Manual: Legend of atom groups


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Diamond Version 5 User Manual: Display of structure picture

Legend of atom groups

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A legend listing all atom groups (atom types) of the current structure can be displayed at an arbitrary position of the structure picture.

"Settings" describes how to switch on or off the display of the legend, to define the position, size and other settings.

"Relative vs. Absolute Positioning" compares between the two kinds of positioning the legend.

Settings

You define all settings for the legend of atom groups (or atom types) in the Legend dialog. To open this dialog, choose the Legend command from the Objects menu. If the legend is already displayed, you can also open the dialog with a double-click into the legend, or with a right-click into the legend and choosing Legend from the context menu.

Switching the legend on or off

The main switch in the Legend dialog is the checkbox Display legend. This determines if the legend is displayed or not. If not, all other controls in the dialog box are unavailable.

Position of the legend

The position of the legend refers either to the center of the structure picture or to one of the four corners. This is defined by the setting in the combo box Relative to:

center of picture	the values in X and Y define the horizontal and vertical distance of the centerpoint of the legend from the center of the structure picture or the center of the structure window, rsp., in centimeters.
top left	the values in X and Y define the horizontal and vertical distance of the upper left corner of the legend from the upper left corner of the structure picture or the structure window, in centimeters. This means, the position of the legend depends on the size of the structure window (or of the page, if page view mode is used or when printed).
top right	the values in X and Y define the horizontal and vertical distance of the upper right corner of the legend from the upper right corner of the structure picture or the structure window, in centimeters.
bottom left	the values in X and Y define the horizontal and vertical distance of the lower left corner of the legend from the lower left corner of the structure picture or the structure window, in centimeters.
bottom right	the values in X and Y define the horizontal and vertical distance of the lower right corner of the legend from the lower right corner of the structure picture or the structure window, in centimeters.

The position of the legend relative to the center or a corner of the structure window or picture is defined in the two input fields Position X and Y, rsp. These values are given in centimeters. Positive values grow to the right and top, rsp., negative values to the left and bottom ,rsp.

Size of the legend

The size of the legend is indirectly determined by the sum of the radii for the atoms to be displayed in the legend. From the combo box Atomic radii, you can choose between two kinds of radii:

fixed	All atoms in the legend have the same size (the radius is given in Radius in centimeters).
atom-group-specific	The radii are used which have actually been used for drawing, that means the legend's size depends on the current enlargement factor.

If you are using a "fixed" radius, every atom that is displayed in the legend, will use the radius given in the input field Radius in centimeters. Otherwise the radius depends on the radius defined for the atom group and increases or decreases when the enlargement factor is changing.

Legend example #1 with atom radii of 0.25 cm

Legend example #2 with atom radii as given for their atom groups

The same legend of atom groups: The upper one using fixed radii (0.25 cm, font: 0.4 cm), the lower one with "atom-group-specific" radii and an enlargement factor of about 1.3 cm/Å.

Settings for the atom type label text

To change the font used for the atom type label text, push the Font button. The size of the text is determined by the value in the input field Font size in centimeters. Please note that the point size field of the font in the MS Windows standard font dialog will be ignored. The attributes bold and italics will be ignored, too. The color of the text is defined by the color select box Color.

Color and thickness of legend's border

The color of the legend's border is determined by the color select box Color, that means the font uses the same color as the border. The thickness in millimeters is given in the input field Border width. Use a value of zero, if you want no border to be drawn.

Formatting the atom group symbols

Diamond accesses the symbols that have been defined with the atom groups. (Usually these are default symbols made up from element symbol plus charge as far as defined. To change an atom group symbol, see "About atoms, atom groups, bonds, and bond groups".) If the atom group symbol begins with an element symbol, the rest of the symbol can be superscripted or subscripted, according to the setting in the combo box Symbols:

(no re-formatting)	The atom group symbol is not re-formatted.
superscript extension	If the atom group symbol consists of an element symbol and an attached extension (e.g. the oxidation number), the extension will be superscripted.
subscript extension	ditto, but subscripted.

With the Select button, you can open the Select Atom Groups for Legend dialog and choose, which atom groups may appear in the legend or if only those atom groups with at least one corresponding created atom in the structure picture will be listed (checkbox Hide atom groups not used in structure picture). Otherwise, all atom groups of the atom group list will be listed.

Setting default values

The button Reset defaults resets all settings including the Display all checkbox to the "factory" settings, i.e. the settings that Diamond uses after it has been installed for the first time.

Relative vs. Absolute Positioning

The position of the legend of atom groups refers to either the center of the structure picture (or the structure window, rsp.) or to one of its four corners. If you want to align the legend to special objects of the structure picture, you should set the combo box Relative to to "center of picture". In this case the position remains even if you change the window's size or if you change the layout of the picture or if you print the structure picture. When using relative positioning, the legend's position adjusts automatically to its window's size. That leads to different absolute positions of the legend on screen and printout, rsp.

The following screenshots compare the different results of relative positioning for the structure window (upper part) and for the printout (lower part; the printout is simulated by the page view mode). In both case the lower right corner of the legend is fixed with the lower right corner of the structure window and printout, rsp.

Legend example #2 with atom radii as given for their atom groups

Legend example #3 with layout switched from Window to Printout Page

Previous article: Adding text to structure picture
Next article: Coordinate system

References:
ICSD:23119: Jackson P F, Johnson B F G, Lewis J, Nicholls J N, McPartlin M, Nelson W J H. "Synthesis of the Carbido Anion (Os₅ C (C O)₁₅ I)and the X-Ray Crystal Structures of Os₅ C (C O)₁₅ and Ph₃ P)₂ N) (Os₅ C (C O)₁₅ I)". JCCCA, 1980, 564-566 (1980).