PyMOL

PyMOL is a specialized program for 3D molecular visualization. It lets you analyze and display the structures of proteins, nucleic acids, and other biomolecules, with advanced rendering tools.

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• 3D visualization. PyMOL generates three-dimensional representations of molecular structures from X-ray crystallography, nuclear magnetic resonance, or computational model data. Molecules can be displayed in different styles such as spheres, sticks, cartoons, or surfaces.
• High-quality rendering. PyMOL's ray-tracing engine produces images with configurable shading, transparency, and lighting effects. Images can be exported as PNG files with custom resolution settings.
• Structural analysis. Includes tools for measuring atomic distances, bond angles, and dihedral angles. Can also display electron density maps loaded from external files.
• Animations. Lets you create animated sequences of molecular motion, conformational transitions, or simulation trajectories. Movies can be exported as image sequences or MPEG files.
• Python scripting. PyMOL integrates a Python interpreter for automating tasks with scripts. Users can develop custom functions and commands using the program's API.
• Format support. Reads standard formats such as PDB, mmCIF, SDF, and MOL2. It can also load structures and trajectories produced by molecular dynamics packages.
• Surface generation. Calculates molecular surfaces and solvent-accessible surfaces. Represents electrostatic properties through potential maps, using the built-in tools or the APBS plugin.
• Alignment tools. Aligns multiple structures by superimposing their backbones or specific regions. Calculates RMSD values to compare conformations.
• Secondary structure display. Automatically assigns secondary structure elements and shows them with customizable color schemes. Can also display hydrogen bonds and other polar contacts.
• Presentation mode. Offers scenes and a presentation mode for building slide-style sequences with labels and visual effects. Lets you control the visibility of objects in real time.
• Extensions and plugins. Supports plugins and external scripts for added functionality, such as electrostatics calculation, structure modeling, and integration with other bioinformatics tools.

PyMOL was originally developed by Warren Lyford DeLano and first released in the early 2000s. The source code is written mainly in C and Python, with components optimized for graphics processing. DeLano Scientific LLC maintained the project until DeLano's death in 2009, after which Schrödinger acquired it. Schrödinger continues to develop and distribute PyMOL commercially, while the open-source version remains available under a permissive license. Today, PyMOL is used in pharmaceutical research, bioinformatics, and university teaching.

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