Module: Generate Molecular Interface ()

Description:

This module generates a distance-based interface between two molecules or between groups of a chosen level of a single molecule. As results of the computation a Mol Surface and a distance field are generated. Each point on this surface has the same distance to the closest atom of both groups or molecules. Viewing the surface with the Molecule Surface View module allows you to access additional information contained in the surface (e.g., kind of closest atom or kind of group it belongs to). The distance field can be used to color the surface.

Press the Apply button to start the computation.

Connections:

Molecule A [required]
Molecule for which interfaces should be computed. In case of the computation of intermolecular interfaces, this is one of the molecules for which the interfaces should be generated.

Molecule B [optional]
Second molecule for the computation of the intermolecular interface.

Ports:

Distance To

Select the type of interface. Choosing the first option the distance to the van der Waals surface will be considered, otherwise the distance to the atom center, which results in an approximation of the Voronoi diagram.

Levels

This option menu allows you to choose the level of molecular structure for which the intramolecular interfaces should be generated. For example, you might want to compute atomic interfaces on a very low level, or you might just want to generate interfaces between functional groups on a higher level or even between secondary structures. This port disappears if two molecules are connected to the module.

Sampling Options

Voxel Size

Voxel size of the distance field, i.e., measure of discretization. The smaller the voxel size, the longer the processing time.

Cutoff Distance

Largest distance from an atom that should be considered in the algorithm. Points further away than the cutoff distance to any atom will not be considered in the computation.