The default plot style is stick bonds. This style is restored with Rset or on moving to a new entry.
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 Å 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 Å 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.
ShowB shows bond types currently defined for the structure in the following styles:
single: | 1 solid line |
double: | 2 solid lines |
triple: | 3 solid lines |
quadruple: | 4 solid lines |
aromatic: | 2 dashed lines |
delocalised: | 2 dashed lines |
pi: | 1 grey short dashed line |
polymeric: | 5 cyan dashed lines |
contact: | 1 cyan dashed line |
unassigned: | 1 solid grey line |
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:
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.
All labelling and annotation options are reset with 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.
Labl draws labels for all atoms in current plot.
Nola draws 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 in 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. Existing text can also be selcted for moving or deletion.
LABEL MOL has the 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:
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 TOP plot CCDC logo and Refcode at the top of the plot (the default).
STYLE NOTOP do not plot the CCDC logo and Refcode at the top of the plot.
The R and T controls below the menu bar allow the molecule to be rotated (3 degrees increment) and translated in the XY plotting plane.
Zrot+ rotates clockwise about out-of-screen Z view axis.
Zrot- rotates anti-clockwise about out-of-screen Z view axis.
RX+90 rotate by +90 degrees about horizontal X view axis.
RY+90 rotate by +90 degrees about vertical Y view axis.
Zoom+ magnifies the current image by a factor of 1.1.
Zoom- magnifies the current image by a factor of 0.9.
Size scales the plot to fit it within the view area.
VX, Vy, Vz select view along cell axis a, b, c respectively.
Vm selects view of minimum overlap based on mean-plane through all atoms, rotated by up to 30 degrees.
Vp gives mean-plane view through up to 16 selected atoms. Click twice for mean-plane view through all atoms included in plot (inertial axes view).
VIEW XO/YO/ZO defines the view direction along orthogonal axes Xo, Yo, Zo respectively.
VIEW XC/YC/ZC defines the view direction along cell axes Xc, Yc, Zc respectively.
VIEW HOR at1 at2 VER at3 at4 defines a view with the horizontal axis Xp in the direction at1 to at2, and with the vertical axis Yp as near as possible to direction at3 to at4. Note that all four atoms must be given.
VIEW LINE at1 at2 HOR at3 at4 defines a view along the direction at1 to at2, with the horizontal axis Xp in the direction at3 to at4; all four atoms must be given.
VIEW BISECT at1 at2 at3 defines a view along the bisector of the angle at1-at2-at3, towards the atom at2.
VIEW PERP at1 at2 at3 defines a view along the perpendicular to the plane of the atoms at1, at2, at3; all 3 atoms must be given.
VIEW PLANE at1 at2 at3 at4 . . . defines a view normal to the least-squares plane through the set of atoms given. At least 3 atoms must be given, with the upper limit only defined by the number of labels possible to fit on the command line.
XROT, YROT, ZROT allow the user to modify any of the above view directions, by applying successive rotations about the Xp, Yp, Zp axes. Positive angles produce a clockwise rotation of the image. The presence of these keywords will always modify whatever current view direction has been set, so the effect can be cumulative.
Example: VIEW YO XROT 45 will select the view along Yo and then rotate 45 degrees about the horizontal axis Xp.
Example: VIEW BISECT C1 C2 C3 YROT 30 XROT -30
will select the view along bisector C1-C2-C3 , rotate 30 degrees about the vertical axis Yp, and then rotate 30 degrees anti-clockwise about the horizontal axis Xp.
X/Y/Z <n> rotates the image by a specific angle <n> about the axis given. If no value of n is given then the previous value of n is used. If no value of n was given earlier a default of 30 degrees is used. Positive angles cause a clockwise rotation of the image.
VIEW MATrix r11 r12 r13 r21 r22 r23 r31 r32 r33 sets view matrix explicitly as given to generate a required view, where rij are the elements of a rotation matrix. This is sometimes useful when a rotation matrix has been obtained from another calculation. The program checks that the determinant of the matrix is equal to +1.000 within a tolerance of 0.0001.
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.
ColM toggles between COL MOTIF BASE, COL MOTIF ALL and colour-by-motif off modes.
COL colours by element type (C green, H white, O red, N blue, S yellow). Default colour option.
COL NONE colours with default global atom, bond and non-bonded contact colours.
COL DEF n1 n2 n3 changes the default colours for atoms, bonds, and non-bonded contacts (defaults are white, white and cyan respectively). Also restores non-bonded contacts to the default colour.
COL DISP displays the 15 available colours with their code numbers which are set in the pluto configuration file.
COL n sets the global plot colour for all atoms, bonds, non-bonded contacts, labels, unit cell and geometric objects. This effect is cancelled by applying another colour command.
COL BOND at1 at2 highlights 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 sets atom colours for named elements to given values. Other elements are plotted in the default atom colour. Default element colours are restored with COL.
COL PLANE n sets colour n for all planes and vectors (default colour 14, dark grey).
COL PLANE n1 n2 sets colour n2 for plane or vector n1.
COL SYMM colour-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 colours 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. The 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 colours 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 all other residues are plotted in colour 14 (dark grey).
COL STR colours the atoms and unit cell of each structure in a different colour, to identify which atoms and unit cell belong to which structure when more than one structure is displayed simultaneously.
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. The default intermolecular bond colours are restored by COL NONE or COL DEF.
COL MOTIF [mode] [n] [KEYFIX]. In the GSET and RING display, particular motifs may be highlighted by typing COL MOTIF n to highlight the nth motif in the plot key list. Several motifs may be specified on the command line and if no arguments are given all motifs are coloured, unless KEYFIX is specified, in which case the motifs currently selected are not changed. This allows the mode to be changed without changing the selected motifs. Alternatively, individual motifs may be selected for highlighting by clicking on the corresponding entry in the plot key list. The current mode, ALL or BASE, is used if mode is omitted.
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, if the motifs have been generated with the GSET feature.
BASE mode: only the atoms and bonds in the basic motif repeat unit are coloured, and only those molecules which comprise these repeat units are displayed.
ALL mode: this behaves similarly to BASE mode, except that the motif highlighting is propagated throughout all the molecules currently displayed. As a result, all atoms and bonds which are related by symmetry to bonds in the basic motif repeat unit are coloured. This may be used to show how chain motifs form an extended network through a structure. The current molecule list is unchanged.