Excluded Volumes Dialog Box

In the Excluded Volumes dialog box, you can pick atoms to define a volume that should not contain atoms in any active ligand that matches the hypothesis, or generate them using some automated procedures.

  • Using
  • Features
  • Additional Resources

Using the Excluded Volumes Dialog Box

The Excluded Volumes dialog box provides means to add excluded volumes manually to a hypothesis, or to run a program that places excluded volumes automatically at locations defined by the program input.

Manual placement of excluded volumes creates volumes at the location of atoms or at the centroid of a set of picked atoms. First select Pick atoms to create excluded volume, then pick atoms in the Workspace. Each pick adds an excluded volume with the radius specified in the Radius text box (default 1 Å).

To place an excluded volume at the centroid of a set of atoms, shift-click to pick the second and subsequent atoms. After each pick, the centroid of the atom set is calculated and the excluded volume sphere is moved to the centroid. To remove an atom from the set, use control-click. (This is the normal selection behavior for atoms.)

The sphere radius and the coordinates of the bolume are added to the table when it is created and the sphere is colored yellow. You can edit the table cells to change the radius and the centroid location.

There are three automated procedures for placement of excluded volumes.

  • You can place excluded volumes on selected atoms of a receptor structure, to which the reference ligand of the hypothesis must be properly aligned. Include the receptor in the Workspace, then click Receptor, to open the Excluded Volumes from Receptor dialog box.

  • You can place excluded volumes in a full or a partial shell around a set of structures that is aligned to the hypothesis. Include the structures in the Workspace, then click Reference Structures, to open the Excluded Volumes from Reference Structures dialog box.

  • You can place excluded volumes on atoms in a set of inactive ligands that do not occupy the same region of space as atoms in any of a set of active ligands. Click Inactives and Actives to open the Excluded Volumes from Inactives and Actives dialog box.

Excluded volumes from all of these methods are added to the volumes table. You can select multiple volumes either in the table or in the Workspace, with shift-click and control-click. The spheres for the selected rows are highlighted in the Workspace.

You can move the excluded volume spheres in the Workspace:

  1. Select Pick excluded volume to translate.

  2. Select the excluded volumes in the table or in the Workspace.

    The volumes are colored red. Use shift-click and control-click to select multiple volumes.

  3. Drag in the Workspace with the right mouse button.

Dragging excluded volumes only moves them in the viewing plane. You can use View → Rotate → X 90 or View → Rotate → Y 90 to switch planes to one of the orthogonal planes.

To delete volumes, select them in the table and click Delete. You might want to delete volumes from the automated procedures that overlap with each other, for example. Deleting redundant volumes reduces the time required to apply these volumes when screening structures for matches to the hypothesis.

Excluded Volumes Dialog Box Features

Pick atoms to create excluded volume option

Select this option to start picking atoms in the Workspace to define an excluded volume. To create an excluded volume on an atom, click on the atom. To create an excluded volume at the centroid of a set of atoms, click on the first atom, and shift-click on the subsequent atoms. A sphere with the default radius is placed at the centroid and is moved to the new centroid at each pick. The atoms in the current set are marked with small spheres. If you want to remove an atom from the set, control-click the atom.

Radius text box

Specify the default radius for new spheres. You can edit the radius later in the table.

Pick excluded volumes to translate option

Select this option to pick and drag excluded volumes to a new location in the Workspace. You can only move them in the current viewing plane, so to move them in other planes you must rotate the hypothesis. You can move multiple excluded volumes by selecting them with shift-click, then dragging.

Create volumes for buttons

Create excluded volumes using an automated procedure based on atoms in one or more structures. Each button opens a dialog box in which you can set up and run the procedure. The excluded volumes are appended to the Volumes table. The buttons are:

Volumes table

Lists the excluded volumes for the hypothesis. You can edit the values in the cells to change the coordinates or radii of the spheres, and you can select multiple spheres in the table to apply an action.

Delete button

Delete the excluded volumes that are selected in the volumes table.

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