Atom Label Editor

The Label Editor button can be found on the Tools toolbar.

Use this button to perform the following actions:

  • Formatting the atom label

  • Replacing or overwriting any atom or atom label in a structure with a formatted:

    • Abbreviation group

    • List/NOT list

    • R-group

    • Alias

    • Pseudo atom

Only the default and user-defined abbreviation groups can be formatted.

Change an Atom Label

To change an atom label, follow the steps below.

  1. Click the Label Editor button, which is located on the Tools toolbar. Alternatively, the label editor can be used through the context menu.

  2. Hover the cursor over an atom and click to open its atom label text field.

  3. Enter a new label or change an existing one as needed.

  4. When finished, click on the canvas or click the green checkmark below the textbox to close the text field.

Formatting

When opening an atom label field, a formatting toolbar appears containing several options.

Some shortcuts can be used inside the textbox for formatting, too.

Formatting function

Button

Shortcut

Bold

images/download/thumbnails/1802492/bold24.png

Ctrl+B

Italic

images/download/thumbnails/1802492/italic24.png

Ctrl+I

Subscript

images/download/thumbnails/1802492/subscript24.png

Alt+↓

Superscript

images/download/thumbnails/1802492/superscript24.png

Alt+↑

Symbols

images/download/thumbnails/1802492/symbol16.png

N/A

Alias atom

Alias

N/A

Pseudo atom

Pseudo

N/A

The symbol map is active only when a text box is open for editing, The twelve most recently used characters appear at the top of the window. A character may appear more than once in this section if the versions use different font styles.

To insert a character, simply select the character from the table and click Insert.

Text attributes like font type and color can be set in the Format dialog box which can be opened from the contextual menu.

Replacing and Overwriting

MarvinSketch automatically tries to interpret chemically the atom labels including the abbreviation groups (user-defined ones as well) and templates.

If this interpretation fails, a message notifies the user that the label will be recognized as an alias.

Restrictions and tips on changing atom labels are summarized in the table below.

Atom label

Description

Atom/element

It is possible to change an atom label to an element symbol. However, it can be done more easily by placing the cursor on the selected label and typing the desired atom symbol.

The elements must be entered without explicit hydrogens.

Those elements which are used as an abbreviated group, that is, Ac or No cannot be introduced using the atom label editor.

To introduce them, simply overwrite a label with them in selection mode.

When formatting an element it becomes its alias atom.

Abbreviated group

It is possible to change an atom label to an abbreviated group by using the label editor. However, it can be done more easily by placing the cursor on the selected label and typing the desired abbreviation.

Formatting is only allowed for default and user-defined abbreviation groups.

Atom list/Not list

Atom list/NOT list cannot be formatted, only editing is allowed.

It is possible to change an atom label to an Atom list/NOT list using the Atom label editor. However, it can be done more easily by placing the cursor on the selected label and typing the definition.

R group

Only the R groups in the query structures can be formatted and not those in the R group definitions.

Pseudo atom

Pseudo labels by default are displayed as italic text.