Data visualization is a pivotal component of a structural biologist's arsenal. The Mol* Viewer makes molecular visualizations available to broader audiences via most web browsers. While Mol* provides a wide range of functionality, it has a steep learning curve and is only available via a JavaScript interface. To enhance the accessibility and usability of web-based molecular visualization, we introduce MolViewSpec (molstar.org/mol-view-spec), a standardized approach for defining molecular visualizations that decouples the definition of complex molecular scenes from their rendering. Scene definition can include references to commonly used structural, volumetric, and annotation data formats together with a description of how the data should be visualized and paired with optional annotations specifying colors, labels, measurements, and custom 3D geometries. Developed as an open standard, this solution paves the way for broader interoperability and support across different programming languages and molecular viewers, enabling more streamlined, standardized, and reproducible visual molecular analyses. MolViewSpec is freely available as a Mol* extension and a standalone Python package.

Department of Chemistry and Chemical Biology Rutgers The State University of New Jersey Piscataway NJ 08854 United States

National Centre for Biomolecular Research Faculty of Science Masaryk University Brno 625 00 Czech Republic

Protein Data Bank in Europe European Molecular Biology Laboratory European Bioinformatics Institute Hinxton Cambridge CB10 1SD United Kingdom

Research Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine Rutgers The State University of New Jersey Piscataway NJ 08854 United States

Research Collaboratory for Structural Bioinformatics Protein Data Bank San Diego Supercomputer Center University of California La Jolla CA 92093 United States

Rutgers Artificial Intelligence and Data Science Collaboratory Rutgers The State University of New Jersey Piscataway NJ 08854 United States

Rutgers Cancer Institute Rutgers The State University of New Jersey New Brunswick NJ 08901 United States

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