• MolViewSpec is an open standard for describing molecular scenes:
  • ribbons and atomic representations
  • pseudobonds and labels
  • volumes (density maps)
  • geometric shapes
• freely available [MIT license] as a Mol* extension [github] and a standalone Python package [github]
• collaboration effort by the PDBe, RCSB PDB, and National Centre for Biomolecular Research (NCBR)/Central European Institute of Technology (CEITEC) in the Czech Republic

MolViewSpec separates the creation of complex molecular scenes from viewer-specific details; the open standard enables extending viewers other than Mol*. A "MolViewSpec State" (MVSS) is a scene description.

Features currently include:

• specifying data source and format, with focus on PDBx/mmCIF, BinaryCIF, and PDB
• constructing molecular structures, including the specification of asymmetric unit, biological assembly, or crystal symmetry
• defining selections via predefined structure components (protein, ligand, nucleic acids, carbohydrates, etc.) or lists of atoms, residues, chains, or molecular entities
• specifying 3D molecular representations (cartoons, ball and stick, surfaces, etc.)
• volumetric data rendering (isosurfaces)
• labeling and coloring individual selections
• visualization of geometrical primitives (meshes, lines, spheres, distance/angle measurements, etc.)
• specifying coordinate transformations to enable superposition
• controlling camera position within the scene, allowing either a static viewpoint or automatic focus on a specific selection
• transitions between multiple views to create visual narratives

The MolViewSpec Mol* Viewer extension allows:

• loading a MolViewSpec State into Mol* by drag-and-drop or GUI menu
  
  
• including a link or embedded MVSS as part of the browser URL
  
  
• using JavaScript to specify or load MVSS into a Mol* instance embedded in external applications
  
  
• using a command-line utility to render MVSS as PNG or JPEG without a web browser

The MolViewSpec toolkit has three parts:

• MolViewSpec State JSON schema: defines the properties of individual nodes of the tree data structure stored in files with .mvsj and .mvsx extensions
• MolViewSpec API: provides a mechanism for building and validating MVSS stored in JSON format as defined by the schema. The API is available in Python and JavaScript/TypeScript.
• MolViewSpec Mol* Viewer extension implemented in TypeScript, for rendering MVSS in a web browser

MolViewSpec can installed from PyPi.

• [ interactive version ]

• [ interactive version ]

Several examples are available at the MolViewSpec website. Code for the examples is available on github.

• actively addressing community requirements as they arise
  
  
• standardizing molecular visualization color schemes (currently user-defined)
  
  
• supporting programming languages other than JavaScript/TypeScript and Python, e.g. Java or C#
  
  
• coordinating with developers of major 3D viewers like PyMOL and ChimeraX to facilitate MolViewSpec cross-platform support and enhance interoperability, allowing researchers to create consistent and reusable visualizations
  
  
• creating a user-friendly interface for building MolViewSpec States to broaden accessibility beyond the developer community