Module: Tube View ()

Description:

With the Tube View module you can connect an arbitrary set of consecutive atoms with a tube through interpolated atom coordinates. To define the atom set, you can use atom expressions. The order with which the atoms are connected is determined by their sequence.

Selecting and Highlighting: Parts of the molecule can be selected by clicking onto specific regions in the selection mode (you can switch to the selection mode of the viewer by pressing the ESC key). A detailed description of the selection concept can be found in the section visualization of molecules. Selected structures will be highlighted in the color that you choose in the port Highlighting Color.

Connections:

Data [required]
The molecule you want to be shown.

Ports:

Display Options

Part

This port lets you enter an atom expression. The atom expression will determine the set of atoms that will be connected. The default value is backbonereduced, which means that the tube will indicate the location of polypeptide and RNA/DNA backbone atoms.

To restrict the display to just a few atoms it is more convenient to use the filter that can be accessed with the Selection Browser. To include atoms in the sequence to be shown it must be active in the set defined by the atom-expression as well as the filter.

Distance Cut Off

All atoms that are further away than the specified value will not be connected.

Radius

This port specifies the radius of the tube.

Complexity

This port specifies the complexity of the tube triangulation as well as the number of interpolation points to be added between each atom coordinate. The higher the value the better the display quality but the slower the rendering.

Interpolation Method

The tube coordinates will be interpolated by using the atom coordinates as base points. This port lets you choose the interpolation method. B-Spline interpolation is generally smoother than cubic interpolation but the tube will not necessarily run through the atom coordinates.

Coloring

Coloring




You will find the description of the four ports above in the section on visualization of molecules.

Selection

Highlighting

This port lets you select tube sections with a lasso style selection mechanism or a ROI box.

Highlighting Color

Tube sections that belong to atoms that have been highlighted with the Selection Browser will be shown in this color.