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Jmol enhanced figure toolkit - a manual for authors

[Example graphic]

Toolkit options reference

All the options presented in the toolkit interface are described for the beta 2 release version of the Jmol toolkit. Significant changes to these may follow user feedback during the beta test phase.

The preview tab

This is the first tab, and is the one that is open when you load (or reload) the editor page (Fig. 39). It allows you to preview the effect of the scripts associated with the enhanced figure. When a structure is first loaded, it contains two of the standard buttons that will always be created for an enhanced figure.

[Fig. 39]
Fig. 39
The preview tab.

'Reset view' reloads the initial view that is saved whenever the 'Primary save' option is selected. This is also the view that is recorded as a static image for incorporation into the PDF edition of the journal. (The online enhanced figure also contains a 'static view' button that shows this static figure. It is absent from the preview pane since it serves no useful purpose here.)

'Toggle spin' rotates the view if it is stationary, or stops it if it is currently rotating. Since this is one of the most common requirements of an enhanced figure, it is provided as standard.

Below these buttons, any scripts that you create and link to buttons, checkboxes or radio buttons will appear, to allow you to test their effects before saving the enhanced figure.

The general tab

This tab provides options to change global aspects of the figure (Fig. 40). In general you will start here.

[Fig. 40]
Fig. 40
The general tab.

black background

A check box to select a black background in the visualization window. Other background colours may be set from within the applet using the Jmol menu. By default, a white background is set, in the style of traditional static figures. Black may be selected to emphasise colour or translucency effects. Other background colours will not usually be accepted unless there is a compelling reason.

rotate structure

A checkbox allowing rotation about a vertical axis in the plane of the image (around the y axis). This is a useful feature to allow the author to see how a rotating structure will appear. Normally, however, you will unset this option before saving, so that the preferred orientation is saved in the static image. Note that the enhanced image page will always have a 'toggle spin' button, so that the reader may always choose a rotating view.

show perspective view

A checkbox to force a linear perspective depth representation. The Jmol default setting 'set cameraDepth 3.0' may be modified using the console if a more or less exaggerated perspective is required.

Orientation

A menu specifying projections along the main crystallographic axes. Jmol uses the designations 'front', 'back', 'left', 'right', 'top' and 'bottom', which are explicitly described in the menu options.

Stereo view

A menu allowing stereoscopic views to be set up as side-by-side (cross-eyed or wall-eyed) pairs, or as red/blue, red/cyan or red/green superimpositions.

Style of atoms and bonds

colour scheme

The menu options are 'by element' (the default for small molecules and inorganics), 'by alternative location' (typically where positional disorder is present), 'by the molecule', 'by formal charge', and 'by thermal displacement'. Biological macromolecules also have 'by amino acid', 'by secondary structure' and 'by chain'. The default for biological macromolecules is to colour residues along a rainbow gradient, from blue (at the N or 5' terminus) to red (at the C or 3' terminus). Other colouring schemes for macromolecules are available in the structure tab.

overall style

The common menu options are 'ball-and-stick', 'stick, 'wireframe' and 'CPK Spacefill'. For inorganic and small-molecule structures there are also 'displacement ellipsoids' and 'displacement ellipsoids (H atoms as small spheres)'. For proteins there are also 'cartoon' (the default), 'ribbon' and 'strands'. Additional abstract representations are available for biological macromolecules through the structure tab. Note that if you wish to display a crystallographic packing diagram, you should first set up the desired view using the crystallography tab, then return here to change the rendering style.

atom radii

This menu allows a number of settings of atomic radii, either as a fraction of the van der Waals radius, or proportional to the ionic radii. 'default' for small-molecules and inorganics is 20% of the van der Waals radius. For macromolecules, atom and bond rendering is off by default (since the usual starting representation is a cartoon or other abstract view).

bond widths

The menu provides a number of bond width values in ångström units. The default for inorganics and small molecules is 0.15 Å. For macromolecules, the default is to turn bonds off - this means that they must explicitly be turned on in this menu if a 'vine' or 'ball-and-stick' representation is desired.

hydrogen bonds

(Biological macromolecules only.) The menu allows you to select whether hydrogen bonds are displayed or not, and a bond width to assign to them. In the current release of Jmol, 'hydrogen bonds' are currently limited to certain types of calculated bonds in biological macromolecules, specifically: (a) between protein amide NH and protein amide carbonyl oxygens and (b) between nucleic acid base pairs.

disulfide bonds

(Biological macromolecules only.) Specifies whether disulfide linkages are shown, and what radii (in Å) they should have.

Molecular surface representation

These options allow the display of a number of slightly different molecular envelopes.

type of surface

The 'van der Waals' surface is formed from the individual atomic van der Waals radii. The 'solvent' surface is that traversed by a spherical probe that rolls over the currently selected atoms. The 'solvent-accessible' surface is the locus of the centre of a spherical probe that rolls over the currently selected atoms. For these two cases the radius of the probe is taken to be the default Jmol radius of 1.2 Å; it may be changed in the Jmol console using the 'set radius' command. The 'molecular' surface is the same as the solvent surface for a probe of fixed radius 1.4 Å. The 'dot surface' option renders the surface by discrete dots.

colour

Sets the molecular surface to a selected colour. If the surface is represented by dots, these will retain colouring by element. This behaviour may be changed, if necessary, by issuing a 'colour dots' command within the console.

translucency

A menu allowing levels of translucency to be set from 0 (opaque) to 100% (invisible) for the molecular surface.

Labelling

A number of options are presented to modify the labelling conventions for the figure as a whole. These would normally only be of use for a single, relatively small, molecule. To label individual atoms or parts of the structure, one should use instead the options on the select/label tab. The options available fall into three groups.

labels off
chemical symbol
atom name
atom number
symmetry operator
element and symop
atom name and symop

The options are largely self-descriptive. 'Atom number' is a sequential number assigned by Jmol; 'atom name' is the label found in the CIF. Symmetry operators are given in the form 2556, for example, where the '556' represents the cell offset from the base coordinate set at 555 (i.e. in this example it refers to a translation of one unit cell along the c axis). The initial integer is the sequence number of the symmetry operation in the ordered list in which it appears in the CIF - i.e. here, symmetry operation number 2. In line with current journal policy, these labels are applied only to non-hydrogen atoms.

label H atoms

Provides an option to label H atoms. In this case, all atoms are labelled by atom name. To change this behaviour, one should select individual atoms and label them using the options available on the select/label tab.

monochrome labels
inherit colour

By default, Jmol creates labels in the same colours as their parent atoms. The 'monochrome' option allows a global choice of black on a white background (the usual journal default for printing) or white on a black background.

The crystallography tab

This tab provides options for generating crystal packing diagrams and for identifying or annotating symmetry-related features (Fig. 41). It is a good starting place if the main objective of your figure is to show the crystal packing.

[Fig. 41]
Fig. 41
The crystallography tab.

unit cell
show cell parameters
hide cell parameters

An outline of the unit cell may be drawn or hidden. By default, it is generated when small-molecule and inorganic compounds are first loaded, but not for biological macromolecules. A legend displaying the space group and cell parameters may be displayed in the top left-hand corner. By default, IUCr journal style is not to display this information.

Cell packing

The menu provides a list of options to display: the asymmetric unit only; the unit-cell contents when all symmetry operations have been applied (this will display atoms lying outside the basic unit-cell boundary); the contents of the central cell of an extended lattice (this will show only atoms located within the unit-cell boundaries, which may of course include portions of symmetry-generated molecules that lie mostly in adjacent unit cells); and a selection of planar or cubic packing nets. The limit provided in the menu is 3 x 3 x 3 unit cells. More extended lattices can be generated using the console, but you should remember that the computational demands in generating and manipulating large numbers of atoms in real time may make this impractical for readers with limited computing facilities.

Offset unit cell

The menu allows the unit cell to be re-located.

Symmetry

A small number of utilities are provided that allow you to display or highlight part of the symmetry-generated contents of the crystal lattice.

Display: first molecule
asymmetric unit
symmetry-derived
all

Various portions of the lattice are displayed. 'First molecule' examines the list of atoms, applies bonding rules to identify one or more discrete molecules, identifies the molecule that is first in the list (i.e. that contains the atom numbered 1 in sequence), and shows all symmetry mates of that molecule. The Jmol command that is executed to achieve this effect is 'restrict within(molecule,atomno=1)'. Another molecule may be chosen by specifying a suitable atom sequence number in the console.

'Asymmetric unit' displays only the atoms occupying the asymmetric unit; no symmetry operations are applied. 'Symmetry-derived' displays the symmetry mates to the asymmetric unit; 'all' displays the complete contents of the lattice.

Highlight: original
symmetry-derived
first-molecule
by molecule
none

These options are largely complementary to the previous set. Instead of displaying or hiding parts of the lattice, they highlight the selected items with different colours.

The select/label tab

This is possibly the most useful tab in allowing you to highlight particular portions of the structure. It is also at first glance the most complicated. However, the various options are collected into logical groups, and you will only need to use the ones that are relevant for your purpose (Fig. 42).

[Fig. 42]
Fig. 42
The select/label tab.

You can also, of course, simply use the selection options available through the Jmol pop-up menu, or perform explicit selection, labelling and measurement commands through the Jmol console.

Note that the options on this page invoke either or both of the Jmol 'select' and 'set picking' sets of commands, often in complex ways. When you have finished working with these options, we recommend that you click the buttons 'all' (under 'Select items') and 'enable measurements' (under 'Display geometric measurements'). You cannot select both together, but if you click on each in turn, you will restore the behaviour of Jmol to the one with which most users will be familiar (i.e. all atoms are selected, and the user may click on atoms to measure distances and angles between them).

Highlight selected items

selection haloes on
selection haloes off

It will be much easier to understand what atoms will be affected by a command if you turn selection haloes on - each atom selected will be surrounded by a yellow sphere. Normally you will want to turn selection haloes off when you have finished manipulating the molecule, so that they do not appear in the static figure.

Select items

The options in this section allow you to select particular parts of the structure, and to show or hide the parts selected.

all
none

These are global settings. When you have finished working on this page, you should normally select 'all' so that any operations that the reader performs through the standard Jmol menu will have the anticipated effect of acting on the structure as a whole. By default, all the atoms will initially be selected, so you may wish to select the 'none' option before you begin to select individual atoms or groups of atoms.

invert selection
show only selected
hide selected
hide none

These options affect the display of the selected objects, and allow you to invert the sense of selection - i.e. to select the complementary set of objects.

individual atoms
individual molecule
by element

These options establish the 'picking mode' that allows you to make interactive selections by clicking on objects in the structure with your mouse. If you click on 'individual atoms' then each mouse click will add another atom to the set selected (clicking a second time on any atom removes it from the selection set). The 'individual molecule' setting will select all atoms in the same molecule as the one that you click on (note that the 'molecule' will be that established by Jmol's own connection rules). The option 'by element' selects all atoms of the same elemental type as that clicked on. These actions are additive - if you select 'by element' and click on a C atom, then an N, all carbon and nitrogens will be selected. They are also reversible - if you decide that you didn't want the carbons, click again on a C atom and all will be deselected.

(Biological macromolecules only)

backbone
side chains
polar residues
non-polar residues
hetero groups
solvent
water
ligands
non-aqueous hetero groups
non-aqueous solvent

Several options are provided to help in selecting portions of a protein or nucleic acid structure, including solvent water molecules, all solvent (including free phosphate and sulfate ions), hetero groups and ligands, and particular components of the polypeptide or polynucleotide molecules. Note that they all rely on correct designation of these components in the loaded mmCIF.

show hydrogen atoms
hide hydrogen atoms

Because it is very common to suppress H atoms from display, a separate option is provided to display or hide all hydrogens.

Colour/style of selected items

Once you have made a selection, you will usually wish to change some aspects of its representation.

colour

This option provides a selection of colours, as well as 'translucent' (70% translucency) and 'opaque'. The colour applies to all items selected, which may not always be what you want. If you select two atoms and a connecting bond, and change the colour of the selection by this menu, the selected atoms and the bond between them will change to the desired colour. However, by default Jmol colours a bond in two halves, each corresponding to the colour associated with the atom immediately adjacent. If you use this option to change the colour of a selected C atom from grey to red, for example, you may be surprised when the other bonds from the selected carbon also change to red. In that case, you will wish to use the other options in this section for more control over individual atoms and bonds.

atoms: radii
colour
translucency
These options provide greater control over the atomic spheres in the selection. You may change their radii, colours and translucencies through a range of values.

bonds: width
colour
translucency
bond order

These options provide greater control over the bonds in the selection. You may change their widths, colours and translucencies through a range of values. You may also assign different representations corresponding to an assigned bond order - single, double, aromatic etc. You may hide individual bonds. Note that you may also use these options to draw a line between any two atoms - no checking is done as to whether the connection satisfies chemical bond length constraints. To do this, first 'select none', then 'select by individual atoms'; click on the two atoms you wish to connect, and then select under the 'bonds: width' menu the option 'connect all selected'.

Label selected items

These options allow you to label individual atoms or groups of atoms, and to make limited changes to the style of the label. Note that the labelling styles offered by Jmol do not always correspond to the requirements of the IUCr journals, so labelling should be used sparingly, particularly on the main figure (which will be published also in the PDF edition of the journals).

labels off
chemical symbol
atom name
atom number
symmetry operator
element and symop
atom name and symop

These specify the content of the label, and are largely self-explanatory. 'Atom number' represents the sequence number of the atom in the coordinate list, and is probably of little use in a publication. See also Section 9.2.5 for discussion of the format of the labels.

monochrome labels
inherit colour

By default, Jmol renders atom labels in the same colour as their parent atom. IUCr journals prefer black labels (on a white background) or vice versa, which are supplied by the 'monochrome labels' option.

centred
upper right
lower right
upper left
lower left
label size

A number of standard offsets are provided for the label. If these are not sufficient to prevent the label colliding with some other object, you may wish to use a scripting command such as 'set labeloffset 12 0' to set the label 12 pixels to the right of the atom (the arguments to the 'set labeloffset' command are the x and y displacements in pixels; 12 is the default value).

The label size may also be changed; 20 pixels is the default value.

Display geometric measurements

One of the most useful features of Jmol as a visualization tool is the ability for the user to click on two, three or four atoms and see a representation of bond distances and angles. This is achieved by the default setting 'select picking measure', which will be turned off if you have used any of the options provided for selecting individual atoms or groups through mouse clicks. If you have done so, you should click on the 'enable measurements' option on this tab before saving what you have done (unless you intend the reader to use the select picking mode currently in use).

These options also allow you to render some geometric information in your saved enhanced figure.

enable measurements
delete measurements
colour
linewidth
font size

To draw measurements between two atoms, select the 'enable measurements' option and click once on each of the atoms. To select three or four atoms, double-click on the intervening ones.

You may set the colour and line width (in Å) of the measurement lines, and the font size (in pixels) of the associated labels. If you select 'hide' on the font size menu, you may use this technique as an alternative way to draw lines between arbitrary atoms. Note that the 'thin dotted' menu item under the 'linewidth' option allows you to draw a dotted line; Jmol, however, does not currently provide options for changing the width of such a dotted line.

Special features

centre selected atom
rotate about selected atom
stop rotation

These options are occasionally useful for recentring the view on a specific atom. 'Rotate about selected atom' locates the rotation axis on the selection, and causes the structure to rotate about that axis, so that you can check that it behaves as expected. You may wish, however, to 'stop rotation' in order to save a specific initial view. The reader will always be able to restart the rotation using the standard 'toggle spin' button on the enhanced figure.

The ellipsoids tab

(Inorganic and small-molecule compounds only.)

These options allow you to change the style of atomic displacement ellipsoids (Fig. 43).

[Fig. 43]
Fig. 43
The ellipsoids tab.

probability(%)

The probability envelope represented by the ellipsoids.

style

Jmol offers a wide choice of representations. The default (cutout octants with axes) displays ORTEP-style ellipsoids; the principal ellipses can be distracting especially against black backgrounds, and may be inhibited using the simple 'cutout octants' style. Other options allow increasingly schematic views of the ellipsoids, or in the case of 'intersecting axes' the axes only. Some of the representations can be combined.

colour
translucency

A selection of colour and translucency schemes may be applied. Colour 'by temperature' applies a graduated scale from blue through red to white for atoms with progressively greater displacement modulus.

hydrogen atoms

H atoms may be represented as small spheres (the default); with ellipsoids if the refinement warrants it; purely by position (i.e. shown as capped sticks); or suppressed altogether.

show outlines only while manipulating figure

Because of the high computational effort needed to render ellipsoids, it can take time to move the molecule around. If you select this option, the ellipsoids will be shown in outline only during manipulations of the figure, making it much easier to decide an optimal view direction.

The polyhedra tab

(Inorganic compounds only.)

These options allow limited control over the display of coordination polyhedra in inorganic structures (Fig. 44). For more control, you should consult the detailed Jmol documentation.

[Fig. 44]
Fig. 44
The polyhedra tab.

Polyhedra based on distance

The current menus support coordination polyhedra with a variable number of vertices based on the radius from a central atom.

maximum radius (flat faces)
maximum radius (collapsed faces)

Normally you will wish Jmol to calculate polyhedra based on default bond lengths. The optional radii, which extend from 1.0 to 5.0 Å, may nevertheless be useful for constructing polyhedra of a desired size around a selected subset of atoms in the crystal (use the select/label or crystallography tabs to make selections). The 'flat face' rendering draws convex polyhedra. 'Collapsed faces' draws concave figures, making it easier to see the central atom.

colour
translucency

These menus allow you to modify the appearance of the edges and faces of the polyhedra.

highlight edges
highlight front edges

These options emphasise the edges (or the visible edges) of the polyhedra to make their three-dimensional outlines clearer.

The structure tab

(Biological macromolecules only.)

These options determine the style of various schematic representations of secondary structure in proteins and nucleic acid molecules (Fig. 45). They can be applied to portions of the structure previously defined by options on the select/label tab.

[Fig. 45]
Fig. 45
The structure tab.

backbone
trace
cartoon
  alpha helices as ribbons
  alpha helices as cylinders
meshribbon
rocket
ribbon
strands

The 'backbone' representation draws a zigzag line through the α carbon atoms of polypeptides or the P atoms of polynucleotides. The thickness may be set from the menu using a range of values expressed in Jmol's internal dimension units (250 units = 1 Å). The 'trace' is a smooth curve interpolated between the α carbon or phosphorus atoms. In this case the thickness may be selected from a range of values in Å units.

The 'cartoon' representation uses ribbons with an arrowhead for α helix and β strand stretches, and trace for the remaining turns, loops and random coils. For nucleic acids, the nucleotides are displayed as flat molecular templates. The rendering may be modified to show 'alpha helices as cylinders', i.e. as arrowed cylinders in the style of 'rockets'. The 'rocket' representation displays only polypeptides; it uses arrowed cylinders for α helices, straight 'planks' with an arrowhead for β strands, and trace for the remainder.

'Ribbon', 'strands' and 'meshribbons' display ribbons following the trajectory of the interpolated curve that defines the trace. They employ respectively solid ribbons, ribbons made of parallel threads, or ribbons made of crossing threads. All may be used for polypeptides and polynucleotides.

The available colour schemes for each of these representations are: 'by element' (so that proteins appear grey from the α carbons, nucleic acids orange from P); 'by amino acid' (bright colours are used for polar amino acids, dark for hydrophobic ones; nucleosides all have the same brown colour); 'shapely' (an alternative colouring scheme used by RasMol and other software to colour residues by amino acid property; nucleosides are also coloured); 'by secondary structure' (helices are pink, β strands or sheets yellow, turns in blue, the remainder white; DNA and RNA are coloured purple and red); 'by chain'; and 'gradient' (a rainbow from blue at the N or 5' terminus to red at the C or 3' terminus). Each selection may also be coloured from a menu of single hues.

In addition, each representation can be assigned a translucency.

The special tab

The special tab (Fig. 46) provides a small collection of 'special effects' achievable through Jmol scripting. The intention is not necessarily to provide features that will be of widespread use, but rather to illustrate some of the more unusual functions that can be used to good effect to illustrate particular features of a structure. This selection may grow if users can suggest novel examples.

[Fig. 46]
Fig. 46
The special tab.

Slabbing

The effect of this option is to slice the model through a plane parallel to the plane of the display. It has the effect of a 'bacon slicer', removing the top or rearmost portion of the model, and is perhaps most effective when the model is rotating (and especially if rendered in some space-filling view).

slice from front
slice from rear

A range of values is provided for illustrative purposes. As with all the options on this tab, the author may use these as examples, and specify more precise commands through the use of the Jmol console.

Crystal plane surfaces

This is similar to the slabbing mode, but it provides slices through a crystal structure parallel to particular Miller planes.

remove atoms from above
remove atoms from below

Again, the Miller planes available through the drop-down menus are for illustrative purposes only. Authors may wish to modify the indices to demonstrate a particular plane of interest in their structure.

Cavities

show cavities
colour
translucency

In this version of the toolkit, the 'show cavities' option is essentially equivalent to the solvent-accessible surface that can be drawn on the general tab. It is hoped in future releases to include the cavity slabbing facility beautifully demonstrated on Alan Hewat's web page at http://icsd.ill.fr/slabslider/slab3d.html.

Fig. 47 shows an example of what is achievable using some of the options on the special tab.

[Fig. 47]
Fig. 47
A slice through the crystal packing along the (202) plane displayed and highlighted using options from the special tab.

Advanced users

The final option on the special tab (Fig. 48) allows access to the stored graphics state of the main figure. It is the information that was stored when the last save was made using the primary save button. Its main use would be to restore the saved view without reloading the application, using the 'Activate' button at the bottom of the text field (for example, if you wished to use the same starting view as the basis for a number of different views stored in the various button and checkbox scripts). It is also possible to replace the stored view with the current one using the 'Update state script' button. This is equivalent to making a primary save.

[Fig. 48]
Fig. 48
Access to the saved graphics state through the 'Advanced users' option of the special tab.

It is expected that this will be of use only to those who understand in some detail how the graphics state may be manipulated, and it is therefore concealed from view unless the user specifically wishes to display it.

The button scripts tab

This tab (Fig. 49) provides space for the author to supply up to four Jmol scripts that will be associated with buttons on the enhanced figure page. The buttons will be labelled (a), (b), (c) and (d). Each script has an associated caption, which you should also supply through this tab.

[Fig. 49]
Fig. 49
The button scripts tab.

Against each script field (on this and the other script tabs) is a button, 'import view', which will transfer the graphics state of the current view in the visualization window into the script box. This means that you can use all the options on the other tabs to generate a completely new view of the structure, which you can store as one of the scripts that you supply for the reader to run. Be aware, however, that this can create a very large script; and also that it will completely define the graphics state of the visualization, which might conflict with some of the settings that you attempt to provide through other scripts.

The software places no constraints on what Jmol scripts you may load in these fields. They can be very simple indeed ('stereo on'); they can be complex views created using the tools in this toolkit and imported through the 'import view' button; or they can be arbitrarily complex scripts involving animations and other advanced features of Jmol provided by an expert.

However, it is important to meet the reader's expectations of what will happen when the various mechanisms for activating these scripts are used. The scripts on the current tab are associated with buttons on the enhanced figure page. The reader will not be surprised, when a button is clicked, if a completely new view of the structure is presented, or some 'one-off' animation is run. Therefore, these button scripts should be used when you wish to demonstrate quite distinct views of the structure. They may be the ones that rely most on the 'import view' facility to allow you to set up quite complex views that are very different from that of the main figure.

If, on the other hand, you want the reader simply to be able to change aspects of the structure that they are currently viewing, it may be better to create smaller scripts that are accessed as checkboxes or radio buttons (see the descriptions of the other script tabs for further discussion of this point).

The checkbox scripts tab

This tab (Fig. 50) provides space for the author to supply up to four Jmol scripts that will be associated with checkboxes on the enhanced figure page. Normally, you will supply a script to run when the checkbox is selected, and another to run when the checkbox is unselected. In keeping with the principle that the reader's expectations should not be upset, you will probably want to provide complementary on/off functions through these paired scripts ('stereo on', 'stereo off' etc.).

[Fig. 50]
Fig. 50
The checkbox scripts tab.

Supply a caption for each checkbox that you create.

You will normally to use checkboxes to provide the reader with features that can be turned on or off independently of other aspects of the current view, and that therefore are 'additive'.

As with other script fields, you may import the current view from the visualization window using the 'import view' button alongside each script field. In general, though, you will probably want to provide more lightweight Jmol scripts using this tab. See Section 6.4 for some suggestions on how to go about this.

The radiobutton scripts tab

This tab (Fig. 51) provides space for the author to supply one or two groups, each with up to six Jmol scripts that will be associated with radiobuttons on the enhanced figure page. 'Radio buttons' are normally used in web forms to select one among a set of mutually exclusive options. You should therefore structure any scripts offered to the reader through this interface along the same principles.

[Fig. 51]
Fig. 51
The radiobutton scripts tab.

Note that you are not obliged to do so; any Jmol script can be inserted in any of the script fields. However, the reader is likely to become very confused if your scripts do not behave in the exclusive manner suggested by the radiobutton interface.

In that spirit, you should arrange that the scripts you provide in each group of radiobuttons select mutually exclusive options for a single feature. In the (optional) title for each radiobutton group, you can specify what that feature is.

As with other script fields, you may import the current view from the visualization window using the 'import view' button alongside each script field. In general, though, you will probably want to provide more lightweight Jmol scripts using this tab. See Section 6.4 for some suggestions on how to go about this.

The scratch tab

The scratch workspace (Fig. 52) is a text-entry field in which you can experiment with Jmol scripting. If you enter any commands in this box and then click the 'Test' button at the bottom, those commands are applied to the current view. The 'import view' button at the top of the scratch area imports the complete graphics state represented by the current view (note that this will completely overwrite anything already in the text entry box). This workspace can also be used as a convenient area into which to paste existing scripts, to test or modify them further.

[Fig. 52]
Fig. 52
The scratch tab.

The contents of the workspace are saved whenever either of the primary or secondary save buttons are clicked. This may therefore be used as a persistent notebook for storing ideas or experiments between editing sessions.

The help tab

The help tab provides a concise summary of how to use the software (Fig. 53).

[Fig. 53]
Fig. 53
The help tab.

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