ChemDoodle 3.2.1 has been released! We provide this upgrade, free of charge, to our existing customers. When we find bugs in ChemDoodle, we fix them immediately. Unlike our competitors, we would never charge our customers to fix our mistakes.

Executive Summary

ChemDoodle 3.2.1 is primarily a bug fix release. While few, the added features are powerful and improve the drawing system. Site licensees must upgrade to 3.2.1 prior to activating with a renewed activation code.


  1. A new setting has been added to turn off the starting atom requirement. The starting atom setting is intended for users new to chemical drawing programs. More experienced users find they can more quickly draw figures if they turn off this starting atom requirement. This option is provided in the General tab of the Preferences window.
  2. A new right-click menu item has been added to quickly show/hide Carbon labels without opening preferences. This option only appears for “C” labels.
  3. A new option has been added to show/hide borders on Rectangles, Ovals, Text Areas and HTML Areas. This option is disabled by default for Text Areas and HTML Areas so they are now borderless by default.
  4. A new spectrum mouse gesture, shift+drag, will translate the spectrum along the x-axis.
  5. Integration lines can now be rendered for NMR spectra. Color and thickness are editable.
  6. Grids can now be rendered for spectra. Color and thickness are editable.
  7. ChemDoodle Web Components v3.5 is included.


  1. Fixed major issue when renewing a Site License activation where an innocuous error is displayed, making it seem like an error had occured when really everything renewed correctly.
  2. Fixed bug where the Line Notation Pad widget would go blank if an atom with an isotope defined was input.
  3. Isotopes are now supported in ChemSketch files.
  4. Improved the interpretation of coordinates from JCAMP-CS files.
  5. Fixed the reading of negative abscissa values from JCAMP-DX files.
  6. Fixed issue reading element types from SKC files with atomic numbers greater than 107.
  7. Improved the performance of line notation readers.
  8. Line notation readers now warn of multiline input.
  9. Fixed SMILES input issue where the ring closing bond type is specified before a ring declaration.
  10. Improved ROSDAL reading.
  11. Fixed the reading of mass numbers and radicals from InChI strings.
  12. Fixed the writing of radicals to InChI strings.
  13. Fixed bug where changing the bond width or texture thickness to values not available in the Strokes toolbar had no effect.
  14. Single bonds in condensed labels are no longer superscripted.
  15. Charges are now set when expanding condensed labels with charges defined.
  16. Abbreviations now trump elements, so “Ac” is interpreted as an acetyl group instead of Actinium.
  17. Improved condensed notation interpretation to recognize abbreviations at the beginning of atom labels.
  18. Improved handling of abbreviations with different interpretations depending on connectivity, for instance “CO2” can be either carbon dioxide or part of a ester or carboxyl group.
  19. Fixed rendering of orbitals and ovals in PICT output.
  20. Fixed shape rotation issues in PICT output.
  21. Fixed bug where SSSR linear independence was incorrectly determined by atom sets. The linear independence is now correctly determined by bonds.
  22. Keyboard atom shortcuts alt+3 and alt+8 now correctly place cyclopropene and cyclooctatetraene, respectively.
  23. Fixed bug where the window would go blank when trying to determine the stereochemistry of a fully substituted double bond.
  24. Fixed bug where text input components remained and could not be removed if clearing the Doodle Board while a text input component was active.
  25. Fixed bug where zooming in on a flipped x-axis spectrum in the Spectrum Edit window caused the spectrum to incorrectly flip and display crossing tails.
  26. Removed the rendering of infinite tails at the end of spectra that may be incorrectly interpreted as data. The spectrum now stops at its ends.
  27. Fixed the display of the Degree of Unsaturation descriptor in the Properties widget.
  28. Improved the calculation of the Hydrogen Bond Acceptor descriptor.
  29. Improved small case issues in aromaticity detection.
  30. Fixed bug in calculating Morgan indices.
  31. Fixed issue where the main window sometimes lost focus when trying to use keyboard accelerators and shortcuts.
  32. Fixed minor issues where modifier keys didn’t show immediate feedback when transforming lasso content.
  33. Slightly improved Statistics widget scrolling and selecting.
  34. Raster image output now correctly conforms to the advanced specifications for document rendering.
  35. Removed HTML Area highlight decorations from appearing in image output.
  36. Fixed bug where second token in superatoms didn’t stack if that superatom is the first entity in a label.
  37. Dragging after placing an atom will now correctly hover/dehover it.
  38. The atom the mouse is under is now automatically hovered after a template or ring is placed.
  39. Fixed minor issue when searching ChemExper where results without coordinates were displayed.
  40. Fixed issue when searching ChemSpider where short bonds to Hydrogens were being considered when scaling structures to the preferred bond length causing structures to be somewhat larger than preferred.
  41. Fixed minor issue where shadow settings were displayed for shapes that did not support shadows.
  42. Fixed issue where some spectrum visual specifications were mistakenly global.
  43. Expanding the spectrum to fit in the Spectrum Edit dialog now refreshes the tick spacing controls.
  44. Negative values in spectra no longer offset the baseline.
  45. Closing the Preferences window by using the top bar’s close icon will now work just like the Done button.
  46. Fixed bounds calculation for rotated label shapes.
  47. Enabling/disabling chemical warnings now give immediate visual feedback.
  48. Added lasso decorations for orbitals.
  49. Removed lag when checking for updates when no internet connection is found.
  50. Displaying the update changelog when new updates are announced is now instantaneous.