A file will not open
Athanor says why a file did not open, in the notice. Check the extension matches the format, try saving it from the other program as CDXML or MOL V3000, and if it still fails, report it with the file.
When a file does not open, the notice says why. Find the start of the message below.
The messages
| The notice says | What it means | What to try |
|---|---|---|
| "Could not tell what kind of file this is." | The extension is missing or unknown, so Athanor tried it as SMILES and that failed too. | Rename it with the right extension (.cdxml, .mol, .sdf, .smi and so on). The notice lists what is supported. |
| "Could not read that ChemDraw file." | The CDX or CDXML is damaged or uses something Athanor cannot read. | Open it in ChemDraw and save it again as CDXML. |
| "That ChemDraw file holds nothing Athanor can open: no structures, arrows or text." | It holds only pictures or shapes. | Add it from the library's + to bring its drawings in as icons. |
| "This ChemDraw style sheet holds no drawing." | A .cds style sheet is a set of styles, not a document. |
Add it from the library's + as a document type. |
| "Could not read that molfile." or "Could not read that SD file." | The MOL or SD file is damaged, or the first record is. | Open it in the program that made it and save it again as MOL V3000. |
| "This is a binary file and could not be read as text." | A binary file with a text extension. | Check that it is the file you meant. |
| "Could not read that Marvin file", "…CML file", "…RXN file", "…RDfile" | That file's contents could not be read. The rest of the message says where. | Save it again from its program, or as MOL or CDXML. |
| "Could not read the file. It may be damaged or in a format this version cannot read." | Anything else. | Try the steps below. |
It opened, but something is missing
- A ChemDraw file: Athanor opens structures, arrows and text. The notice names what it left out, for example "Left out: …".
- "Some structures could not be read": the rest opened. The message gives the reason for the ones that did not.
- "Read as SMILES. It carries no coordinates, so the layout is ours, not yours.": a SMILES file has no drawing, so Athanor lays the structure out itself.
- An SD file opens every record. If only some appear, the others may be damaged.
Still will not open
- Check the supported formats.
- Save it again from the program that made it, as CDXML or MOL V3000, and open that.
- Report the problem and attach the file, if you can share it.
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Last updated Nov 12, 2026
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