Module: H Bond View ()

Description:

The H Bond View module allows you to display hydrogen bonds using two different representations: dashed lines or tubes.

If the connected molecule does not contain information about hydrogen bonds, the bonds can be computed internally on the fly. These bonds will not be inserted into the original molecule.

A hydrogen bond is displayed using 5 differently colored parts called "sticks". The middle section represents the hydrogen atom that is being shared by the two atoms that this bond is connecting.

Connections:

Data [required]
The molecule whose hydrogen bonds should be displayed.

Continuous CM [optional]
Optional colormap used for mapping float data to colors.

Discrete CM [optional]
Optional colormap used for mapping discrete attributes to colors.

Ports:

Type

Selects the display mode: lines or tubes.

HBond Source

Selects the source from where the hydrogen bond information is taken. HBonds level means that the level 'hBonds' in the molecule is used. This only works if such a level has been computed beforehand. Compute means that the hydrogen bonds are computed internally. This makes sense when your molecule is part of a trajectory for which the hydrogens bonds may change between timesteps. With 'automatic' the level 'hBonds' is used if it exists and else the bonds are computed internally.

Advanced

Line Width

Specifies the width of the lines.

Complexity

Specifies the complexity of the tubes. Higher complexity will produce more attractive results, but will take longer to draw.

Tube Radius

Specifies the radius of the tubes.

Animation

Starts an animated view of the hydrogen bond when using the tube display mode. To visualize the sharing of the hydrogen atom between the two atoms, the middle section representing the hydrogen atom will move slowly back and forward in the two directions of the atoms involved in this bond.

Appearance

Coloring




For an explanation of the four ports above, see the description in the general section on display of molecules.