Installation

Unpack the TomoPlane into your extension directory. If you do not have an extension directory, create one and add it to Chimera using the "Locations" panel of the "Favorites / Add to Favorites" menu entry. TomoPlane must be a directory inside the extension directory.

The TomoPlane extension is invoked using the menu item "Tomographic cut plane" in the "Tools / Volume Data" menu.

Selecting a data set

Select a volume data set from the menu. Cut planes can be oriented initially along the xy, xz, or yz pair of axes. The initial size of the cut plane is taken from the size of the data volume. Click on "Create" to create the initial plane.

Moving the plane

The cut plane can be translated along its normal using the slider. Initially, it is positioned in the center of the data set, and the slider is scaled according to the data volume size.

The cut plane will show up as a model in the Model Panel. It can be manipulated using the mouse like any other model, and when it is moved relative to the map, it will reflect the different density levels.

If the cut plane is manipulated using the mouse, the slider will stay at the same position. Moving the slider will continue the motion at the new position of the cut plane. This allows you to position the cut plane at a point of interest and smoothly move it a predetermined range around it. The range of the slider can be changed by the text entry fields.

The position of the cut plane is indicated in the Tomo Plane dialog. The angular orientation is expressed in terms of the angles that its normal vector forms with the three coordinate axis of the volume data set. In addition, the position of the center of the cut plane in the volume data set's coordinate system is given.

Controlling the coloring of the plane

The representation of densities on the plane can be controlled by manipulating a set of markers on a histogram of the data sets values in the same way as in the Volume Viewer dialog (solid mode).

The plane itself is represented in Chimera in the same way as isosurfaces on volume data sets. This makes coloring somewhat inefficient.

Placing markers

In conjunction with the "Volume Path Tracer" tool, TomoPlane can be used to place markers restricted to the plane. This is activated by the check box "Place markers on place". Once the box is checked, the marker placement button defined there will place markers on the plane, not on the data density.