Manage Excluded Volumes Panel
Create, modify, move, and delete excluded volumes for a hypothesis.
To open this panel, click the H button in the Entry List panel and choose Show → Manage Excluded Volumes. The hypothesis must be included in the Workspace.
- Using
- Features
- Additional Resources
Using the Manage Excluded Volumes Panel
You can create new excluded volumes for a hypothesis by placing them on atoms in a Workspace structure. First, you must add the structure to the Workspace, without removing the hypothesis (use control-click). Then select the atoms on the structure where you want to place the spheres, enter a radius for the spheres, and click Selected Atoms.
Existing excluded volumes can be repositioned or deleted. You can select multiple excluded volumes, either in the Workspace (select Pick sphere to translate and use control-click or shift-click to add spheres) or in the table, and reposition (translate) them together or delete them.
Excluded volumes can be added to hypotheses when you create them in the Develop Pharmacophore Model Panel.
Manage Excluded Volumes Panel Features
- Create excluded volumes using tools
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Create new excluded volumes for the hypothesis. The new spheres are added to any existing spheres unless they are redundant.
- Selected Atoms button
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Select atoms on a structure in the Workspace and click this button to add excluded volumes to the selected atoms. You must have a structure included in the Workspace as well as the hypothesis.
- Radius text box
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Specify the radius of the excluded volume spheres, in angstroms.
- Receptor button
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Create excluded volumes from a receptor that complements the hypothesis. Opens the Excluded Volumes from Receptor Dialog Box.
- Reference Structures button
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Create excluded volumes in a full or partial shell around one or more reference structures. Opens the Excluded Volumes from Reference Structures Dialog Box.
- Inactives and Actives button
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Create excluded volumes for a Phase hypothesis in regions occupied by atoms in a set of inactives that do not overlap with atoms in a set of actives. Opens the Excluded Volumes from Inactives and Actives Dialog Box.
- Excluded volumes section
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This section allows you to manage existing excluded volumes.
- Pick sphere to translate option
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Select this option to pick spheres in the Workspace and drag them to a new location. You can use shift-click and control-click to select multiple spheres. Use the same mouse button as you use for translating a structure. If you want to change the camera view to translate in a different plane, deselect this option, then change the view, and reselect the option to translate again. When you pick spheres, the corresponding rows are also selected in the table.
- Excluded volumes table
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Lists the excluded volume spheres with their radii and coordinates. You can edit the table cells (double-click) to change the radius and coordinates. You can select multiple rows to delete or translate the volumes. Selecting rows in the table also marks them in the Workspace.
- Delete button
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Select excluded volumes in the table or the Workspace and click this button to delete the volumes.
- Reset button
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Revert all changes made to the excluded volumes, and reset the panel settings to their opening state.