Plot rendering

Plot styles

The default plot style is stick bonds. This style is restored on Rset or on moving to a new entry.

Menu buttons

Sol Solid (ball-and-spoke) style. Stick style appears when this button is toggled off.

Shad Ball-and-spoke style, with line-shadow shading.

Atm- reduces the current size of atom circles as displayed in SOLid style.

Atm+ increases the current size. The increment is 0.1 Angstroms in radius.

Adef uses default sizes for atoms based on a fraction of the bonding radius.

VdW uses Van der Waals radii for atoms.

Bon- reduces the current thickness of bonds as displayed in SOLid style.

Bon+ increases the current thickness of bonds. The increment is 0.02 Angstroms in the radius.

Nbo- reduces the current thickness of the non-bonded contact lines.

Nbo+ increases the current thickness of the non-bonded contact lines. This may be useful in emphasising a network of contacts, such as H-bonds.

Ster draws a stereo pair with separation approximately 60mm. When toggled off the drawing is a single frame, with no perspective.

Style provides options for customising the plotting style. This is useful for preparing diagrams for overhead slides and publications. The style changes applied before the first plot passed through to the Postscript output file. However, further style changes are not reflected in subsequent postscript plots. Options available are:

L
linewidth for all plot lines, e.g. 2, 3, 4, etc.
C
character size, e.g. 100 (default is 60)
P
plot step for circle drawing (default is 0.5, smaller values providing better quality display and hardcopy resolution and diminishes 'polygon' effect with small circles)

Typed commands

STEREO has the same effect as menu button Ster.

STEREO COLour plots molecules, unit cell, geometric objects and labels as an overlapping red-green stereo pair.

MONO returns to standard size single plot mode.

Labelling and annotation

All labelling and annotation options are reset on Rset or on moving to a new entry with the exception of the Labl menu toggle.

Individual atoms may be labelled by clicking on the atom position in the plot.

Menu Buttons

Labl draw labels for all atoms in current plot.

Nola draw no labels for atoms, molecules or residues.

Labm draws labels Mm at molecular centres, and gives a list of the residue numbers and the symmetry operators (n) and translations (tx,ty,tz) which generate each molecule from the base residues.

Nodi removes distances and angles from the plot and clears the distance key in the top left corner of the plot.

Title allows a title to be typed which is displayed at the bottom left corner of the plot.

Text allows text to be typed to annotate plot. Select position for start of text and then type text. May also select start of existing text to move or delete.

Typed commands

LABEL MOL has same effect as menu button Labm.

LABEL RES labels each crystallographically independent residue as A, B, C etc.

LABEL RESNUM labels each crystallographically independent residue as 1, 2, 3 etc.

LABEL SYMM labels each molecule with a symbol to show the operator used to generate it from the corresponding base molecule. The codes are as follows:

T
translation
I
centre of symmetry (inversion centre)
G
glide plane
M
mirror plane
nS
n-fold screw axis
nR
n-fold rotation axis
nI
n-fold inversion axis

LABEL NUM labels all atoms with their number position in the atom table, 1, 2, 3 etc. This may be useful in identifying an atom uniquely for a typed command since several atoms may have the same label in a packing diagram.

STYLE (NO)TOP Plot/do not plot CCDC logo and Refcode at top of plot.

Colour Modes

In general, colour settings apply to atoms. In solid mode the atoms are coloured and the bonds and non-bonded contacts are shown in default colours. In stick mode, the split bonds are coloured on the basis of the atom colours.

Menu buttons

The menu button Colr toggles between the COL and COL NONE modes.

Typed commands

COL Colour by element type (C green, H white, O red, N blue, S yellow). Default colour option.

COL NONE Colour with default global atom, bond and non-bonded contact colours.

COL DEF n1 n2 n3 Change default colours for atoms, bonds, and non-bonded contacts (defaults white, white and cyan respectively). Also restores non-bonded contacts to default colour.

COL DISP Displays the 15 available colours with their code numbers.

COL n Set global plot colour for all atoms, bonds, non-bonded contacts, labels, unit cell and geometric objects. Effect is cancelled by applying another colour command.

COL BOND at1 at2 Highlight a particular bond between atoms at1 and at2 (atom labels) in a base molecule in both solid and stick mode. A maximum of 20 bonds may be coloured in this way in separate command lines. Highlighting may be removed by command COL NONE.

COL ATOM el1 n1 el2 n2 Set atom colours for named elements to given values. Other elements plotted in default atom colour. Default element colours restored with COL.

COL PLANE n Set colour n for all planes and vectors (default colour 14, dark grey).

COL SYMM Colours-codes atoms by the type of symmetry operator generating the atom from the corresponding atom in the crystallographic asymmetric unit of the base molecule. This allows internal crystallographic symmetry in molecules and symmetry relationships in packing diagrams to be investigated. Symmetry elements are identified by means of a colour key.

COL MOL n colour-name Colour atoms in just one molecule n for highlighting. Colour-name may be one of RED, BLUE, GREEN, CYAN, MAGENTA, YELLOW and ORANGE, e.g. COL MOL 4 RED. Remaining molecules are plotted in colour 14 (dark grey). Labm button or command LABL MOL may be used to obtain molecule numbers. Only one molecule may be highlighted at a time.

COL RES n colour-name Colour atoms in all occurrences of a particular residue n, e.g. to highlight a particular residue in a packing diagram. Colour-names as for COL MOL. Only one residue may be highlighted at a time and other residues are plotted in colour 14 (dark grey).

COL HBOND Crystallographically-equivalent H-bonds or other non- bonded contacts are colour coded. This allows the path traced by a particular contact to be followed through a structure using the Expand or Pack functions. Current atom and bond colours are unaffected. Default intermolecular bond colours restored by COL NONE or COL DEF.

COL MOTIF n In the GSET display, particular motifs may be highlighted by typing COL MOTIF m for first level, or mn for second level patterns >n>m or n&m and -mn for >m<n. Several motifs may be specified on the command line and if no arguments are given all motifs are coloured. Both atoms and bonds are coloured, even in Solid mode. Where motifs overlap, the colour of the first motif in the list of those to be displayed takes precedence. The motif colours correspond to the graph set colour key and the first level motif colours to the H-bond colours obtained with the COL HBOND command.