Athanor by arbastro
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How to save and open MOL and SDF files

Select the structure, press Ctrl+Shift+E, search for MOL or SDF, and choose V2000 or V3000 under Molfile. Copy as molfile puts a V3000 molfile on the clipboard. Opening an SD file places every record on the page, named from its Name field.

On a Mac, Ctrl is Cmd.

Save a MOL or SDF file

  1. Select the structures, or nothing for the whole page.

  2. Press Ctrl+Shift+E (Export), type MOL in Search formats, and choose MOL (or SDF).

  3. Under Molfile, choose V2000 or V3000. The preview shows the file as it will be written.

    The Export panel for MOL: the molfile preview, what it keeps and loses, and the Molfile switch set to V2000.The Export panel for MOL: the molfile preview, what it keeps and loses, and the Molfile switch set to V2000.

  4. Press Export MOL, or Copy to put the text on the clipboard.

A molfile keeps atoms, bonds, charges, coordinates and stereo. It loses arrows, text, colors and layout around the structures: for those, keep the .athanor file.

V2000 or V3000?

V2000 V3000
Read by Almost every chemistry program Most current programs
Limits 999 atoms and 999 bonds per structure No practical limit
Stereo groups (and, or) Not kept Kept

Pick V2000 when the file goes to an older program, and V3000 otherwise.

Copy a molfile

Select the structure, press Ctrl+K and choose Copy as molfile. It copies a V3000 molfile. See copy as SMILES, InChI or a molfile.

Open a MOL or SDF file

Press Ctrl+O or drag the file onto the window. Athanor reads V2000 and V3000 (.mol, .sdf, .sd).

An SD file with many records opens with every record on the page, one after another. Each is named from its Name data field, or its title line when it has none.

If a file does not open, see A file will not open.

Files and formatsSupported file formatsExport (Ctrl+Shift+E) writes images (PNG, SVG, PDF, TIFF, EMF, EPS, JPEG, WMF), ChemDraw CDXML and CDX, chemistry files (MOL, SDF, SMILES, InChI, InChIKey, CML, Marvin, RXN, RDF) and computation files (XYZ, PDB, MOL2, Gaussian, ORCA).Files and formatsHow to export a figure or structure filePress Ctrl+Shift+E, pick a format (Ctrl-click to pick several), read what it keeps and loses, then press Export or Copy. Export again (Ctrl+Alt+E) repeats the last choice.Names, properties and checksHow to copy a structure as SMILES, InChI or a molfileSelect the structure and use Edit › Copy as: Copy as SMILES (Ctrl+Alt+C), InChI, InChIKey, molfile, CDXML, chemfig or mhchem formula. Then paste it wherever you need it.Atoms, bonds and ringsHow to mark stereo groups (AND, OR, absolute)Select the drawn stereocenters and choose Object › Stereo group: absolute, Stereo group: new AND (racemic) or Stereo group: new OR (one of two, unknown which). Stereo group: clear removes the mark.

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Last updated Nov 12, 2026