Some examples of the SIZE command are:-

SIZE 250
SIZE 250 SCALE 10
SIZE 250 CHAR 5 XMIN -5.0 XMAX 5.0

2.5 Commands used for plotting

Data can be typed in from the terminal or read in from a disk dataset. In both cases, if the first character on the first data line is an #, Cambridge database format is assumed. If it is not an #, FREE Format is assumed. When input comes from the terminal, the program will first prompt you to type in the 3 characters, 'VDU', in order to set flags correctly. Then a FREE FORMAT dataset can be entered. It consists of the following records:-

TITLE record
CELL record
SYMM record(s)
Atomic coordinate records
END record>

*** Note : records 1,4,5) are mandatory.

1) TITLE record

This record must have TITLE in columns 1 - 5, but the rest of the record can contain any text for identification, up to a maximum of 74 characters.

2) CELL record

This record must have CELL in columns 1-4, followed by the values of the axial lengths (a, b, c) and the interaxial angles (alpha, beta, gamma). If the CELL record is omitted, the program sets six default values (1 1 1 90 90 90) which correspond to the input of orthogonal angstrom coordinates. Some examples of this record are as follows:-

CELL 12.90 3.91 28.54 90 90 90
CELL 12.901 3.952 28.543 99.12 121.34 102.6

3) SYMM record

There are two alternative forms for this record:-

a) SYMM in columns 1-4 followed by the general equivalent positions (GEP) as specified in the International Tables for X-ray Crystallography, volume 1. The full set of GEP is required including those related to the basic set by a centre of symmetry at the origin and by lattice centring. The first GEP in the list must be X, Y, Z. Each GEP is separated from the next by '*'. If more than one record (up to 80 characters long) is needed then each record starts with SYMM. Fractions can be coded as decimal numbers or as fractions, but the coding for a GEP must not be split between two successive records. Some examples of these SYMM records are as follows:-
```
SYMM X,Y,Z * l/2-X,l/2+Y,Z * ... 
SYMH X,Y,Z * 0.5-X,0.33333+Y,Z * ...
```
b) SYMM in columns 1-4 followed by the numeric symmetry operators which relate xp, yp, zp to the first general equivalent position X, Y, 2 by the expressions:-
```
xp = R11.X + R12.Y + R13.Z + Tl
yp - R21.X + R22.Y + R23.Z + T2
zp = R31.X + R32.Y + R33.Z + T3
```
The terms Rij and Ti are the elements of the rotation matrix R and the translation vector T connecting the symmetry points. Note that only one operator can be present on this type of record and that if SYMM records are absent, the default setting of the program is one GEP of X, Y, Z. An example of this type of record is as follows:-
```
SYMM -1 0 0 0.5 0 1 0 0.0 0 0 -1 0.5 
```
This represents the GEP 1/2-X, Y, 1/2-Z.

4) Atomic coordinates record

This record begins with a mandatory atom label which starts in column 1. The specification of labels obeys the following Cambridge rules. The label consists of two parts, the first being usually a conventional chemical symbol for the type of atom but you can define your own labels. The second part of the label consists of one or more numeric characters to identify each atom of a particular type. The total length of the label must be 6 characters or less.

Nl 
C12
BR3

If an atom is symmetry related to a member of the basic set then another one or two letters are added to the label to distinguish between atoms of different symmetry. Each letter added identifies the number of the symmetry operation used to generate the atom. For example, letter A goes with the first operation, B with the second and so on. Examples are:-

C12A
BR3F 
N1AB

The record also contains the fractional atomic coordinates x/a, y/b, z/c referred to unit cell axes in the coordinate system XC,YC,ZC. These three values must be separated from the atom label and from each other by at least one blank character. An example of this record is as follows:-

C1 0.01 -0.02 0.03

5) END record

This record must have END in columns 1 - 3, and it indicates the end of current data entry. No calculation takes place until this record is read.

*** Note: when the current set of free format data needs to be replaced, you must reset the data-in-core flag by using the command DCLEAR before typing in the next set of data. You may run the program using several Free Format datasets in a disk file, but PLOT ENTNO XX will only be obeyed after DCLEAR is given. Otherwise 'ENTNO XX' will be ignored and the current dataset will be reused.

2.6 Data Entry Commands using FREE Format

This example is of the first plot ( 1.2) of entry number 23 (BAOXLM) in the test dataset of structures. See >section 2.5 for a description of the format of each record. The TITLE, atomic coordinates and END records are mandatory, and there must be at least 3 sets of atomic coordinates to define a plane.

TITLE BAOXLM FREE FORMAT DATA
CELL 10.10 7.96 6.83 90 121.96 90
SYMM X,Y,Z * X+1/2,Y+1/2,Z * -X,Y,-Z * -X+l/2,Y+l/2,-Z
BA1 0.2175 0.0 0.3153
C1 0.3615 0.403 0.2405
O1 0.4133 0.3346 0.1305
O2 0.3102 0.33 0.3516
O3 0.4712 0.0 0.2439 
C1F 0.3615 0.5970 0.2405 
O1F 0.4133 0.6654 0.1305 
O2F 0.3102 0.67 0.3516 
END

This format can be typed in interactively from the terminal and then plotted immediately by PLUTO78. If the data is to be stored, the command FR80 can be used AFTER the first plot. However, it is probably easier to prepare the data using the editor, and then plot it as a file of data read in from disk.

2.7 MACRO commands

A PLUTO78 MACRO command is defined as a set of commands preceded by, and terminated by special records. The start of the MACRO command is indicated by the characters '* MACNAM', where MACNAM is any set of up to 6 characters. The end of the MACRO is indicated by '*END'. Between these delimiters, you may define any collection of valid PLUTO78 commands. The MACRO'S are held in a file and MUST be defined before the program is run. On CMS the file is called 'PLMACRO COMMAND' and if you haven't made such a file on your minidisk, the default on the PLUTO78 disk will be used. On the GEC's the file is called '.MACROCOM'. The file may contain more than one MACRO command and each is called by its name. For example, if you want to define a MACRO which sets up coloured bonds add the following to your MACRO file:-

* COLBND
COLOUR ON C CYAN O RED H YELLOW N MAGENT
COLOUR BONDS
*END

At any point during the running of the program you can type in reply to the 'COMMAND?' prompt:-

* COLBND

remembering to start in column one. This command input will result in the MACRO file being searched to find '* COLBND'. If is is found, the commands up to '*END' will be obeyed. If it is not found, the program will output the lines:-

*** EOF ON MACRO COMMAND FILE ***
*WARNING* UNRECOGNISED CARD

to the terminal and then the 'COMMAND?' prompt will be given.

*** Note: This MACRO file is NOT the same as the file used when you want to run your command sets from disk, instead of from the terminal. If you specify the MACRO file when you mean the file of command sets, the program will produce unpredictable results. A typical file of command sets is 'PLDEMO COMMAND' on CMS, and '.PLDEMCOM' on GEC's.

3.1 CMS use of PLUTO78

3.1.1 Introduction

This document briefly describes how to use PLUTO78, the molecular drawing program from Cambridge in its 1978 version. It runs interactively under CMS and also on the RAL BATCH system. Under CMS, PLUTO78 lets you look at molecular data and decide which set of drawing instructions (called command sets) give useful plots. These instructions and data can then be sent to the batch system to produce high quality microfiche, 16/35 mm black + white or colour film, and hard copy paper output on the FR80 microfilm recorder.

3.1.2 Getting started on CMS

You need a valid identifier and account for CMS in order to use PLUTO78. If you want to use the FR80, you also need a valid identifier and account on the BATCH system. The document entitled 'An introduction to CMS on the RAL coupled system' (RL-80-008, second edition) gives all the necessary information for interactive use, and a copy of it is given to new users. When you run PLUTO78 under CMS you need a virtual machine (vm) of 1 megabyte, but your initial vm size will probably be 512kb. To change this temporarily during the session you must type in the command:-

DEFINE STORAGE 1M

and follow this by typing:-

IPL CMS

to recreate your vm. Then type return. To change your vm size permanently you must type in the command:-

DIRM STORAGE 1M

and then logout and logon again. To check your vm size, type the command:-

Q STOR

To run the program you must have access to PLUTO78 EXEC, PLUTO78 MODULE and PLUTO78 HELPCMS.

In order to use PLUTO78 EXEC and HELPCMS you must access the U-disk at the start of your session. To do this type the command:-

UDISK (MODE U

The U-disk is now accessed as your U minidisk.

You must now type in the command:-

PLULINK

to link to the disk containing PLUTO78 MODULE. By default this disk will be linked as your D-disk. There are two files on the U -disk called PLULINK EXEC and PLULINK HELPCMS that you can access if you want more information.

If you want to run the program using the test option or with permanently stored data, see sections 3.1.14,15.

*** Note : running on a graphics device will probably use a lot of your accounting units. If you just want to see what sort of output PLUTO78 can produce on a tektronix 4010, type in 'GVIEW PLUTO78 GRAPHICS', or see sections 3.1.3), part f) , 3.1.11) for more information.

3.1.3 PLUTO78 components

PLUTO78 consists of six parts :-

a) PLUTO78 MODULE ......  this is the non-  relocatable load MODULE,
                          stored on the PLUTO78 minidisk  (see section
                          3.1.2 for linking information).
b) PLUTO78 EXEC ........  this EXEC is stored on the CMS U- disk (see
                          section 3.1.2) and runs the MODULE when you type in the command:-
                            PLUTO78
c) PLUTO78 HELPCMS .....  this is the HELPFILE which is stored on the
                          U- disk. (see section 2). It briefly describes 
                          what PLUTO78 is and contains the various HELP facilities 
                          called by the program. It will run under the CMS HELP 
                          system when you type in the command:-
                            HELP PLUTO78
d) PLSECT31 SCRIPT .....  is this section of the user manual.  This is
                          available on the PLUTO78 minidisk.
e) PLSECT2 SCRIPT ......  this document contains all the commands and
                          specifications for free format data entry.
                           It is on the PLUTO78 minidisk.
f) PLUTO78 GRAPHICS ....  this  is  a set of  demonstration plots,
                          suitable for viewing on a tektronix 4010, using the 
                          CMS GVIEW command (see section 3.1.11). It can be 
                          viewed from the PLUTO78 minidisk.

3.1.4 The Cambridge user manual

A copy of the 1978 Cambridge manual is available for reference in the Atlas centre, RAL. Ask either Mrs K M Crennell or Dr G M Crisp.

3.1.5 Device types and line speeds

To produce graphical output you need a tektronix 4010 or a sigma 5660/70. If you want to use either the test option (see section 3.1.11) or submit a job to BATCH (see section 3.1.14), then you need only an ASCII terminal or a teletype. Available line speeds are:-

300, 1200, 2400,4800 Baud

if you access CMS from SERCNET.

3.1.6 The EXEC

The EXEC runs the MODULE and allows you to interrogate

a) the HELPFILE.
b) the valid device types and speeds.
c) the valid data/ command file formats.
d) to link/ detach disks (CMS and OS) and query which disks you can access.

3.1.7 The HELP facility

You can list the HELP file - PLUTO78 HELPCMS - from the terminal by typing in the command:-

HELP PLUTO7B

The EXEC lists the HELP file when you type in:-

HELP

in response to certain EXEC prompts. The PLUTO78 program uses the HELP file slightly differently, in that you can look at particular sections of the file when you type in:-

HELP XXX

in response to either of the program prompts:-

COMMAND? 
DATA?

XXX indicates any valid name in the HELP file and if you want to find out what HELP is available, just type in:-

HELP

3.1.8 Data

You can type data interactively from the terminal if you have specified the terminal in response to the appropriate EXEC prompt. If you specify an existing CMS or OS- disk, then the program will take data from this source. The program asks you whether the data file consists of a single set or many sets of molecular data. If many sets of data are expected, the program asks you whether a single set or many sets of commands will be used. A single set of data has only many sets of commands, but many sets of data can have either:-

a) a single command set, so that all the molecular data is processed in the same way. You can find this useful if you want to look through all your data without re-typing the command sets.

b) many sets of commands, so that each set of molecular data can have any number of command sets by which it is processed. You can use this to find out which command set bests suits the current set of molecular data, before storing the commands in a file for use on the FR80 (see section 3.1.12).

3.1.9 Commands

You can type commands interactively from the terminal, if this has been specified in the EXEC, or you can read the commands in from a file which already exists on CMS or OS- disks. Section 1.2 of this manual gives several PLUTO78 example plots, including their sets of commands. These commands are stored in PLDEMO COMMAND on the PLUTO78 disk.

3.1.10 Test option

A simple test option exists in the CMS version of PLUTO78 which bypasses the graphics routines. It can be used when specified in response to the appropriate prompt from the program. This option is an aid to debugging data, in addition to the 'OPT' keyword qualifier 'DEBUG', and provides one line output when entering routines associated with data input and handling. This allows you to monitor the progress of the progam. A typical one line output is:-

*** ENTERING INTERP. 1ST CALL ***

*** Note This option is in addition to the DEBUG command which outputs variables and arrays.

3.1.11 Storing graphical output

You can store graphical output in a file for viewing later if you specify a filename when the EXEC prompts you to initialise the graphics device. The filename must only have up to 5 alphanumeric characters, because the system appends a three digit version number to make the file unique. You specify this name after the device speed, and you need all the parameters specified. For example if you type in the command:-

T4010 4800 TKOUT

when prompted, the system stores your graphical output in a file -TKOUT001 - in the common GRAPHICS filestore. You can look at this file, on a tektronix, by typing in the command:-

GVIEW TKOUT

The system erases the file after 15 days, but you can save it by copying it to your CMS minidisk by typing in the command:-

GCOPY TKOUT AS MYTEK

This gives you a copy of - TKOUT - known as - MYTEK GRAPHICS A - on your minidisk.

To view this file type in the command:-

GVIEW MYTEK GRAPHICS

For more information type in the CMS commands:-

HELP GVIEW
HELP GCOPY

A set of example plots, suitable for display on a tekronix 4010 and generated from commands similar to those in 'PLDEMO COMMAND D', are held in 'PLUTO78 GRAPHICS D' on the PLUTO78 D-disk. The command to type in to view these is:-

GVIEW PLUTO78 GRAPHICS D

3.1.12 Use of the FR80 microfilm recorder

PLUTO78 allows you to use the FR80 by submitting a batch job from CMS. This job file contains JCL, and your command sets and molecular data (if necessary) are taken from CMS disk files. You create these files when prompted from the EXEC, but in case you forget to do this the system creates default files in your filestore with names such as:-

FILE FT10F001

where the filename is - FILE - and the filetype indicates that output comes from FORTRAN stream 10 in the program. Stream 10 outputs commands and stream 11 outputs data. When running the program you send your current command (and terminal data) set to the files by typing in the CMS command:-

FR80

every time you want to save the current command set. Note that if you are using FREE format data, it can only be saved immediately after the current set has been closed and the first plot made.

3.1.13 BATCH job submission

You submit jobs to the BATCH system by typing either of the commands:-

PLANT FRCOM JOB A 
PLANT FRCOMDAT JOB A

The use of PLANT rather than XPLANT is to maintain compatibility with the use of PLUTO78 on the GEC's. The files - FRCOM, FRCOMDAT - both contain the same JCL but the first needs to include only command sets, whereas the second needs both command and data sets. A copy of each of these files is stored on CMC's D disk (see section 3.1.2).

The system EXEC - PLANT - prompts you for the following input:-

JOBNAME   - (e.g. MYPLUTO1) 
ACCOUNT   - (MYACC) 
ID        - (MYID)
CAMERA    - (MFCH (microfiche) is the default and the user will have to 
             supply this explicitly in response to 'USER ARGUMENTS>'
             e.g. CAMERA=HCM (hard copy many))
DATANAME   - (USER.ID.MEMBER (OS) or FR80 DATA (CMS)) 
DISKNAME   - (RHEL03) 
COMMANDS   - (FR80COM DATA) 
M/S_DAT?   - (M, for a multiple set of data, S, for a single set.)
M/S_COM?   - (M, for a mutliple set of commands, S, for a single set.)

For more information on cameras available, type in the CMS command:-

HELP GRAPHICS

FR80 output is routed by Operations to the user with identifier MYID, in this example.

3.1.14 Sample session using the Test option

This sample session does not try to present a complete picture of the way in which you can use PLUTO78, but rather to illustrate the salient features. In the following text your input is indicated by the characters:-

->

which are not part of the CMS prompt. Any input such as <XXX> means that you type XXX, <CR> means type return. After you log on and CMS is ready to receive your input, the short ready message (R;) and the prompt (.) are displayed. If you access CMS via the network, then the prompt may be absent.

R;
-> PLUTO78
DEVICE TYPE AND SPEED?, OR <CR>
-> <CR>
ALLOWED TYPES ARE :- TEKT T4010, T4014, SIGMA S5600, S5660, S5674, S5671
                     S5470, CALCOMP CALC81, CALC81R, HELP, Q, END
EXAMPLES :-
1) T4010 4800 ... ... (TEKT. 4010 AT 4800 BAUD)
2) TERM ... ... ..... (DEFINES TELETYPE OR RETAINS CURRENT DEVICE)
3) HELP ... ... ..... (INVOKES CMS HELP FACILITY)
4) Q ... ... ... .... (QUERIES GRAPHICS DEVICE)
5) END ... ... ...... (ENDS EXEC)
6) T4010 4800 TKOUT . (GRAPHICS OUTPUT SENT TO FILE TKOUT001)
ALLOWED SPEEDS ARE :- 300, 1200, 4800 
DEVICE TYPE AND SPEED?, OR <CR>
-> TERM
PLUTO DATA FILENAME?, OR <HELP>
-> HELP
FILENAMES ARE DEFINED AS :- INPUT NAME1 NAME2 NAMES NAME4 NAME5
WHERE :- INPUT IS ONE OF, TERM, CMS, OS, END, HELP.
WHERE :- NAME1, ..NAME5 ARE PARTS OF FILENAME ON CMS, OS-DISKS.
EXAMPLES :-
1) TERM ... ... ... . (INPUT FROM TERMINAL)
2) CMS MYFILE FTYPE . (CMS FILE WITH NAME - MYFILE, TYPE - FTYPE)
3) OS JAN IDFRED .... (OS FILE JAN . IDFRED ON FREEDISK. ... ... ... ... ... LINK TO DISK LATER)
4) END ... ... ... .. (ENDS EXEC FOR PLUTO DATA + COMMANDS,
  ... ... ... ... ... BUT BYPASSES FR80 OUTPUT FILES)
5) HELP ... ... ... . (INVOKES THIS PART OF EXEC)
PLUTO DATA FILENAME?, OR <HELP>
-> CMS PLUTO78 DATA
PLUTO COMMAND FILENAME?, OR <HELP>
-> TERM
FR80 COMMAND FILENAME?, OR <HELP>
-> CMS FR80COM DATA
FR80 DATA FILENAME?, OR <HELP>
-> END
FILEDEF 8 DISK PLUTO78 DATA *
FILEDEF 1 T
FILEDEF 4 DISK FR80COM DATA *
FILEDEF 2 T
FILEDEF 9 T
FILEDEF 6 T
FILEDEF 3 DISK PLUTO78 HELPCMS *
FILEDEF 10 DISK XY20UT DATA *
FILEDEF 11 DISK ANGOUT DATA *
PLUTO78
ENTER DEVICE TYPE ONE OF TEST,4010,4014,5600,5660,5674,5671,5470,CALC8l, CALC81R
-> TEST
-** BYPASSING CRTPLT + OPTION. 1ST CALL *** 
SINGLE OR MULTIPLE DATASETS ? ENTER <S/M>
-> M
DATASETS TO BE RUN UNDER SINGLE/ MULTIPLE COMMAND INPUT ? ENTER <S/M>
-> M
-** ENTERING INTERP. 1ST CALL ***
-** FOR HELP, ENTER <HELP> *** 
COMMAND?
-> HELP
PLUTO HELP FACILITIES ARE AS FOLLOWS:-
COMMANDS - LISTS AVAILABLE COMMANDS  (ABBREVIATION COM)
NEWS     - CURRENT NEWS              (ABR. NEW)
WHOSWHO  - WHO TO CONTACT            (ABR. WHO)
DISKS -    USE OF CMS/ OS- DISKS     (ABR. DIS)
DATA -     FREE FORMAT DATA ENTRY    (ABR. DAT)
TIME -     BATCH/ FR80 OUTPUT TIMES  (ABR. TIM)
CAMERA -   FR80 CAMERA TYPES         (ABR. CAM)
OUTPUT -   FR80 OUTPUT TIPS          (ABR. OUT)
BUGS -     CURRENT KNOWN BUGS        (ABR. BUG)
FOR MORE INFORMATION ABOUT THESE FACILITIES ENTER 'HELP XXX' 
IN RESPONSE TO 'COMMAND?' OR 'DATA?', WHERE XXX IS THE REQUIRED 
FACILITY.
FOR USERS RUNNING PLUTO78 FOR THE FIRST TIME ENTER 'HELP START' 
COMMAND?
-> GOPT NOLABEL SOLID
CONTROL CARD...GOPT NOLABEL SOLID
COMMAND?
-> PLOT ENTNO 1
CONTROL CARD...PLOT ENTNO 1
*** ENTERING READ1. 1ST CALL ***
READING DATA. IF ENTRY FROM TERMINAL ENTER <VDU>
NOW READING FDAT ENTRIES FROM UNIT 1
ENTNO=   1  ACNTBP   SPG=P21/C Z=  4 ATOMS= 29 INTF=3 AS=1 R-FACTOR(MIN,
MAX) = 0.045 0.045
*** ENTERING PLANE. 1ST CALL ***
*** ENTERING MINOV. 1ST CALL ***
RESIDUE  0 MIN. OVERLAP VIEW MATRIX 0.28176-0.95849-0.04377/ 0.95598 0.27654
0.09813/ -0.08195-0.06949 0.99421
GENERATING MOLECULES WITH OPERATOR 1 0. 0. 0.
TOTAL NUMBER OF ATOMS   29
VIEW ROTATION MATRIX   0.28176-0.95849-0.04377/ 0.95598 0.27654 0.09813/
-0.08195-0.06949 0.99421
SIZE OF PLOTTING AREA =   12.49 ANGSTROMS = 220.00 MM. SCALE FACTOR =
14.0942 MM/A
*** ENTERING BELLA. 1ST CALL ***
*** COMPLETED DRAWING NO.  1 - COPY NO.  1 - TRACE NO.  1

3.1.15 A quick introduction to using PLUTO78 with permanently stored OS- test data

You may run PLUTO78 with a permanently stored dataset, called USER.NW.PLUTODAT which contains 180+ compounds, on OS- disk RHEL03, or a smaller set of 24 compounds on CMS disk in PLUTO78 DATA on the PLUTO78 disk. Find a tektronix 4010 or a sigma 5660/70, switch on and log onto CMS. Before running the program check your virtual machine size and make sure that you access both the U-disk and then the PLUTO78 disk (see section 3.1.2). The example which follows uses a small molecule containing carbon, oxygen and barium and has an entity number (ENTNO) of 23 in the dataset. A demonstration command set is stored in PLDEMO COMMAND on the PLUTO78 minidisk. Only the EXEC/ program output which prompts you for input is given below. Your input begins following the characters:-

->

which are only used to indicate the lines you type in, but are not part of that input. When CMS is ready for input you type:-

-> PLUTO78
DEVICE TYPE AND SPEED?, OR <CR>
-> T4010 4800
PLUTO DATA FILENAME?, OR <HELP>
-> OS USER NW PLUTODAT (or CMS PLUTO78 DATA *) 
PLUTO COMMAND FILENAME?, OR <HELP>
-> TERM     (or CMS PLDEMO COMMAND * for the demo command set 
            when PLUTO78 DATA is specified above)
FR80 COMMAND FILENAME?, OR <HELP>
-> END
FR80 DATA FILENAME?, OR <HELP>
-> END
LINK/ DETACH ANOTHER OS- DISK?, OR <HELP> 
-> LINK RHEL03 K
DASD 120 LINKED R/O ; R/W BY FEM 
*** RHEL03 ACCESSED , MODE K ***
LINK/ DETACH ANOTHER OS- DISK?, OR <HELP>
-> NO
FILEDEF 8 DISK USER NW PLUTODAT *
FILEDEF 1 T
FILEDEF 2 T
FILEDEF 9 T
FILEDEF 6 T
FILEDEF 3 DISK PLUTO78 HELPCMS *
FILEDEF 10 DISK XYZOUT DATA *
FILEDEF 11 DISK ANGOUT DATA *
ENTER DEVICE TYPE ONE OF TEST,4010,4014,5600,5660,5674,5671,5470,CALC81,
                         CALC81R
-> 4010
The terminal screen clears at this point and the bell sounds. To
continue, type return.
SINGLE OR MULTIPLE DATASETS ? ENTER <S/M>
-> M
DATASETS TO BE RUN UNDER SINGLE/ MULTIPLE COMMAND INPUT ? ENTER <S/M>
-> M
*** FOR HELP, ENTER <HELP> *** 
COMMAND?
-> GOPT
CONTROL CARD...GOPT 
COMMAND?
-> PLOT ENTNO 23
CONTROL CARD...PLOT ENTNO 23

*** Note : spaces in command lines are important.

Data about the molecule is displayed on the terminal, and when this stops a prompt appears and the bell sounds. The prompt is displayed at the top left hand corner of the tektronix screen and as normal text on the lowest line of the sigma alpha screen. The prompt is:-

>>> TYPE RETURN TO CLEAR SCREEN + NEXT PLOT

When you have looked at this data and wish to continue, type return.

The program plots the molecule and when this is done, a new prompt appears at the top of the screen and the bell sounds again. This prompt is:-

>>> TYPE RETURN FOR NEXT COMMANDS

When you have finished with this plot, type return to continue and you will be asked for another command. To stop the program, type in:-

STOP

The first prompt appears and the bell sounds, and when you type return you will be back in CMS.

*** Note : on some terminals which emulate a tektronix 4010 the bell may not sound when the prompt is given.

3.2 ICF GEC use of PLUTO78

3.2.1 Introduction

This document briefly describes how to use PLUTO78, the molecular drawing program from Cambridge in its 1978 version. It runs interactively on the ICF GEC's under OS4000 and also on the RAL batch system. On the GEC's, PLUTO78 lets you look at molecular data and decide which set of drawing instructions (called command sets) give useful plots. These instructions and data can be sent to the BATCH system to produce high quality microfiche, 16/ 35 mm black + white or colour film, and hard copy output on the FR80 microfilm recorder.

3.2.2 Getting started on GEC's

You need a valid identifier and account on the GEC, and also on RAL BATCH for FR80 output, in order to use PLUTO78. The document entitled 'An Introduction to OS4000' gives all the necessary information for using the GEC's, and a copy of it can be obtained from your local ICF GEC manager. You can use PLUTO78 interactively on a demonstration account which is set up at QMC (on ZMGA) under the ID/PASSWORD of NTIN22/PHENAZ. The maximum time and CPU available are 30 minutes and 100 IEU's. See sections 3.2.14, 3.2.15 for sample sessions.

3.2.3 PLUTO78 components

On the ICF GEC's PLUTO78 consists of seven parts:-

a) .BPLUTO78 ........... this is the compiled + linked binary program.
b) .MPLUTO78 ........... this is the MACRO file which runs the program.
c) .PLUHELP ............ this is the GEC version of the HELPFILE.
d) .PLCOMOUT ........... this is an empty file which receives command
                         sets when the command 'FR80' is used.
e) .PLDATOUT ........... this is an empty file which receives any FREE
                         FORMAT data when the command 'FR80' is used 
                         for the first time on the current set of data.
f) .PLXYZOUT ........... this is an empty file which receives bond
                         data when the command 'ROTATE SAVE' is used.
g) .PLANGOUT............ This is an empty file which receives angle
                         calculations when 'ANGLE' is used in the OPT 
                         command.

3.2.4 The user manual

A copy of the 1978 Cambridge manual is available for reference in the Atlas centre, RAL. Ask either Mrs K M Crennell or Dr G M Crisp.

3.2.5 Device types and line speeds

To produce graphical output you need a tektronix 4010/14 or a sigma 5600/60/74. If you want to submit a job to RAL BATCH (see section 14), then you only need a vdu (without graphics) or a teletype. Available line speeds are:-

300, 600, 1200, 2400, 4800  Baud

You need to use the local convention for connecting to a node of the SERC X25 network. You can then call the GEC at QMC by typing in '!!ZMGA'.

3.2.6 The MACRO

The MACRO runs the BINARY file and allows you to interrogate :-

a) Which files you have available through the EXAMINE command.
b) Which datafile you want to use when the program runs (either from the filestore or the terminal)
c) Which BINARY file is to be run (in case there are several, such as old and new versions), or the default.
d) Which command file is to be used (either from the filestore or the terminal).

3.2.7 The HELP facility

You can use the HELP file, .PLUHELP, from within the program when prompted by the output:-

'COMMANDS?' 
'DATA?'

You type in either of the replies:-

HELP 
HELP XXX

where the first form gives information on what help is available, and the second allows you to look at particular parts of the file. The XXX is the name of the part of the file which is of interest, for example COMMANDS, and names can be shortened to a minimum of 3 or 4 unique characters. You can also VIEW the HELP file from the terminal by using the GEC 'VIEW' command. This allows you to look through the file in pages of 23 lines, both forward and back, and to search for strings. Use 'HELP COMMAND VIEW' for more information.

3.2.8 Data

You can type in data interactively from the terminal, if you have specified the terminal in response to the appropriate MACRO prompt. If you specify a disk file which already exists, then the program will take data from this source. The program asks you whether the data file consists of a single set or many sets of molecular data. If many sets of data are expected, the program asks you whether a single set or many sets of commands will be used. A single set of data has only many sets of commands, but many sets of data can have either:-

a) a single command set, so that all the molecular data is processed in the same way. You can find this useful if you want to look through all your data without re-typing the command sets.
b) many sets of commands, so that each set of molecular data can have any number of command sets by which it is processed. You can use this to find out which command set bests suits the current set of molecular data, before storing the commands in a file for use on the FR80 (see section 3.2.12).

3.2.9 Commands

You can type commands interactively from the terminal, if this has been specified in the MACRO, or you can read the commands in from a file which already exists on disk. For more information on the commands available, see sections 2 and 5.5, 5.6 of this manual. Some 12 sets are given as examples in section 1.2.

3.2.10 Test option

A simple test option exists in the GEC version of the program, which bypasses the graphics routines. It can only be used when specifying the device, 'TEST', when prompted by the program. This option is an aid to debugging data, in addition to the 'OPT' keyword 'DEBUG', and provides one line output when entering routines associated with data input and handling, allowing you to monitor the progress of the program. A typical one line output is:-

*** ENTERING INTERP. 1ST CALL ***

3.2.11 Storing graphical output

At present graphical output from PLUTO78 can only be displayed directly onto the screen. There is no facility to divert this output to a disk file, at the MACRO level.

3.2.12 Use of the FR80 microfilm recorder

PLUTO78 only allows you to use the FR80 when you submit a job to the RAL BATCH system from the GEC. This job file contains JCL, and your command sets and molecular data (if necessary) are taken from GEC disk files. Two empty files, .PLCOMOUT and .PLDATOUT, receive FR80 commands and free format data when you run the program. If these files do not exist then the macro, .MPLUTO78, will create them, and if the files do exist then the macro will empty them. If you want to keep the commands +/or data after the program has run, you MUST copy either or both .PLCOMOUT, .PLDATOUT to more permanent files. When running the program you send your current command (and terminal data) set(s) to the files by typing in the command:-

FR80

This must only be typed when the current set has been closed, for example by the command:-

PLOT ENTNO XX

3.2.13 BATCH job submission

You submit jobs to RAL batch by typing either of the commands:-

PLANT FROM .FRCOM 
PLANT FROM .FRCOMDAT

The files, .FRCOM and .FRCOMDAT, both contain the same JCL but the first needs to include only command sets, whereas the second needs both command and data sets. The system macro, PLANT, prompts you for the following input:-

JOBNAME   - (e.g. MYPLUTO1) 
ACCOUNT   - (MYACC) 
ID        - (MYID)
CAMERA    - (MFCH (microfiche) is the default and the user will have to 
             supply this explicitly in response to 'USER ARGUMENTS>' 
             e.g. CAMERA=HCM (hard copy many) 
             ?Z
             Note: '?Z' closes this part of the MACRO)
DATANAME  - (USER.ID-MEMBER (BATCH disk) for .FRCOM
            .FRDATA (GEC disk) for .FRCOMDAT) 
DISKNAME  - (RHEL03, this prompt is only
             given for .FRCOM) 
COMMANDS  - (.FRCMD) 
M/S_DAT?  - (M, for multiple sets of data,
             S, for single sets.)
M/S_COM?  - (M, for multiple sets of commands, 
             S, for single sets.)

Unless the output file is specified in the 'TO' parameter of the PLANT macro, output will go to a temporary file '&LIST'. This can be submitted to the RAL batch system by typing in the GEC command:-

IBMJOB &LIST

*** Note : All replies to PLANT must be upper case. For more information on cameras available, see the document:-

GEC GRAPHICS USER 14

FR80 output is routed by Operations to the user with identifier MYID in the example above.

3.2.14 Sample session using the Test option

This sample session does not try to present a complete picture of the way in which you can use PLUTO78, but rather to illustrate the salient points. In what follows, your input is indicated by the characters:-

->

which are not part of the GEC prompt. Any input such as <XXX> means that you type XXX. <CR> means type return. After you log on and the GEC is ready to receive your input, the ready message (Ready) is displayed.

Ready
-> .MPLUTO78
*************PLUTO78 CAMBRIDGE RAL MOLECULAR DRAWING PROGRAM ********* 
*************GEC COLOUR VERSION                              *********
Do you wish to EXAMINE files. Type in YES or NO.
-> NO
Select a datafile. Type in one of the following:-
1) Return for the default .PLUTODAT
2) A filename in the filestore
3) * for data input from the terminal
-> <CR>      (Carriage return is typed in) 
Type in one of the following:-
1) Return for the current program
2) The filename of a previous version
-> <CR>
Select a command file. Type in one of the following:-
1) Return to run the demonstration
2) A command filename from the filestore
3) * for command input from the terminal
-> *
ENTER DEVICE TYPE ONE OF TEST,4010,4014,5600,5660,5674,5671,1302,1332 
-> TEST
SINGLE OR MULTIPLE DATASETS . ENTER S/M
-> M
DATASETS TO BE RUN UNDER SINGLE/ MULTIPLE COMMAND INPUT . ENTER S/M
-> M
-** ENTERING INTERP. 1ST CALL ***
-** FOR HELP, ENTER HELP *** COMMAND?
-> HELP
PLUTO HELP FACILITIES ARE AS FOLLOWS:-
COMMANDS - LISTS AVAILABLE COMMANDS (ABBREVIATION COM)
NEWS     - CURRENT NEWS             (ABR. NEW)
WHOSWHO  - WHO TO CONTACT           (ABR. WHO)
DISKS    - USE OF GEC DISKS         (ABR. DIS)
TIME     - BATCH/ FR80 OUTPUT TIMES (ABR. TIM)
CAMERA   - FR80 CAMERA TYPES        (ABR. CAM)
OUTPUT   - FR80 OUTPUT TIPS         (ABR. OUT)
DATA     - FREE FORMAT DATA ENTRY   (ABR. DAT)
BUGS     - CURRENT KNOWN BUGS       (ABR. BUG)
FOR MORE INFORMATION ABOUT THESE FACILITIES ENTER 'HELP XXX' IN 
RESPONSE TO 'COMMAND?' OR 'DATA?', WHERE XXX IS THE REQUIRED 
FACILITY.
FOR USERS RUNNING PLUTO78 FOR THE FIRST TIME ENTER 'HELP START' 
COMMAND?
-> GOPT NOLABEL SOLID
CONTROL CARD...GOPT NOLABEL SOLID
COMMAND?
-> PLOT ENTNO 1
CONTROL CARD...PLOT ENTNO 1
*** ENTERING READ1. 1ST CALL ***
READING DATA. IF ENTRY FROM TERMINAL ENTER VDU
NOW READING FDAT ENTRIES FROM UNIT 1
ENTNO=   1  ACNTBP  SPG=P21/C Z=  4 ATOMS= 29 INTF=3 AS=1 R-FACTOR(MIN,
MAX) = 0.045 0.045
*** ENTERING PLANE. 1ST CALL ***
*** ENTERING MINOV. 1ST CALL ***
RESIDUE  0 MIN. OVERLAP VIEW MATRIX 0.28176-0.95849-0.04377/ 0.95598 0.27654
0.09813/ -0.08195-0.06949 0.99421
GENERATING MOLECULES WITH OPERATOR 1 0. 0. 0.
TOTAL NUMBER OF ATOMS   29
VIEW ROTATION MATRIX   0.28176-0.95849-0.04377/ 0.95598 0.27654 0.09813/
-0.08195-0.06949 0.99421
SIZE OF PLOTTING AREA =   12.49 ANGSTROMS = 220.00 MM. SCALE FACTOR =
14.0942 MM/A
*** ENTERING BELLA. 1ST CALL ***
*** COMPLETED DRAWING NO.  1 - COPY NO.  1 - TRACE NO.  1
COMMAND?
-> FR80 
COMMAND?
-> STOP
CONTROL CARD...STOP
INTERP ENDS. END OF COMMANDS/ DATA
Ready

The file, .PLCOMOUT, on GEC disks contains the command lines:-

GOPT NOLABEL SOLID 
PLOT ENTNO 1

the ENTNO keyword in the PLOT command must be used for the batch version of PLUTO78, otherwise the system may process all the molecular data with a single command set. The file .PLDATOUT will contain any FREE Format data, whilst .PLXYZOUT and .PLANGOUT contain output from the rotation command and the ANGLE keyword on the OPT/ GOPT command. All these are temporary files and are emptied at the start of each PLUTO78 run. To save them, copy the files to permanent ones.

3.2.15 A quick introduction to using PLUTO78 with permanently stored GEC test data

This section lets you run PLUTO78 with a permanently stored dataset, called .PLUTODAT which contains 180+ compounds. Find a tektronix 4010/14 or a sigma 5600/60/74, switch on and log onto the GEC. The example which follows uses a small molecule containing carbon, oxygen and barium, which is entry number (ENTNO) of 23 in the dataset. Only the MACRO/ program output which prompts you for input is given below. A demonstration command set is stored in .PLDEMCOM. Your input begins following the characters :-

->

which are only used to indicate the lines you type in, but are not part of that input. When the GEC is ready for input you type:-

-> .MPLUTO78
********* PLUTO78 CAMBRIDGE RAL MOLECULAR DRAWING PROGRAM **************
********* GEC COLOUR VERSION                              **************
Do you wish to EXAMINE files. Type in YES or NO.
-> NO
Select a datafile. Type in one of the following:-
1) Return for the default .PLUTODAT
2) A filename in the filestore
3) * for data input from the terminal
-> <CR>       (Carriage return is typed in) 
Type in one of the following:-
1) Return for the current program
2) The filename of a previous version
-> <CR>
Select a command file. Type in one of the following:-
1) Return to run the demonstration
2) A command filename from the filestore
3) * for command input from the terminal
-> *    ( or <CR> to run the demonstration from commands held in .PLDEMCOM )
ENTER DEVICE TYPE ONE OF TEST,4010,4014,5600,5660,5674,5671,1302,1332
-> 4010
SINGLE OR MULTIPLE DATASETS ? ENTER S/M
-> M
DATASETS TO BE RUN UNDER SINGLE/ MULTIPLE COMMAND INPUT ? ENTER S/M
-> M
*** FOR HELP, ENTER HELP *** 
COMMAND?
-> GOPT
CONTROL CARD...GOPT 
COMMAND?
-> PLOT ENTNO 23
CONTROL CARD...PLOT ENTNO 23

*** Note : Spaces in command lines are important. All commands BEGIN in COLUMN 1

Data about the molecule is displayed on the terminal, and when this stops a prompt appears and the bell sounds. This prompt is displayed at the top left hand corner of the tektronix screen and as normal on the sigma alpha screen. The prompt is:-

>>> TYPE RETURN TO CLEAR SCREEN + NEXT PLOT

When you have looked at this data and wish to continue, type return. The program plots the molecule and when this is done, a new prompt appears at the top of the screen and the bell sounds again. This prompt is:-

>>> TYPE RETURN FOR NEXT COMMANDS

When you have finished with this plot, type return to continue and you will be asked for another command. To stop the program, type in:-

STOP

*** Note : on some terminals which emulate a tektronix 4010 the bell may not sound when the prompt is given.

4.1 Definition of Cambridge data format

The following section is taken directly from the PLUTO78 Cambridge User Manual. It defines the format of the Cambridge data file, which is usually referred to as the FDAT file.

Each published set of data to be included in the FDAT file is CRITICALLY EVALUATED FOR INTERNAL CONSISTENCY using a program called UNIMOL. This evaluation involves the calculation of the crystal connectivity and the re-calculation of all bond lengths. The latter are compared with the published values and all major discrepancies are investigated.

If the source of the discrepancy can be found then the corrected numeric data are input to the FDAT file. Otherwise flags are set (in the directory record) and comments introduced, as necessary, so that the user can be warned that a given entry is an error set.

For error-free, non-polymeric structures, the published coordinates are transformed, if necessary, so that the list which is stored (in record type 6) in FDAT refers to a single chemical entity rather than to a crystallographic asymmetric unit. Furthermore, the coordinates of atoms which are symmetry related and bonded to atoms of the asymmetric unit are added to the list. This means that the atomic coordinates in FDAT are directly usable by non-specialists without having to apply complicated symmetry operations.

Assessment of Reliability of an Entry

Certain items, described in detail later, give an indication of the reliability of the data in an entry.

The most important is the error status in col.61 of card type 1.

If this flag is set to 1 the entry is in error and the user should handle the data with caution.

It should be stated, however, that the error might be, for example, an error in only one atomic coordinate. Nevertheless this could be sufficient to make the entry an error set.

An entry is an error set if any one of the following conditions apply:-

(a) bond matching problem                    (col.69 of card type 1}
(b) valency check error                      (col.71 of card type 1)
(c) short bond                               (col.72 of card type 1)
(d) bond length discrepancy, level 2         (col.74 of card type 1)

The internal consistency check afforded by the UNIMOL program can be considered to have 2 levels of checking.

(i) full check for (a) - (d)
(ii) partial check for (b) and (c)

For (i) the entry must contain cell dimensions, space group, atomic coordinates and bond lengths

For (ii) the entry lacks bond lengths

If cell dimensions or space group or atomic coordinates are absent then no UNIMOL checking is done and the entry is "error-free" with col.61 set to zero in card type 1.

Othe useful information relating to the reliability may be contained in the REMARK and ERROR fields of the text (card type 3).

In addition the following can be noted:-

(i)  INTF in col.58 of card type 1      :  Value 3 should be better 
                                           than 2 than 1, for a 
                                           given crystal
(ii) AS in col.67 of card type 1        :  Value of 1 is better 
                                           than 2 than 3 than 4
(iii) The R-FACTOR field in card type 3 :  R-factors < 0.10 generally
                                           correspond to well-refined 
                                           structures.

Overall Entry Structure

Each entry is composed of 80-column card images as follows:-

Card type 1 :  Directory
Card type 2 :  Unit cell parameters
Card type 3 :  Text
Card type 4 :  Symmetry positions
Card type 5 :  Radius values
Card type 6 :  Atomic coordinates
Card type 7 :  Bond  lengths
Card type 8 :  Crystal  connectivity

Notes:-

(i) An example of an FDAT entry is shown on page 4.27.

(ii) Card type 1 is mandatory; all others are optional. Card type 1 acts as a directory to the entry and as an indicator of important flags which summarise the error status and reliability of the entry.

(iii) Card types 1, 2 and, normally, 5 are single cards. Card types 3, 4, 6, 7, 8 may each require more than one card for the storage of the information.

(iv) Card type 4 is normally present only when space group and card type 6 are present.

(v) Card type 5 is normally present only when card types 6 or 7 are present.

(vi) Card type 8 is present only when card type 6 is present, entry is error-free and structure is non-polymeric.

Record 1: Directory

Format:  (1H#,A8,2I1,I6,6X,11I3,22I1,I2)

Cols.	Item	Meaning	Values/Comments
1	#	Start entry
2-9	REF	Reference code	e.g.ABCDEF01
10	SYS	Crystal system	0,1,2,3,4,5 or 6
11	CAT	Structural category	3
12-17	ADAT	Access date	e.g. 771231
18-23	IW		Not yet used
24-26	NCARDS	No. of cards in entry, incl. directory
27-29	NRFAC	No of characters in R-FACTOR field	in card type 3
30-32	NREM	No. of characters in REMARK field	in card type 3
33-35	NDID	No. of characters in DISORD field	in card type 3
36-38	NERR	No. of characters in ERROR field	in card type 3
39-41	NOPR	No. of symmetry positions	in card type 4
42-44	NRAD	No. of elrment types in RADIUS values	in card type 5
45-47	NAT	No. of atom	in card type 6
48-50	NSAT	No. of symmetry-related atoms	in card type 6
51-52	NBND	No. of bond lengths	in card type 7
54-56	NCON	No. of crystal connectivity integers	in card type 8
57	CELL	Absence or presence of cell (card type 2)	0 or 1
58	INTF	Intensity measurement type	0,1,2 or 3
59	ATFOR	Atom coordinate format type	0,1 or 2
60	CENT	Centre of symmetry at origin	0,1 or 2
61	ERR	Error status	0 or 1
62	RPA	Refer problem to author	0 or 1
63	TD	Total disorder	0 or 1
64	PD	Partial disorder	0 or 1
65	PC	Partial connectivity	0 or 1
66	CBL	Corrected bond lengths in paper	0 or 1
67	AS	Average σ (C-C	0,1,2,3 or 4
68	POL	Polymer flag	0 or 1
69	BM	Bond matching flag	0 or 1
70	IG	Ignore checks	0,1 or 2
71	VAL	Valency check error	0 or 1
72	SB	Short bonds	0,1,2 0,<10, ≥10
73	BC1	Bond length discrepancy, level 1	0,1,2 for 0, <10, ≥10
74	BC2	Bond length discrepancy, level 2	0,1,2 for 0, <10, ≥10
75	IAC	Author error correction flag	0 or 1
76	IX		Not yet used, set to 0
77	IY		Not yet used, set to 0
78	IZ		Not yet used, set to 0
79-80	YEAR	Year of publication	e.g. 78

Cols.	Item	Notes
		If an item is inapplicable or if its value is unknown then in the directory record it is set to 0. However cols.18-23 are set to blank.
10	SYS	The crystal system takes the values:- 0 if unspecified by author 1 for anorthic unit cell 2 for monoclinic unit cell 3 for orthorhombic unit cell 4 for tetragonal unit cell 5 for hexagonal or rhombohedral unit cell 6 for cubic unit cell
11	CAT	The structural category is always 3, indicating that the entry corresponds to a structure determination.
12-17	ADAT	The accession date is the date when the entry was added to the file. It takes the form e.g. 771231 for 31 December 1977 Entries added to the file before December 1971 all have the same accession date, viz. 711231.
24-56		These indicate whether various information types are present or not, or how many columns they occupy on the cards.
27-29	NRFAC	This relates to the text {card type 3)
30-32	NREM	This relates to the text {card type 3)
33-35	NDID	This relates to the text {card type 3)
36-38	NERR	This relates to the text {card type 3)
39-41	NOPR	This relates to the symmetry positions (card type 4)
42-44	NRAD	This relates to the radius values (card type 5)
45-47	NAT	This relates to the atomic coordinates (card type 6)
48-50	NSAT	This relates to the atomic coordinates (card type 6)
51-52	NBND	This relates to the bond lengths (card type 7)
54-56	NCON	This relates to the crystal connectivity (card type 8
57	CELL	If this is 0 then card type 2 is absent
58	INTF	The intensity measurement type takes the values:- 0 if unspecified by the author 1 for visual intensity measurement 2 for densitometer intensity measurement 3 for diffractometer intensity measurement
59	ATFOR	The atom coordinate format type takes the values:- 0 if card type 5 is absent 1 for format (a) in card type 6 2 for format (b) in card type 6
60	CENT	The centre of symmetry at origin takes the values:- 0 if card type 4 is absent 1 for centre of symmetry at origin 2 for no centre of symmetry at origin In geometry calculations this flag is used in conjunction with the symmetry positions (card type 4)
61	ERR	0 indicates that the entry is error-free 1 indicates that the entry is an error set. For further discussion of the error status see page 4.2.
62	RPA	Certain types of error can only be corrected by referring the problem to the author. In such a case RPA is set to 1. In Cambridge we do make such referrals to authors and the response is now fairly good. On receipt of details from the author we reprocess the entry through UNIMOL.
63	TD	If this flag is set to 1 it indicates that the organic part of the structure is totally disordered. In such a case no atomic coordinates or bond lengths are input to the entry.
64	PD	If this flag is set to 1 it indicates that the structure is partially disordered. The nature of the disorder is described in the text (card type 3). Usually atomic coordinates and bond lengths are not input to the entry for the disordered atoms. However, if the author reports coordinates for two sites with occupancy factors of, e.g. 0.8 and 0.2, then we input the set for 0.8 and make a note of the handling of the situation in the text (card type 3) .
65	PC	If this flag is set to 1 it indicates that the atomic coordinates in the entry describe only part of the chemical system. By chemical system we mean those residues of the structure which are of importance i.e. would be classified in the FBIB file. A common example would be a case of partial disorder (e.g. the side chain in a steroid) where the atomic coordinates of the disordered atoms are not included in the entry.
66	CBL	CBL set to 1 indicates that the author has published bond lengths corrected for thermal vibration even though we do not hold them in the FDAT file.
67	AS	This flag is a useful indicator of the precision of the experiment. It provides, in coded form, an indication of the average σ(X-Y) where X,Y are light atoms - C,N,O etc 0 indicates not reported or inapplicable 1 indicates σ(C-C) in range 0.001 - 0.005 angstroms 2 indicates σ(C-C) in range 0.006 - 0.010 angstroms 3 indicates σ(C-C) in range 0.011 - 0.030 angstroms 4 indicates σ(C-C) in range 0.03l angstroms -
68	POL	POL set to 1 indicates that the structure is polymeric.
69	BM	BM set to 1 indicates that, in UNIMOL checking, a bond matching problem was encountered i.e. bond(s) in card type 7 not found in calculation. Prior to July 1977 there may be entries which are error-free but with BM set to 1. The majority of these are genuinely error-free but in a few cases these entries should have been classed as error sets.
70	IG	The IG flag controls the ignoring of certain checks when an entry is reprocessed by UNIMOL. If set to 0 then all checks are performed If set to 1 valency checking is ignored If set to 2 all checking is bypassed.
71	VAL	If set to 1 this indicates that a valency check error was detected in the UNIMOL processing.
72	SB	A bond length d(A-B), calculated by UNIMOL, is declared short if d(A-B) < r_A + r_B - T where r_A, r_B are radii of elements A and B, T is tolerance (see ITOL in card type 2) SB = 0 if number of short bonds = 0 SB = 1 if number of short bonds < 10 SB = 2 is number of short bonds >= 10
73	BC1	Let d_A be bond length reported by author (card type 7) } Let d_C be bond length calculated by UNIMOL program. Let Delta = \|dc - d_A Bond comparison is at level 1 if 0.02 <= Delta < 0.05 angstroms BC1 = 0 if number of bond comparisons at level 1 = 0 BC1 = 1 if number of bond comparisons at level 1 < 10 BC1 = 2 if number of bond comparisons at level 1 >= 10
74	BC2	As above, but Bond comparison is at level 2 if Delta >= 0.05 angstroms BC2 = 0 if number of bond comparisons at level 2 = 0 BC2 = 1 if number of bond comparisons at level 2< 10 BC2 = 2 is number of bond comparisons at level 2 >= 10
75	IAC	The author correction flag is set-to 1 if the entry was corrected by referring the problem to the author.
79-80	YEAR	The year of publication of the entry is held in cols. 79-80, e.g. 78 for 1978. Normally users will access entries by date via FBIB, but it can be useful, especially in Cambridge, to have a mechanism for easy retrieval of all data entries for a given year.

Record 2: Unit Cell

Format:  (6I6,6I1,6I2,2I3,I3,A8,I3,I2,4X)

Cols.	Item	Meaning
1-6	IA	a × 10^P1
7-12	IB	b × 10^P2
13-18	IC	c × 10^P3
19-24	IALF	α × 10^P4
25-30	IBET	β × 10^P5
31-36	IGAM	γ × 10^P6
37-42	IP	Precision digits P1---P6
43-44	ISA	σ(a) × 10^P1
45-46	ISB	σ(b) × 10^P2
47-48	ISC	σ(c) × 10^P3
49-50	ISALF	σ(α) × 10^P1
51-52	ISBET	σ(β) × 10^P4
52-54	ISGAM	σ(γ) × 10^P5
55-57	IDM	100Dm
58-60	IDX	100Dx
61-63	NSPG	Space group number
64-71	SPG	Space group symbol
72-74	X	Z i.e. number of formula units/cell
75-76	ITOL	Tolerance × 100
77-80	blank

Notes

(i) If none of the above items are available then card type 2 is absent and CELL is set to zero in col.57 of the director-y card.

(ii) If any item in integer format is absent, then it is set to zero.

(iii) The unit cell dimensions a, b, c, α, β, γ, are recorded in coded form in cols.1-36.

Their correct interpretation is controlled by the precision digits P1, P2,.....P6 in cols.37-42.

All six parameters are recorded irrespective of the crystal system.

The standard deviations of the unit cell parameters are recorded in coded form in cols.43-54 and these also are "controlled" by the precision digits.

The precision digits can take the values 0, 1, 2, 3, 4 or 5.

The system of coding can be illustrated by some examples:-

a = 12.3456 ± 12      P1 = 4     IA = 123456     ISA = 12 
a = 12.345 ± 6        P1 = 3     IA = 12345      ISA = 6 
a = 12.0              P1 = 1     IA = 120        ISA = 0 
a = 12                P1 = 0     IA = 12         ISA = 0 
α = 123.456° ± 21     P4 = 3     IALF = 123456   ISALF = 21
α = 95.6° + 2         P4 = 1     IALF = 956      ISALF = 2
α = 95.0°             P4 = 1     IALF = 950      ISALF = 0
α = 90°               P4 = 0     IALF = 90       ISALF = 0
γ - 120°              P6 = 0     IGAM = 120      ISGAM = 0

Angles fixed by symmetry are recorded, as shown above, for α = 90°, γ = 120° etc.

(iv) For the measured density Dm and the calculated density Dx we record the published values, rounded to 2 decimal places, multiplied by 100.

(v) The space group number is the number of the space group in International Tables for X-ray Crystallography.

(vi) The space group symbol is based on the Hermann- Mauguin notation.

Examples are:-

P-1       for       PT
P21                 P2₁
P21/C               P2₁/c
B112/M              B2.m (see note below)
I41/AMD             I4₁/amd
R3C                 R3c
R3CR                R3c (see note below)

Note that for monoclinic with a-axis or c-axis unique we record the full space group symbol.

The last example illustrates the convention for the situation where the unit cell is rhombohedral. The previous example implies a hexagonal unit cell.

If the space group is absent then SPG is blank and NSPG = 0.

The tolerance is used by the UNIMOL program in assessing whether an interatomic distance corresponds to a covalent bond. See notes on the radius record (record 5). The normal value of ITOL is 40.

Record 3: Text

Format:  (80A1)

The text information in considered to be divided into 4 fields:-

(a) R-FACTOR field : controlled by NRFAC in cols.27-29 of record 1

(b) REMARK field : controlled by NREM in cols.30-32 of record 1

(d) ERROR field : controlled by NERR in cols.36-38 of record 1

(a) An example might be as follows:- R=0.123,RW=0.145.

(b) The REMARK field is used for general remarks and comnents.

(c) The DISORDER field is used to describe the nature of partial disorder when PD is set to 1 in col.64 of card type 1. e.g. PERCHLORATE GROUP IS DISORDERED.

(d) The ERROR field is used to indicate the correct value or possible correct value of some parameter which is wrong in the publication. If the correct value has been supplied by consultation with the author then IAC is set to 1 in col.75 of card type 1. e.g. Z-COORDINATE OF N12 SHOULD BE -.2468.

Notes

(i) There is no blank between successive fields and the text continues from col.80 of one card image to col.l of the next.

(ii) Blank characters are added to the end of the text, as required, so that the total number of characters is divisible by 4.

(iii) If one or more fields is absent then no characters are present for these fields and corresponding items in card type 1, e.g. NRFAC, are set to zero.

(iv) If all fields are absent then card type 3 is absent and the four items in the directory card, NRFAC, NREM, NDIS, NERR are all set to zero.

Record 4: Symmetry

Format:  (5(3I1,I2,3I1,I2,3I1,I2),5X))

Cols.	Item	Meaning
1-3	R11 R12 R13	Components of 1st symmetry operator
4-5	T1
6-8	R21 R22 R23
9-10	T2
11-13	R31 R32 R33
14-15	T3
etc		Components of further symmetry operators
76-80

Notes

(i) This card type which may, in fact, occupy several cards carries, in coded form, the general equivalent positions for the space group setting used by the author, Positions related by lattice-centring are included but not those related by a centre of symmetry at the origin.

(ii) The record is present only when the entry contains atomic coordinates (card type 6) and the space group.

(iii) Each position (xp yp zp) can be represented by:-

_  _     _               _  _ _     _  _
|xp|     | r11  r12  r13 |  |x|     |t1|
|yp|  =  | r21  r22  r23 |  |y|  +  |t2|  where rij =0 or ±1
|zp|     | r31  r32  r33 |  |z|     |t3|
-  -     -               -  - -     -  -
The coding convention uses Rij = rij + 1
                           Ti  = ti × 12

(iv) As an example, the position -x, y - x, 1/3 - z is coded as:-

 011B0 021B0 110B4   where B is blank

Record 5: Radii

Format:  (16(A2,I3))

Cols.	Item	Meaning
1-2	EL1	Symbol of 1st element
3-5	RAD1	(Bonding radius × 100) of 1st element
6-7	EL1	Symbol of 2nd element
8-10	RAD1	(Bonding radius × 100) of 2nd element
etc	etc	etc

Notes

(i) This record is present only if the entry contains atomic coordinates (card type 6) or bond lengths (card type 7).

(ii) The above format allows for 16 element-radius pairs and, at present, no entry contains more than this.

If the need arose further card(s) could be read by recognising that NRAD in the directory card >16.

(iii) These radii are used in the calculation of the crystal connectivity, according to the following criterion:-

The distance d(A-B) between two atoms A and B is accepted as a covalent bond if:-

rA + rB - T ≤ d(A-B) ≤ rA + rB + T where rA, rB are the bonding radii of elements A and B, T is a tolerance (usually 0.40angstroms), whose value is recorded in cols.75-76 of card type 2.

(iv) In a very few entries the element symbol is X or Z. This situation is described in the notes on the atomic coordinates (card type 6).

Record 6: Atom Coords

(a) If ATFOR = 1 Format:  (4(A5,3I5))
(b) If ATFOR = 2 Format:  (A5,3I7,1X,A5,3I7,1X,A5,3I7)

Type (a)

Cols.	Item	Meaning
1-5	ALAB	Atom label 1 (left adjusted)
6-10	NX	x/a × 10000
11-15	NX	y/b × 10000
16-20	NX	z/c × 10000
21-25	ALAB	Atom label 2 etc

Type (b)

Cols.	Item	Meaning
1-5	ALAB	Atom label 1 (left adjusted)
6-12	NX	x/a × 10000
13-19	NX	y/b × 10000
20-26	NX	z/c × 10000
27	blank
28-32	ALAB	Atom label 2 etc

Notes

(i) The format is controlled by the directory flag ATFOR. Format 1 is used when all coordinates are in range -.9999 to 9.9999 and no coordinate contains more than 4 decimal places. Format 2 is used otherwise and accommodates coordinates in the range -9.99999 to 99.99999.

(ii) The atomic coordinates are in fractional units with respect to the crystallographic axes.

(iii) If NAT=0 then ATFOR=0 and card type 6 is absent.

(iv) If symmetry-related atoms are generated by UNIMOL then these NSAT atoms follow, without a break, the NAT "basic" atoms. This applies only to error-free entries and non-polymeric structures.

(v) The. atom label can take two forms according to whether

(a) the atom is one of the basic set (asymmetric unit)

(b) the atom is symmetry-related and bonded to one of the atoms of the basic set.

(a) For a basic atom the label takes the form:- element symbol number sometimes ' e.g. C12 BR3 N1'

Note that in a very few cases an atom may have a label of the type N1''.

(b) For a symmetry-related atom the label takes the form:- element symbol number sometimes ' one or two letters e.g. C12A BR3F N1'AB.

C12A implies that this atom is related to atom C12 by a symmetry operation whose (internal) label is A. etc. etc.

These schemes for atom-labelling imply that very often the labels in FDAT differ from those used by the author.

In a very few entries the element symbol is X or Z. This convention is used when the author could not determine whether an atom is, for example, carbon or nitrogen.

In such cases the element symbol X or Z is also used in the radius card (card type 5).

(vi) Atomic coordinates have not been input to FDAT for clathrate compounds.

(vii) For the complete list of atomic coordinates in an entry each atom is considered to have an implicit sequential number.

The 1st atom in the list has sequential number 1. The 2nd atom in the list has sequential number 2. etc. etc.

These sequential numbers are used in the bond lengths card (card type 7) as atom labels for format (a).

(viii) For a variety of reasons the handling of hydrogen coordinates can be rather troublesome. Very often an author will publish hydrogen coordinates which correspond to an earlier stage of refinement than the published non-hydrogen coordinates.

If, in the course of UNIMOL processing, we find such difficulties with hydrogen coordinates then we delete them from the entry. There should be a REMARK in the text card (card type 3) indicating that such action has been taken.

Record 7: Bond Lengths

(a) If NAT > 0 Format:  (10(2I3,I4))
(b) If NAT = 0 Format:  (5(2A5,I4,10X))

Type (a)

Cols.	Item	Meaning
1-3	IAT	Atom sequential number in the atom coordinate list
4-6	JAT	Atom sequential number in the atom coordinate list
7-10	DIJ	Bond Length × 1000 between atoms IAT and JAT
etc	etc	etc

Type (b)

Cols.	Item	Meaning
1-5	ALABI	Atom label (left adjusted)
6-10	ALABJ	Atom sequential number in the atom coordinate list
11-14	DIJ	Bond Length × 1000 between atoms ALABI and ALABJ
etc	etc	etc

Notes

(i) The format is controlled by the value of NAT in the directory card.

(ii) If NBND=0 in the directory card then card type 7 is absent.

(iii) The bond lengths are uncorrected for thermal vibration and are actual values (in angstrom) not average values.

(iv) The atom sequential number is described in the notes on the atomic coordinates (card type 6).

(v) The atom labels in format (b) take the form described in the notes on the atomic coordinates (card type 6).

(vi) There is a special case in format (a) which is best described with reference to an example:-

Suppose there is a centre of symmetry at mid-point of bond joining rings 1 and 2.

The asymmetric unit consists of the atoms of ring 1.

However at input time we must input:-

coordinates of atoms 1-6
bond lengths in ring 1
and bond length for bond C5-C5*

Note that we do not know in advance what label UNIMOL will assign to C5*. It might be C5A, C5B, etc. etc.

Since the label C5* does not appear in the list of atomic coordinates (before or after UNIMOL) a special convention is needed to assign an atom sequential number to this atom in the bond length record.

The convention is as follows:-

Let sequential number of atom C5 be 13
The sequential number of atom C5* is 513 (i.e. add 500)
Bond length C5-C5* = 1.5428angstroms is stored as 135131542

Record 8: Bond Connectivity

(a) If 0 < 0 < 100 Format:  (40I2)
(b) If NAT ≥ 100  Format:  (26I3,2X)

Type (a)

Cols.	Item	Meaning
1-2	N1	Sequence of NCON integers N1, N2, ...
3-4	N2
etc	etc	etc

Type (b)

Cols.	Item	Meaning
1-3	N1	Sequence of NCON integers N1, N2, ...
4-6	N2
etc	etc	etc

Notes

(i) The crystal connectivity is generated by the UNIMOL program from the atom coordinates and bonding radii. If there are no atomic coordinates NCON=0 and card type 8 is absent.

(ii) The connectivity is described by NCON integers Nl, N2,... The integers are stored in the above formats depending on the value of NAT in the directory card.

The integers are, in fact, the sequential numbers of the atoms in the atomic coordinates list (card type 6).

(iii) The scheme is described, with reference to an example, on the following page:-

Example

In the diagram the numbers correspond to the sequential numbers of the atoms in the atomic coordinates list.

NAT=8

The first 8 integers in the connectivity list are:-5 1 7 7 6 8 2 4

These indicate atom 1 bonded to atom 5, atom 2 bonded to atom 1 , ... atom 8 bonded to atom 4.

At this stage the bonds 1-6 and 3-8 are undefined.

The next integers in the connectivity list are the pairs of integers needed to define the remaining bonds i.e. 1 6 3 8

In summary, above structure has NCON=12 and its crystal connectivity is:-

5 1 7 7 6 8 2 4 1 6 3 8

Since the order of recording atomic coordinates (basic set) in card type 6 is arbitrary some of the first NAT integers may be zero. These are ignored in decoding the connectivity.

If users wish to assign a residue number to each atom then a subroutine is available in the program PLUTO78.

4.2 Example of Cambridge data formats

Two examples of this format are given, which Cambridge usually refer to as FDAT data. The two molecules cited are ACNTBP and BAOXLM which were used for example plots in section 1.2. They are entries numbered 4 and 23 in the dataset. Above each example are column indicators which will enable you to decode the format, using section 4.1, but these are not part of the input.

0        1         2         3         4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
#ACNTBP  23740930       19  8  0  0  0  2  4 29  0 18 31132100000010000000000074 
 12146 12647  7812    90  9433    90333020 1 1 1 0 1 0134129 14P21/C     440
R=0.045 
211 0121 0112 0011 0121 6110 6   
C 68H   20N  680  68       
Cl     22850 -45440  38580 C10    34740 -77300  37430 C11   24370 -75190  43150
C12    20480 -64970  43620 C13    39360 -88210  36420 C14   31950 -97560  38080
C2     12340 -42040  32760 C3      8870 -31690  33970 C4    16120 -24220  41000
C5     26620 -27140  46900 C6     29940 -37590  45780 C7    26770 -56560  38290
C8     37220 -58670  32790 C9     41100 -68890  32460 H11   19700 -80800  46800
H12    13100 -63400  48100 H14    35500-102700  35900 H141  26300 -97500  27700
H142   28500 -97800  49900 H3      2200 -30300  30600 H4    13600 -17300  41500
H5     32000 -21800  55500 H6     37600 -40000  52500 H8    41500 -53100  28100
H9     48000 -70400  27500 Nl      4470 -49550  24130 O1     5060 -49270  28130
O2      7720 -55490  13300 O3     49090 -89260  34100  
 2   51494  3  41378 28 261219  1  71390  1 111404  1 121485 7  81381  8  91376
 9  101374 10 111386 12 131396 12  41392 13 141376 14  21387 2  31394 26  71475
 5   61498  5 291216       
7 3  412 2 5 8 91011 1 11213 3 4 6 6 6 8 910111314 72626 5 214
0        1         2         3         4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
#BAOXLM  23740930        9  8  0  0  0  4  3  5  3  3  8111100000000100000000074
  1010   796   683    90 12196    90222020 2 2 2 0 0 0343340 12C2/M      440
R=0.086
211 0121 0112 0211 6121 6112 0011 0121 0110 0011 6121 6110 0 
BA134C  680  68
BA1   2175    0 3153C1    3615 4030 240501    4133 3346 130502    3102 3300 3516
03    4712    0 2439C1F   3615 5970 240501F   4133 6654 130502F   3102 6700 3516
  2  31240   2 41260  25021550 
 0 6 2 2 0 0 6 6

5.1 Definitions of VIEW with minimum overlap

The minimum overlap view is derived by calculating the matrix of inertia using unit weights for all atoms and treating each molecule separately. The principal axes of inertia are found by a subroutine for finding eigenvectors of a symmetric matrix. The axis with the largest latent root is the axis about which the molecular framework has maximum moment of inertia. The rotation matrix for converting the cell orthogonal coordinates to the plotting coordinates is printed.

A test for overlapping atoms in projection is then carried out. Overlap is defined here as a distance of less than 0.25 angstroms between atoms in projection. If no overlap is detected then the program plots the least squares plane view for the molecule without further modification. If overlap occurs then a simple overlap function is calculated to select a view of minimum overlap within +,-30 degrees of rotation from the least squares plane view. The function is:-

F(a1,a2) = Σ Σ dij^-2
           i j

for the non-redundant list of distances between atoms i and j in the ZP projection. The rotations are a1 about the XP axis and a2 about the YP axis. Positive rotation is clockwise movement of the atoms when looking along the axis from the positive end towards the origin. It has been found that the minimum position is not greatly affected by truncating the summation with dij less than 1 angstrom and using only points (a1,0) and (a2,0) ( thus saving computing time ). The values a1 and a2 run from -30 to +30 degrees in steps of 10 degrees. The program then orients the molecule at the position on this grid giving minimum F.

5.2 Bonding radii used by default

The following list consists of the atom type identifiers and their bonding radii, in angstroms, used by the program as default values. Cambridge data format specifies the radius for each atom type, but the calculation of connections for FREE Format data depends on these values unless overridden in the command set, by JOIN and CALC. *** Note : the program only recognises the atom as 1 or 2 UPPER CASE letters.

TYPE  RADIUS   TYPE   RADIUS    TYPE  RADIUS    TYPE  RADIUS
Ac....1.88      Ag....1.59      Al....1.35      Am....1.51 
As....1.21      Au....1.50       B....0.83      Ba....1.34
Be....0.35      Bi....1.54      Br....1.21       C....0.68
Ca....0.99      Cd....1.69      Ce....1.83      Cl....0.99
Co....1.33      Cr....1.35      Cs....1.67      Cu....1.52
 D... 0.23      Dy....1.75      Er....1.73      Eu....1.99
 F....0.64      Fe....1.34      Ga....1.22      Gd....1.79
Ge....1.17       H....0.23      Hf....1.57      Hg....1.70
Ho....1.74       I....1.40      In....1.63      Ir....1.32
 K....1.33      La....1.87      Li....0.68      Lu....1,72
Mg....1.10      Mn....1.35      Mo....1.47       N....0.68
Na....0.97      Nb....1.48      Nd....1.81      Ni....1.50
Np....1.55      Pb....1.54      Os....1.37       P....1.05
Pa....1.61       O....0.68      Pd....1.50      Pm....1.80
Po....1.68      Pr....1.82      Pt....1.50      Pu....1.53
Ra....1.90      Rb....1.47      Re....1.35      Rh....1.45
Ru....1.40       S....1.02      Sb....1.46      Sc. ..1.44
Se....1.22      Si....1.20      Sm....1.80      Sn....1.46
Sr....1.12      Ta....1.43      Tb....1.76      Tc. ..1.35
Te....1.47      Th ...1.79      Ti....1.47      Tl....1.55
Tm....1.72       U....1.58       V....1.33       W....1.37
 Y....1.78      Yb ...1.94      Zn....1.45      Zr....1.56

5.3 Hints + tips on using PLUTO78

The following hints and tips are intended as a guide to allow you to get the best out of the program and avoid some of pitfalls which occur from time to time. This list is probably incomplete and cannot hope to cover all possible unstable states of the program/ data. However, the program to date has been very robust and its recovery after errors is good. The following tips are intended for terminal use of PLUTO78 unless batch use is indicated.

a) Single and Multiple Datasets

If your dataset contains more than 1 set of molecular data, you can operate the program in 2 separate ways. The first plots all the data under the control of a single command set, and the second allows you to plot each molecule with different sets of commands. These two methods of working cannot be selected together. To initiate a plot in the first way you use 'PLOT', and in the second you use 'PLOT ENTNO xx' ( where xx is the xx'th molecule in the dataset ). The option of 'ENTNO' is very important in the batch program, and failure to specify it, when many command sets are being used, may result in all subsequent molecules being plotted under its control. This effect will be repeated on any following sets of commands.

b) BATCH CPU time needed

Good ball + spoke plots require SEGMENT 20, space filling plots need SEGMENT 50 if unshaded and SEGMENT 150 if half-tone shaded. The default SEGMENT is 8 to enable you to plot quickly. You can use SEGMENT OFF for the highest quality, but the plot will take much longer. In batch, defaults are set up in a different way. All the cameras, except 'hard copy single1, use SEGMENT 50 for most plots, but SEGMENT 150 when the plot is to be space filling and shaded. The 'hard copy single' camera uses SEGMENT OFF exclusively, so that the best possible plots are produced. As a guide, plotting times for 'hard copy many' output of a 30 atom molecule are :-

1) ball + spoke = 2 secs.
2) ball + spoke shaded = 3-4 secs.
3) shaded space filling SEGMENT 150= 6 secs
4) most other plots = 1-2 secs.

For 'hard copy single', the output times are:-

1) ball + spoke shaded = 9 secs.
2) shaded space filling SEGMENT OFF = 40 secs.
3) most other plots = 2-3 secs.

*** Note 1 : you can override the defaults on any FR80 camera by using 'SEGMENT xx FR80', where xx is any valid value.

*** Note 2 : remember to scale these times appropriate to the number of atoms in the molecule.

The 35mm cameras take about half the time of the 'hard copy many' output. The 16mm cameras require about half the 35mm times.

c) Control of shading line spacing

Half-tone and colour needs DENSITY 2 for solid shading, but DENSITY -2, -4 will give fast plots for a quick look. On a terminal, with a complicated plot in colour, it may be better to use the values -2 or -4 if you want to take a picture from the screen, or via the DUNN camera at RAL. The FR80 has DENSITY set up to give good full shaded plots using the minimum CPU time.

d) Changing sizes of plot

Plotting a molecule as large as possible needs SIZE 250 SCALE n, where 'n' specifies the scale of the plot in mm per angstrom. The default value will have been given in the last line of output for the previous plot, so you can decide what value 'n' has to be used. The plot has no enclosing box and to remove the title, which may restrict the size of the output, use NOTITLE in the OPT/ GOPT command.

e) Default plot sizes

Single plots are 250 units square with no commands output down the right hand side. Nominally the units are in millimetres, but this cannot be guaranteed because of the mapping onto a particular device. With commands output to the plot, the size is reduced to 220 units. The maximum boxed plot is 350 units. Stereo output is 110 units for each plot of the pair and no command output is allowed. The maximum stereo size is 170 units. These sizes refer to tektronix 4010 and sigma devices. On tektronix 4014, On approximately double these sizes.

f) Input data

Do NOT mix CAMBRIDGE and FREE FORMAT data in a single file because the file type will be determined by the first set of data. If this is CAMBRIDGE data then FREE FORMAT will be ignored, and vice versa.

g) Saving FREE Format data

If you use the GEC version and wish to SAVE data in '.PLCOMOUT', 1.FLDATOUT', '.PLXYZOUT','.PLANGOUT', then ALWAYS copy these files before running PLUTO78 again. This is a precaution because the MACRO empties these files at the start of each run. On CMS, the 'XYZOUT DATA' and 'ANGOUT DATA' files are not user definable and may be overwritten on each run.

h) Changing colours on the screen

When using the Sigma colour terminal (5660) on the GEC's you can use the terminal hardware to change the colours displayed on the screen. To do this let the current plot finish, and then type the <return> key to obtain the 'COMMAND?' prompt. Type in the following character string:-

+-*/JGxabc0<return>

where 'x' is the GINO colour number and 'abc' the hexadecimal value of RED, GREEN and BLUE to be output. Each of a,b,c can have the values 0,1,2,3,4,5,6,7,8,9,A,B,C,D,E,F. 0 is for zero output and F the maximum. The current GINO colours are:-

BLACK (C)  = 0,  CYAN (BR)   = 1, YELLOW (S)= 2,
GREEN (CL) = 3,  MAGENTA (P) = 4,  BLUE (N) = 5,
RED (O)    = 6,  WHITE (H)   = 7

The labels in brackets are the atom types which go with the colours. To change the oxygen atoms from red to orange type in:-

+-*/JG6FC00<return>

5.4 LOCAL command summary

Cambridge commands are indicated by a 'C' in the command name column, and additional RAL commands by 'R'. A summary of the Options Keywords and Qualifier command names follows :-

OPT  COMMAND   KEYWORD   MEANING
00C)..OPT.......................Set up default options.
01R)............ANGLE...........Calculate bond angles and print them out.
02C)............CELLPLOT........Plot outline of unit cell.
03C)............DEBUG...........Invokes debugging facility.
04C)............NOHYD...........Omit all H atoms.
05C)............NOLABEL.........Suppress all labelling.
06R)............NOTITLE.........Suppresses output of title.
07C)............PACK............Plot packing diagram.
08R)............PFRED...........Print free format data on terminal when input 
                                is from disk.
09C)............SEPRES..........Treat each bonded residue by itself.
10C)............SOLID...........Plot ball + spoke model.
11C)............STEREO..........Plot side-by-side  stereo pair. 
12C)............VIEWS...........View  down shortest of XO,YO,ZO. 
12C)............VIEWX...........View along XO.
14C)............VIEWY...........View along YO.
15C)............VIEWZ...........View along ZO.
16C)..C.........TEXT............Comment record.
17C)..CALC......BOTH............Calculate connectivity.
18C)..COLOUR....KEYWORDS........Specify colour of lines for plotting.
19R)..DCLEAR....NONE............Erase current Free-format data-in-core and reset 
                                flags and variables for next set of data.
20R)..DIRCOS....KEYWORDS........Specify a vector within the molecule and calculate 
                                its direction cosines, or form a right-handed set of 
                                axes, or calculate the crystal diamagnetic susceptibility.
21R)..DIST......BOTH............Specify two atoms and find the distance  between them, 
                                or define plotting of the distance on the device.
22C)..EXCL......KEYWORDS........Exclude the specified elements.
23R)..FR80......NONE............Send current commands/ data to file.
24R)..HELP......KEYWORDS........Invokes the help facility.
25C)..INCL......KEYWORDS........Include the specified elements.
26C)..JOIN......KEYWORDS........Specify connectivities.
27C)..LABEL.....KEYWORDS........Plot specified element labels only.
28C)..MATRIX....VALUES..........Specify rotation matrix.
29C)..MOLE......VALUES..........Specify molecules for packing.
30C)..PERSP.....VALUES..........Plot with perspective.
31C)..PLOT......BOTH............Initiate plotting.
32C)..PRINT.....................Print out geometry + connectivity.
33C)..RADII.....BOTH............Specify radii of atoms, bond cylinders, or the inclusion 
                                of a stick plot overlaid on a space filling plot. 
34C)..RANGE.....VALUES..........Specify range of unit cell for packing. 
35C)..SHADE.....VALUES..........Shade atom circles.
36C)..STEREO....COLOUR..........Specify red/ green stereo pair.
37R)..STEREO....VIEWER..........Specify Open University stereo pair.
38C)..STOP......NONE............Closes output files + stops program.
39C)..TITLE.....TEXT............Print specified title at top of plot.
40C)..VIEW......BOTH............Specify view direction.

5.5 GLOBAL command summary

These commands remain in force over many plots unless reset by the GLOBAL options command GOPT (which has the same keywords as OPT), or changed by using the command to redefine keywords and values. As in the case of the LOCAL command, GLOBAL ones are distinguished by 'C' for Cambridge and 'R' for RAL. A summary of the GLOBAL command names follows :-

COMMAND NAME  KEYWORDS         MEANING
              +VALUES
00R)..GOPT........SAME.AS.OPT...Set up  default options.
01R)..COLOUR........KEYWORDS....Specify atom/ colour pairs.
02RJ..COMPLOT.......KEYWORDS....Commands are listed on the plot. 
03R)..DEMO...........VALUES.....Set up a continuous demonstration with 
                                a variable amount of time between plots. 
04R)..DENSITY........VALUES.....Specify the spacing  of lines which shade atoms. 
05R)..INTENSITY......VALUES.....Set up scaled intensities for all colours on FR80. 
06R)..INTHIT..........BOTH......Set up absolute intensities + hits of colours on FR80. 
07R)..MANYUP.........VALUES.....Set up the FR80 hard copy many subdivisions. 
08R)..MOVE............BOTH......Allows you to move molecules within the unit 
                                cell and move the origin of the whole plot. 
09R)..ROTATE..........BOTH......Specify bond rotation.
10R)..SEGMENT.........BOTH......Specify the  number of segments in the atom circles. 
11C)..SIZE............BOTH......Set up the size of the plot.