Advanced Molecular Visualization System

Introduction to PyMOL

PyMOL is an open-source molecular visualization system, maintained and distributed by Schrödinger. It excels in creating high-quality 3D structural images of small molecules and biological macromolecules, particularly proteins. Used globally by scientists, PyMOL is renowned for its ease of use and effectiveness in protein structure visualization. Explore mre at PyMOL GitHub.

Key Features of PyMOL

  • Cross-Platform Support: Compatible with Unix, Macintosh, and Windows, utilizing OpenGL and Python.
  • Atomic Selection and Editing: Facilitates centralized visualization and editing using arbitrary logical expressions.
  • Molecular Splitting/Joining: Dynamic manipulation of structures and reassembly, with standard file outputs like .PDB.
  • Cartoon Ribbon Rendering: Provides aesthetically pleasing and easy-to-create molecular cartoons.
  • Advanced Scripting: Control through scripts written in command language or Python for complex tasks.
  • High-Quality Rendering: Built-in ray tracer for enhanced depth and shadow effects in 3D scenes.

Applications and Services

  • Visualization Presets: Offers a variety of preset visualizations for different aspects of molecular scenes.
  • Artistic Rendering: High-resolution image rendering for presentations and publications.
  • Measurements and Analysis: Measures distances, angles, dihedrals, and evaluates molecular interactions.
  • Interactive Molecular Data Presentations: Assists in creating interactive molecular data for collaborative and educational purposes.


  • Molecular Object Editing: Creation and modification of bonds, atoms, residues, and chemical groups, with structure optimization using MMFF.
  • Output for Various Media: Direct export of PNG files for integration into presentation tools like PowerPoint.


Tags for PyMOL

  1. Molecular Visualization
  2. 3D Structural Imaging
  3. Protein Structure Analysis
  4. Scientific Rendering
  5. Interactive Molecular Presentations

Learn More about Molecular Visualization with PyMOL

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