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Manage Highlights Panel |
In this panel you can create, delete, and edit highlights for sets of atoms.
To open the Manage Highlights panel, you can:
Choose Workspace → Highlights in the main window.
Click the Highlights button on the Labels toolbar in the main window.
Choose Settings from the
Quick Highlights button menu on the
Labels toolbar in the main window
To create a highlight, click New. A dialog box opens, in which you can name the highlight. The highlight is listed in the table and is selected. Next, choose a highlighting method from the Method option menu, then use the Highlight atoms picking tools to define the atoms to highlight. If you want to change the settings used for the highlight, use the tools below the Highlight atoms section or in the Settings tab.
To edit a highlight, select it in the table. You can then edit the name in the table, or change any of the settings in the Atoms, Text, or Arrow tabs.
To create a highlight from an existing highlight, select the source highlight in the table and click Duplicate, then edit the duplicated highlight.
You can add text to the highlight in the Text tab, and set the font, background method, and text color. If you have text, you can also add an arrow from the text box in the Workspace to a location relative to the structure. The head of the arrow is defined as a point in 3D space, so it moves as you rotate or translate the structure. The text does not move with the structure, but you can relocate it by dragging. You can reposition multiple text boxes by selecting them with shift-click and control-click, and dragging.
Highlight text can be edited by double-clicking it in the Workspace, or right-clicking and choosing Edit. The Edit Highlight Text dialog box opens, in which you can change the text, background, and font.
If you want to delete highlight text, select the text in the Workspace and press Delete, choose Highlight Text from the Delete button menu, or Delete Selected Highlight Text from the highlight text shortcut menu. You can select multiple text boxes to delete, with shift-click and control-click.
To add a highlight that just consists of text and an arrow, you could for example create a silhouette highlight and set the transparency to 100%. Another approach is to create a highlight with no atoms, add text and an arrow, and ensure that Show only when atoms are highlighted is deselected in the Text tab.
To show or hide highlights, use the Show column checkboxes in the table.
To delete a highlight, select it in the table and click Delete.
In this tab, you can set up and edit highlights.
This table lists the highlights defined in the project. The highlights are displayed in the Workspace when the check box in the Show column is checked. The columns cannot be edited directly, but their content can be changed with the tools in the panel or the shortcut menu. The shortcut menu for the table has four items: the standard Export Table Data; Delete, to delete the highlight; Duplicate, to make a copy of the highlight; and Rename, to rename the highlight.
You can select a single row in the table. When you select a row, the controls in the tabs below the table are updated to reflect the selections or choices made for the selected row.
Click this button to add a new highlight. The New Highlight dialog box is displayed, in which you can name the highlight. When you click OK, a row is added to the Highlights table with the default method.
Make a copy of the selected highlight. A default name is generated by adding -dupN to the name of the original highlight. When the copy is created, it is selected in the table instead of the original. This allows you to immediately start making changes in the copy.
Delete the selected highlight.
In this tab, you select the atoms to be highlighted, the highlight method, and the color and transparency of the highlight.
Choose the highlighting method to use:
The controls that appear below the picking tools depend on the choice made from this option menu.
Select the atoms to highlight in the Workspace with the tools in this section. Picking atoms in the Workspace creates a highlight that is specific to the entry whose atoms you picked. If you want a highlight that can be applied to different entries, you should enter an ASL expresssion in the text box, or compose the ASL expression in the Atom Selection dialog box, by clicking the common objects button and choosing Select. For example, you could use atom sets or SMARTS patterns to define a particular functional group to highlight.
Choose a color for the highlight by clicking Edit, which opens a standard color selector. The new color is displayed in the patch when you click OK. Only displayed when Silhouette is chosen from the Method option menu.
Change the transparency of the highlight with this slider. Only displayed when Silhouette is chosen from the Method option menu.
In this tab, you can enter text that is added to the caption. The text is displayed in a box in the Workspace, with an optional arrow pointing to a location in the highlight. You can select multiple text boxes in the Workspace and drag them to a new location or delete them.
Enter the desired text in this area, or edit existing text. You can paste text into this area in the usual way (middle-click on Linux, Ctrl+V (⌘V) on Windows).
Select an option for the text background. Selecting Automatic chooses a background color that contrasts with the text color. Selecting No fill (transparent) makes the background of the text transparent, which means that anything that is behind the text will be visible through the text.
Choose font settings for the text: font type, point size, and style.
Set the color for the text. Click Edit to choose the color in a standard color selector. The color is displayed in the color patch.
Show the text only when there are atoms in the Workspace that are highlighted with this highlight (i.e. there is a match to the ASL expression for the highlight). If deselected, the text is shown regardless of whether the highlight is shown, provided Show is selected for the highlight in the Highlights table.
In this tab, you can specify the location of the head of the arrow that points from the text to the highlighted atoms. The arrow is not drawn if there is no text.
Pick atoms to define the location of the arrow head. The atoms need not be the same as the highlighted atoms. The head is placed at the centroid of the picked atoms, and moves as you translate or rotate the structure.
Set the color for the arrow. Click Edit to choose the color in a standard color selector. The color is displayed in the color patch.
In this section, you can make global settings that affect all relevant highlights.
This section contains a Contrast slider, which you use to change the contrast between the highlighted atoms and the other atoms for the contrast highlight type. The setting applies to all contrast highlights.
This section contains a Saturation slider, which you use to change the color saturation of the non-highlighted atoms for the saturation highlight type. The setting applies to all saturation highlights.
This section has three sliders, for controlling the width of the silhouette for different atom and bond types. The units of the width are angstroms. The Bond line border width setting applies to wire frame bonds. The Bond tube border width setting applies to bonds in both tube and ball-and-stick representation. The Atom sphere border width setting applies to atoms in both CPK and ball-and-stick representation.
This section has options for the direction of the arrow head when arrows are displayed. Flat means that the arrow is drawn in the plane of the highlight text, and points to the x,y coordinates of the chosen head location. Pointing means that the head points to the x,y,z coordinates of the chosen head location.
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