PyMOL

PyMOL visualizes biomolecular structures and generates publication-quality images to support structural analysis and communication of protein molecular structures.

Key Features:

• Extensive Shortcut Collection: The pymolshortcuts repository contains 241 Python functions ("shortcuts") that extend PyMOL's functionality.
• Functional Clustering: The shortcuts are organized into 25 functional groups to streamline retrieval and categorization.
• Innovative Molecular Representation Styles: A subset of shortcuts produces new molecular representation styles for visualization and structural analysis.
• Automated File Management: Shortcuts automate file saving by appending timestamps to filenames to prevent overwriting and standardize output.
• Web Integration: Shortcuts enable submission of search terms from PyMOL to a web browser to access online resources relevant to structures.

Scientific Applications:

• Structural visualization: Generation of detailed images and alternative representations of biomolecular structures, including proteins.
• Representation-driven analysis: Use of custom molecular representation styles to highlight structural features for analysis and presentation.
• Workflow automation: Automation of routine tasks such as timestamped file saving to support reproducible file management.
• Online resource linkage: Programmatic submission of queries to web resources to facilitate retrieval of external structural information.
• Productivity for analysis: Reduction of repetitive command assembly to allocate more researcher time to interpretation and analysis.

Methodology:

Development consists of creating Python functions that extend PyMOL; these functions are organized into functional groups and invoked by name at the PyMOL command prompt.