Athanor by arbastro
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How to clean up a structure

Select the structure and press Ctrl+Shift+K (Clean up structure). Bond lengths and angles become regular; the atoms and bonds stay the same.

On a Mac, Ctrl is Cmd.

Ctrl+A, then Ctrl+Shift+K redraws a roughly drawn chain.

Steps

  1. Select the structure: click it with Select (V), or press Ctrl+A for everything on the page.

    A roughly drawn chain with uneven bond angles.A roughly drawn chain with uneven bond angles.

  2. Press Ctrl+Shift+K, or choose Object › Chemistry › Clean up structure.

    The same chain after Clean up structure, redrawn with regular angles.The same chain after Clean up structure, redrawn with regular angles.

Clean up changes only where atoms sit. The formula, the bonds, wedges and labels stay as they were, so it is always safe to use, and Ctrl+Z puts the old layout back.

Check it too

Check structure (Shift+K) looks for chemistry problems in the selected structure, such as an atom with too many bonds, and lists each one. A clean structure gets "No problems found." Problems are also counted in the issues badge at the bottom left of the canvas; Athanor flags them and leaves the fix to you.

Reaction schemes

For a whole reaction scheme, select its arrow and use Clean up reaction in the same menu.

Switching from ChemDrawChemDraw commands and their Athanor namesMost ChemDraw commands have an Athanor command with the same or a similar name. Type ChemDraw's name into Search everything (Ctrl+K) and the Athanor command comes up, with its menu path and shortcut.Switching from ChemDrawWhat works differently from ChemDrawAthanor saves as you work, flags valence and stereo problems instead of silently changing your structure, shows actions for the selection in a bar beside it, and finds commands by ChemDraw's names in Search everything.

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Last updated Nov 12, 2026