Converting AlphaFold3 CIF to PDB

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The AlphaFold3 Server predicts models only in the mmCIF format (filename ending .cif). These files can be uploaded to iCn3D, or displayed in PyMOL or ChimeraX.

Only FirstGlance in Jmol and iCn3D color by confidence/pLDDT correctly (blue for high confidence, red for low confidence). See Visualizing Predicted Structures.

FirstGlance also makes it easy to get the average pLDDT for any range of residues that you specify.

In 2024, FirstGlance in Jmol requires the older PDB format. If you wish to display AlphaFold3 predicted structures in FirstGlance, here is how to convert them to PDB format:

  1. Get the Jmol.jar Java application running on your computer by following the instructions at Jmol/Application.
  2. Create a working folder (directory), and put Jmol.jar in it.
  3. Download the zip file from the AlphaFold3 Server.
  4. Double-click the zip file to unzip it.
  5. In the newly unzipped folder, find the file with a name ending _model_0.cif. Drag it into your working folder.[1]
  6. Double-click Jmol.jar to run it.
  7. Drag the _model_0.cif file and drop it into the black window of Jmol. The model should appear.
  8. In the white Jmol Script Console, enter the command write af3-jobname.pdb, where jobname is a unique identifier for this model.
  9. Upload the af3-jobname.pdb to FirstGlance in Jmol.

See Also

Notes

  1. ↑ Each job produces 5 .cif files. The file with a name ending   _model_0.cif is one of those with the highest overall pTM quality score. The pTM quality score is in the corresponding _summary_confidences_0.json file. Open this file in a text editor. Look for the third-from-last line, which begins "ptm": (including the quotes) followed by the overall pTM confidence value. See the FAQ at the AlphaFold3 Server for how to interpret pTM.

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

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