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Clipping Planes Window |
The Clipping Planes window is located in the lower-right corner of the Workspace. By default, it is not displayed. You can display it by choosing Window → Clipping Planes.
"Clipping" is used to automatically limit the parts of a structure that are displayed in the Workspace. This is done by defining clipping planes, and displaying only the parts of the graphical image that are between these planes. Anything that is in front of or behind these planes is not displayed. Clipping can be useful when working with large structures containing many atoms, in which it can be hard to see certain atoms and even harder to pick those atoms.
The display in the clipping planes window consists of the following features:
Top view of structures: A representation of the structures in the Workspace, drawn in the wire frame representation. The view of the structures is from the top, that is, from the positive y direction looking down to the negative y direction. Thus, the back of the structure is in the upper part of this window while the front is in the lower part of this window.
Translation in y doesn't affect the display, but x and z-translation moves the displayed structures.
By default, the structures are displayed at the same size regardless of zoom. You can, however, zoom in on the top view by setting a preference in the Preferences panel, to zoom in on the top view whenever zooming in the Workspace.
Clipping planes: These are horizontal lines that mark the planes where the graphical image is clipped. The lower line marks the plane that is closest to the viewer, and the upper line is furthest from the viewer. The planes can be moved by dragging the horizontal lines.
To move both planes simultaneously in the same direction (i.e. in parallel), hold down the CTRL key and drag one of the planes or use the mouse wheel, or use the = and - keys.
To move both planes in opposite directions, hold down the SHIFT key and drag one of the planes or use the mouse wheel, or use the F and G keys.
You can also move the clipping planes by using the View → Move Clipping Planes menu, which also has items to adjust the clipping planes to show all atoms, the selected atoms, or the ligands.
The clipping planes are automatically adjusted with any of the following actions:
All but the first of these are controlled by a preference in the Workspace – Clipping planes tab of the Preferences panel. To zoom out again, ensure that nothing is selected in the Workspace, and perform a fit to Workspace.
Viewing volume indicator: This is a green box that represents the viewing volume. As you zoom in on the structure, the box shrinks. If you have perspective enabled, the viewing volume box is trapezoidal, with the small side at the bottom.
Clipping can be applied selectively, as well as to all graphical objects. To choose what clipping is applied to, right-click in the clipping planes window and make your choice from the shortcut menu that is displayed. The choices are:
All—Apply clipping to all objects (structures and surfaces). Clipping planes are drawn as horizontal orange lines, and can be adjusted by dragging.
Surfaces— Apply clipping to surfaces but not to structures. There are four clipping planes: front, back, left, and right. These planes are drawn as horizontal and vertical purple lines, and can be adjusted by dragging.
If you want to clip individual surfaces, you could instead consider using the Limit feature for the surface. See the Limit Surface Panel topic for more information.
Surfaces to selected atoms— Apply clipping to the surfaces using a cube centered on the selected atoms. For example, you might select just the ligand in a ligand-receptor complex, and the surface will be clipped to a cube that contains the ligand. The outline of the cube is displayed in cyan. You can resize the cube by dragging horizontally.
Selected atoms—Apply clipping only to the selected atoms. For example, you could select the receptor in a complex, and leave the ligand unclipped. Clipping planes are drawn as horizontal cyan lines, and can be adjusted by dragging.
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