Module: Mean Molecule ()

Description:

This module computes the mean molecule of a molecular trajectory by averaging the atom positions. In order to do this, the molecules need to be transformed to a common coordinate system. This can be done either by aligning all time steps to some reference molecule, or by computing transformations with the Precompute Alignment module.

Press the Apply button to start the computation.

Connections:

Data [required]
Molecular trajectory for which the mean molecule should be computed.

Align Master [optional]
In order to compute the mean molecule, all molecules of the trajectory need to be aligned with respect to a certain molecule. This is done by right-clicking on the white square of the module icon in the Project View, selecting Align Master, and connecting it to a molecule in the Project View.

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

Ports:

Time Steps

Specify the range of molecules used for the computation.

Option

Select this option if you want to iteratively improve the mean molecule.

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.