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Path Analyzer#

Path Analyzer is a SAMSON app for exploring paths and molecular dynamics trajectories directly inside your document. It combines an Analysis Builder, an Analysis Tray, and an interactive dashboard so you can go from a selection to a useful plot in just a few clicks.

Use it to measure geometric observables, inspect structural changes, compare saved analyses, build density maps, and explore energy landscapes without exporting your data first.

Path Analyzer

Opening Path Analyzer#

After installing the Path Analyzer extension, open it from Home > Apps and choose Path Analyzer.

Path Analyzer works with paths already present in the active document. These paths may come, for example, from imported trajectories, from external tools, from conformations converted to a path, or from subset paths created inside Path Analyzer itself.

The main parts of the interface#

  • Analysis Builder: choose an observable, choose a path when needed, define selections, and add a new card.
  • Analysis Tray: keep reusable saved analyses that can later be combined into a Custom scatter, Density curve, 2D density map, or Energy landscape.
  • Dashboard: explore the resulting cards, move and resize them, change settings, and export them.

Typical workflow#

  1. Choose an Observable in the builder.
  2. Choose a Path when the analysis is path-based.
  3. Define the required targets. For example, two groups for Distance, a measured set and a fit set for RMSD, or saved analyses from the Analysis Tray for Custom scatter.
  4. Click the action button to create the card. The button label adapts to the selected observable, for example Add Time Series, Add Scatter, Add Heatmap, Add RDF, or Add Energy Landscape.
  5. Reuse the saved analysis later if you want to derive higher-level views from it.

How Path Analyzer interprets a selected group#

This is important: a selected group is not always converted the same way in every analysis.

  • In Angle and Dihedral, each selected group is converted to a single representative position. One atom gives one atomic position; a multi-atom group is reduced to its center of mass.
  • In Distance with the Centroids mode, each group is represented by its centroid, i.e. the simple geometric average of the atom positions.
  • In Distance with Minimum, Minimum along X, Minimum along Y, or Minimum along Z, Path Analyzer does not reduce the group to one point. Instead, it compares the full atom sets and takes the minimum pairwise separation.
  • In analyses such as RMSD, RMSF, Contacts, Contact persistence, and RDF, Path Analyzer generally works on the full selected atom sets rather than replacing each group by a single representative point.

This means that changing the size or composition of a selection can affect the result in very different ways depending on the chosen observable.

What Path Analyzer does especially well#

  • It keeps plots linked to the current path whenever the analysis is frame-resolved.
  • It automatically uses time on the x-axis when the path provides meaningful time values, and falls back to frame indices otherwise.
  • It lets you keep several complementary cards side by side, for example a Distance series, a RMSD series, and an Energy landscape built from those saved analyses.
  • It stays useful both for quick inspection and for publication-oriented export.

Interacting with the dashboard#

  • Clicking a point in a frame-resolved time series or scatter plot moves the source path to the corresponding frame.
  • Clicking a cell in RMSD (pairwise) moves the path to the later of the two selected frames.
  • Double-clicking certain plots selects the corresponding feature in SAMSON, for example a residue in a Ramachandran plot or a feature in a RMSF profile.
  • Brushing points can create a frame subset, and that subset can be promoted to a new path.
  • Cards can be moved and resized freely in the dashboard.

Card settings and export#

Each card can expose settings that are specific to the selected analysis:

  • axis titles
  • series colors
  • heatmap color scale
  • energy, force, or velocity units
  • energy component and energy view mode
  • Ramachandran background
  • current-frame indicator visibility
  • contour-line visibility and color for energy landscapes

You can export each card as:

  • CSV
  • PNG
  • SVG

Picking the right analysis#

Geometry#

  • Distance: follow a separation between two groups.
  • Angle: monitor a three-point angle.
  • Dihedral: monitor a torsion angle defined by four groups.

Structural and trajectory observables#

Distribution, density, and comparison#

Energetics and dynamics#

Tip

  • Start with scalar analyses such as Distance, RMSD, Energy, or Radius of gyration. They combine especially well later.
  • For RMSD and RMSF, choose the fit set deliberately: it defines what motion is treated as overall rigid-body motion and what motion is treated as internal change.
  • For Contacts and Contact persistence, use chemically meaningful root selections such as residues, ligands, domains, or chains, so the map and timeline remain readable.
  • For RDF, provide a path with valid unit-cell information when possible, since that enables a properly normalized g(r).
  • Use the Path Analyzer reference when you want details for one specific plot type.