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ChemDoodle can also parse IUPAC names into structures. Round trip editing. Embed your data into Microsoft Office, Mac OS X applications, OpenOffice and others. Incredibly convenient and no need to save separate files. ChemDoodle contains all of the features you would expect from the most professional software and more.

ChemDoodle 3D

3D Chemical Graphics, Animations and Modeling

Click the play button to watch an introduction video

Main Features

ChemDoodle 3D is a powerhouse for working with chemistry in 3D with industry leading molecular modeling tools and best-in-class graphics.

• • We spend a very long time scrutinizing the graphics output in ChemDoodle 3D. Take a close look at the renderings as you are rotating them to watch bonds orient towards the camera; every object mesh in the scene is built to merge with the others; and our models are some of the most gorgeous generated by any software in this industry.

  • All of the rendering in ChemDoodle 3D is controlled by styles that are defined by you. The styles can apply to the entire scene, selected content or individual objects.

  • ChemDoodle 3D’s advanced 3D graphics engine can render text beautifully. Use this to show atom labels and more. You have full control over font, size and color.

  • In addition to the predefined Jmol, Rasmol, PyMOL and CDK color sets, you can also manually define your own elemntal color set to apply to molecule rendering.

  • Shadows

    Fully customizable, real-time, dynamic shadows add a major sense of realism to your graphics.

  • Define fogging using linear, exp1 and exp2 algorithms. Give incredible depth to your graphics or focus on specific sections with these features.

  • Include a compass on the bottom left of the graphic, or in the center overlaying the content to describe orientation.

  • Shaders are advanced instructions on how 3D graphics are generated. ChemDoodle 3D provides you with several built-in shaders to render your graphics, from realistic styles like plastic, to unrealistic styles like cartoon.

  • After effects are multipass shader options that provide additional graphical effects. Blurring and outlining are currently available.

  • Both orthographic and perspective projections are available and can be switched instantly.

  • You can quickly change between various quality levels to benefit graphics output or to speed up performance.

  • ChemDoodle 3D can generate a number of surface types and color functions for any number of atoms. Visualize the space of your structures in ways other editors cannot.

    You can customize mesh algorithms, display types, normals, colors and more.

    Different types of surfaces are available, including van der Waals (VDW), solvent accessible surfaces (SAS) and solvent excluded surfaces (SES, Connolly).

    Color your surfaces through various functions to provide a physical perspective on the structure. Functions include by atom color, charges (Gasteiger, QEq, QTPIE), lipophilicity (AlogP98) and molar refractivity (AMR98).

  • View atomic orbital models based on quantum numbers with the Orbitals widget. Many options are available for customizing the graphics, which can then be output to an image. A great way to view the different orbital shapes.

• Interact with your structures in real-time with advanced physical simulations

  Accurate Force Field Implementations

  Both the Universal Force Field (UFF) and Merck Molecular Force Field (MMFF98) are implemented. Our implementations are some of the most accurate and consistent in the industry. Quickly generate relevant 3D coordinates for your built structures.

  Real-time Optimization

  Choose from various optimization functions to minimize your energies including steepest descent, conjugate gradients, and BFGS, with several line search options. These optimization procedures can be run in real time (using the Minimizer widget) so you can interact with molecules while you are building them or easily change between conformations.

  Algorithm Transparency

  ChemDoodle 3D will automatically map atom types for you, and will let you know when a structure is not compatible with a force field. While optimizing structures, ChemDoodle 3D can render force vectors and atom types for reliability and referencing.

• • ChemDoodle 3D’s building controls are made to clearly model the atoms and bonds they manage. Copious visual feedback is provided. There are also many options for customizing the building tools to your preference.

  • Intuitive selection tools allow you to quickly trace, select and edit objects in 3D. For even more accuracy, use the Selector widget for a comprehensive organization of all the objects in the scene, allowing you to precisely investigate and select content.

  • 6 physically relevant bond types are provided to create any type of chemical representation. No other program compares.

  • ChemDoodle 3D renders multiple bonds that are able to orient themselves towards the camera for the most descriptive graphics.

  • When building 3D structures, ChemDoodle 3D will automatically suggest the best place in three dimensions to add an atom connection. This helps you quickly build molecules. You can then simply turn on the minimizer to optimize physical coordinates. No other program has an optimize zone like ChemDoodle 3D’s!

  • You have full control over how atoms and bonds are rendered, and you can quickly choose from predefined representations, such as van der Waals spheres, ball and stick, stick, wireframe and line.

  • ChemDoodle 3D’s advanced graphics engine can render text beautifully. Use this to show atom labels. You have full control over font, size and color.

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  • Hydrogens will be added for you to your structures in appropriate 3D locations.

  • Implicit hydrogens are automatically tracked for your structures, but you can also override them as appropriate.

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  • Use toruses for aromatic circles or use resonance bonds that automatically orient to the center of rings.

  • Perceive stereochemistry for 3D structures. CIP stereochemistry is determined for chiral centers and double bonds using our advanced and accurate CIP algorithms. Common cis/trans stereochemistry can also be determined for double bonds.

  • Quickly generate 3D coordinates for your structures using several algorithms.

  • Measure distances, angles and torsions in your structures.

  • Quickly access powerful functions to help modify your graphics: saturation, Kekulization, ring perception, distance geometry embedding, and more.

  • Search databases (PubChem, ChemSpider, ChemExper) for chemical structures and drag them right into your 3D scene using the MolGrabber widget.

• In addition to creating beautiful graphics for small molecule structures, ChemDoodle 3D will also help you to edit and create graphics for protein and nucleic acid macromolecules. The above image was rendered in ChemDoodle 3D of Protein Data Bank entry 5LRS with two solvent accessible surfaces rendered for the protein chains and using the None shader.

  • ChemDoodle 3D reads protein and nucleic acid information from PDB files and generates high quality meshes that are superimposed over the atom and bond coordinates.

  • ChemDoodle 3D also fully supports the RCSB Macromolecular Transmission Format for incredibly fast input of Protein Data Bank files with full bond order information.

  • Beautiful protein ribbons and traces are generated. Tubes, cylinder and plank models and cartoon models can also be generated. These models can be segmented, colored and completely controlled through styles. For instance, you can change the ribbon thickness or the alpha helix width.

  • Accurate nucleic acid ladder models are generated. These models can be colored and completely controlled through styles. For instance, you can change the backbone thickness or the platform height.

  • ChemDoodle 3D can use either a B-Spline algorithm or the Catmull-Rom algorithm for generating models. The Catmull-Rom spline creates more accurate models, but the B-Spline algorithm produces smoother and more aesthetic results.

  • Control residue atoms and bonds separately from the rest of the structures for unique graphics.

  • Show and hide water atoms defined in PDB files and represent them with stars instead of spheres.

• Unit cells are a great way to investigate repeating structures and crystals. The above image was rendered in ChemDoodle 3D of the zeolite Si-O framework, MFI, propagated along the z-axis with exponential fogging using the standard Blinn-Phong shader.

  • ChemDoodle 3D reads periodic data from CIF files and can fully resolve point groups and symmetries. Unit cells for any symmetry geometry are extracted.

  • Unit cells are rendered and supercells can be generated. Use an orthographic projection to get the best view.

  • Build armchair, zigzag and chiral nanotubes with several options. Periodic systems of nanotubes are automatically generated. A great way to output nanotube geometries for other applications.

• ChemDoodle 3D is designed to perform everywhere for everyone

  • High DPI Support

    Full support for high resolution displays, such as Retina Macs and the Microsoft Surface Pro.

  • Control interface colors, interface font sizes, define cursors and a cursor left-handed and right-handed mode make it comfortable for most users to use the software. You can also fully define all of the menu item accelerators (except the ones forced by the operating system) and tool shortcuts.

  • A ChemDoodle license includes access to our ChemDoodle Mobile app companion for iOS (iPod/iPhone/iPad), Android and other mobile devices.

  • ChemDoodle 3D works with several partners to help you improve your workflow. These partners include databases like PubChem, ChemExper and ChemSpider, ELNs such as LabArchives and social networking services like Twitter.

  • Quickly tweet your selected content from ChemDoodle 3D.

  • We are always adding new features, and our customers continuously enjoy new updates with great new innovative solutions and tools that they have requested. Your license entitles you to all updates.

  • Read and write many popular 3D chemical file types for working with the applications you use:

    Beilstein ROSDAL (.ros), Crystallographic Information Format (.cif), CHARMM CARD File (.crd), Chemical Markup Language (.cml), Daylight SMILES (.smi, .smiles), ChemDoodle 3D Scenes (.ic3), ChemDoodle Javascript Data (.cwc.js), IUPAC InChI (.inchi), MDL MOLFiles, both V2000 and V3000 connection tables (.mol, .mdl), MDL SDFiles (.sdf, .sd), RCSB MacroMolecular Transmission Format (.mmtf), RCSB Protein Data Bank Files (.pdb, .ent), Schrödinger MacroModel (.mmd, .mmod), Tripos Mol2 (.mol2, .ml2, .sy2), Tripos Sybyl Line Notation (.sln), XYZ Files (.xyz)

  • Write a large number of bitmap (also known as raster or pixel) images for use with other applications. Some formats have additional options, such as controlling output resolution in PNG, JPEG, and TIFF images.

    1. CompuServ Graphics Interchange Format {.gif}
    2. Joint Photographic Experts Group {.jpg, .jpeg, .jpe, .jfif, .jfi, .jif}
    3. Microsoft Bitmap {.bmp, .dib}
    4. Portable Network Graphics {.png}
    5. Tagged Image File Format {.tiff, .tif}
    6. UNIX Portable PixMap {.ppm, pnm, pbm, pgm}
    7. Wireless Bitmap {.wbmp}

  • Produce 3D ChemDoodle Web Components, which are high-quality, interactive, HTML5 components for websites and web apps that work in Microsoft Edge, Mozilla Firefox, Google Chrome, Apple Safari and Opera, and even on Mobile Safari on iOS and Chrome for Android.

  • All of the resources we use to develop the algorithms in ChemDoodle 3D or the choices we make for the software are documented in the Help menu. This way you can evaluate the quality of our work.

  • A thorough user manual is free to download. It is in PDF format, fully searchable with a fully linked table of contents and index.

A free trial for ChemDoodle 3D lasts for 14 days with some features restricted. The trial is not an obligation and we require no identifying or financial information to start a trial. After 14 days, the trial will no longer open. Our free trials are only for evaluation purposes and any output from the trial will contain a watermark and is copyright of iChemLabs.

To start your trial, simply download ChemDoodle 3D for your operating system below, install and open it. Then accept the EULA. The next page will ask for a license code, instead click the Free Trial button to begin.

System Requirements

• Windows Vista/7/8/10+, macOS 10.11+ (El Capitan, Sierra, High Sierra, Mojave, Catalina or more recent), or Linux.
• A 64 bit system is required (all modern systems are 64 bit).
• ChemDoodle 3D requires OpenGL v2+ drivers.
• A minimum of 1GB of memory.