Manual: Labelling atoms and bonds


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Diamond Version 5 User Manual: Display of structure picture

Labelling atoms and bonds

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Overview

This article deals with the use of atom and bond labels and will tell you:

- how to add labels to atoms and bonds,

- what atom and bond label texts can consist of,

- how to define the size, position, and style of the label,

- how to shift the label with the mouse,

- how to change the label text, size, position, and style of an existing label,

- how to delete atom and bond labels.

Adding Labels

There are several ways how you can add labels to atoms or bonds or to both atoms and bonds:

Labelling all selected atoms and bonds

To label all selected atoms and bonds, push the (red marked) button Add Labels toolbar button in the Picture toolbar, or use the "hotkey" Shift+Ctrl+L. With this quick method, the new atom and bond labels get the latest atom label and bond label settings, rsp., or the default settings.

Labelling all selected atoms or bonds

If objects of different kinds (atoms, bonds, etc.) have been selected, but you want to label the selected atoms or the selected bonds only, or if you want to add labels and define new settings (text, size, position, style), right-click into one of the selected atoms or bonds, and choose the appropriate command from the context menu, that means either the Atom label(s) or the Bond label(s) command, rsp., from the Add sub-menu of the context menu.

You may also choose the Atom labels command from the Objects menu. Both commands open the Add Atom Label dialog, where you can change the default or latest settings, rsp., and start the generation of labels with the OK button. If the Update existing label definitions checkbox is checked, existing labels will be overwritten using the current settings.

The Bond Labels command in the Objects menu does the same for bonds rather than atoms, using the Add Bond Label dialog instead.

Atom Label Text

To define the text for a new atom label or to edit the contents of an existing atom label, use the controls in the Text group of the Add Atom Labels dialog box or the Edit Atom Labels dialog box, rsp.

The atom label can either have individual text or pre-defined text such as the atom symbol. Content determines the kind of information to be supplied, whereas Format decides how the information will be formatted.

Mixed site decides, if to show only the label for the representative of mixed atom site (or the single component to show at a certain position) or of all components of a mixed atom site, separated with '/', ',', or '+' character each.

You may select from:

Content	Format	Description
Element symbol	Fe	Formats the element symbol: First letter uppercase, second (if defined) lowercase.
	FE	Both letters (as far as defined) uppercase.
Atom symbol	Fe 1	Formats the atom symbol without any change.
	Fe1	Formats the atom symbol, but removes blanks, e.g. blanks between an element symbol and additional identifiers.
	Fe^1^	Formats the atom symbol with the non-element part of the symbol as far as possible as superscript.
	Fe~1~	dito, but as subscript.
Atom identifier	AXYZSSB	Formats the atom coderef_atomcode.
	PARM #	Formats the sequential number of the atom in the parameter list (beginning with #1).
	ATOM #	Formats the sequential number of the atom in the list of created atoms (beginning with #1).
Element/Charge	Fe+2	Displays the element symbol plus charge or (formal) oxidation number. Charge is added to the element symbol directly as integer with sign (even if positive).
	Fe(+2)	The integer charge following the element symbol is enclosed in parentheses.
	Fe+2.345	Charge is added to the element symbol without rounding.
	Fe(+2.345)	The charge is enclosed in parentheses and not rounded.
	Fe^+2^	Like Fe+2, but with charge as superscript.
	Fe^+2.345^	Like Fe+2.345, but with charge as superscript.
	Fe^2+^	Charge is rounded and superscripted with sign following the charge.
Charge	+2	Displays the charge (or formal oxidation number), as far as defined. Charge is rounded and signed even if positive.
	2	Charge is rounded and signed if negative.
	+2.345	Charge is signed even if positive but not rounded.
	2.345	Charge is signed if negative and not rounded.
Composition	0.5678Fe(+2)	Displays (component's) site occupation factor (unless 1.0), followed by element symbol and charge/oxidation number (if defined).
	0.5678Fe^+2^	Charge or oxidation number as superscript.
	0.5678(5)Fe(+2)	The site occupation factor is followed by standard uncertainty, if defined.
	0.5678(5)Fe^+2^	Both site occupation factor with standard uncertainty and charge/oxidation number as superscript.
(Individual text)		The label contains individual text which has to be entered or changed in the input field Individual text.

Bond Label Text

To define the text for a new bond label or to edit the contents of an existing bond label, use the controls in the Text group of the Add Bond Labels dialog box or the Edit Bond Labels dialog box, rsp.

The bond label can either have individual text or pre-defined text such as the bond length. Content determines the kind of information to be supplied, whereas Format decides how the information will be formatted. You may select from:

Content	Format	Description
Bond length	1.234	Formats the bond length in Angstroems with 3 decimal places and without unit symbol.
	123.4	Formats the bond length in picometers with 1 decimal place and without pm symbol.
	1.234 Å	Formats the bond length in Angstroems with 3 decimal places and with unit symbol.
	123.4 pm	Formats the bond length in picometers with 1 decimal place and with pm symbol.
	1.2345	Formats the bond length in Angstroems with 4 decimal places and without unit symbol.
	123.45	Formats the bond length in picometers with 2 decimal places and without pm symbol.
	1.2345 Å	Formats the bond length in Angstroems with 4 decimal places and with unit symbol.
	123.45 pm	Formats the bond length in picometers with 2 decimal places and with pm symbol.
	1.234(5)	Like 1.234 but with standard uncertaintyref_esd, as far as defined.
	123.4(5)	Like 123.4 but with standard uncertainty, as far as defined.
	1.234(5) Å	Like 1.234 Å but with standard uncertainty, as far as defined.
	123.4(5) pm	Like 123.4 pm but with standard uncertainty, as far as defined.
	1.2345(6)	Like 1.2345 but with standard uncertaintyref_esd, as far as defined.
	123.45(6)	Like 123.45 but with standard uncertainty, as far as defined.
	1.2345(6) Å	Like 1.2345 Å but with standard uncertainty, as far as defined.
	123.45(6) pm	Like 123.45 pm but with standard uncertainty, as far as defined.
	1.234(2..19)	Formats the bond length in Angstroems with standard uncertainty in the range (2) through (19) with variable number of decimal places, no unit symbol used.
	123.4(2..19)	The same as above but in picometers.
	1.234(2..19) Å	The same as above in Angstroems and with unit symbol.
	123.4(2..19) pm	The same as above but in picometers and with pm symbol.
Identifier	BOND #	The sequential number of the bond in the list of created bonds (beginning with #1).
(Individual)		The label contains individual text which has to be entered or changed in the input field Individual text.

Style, Size, and Position

To define the size, position, and style for a new atom or bond label or to edit the size, position, or style of an existing atom or bond label, use the controls in the Style group of the Add Atom/Bond Labels dialog box or the Edit Atom/Bond Labels dialog box, rsp. See "Adding Labels" and "Changing Label Text, Style, or Size After Creation" how to add labels or how to edit existing labels, rsp.

Both size and position of an atom or bond label are defined in Angstroem units rather than in centimeters or millimeters, that means both position and size of the label depend on the current enlargement factor of the structure picture. If central projection is used, labels in the front may appear larger than those in the rear. If you rotate or shift a structure, the labels follow the movements of their associated atoms and bonds, rsp.

Defining the label's position

The position of an atom or bond label is defined as the vector between the reference point of the label and the center of the associated atom or the center of the associated bond, using the components x, y, and z in Angstroem units. x determines the horizontal, y the vertical distance. Positive values mean shift to the right and top rsp. The reference point of the label is defined by Alignment.

The third parameter, z, is used only for rendered structure pictures to define the 3D position of the text relative to the 3D coordinates of the corresponding atom or bond. Since rendered representation uses a Z buffer to calculate the overlap of objects, parts of a label may interpenetrate its associated atom or bond, if it is "too near". To avoid this, use a value of about 0.5 or higher to ensure drawing of the label in front of the atom or bond, rsp. Since x, y, and z refer to the view coordinate system, the label does not rotate with the atom or bond, when the structure is rotated.

The Alignment defines the reference point within the rectangle that surrounds the label text. The label may be aligned in different ways:

Centered	the horizontal and vertical center of the label
Right	the left edge and the vertical center (text appears right from the reference point)
Left	the right edge and the vertical center (text appears left from the reference point)
Parallel	the label text is rotated with the bond axis

Normally, labels do not rotate when the structure is being rotated. Especially for bond labels, you can assign an alignment that rotates bond labels automatically so that the text is parallel with the bond axis.

Defining the label size

Like the position, the size of the label text is defined in Angstroem units. The real size of the label (in centimeters) in the structure picture is calculate with the current enlargement factor. If central projection is used, labels in the front may appear larger than those in the rear. Changing the enlargement factor of the structure picture leads to a equivalent increase or decrease of the label size. Use the input field Text size to set the label text size.

Defining the label color

Use the color select box Color to select an existing color or define a new color for the label.

If you are adding new labels, you can constrain the label's color with the atom's or bond's main color, instead. For that, check the checkbox Use atom's main color. The main color is derived from the atom's or bond's design: The main color is the interior color of atoms and thick bonds. (For thin bonds, only one color is available.) If the atom or thick bond is hollow or has black or white as interior color, Diamond takes the edge color instead.

Defining font and other attributes

Push the Font button to open the MS Windows standard font dialog to define the font and attributes like bold and/or italics. If the text shall appear underlined, check the Underline checkbox. Use Strike out to strike out the text. If the checkbox Opaque is checked, the label text will be opaque, which means that the background of the label text will be filled with the current background color. Otherwise (default) it is transparent.

Defining a default style for labels

When you are editing an existing label, check the checkbox Use this design as default for new labels to make the current options (text, size, position, styles) the default settings for new labels. These default settings apply automatically, if you add labels with the quick method (compare "Adding Labels"). The checkbox is not available in the Add Atom/Bond Labels dialog.

Shifting Label Position With Mouse or Cursor

You can shift the position of an atom label or bond label with the mouse. If you select multiple atom or bond labels, you can shift these labels simultaneously. Shifting the position means here changing the x and y coordinate of the label(s).

To shift a single label, move the mouse cursor into the rectangle that surrounds the label text, then press down the left mouse button and shift the label with left mouse button down to the desired position. When you have reached the desired position, release the left mouse button.

To shift multiple labels simultaneously, first select the labels, then move the mouse cursor into one the label markers, and continue like for a single label.

Changing Label Text, Size, or Style After Creation

To edit the properties of one or more atom or bond labels, do the following:

If you want to edit one label, the easiest way is to double-click into the rectangle that surrounds the label text. Or click with the right mouse button into that rectangle, and then choose the Atom/bond label(s) command from the Edit sub-menu of the context menu, or choose the Atom labels or Bond labels command, rsp., from the Objects menu.

If you want to edit more than one label at a time, first select the labels, then either double-click into one of the markers or click with the right mouse button into one of the markers and choose the Atom/bond label(s) command from Edit sub-menu of the context menu, or choose the Atom labels or Bond labels command, rsp., from the Objects menu.

All methods open the Edit Atom Labels dialog or Edit Bond Labels dialog, rsp.

If you edit one label only, change the settings you want to alter, and confirm with OK. If multiple labels have been defined, those settings keep blank that are not unique. If for example two labels have been selected with identical settings, but one label in red, the other in yellow, the color select box will be empty.

Removing Labels

To delete one or more atom or bond labels, select the labels, and then either press the Delete key, or click with the right mouse button into one of the markers, and choose the Atom/bond label(s) command from the Destroy sub-menu of the context menu.

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Next article: Adding text to structure picture