Module: Molecule View ()

Description:

The Molecule View allows you to display molecules in three different representations: atom spheres, wire frame, and ball-and-stick. For each of these representations there are two Quality modes, fast and correct.

Atoms can be colored according to the groupings defined on the molecule, e.g., atoms, residues, and chains. Moreover, the displayed part of the molecule can be restricted by using the selection browser as well as by interaction in the viewer.

In addition to just visualizing molecules, this module provides tools that facilitate interaction with the molecule. For example, you can select atoms to find out which index they have and which group they belong to. The ability to select atoms is also a precondition for the alignment procedure described in the section on aligning molecules.

In order to measure distances and angles in the molecule, right-click the Molecule View in the Project View, which will open a popup menu with the entry Molecule Measurement.

Connections:

Data [required]
The molecule to be visualized.

Reference Molecule [optional]
A reference molecule must be connected if you want to study the alteration of the torsion angles from one time step of a molecular trajectory to another (see the Options port below for more information).

Continuous CM [optional]
The colormap that is used to map values of float attributes to colors.

Discrete CM [optional]
The colormap that is used to map values of discrete attributes, e.g., integers and strings, to colors.

Ports:

Mode

Select one of three main display modes: balls, sticks, or balls and sticks. The default is sticks.

Display Options

Quality

The appearance of the balls and sticks can be altered by selection of one of two different qualities, a fast mode and a correct mode. The fast mode shows sticks as lines and spheres by rendering a square with the image of the sphere. This permits the display of large numbers of spheres at interactive speed. However, showing the image of a sphere means the 3D expansion of the sphere in only two directions is taken into account. As long as none of the spheres intersect, there will be no visible difference between spheres drawn in fast mode and spheres drawn in correct mode. In the correct mode, spheres are represented by textured triangular meshes and sticks by cylinders. This port is not available when raycasted spheres options is selected in preferences and display mode is set to balls.

Options

Single radius: display all atoms with the same radius.
Bond type: display bond type, e.g., single, double, triple, or aromatic.
Torsion angles: display torsion angles by the use of a coil around the stick.

Atom Radius

If the option single radius is selected, the value given here will be interpreted as the sphere radius for all atom spheres. Otherwise, the value scales the van der Waals radius of the atom.

Bond Radius

Radius of cylinders representing bonds (only visible in correct display mode).

Twist Factor

Allows adjustment of the twist of the coil.

Coloring




The four ports above are described in the general section on visualization of molecules.

Selection

Method

This port provides functionality for selecting (or highlighting) atoms in the viewer window. For more information, see the description of the highlighting port in the general section on visualization of molecules.

Highlight Size

This port provides functionality for selecting the intensity of highlight.

Buffer

This port is the front end to a filter that determines the set of atoms being displayed by the Molecule View. The buttons are described in the section on visualization of molecules.

Commands:

setTextureAntiAliasing <value>
This command enables (1) or disables (0) antialiasing for the textures used in fast sphere mode. Antialiasing has no impact on the rendering speed. However, if antialiasing is enabled and you have many different colors, the generation of the textures might be considerably slower.