Athanor by arbastro
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How to check a structure for errors

Select the structure and press Shift+K (Check structure). Athanor lists each problem it finds, such as a carbon with five bonds, with a suggestion. A clean structure gets "No problems found.

On a Mac, Ctrl is Cmd.

Steps

  1. Select the structure with Select (V), or press Ctrl+A for everything.

  2. Press Shift+K, or choose Object › Chemistry › Check structure.

  3. If all is well, a message says No problems found.

    The message No problems found after checking caffeine.The message No problems found after checking caffeine.

  4. If something is wrong, a box lists each problem with what to do about it, for example "Error: This C has 5 bonds. C takes 4. Remove a bond, or add a charge if you meant an ion." Press OK and fix it.

    A check that found a carbon with five bonds, with the suggestion to remove a bond or add a charge.A check that found a carbon with five bonds, with the suggestion to remove a bond or add a charge.

Athanor never fixes a structure for you: it tells you what it found and leaves the decision to you. The same problems are counted all the time in the issues badge at the bottom left of the canvas. See Why an atom is flagged.

Troubleshooting and FAQWhy an atom is flaggedThe badge at the bottom left of the canvas counts problems in what you drew, such as a carbon with five bonds (an error) or a stereocenter with no wedge (a warning). Click it to see the list. Athanor flags problems and never changes your structure on its own.Drawing basicsHow to clean up a structureSelect the structure and press Ctrl+Shift+K (Clean up structure). Bond lengths and angles become regular; the atoms and bonds stay the same.

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Last updated Nov 12, 2026