To help you get started, we've collected the most common ways that 3dmol is being used within popular public projects.

Autodesk / molecule-3d-for-react / src / components / molecule_3d.jsx View on Github

render3dMol() {
    if (!this.glviewer && Molecule3d.isModelDataEmpty(this.props.modelData)) {
      return;
    }

    const glviewer = this.glviewer || $3Dmol.createViewer(jQuery(this.container), {
      defaultcolors: $3Dmol.elementColors.rasmol,
    });

    const renderingSameModelData = moleculeUtils.modelDataEquivalent(
      this.oldModelData, this.props.modelData
    );
    if (!renderingSameModelData) {
      this.lastStylesByAtom = null;
      Molecule3d.render3dMolModel(glviewer, this.props.modelData);
    }

    const styleUpdates = Object.create(null); // style update strings to atom ids needed
    const stylesByAtom = Object.create(null); // all atom ids to style string
    this.props.modelData.atoms.forEach((atom, i) => {
      const selected = this.state.selectedAtomIds.indexOf(atom.serial) !== -1;
      const libStyle = libUtils.getLibStyle(

View more ways to use 3dmol

3Dmol.js

3Dmol.js is an object-oriented, WebGL accelerated JavaScript library for online molecular visualization.

Since 3Dmol.js is licensed under the permissive BSD open-source license, you are free to use it in any project, as long the code is properly acknowledged and cited.

With 3Dmol.js, you can add beautifully rendered molecular visualizations to your web applications. Features include:

• support for pdb, sdf, mol2, xyz, cif, cdjson, mmtf, prmtop, gro, pqr, cube, and vasp formats
• parallelized molecular surface computation
• sphere, stick, line, cross, cartoon, and surface styles
• atom property based selection and styling
• labels
• clickable interactivity with molecular data
• geometric shapes including spheres and arrows

See the documentation to learn how to use 3Dmol.js as a hosted viewer, embeddable viewer, or as a component of a larger application.

Examples

HTML

     
 
 <div data-surface="opacity:.7;color:white" data-style="cartoon:color=spectrum" data-pdb="4N8T" class="viewer_3Dmoljs" style="width: 400px; height: 400px;"></div>

JavaScript

We support the use of both PDB queries as well as PDB files.

First you simply create the viewer with a div's id.

var viewer = $3Dmol.createViewer($("#div"));

Then you can download a protein data bank model (here pdb:1MO8) and display it with the styling of your choosing.

$3Dmol.download("pdb:1MO8",viewer,{multimodel:true, frames:true},function(){
	viewer.setStyle({}, {cartoon:{color:"spectrum"}});
	viewer.render();
});

Surfaces

We also support the use of surfaces that are asynchronously loaded and support different color schemes

viewer.addSurface($3Dmol.SurfaceType.VDW, {
    opacity:0.85,
    voldata: new $3Dmol.VolumeData(volumedata, "cube"),
    volscheme: new $3Dmol.Gradient.ROYGB(range[1],range[0])
},{});

Shapes

The use of different shapes and styles is supported.

viewer.addCylinder({start:{x:0.0,y:2.0,z:0.0},
    end:{x:0.0,y:10.0,z:0.0},
    radius:0.5,
    fromCap:false,
    toCap:true,
    color:'teal'});
viewer.addCylinder({start:{x:15.0,y:0.0,z:0.0},
    end:{x:20.0,y:0.0,z:0.0},
    radius:1.0,
    color:'black',
    fromCap:false,
    toCap:false});

Documentation

Please check out our documentation at 3dmol.js. We have tutorials, as well as the stable release of the platform.

Contact

Please address any questions or concerns to dkoes@pitt.edu. You may also submit an issue on github.

Citing

If you use 3Dmol.js, please cite our Bioinformatics paper.

Funding

3DMol.js is funded through R35GM140753 (and previously R01GM108340) from the National Institute of General Medical Sciences. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute of General Medical Sciences or the National Institutes of Health.