PyMOL

PyMOL is an industry-leading, user-sponsored molecular visualization system built on an open-source foundation, maintained and distributed by Schrödinger. Hundreds of thousands of scientists worldwide rely on PyMOL to view, share, and analyze molecular data. Lightweight and fast, PyMOL delivers peerless visualization quality while offering the flexibility of Python-based development and broad scalability, making it the tool of choice for researchers working with proteins, nucleic acids, and other complex molecular structures.

PyMOL 3 represents a modern advance in molecular visualization and animation, introducing a redesigned interface and powerful new tools that make it easier than ever to produce publication-quality images, manage scenes, and create compelling movies that communicate the complexity of three-dimensional biological systems.

Publication-Quality Image Creation

• Highlight important interactions, helpful representations, and key labels for any area of interest within a structure
• Produce stunning ray-traced images that add depth and realistic shadowing to any molecular structure
• Generate consistent figures that are straightforward to reproduce and modify across projects

Scene Management

• Store snapshots of the current workspace as scenes for easy recall at any time
• Use convenient thumbnail previews to quickly distinguish between stored scenes at a glance
• Add scenes directly to the timeline to build movies in only a few clicks

Movie Creation and Animation

• Create visually stunning movies that convey the full complexity of three-dimensional molecular systems
• Use the new Timeline feature to produce basic movies quickly by adding scenes to the main camera track, or explore advanced controls to unlock its full potential
• Animate dynamic processes such as micelle formation, Cas9 inhibition, docking poses, and molecular binding events

New Interface Features in PyMOL 3

• Top Toolbar: Provides quick access to common actions including changing the selection mode, reorienting the camera, and launching various panels
• Scenes Panel: Allows users to rapidly store and recall workspace snapshots, now featuring thumbnail previews for at-a-glance recognition
• Contents Panel: A redesigned panel that displays all objects and selections currently loaded into PyMOL, with ASHLC buttons enabling users to show or hide representations, apply colors, find interactions, and perform a range of additional actions
• Timeline: A new tool used to interpolate between values, visualize changes over time, and create insightful movies that bring otherwise static molecular systems to life

Training, Documentation, and Community Resources

• An online certification course — Visualizing Science with PyMOL 3 — teaches users how to unlock the full power of movie making within PyMOL
• The PyMOL Wiki is a community-run support site offering detailed pages on features and commands, with additional resources and examples available in the Quick Links section
• Official documentation, support channels, and updates and releases are available through Schrödinger's platform

PyMOL is suitable for life science researchers across academia and industry who need high-quality visual representations of molecular structures for visualizing, analyzing, exploring, and interpreting complex biological data. As an open-source-based platform distributed by Schrödinger, it combines community-driven development with professional-grade support and training resources.