We are pleased to introduce version 7.1 of our ChemDoodle 3D software. This update is free for all ChemDoodle subscriptions, Lifetime and Site licenses. Licenses are as little as $19, and we have a free trial available at: https://www.chemdoodle.com/3d


Different atomic surface, isosurface and molecular orbital representations in ChemDoodle 3D.

Executive Summary

ChemDoodle 3D v7.1.0 focuses on surfaces and volumetric data. Support for Gaussian Input and Cube files has been implemented. Isosurfaces, including molecular orbitals, can now be generated from Cube files. New smoothing algorithms and surface coloring options have been added. Other new features allow access to the right-click context menu directly from the Selector widget, more filetype options, and the ability to lock atoms and electrons within the optimization engine.


  1. ChemDoodle 3D now supports a new surface type, isosurfaces, in additional to atomic surfaces. Isosurfaces are input from volumetric data files, such as Gaussian Cube files, which are now supported. The volumetric data will be included and rendered as an isosurface or molecular orbital, but may also be used as data to color other atomic surfaces and isosurfaces within the scene. Please see chapter 9 of the user guide for detailed instructions.
  2. A much more advanced surface smoothing system has been implemented, leading to much smoother surfaces in the software. Included algorithms are 'Laplacian', 'HC' and 'Taubin'. 'Taubin' produces the best results without shrinkage, and is now the default. Please see section of the user guide for more information.
  3. More data-based coloring options have been added for surfaces, including 'white-black' and 'rainbow'. You now also have the ability to reverse the colors. Please see section of the user guide for more information.
  4. Gaussian Input files (.gjf, .gau, .gzmat, .com) are now fully supported in ChemDoodle 3D, including cartesian and z-matrix formats. Different atom ID types and variables are fully supported for both input and output.
  5. Gaussian Cube files (.cub, .cube) are both read and written, including molecular data and volumetric data. Volumetric data will be input as Isosurface shapes.
  6. Using the Minimizer widget, you may now lock atoms and electrons in the scene while performing optimizations. You are still able to move locked atoms and electrons, but the opitimizer will preserve those coordinates during energy minimization. Please see section of the user guide for further instructions.
  7. Shapes and surfaces can be shown or hidden using styles.
  8. More filetype options have been added, mirroring relevant options from ChemDoodle 2D.
  9. You may now right-click on the Selector widget to see the same context menu functions as you would when right-clicking on the scene itself. This is helpful for quickly hovering an object in the Selector widget to change properties.


  1. Fixed bug where odd cumulene stereocenters were not handled correctly from 3D coordinates.
  2. Fixed bug where opening styles and cancelling reverts to defaults any surfaces that are not selected.
  3. Fixed bug where color function fails if atoms from multiple discrete structures are used to create the surface.
  4. Escape key now correctly cancels previews when using the element tools to draw a bond to an element.
  5. Corrected Window tab menu items enabled and disabled states.
  6. Corrected Optimize PDB to JSON window where file choosers appeared behind the window.
  7. The Selector widget can no longer be hovered when the right click menu is showing, leading to errors.
  8. Fixed issue where first autosave loaded does not retain styling, and reverts back to the default.