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Converting AlphaFold3 CIF to PDB

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<li> Drag the .cif file and drop it into the black window of Jmol. The model should appear.
<li> Drag the .cif file and drop it into the black window of Jmol. The model should appear.
<li> In the white ''Jmol Script Console'', enter the command '''write jobname.pdb''', where ''jobname'' is a unique identifier for this model.
<li> In the white ''Jmol Script Console'', enter the command '''write jobname.pdb''', where ''jobname'' is a unique identifier for this model.
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<li> [http://firstglance.jmol.org/where.htm#uploading Upload] the jobname.pdb to [http://firstglance.jmol.org FirstGlance in Jmol].
+
<li> [http://firstglance.jmol.org/where.htm#uploading Upload] ''jobname.pdb'' to [http://firstglance.jmol.org FirstGlance in Jmol].
</ol>
</ol>

Revision as of 00:52, 12 January 2026

The AlphaFold3 Server predicts models only in the mmCIF format (filename ending .cif). In addition, a small percentage of models in the wwPDB are available only in mmCIF format. These files can be uploaded to iCn3D, or displayed in PyMOL or ChimeraX.

Only FirstGlance in Jmol and iCn3D color AlphaFold-predicted models 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 2025, FirstGlance in Jmol requires the older PDB format. If you wish to display AlphaFold3 predicted structures in FirstGlance, here is how most of them* can be converted 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. Get the .cif file to convert. If you have downloaded a .cif file from the wwPDB, you can skip the next 3 steps.
    1. Download the zip file from the AlphaFold3 Server.
    2. Double-click the zip file to unzip it.
    3. In the newly unzipped folder, find the file with a name ending _model_0.cif. Drag it into your working folder.[1]
  4. Double-click Jmol.jar to run it.
  5. Drag the .cif file and drop it into the black window of Jmol. The model should appear.
  6. In the white Jmol Script Console, enter the command write jobname.pdb, where jobname is a unique identifier for this model.
  7. Upload jobname.pdb to FirstGlance in Jmol.

See Also

Notes

*Models with > 99,999 atoms or > 62 chains will not fit in the legacy PDB format.

  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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