RMSD
Tracks structural drift from a reference. A stable plateau is often reassuring; a continuing climb deserves inspection.
Trajectory analysis
Analysis turns motion into evidence.
PyMACS generates stability metrics, flexibility plots, compactness traces, contact maps, interaction summaries, ligand-centered network diagrams, and figurebooks.
RMSF
Reports residue or atom flexibility. Peaks often indicate loops, termini, or contact regions that move substantially.
Rg
Measures compactness. It helps detect expansion, collapse, or large-scale breathing behavior.
Contacts
Identifies residues near the ligand or partner over time, separating persistent interactions from brief encounters.
Output gallery
Representative PyMACS analysis products.
Protein RMSD
Tracks global backbone stability after alignment. A plateau usually suggests the protein has settled into a stable conformational regime.
Ligand RMSD
Shows whether the ligand preserves its starting binding pose, samples nearby sub-poses, or leaves the pocket.
Radius of Gyration
Measures compactness for the protein, ligand, and full complex as the trajectory evolves.
Contact Frequency
Ranks binding-pocket residues by how persistently they contact the ligand across the sampled trajectory.
Interaction Heatmap
Summarizes how interaction types and residues distribute through time.
NETWORX Panel
Converts contact tables into a ligand-centered network view for interpretation and reporting.