Module: Rank Time Steps ()

Description:

This module takes an object of type Molecule Trajectory as input and either sorts all molecules in the trajectory or selects a single molecule from the trajectory. Selection and sorting can either be done using the observable values of the trajectory or the rmsd value in comparison to a specific molecule, which then needs to be connected to the module.

The module is, e.g., very helpful in conjunction with the module for the computation of the Mean Molecule. It allows you to find the time step in the trajectory that best approximates the mean molecule.

Press the Apply button to start the search (and sorting). When pressing the button for the first time, a new object of type Molecule, connected to the trajectory, will be added to the Project View. This molecule is used to set the index of the molecule with min value, max value or according to the index of the sorted list.

Connections:

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

Align Slave [optional]
This connection is only required if you want to search the trajectory according to the rmsd value with respect to a reference molecule. If the reference molecule has a different topology than the time steps of the trajectory, an atom correspondence is needed for the alignment and the rmsd computation. To define this correspondence, one needs a selection in the align master and the align slave, where the align slave should be a time step of the trajectory.

Align Master [optional]
This connection is only required if you want to search the trajectory according to the rmsd value, since then you will need a reference molecule.

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.

Ports:

Sorted Timesteps

This slider allows you to step through the time steps after sorting. Time step 0 is that having the minimal value.

Search Option

Search Option

The two options allow you to specify which kind of value, root mean square deviation (rmsd) or some observable value, should be used for ranking the time steps of the trajectory. The observable type needs to be further specified by the Observable port.

Sorting

Three options are possible. The first two allow you to search for a single time step with either minimum of maximum value. The last option, all sorted, gives you the most flexibility and is therefore the default.

Observable

This port allows you to select the observable you are interested in.

Alignment



The three ports above specify how the molecules are transformed before computing the rmsd value. See the description in the general section on alignment of molecules for a detailed explanation.