Path Analyzer Reference#

This reference complements the main Path Analyzer page. It contains one page per Path Analyzer analysis type, with the required inputs, supported card views, interpretation advice, and practical tips.

Path Analyzer

Geometry#

Angle: measure a three-group angle along a path.
Dihedral: measure a four-group torsion angle along a path.
Distance: measure centroid or minimum distances between two groups.

Structural and Trajectory Observables#

Asphericity: monitor how far a selected group deviates from a spherical shape.
Contact persistence: inspect which contact pairs remain present over time and how persistent they are.
Contacts: follow the number of contacts over time and inspect pair occupancies in a contact map.
Ramachandran: inspect phi/psi conformational states of protein residues.
Radius of gyration: monitor compactness of a selected group.
RMSD: track structural deviation relative to the first frame after fitting.
RMSD (pairwise): compare every frame with every other frame.
RMSF: compute the fluctuation profile of the measured features after fitting.
SASA: track solvent-accessible surface area.
Secondary structure content: follow alpha, beta, and unstructured fractions through time.
Shape parameter: inspect how elongated or flattened a selected group becomes.

Distribution and Density#

2D density map: combine two saved scalar analyses into a two-dimensional density estimate.
Density curve: estimate a smooth one-dimensional density from a saved scalar analysis.
RDF: compute the radial distribution function between two groups.

Energetics and Dynamics#

Average force: follow mean force magnitudes for a selected group.
Average velocity: follow mean velocity magnitudes for a selected group.
Energy: inspect potential, kinetic, or total energy along the path.
Energy landscape: project path energy onto two saved scalar analyses.

Comparative#

Custom scatter: compare two saved scalar analyses directly against each other.