PyMOL

PyMOL visualizes and animates three-dimensional biomolecular structures to support interpretation of molecular simulations, structure prediction, and protein design.

Key Features:

• 3D rendering and animation: Renders and animates atomic-resolution three-dimensional structures of biomolecules.
• Real-time simulation visualization: Updates molecular visualizations in real time to reflect simulation progress and structural changes.
• Rosetta integration via UDP sockets: Receives coordinate updates from Rosetta transmitted over UDP network sockets to enable inter-process communication.
• UDP socket listener: Listens on a UDP socket to accept incoming coordinate data streams from remote processes.
• Coordinate interpretation and update: Interprets incoming coordinate data and applies updates to displayed molecular structures.
• Remote execution support and energy visualization: Supports remote execution workflows by visualizing on-demand biomolecular structures and associated energy information.

Scientific Applications:

• Biomolecular structure visualization: Visualizes three-dimensional biomolecular structures for analysis of atomic arrangements.
• Structure prediction and design: Provides on-demand visualization during computational structure prediction and design of proteins and protein–protein complexes, including workflows with Rosetta.
• Simulation monitoring: Enables monitoring of structural changes during simulations by reflecting coordinate updates in real time.
• Energy interpretation: Displays energy information alongside structural updates to aid interpretation of simulation results.

Methodology:

Rosetta detects changes in protein structure and transmits new coordinates over a UDP network socket to a PyMOL instance running a UDP socket listener; PyMOL interprets the incoming coordinate data and updates the molecular visualization in real time.