Module: Configuration Density ()

Description:

This module enables you to compute a probability density for the positions of atoms and bonds within a molecular trajectory. The input is an object of type Molecule Trajectory. As output either a scalar field or a color field is generated. In order to visualize the computed density you can, for example, apply the volume rendering module, Volume Rendering.

Since the time steps of the molecular trajectory can be arbitrarily rotated and translated, we must perform an alignment for each time step to fit it best to some chosen reference. This is done internally, but you must specify how the molecules should be aligned to each other. There are four options from which to choose. The first uses all atoms for alignment, which is the recommended option. In the second you can select a few atoms (see below for more information). The third and fourth use none and center of gravity alignment, respectively.

For the representation of the molecule two kinds of geometric objects can be used: spheres and sticks. Here, spheres represent the positions of the atomic nuclei and the sticks the existing bonds within the molecule. You can compute the density for sticks, atoms, or sticks and atoms.

Connections:

Data [required]
The molecular trajectory for which the density should be computed.

Align Master [optional]
The molecule to which each time step of the trajectory will be aligned.

Precomputed Alignment [optional]
Instead of aligning all time steps of a trajectory to the AlignMaster molecule, you can use a precomputed alignment to align the time steps.

Continuous and DiscreteColormap [optional]
These two colormaps are used for the color management of the computed volume, in case a color field should be generated.

Ports:

Time Steps

Specifies range of time steps for which the density should be computed.

Voxel Size

This value determines the size of a voxel, i.e., its height, width, and depth, of the field storing the probability density.

Grid Dimension

The dimension of the field grid resulting from the specified voxel size.

Output Options

Output Data

• Since for the computation of the grid dimension all molecules need to be aligned, for a long trajectory this might take some time. So it may not be desirable to recompute the grid dimension all the time. If you are interested in the size of the grid before invoking the computation of the field, the BBox checkbox must be checked. The bounding box of the field, including all alignments, will be computed on apply and from this, the grid dimension.
• Check the Field box to compute the field. If the grid dimension is not up to date, it will be computed first.

Field

This menu contains two options, Scalar Field and Color Field. Choose the first if you only want the density. If you choose the second option, in addition to the density, the color information will be stored according to the color scheme (see Atom Colors port).

Atom Colors

Determines how the field regions will be colored. For more information see the description of Color port in the section on displaying molecules.

Colormaps


These two colormaps are used to color the atoms and sticks according to the selected color scheme in Atom Colors. See the description in the section on display of molecules for a detailed explanation.

Define Color

The port is described in the section on display of molecules.

Alignment

The three ports above specify how the molecules are aligned to each other. See the description in the general section on alignment of molecules for a detailed explanation.

Shape Options

Shape

Choose the geometry used to represent the molecule. If you have a highly varying trajectory, the recommended shape is cylinders.

Radius Options

Use a unique radius for all atom spheres (fixed) or take for each sphere the van der Waals radius scaled by the value of port Atom Radius (atom class dependent).

Atom Radius

Radius of the atom spheres.

Bond Radius

Radius of cylinders representing bonds.