PyMOL
PyMOL is an open-source molecular visualization system. It can produce high-quality 3D images of small molecules and biological macromolecules such as proteins. PyMOL is designed for interactive visualization and generating publication-quality images and animations.
molecular-visualization
protein-structure
molecular-graphics
3d-structure
PyMOL: Open-Source Molecular Visualization System
PyMOL is an open-source molecular visualization system. It can produce high-quality 3D images of small molecules and biological macromolecules such as proteins. PyMOL is designed for interactive visualization and generating publication-quality images and animations.
What is PyMOL?
PyMOL is a popular open-source molecular visualization system created by Warren DeLano and currently maintained by Schrödinger. It is designed specifically for visualizing and animating 3D structures of small molecules and biological macromolecules such as proteins and nucleic acids.
Some key features and capabilities of PyMOL include:
- High-quality rendering and ray tracing for publication-ready images and movies
- Support for a wide range of molecular data file formats
- Interactive visualization with rotations, selections, coloring, etc.
- Measurement tools for distances, angles, surface areas, etc.
- Sequence and structure alignment capabilities
- Integrated Python scripting for automation and customization
- Plugins and library for advanced features like electrostatics and visualization of large structures
PyMOL can be used on Windows, Mac, and Linux systems. The intuitive GUI combined with flexible scripting has made it one of the most widely used platforms in molecular modeling, structural biology education, and molecular visualization in research publications and presentations.
Some alternatives with similar functionality include UCSF Chimera, VMD, Swiss PDB Viewer, and others. But PyMOL remains popular as a free tool for high-quality molecular graphics and flexible customization via scripting.
PyMOL Features
Features
- Molecular visualization and modeling
- High quality rendering
- Support for animations and movies
- Plugin architecture for extensibility
- Python scripting interface
- Command line interface
- Support for multiple structure alignment
- Measurement tools
- Session saving
Pricing
- Free
- Open Source
Pros
Powerful visualization capabilities
High quality graphics
Extensive scripting options
Cross-platform availability
Free and open source
Cons
Steep learning curve
Limited support and documentation
Some features only in paid versions
Can be resource intensive for large structures
Official Links
The Best PyMOL Alternatives
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