{
  "name": "Structural Biology Molecular Visualization Software Architectural Specifications",
  "description": "Comparative matrix of leading computational structural biology visualization frameworks, compiling rendering engines, Jupyter notebook integration mechanisms, primary input file formats, surface calculation capabilities, programmatic export types, licensing, and primary research workflows based on peer-reviewed methods papers and official developer documentation.",
  "page": "https://casrai.org/guides/py3dmol",
  "publisher": "CASRAI",
  "license": "https://creativecommons.org/licenses/by/4.0/",
  "dateModified": "2026-11-14T01:25:23Z",
  "temporalCoverage": "2015/2026",
  "spatialCoverage": "Global",
  "columns": [
    {
      "name": "Software Package",
      "unit": "",
      "description": "Name of the molecular visualization tool or library"
    },
    {
      "name": "Primary Developer & Institution",
      "unit": "",
      "description": "Lead research group, university, or organization developing the package"
    },
    {
      "name": "Graphics Engine",
      "unit": "",
      "description": "Underlying graphics API and rendering pipeline"
    },
    {
      "name": "Jupyter Integration Mode",
      "unit": "",
      "description": "Mechanism utilized for embedding views inside Jupyter notebooks"
    },
    {
      "name": "Key Coordinate Formats",
      "unit": "",
      "description": "Primary atomic structure and volumetric grid formats supported"
    },
    {
      "name": "Surface Algorithms",
      "unit": "",
      "description": "Client-side or native surface generation types supported"
    },
    {
      "name": "Standalone Export Formats",
      "unit": "",
      "description": "Autonomous output and image formats generated programmatically"
    },
    {
      "name": "Software License",
      "unit": "",
      "description": "Open-source or academic software distribution license"
    }
  ],
  "rows": [
    {
      "Software Package": "py3Dmol",
      "Primary Developer & Institution": "University of Pittsburgh (Koes Lab)",
      "Graphics Engine": "WebGL 1.0/2.0 via 3Dmol.js",
      "Jupyter Integration Mode": "Static HTML/JavaScript (Kernel-Free)",
      "Key Coordinate Formats": "PDB, mmCIF, SDF, MOL2, XYZ, PQR, CUBE",
      "Surface Algorithms": "VDW, MS, SAS, SES",
      "Standalone Export Formats": "HTML (write_html), base64 PNG (png())",
      "Software License": "MIT / BSD 3-Clause"
    },
    {
      "Software Package": "NGLView",
      "Primary Developer & Institution": "ASBMB / NGL Development Team",
      "Graphics Engine": "WebGL via NGL.js",
      "Jupyter Integration Mode": "Bidirectional ipywidgets (Active Kernel Required)",
      "Key Coordinate Formats": "PDB, mmCIF, GRO, TRR, XTC, DCD, MMTF",
      "Surface Algorithms": "Molecular Surface, SAS, Gaussian Surface",
      "Standalone Export Formats": "PNG, animated GIF, MP4",
      "Software License": "MIT License"
    },
    {
      "Software Package": "Mol* (Molstar)",
      "Primary Developer & Institution": "RCSB PDB, PDBe, CEITEC",
      "Graphics Engine": "WebGL2 / WebGPU via TypeScript Engine",
      "Jupyter Integration Mode": "WebComponent / molstar-python wrapper",
      "Key Coordinate Formats": "mmCIF, BinaryCIF, PDB, SDF, CCP4, DSN6",
      "Surface Algorithms": "Molecular Surface, Gaussian Surface, ED Density",
      "Standalone Export Formats": "PNG, MP4, glTF 3D mesh, State JSON",
      "Software License": "MIT License"
    },
    {
      "Software Package": "PyMOL Open-Source",
      "Primary Developer & Institution": "Schrödinger, Inc. / Community",
      "Graphics Engine": "Desktop OpenGL (C/C++ native)",
      "Jupyter Integration Mode": "External window or IPyMOL static PNG",
      "Key Coordinate Formats": "PDB, mmCIF, MOL, MOL2, SDF, CCP4, DX",
      "Surface Algorithms": "Connolly, Solvent-Excluded, Gaussian, VDW",
      "Standalone Export Formats": "Ray-traced PNG, VRML, POV-Ray, OBJ, PSE",
      "Software License": "Open-Source (Python-style / BSD-like)"
    },
    {
      "Software Package": "UCSF ChimeraX",
      "Primary Developer & Institution": "UCSF Resource for Biocomputing (RBVI)",
      "Graphics Engine": "Desktop OpenGL 3.3+ via Qt GUI",
      "Jupyter Integration Mode": "External GUI or REST chimerax-web interface",
      "Key Coordinate Formats": "PDB, mmCIF, MRC, CCP4, EM, BRIX, MTZ",
      "Surface Algorithms": "Solvent-Excluded, Molecular, Density Meshes",
      "Standalone Export Formats": "High-res PNG, TIFF, MP4, VRML, GLTF, STL",
      "Software License": "Free for Academic / Non-Commercial"
    },
    {
      "Software Package": "JSmol / Jmol",
      "Primary Developer & Institution": "Jmol Development Team",
      "Graphics Engine": "HTML5 2D Canvas / WebGL (Java transpiled)",
      "Jupyter Integration Mode": "Via jupyter-jmol extension",
      "Key Coordinate Formats": "PDB, CIF, MOL, XYZ, Gaussian, CUBE",
      "Surface Algorithms": "Connolly, Molecular Surface, Isosurface",
      "Standalone Export Formats": "PNG, JPG, Jmol Script (.spt), HTML export",
      "Software License": "GNU LGPL v2.1"
    }
  ],
  "sources": [
    {
      "title": "3Dmol.js: molecular visualization with WebGL (Bioinformatics)",
      "url": "https://doi.org/10.1093/bioinformatics/btu829",
      "accessed": "2026-11-13"
    },
    {
      "title": "3Dmol.js GLViewer API Reference and Documentation",
      "url": "https://3dmol.org/doc/GLViewer.html",
      "accessed": "2026-11-13"
    },
    {
      "title": "NGLView: An IPython/Jupyter widget to interactively view molecular structures and trajectories (Bioinformatics)",
      "url": "https://doi.org/10.1093/bioinformatics/btx789",
      "accessed": "2026-11-13"
    },
    {
      "title": "Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures (Nucleic Acids Research)",
      "url": "https://doi.org/10.1093/nar/gkab314",
      "accessed": "2026-11-13"
    },
    {
      "title": "The PyMOL Molecular Graphics System, Version 2.0 (Schrodinger, LLC)",
      "url": "https://pymol.org/",
      "accessed": "2026-11-13"
    },
    {
      "title": "UCSF ChimeraX: Meeting modern challenges in visualization and analysis (Protein Science)",
      "url": "https://doi.org/10.1002/pro.3998",
      "accessed": "2026-11-13"
    },
    {
      "title": "Jmol: an open-source Java viewer for chemical structures in 3D",
      "url": "http://jmol.sourceforge.net/",
      "accessed": "2026-11-13"
    }
  ]
}