ChemDoodle 5.1.0 has been released! We provide this upgrade, free of charge, to our existing v5 customers.

Executive Summary

This update addresses several issues brought to our attention and adds a bunch of minor features. Support is added for ChemDoodle Web Components v5.


  1. Updated ChemDoodle Web Components support to version 5.
  2. It is now easy to copy/paste ChemDoodle JSON (for easier interaction with the web sketcher on a webpage) directly from the Edit menu.
  3. Added a Paste and Match Style menu item to the Edit menu to paste content and match the current style sheet.
  4. Zero order bonds are now rendered as a line of dots.
  5. Bonds can now easily be drawn between two atoms by just dragging the mouse close to the second atom when drawing.
  6. Half-arrows can now be drawn on bezier curves.
  7. Added 31 new glassware templates.
  8. You can now change the arrow type (full/half) in the shapes settings dialog.
  9. Added rearrangement arrow option to the shapes settings dialog.
  10. In the General panel in Preferences, you can now control the highlight, selected, preview and error colors.
  11. When using the Carbon Chain tool, the carbon chain will now invert in half portions depending on where the mouse is located. More angles are now allowed.
  12. Added a Delocalize menu item to the Structure menu to delocalize a Kekule structure.
  13. Added a menu accelerator for Copy as SMILES and Paste as SMILES.
  14. Improved the bitmap rendering of straight arrows.
  15. Minor graphical improvements inlcuding line highlighting and anchor rendering.


  1. Improved PubChem results.
  2. Implicit hydrogens are now preserved in MolGrabber if they help to define stereocenters.
  3. Fixed issue where fusing rings to bonds did not always choose the best orientation in the optimize zone.
  4. Mass calculations now take into account atom charges.
  5. Improved NMR simulation chemical shift accuracy for acetylene and aldehyde protons.
  6. Fixed bug where pasting chemically interpretted atoms would ignore formatting.
  7. Fixed issue where switching to new document when a text field is open reopens the old text field.
  8. Fixed bug where formatting a carbon label caused file corruption.
  9. Fixed bug where closing a blank formatted atom field would cause an error.
  10. Editing arrows using the shape settings window can now be undone.
  11. Reduced the width of the Unicode button in the Symbols widget to facilitate resizing.
  12. Resolved issues where using the shift key on Windows would cause some issues when editing content with a selection tool.
  13. Resolved issues where using the alt key on Windows would cause some issues when selecting content with a selection tool.
  14. Removed the invisible rotation anchor that would be present for single selected atoms.
  15. Decorated reaction arrows now correctly shift text to avoid overlaps.
  16. Fixed issue where using the atom start select tool in the Line Notation Pad widget would cause it to crash on rare occasions.
  17. Selection tools no longer allow the hovering of attributes when selecting single objects.
  18. Fixed issue when url encoding was required to properly query ChemExper.
  19. JCAMP spectra units are now detected regardless of case.
  20. Fixed Kekulizer issue where errors could occur.
  21. Improved detection of MOLFile variations.
  22. Minor textual corrections.