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Non-Bonded Interactions Panel |
This panel is used for displaying H-bond, halogen bond, contact, and pi interaction markers, and set the colors for the markers.
To open the Non-Bonded Interactions panel, you can:
Choose Tools → H-Bonds and Halogen Bonds in the main window.
Choose Tools → Contacts in the main window.
Choose Tools → Pi Interactions in the main window.
To display markers for a particular interaction, select the option for the interation.
To change the color of the markers for a particular interaction, click the color button next to the option for the interation, and choose a new color.
To define the atom sets between which to display interactions, choose an item from the option menu for the interaction type.
To add properties to the project for the count of occurences of each interaction, click Create Property and select the interaction types in the dialog box that opens.
To set the paramaters that define each interaction type, click Preferences and make settings in the Preferences panel.
The panel has three sections, for the three different kinds of non-bonded interactions. Each section has the same layout and types of controls.
The display options control which interaction types are displayed in the Workspace. The overall Display option in each section can be used to turn on and off all interaction markers of that type. The individual options can be used to control which specific interactions are shown.
The display options are also available from the HBonds button, Contacts button, and Pi button on the Measurements toolbar, and in the Pose Viewer panel. Changing an option in any of these places changes it in all of them.
These buttons allow you to set the color of the marker for each specific interaction. Clicking the button opens a standard color selector in which you can set the color. The chosen color is displayed on the color button.
This option menu allows you to choose the atom sets for which the interactions are displayed:
Click this button to add properties to the selected entries in the Project Table. Opens a dialog box in which you can select the interaction types for which to calculate the properties. The property created for each interaction is the number of interactions that exist between the sets of interacting atoms. If the property already exists, it is updated. Properties for all interactions of the selected types are created (not just the ones that are displayed).
Set up the criteria used to find interactions of each type. Opens the Preferences panel at the Non-bonded interactions – Criteria section.
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