Module: Molecule Measurement ()

Description:

This module lets you determine distances, angles, and dihedral angles between atoms of the molecule.

To obtain a measurement, you need to select the atoms that are to be examined. You can read more about selecting atoms in the documentation of the Molecule View and the Selection Browser. The order of the selected atoms is important for angles and dihedrals. It is determined by the sequence that the atoms were selected. If the Measurement module is connected to two molecules, the selected atoms of the first molecule come first.

Connections:

Module [required]
The molecule in which you want to take measurements.

Data2 [optional]
You can connect a second molecule. This allows you to take intermolecular measurements.

Ports:

The following ports will only be visible if you have selected two atoms for distance measurement, three atoms for angle measurement, or four atoms for measurement of dihedral angles.

Selected atoms

This port shows the indices and sequence of the atoms that are used for the measurement. If two molecules are connected it also shows the index of the molecule (1 or 2).

Options

This port is visible if your base molecule is derived from a trajectory. If you activate the toggle, not only the measurement of the currently active time step, but also the mean value of the complete trajectory and its standard deviation will be evaluated. For large trajectories this may take some time as all atomic coordinates have to be loaded for each time step. So if you do not need this option, leave it unchecked.

Angle

This port shows the value of the measurement. For two selected atoms, this is the distance; for three, the angle; and for four atoms, their dihedral angle. (The dihedral angle is defined as the angle between the two planes determined by the first three selected atoms and the last three selected atoms). The distance is given in angstroms, the angles in degrees.

Time-Mean

This port is visible if your base molecule is derived from a trajectory and the Time-mean toggle is activated. It will show the mean value of the measurement by determining the arithmetic mean over all molecules that are part of the trajectory. In addition, the standard deviation of the time-mean will be shown.

Time Plot

Like the time-mean port, this port is only visible for trajectories. By pressing the Show button you can see the plot of the measurement against the time steps of the trajectory. The vertical line of the plot indicates the position of the currently shown time step. The horizontal lines show the mean and the standard deviation.

Selection

With the Clear button you can deselect all atoms.

Observable

Observable Name

If the molecule is part of a trajectory, then you can create an observable of the measurement, that contains the value of the measurement for each time step. This observable will be added to the trajectory data object. The observable's name needs to be entered in the text field.