Version History


April 14, 2019

Executive Summary

ChemDoodle 3D v4 is a major update to ChemDoodle 3D with a significant amount of work invested in the molecular modeling engine. Other notable features include a new widget for creating atomic orbital graphics, new protein models, Connolly surfaces and surface color functions, and the generation of armchair/zigzag/chiral carbon nanotube geometries. Check out all the new features below. This update also includes all of the API improvements to our application engine present in ChemDoodle v9, such as customizable shortcuts and native file choosers on macOS.


  1. Building and Modeling
    1. A very accurate implementation of the MMFF94 and MMFF94s force fields can now be used by the Minimizer widget when building molecules. When comparing calculations by ChemDoodle 3D to the author’s MMFF94 dataset, only 6 of 761 structures do not match to the ten-thousandths place, with the largest difference being 0.0061 kcal/mol. When compared to the author’s MMFF94s dataset, all 265 structures match to the ten-thousandths place. This makes ChemDoodle 3D one of the most accurate implementations of the MMFF94 and MMFF94s force fields in the industry. An option is provided to include or exclude published MMFF94 Bond Reduction Factors.
    2. You can now set which optimizer function is used, between steepest descent, conjugate gradients and BFGS.
    3. You can now set which line search function is used, between coarse, fine and Newton.
    4. You can now control whether a cutoff distance is used to throttle non-bonded interactions (vdW and electrostatic) and control that cutoff distance value.
    5. There is a new option to use a Morse oscillator for the bond stretch function for the Universal Force Field.
    6. The Minimizer widget now presents an option to display force field specific atom typing labels for the referenced structure. For the MMFF94 force fields, both the generic Numeric and specific Symbolic atom types are properly attributed in ChemDoodle 3D.
    7. When optimizing structures, the Minimizer widget will now display an error when a unknown atom type is present.
    8. The select and manipulate states have been merged to make building molecules significantly faster and easier. Simply use a selection tool to make selections for editing, or hover individual atoms and bonds to move and manipulate them.
    9. An advanced system has been added to place new bond connections to atoms in the most optimal location in 3D around the atom. Use this to efficiently create molecules and quickly build coordination complexes.
    10. Implicit hydrogen counts can now be set for atoms. Implicit hydrogen overrides will be displayed in a label on the atom.
    11. The escape key will cancel previewed actions.
    12. The delete/backspace key now erases selections.
  2. Macromolecular Structures
    1. New model types for proteins, including an advanced cylinder and plank model as well as a cartoon model. The cylinder and plank model allows for many customizations, including an exclusive method for rendering the void spaces of helices.
    2. Generate armchair, zigzag and chiral nanotubes based on an improved Tubegen algorithm. Build periodic systems of nanotubes and calculate various properties of the structure. Related graphene sheets can also be generated.
    3. You can now color PDB files by chain. Multicolored meshes are now possible for models. Color by rainbow.
    4. Chain residues are now numbered in the Selector widget.
  3. Surfaces – Solvent excluded surfaces (Connolly) can now be generated. Surfaces can now be colored by function, including: Gasteiger charges, QEq, QTPIE, AMR98 and AlogP98.
  4. Periodic – Unit cells now act like individual shapes, and can be edited accordingly with multiple unit cells in the same scene. Supercell dimensions are now better controlled with bounds instead of multiplicities.
  5. Graphics and Interface
    1. A new Orbitals widget is provided for creating advanced atomic orbital graphics based on quantum numbers.
    2. Shapes can now be copied and pasted along with structures.
    3. Automatic shapes are now removed when their constituents are deleted.
    4. Context sensitive cursors are now implemented across the tools, with accessibility options.
    5. Controlling the light direction now properly adheres to the rotation algorithm set in General preferences.
    6. Atom labels will now properly disappear if the atom rendering is hidden.
    7. Fixed the location of dropped molecules from the Molgrabber widget.
    8. Updated elemental data, including Allred-Rochow electronegativities for better calculations.
  6. Chemical Files – Significant improvements to the MMTF interpreters, fixing all reported and known issues. Improvements to the CIF interpreters to read a wider range of files. Also fixed a centering issue with CIF input.


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.