The angle between the three specified atoms with atom-name2 as apex is calculated. The three atoms are not necessarily bonded atoms, but should be present in the current atom list. This list can be inspected with a LIST ATOMS instruction. An individual angle may be calculated as an aid in the analysis of the geometry of the structure. Exhaustive geometry listings may be obtained with the companion program PLATON. (See olso the GEOM instruction)

Example: ANGLE C(2) O2 N(2)

The following data are in orthogonal Angstrom units after multiplication with 'scale'.

The 'scale' should be adequate riIn order to fit in the automatic connectivity search based on the build-in covalent radii.

This instruction adds in a cumulative fashion asymmetric residue units (aru's) to the list of aru's to be drawn. It allows the user to have direct control over the list of residues to be drawn. This instruction is needed only when the automatic maintenance of this list with the JOIN RADII and/or PACK instructions is found to be not adequate. The ARU list may be inspected with the LIST ARU instruction. ARU's (e.g. aru1) are designated by a composite number (ARU) that may be split up into five parts: ARU = S*1000 + TX*100 + TY*10 + TZ + 555 + R*0.01, where S is the serial number of the symmetry operator (from the complete list to be inspected with a LIST SYMM instruction) to be applied to the input list of coordinates; TX, TY, TZ are the unit cell translations and R is the residue number. A negative sign of ARU means that the specified residue should not be drawn in the following plots, and may be used to eliminate residues temporarily from the list of residues to be plotted. This may useful in conjunction with the pack instruction.

Often residue numbers are not explicitly indicated and the fractional part of ARU effectively set to zero. In this form the complete asymmetric structure unit (ASU) is meant.

Examples: ARU 3555 7564 -1555 ARU 3564.01

Note: for packing reasons, the number of residues that can be coded is restricted to 9 with corresponding change in aru coding.

The effective ARU list is emptied with the NONE sub-keyword. (A LIST ARU will show that all ARU's now have negative values). The list is reset to what it was after a previous JOIN RADII UNIQUE or INTER instruction with the UNIQUE or INTER keywords respectively. A RESTORE sub-keyword resets all negative entries in the molecule list to their absolute value, so that they are active again.

If the effective ARU list is empty when the PLOT instruction is read, a ARU 1555 instruction will be executed automatically.

Example: ARU NONE

By default the drawing will be surrounded with a rectangular box outline. This setting may be changed with the ON and OFF sub- keywords. The structure is drawn with a shrinkage factor of 90 percent relative to the automatic scale factor that fits the drawing within the BOX-outline to provide a margin. This default percentage may be changed with the SHRINK shr option. This option may be also of use when a drawing which a non-default scale is required. The three numbers shown in the bottom right, top left and bottom left corner of the box are the cumulative rotation angles xr, yr and zr respectively. These numbers may be used to reconstruct this particular orientation in a later session directly from the default UNIT orientation via a VIEW UNIT XR xr YR yr ZR zr instruction. The default horizontal to vertical size ratio of the box is 4/3. A ratio of 1.0 results in a square box.

Example: BOX RATIO 2 SHRINK 80

An alternative to color coding of atom types is a distinction of atom types with different patterns drawn on the spheres representing the atoms. This is useful for black-and-white hardcopy and publication drawings. The current (default) settings may be inspected with the LIST TYPES instruction. Available options for bwc are contour, net, shade, segment, dots, black, cross, parallel, globe, meridian, horizontal, vertical, mesh, diagonal, slant, textile and void.

Example: BWC Pd GLOBE

BWC ON/OFF toggle.

This instruction may be used to change the default color (normally BLACK for plotters & laser printers and WHITE for terminal screens) of the plot into the one chosen (subject to the availability of colour with the actual graphics facility). This color is used for bonds, atom circumference and text.

Example: COLOR RED

The color setting of an atom-type, as shown with a LIST TYPES instruction, may be modified with the COLOR TYPE instruction. Available values for col are: BLACK(WHITE)/RED/GREEN/BLUE/YELLOW/ORANGE/VIOLET/BROWN.

Example: COLOR TYPE C black O red

On/off toggle for display of residue colors.

On/off toggle for color per ARU.

Color on/off toggle.

List geometry about 'atom-name'

This sets parameters for a space-filling model (Corey-Pauling- Koltum) with atomic radii that are taken by default from internal tables and optionally with RADII ATOMS instructions. The surface may be either globally Shaded, Coloured, Dotted, drawn with Contours, segments, a Net structure etc. or with a pattern dependent on the atom type (BWCOL). The keyword SHADE causes the drawing of shade lines representing shadow from a light source whose position is given by the two angles a1 and a2. The setting of both angles to zero models a light source coming directly towards the viewer along the ZP axis, so that the whole atom is shaded. The angles a1 and a2 are rotations of the light source about YP and ZP respectively and in that order, and d is the spacing in cm between shading lines. Default settings are 120, -45, 0.15.

The atoms may be coloured as a function of their atom type. This feature is implemented as the SHADE option with a1=a2=0 and d = 0.05 in the absence of other sub-keywords with the COLOR sub- keyword.

The NET sub-keyword produces a NET with two sets of perpendicular great-circles drawn on the surface (colored in combination with the COLOR sub-keyword). the number of horizontal and vertical circles may be modified with nh and nv.

The GLOBE sub-keyword produces a polar grid surface, combined with shading.

The CONTOUR sub-keyword produces a set of parallel circles on the surface.

The BWCOL sub-keyword may be used to differentiate between atom types in a black-and-white plot.

The SPOT sub-keyword asks for a light reflexion spot on the surface.

The STICK keyword produces a CPK plot combined with a STICK frame to show the chemistry of the molecule.

Example: CPK NET COLOR SPOT

Note: CPK COLOUR DOTS will generate white dots on the colored atomic spheres.

CROTX will produce a stick model rotating about the horizontal X- axis. CROTYM gives a model rotation about y, anti-clockwise). Bonds may be colored as a functions of the atomtypes at their end-points with the COLOR sub-keyword.

Example: CROTX COLOR

This instruction allows the elimination of bonds from the bond list, such as those resulting from intermolecular contact searches or between non-bonded metals.

Example: DETACH CA C

The deletion of undesired intermolecular bonds may require special treatment. The first step involves finding the exact entry in the bond-list (use LIST BONDS) to be deleted.

Example: to delete the bond O1 H1A a from the list, issue DETACH O1 H(1A)a.

Replace set of bonds by one bond to the centre of gravity of the specified atoms. This is particularly useful to represent the eta-5 bond of a metal to a cyclopentadienyl ring:

Example: DEFINE Ti TO C1 C2 C3 C4 C5

Delete specified items.

The distance between the specified and not necessarily bonded atoms is calculated. Both atoms should be in the current atom list (to be checked with a LIST ATOMS instruction) or explicitly generated using the optional aru designator.

Example: DIST C1 C3 DIST C1 C3 2555.01

End of plot instructions for this data set. The next data set following an ENDS card is loaded when the SPF-file contains multiple data sets. The program terminates when no data are left; information on the produced files will be shown. Direct termination is achieved with QUIT or STOP instructions.

Instruction to manage multi-entry data sets (e.g. from CSD).

Exclude the specified atoms from the atom list. ORIG means all the atoms originally input; UNIQUE means atoms generated by JOIN RADII UNIQUE; INTER means atoms generated by JOIN RADII INTER. Bonds are only drawn between included atoms, except that bonds to UNIQUE and INTER atoms are drawn even if these atoms are omitted. Usually, generated atoms need not be specifically included because they duplicate original atoms in generated molecules. The effect of successive INCLUDE and EXCLUDE instructions is cumulative. INCLUDE ALL and EXCLUDE NONE are synonymous; so are INCLUDE NONE and EXCLUDE ALL. The default is INCLUDE ALL.

Example: EXCLUDE H

Interactive calculation of geometry around atom, i.e bond distances and bond angles.

This gives on-line help on the specified type of instructions. In particular HELP GRAPHICS will inform on the way the graphics is implemented. HELP SPGR gives a listing of all the space group names known to the program. HELP ALL gives the full list of available instructions.

Example: HELP STYLE

Include the specified atoms in the atom list. See EXCLUDE.

Instruction modifies defaults to suitable values for inorganic compounds.

A PLOT instruction that, since the start of the program or after a RESET, was not preceded by any JOIN instruction will automatically invoke the execution of a JOIN RADII UNIQUE EXPAND instruction. This automatically produces a list of connections, an ARU-list and an atom list for the possibly symmetrical molecule(s) in the structure, based on internal covalent atomic radii. All distances between two, possibly symmetry transformed, atoms less than the sum of the covalent radii for the two atoms plus a tolerance (by default tol = 0.2 Angstrom per atom) will be entered in the connection list and related changes or additions are made to the molecule and atom lists. Atoms are moved (unless NOMOVE disables it to do so) to symmetry-equivalent positions in order to form connected fragments. If the molecule has symmetry coincident with space group symmetry operators and only the asymmetric coordinate set supplied, the program will look for connections between the symmetry-related portions of the molecule. This involves the generation of dummy atoms and modification of the molecule list as well so that the PLOT instruction will show the complete molecule. The radii used for the automatic JOIN instruction can be inspected with the LIST TYPES instruction. The user may override this automatic feature by explicitly specifying the required JOIN instruction(s) before the first PLOT instruction. When the EXPAND sub-keyword is left out the molecules will not be fully symmetry expanded as is needed for molecules exceeding threefold site symmetry. Symmetry is not taken into account when in addition to this the UNIQUE sub-keyword is left out so that the user is held responsible to provide the correct set of atomic coordinates assumed to be already in bonding distance. Also the atomic radii used may be changed by their explicit specification:

JOIN RADII C 0.85 BR 1.35 H 0.4

This will find all C-C bonds less than 1.7, C-H less than 1.25 and C-Br less than 2.2 Angstrom. Tolerance values are not added to explicitly specified radii.

The ARU list is reset to the input set before entering the connection search routine when a JOIN RADII instruction is read and the connection list is also emptied.

The TOL sub-keyword may be used to change the value of tol to be used along with the radii drawn from the internal tables (see Appendix V). The single keyword instruction JOIN is equivalent with the expanded form JOIN RADII UNIQUE EXPAND.

When appropriate an additional 0.7 Angstrom is added to the tolerance value in the automatic radii mode to catch (earth-) alkali to non-metal contacts.

To generate intermolecular connections (e.g. Hydrogen bonds), the keyword INTER must follow RADII. This also involves generating dummy atoms and modifying the molecule list so that a subsequent plot will show several molecules unless the list is changed by a MOLES or PACK instruction.

Example: JOIN RADII INTER N 1.5

would form the unique molecule first and then find all potential hydrogen bonding interactions between nitrogen atoms less than 3 Angstrom. Alternatively, the sub-keyword HBONDS may be used for which only H to acceptor contacts are generated:

JOIN RADII INTER HBONDS

For JOIN RADII INTER, the molecule list is reset to the list generated by a previous JOIN RADII UNIQUE; the connection list remains at the current setting and the intermolecular connections are added to the list as they are found.

When no explicit radii are given on a JOIN RADII INTER card the program will use radii equal to the covalent radii + 0.8 + tol. When only part of the inter radii is specified it is implied that the radii for the remaining atom types is to be set to zero. The instruction JOIN HBONDS is equivalent to the expanded form JOIN RADII INTER HBONDS.

The first atom on the JOIN card is joined to each of the others.

Example: JOIN Mn1 TO C1 C2 C3 C4

This instruction sets up connections explicitly, adding them to those already existing. Each atom is to be joined to the one preceding it and the one following it in the list. Thus to draw a benzene ring with atoms C1, C2, C3, C4, C5 and C6:

JOIN C1 C2 C3 C4 C5 C6 C1

Option for dashed bonds.

A JOIN INTRA instruction deletes intermolecular connections (those generated by JOIN RADII INTER), leaving only intramolecular bonds, including those between symmetry-related parts of a molecule (generated by JOIN RADII UNIQUE).

JOIN NONE empties the connection list.

The specified atoms are added to the current list of atoms to be labelled. The program tries to find a suitable position for the label close to the atom giving minimum overlap by other plot items. The sub-keyword MOLES causes the symmetry code of the molecules to be plotted against the first atom of each molecule.

Examples:

     LABEL Cu N O
     LABEL C1 C2 C3 N4 C5
     LABEL ARU
     LABEL ALL
     UNLABEL *

The effect of successive LABEL instructions is cumulative.

These label instructions are global. The ALL sub-keyword gives labelling of all atoms and is undone with UNLABEL ALL. ON and OFF have the same effect. Atom labels may be plotted with or without (default) parentheses.

This causes some of the lists held by the program to be displayed for inspection. The same lists are sent automatically to the trailer output file when a PLOT instruction is executed.

The ATOMS option gives a list of the input atoms together with any dummy atoms generated by a JOIN instruction. For each atom, the coordinates and atom radius are shown, together with flags to show whether the atoms are currently included and/or to be labelled.

BONDS list all the (active) connections currently held with their distance and plot style parameters.

LINES lists the information set up by RADII BONDS instructions.

MATR gives the current orientation matrix and the three decomposition angles to reconstruct this orientation with a VIEW UNIT XROT xr YROT yr ZROT zr instruction.

ARU gives the list of molecules.

STATUS list various parameter settings and other relevant data.

SYMM gives a list of all equivalent positions, preceded by their internal sequence number that is used in conjunction with the ARU instruction.

TYPES gives a listing of all atom-type dependent setting such as radii and colours. If none of the above keywords is given, all the information is shown.

Example: LIST ATOMS BONDS

This lists atom data from the atom list for the specified atom or atom-type.

Example: LIST ATOM O

This lists bond data for the specified bond from the bond list.

Example: LIST BOND C3 C4

This displays the current cell parameters for inspection.

List symmetry operations and related data.

Option to list an internal parameter value held in the PAR list. A range is listed when two numbers have been specified or the full list is case that none was specified. New values may be assigned with the SET PAR instruction.

Example: LIST PAR 5

Option to list an internal parameter value held in the IPR list. A range is listed when two numbers have been specified, or the whole list is case of no range specification. New values may be assigned with the SET IPR instruction.

Example: LIST IPR 3 5

A single perspective drawing is to be produced as seen from a point at d cm. along the ZP axis, above the centre of the drawing. The default setting is 10000 cm. (effectively infinity) but may be set to 60 cm. for convenient perspective viewing. The actual value is plotted in the top right corner of the plot (zero for infinite perspective) to avoid confusion.

Nomove toggle.

No atom list sorting toggle.

All atoms with their centres outside the box defined by the fractional coordinates xmin,...,zmax are omitted from the drawing, together with any bonds to them. This is useful as a 'window' on a packing diagram. The window may be reset by another OMIT OUTSIDE instruction, or cancelled alltogether by OMIT OUTSIDE 0. Note that molecules lying across the edge of the window will be drawn incomplete. An alternative option is the exclusion of all atoms with their centres outside a sphere with radius r around a specified atom.

Example: OMIT OUTSIDE C(1) 5
         OMIT OUTSIDE 0.5 1 0.5 1 -.25 .25

Omit the specified items from the 'plot-list'.

Set default parameters for type organic structure.

The overlap margin (non-bonded bond-bond, atom-atom, atom-bond overlap) is set by default to the value mrg = 0.1 cm and the incoming bond shadow margin to shad = 0 cm. Overlap calculations (by default) may be turned off for fast testruns. This should be specified before plotting and after the specification of the plot-style.

Example: OVERLAP OFF

This causes a search for all ARU's having their centres inside the box defined by the fractional coordinates given. By default PACK RANGE displays the contents of a unit cell. However, this will not show the complete packing arrangement of the crystal; it is necessary to supply a range that will ensure that a pair of translated molecules will be found in each axial direction. This is achieved by giving a range of cell translations. In most structures, the result of a range of two in each axis is usually too congested to be of any use, so that it is best to restrict the range to one on the axis closest to the view direction.

e.g. PACK RANGE -0.5 1.5 -.5 1.5 0 1

might be appropriate for a z-axis projection. The instruction PACK generates by default all ARU's with their centre within the unit cell.

The ARU's that obey the conditions are added to the ARU list. The ARU list is reset to ARU UNIQUE at the beginning of the search. No other lists are affected. The ARU list may be displayed by the LIST ARU instruction.

ARU's are put in the moles list that satisfy the condition of lying within the range xmin,...,zmax and in the neighborhood of the specified hkl-plane (d1 and d2 are in Angstrom).

Example: PACK PLAN 1 1 1 -.5 .5 RANGE -1 2 -1 2 -1 2

This produces a drawing using the information set up by the previous instructions on either the current graphics medium (default) or on the specified medium (Display, Plotter or Meta- file). The default medium is either the one previously set or the display by default. An automatic JOIN RADII UNIQUE EXPAND instruction is executed when no previous JOIN instruction was given and a VIEW MIN instruction is case of no previously given VIEW instruction. The MOGLI option may be used to generate DGE and OBY files to be used to view the molecule in 3D with the PSSHOW program of the MOGLI package on a PS300 display (use PLOT CAL MOGLI to generate the files without display or plotter output).

The special instruction PLOT CAL 3 will generate a file with full 3D vector information for a ROD-style plot, independent of previous parameter settings.

This gives immediate exit from the program.

This globally sets the atomic radii (Angstrom) for the plotting of the spheres in the SOLID, ROD and CPK style. The appropriate instruction is normally executed automatically. In the SOLID and ROD mode spheres are drawn at 0.5 times their covalent radius and in the CPK mode at the covalent radius + 0.8.

This instruction may be used to input user defined radii for the spheres to be drawn. The actual values may be listed with a LIST TYPES instruction.

Bonds in SOLID or ROD drawings have cylindrical radius r Angstrom (default 0.04 and 0.2 resp.) and are drawn with n (default n = 8) lines along the circumference of the cylinder, spaces (180/(n+1)) degrees apart on the visible side of the cylinder. This instruction resets r and n for all bonds.

This sets r and n for all bonds to a particular atom or atom type. This may be useful to emphasize coordination of a particular atom. To produce single-line bonds, set r - 0 and n = 1. Bonds with n = 0 are omitted.

This sets r and n for a particular bond already in the connection list.

This sets r and n for all intermolecular bonds created by a JOIN RADII INTER instruction. This is useful, for example, in distinguishing hydrogen bonds.

RADII BONDS ALL not only resets r and n for all bonds, but also cancels all other RADII BONDS instructions which have already been given, i.e. 'all' really means all. To reset r and n for all bonds EXCEPT special ones, use this instruction instead.

When the program is drawing the bonds, it looks though the list of the RADII BONDS instructions and assigns the r and n values of the last instruction given which is relevant to the bond being drawn. In this way the result of conflicting instructions can be controlled by the order in which the data card are given. An example of such a list of instructions:

     RADII BONDS ALL 0.05 5
     RADII BONDS INTER 0.02 2
     RADII BONDS TO CU1 0 1
     RADII BONDS TO NA 0.03 2
     RADII BONDS CU1 O4 0.06 10

Note, however, that if a particular RADII BONDS instruction is given a second time with different values of r and n, this resets r and n without altering the order of the RADII BONDS instructions. E.g., the sequence

     RADII BONDS TO H 0.02 4
     RADII BONDS INTER 0 1
     RADII BONDS TO H 0.03 7

is equivalent to

     RADII BONDS TO H 0.03 7
     RADII BONDS INTER 0 1

i.e. the second RADII BONDS TO H instruction directly replaces the first.

In order to enhance the perspective effect of drawings (see MONO and STEREO options), bonds are drawn with an exaggerated taper, the degree of exaggeration being set by the parameter taper. taper = 2 gives maximum exaggeration. The default setting is 0.250. Tapering is applied even if the viewing distance is effectively infinite, unless taper = 0.

Before any plotting instructions are read, various default parameters for plotting must be set. This is automatically done at the beginning of the program, but can also be done at any time by use of RESET.

Labels are retraced n times.

This prepares for a ROD-style plot with atoms optionally shaded, coloured, drawn with a net or contoured surface or individually characterized (see CPK for further information).

This instruction may be used to save instructions to be used on other data sets as well. This feature is useful when examining a series of structures taken from the crystallographic data base. All instructions following a SAVE instruction until an END are saved.

Plotstep and substep are parameters that determine the accuracy of the plot, the speed and the computing time needed for the plot. Testing for overlap is done in steps of size plotstep. When a problem is encountered the testing will be redone in steps of size plotstep/substep. The default values are 0.1 cm and 4 steps respectively. For accurate plots, in particular on either the plotter or the meta-file, values of 0.01 cm and 1 are recommended for the above parameters.

This instruction is not meant for general use. It provides a facility to modify internal parameters, in particular those with no equivalent (sub)keyword.

The default character size (ch = 0.25 cm) may be changed with a SIZE 0 CHAR ch instruction.

Similarly, the default character size of the title (ti = 0.4 cm) may be changed with the TITLE sub-keyword: SIZE 0 TITL ti.

The cm/Angstrom scale may be specified with SCALE

Example: SIZE 0 SCALE 1.0

This gives a vintage-PLUTO-style bond-and-stick plot.

See the CPK instruction for other keywords.

Example: SOLID COLOUR CONTOUR 0

for a colored atom outline. (nc = number of contours)

This produces a stereo pair, as seen by an observer with eye- separation of 6 cm. at a distance d ( default 60) cm along the ZP axis. If the keywords RG or GR are present, the left-eye and right- eye views are superimposed instead of being placed side-by-side, but are drawn in different colors, so that the stereo effect can be observed using appropriate red/green or green/red filters. The sub- keyword CROSSED allows for crossed eye vision.

This asks for a stick model drawing, i.e. one in which the atoms are points and the bonds single lines. A succession of such drawings requires very little computing and plotting time, and is useful as a preliminary run for checkout and to find a good view direction.

Note: since atoms are represented by points in this presentation, as are bonds when viewed along their direction, non-bonded atoms and some linear molecules viewed from the end are not shown in STICK plots.

This gives an immediate EXIT from the program.

The title of the plot is normally taken from the TITL card that preceded the coordinate data. It can be overruled with a new TITL instruction.

The dihedral angle (not necessarily involving bonded atoms) for the specified atoms is calculated as an aid to analyze the geometry of the structure (exhaustive geometry listings may be obtained with the companion program PLATON).

Example: TORSION C(2) O2 N(2) C(4)

This allows a unit cell outline to be drawn. The outlines are treated as bonds (in terms of radius and number of lines drawn on the bond).
Their default setting is: rbo = 0.01 and nli = 2.

This instruction may be used to unlabel. see LABEL.