Over 10,000,000 page views! Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only web application utilizing jQuery, a Java applet, a stand-alone Java program (Jmol.jar), and a "headless" server-side component (JmolData.jar). Jmol can read many file types, including PDB, CIF, SDF, MOL, PyMOL PSE files, and Spartan files, as well as output from Gaussian, GAMESS, MOPAC, VASP, CRYSTAL, CASTEP, QuantumEspresso, VMD, and many other quantum chemistry programs. Files can be transferred directly from several databases, including RCSB, EDS, NCI, PubChem, and MaterialsProject. Multiple files can be loaded and compared. A rich scripting language and a well-developed web API allow easy customization of the user interface. Features include interactive animation and linear morphing. Jmol interfaces well with JSpecView for spectroscopy, JSME for 2D->3D conversion, POV-Ray for images, and CAD programs for 3D printing (VRML export).


  • Active, helpful, world-wide user group; approximately 100,000 downloads/year
  • HTML5/canvas graphics for all modern browsers, including iOS and mobile
  • Extremely low footprint option (50K) for simple interactive structure display
  • Additional server-side Java, stand-alone Java, and signed Java applet options
  • Full crystallographic symmetry capability
  • Load many surface formats and creates and displays surfaces on the fly
  • Easily customizable web-based interface compatible with (and requires) jQuery
  • Well documented scripting language with over 1000 tokens
  • Reads over 60 file formats, including PyMOL (PSE) session files
  • Creates highly compressed (300:1) surface files from volumetric (CUBE) data
  • Exports to GIF, JPG, PNG, PDF, WRL, POV-Ray, OBJ formats
  • Uses customized, optimized Java-to-JavaScript compilation for pure HTML5 app
  • Generalizable JavaScript library for Swing and PDF export in client-side JavaScript
  • JSpecView module features:
  • Reading of JCAMP-DX, CML, AnIML formats
  • Interactive real and predicted 1H NMR spectra
  • Interactive IR, Raman, NMR, GC/MS, UV/VIS spectra
  • Spectra generated in PDF format

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User Ratings

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User Reviews

  • Excellent very well written no bugs and gives solutions the way it supposed to. Very useful tool for understanding molecules.

  • A great software for displaying proteins (usually from RCSB PDB files in my case). Has an easy-to-learn scripting language to select and color stuff. You can also easily do stuff like show the secondary structure as a cartoon (instead of showing single atoms). If you like this AND the internet, take a look at JSMol as well. We use that on the PTGL protein topology web server. Suggestion to the authors: add some cool view presets to the menu (if a suitable molecule is loaded), so new users can more easily see how cool the software is. Something like "View => Presets => Secondary structure colored by SSE type".

  • Thanks for Jmol, it's wonderful!

  • Thanks for great project! Simply the best.Good,good,good.+1

  • very good project, thanks!Good,good,good.+1

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