Version History


April 30, 2017

Executive Summary

ChemDoodle 3D v3 is finally here! Build and play with your molecules in real time in 3D. Generate the best graphics for your scientific figures. This is the 3D chemistry software you have been waiting for! Check out all the new features below.


  1. Faster and more advanced shaders for the most realistic graphics or captivating cartoon rendering. There are now 6 shaders to choose from.
  2. Fully customizable and dynamic real-time shadow rendering.
  3. Molecules can now be built using intuitive tools and a continuous running optimization (using the new Minimizer widget) to allow you to build accurate models and the specific conformations you desire. It is a lot of fun to physically interact with the structures you build!
  4. New bond types, more aromatic ring representations, more cheminformatics functions.
  5. Distances can now be measured between any combination of bond centers and atoms; previously only atoms were allowed. Visual specifications for all shapes can now be independently edited.
  6. Fully customizable surfaces can now be built for selections of atoms.
  7. Selector tools have been added, and you can now select objects by lasso and rectangular marquee.
  8. Our interface engine is now fully implemented including drawing toolbars, widgets, autosaving, workspace control and more.
  9. Style sheets (and scene settings files) can now be created, saved and loaded.
  10. Quaternions can now be used for all rotations, instead of just X-Y axis rotation.
  11. Full support for the new RCSB Macromolecular Transmission Format.
  12. A more advanced copy and paste system.
  13. After effects are new multipass shader options that provide additional graphical effects. Blurring and outlining are currently available.
  14. Outlines are now rendered for highlighted and selected objects.
  15. Model settings in the Visuals panel in Preferences are now organized by model type.
  16. A new Custom Element Color Set. Color choosers have been upgraded and now affect graphics in real time. Improved MacOS look and feel.
  17. Added the last of the new element names recommended by IUPAC. Added more published van der Waals values.
  18. Polishing, new icons, and performance improvements affecting just about every asproect of the product, from picking to animations to rendering and saving images.


May 04, 2016

Executive Summary

This is a bugfix update mainly addressing HTTPS protocol issues with NIH Cactus and related issues.


January 19, 2016

Executive Summary

ChemDoodle 3D v2 is a massive update from the first version included in ChemDoodle 7 and can be used independently from ChemDoodle desktop. The graphics and data were the focus of this update. Protein and nucleic acid models can be loaded from PDB files and periodic systems can be loaded from CIF files in addition to small molecules. All of the graphics are customizable, including the models. More graphics capabilities include fogging and compasses. An entire advanced selection system has been implemented to select content by mouse, function or list. Enjoy and please spread the word!

New Features

  1. A Java installation is no longer required.
  2. Full Retina display support on Mac OS X.
  3. Support for high DPI Windows hardware.
  4. The visual specifications of the scene can now be applied to selected content, or individual objects, as opposed to the entire scene. Right-click on objects and select the Format… menu item to show visual options for that object. New representation quick buttons are now available for modifying residue atoms and bonds, ribbon models and nucleic acid models in addition to non-residue atoms and bonds.
  5. Protein and nucleic acid information can now be loaded from PDB files. Ribbon, trace and tube models can be generated for proteins. Ladder models can be generated for nucleic acids. The models are fully customizable. Control dimensions, alpha helix widths, coloring and more. Both B-spline and Catmull-Rom splines can be used to generate models. Water can be displayed as stars. Residue atoms can be controlled separately from hetatoms. Load PDB files by PDB id.
  6. Periodic data can now be loaded from CIF files. Unit cells of any geometry are resolved. Functions for periodic systems will be provided in the Periodic menu. Build supercells.
  7. An advanced selection system has been implemented. Select, deselect and reselect content. Select all, next molecule, inverse and by SMARTS. Use the new selection mode to select content or use the selection window to list the contents of the scene and select the content you wish to work with. The selection window is very advanced and will show you what you are currently hovering.
  8. Fogging can now be defined in scenes using linear, exp1 or exp2 algorithms. Fog color can be defined as well as fog ranges.
  9. A compass can be added on the bottom left of the scene or through the camera’s origin.
  10. 3D scenes can now be printed.
  11. Added quick quality options in the View menu to quickly switch between a range of higher and lower quality rendering settings to allow you to improve graphics or performance.
  12. Image export now allows for transparent backgrounds in capable image types. This allows you to easily use ChemDoodle 3D generated graphics in various media with custom backgrounds.
  13. Many new smaller features: added an option to remove shadows from text, added projection menu items, certified the correct 3D stereochemistry is generated from 2D drawings, picking can now handle any number of objects, and more.
  14. Updated to support ChemDoodle Web Components v7. Shapes can now be read/written using ChemDoodle JSON.
  15. Your iChemLabs account can now be accessed from ChemDoodle 3D. ChemDoodle 3D customers receive a free account for accessing ChemDoodle Mobile. If you also have ChemDoodle desktop, this is the same account.
  16. Dozens more improvements and additions.