ChemDoodle 3D

3D Chemical Graphics, Animations and Modeling

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Main Features

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

  • 3D Visualization

    A new perspective on chemistry

    • Beautiful Scientific Models

      We spend a very long time scrutinizing the models generated 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 gorgeously crafted by any software in this industry.

    • Completely Customizable

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

    • Advanced Text System

      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.

    • Custom Element Color Sets

      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.

    • Compasses

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

    • Projections

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

    • Mesh Quality

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

    • Transparency

      Transparency effects are just that, they let you see through objects in the scene. ChemDoodle 3D allows you to render transparent objects with or without back faces.

    • Surfaces

      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).

    • Orbitals

      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.

    • Gamma Correction

      Gamma correction alters the brightness model of the graphics to compensate for the non-linear brightness physics of your monitor. ChemDoodle 3D defaults to a standard value of 2.2, but you can change this as appropriate for your screen.

  • Art

    Easily create ultra-realistic images, sketches, cartoons, paintings and more artistic illustrations

    • Shader Programs

      Shader programs are advanced instructions sent to the graphics card on how 3D graphics are generated. ChemDoodle 3D provides you with several built-in shaders to render your graphics, to create realistic styles like plastic and unrealistic styles like cartoons. Shaders in ChemDoodle 3D also provide additional features, such as outlining and shadows.

    • Lighting

      Control the color and direction of the lighting.

    • Shading Model

      A shading model is the method for converting the scene information into colors implemented by the shader program. Ambient-Diffuse-Specular (ADS) theory can be implemented in many different ways to create shaders that produce realistic graphics and non-realistic graphics. ChemDoodle 3D implements the following shading model types to choose from, all based on the ADS shading model:

      • None
      • Flat
      • Cartoon
      • Gouraud
      • Phong
      • Blinn-Phong

    • Renderers

      A renderer is the complete procedure in which we communicate with the graphics card using one or more shaders to produce a final image. In the simplest procedure, a single call is made to the graphics card where we pass in the scene data and produce an image with a single shader program. This is what we call a forward renderer.

      The downside of a forward renderer, is each pixel is calculated in isolation, limiting the techniques we can achieve. We can instead chain several rendering passes through the graphics card together, using the output of one complete pass as input into another. This allows the software to produce some advanced effects.

      In ChemDoodle 3D, you will find styles for 3 different types of renderers: (1) the forward renderer (2) the deferred renderer and (3) after effects.

    • Anti-aliasing

      Anti-aliasing smooths out the rough pixel edges in graphics (known as jaggies). ChemDoodle 3D supports both hardware (MSAA) and software (FXAA) anti-aliasing.

    • Shadows

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

    • Fogging

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

    • Screen Space Ambient Occlusion

      Screen space ambient occlusion (SSAO) simulates the occlusion of ambient light in corners and crevasses of 3D objects. If you look in the corner of your room, it will appear slighly darker than the centers of the walls. This technique adds a significant amount of realism to the image and greatly helps with perception of topography. This technique is fully customizable in ChemDoodle 3D.

    • Outlining

      Outline effects are created by finding significant changes in cached data values from pixel to pixel. There are two types of outline algorithms provided in ChemDoodle 3D: Trace and Artistic. You can control colors, thicknesses, sketchiness and more!

    • Depth of Field

      A depth of field effect focuses in on a specific portion of your scene, emulating images made with camera lenses. You can define the beginning and ending focus depths as well as the extent of the unfocused blur and dilate effects.

    • After Effects

      After effects are advanced image filters. ChemDoodle 3D includes the following after effects:

      • Blur (Gaussian)
      • Blur (Kuwahara)
      • Blur (Median)
      • Dilate
      • Edge Detection
      • Pixelize
      • Posterize
      • Sharpen

  • Modeling

    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.

  • Small Molecules

    Build and visualize your molecules in 3D

    • Intuitive Controls

      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.

    • Advanced Selections

      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 Bond Types

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

    • Smart Bonds

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

    • Optimize Zone

      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!

    • Balls and Sticks

      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.

    • Show Labels

      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.

    • Add Hydrogens

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

    • Implicit Hydrogens

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

    • Aromatic Representations

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

    • Stereochemistry

      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.

    • Optimize Structures

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

    • Measurements

      Measure distances, angles and torsions in your structures.

    • Cheminformatics Functions

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

    • Database Lookup

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

  • Macromolecules

    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.

    3D scientific graphics, big and small!

    • Protein Data Bank Format

      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.

    • Macromolecular Transmission Format

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

    • Protein Ribbon Models

      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.

    • Nucleic Acid Ladder Models

      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.

    • Interpolation Algorithms

      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.

    • Residue Atoms and Bonds

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

    • Water

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

  • Periodic Systems

    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.

    Infinitely repeating chemistry

    • Crystallographic Information Format

      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 and Extrapolated Supercells

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

    • Nanotubes

      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.

  • Universality

    ChemDoodle 3D is designed to perform everywhere for everyone

    • Operating Systems

      Fully supported on Windows, macOS and Linux.

    • High DPI Support

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

    • Accessibility

      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.

    • Mobile Devices

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

    • 3rd Party Integration

      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.

    • Twitter Integration

      Quickly tweet your selected content from ChemDoodle 3D.

    • 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. Your license entitles you to all updates.

    • Chemical Files

      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)

    • Bitmap (Raster, Pixel) Images

      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}

    • Web Components

      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.

    • References

      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.

    • Thorough Documentation

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


Windows interface
macOS interface
Linux interface
Interface: Building a molecule
Interface: Working with Protein Data Bank entry 3N4B
Interface: Generating a chiral carbon nanotube
Different models rendered for the Protein Data Bank entry 1CRN
Different surface representations for the antibiotic ampicillin
A ball and stick representation of aspirin, with several measurements shown
Visualizing the internal channels of the zeolite LTA, using a molecular surface on the (-1->1) supercell, with two distances measured and rendered with a Blinn-Phong shader
A MMFF94 optimized model of sildenafil shown with aromatic circles and a Connolly surface (QEq color function) rendered with the Cartoon shader
The PDB entry 5GZC, showing a ribbon trace through the ball and stick representation of the protein rendered with the Blinn-Phong shader
PDB entry 2NDO, with a grey background and slight fogging, tubes and stick models for the chain and a vdW model for the small molecule, rendered with the Blinn-Phong shader
PDB entry 3QDU, with 4 solvent accessible surfaces surrounding each chain, rendered with the Phong shader
PDB entry 5F60, rendered with a cartoon shader, showing a vdW surface on the largest small molecule, with line and ribbon rendering for the chain, slight fogging and labels shown in an artistic style
PDB entry 3N4B with flat ribbons in rainbow color, rendered with a "none" shader, with SSAO on and SSAO blur off (to show a pastel pad texture), and a sketchy outline added to produce a nice hand-drawn effect
An acetaminophen molecule with Connolly surface, with water molecules in the background blurred with a depth of field technique
PDB entry 2POR, rendered in an artistic outline, with soft strokes and increased thickness closer to the camera
PDB entry 3N4B with a Taylor amino acid color set, with a Kuwahara blur on top of a depth of field technique, to create a water painting look where colors bleed into each other
A spacefilling model of PDB entry 3N4B, rendered with SSAO and a Kuwahara blur to produce an oil painting effect
The drug paxil, rendered with a cartoon shader and trace outlines
A realistic looking spacefilling render of PDB entry 6U4V, made to look like a plastic model, with SSAO, shadows and a high shininess value
A ball and stick model of molecule DDT, rendered with SSAO and shadows
A spacefilling model of molecule DDT, rendered with SSAO and shadows
Showing how shadows and SSAO greatly benefit topography percecption for PDB model 2POR
General preferences
Styles Preferences
Advanced preferences

Try ChemDoodle 3D before you buy

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.

When you are ready, you may purchase a ChemDoodle license here:

Version 6.0.0

Version History


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.