UCSF ChimeraX is a next-generation software for visualizing and analyzing molecular structures, density maps, 3D microscopy, and related data. It addresses challenges in handling large and diverse data sets from cutting-edge experimental methods, offering advanced rendering options and professional software design. The software provides interactive ambient occlusion, reliable molecular surface calculations, and supports various data types, including density maps, 3D imaging, and integrative hybrid modeling. ChimeraX is free for non-commercial use and available on Windows, Mac, and Linux. ChimeraX builds on the successful UCSF Chimera visualization system, which has been widely used in the scientific community. It offers an integrated multiscale modeling environment for researchers to interactively access, visualize, and analyze structural data across scales from atomic to cellular. It supports various data types, including protein sequences and hybrid-modeling restraints, using integrated tools that link disparate data types. ChimeraX uses standard software toolkits with advanced GPU capabilities and parallel computing to handle large data sets. ChimeraX includes features such as interactive ambient occlusion, molecular surface calculations, and new algorithms for depicting secondary structures. It also supports 2D plots that interact with 3D graphics, enabling efficient exploration of complex structures. The software integrates with external packages for more sophisticated analyses, such as Cytoscape for network visualization. ChimeraX supports virtual reality headsets, allowing immersive 3D visualization of molecular and cellular data. It uses the Qt windowing system for a native-like interface and supports HTML and command-execution links for easy access to functions and custom demos. The software is designed for extensibility, with a "toolshed" where developers can deposit and share new tools. ChimeraX is available for Windows, Mac, and Linux, and is open source and free for non-commercial use. It includes many capabilities from the predecessor Chimera, including interfaces to web services for electrostatic potential, ligand docking, comparative modeling, and multiple sequence alignment. New capabilities are under development for 3D light-sheet microscopy, model building in atomic-resolution cryoEM density maps, integrative hybrid modeling, and alternative depictions of multiple sequence alignments. ChimeraX is designed to handle large data sets efficiently, using memory-efficient data structures and high-performance algorithms. It supports various data formats, including mmCIF, and includes a hierarchical representation for integrative hybrid modeling. The software is also designed for community development, with a toolshed for distributing new tools and extensions.UCSF ChimeraX is a next-generation software for visualizing and analyzing molecular structures, density maps, 3D microscopy, and related data. It addresses challenges in handling large and diverse data sets from cutting-edge experimental methods, offering advanced rendering options and professional software design. The software provides interactive ambient occlusion, reliable molecular surface calculations, and supports various data types, including density maps, 3D imaging, and integrative hybrid modeling. ChimeraX is free for non-commercial use and available on Windows, Mac, and Linux. ChimeraX builds on the successful UCSF Chimera visualization system, which has been widely used in the scientific community. It offers an integrated multiscale modeling environment for researchers to interactively access, visualize, and analyze structural data across scales from atomic to cellular. It supports various data types, including protein sequences and hybrid-modeling restraints, using integrated tools that link disparate data types. ChimeraX uses standard software toolkits with advanced GPU capabilities and parallel computing to handle large data sets. ChimeraX includes features such as interactive ambient occlusion, molecular surface calculations, and new algorithms for depicting secondary structures. It also supports 2D plots that interact with 3D graphics, enabling efficient exploration of complex structures. The software integrates with external packages for more sophisticated analyses, such as Cytoscape for network visualization. ChimeraX supports virtual reality headsets, allowing immersive 3D visualization of molecular and cellular data. It uses the Qt windowing system for a native-like interface and supports HTML and command-execution links for easy access to functions and custom demos. The software is designed for extensibility, with a "toolshed" where developers can deposit and share new tools. ChimeraX is available for Windows, Mac, and Linux, and is open source and free for non-commercial use. It includes many capabilities from the predecessor Chimera, including interfaces to web services for electrostatic potential, ligand docking, comparative modeling, and multiple sequence alignment. New capabilities are under development for 3D light-sheet microscopy, model building in atomic-resolution cryoEM density maps, integrative hybrid modeling, and alternative depictions of multiple sequence alignments. ChimeraX is designed to handle large data sets efficiently, using memory-efficient data structures and high-performance algorithms. It supports various data formats, including mmCIF, and includes a hierarchical representation for integrative hybrid modeling. The software is also designed for community development, with a toolshed for distributing new tools and extensions.