A powerful solution for molecular modeling and 3D scientific graphics.

ChemDoodle 3D is developed by the same team that produces the popular and critically acclaimed ChemDoodle chemical drawing software. In addition to the vast amount of customizability and control that ChemDoodle tools offer for working with molecules and advanced scientific graphics, we focus on producing a compatible and portable solution that works everywhere. This includes simple installations and universal support so that ChemDoodle 3D serves you and not the other way around.

Packed with Features

ChemDoodle 3D contains thousands of features for working with molecules and scientific graphics. The main uses are listed below. Learn more by selecting the titles to the right.

Continuously Developed

We are always adding new features, and our customers continuously enjoy new updates with great new innovative solutions and tools that they have requested. Try a free trial today!

Major Features:

  • Beautiful graphics. The graphics in ChemDoodle 3D are of the highest quality, we urge you to compare them to other similar software tools.
  • Advanced graphics algorithms. ChemDoodle 3D contains cutting-edge graphics algorithms, including shadows, fogging, creative shaders, text and more.
  • Small Molecules. Many rendering options for atoms and bonds. Several bond types are available. Ball and Stick, vdW, stick, wireframe and line representations are predefined.
  • Surfaces. Generate fully customizable surfaces for groups of atoms. van der Waals, solvent accessible and solvent excluded (Connolly) surfaces are calculated with optional coloring functions.
  • Proteins. Ribbons, tubes, cylinder and plank and cartoon models. Residues can be individually colored and segmented. Many coloring options for custom models.
  • Nucleic Acids. Render ladders for nucleic acid models. Meshes can be controlled for custom models. Platforms can be individually colored.
  • Nanotubes. Build armchair, zigzag and chiral carbon nanotubes with advanced tools that will calculate various geometric data for you.
  • Periodic Systems. Periodic data can be represented through controlled unit cells which allow expansion to create super cells.
  • Thoroughness. ChemDoodle 3D contains all of the features you would expect from the most professional software and more. Found something missing? Tell us and we can add it.
  • Web tools. Build ChemDoodle Web Components for use in interactive and educational websites. Take full advantage of the upcoming HTML5 technologies with ChemDoodle 3D.
  • Comprehensive documentation. In addition to this website, ChemDoodle 3D comes with a thorough and free user guide on how to use ChemDoodle 3D.
  • Fully customizable. You can customize every last detail of the graphics, the modeling engine, and even how the application works.
  • Build Molecules in 3D. Intuitive tools to quickly build 3D molecules. No need to find pre-made files of your molecules before creating your graphics.
  • Real-time Interaction. Interact with your molecules in a physical simulation, see how movements of the atoms and bonds change the configuration in real-time.
  • Molecular Modeling Engine. An expert modeling engine has been created to work with molecules, with industry leading implementations of the UFF, MMFF94 and MMFF94s force fields.
  • Advanced editing system. Easily pick and edit atoms, bonds and molecules directly from your scene. Precise editing can be performed with the Selector widget.
  • Read and write chemical file types. Supports ChemDoodle 3D, MOLfiles, CML, CIF, SMILES, InChI, PDB, XYZ and others. Paste from ChemDoodle for even more file support!
  • Export to high resolution images. Write PNG, TIFF and other bitmap formats. Image transparency and resolution are supported where possible.
  • Full Graphical Control. You can specify any of the features of the graphics, including background colors, anti-aliasing, projections, lighting and more.
  • Shaders. Choose from different shaders for different visual styles from realistic to non-realistic. Industry leading algorithms are implemented for shadows, fogging, text and more.
  • Animations. Help visualize your graphics with continuous animations that you control to highlight specific features of your structures.
  • Easy Site Licenses. Quickly deploy activation codes to your users and easy to setup configurations for campus use make it a breeze to work with ChemDoodle 3D.
  • Multiplatform. Windows, Mac OS X and Linux are fully supported. Need to change operating systems? No problem, ChemDoodle 3D will come with you.
  • Affordable. Even the most cost conscious student can fit ChemDoodle 3D into his or her budget. Site licenses are affordable to any institution.