PyMOL

PyMOL is a cross-platform molecular visualization system widely used in structural biology, bioinformatics and chemistry for viewing, analyzing and producing high-quality renderings and animations of biomolecules. It was originally created by Warren Lyford DeLano around the year 2000, and is now maintained and distributed by Schrödinger, Inc.. The name “PyMOL” reflects the program’s integration with the Python language (so “Py-” indicates Python) and its molecular visualization (-“MOL”).
PyMOL supports a wide variety of file formats (for example PDB coordinate files), allows interactive manipulation of molecular models (rotate, zoom, translate), supports many different representations (cartoons, ribbons, surfaces, sticks, spheres) and is scriptable via a command‐line or Python API—making it both flexible and powerful. Because of these capabilities it has become a standard tool in many labs for tasks such as examining protein structure, preparing publication‐quality images, visualizing docking results, or building molecular animations.
Though originally open source, parts of PyMOL are now under a commercial licensing model (with an “Incentive” version that adds extra support/features for paying users) while still providing an open source core. This hybrid model means that while many users (especially academic users) can access the software (or older builds) freely, organisations and commercial users often pay for full support/licensing.
In many respects PyMOL is valued for:

• Its ability to render elegant, high‐quality 3D images (for publications or presentations)
• Its scriptability, enabling automation or complex workflows in structural analyses
• Wide uptake in the structural biology community, meaning many tutorials, plugins and community contributions exist
• Cross‐platform support (Windows, macOS, Linux)
  For instance, beginner tutorials emphasise the three main components of the interface (display area, command line, and object menu) and note the ease with which users can explore structure, select atoms/residues, and create attractive output images or animations.